AOML's Ocean Chemistry and Ecosystems Division


OCED News

September 16, 2019

News

● Charlene Quenee successfully defended her Master's Thesis last week!.

Manuscripts

● The paper entitled "Satellites will address critical science priorities for quantifying ocean carbon" by Jamie D. Shutler, Rik Wanninkhof, Philip D. Nightingale, David K. Woolf, Dorothee C. E. Bakker, Andy Watson, Ian Ashton, Thomas Holding, Bertrand Chapron, Yves Quilfen, Chris Fairall, Ute Schuster, Masakatsu Nakajima, and Craig J. Donlon was accepted for publication in Frontiers In Ecology and Environment. This forward looking paper is an outcome of the working group sponsored by the International Space Science Institute (ISSI). A press release by the European Space Agency (ESA) is planned.

Meetings

● Dr. Jim Hendee and Frank Muller-Karger will be at OceanObs'19 meeting in Honolulu, Hawaii from September 16-20 to represent the compendium of coral monitoring efforts, entitled, "Coral Reef Monitoring, Reef Assessment Technologies, Ecosystem-Based Management" by many authors, including D. Obura, N. Amornthammarong, J. Bishop, P. Fletcher, L. Gramer, J. Halas, J. Hendee, G. Hodgson, and F. Muller-Karger.

● Dr. Luke Thompson will be attending OceanObs'19 meeting in Honolulu, Hawaii from September 16-20. He will contribute to breakout sessions on UN Sustainable Development Goals, Community Building and Dialogue, Ecosystem Health and Biodiversity, and Biological Observing.

● Dr. Rik Wanninkhof will be attending the OceanObs'19 meeting in Honolulu, Hawaii from September 16-20. He will contribute to breakout sessions on Observational Needs of Surface CO2 Monitoring.

● Dr. Derek Manzello will be attending the OceanObs'19 meeting in Honolulu, Hawaii from September 16-20. He will contribute to breakout sessions on NOAA's National Coral Reef Monitoring Program: Monitoring the Ecological Response of Coral Reefs to Ocean Acidification.

● Dr. Chris Kelble will be attending the Habitat Focus Area workshop in Cambridge, MD on September 17 and 18. He will be presenting on our progress with the Biscayne Bay Habitat Focus Area and serving on a panel on cross line office collaboration in HFAs.

● Dr. Chris Kelble will be presenting at the Biscayne Bay Marine Health Summit at FIU on September 20 and serving on a panel discussing the current state of Biscayne Bay.

● The manuscript entitled "Participatory approaches to coral reef management: Lessons learned from coral reef monitoring stations the Wider Caribbean", by P. Fletcher, J. Hendee, A. Jones, M. Jankulak, N. Amornthammarong, J. Bishop and R. van Hooidonk, was accepted for presentation at the 14th International Coral Reef Symposium (Bremen, Germany, July, 2020).

● The manuscript entitled "Multi-agency collaboration in support of near real-time environmental monitoring of dredging projects in SE Florida", by X. Serrano, D. Condon, A. Priestas, P. Dickhudt, J. Karazsia, L. Gramer, J. Hendee, N. Amornthammarong, and M. Soden, was accepted for presentation at the 14th International Coral Reef Symposium (Bremen, Germany, July, 2020).

● The manuscript entitled "The Opuhala Project: Improving Satellite Projections Using In Situ Synoptic Coral Reef Temperatures From Around the World" by J. Hendee, N. Amornthammarong, R. van Hooidonk, D. Trespalacios, J. Lang, P. Fletcher, and M. Jankulak was accepted for presentation at the 14th International Coral Reef Symposium (Bremen, Germany, July, 2020).

Field Work

● Nikki Besemer and Graham Kolodziej are undertaking NCRMP field operations in St. Croix the week of September 9th along with colleagues from the University of the Virgin Islands. Nikki and Graham will be recovering and replacing subsurface temperature recorders (STRs), Bioerosion Monitoring Units (BMUs), and Calcification Accretion Units (CAUs) around the island, as well as establishing Reef Budget survey transects and deploying Subsurface Automatic Samplers (SAS) at Salt River Bay National Historical Park and Ecological Preserve.

● The next South Florida Ecosystem Restoration Research survey aboard the R/V Walton Smith is scheduled for Sept. 23-27. This cruise is being conducted in collaboration with the State of Florida HAB program at the Florida Fish and Wildlife Research Institute (FWRI). FWRI collaborators will likely provide funding to extend the survey and will collect measurements with an imaging flow cytobot to quantify the phytoplankton community and iron measurements to help understand the role iron may play in initiating red tide blooms.

September 9, 2019

Manscripts

● "A novel low-cost, high-precision sea temperature sensor for coral reef monitoring," by N. Amornthammarong and J. Hendee has been selected for Honorable Mention in the competition for the 2019 Excellence in Technology Transfer award. Mana Amornthammarong, who invented the sensor, will fly to Milwaukee for the Regional Meeting on October 16th and 17th at the Hyatt Regency Milwaukee to to receive the certificate of Honorable Mention for Excellence in Technology Transfer.

Field Work

● Ian Smith, Kelly Montenero, and Aly Thompson will be conducting the next juvenile sportfish monitoring survey in Florida Bay on September 10-13.

September 3, 2019

News

● CONGRATULATIONS to Dr. Ian Enochs for receiving the Silver Medal Award for development of a low-cost, open source subsurface autosampler (SAS) that eliminates barriers to water sampling and increases research capacity for all oceanographers. This cost-effective observing tool is being used to conduct research in the waters around coral reefs. We have also requested an award for Nathan Formel of CIMAS who was a key collaborator in the development of this instrument.

● Charline Quenee is scheduled to defend her M.S. Thesis on September 11 at 12pm at RSMAS.

Manuscripts

● The paper entitled "The development of habitat suitability models for fiddler crabs residing in subtropical tidal flats" was accepted in Ocean and Coastal Management.

Hsing-Juh Lin, Tung-Yun Chen, Gwo-Wen Hwang, Anderson Mayfield, Chang-Po Chen (in press). The development of habitat suitability models for fiddler crabs residing in subtropical tidal flats. Ocean and Coastal Management.

Meetings

● Dr. Chris Kelble will be attending the Habitat Focus Area workshop in Cambridge, MD on September 17-18. He will be presenting on our progress with the Biscayne Bay Habitat Focus Area.

● Dr. Chris Kelble will be presenting at the Biscayne Bay Marine Health Summit at FIU on September 20 and serving on a panel discussing the current state of Biscayne Bay.

● The Omics meeting scheduled for this week has been cancelled due to Hurricane Dorian.

August 26, 2019

Meetings/Seminars

● The 2019 SEFSC-AOML Collaborative Omics Workshop will take place on Wednesday September 4 and Thursday September 5 in the RSMAS Library. The goal of this workshop is to advance collaborations between SEFSC and AOML in the area of Omics. The workshop will focus on collaborative project areas at the intersection of the missions of both centers, including both fisheries and conservation applications, with samples from macro-organisms, micro-organisms, and environmental DNA. The first morning session will consist of seminars about progress in these project areas, followed by a discussion of resources required for continued success and growth. The next two half-day sessions will consist of targeted discussions of study questions and hypotheses, study designs, and resource needs for two broad categories of projects: Organismal Omics and Environmental Omics. The final afternoon session will close the workshop with the formation of collaborative action plans. GoToMeeting access:

● Dr. Anderson Mayfield will be giving a talk entitled "Assessing coral health in an era of changing global climate" on Tuesday August 27 at 10AM in the first floor conference room.

● The first Artificial Intelligence Informal Research Report will be given by Jebb Stewart, ESRL's Informatics and Visualization Section Chief, on Tuesday, August 27 at 1pm in the first floor conference room.

● Dr. Kelly Goodwin will provide a "NOAA Omics Taskforce Update" at GLERL on August 28 and at AOML on September 6, 2019 (time to be announced).

Field Work

● Dr. Derek Manzello, Dr. Anderson Mayfield, and Graham Kolodziej of AOML, alongside Ph.D. students Shelby Gantt (U. Alabama-Birmingham) and Yingqi Zhang (U. Southern California) successfully collected gamete bundles from spawning corals (Orbicella faveolata) at Cheeca Rocks the night of 22 August 2019 from 23:15-23:50. This research is part of the NOAA Omics program project being led by Derek Manzello and is a collaboration with Dana Williams at SEFSC, Carly Kenkel (USC), and Dusty Kemp (UAB). Cheeca Rocks is an inshore patch reef that has exhibited a marked resilience to recent bleaching and has maintained high coral cover (~30%) and a large population of the ESA threatened coral species, O. faveolata. From the gamete bundles, the scientists will generate larvae and conduct heat stress experiments to compare the thermal tolerance of the inshore, bleaching-resilient corals with those from offshore. Previous research by Manzello and colleagues has shown an increased thermal tolerance of the inshore corals, such that they can tolerate temperatures up to 1 deg C more than the offshore corals without bleaching. As such, these coral genotypes may be important for restoration of bleaching impacted areas. Larvae of O. faveolata lack algal symbionts until settlement, so these experiments will provide information on how much of the thermal tolerance of the inshore corals is directly due to the role of the coral host as opposed to the algal symbion and what genes are responsible for this heat resistance. The scientists will also attempt to cross the inshore larvae with those from offshore that were collected by Dana Williams and the SEFSC-led team to try and create hybrid corals with high heat tolerance in addition to the traits that have allowed the offshore corals to thrive before recent warming.

News

● Florida Fish and Wildlife Conservation Commission's Fish and Wildlife Research Institute as well as NOAA's National Coral Reef Monitoring Program will be implementing indicators developed by AOML's Florida Keys Integrated Ecosystem Assessment (FKIEA) team (Kelly Montenero, Chris Kelble and Charline Quenee). The FKIEA, with a team including academic and agency experts, developed a vetted list of ecological, socioeconomic and human use indicators for the status and condition of the Florida Keys National Marine Sanctuary.

August 19, 2019

Manuscripts

● The manuscript entitled "A novel low-cost, high-precision sea temperature sensor for coral reef monitoring" was accepted for publication in the Bulletin of Marine Science.

Hendee, J, N. Amornthammarong, L. Gramer and A. Gomez. A novel low-cost, high-precision sea temperature sensor for coral reef monitoring. Bull. Mar. Sci. [final citation not yet known]

● Dr. Anderson Mayfield has two articles coming out this month on reef coral health. 'The Coral Hospital' is a review article fused with a proposal to humor the idea of actively rehabilitating sick corals, whereas the second manuscript highlights the need to compare coral behavior in the field and in the aquarium setting (an especially pertinent topic for those undertaking environmental challenge experiments, as well as those seeking to rear corals in husbandry facilities).

Mayfield, Anderson B., Sujune Tsai, and Chiahsin Lin. "The Coral Hospital." Biopreservation and biobanking (2019). https://www.liebertpub.com/doi/10.1089/bio.2018.0137.

Lin, Chiahsin, Sujune Tsai, and Anderson B. Mayfield. "Physiological Differences Between Cultured and Wild Coral Eggs." Biopreservation and biobanking (2019). https://www.liebertpub.com/doi/full/10.1089/bio.2019.0045.

Meetings

● Dr. Chris Kelble will be attending the Florida Sea Grant workshop, "A forum for harmful algal bloom scientists to assess the current state of the research for Florida's HABs," in St. Petersburg on August 20-21.

● Kelly Montenero and Charline Quenee will be attending the Florida Keys National Marine Sanctuary Advisory Committee meeting in Marathon on August 20. The draft environmental impact statement will be released at this meeting and includes indicators developed at AOML for the Florida Keys Integrated Ecosystem Assessment.

Field Work

● Dr. Anderson Mayfield will be gaining field experience in coral spawning collection and research alongside SEFC scientist Dr. Dana Williams and her team in Key Largo on August 19 and 20.

● Dr. Anderson Mayfield, Graham Kolodziej, and Mike Jankulak will be sampling massive coral colonies (Orbicella faveolata) across both offshore and inshore sites of the Upper Florida Keys as part of a long-term monitoring project aimed at 1) understanding the molecular basis of coral resilience to high temperatures and 2) developing the technological capacity to predict which corals will bleach and which will not.

● Dr. Anderson Mayfield, Graham Kolodziej, and Dr. Derek Manzello will be conducting field work off Islamorada (Upper Florida Keys) with a team of scientists from the University of Southern California (Carly Kenkel and Yingchi Zhang) to catch eggs and sperm spawned from stony coral (Orbicella faveolata) colonies, later conducting cross-fertilization experiments with this biological material (August 21-22).

● Nathan Formel, Dr. Anderson Mayfield, and Ian Enochs will be traveling to Mayreau, Grenadines at the end of September to describe a high-CO2 vent impacting nearby reefs. They will be collecting coral tissue samples to investigate the molecular responses of corals experiencing localized acidification and heat stress.

● Dr. Mana Amornthammarong and Dr. Jim Hendee will be traveling to Union Island, St. Vincent & the Grenadines, September 25 - 30 to re-program the CREWS buoy and meet with officials of the Tobago Cays Marine Park to discuss collaborative work in the coming year.

News

● Professor Kitack Lee of Pohang University, Korea was elected fellow of the American Geophysical Union (AGU). Kitack obtained his PhD. under Prof. Frank Millero of RSMAS and worked at AOML as CIMAS postdoc and Research Associate from 1997 to 2001. He was chief scientist on the AOML led CLIVAR cruise A5 and published his seminal work on interannual variability of ocean carbon fluxes while at AOML.

Lee, K., Wanninkhof, R., Takahashi, T., Doney, S., and Feely, R. A.: Low interannual variability in recent oceanic uptake of atmospheric carbon dioxide, Nature, 396, 155-159, 1998.

● These are some recent pictures that Dr. Luke Thompson took while conducting his omics/bioinformatic work aboard the RV Kronprins Haakon: https://flic.kr/s/aHsmFdNPZP.

August 12, 2019

Manuscripts

● The manuscript entitled "Coral Reef Monitoring, Reef Assessment Technologies, and Ecosystem-based Management" was accepted for publication in Frontiers in Marine Science..

David Obare Obura, Ward Appeltans, Natchanon Amornthammarong, Greta Aeby, Nicholas J Bax, Joe Bishop, Russel E Brainard, Samuel Chan, Pamela Fletcher, Timothey A.C. Gordon, Lew Gramer, Mishal Gudka, John Halas, James Hendee, Gregor Hodgson, Danwei Huang, Mike Jankulak, Albert Jones, Tadashi Kimura, Joshua Levy, Patricia Miloslavich, Loke Ming Chou, Frank Edgar Muller-Karger, Kennedy Osuka, Stephen Simpson, Karenne Tun, Supin Wongbusarakum. 2019. Coral Reef Monitoring, Reef Assessment Technologies, and Ecosystem-based Management. Frontiers in Marine Science. [Final citation not yet attributed]

● The manuscript entitled "Children Exposure-Related Behavior Patterns and Risk Perception Associated with Recreational Beach Use" has been published in the International Journal of Environmental Research and Public Health. To view the online publication: https://doi.org/10.3390/ijerph16152783.

Ferguson A, Del Donno C, Obeng-Gyasi E, Mena K, Kaur Altomare T, Guerrero R, Gidley M, Montas L, Solo-Gabriele HM. Children Exposure-Related Behavior Patterns and Risk Perception Associated with Recreational Beach Use. International Journal of Environmental Research and Public Health. 2019; 16(15):2783.

● Dr. Stephanie Rosales was co-author on the manuscript entitled "Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov" which was published in ISMEJ (ISME Journal, Multidisplinary Journal of Microbial Ecology). This paper describes a new bacteria from the genus Rickettsiales that has parallels with Wolbachia. Its genome suggests that this bacterium is parasitic in nature and by analyzing publicly available databases we found that it is globally distributed in aquatic invertebrates. To view the online publication: https://www.nature.com/articles/s41396-019-0482-0.

J. Grace Klinges, Stephanie M. Rosales, Ryan McMinds, Elizabeth C. Shaver, Andrew A. Shantz, Esther C. Peters, Michael Eitel, Gert Worheide, Koty H. Sharp, Deron E. Burkepile, Brian R. Silliman & Rebecca L. Vega Thurber. Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov. The ISME Journal (2019).

Meetings

● Dr. Chris Kelble will be attending the NOAA Leadership seminar August 12-16 in Warrenton, VA.

● The Port Everglades Ecosystem Response Study (PEERS) has its first teleconference on Wednesday, August 14, to discuss plans to install the first CREWS buoy, and other subjects. This project has representatives from OCED (Dr. James Hendee, Dr. Mana Amornthammarong, Joe Bishop, and Madison Soden), PhOD (Ulises Rivero, Pedro Pena), HRD (Lew Gramer), NMFS (Habitat Conservation Division, Jocelyn Karazsia, and PE POC for NOAA).

News

● A great article about Dr. Leticia Barbero: https://research.noaa.gov/News/Scientist-Profile/ArtMID/536/ArticleID/2440/Leticia-Barbero

● Nicole Besemer will be joining the ACCRETE group as the new National Coral Reef Monitoring Program's Caribbean Climate Operations Coordinator.

● Albert Boyd joined the OCED ACCRETE group. He will be working on carbonate chemistry analysis, as well as instrument calibration and maintenance associated with the National Coral Reef Monitoring Program.

● Nash Soderberg joined the OCEDACCRETE group. He will be working on projects pertaining to coral reef restoration, as well as the maintenance of experiments in the Experimental Reef Lab.

● National Research Council post-doc Ana Maria Palacio Castro will be joining OCED on Monday, August 12.

August 5, 2019

Manuscripts

● Dr. Kelly Goodwin is a co-author on the manuscript entitled "Global Observational Needs and Resources for Marine Biodiversity" which was published in Frontiers in Marine Science. To view the online publication: https://doi.org/10.3389/fmars.2019.00367.

Global Observational Needs and Resources for Marine Biodiversity. Gabrielle Canonico, Pier Luigi Buttigieg, Enrique Montes, Carol A, Stepien, Dawn Wright, Abigail Benson, Brian Helmuth, Mark John Costello, Frank Edgar Muller-Karger, Isabel Sousa Pinto, Hanieh Saeedi, Jan A Newton, Ward Appeltans, Nina Bednarsek, Levente Bodrossy, Benjamin Dale Best, Angelika Brandt, Kelly Goodwin, Katrin Iken, Antonio Marques, Patricia Miloslavich, Martin Ostrowski, Woody Turner, Eric 'Pieter Achterberg, Tom Barry, Omar Defeo, Gregorio Bigatti, Lea-Anne Henry, Berta Ramiro Sanchez, Pablo Duran Munoz, Maria Mar Sacau Cuadrado, Telmo Morato, Murray Roberts, Ana Garralda Garcia-Alegre, Bramley J. Murton. Frontiers in Marine Science (2019).

● Dr. Kelly Goodwin is a co-author on the manuscript entitled "Systematic Review and Meta-Analysis of Decay Rates of Waterborne Mammalian Viruses and Coliphages in Surface Waters" which was published in Water Research. To view the online publication: https://www.sciencedirect.com/science/article/abs/pii/S0043135419306724.

Systematic Review and Meta-Analysis of Decay Rates of Waterborne Mammalian Viruses and Coliphages in Surface Waters. Boehm AB, Silverman A, Schriewer A, Goodman KD. Water Research (2019), 114898.

Field Work

● Kelly Montenero, Ian Smith, Alyssa Thompson, and Charline Quenee will be conducting the next juvenile sportfish survey in Florida Bay on August 6-9.

July 29, 2019

Meetings

● Dr. Kelly Goodwin will brief the NOAA Research Council on NOAA's Omics Strategy on July 30, 2019.

● Dr. Kelly Goodwin will brief the NOAA Biodiversity Beyond Areas of National Jurisdiction Marine Genetic Resources Team (BBNJ MGR) August 2, 2019.

● Dr. Luke Thompson and Dr. Ruben van Hooidonk will be attending the NOAA cloud computing workshop in Boulder, CO on July 30 - August 1.

Field Work

● Kelly Montenero, Alyssa Thompson, and Ian Smith will be leading the next south Florida Ecosystem Restoration Research Cruise aboard the R/V Walton Smith from July 29-August 2. This cruise will be surveying the area where the dead zone was observed from August through November of last year to make a preliminary determination of whether low DO is present. These results will be communicated once the ship return to the fishing community on the southwest Florida shelf through the Florida Commercial Watermen's Conservation.

News

● Dr. Stephanie Rosales along with Nicole Carmouze, a SEFSC intern, set up a PCR room at AOML in order for both AOML and SEFSC to have the capacity to perform 'Omics work in-house.

Outreach

● Dr. Ian Enochs spoke with a group of students and interns at MacArthur Beach State Park, through a Skype with a Scientist session. He answered questions about the effects of ocean acidification, bleaching, and nutrients on coral reefs.

July 22, 2019

Meeting

● Dr. Kelly Goodwin will present a seminar on the NOAA Omics Roadmap Taskforce at PMEL on Monday July 22.

● Dr. Chris Singalliano, Dr. Maribeth Gidley and student researcher Anthony Bonacolta will meet with a GeneDisc production development team from the Pall Corporation on Thursday, July 25. This meeting is a part of the on-going NOAA AOML Technology Transfer program that is transitioning molecular microbial source tracking technology tot he commercial sector under a CRADA agreement.

July 15, 2019

Manuscripts

● The manuscript "Using Spatial Variability in the Rate of Change of Chlorophyll a to improve water quality management in a Subtropical Oligotrophic Estuary" with authors Dr. Nicole Millette, Dr. Christopher Kelble, and Lindsey Visser was accepted for publication in Estuaries and Coasts. This manuscript provides a robust statistical analysis to conclude that Biscayne Bay, a NOAA habitat focus area, is slowly eutrophying with steadily increasing chlorophyll a over the past 20 years. This increase is greater in the nearshore and semi-enclosed areas of Biscayne Bay indicating the eutrophication is due to land-based sources. The paper highlights the need for urgent nutrient management actions in certain areas of Biscayne Bay to halt eutrophication before it causes a regime shift. The paper is the result of a collaborative project between AOML and NGI and is a significant step towards accomplishing Goal 1 of the Biscayne Bay Habitat Focus Area Implementation plan.

● The manuscript "The Global Ocean Ship-Based Hydrographic Investigations Program (GO-SHIP): A Platform for Integrated Multidisciplinary Ocean Science" has been accepted by Frontiers in Marine Science. The paper describes current state, vision and socio-economic relevance of the Global Ocean Ship-Based Hydrographic Investigations Program (GO-SHIP). GO-SHIP provides a globally coordinated network and oversight of 55 sustained decadal repeat hydrographic reference lines. GO-SHIP is part of the global ocean/climate observing systems (GOOS/GCOS) for study of physical oceanography, the ocean carbon, oxygen and nutrient cycles, and marine biogeochemistry. GO-SHIP enables assessment of the ocean sequestration of heat and carbon, changing ocean circulation and ventilation patterns, and their effects on ocean health and Earth's climate. This paper is a contribution to the OceanObs 2019 conference. AOML scientists are lead authors and major contributors to many of the solicited white papers for the conference.

Sloyan BM, Wanninkhof R, Kramp M, Johnson GC, Talley LD, Tanhua T, McDonagh E, Cusack C, O'Rourke E, McGovern E, Katsumata K, Diggs S, Hummon J, Ishii M, Azetsu-Scott K, Boss E, Ansorge I, Perez F, Mercier H, Williams MJM, Anderson L, Lee JH, Murata A, Kouketsu S, Jeansson E and Hoppema M (2019). The Global Ocean Ship-Based Hydrographic Investigations Program (GO-SHIP): A Platform for Integrated Multidisciplinary Ocean Science. Front. Mar. Sci. 6:445. doi: 10.3389/fmars.2019.00445.

News

● Indicators from the OCED's Florida Keys Integrated Ecosystem Assessment project will be used in the Draft Environmental Impact Statement for the Florida Keys National Marine Sanctuary. The draft Environmental Impact Statement is still undergoing internal review and is scheduled to be released at the August 20 Sanctuary Advisory Council Meeting. The Florida Keys Integrated Ecosystem Assessment was funded by the Coral Reef Conservation Program and NOAA IEA program.

● Projections of coral bleaching using global climate models will be included in a new syllabus for Year 12 Marine Science students in Queensland, Australia with the goal of having students understand why limiting climate change to 1.5°C is important. The projections are derived from the following manuscript: Ruben van Hooidonk, Jeffrey Allen Maynard, Yanyun Liu, Sang-Ki Lee. 2013. Downscaled projections of Caribbean coral bleaching that can inform conservation planning. Global Change Biology, Volume 21, Issue 9.

● Coming back from a meeting in Woods Hole, the Ocean Carbon Group will participate in an inter-comparison exercise for pH measurements to get a better idea on how well we know this parameter.

July 8, 2019

News

● Dr. John Cortinas officially starts his tenure as AOML director on July 8.

Manuscripts

● The manuscript "Rediscovering the ocean carbon sink: satellites will enable us to watch the global oceans breathe" by Shutler, J. D., R. Wanninkhof, P. D. Nightingale, D. K. Woolf, D. C. E. Bakker, A. J. Watson, et al. (2019) (FEE18-0294) has been accepted by Frontiers in Ecology and the Environment. The paper is a comprehensive review of the use of satellites in ocean carbon cycle research. This is a product of the International Space Science Institute (ISSI) Working Group on this topic, and geared towards the international community and policy makers. A press release by the University of Exeter coinciding with the release is forthcoming.

● Dr. Luke Thompson is a co-author on the manuscript "QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science", which was accepted for publication in Nature Biotechnology. The manuscript describes the next generation of the program QIIME (Quantitative Insights Into Microbial Ecology), the most popular software tool for analyzing amplicon sequencing data.

Authors: Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andres Mauricio Caraballo-Rodriguez, John Chase, Emily K Cope, Ricardo Da Silva, Christian Diener, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Sean M Gibbons, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin D Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie T Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, II, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vazquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Charles HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J Gregory Caporaso.

Field Work

● Ian Smith, Kelly Montenero, and Rachel Martin will be conducting the juvenile sportfish sampling in Florida Bay on July 9-12.

● Dr. Derek Manzello, Graham Kolodziej, Mike Jankulak, Dr. Anderson Mayfield, and NOAA Corps officer Alyssa Thompson will conduct field operations down at Cheeca Rocks Reef, Islamorada, FL, aboard the R/V GBN1 from July 10-12. The activities are part of the in situ climate change and ocean acidification monitoring of the National Coral Reef Monitoring Program, that is led by AOML/OCED for US coral reefs in the Atlantic Ocean. The team will conduct CaCO3 budget surveys, and collect photomosaics of the sites. These are the first CaCO3 budget surveys conducted at Cheeca Rocks Reef since the outbreak of the Soft Tissue Loss Disease event in the Florida Keys, so potential impacts of the disease event might be seen in this year's surveys. Additionally, Anderson Mayfield will lead tissue sampling collection operations for the coral species Orbicella faveolata to acquire samples for transcriptomics and proteomics work in anticipation of a potential bleaching event this year.

Meetings

● On July 11th, Dr. Maribeth Gidley will be giving a presentation at the Climate Design Lab discussing the potential public health impacts of climate change and sea level rise in South Florida. Miami-Dade Public Schools (MDCPS), partnering with CLEO and the Van Alen Institute, is hosting the Climate Design Lab, a three-week immersive summer program for high school students to learn about the role innovative design can play in addressing sea level rise in the Miami region and beyond.

Upcoming

● Dr. Luke Thompson and Dr. Ruben van Hooidonk will be attending the NOAA cloud computing workshop in Boulder, CO on July 30 - August 1.

● Dr. Kelly Goodwin will be presenting a seminar on AOM's 'omics at PMEL on July 22, 2019.

July 1, 2019

Manuscripts

● The paper co-authored by R. Wanninkhof, D. Pierrot, and L. Barbero entitled "A surface ocean CO2 reference network, SOCONET and associated marine boundary layer CO2 measurements" has been accepted for publication in Frontiers in Marine Science, section Ocean Observation.

Authors: Rik Wanninkhof, Penelope Pickers, Abdirahman Omar, Adrienne J Sutton, Akihiko Murata, Are Olsen, Britton Stephens, Bronte Tilbrook, David Munro, Denis Pierrot, Gregor Rehder, J. Magdalena Santana Casiano, Jens Daniel Muller, Joaquin A. Trinanes, Kathy A Tedesco, Kevin M. O'Brien, Kim Currie, Leticia Barbero, Maciej Telszewski, Mario Hoppema, Masao Ishii, MELCHOR GONZALEZ-DAVILA, Nicholas Robert Bates, Nicolas Metzl, Parvadha Suntharalingam, Richard Alan Feely, Shin-ichiro Nakaoka, Siv Lauvset, Taro Takahashi, Tobias Steinhoff, Ute Schuster.

Field Work

● Dr. Stephanie Rosales along with researchers from SEFSC and UM will be in the Upper Florida Keys on Monday and Tuesday collecting tissue samples from Acropora for their ongoing project evaluating outplant health from coral nurseri.

News

● The Celebrity Flora, a cruise ship outfitted with oceanographic instrumentation including an OCED underway pCO2 system set sail this week on the Galapagos. This effort, including OCED's contribution is highlighted in the below joint press release from the University of Miami and AOML. https://news.miami.edu/rsmas/stories/2019/06/one-of-a-kind-floating-laboratories-track-marine-environmental-change.html

● JMP, a statistical analysis software company, has published an article on Anderson Mayfield from his time at the Living Oceans Foundations. The article discusses how Dr. Mayfield analyzed coral reef datasets with JMP statistical software to identify critical survival factors for corals. The article can be found here: https://www.jmp.com/en_us/customer-stories/living-oceans-foundation.html

● CIMAS is looking for a post-doc for the Gulf of Mexico Integrated Ecosystem Assessment. The post-doc can have an ecological or oceanographic background and their initial responsibility will be to quantitatively test a variety of hypotheses regarding red tide blooms on the southwest Florida shelf using remotely sensed and in situ datasets. To apply visit the link here: https://umiami.wd1.myworkdayjobs.com/en-US/UMCareerStaff/job/Miami-FL/RSMAS---Postdoctoral-Associate---CIMAS_R100033175.

● CIMAS is searching for an Assistant Scientist to lead the eDNA for EBFM 'omics project and enhance our 'omics related work with SEFSC. Please forward to anyone who might be interested. To apply visit the link here: https://umiami.wd1.myworkdayjobs.com/en-US/UMCareerStaff/job/Miami-FL/RSMAS---Postdoctoral-Associate---CIMAS_R100033175.

June 24, 2019

Manuscripts

● Dr. Kelly Goodwin is a co-author on a manuscript entitled "In-situ Autonomous Acquisition and Preservation of Marine Environmental DNA Using an Autonomous Underwater Vehicle" which is in press in Frontiers in Marine Science (Yamahara et al.). The paper demonstrated the ability to collect in-situ eDNA samples from an autonomous mobile instrument, allowing observations of complex biological processes at fine-scale temporal and spatial resolutions that are not possible to accomplish using conventional sampling methods.

Meetings

● Dr. Kate Hubbard, the State of Florida's red tide coordinator was at AOML June 24, to talk about ongoing and future collaborations with AOML.

● Dr. Kelly Goodwin was invited to speak at an international workshop on the marine microbiome for the Atlantic Ocean Research Alliance (AORA) on June 27, 2019. AORA is an alliance between Canada, the European Union and the United States in order to advance the vision of the Galway Statement on Atlantic Ocean Cooperation (https://www.atlanticresource.org/aora).

● Dr. Kelly Goodwin will travel to the Monterey Bay Research Aquarium during the week of June 24, 2019 for a post-cruise meeting.

Field Work

● Ian Smith, Kelly Montenero, and Rachel Martin (Hollings Scholar) conducted the next juvenile sportfish survey in Florida Bay on June 25-28.

June 17, 2019

Manuscripts

● Dr. Kelly Goodwin is a co-author on an a paper accepted for publication in Frontiers in Marine Science, Ocean Observation section entitled "Global Observational Needs and Resources for Marine Biodiversity" (G. Canonico et al.).

Meetings

● Dr. Chris Kelble, Kelly Monetenero, and Charline Quenee will be giving a presentation to the Florida Keys National Marine Sanctuary Sanctuary Advisory Committee (FKNMS-SAC) on Tuesday, June, 18. The presentation will update the FKNMS SAC on the Florida Keys IEA we have been conducting. This will include showing them the selected indicators for the condition report and time series for the indicators related to human activities.

● Dr. Chris Kelble, Kelly Monetenero, and Charline Quenee will be giving a presentation to the Florida Keys National Marine Sanctuary Sanctuary Advisory Committee (FKNMS-SAC) on Tuesday, June, 18. The presentation will update the FKNMS SAC on the Florida Keys IEA we have been conducting. This will include showing them the selected indicators for the condition report and time series for the indicators related to human activities.

● OCED will be hosting an 'omics meeting on Monday, June 17th at 1pm in the 2nd floor conference room to discuss 'omics sampling for the coming year and potential equipment purchase to make sample processing more efficient.

● Dr. Catalina Aguilar and Dr. Stephanie Rosales will be presenting at the 3rd annual MDC, Homestead Campus, Microbiology Girls Club this week as part of a 2-day summer workshop to engage twenty-four, 8th to 12th grade girls in STEM fields from local schools. The workshops are sponsored by the international cosmetics company, L'Oreal USA and the American Association of University Women.

News

● Dr. Maribeth Gidley gave an AOML presentation on June 17 on "Measles 2019" and how it could impact AOML operations or travel plans.

● CIMAS scientist Dr. Lew Gramer will be transitioning to AOML's Hurricane Research Division as of Monday, June 17. Lew will leverage the years of experience he has gained in both scientific research and computing with AOML's OCED, and with PhOD before that, to contribute to the hurricane modeling mission in HRD.

June 10, 2019

Manuscripts

● The paper entitled "Hurricane Irma Impact on Water Quality and Phytoplankton Communities in Biscayne Bay (Florida, U.S.A.)" was accepted for publication in Estuaries and Coasts with AOML/OCED co-author Dr. Chris Kelble. This paper found that the passage of Hurricane Irma produced a pulse of freshwater flow into Biscayne Bay resulting in lower inshore salinities and increased nutrient loading as evidenced by higher nutrient concentrations. These changes were accompanied by only a modest increase in phytoplankton biomass (chl a) relative to other estuaries. However, there were changes to the phytoplankton community composition with the relative abundance of diatoms decreased while cyanobacteria and chlorophytes increased. These effects were relatively short-lived with water quality and phytoplankton communities returned to pre-hurricane status within 9 weeks. This suggests that Biscayne Bay phytoplankton communities are resilient to hurricane impacts. This paper is a direct output from the Biscayne Bay Habitat Focus Area.

● The paper entitled "Pacific anthropogenic carbon between 1991 and 2017" has been published in Global Biogeochemical Cycles. The results are based measurements taken on Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP) in which AOML investigators play a major role. The anthropogenic CO2, Canth accumulation rate over the top 1,500mof the Pacific increased from 8.8 (±1.1, 1s) Pg of carbon per decade between 1995 and 2005 to 11.7 (±1.1) PgC per decade between 2005 and 2015. The distribution suggests a substantial enhancement of the accumulation of Canth in the South Pacific by circulation variability and implies that a meaningful portion the reinvigoration of the global CO2 sink that occurred between ~2000 and ~2010 could be driven by enhanced ocean Canth uptake and advection into this gyre.

Carter, B. R., Feely, R. A., Wanninkhof, R., Kouketsu, S., Sonnerup, R. E., Pardo, P. C., et al. (2019). Pacific anthropogenic carbon between 1991 and 2017. Global Biogeochemical Cycles, 33. 597-617https://doi. org/10.1029/2018GB006154

Technical Reports

● The CRCP/CoRIS Technical Report, Coastal Turbidity on the Southeast Florida Shelf - Monitoring Turbid Water Sources and Fates by Satellite, by Lew Gramer and Jim Hendee, has been released to the Web: https://www.coris.noaa.gov/activities/southeast_florida_turbidity/.

Gramer, L.J., and J.C. Hendee, 2018: Coastal turbidity on the southeast Florida Shelf - Monitoring turbid water sources and fates by satellite. NOAA Technical Memorandum, OAR-AOML-105 (doi:10.25923/zqv9-nw98), 31 p.

Field Work

● Dr. Luke Thompson completed his cruise on the R/V Kronprins Haakon. The cruise report can be found here: https://drive.google.com/open?id=1gZHDrOptBvFoZVCkjCsDBELyaDGtb9Z8 This report includes everything that was done on the cruise, including our eDNA work.

● Kevin Sullivan of the Ocean Carbon Cycle group in OCED collaborated with Chip Maxwell and others of the Marine Technology Group (MTG) at RSMAS to install scientific instruments aboard the new Celebrity cruise ship, Flora, which is designed for service around the Galapagos Islands. During a week in the DeHoop shipyard in Schiedam, Netherlands, and for two weeks of the Flora's inaugural voyage the installation of an autonomous instrument to measure pCO2 in surface waters was completed. The instrument operated for most of the voyage between the Canary Islands and St. Maarten, and numerous discrete samples were collected for analyses of additional carbon parameters back in lab. The efforts is in support of carbon cycle and ocean acidifcation reasearch, and in collaboration with Dr. Rafael Bermudez of Galapagos Marine Research and Exploration in Puerto Ayora the Galapagos.

News

● Lea Chomiak's last day with the ACCRETE lab is June 17th. She will be returning to AOML in the fall to pursue a PhD at UM-RSMAS, working closely with PHOD.

June 3, 2019

Manuscripts

● The paper entitled "Remote detection of cyanobacteria blooms in an optically shallow subtropical lagoonal estuary using MODIS data" with AOML/OCED co-author Dr. Chris Kelble was accepted for publication in Remote Sensing of the Environment. The paper describes a new method for detecting cyanobacterial blooms in Florida Bay that was able to accurately classify 75% of cyanobacteria blooms with <1% false positives. Cyanobacterial blooms in Florida Bay are periodic, but cause ecosystem disruptions including the loss of sponges, which increases Florida Bay's vulnerability to ensuing phytoplankton blooms.

Citation: Cannizzaro, JP, BB Barnes, C Hu, A Corcoran, K Hubbard, E Muhlbach, WC Sharp, LE Brand, CR Kelble. Accepted. Remote detection of cyanobacteria blooms in an optically shallow subtropical lagoonal estuary using MODIS data. Remote Sensing of the Environment.

Meetings

● Dr. Derek Manzello is giving an invited presentation at the workshop entitled "Evaluating the Health of the Mesoamerican Barrier Reef using the Reef Budget methodology" in Puerto Morelos, Mexico, June 3-7. The workshop is being co-hosted by Lorenzo Alvarez-Filip of the Universidad Nacional Autonoma de Mexico and Chris Perry of the University of Exeter. Dr. Manzello will present on the use of the ReefBudget methodology as part of the monitoring associated with the Coral Reef Conservation Program's National Coral Reef Monitoring Program.

● On June 4 - 7, Dr. Jim Hendee, Joe Bishop, and Dr. Mana Amornthammarong participated in a CREWS Workshop in Antigua. The purpose of the meeting is to repeat instructions on maintenance of the stations, as well as show how to program the data logger on the stations, as some previous personnel have left the program, and there are new telecommunications carriers that the CREWS stations use to telemeter data back to AOML.

Field Work

● Dr. Luke Thompson is aboard the Norwegian icebreaker the RV KRONPRINS HAKON participating in a cruise focused on using eDNA to characterize a potential new fishery in the mesopelagic layer. This joint project was conceived by the US-Norway Intergovernmental Group on eDNA and is being led by Kelly Goodwin (US-NOAA) and Jon-Ivar Westgaard and Torild Johansen (Norway-IMR).

● Graham Kolodziej, Mike Jankulak, John Morris, Amanda Kirkland, Anderson Mayfield, Nate Formel, Kelly Montenero, and NOAA Corps officer Alyssa Thompson will embark on a research cruise to the Flower Garden Banks National Marine Sanctuary (FGBNMS) in the Gulf of Mexico aboard the R/V Manta from June 3-7 . The activities are part of the in situ climate change and ocean acidification monitoring of the National Coral Reef Monitoring Program, that is led by AOML/OCED for US coral reefs in the Atlantic Ocean. The team will conduct CaCO3 budget surveys, make measurements of diurnal CO2 using Submerged Auto Samplers (SAS) and a SeaFET pH sensor, as well as recover/deploy Calcification Accretion Units (CAUS), Bioerosion Monitoring Units (BMUS), and Subsurface Temperature Recorders (STRS). They will also collect cores from the ESA-listed coral species, Orbicella faveolata, to assess the impact of recent coral bleaching and a separate mortality event on growth of this key reef-builder. FGBNMS is a deep coral reef (> 65') in the Gulf of Mexico that has anomalously high coral cover (~50%) for the Atlantic Ocean, where the majority of coral reefs have lost much of their live coral due to disease and bleaching.

● Dr. Kelly Goodwin and Lauren Valentino are aboard the NOAA Ship Lasker from May 29 to June 7, 2019. During June 3-4, joint operations will be conducted between NOAA and MBARI to field test two eAUVs to collect samples for omic analysis. The mission will also coordinate multiple acoustic platforms, including a MBARI Waveglider and a Saildrone.

News

● Dr. Chris Kelble has been chosen by OAR to attend the very competitive Leadership Seminar to be held in August.

May 27, 2019

Meetings

● Dr. Jason Link, the NMFS Senior Scientist for ecosystem science was at AOML on Wednesday, May 29 to discuss AOML-Fisheries collaborations with AOML. He will be meeting with AOML scientists at 1PM in the second floor conference room to discuss AOML's collaborations with Fisheries currently and in the future.

● On behalf of Dr. Stephanie Rosales, Erinn Muller from Mote laboratory is presenting results at the Association of Marine Laboratories of the Caribbean (AMLC) on the study titled, "The microbiome of corals and sites affected by the stony coral tissue loss disease (SCTLD)." This is work is a collaboration with Mote, FWC, and AOML.

Field Work

● Dr. Luke Thompson is aboard the Norwegian icebreaker the RV KRONPRINS HAKON participating in a cruise focused on using eDNA to characterize a potential new fishery in the mesopelagic layer. This joint project was conceived by the US-Norway Intergovernmental Group on eDNA and is being led by Kelly Goodwin (US-NOAA) and Jon-Ivar Westgaard and Torild Johansen (Norway-IMR).

● Dr. Maribeth Gidley returned from four weeks aboard the NOAA Ship Pisces during the SEAMAP Reef Fish expedition. During this time, she collected nearly 300 water samples for eDNA, along with training science personnel to continue the water collection and filtering for the final leg of the cruise. This is the first gulf-wide water column eDNA collection to support the AOML-SEFSC omics collaborative. The project aims to develop habitat-occupancy relationships from eDNA and models from environmental covariates, and takes advantage of near simultaneous water collection and fish visualization using 360 degree camera arrays.

● Dr. Kelly Goodwin and Lauren Valentino are aboard the NOAA Ship Lasker from May 29 to June 7, 2019. During June 3-4, joint operations will be conducted between NOAA and MBARI to field test two eAUVs to collect samples for omic analysis. The mission will also coordinate multiple acoustic platforms, including a MBARI Waveglider and a Saildrone.

Visitors

● Dr. Denis Pierrot is hosting Dr. Carla Berghoff of the Argentinian Fisheries Institute, INIDEP, in Mar del Plata as part of the Ocean Acidification (OA) Pier2Peer program. Pier2Peer is a scientific mentorship program that matches established researchers in world premier OA laboratories with early career scientists to facilitate the transfer of expertise and know-how, and to provide a platform for international collaborations and capacity building. Funds for Carla's travel were provided by the Ocean Foundation.

News

● Dr. Luke Thompson was selected as the 2019 recipient of the Scripps Institution of Oceanography (SIO) Graduate Teaching Award. The award is a recognition of his considerable and successful efforts in teaching SIO students about data science using the Python programming language. Luke has been teaching the Python course at SIO since 2015. Lessons and video lectures from the course are available from GitHub and YouTube.

● Welcome aboard to Dr. Anderson Mayfield, a new CIMAS Assistant Scientist and Rachel Martin, a NOAA Hollings Scholar. Anderson will conduct Omics funded research in proteomics and coral ecosystems and Rachel will be working with Chris Kelble studying the use of and impact indicators in ecosystem management.

May 20, 2019

Meetings

● Dr. Chris Kelble, Kelly Montenero, Ian Enochs, and Dr. Derek Manzello will participate in the NOAA NCRMP Florida status report meeting at RSMAS on Monday, May 20th.

Field Work

● Dr. Luke Thompson is aboard the Norwegian icebreaker the RV KRONPRINS HAKON participating in a cruise focused on using eDNA to characterize a potential new fishery in the mesopelagic layer. This joint project was conceived by the US-Norway Intergovernmental Group on eDNA and is being led by Kelly Goodwin (US-NOAA) and Jon-Ivar Westgaard and Torild Johansen (Norway-IMR).

● The Omics'-funded collaboration between NOAA/AOML, NOAA/SEFSC, and RSMAS called "Persistence of Resistance" (Rosales et al.) is deploying approximately 20 temperature sensors and 12 bottom current meters ("TCMs") this week and next week, at four reefs in the Upper Florida Keys. Dr. Mana Amornthammarong and Dr. Lew Gramer are working with Annie Peterson and Dana Williams of SEFSC to complete the instrument preparation. Dana, Annie, and Allan Bright completed more than half of the swaps in the field this week. The goal of the project is to understand how physical habitat, coral genetics, and the coral microbiome interact to make for healthy coral outplants (Acropora cervicornis and A. palmata).

Outreach

● Dr. Lew Gramer completed a project to develop a Coral Reef Heat Budget toolkit for the MATLAB programming language, by creating a GitHub repository for the project under the NOAA-CHAMP Profile. This project served as the basis for part of Dr. Gramer's Ph.D. work, and the 165,000 lines of MATLAB code have contributed to three projects undertaken by Lew within OCED since 2013. These projects spanned coral bleaching ecoforecasting in the Keys, upwelling on southeast Florida shelf, and a component for coral habitat suitability mapping throughout south Florida.

Outreach

● Dr. Pamela Fletcher, formally of Sea Grant and AOML, met with students of New River Middle School and Stranahan High School to instruct them on the building of the Opuhala sea temperature sensors designed by Mana Amornthammarong. The sensors they develop will have unique serial numbers, so that the students can follow the temperature recordings of the sensors after they are placed at locations at coral reefs around the world, deployed by Reef Check and the Atlantic Gulf Rapid Reef Assessment groups under a Memorandum of Understanding with AOML.

News

● An NRC Associateship award offer has been sent to Ana Maria Palacio Castro for an Associateship in OCED. Following appropriate security clearing, we expect Ana to start this summer.

May 13, 2019

Meetings

● Dr. Rik Wanninkhof attended the Southern Ocean Carbon Cycle and Modeling (SOCCOM) meeting remotely on May 13 - May 15.

● Dr. Chris Kelble and Kelly Montenero attended the NOAA IEA 10th anniversary meeting in Silver Spring, Maryland on May 13 - May 17. Dr. Kelble gave a presentation on 10 years of IEA science.

Publications

● Dr. Denis Pierrot (NOAA/AOML/Univ. Miami-CIMAS) and Tobias Steinhoff (GEOMAR, Germany) produced a manual to help guide the community on the "Installation of autonomous underway pCO2 instruments onboard ships of opportunity." The manual is published by NOAA.

Pierrot, D., and T. Steinhoff, 2019: Installation of autonomous underway pCO2 instruments onboard ships of opportunity. NOAA Technical Report, OAR-AOML-50 (doi:10.25923/ffz6-0x48), 31 pp.

Field Work

● Charline Quenee and Ian Smith will be conducting the latest survey of juvenile sportfish in Florida Bay from May 14th to 17th.

● Dr. Luke Thompson is aboard the Norwegian icebreaker the RV KRONPRINS HAKON participating in a cruise focused on using eDNA to characterize a potential new fishery in the mesopelagic layer. This joint project was conceived by the US-Norway Intergovernmental Group on eDNA and is being led by Kelly Goodwin (US-NOAA) and Jon-Ivar Westgaard and Torild Johansen (Norway-IMR).

● A MAPCO2 buoy was successfully deployed on May 18, 2019 in Fagatele Bay National Marine Sanctuary by PacIOOS’s Chip Young and OCED’s Michael Jankulak, Graham Kolodziej, and Dr. Derek Manzello. This is the second sentinel ocean acidification monitoring station to be established on a coral reef in the US Pacific in support of NOAA’s National Coral Reef Monitoring Program. The buoy deployment and upkeep is funded by the Ocean Acidification Program and represents a collaborative effort between AOML and NOAA’s Pacific Marine Environmental Laboratory, Coral Reef Conservation Program, National Marine Sanctuaries of American Samoa, PacIOOS, the National Park Service of American Samoa, Department of Marine and Water Resources of American Samoa, and the Coral Reef Advisory Group of American Samoa. All data can be viewed online on PMEL and Pacific Islands Ocean Observing System (PacIOOS) websites and is available to other researchers and the public. NOAA article about the deployment can be found at: https://research.noaa.gov/article/ArtMID/587/ArticleID/2457/New-NOAA-partner-buoy-in-American-Samoa-opens-window-into-a-changing-ocean

Outreach

● Dr. Kelly Goodwin was featured by NOAA Research News. The web story highlights the work of Dr. Kirsten Harper on an AOML/SWFSC pilot project on using eDNA to monitor marine turtles. The story was released on Endangered Species Day, May 17, 2019. The story can be found at: https://research.noaa.gov/article/ArtMID/587/ArticleID/2454/The-DNA-found-in-sea-turtle-poop-could-be-scientists%E2%80%99-newest-monitoring-tool

● Dr. Nate Formel participated in Career Day at Riverside Elementary School on May 14th. He gave the students, who were a mix of excited fourth and fifth graders, a brief presentation about being a marine biologist, how to become one, and shared photos of the work being done by OCED researchers at AOML. Afterwards Nate reported back that enthusiasm as well as concern for our oceans and coral reefs was high, and there is hope for the future generation. Riverside hosts a career day annually and is always looking for more presenters for the kids. If you'd be interested in participating next year contact Nate (nathan.formel@noaa.gov) and he can put you in touch with a Riverside teacher.

News

● On May 16, OCED and RSMAS MBE PhD student John Morris successfully defended his dissertation proposal.

May 6, 2019

Meetings

● Doran Mason and Steve Ruberg of GLERL will visit AOML on Tuesday, May 7th., to discuss Port Everglades monitoring with several AOML participants in the second floor conference room (10am), and give a general overview of GLERL activities for all of AOML in the first floor conference room (1:30pm).

● Dr. Kelly Goodwin will remotely attend the 3rd US-Norway bilateral meeting on eDNA to be held in Bergen, Norway on May 9-10, 2019.

Manuscripts

● Dr. Luke Thompson and Dr. Kelly Goodwin are co-authors on the manuscript "Red Sea SAR11 and Prochlorococcus Single-cell Genomes Reflect Globally Distributed Pangenomes", which was published online April 26 in Applied and Environmental Microbiology. The manuscript presents new microbial genomes and an analysis of these genomes in the context of global ocean metagenomes and metatranscriptomes. Reported are 21 new SAR11 single-cell genomes, including the first genomes from subclades Ib and Id, and 5 new Prochlorococcus single-cell genomes from ecotype HLII. A new method called "OG ordination" is introduced which uses PCA of ortholog group (OG) composition to resolve phylogenetic differences in closely related genomes. Tara Oceans metagenomes are discriminated based on the distribution of Prochlorococcus and SAR11 OGs. Finally, the Baas Becking hypothesis applied to OGs is tested, showing that most OGs from surface ocean Prochlorococcus and SAR11 are distributed widely across the surface ocean.

Thompson, L.R., M.F. Haroon, A.A. Shibl, M.J. Cahill, D.K. Ngugi, G.J. Williams, J.T. Morton, R. Knight, K.D. Goodwin and U. Stingl (2019). Red Sea SAR11 and Prochlorococcus single-cell genomes reflect globally distributed pangenomes. Appl Environ Microbiol. https://doi.org/10.1128/AEM.00369-19.

Field Work

● Patrick Mears is participating in the GO-Ship IO6S research cruise for 39 days, onboard the University of Washington's, RV Thomas G. Thompson as a shipboard analyst measuring Dissolved Inorganic Carbon. You can follow updates from the cruise at: https://usgoship-i06s2019.blogspot.com/.

● Dr. Derek Manzello, Mike Jankulak, and Graham Kolodiez will travel to Pago Pago, American Samoa from 5-15 May to deploy a MAPCO2 buoy in Fagatele Bay National Marine Sanctuary in support of NOAA's National Coral Reef Monitoring Program. This is the second sentinel ocean acidification monitoring station to be established on a coral reef in the US Pacific and represents a collaborative effort with NOAA's Pacific Marine Environmental Laboratory, Coral Reef Conservation Program, Ocean Acidification Program, Pacific Islands Fisheries Science Center, National Marine Sanctuaries of American Samoa, as well as PacIOOS, the National Park Service of American Samoa, Department of Marine and Water Resources of American Samoa, and the Coral Reef Advisory Group of American Samoa.

● On May 1-28, 2019, Dr. Luke Thompson will sail from Cape Verde to Oslo aboard the Norwegian icebreaker the RV KRONPRINS HAKON. The cruise is part of a US-Norway bilateral project on eDNA to investigate a potential new fishery. eDNA analysis will be used to characterize the species composition of the fish community in the mesopelagic layer.

Announcements

● The Global Climate Change Alliance has agreed to fund the Caribbean Community Climate Change Center, headquartered in Belize, for another phase of Coral Reef Early Warning System (CREWS) station installations in the Caribbean. There will be four stations, but which ones of the 14 CARICOM stations has not yet been decided. Site surveys will begin in September, with expected continue participation by AOML personnel Natchanon Amornthammarong, Joe Bishop, and Jim Hendee.

● Dr. Lew Gramer completed a project to develop an Ecological Forecasting Toolkit for the MATLAB programming language, by creating a GitHub repository for the project under the NOAA-CHAMP Profile. This culminates the development and testing of approximately 850 functions and scripts, totaling over 200,000 lines of MATLAB code, during Lew's 12+ years working for OCED. The Toolkit supports the analysis of in situ, model, and satellite environmental data, as well as high-resolution bathymetry and reef habitat data, for reef ecosystems around the world. It stands alone, but will also contribute to future efforts to implement "ecoforecasts" using Python and other open-source components as well.

● Madison Soden has rejoined the OCED CHAMP team as a part-time CIMAS employee. Madison is working with Drs. Amornthammarong and Dr. Lew Gramer, on adapting the EISES ecological forecasting system, newly ported to the Python programming language, for a near-real time ocean monitoring project near Port Everglades (Ft. Lauderdale).

April 29, 2019

Meetings

● Dr. Derek Manzello was invited to be an associate member of the InterSEEP working group. This working group will coordinate interdisciplinary international studies using natural CO2 gradients on seeps worldwide to analyze current data available, plan in situ observations, agree to a set of standard techniques for work in seeps, and establish a foundation for long-term capacity building. Dr. Manzello is the US representative in the group that includes scientists from Spain, England, Australia, Japan, Ecuador, France, Italy, Norway, Colombia, New Zealand, and Japan.

● Kelly Montenero is attending and is on the facilitation team for the Olympic Coast National Marine Sanctuary's ecological indicator vetting workshop in Seattle as a collaboration between IEA regions on April 30-May 3. The Olympic Coast National Marine Sanctuary is going to emulate the indicator selection process Kelly developed for the Florida Keys.

● Dr. Kelly Goodwin gave a talk at SWFSC: "NOAA's 'Omics Roadmap with emphasis on eDNA activities" at the Southwest Fisheries Science Center.

Manuscripts

● A machine learning approach to estimate surface ocean pCO2 from satellite measurements, Chen, S., H. Hu, B. B. Barnes, R. Wanninkhof, W.-J. Cai, L. Barbero, D. Pierrot. Remote Sensing of Environment, RSE 11166.

● Pacific anthropogenic carbon between 1991 and 2017, Carter B.R. Feely, R.A., Wanninkhof, R., Kouketsu, S., Sonnerup, R.E., Pardo, P.C., Sabine C.L., Johnson, G. C., Sloyan, B.M., Murata, A., Mecking, S., Tilbrook, B., Speer, K., Talley, L.D., Millero, F.J., Wijffels, S.E., Macdonald, A.M., Gruber, N., Bullister, J. L. Global Biogeochemical Cycles. Paper #2018GB006154R. Accepted for publication in Remote Sensing of Environment.

This paper explores the use of a random forest based regression ensemble (RFRE) to estimate surface pCO2 in the Gulf of Mexico and after extensive testing under different scenarios and validation with observations finds that this approach is more robust than other approaches such as multi-linear regression (MLR), or principle component regression (PCR).

Field Work

● Patrick Mears is participating in the GO-Ship IO6S research cruise for 39 days, onboard the University of Washington's, RV Thomas G. Thompson as a shipboard analyst measuring Dissolved Inorganic Carbon. You can follow updates from the cruise at: https://usgoship-i06s2019.blogspot.com/.

● Dr. Chris Kelble, Joe Bishop, Ian Smith, and Charline Quenee conducted a South Florida Ecosystem restoration Research Cruise on the R/V Walton Smith on April 29 - May 3. This cruise was modified to sample up to Charlotte Harbor to collect data at the one of the epicenters of the 2018 red tide.

● Dr. Ian Enochs and John Morris conducted fieldwork at three volcanically-acidified coral reefs in the Philippines as part of collaborative work with the University of the Philippines and Dr. Maria Mcglone. The University of Philippines used subsurface autosamplers (SAS) developed at NOAA/AOML to characterize the diel fluctuations in carbonate chemistry. Dr. Enochs gave a presentation on his research into similar reef/vent sites and served as PhD reader for University of Philippines masters student.

April 22, 2019

Meetings

● Dr. Chris Kelble is presenting "Long-term and Short-term trends in juvenile spotted seatrout recruitment in Florida Bay" at the Greater Everglades Ecosystem Restoration conference on Tuesday, April 23.

● Dr. Chris Kelble is hosting the Florida Keys National Marine Sanctuary, Marine Biodiversity Observation Network (MBON) and Integrated Ecosystem Assessment Product Development Workshop on April 24 and 25 in the first floor conference room of AOML.

● Nicole LeBouef, Acting AA for NOS, will be hosting an informational session on NOAA's South Florida Ecosystem Restoration Participation at SALT on Wednesday, April 24 at 5:30 pm.

● Dr. Chris Kelble will attend the South Florida Ecosystem Restoration Task Force Meeting on Friday, April 27. Chris serves on the Science Coordination group for the task force and helps to staff Nicole Lebouef the NOAA Task Force member.

Field Work

● Patrick Mears is participating in the GO-Ship IO6S research cruise for 39 days, onboard the University of Washington's, RV Thomas G. Thompson as a shipboard analyst measuring Dissolved Inorganic Carbon. You can follow updates from the cruise at: https://usgoship-i06s2019.blogspot.com/.

● Dr. Maribeth Gidley will be collecting eDNA on legs 2 and 3 of the Reef Fish Visual Survey aboard the R/V Pisces. This is the first gulf-wide water column eDNA collection to support the AOML-SEFSC omics collaborative. The project aims to develop habitat-occupancy relationships from eDNA and models from environmental covariates.

April 15, 2019

Meetings

● Dr. Chris Kelble met with the Fort Myers Beach City Council on April 15 about his red tide work and collaboration with local fishermen.

● Dr. Chris Kelble met with NGI on April 17 to April 19 to further the project on Biscayne Bay by discussing the next phase which focuses on watershed modeling.

● Dr. Kelly Goodwin spoke at the SWFSC about NOAA's 'Omics Roadmap with emphasis on eDNA activities.

Field Work

● Patrick Mears is participating in the GO-Ship IO6S research cruise for 39 days, onboard the University of Washington's, RV Thomas G. Thompson as a shipboard analyst measuring Dissolved Inorganic Carbon. You can follow updates from the cruise at: https://usgoship-i06s2019.blogspot.com/.

● Dr. Maribeth Gidley will be collecting eDNA on legs 2 and 3 of the Reef Fish Visual Survey aboard the R/V Pisces. This is the first gulf-wide water column eDNA collection to support the AOML-SEFSC omics collaborative. The project aims to develop habitat-occupancy relationships from eDNA and models from environmental covariates.

Instrument Development

● Dr. Natchanon Amornthammarong has further developed his new low cost temperature logger to consume much less power and thus can now operate up to 18 months using three AA batteries. The new sensor is now also easier to build than the previous one. This development comes under the aegis of the Opuhala Project to monitor sea temperatures in situ at coral reefs around the world.

April 8, 2019

Meetings

● Dr. Rik Wanninkhof attended the observation coordination group meeting of JCOMM (JCOMM OCG-10 at the Indonesain Meteorological Institute BMKG in Jakarta, Indonesia from April 8-11. He will present the annual report of GO-SHIP and discuss development of the surface water CO2 reference network, SOCONET.

● Dr. Chris Kelble attended the Center for Coastal and Marine Ecosystems annual meeting in La Jolla, CA on April 11-12. Chris serves as the OAR co-technical monitor for CCME which is a NOAA Office of Education funded program. If anyone is interested in hosting a CCME intern for 12-weeks, please let Chris know before he goes to the meeting.

● Dr. Lew Gramer (CIMAS) participated in the Technical Advisory Committee of the South East Florida Coral Reef Initiative (SEFCRI TAC), at Nova Southeastern University's Oceanographic Center on April 10-11. Lew will be co-hosting Belgian PhD student Thomas Dobbelaere (Universite Catholique de Louvain), who will do a presentation for the TAC on methods and some preliminary results from a high-resolution ocean modeling and Lagrangian particle tracking experiment. The numerical experiment is intended to inform manager responses to the ongoing mass coral disease outbreak in the Florida reef tract ("Stony Coral Tissue Loss Disease" or SCTLD).

Field Work

● Patrick Mears is participating in the GO-Ship IO6S research cruise for 39 days, onboard the University of Washington's, RV Thomas G. Thompson as a shipboard analyst measuring Dissolved Inorganic Carbon. You can follow updates from the cruise at: https://usgoship-i06s2019.blogspot.com/.

● AOML Scientist Dr. Silvia Garzoli assisted CIMAS Scientists Dr. Natchanon Amornthammarong and Dr. Lew Gramer with a test of the 'Xbee' mesh-network temperature sensor package, by allowing one to be installed on her condo roof on Brickell Bay Drive. The sensor will be transmitting temperature data back every 10 minutes from that location ashore to the AOML roof. The aim of the inexpensive new technology is to allow sea temperatures to be measured very densely and in near real-time, to inform management of coral reefs worldwide.

April 1, 2019

Meetings

● Dr. Nancy Williams of PMEL will be visiting AOML and RSMAS as a CIMAS visitor, this Monday and Tuesday (April 1, and 2) and giving a talk: "Bridging observational scales using autonomous biogeochemical platforms (BGC-Argo)". The visit is to inform us about the "next big thing in ocean biogeochemistry" and expanding the utility of profiling floats, with our [AOML/RSMAS/CIMAS] strong interests to gain expertise and become leaders in this area. She has expressed interest in meeting folks interested in BGC Argo. She will be hosted by Dr. Leticia Barbero and Dr. Rik Wanninkhof.

Field Work

● Patrick Mears is participating in the GO-Ship IO6S research cruise for 39 days, onboard the University of Washington's, RV Thomas G. Thompson as a shipboard analyst measuring Dissolved Inorganic Carbon. You can follow updates from the cruise at: https://usgoship-i06s2019.blogspot.com/.

March 25, 2019

Manuscripts

● "Time of detection as a metric for prioritizing between climate observation quality, frequency, and duration", co-authored by Dr. Leticia Barbero was accepted for publication in Geophysical Research Letters. The paper proposes a simple framework for estimating the observational needs of studies assessing climate changes amidst natural variability. This approach aims to connect the Global Ocean Acidification Observing Network "weather" and "climate" data quality thresholds with a single dynamic threshold appropriate for a range of potential ocean signals and environments.

● "Carbon cycling in the North American coastal ocean: A synthesis", co-authored by Leticia Barbero was accepted for publication in Biogeosciences. The article presents recent progress in characterizing carbon fluxes in the coastal ocean and across its boundaries, specifically the air-sea, land-to-coastal-ocean and coastal-to-open-ocean interfaces with a focus on the North American coastal ocean.

Field Work

● This week Mike Jankulak traveled to Key Largo to prepare the Cheeca Rocks MApCO2 buoy for redeployment after its annual swapout and refurbishment on land. Mike spent four days last week removing swapping out components and doing a full test of all systems post-swap. Mike works with a Keys-based contractor who does the boating/diving work for buoy recovery/deployment, and with PMEL personnel who oversee the MApCO2 program. The buoy measures pCO2 of sea and air as well as sea temperatures, pH, salinity, oxygen, turbidity, and other parameters, and its data set dates back to 2011.

● Dr. Derek Manzello, Mike Jankulak, and Graham Kolodziej will travel to Pago Pago, American Samoa from 7-17 April to deploy a MAPCO2 buoy in Fagatele Bay National Marine Sanctuary in support of NOAA's National Coral Reef Monitoring Program. This is the second sentinel ocean acidification monitoring station to be established on a coral reef in the US Pacific and represents a collaborative effort with NOAA's Pacific Marine Environmental Laboratory, Coral Reef Conservation Program, Ocean Acidification Program, Pacific Islands Fisheries Science Center, National Marine Sanctuaries of American Samoa, as well as PacIOOS, the National Park Service of American Samoa, Department of Marine and Water Resources of American Samoa, and the Coral Reef Advisory Group of American Samoa.

● Patrick Mears will be traveling to Cape Town, South Africa at the end of March to participate on the GO-Ship IO6S research cruise for 39 days, onboard the University of Washington's, RV Thomas G. Thompson as a shipboard analyst measuring Dissolved Inorganic Carbon. To learn more about the GO-Ship program: https://www.go-ship.org/About.html

Meetings

● On March 26, Dr. Kelly Goodwin (AOML) and Mark Strom (NWFSC) will give a presentation on the NOAA 'Omics Roadmap at the joint NMFS Science Board/OAR Senior Research Council Bilat meeting in La Jolla, CA (March 26-27).

● This Wednesday Dr. Maribeth Gidley will be attending the University of South Florida Oceans and Human Health Workshop held at the John's Hopkins All Children's Hospital and Research Center in St Petersburg Florida. This workshop was prompted in part by the recent prolonged Red Tide on the Florida west coast, and concerns of its health impacts.

Outreach

● Almost 60 temperature loggers designed by Dr. Natchanon Amornthammarong, OCED, AOML were built by students of two magnet schools in Broward. Many more students and schools will participate in this activity to build more temperature loggers in the near future. This effort is being led by Dr. Pamela Fletcher, Assistant Professor, Broward College. Each temperature logger will be named after the student who build it. After the temperature logger is deployed, the student's name will be shown on our Opuhala website along with the location of the logger on a Google map.

March 18, 2019

Manuscripts

● The paper entitled "Seasonal carbonate chemistry dynamics on southeast Florida coral reefs: localized acidification hotspots from navigational inlets" led by OCED's Dr. Ian Enochs was accepted for publication in Frontiers in Marine Science. Carbonate chemistry measurements were made on a bi-monthly basis from seven sites off of southeast Florida (Miami-Dade and Broward counties), including four reefs and three closely-associated inlets. Significant seasonal fluctuations were observed on reef sites, with elevated pCO2 in the warmer wet season. Periodic pulses of acidified water were observed at inlet sites. These data highlight the important role that inlets play on shallow-water carbonate chemistry dynamics within southeast Florida waters and underscore the degree to which engineered freshwater systems can contribute to coastal acidification on localized scales.

● Full Citation: Enochs IC, Manzello DP, Jones PJ, Stamates J, Carsey T (2019) Seasonal carbonate chemistry dynamics on southeast Florida coral reefs: localized acidification hotspots from navigational inlets. Frontiers in Marine Science, doi: 10.3389/fmars.2019.00160.

Field Work

● Dr. Chris Kelble, Ian Smith, Brianna Alanis (CCME intern), and Charline Quenee will be sampling juvenile sportfish in Florida Bay on March 18-21. This project examines how sportfish in Florida Bay respond to freshwater inflows from the Everglades and evaluates how the proposed changes in freshwater inflow will alter juvenile sportfish habitat suitability in Florida Bay.

Meetings

● Dr. Rik Wanninkhof is in Tokyo, Japan from March 16-22 as an Invited lead NOAA investigator to participate in the Global Ocean Observing System (RECCAP2) workshop.

●Drs. Christopher Sinigalliano and Maribeth Gidley of the AOML Molecular and Environmental Microbiology Program have been invited by the Consul of the Kingdom of the Netherlands to participate in a special "Smart Cities Session on Water Quality and Resilience" to be held aboard the Dutch tall ship Stad Amsterdam while it is docked here in Miami on Wednesday March 20th. They will join a panel of experts from the Netherlands and from South Florida aboard to discuss joint challenges as to water quality and resilience, and to share lessons learned while looking for solutions to help make our cities more resilient. The breakout discussion topics will include: "sea level rise and water quality", "storm water pollution and green infrastructure", "algae and phosphorus", and "governance and water".

Outreach

● A high school student from the School for Advanced Studies shadowed Leah Chomiak and Liz Dutra Monday afternoon and assisted with experimental data acquisition for the ACCRETE Lab's newest experiment in the Environmental Reef Lab.

March 11, 2019

Manuscripts

● Dr. Catalina Aguilar co-authored the paper "Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress" which was published in the journal BMC Genomics. The paper uses transcriptomics to understand the effects of reduced salinity on corals. During extreme floods that are known to occur during the Great Barrier Reef summer, corals can be exposed to salinities below 25 PSU for days. The data presented here highlight the specific metabolic pathways involved in the response of coral adults and juveniles to salinity stress. Corals experience dramatic changes at the molecular level that are similar to the response to extreme heat stress. Press release: https://www.eurekalert.org/pub_releases/2019-02/acoe-rso022419.php.

Aguilar C, Raina J-B, Foret S, Hayward DC, Lapeyre B, Bourne DG, Miller DJ: Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress. BMC Genomics 2019, 20(1):148.

● Dr. Stephanie Rosales and Rebecca Vega Thurber had their manuscript, "A draft genome of phocine herpesvirus-1 sequenced from the brain of a harbor seal" accepted by Microbiology Resource Announcements (full citation not yet known). Phocine herpesvirus (PhHV-1) is a viral pathogen with high prevalence, morbidity, and mortality in harbor seals. In this study, metagenomics was used to assemble the PhHV-1 genome from the brain tissue of a harbor seal. The manuscript presents a 119kb draft genome of PhHV-1 comprising of 76 open reading frames.

● Dr. Luke Thompson traveled to NOAA Headquarters for the OAR Annual Awards Ceremony on Tuesday, March 12, 2019 to receive the Outstanding Scientific Paper Award in the Oceans and Great Lakes category.

● The paper being recognized is: A communal catalogue reveals Earth's multiscale microbial diversity. Nature 551: 457-463, doi:10.1038/nature24621. Thompson, L., Sanders, J., McDonald, D., Amir, A., Ladau, J., Locey, K., Prill, R., Tripathi, A., Gibbons, S., Ackermann, G., Navas-Molina, J., Janssen, S., Kopylova, E., Vazquez-Baeza, Y., Gonzalez, A., Morton, J., Mirarab, S., Xu, Z., Jiang, L., Haroon, M., Kanbar, J., Zhu, Q., Song, S., Kosciolek, T., Bokulich, N., Lefler, J., Brislawn, C., Humphrey, G., Owens, S., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J., Clauset, A., Stevens, R., Shade, A., Pollard, K., Goodwin, K., Jansson, J., Gilbert, J., Knight, R., and The Earth Microbiome Project Consortium.

Seminars

● On March 12, Ana Palacio gave a seminar entitled "Symbiodiniaceae community dynamics: implications for coral bleaching susceptibility and recovery" in the First Floor Conference Room. Ana is a prospective NRC candidate to work as a post-doc in OCED.

● Synopsis: Anticipating increasingly frequent bleaching conditions in the near future, it is essential to assess the role of the endosymbiotic algal communities (family Symbiodiniaceae) in coral bleaching susceptibility, as well as the factors that promote more resistant coral-algal symbiosis. I use highly sensitive qPCR assays to monitor the dynamic changes in Symbiodiniaceae communities during heat stress and recovery, and during the exposure to additional stressors such as elevated nutrients and CO2. During natural bleaching events in Florida and Panama, I evaluate the potential of multiple coral species to increase their temperature tolerance through the acquisition of thermotolerant symbiont communities. Additionally, since annual bleaching conditions are expected to become common in the next decades, I monitor the persistence of acquired thermoresistant symbiont communities under non-stressful temperatures and evaluate how the frequency of heat disturbances affects the community trajectory. Finally, because global warming will likely interact with other local and global stressors, I assess the effect of elevated nutrients and CO2 on pre-bleaching symbiont communities and further bleaching susceptibility. Between predicted back-to-back bleaching events and the likelihood that global carbon emissions exceed RCP4.5, understanding the dynamic relationship between corals and their algal symbionts is key to helping researchers protect the future of coral reefs.

Field Work

● In collaboration with AOML scientists Dr. Stephanie Rosales, Dr. Lew Gramer, Dr. Jia-Zhong Zhang and Dr. Natchanon Amornthammarong, SEFSC scientists Dana Williams, Allan Bright and Annabeth Peterson, and RSMAS scientists Nikki Traylor Knowles, Ben Young, Ana Palacio, and Carly Denison, approximately 500 tissue samples from outplanted Acropora spp. were collected, across four reefs in the Upper Florida Keys. In addition, 44 Opuhala (Natchanon's new design) thermistors were collected and another 40 were redeployed, coral outplant health was assessed, and water samples for nutrient analyses were collected. This is an effort to understand how the environment, host genetics, and host microbiome contribute to outplant success. Following is a graph (admittedly difficult to interpret at this point) of a little section of the time series from the 44 sensors from the project which has so far successfully recovered data from four different reefs in the Upper Keys.

● The ACCRETE Team, in collaboration with the Lirman Lab at RSMAS, initiated two large experiments focused on NOAA CRCP's restoration pillar. The projects will attempt to develop methods for conferring thermal resilience, and quantify genotypic differences in coral performance with the goal of data-informed restoration and outplanting.

March 4, 2019

Meetings

● Dr. Luke Thompson will receive the OAR award for outstanding scientific paper on Oceans and Great Lakes on Tuesday, March 12.

AOML Leadership Changes

● The Deputy Assistant Administrator for Science, Dr. Gary Matlock, will be the official Acting AOML Director effective Monday, March 4, 2019, (upon Bob's retirement) until Dr. Atlas' replacement is chosen. Molly will remain as the AOML Deputy Director. While Molly is on travel in March, Frank Marks will be serving as Acting Deputy Director and Rick Lumpkin will be assisting with the duties of the Deputy Director.

Coral Reef Conservation Program Funding

● OCED will receive $885K from the Coral Reef Conservation Program to conduct research on coral reefs and their ecosystems. This funding includes $470K for the continuation of the National Coral Reef Monitoring Program (NCRMP) efforts in OCED and $415K to support efforts examining land-based sources of pollution and climate change impacts on coral reefs, including how restoration efforts can improve their efficacy.

February 25, 2019

Manuscripts

● Dr. Rik Wanninkhof is a co-author of manuscript aau5153, entitled "The oceanic sink for anthropogenic CO2 from 1994 to 2007" by Gruber et al. This manuscript was accepted for publication in Science. A press release will be initiated by ETH Zurich.

● The paper entitled "Autonomous seawater pCO2 and pH time series from 40 surface buoys and the emergence of anthropogenic trends" with AOML/OCED co-author Derek Manzello was accepted for publication in Earth System Science Data. This paper presents data from 40 individual autonomous moored surface ocean pCO2 time series established between 2004 and 2013. These time series characterize a wide range of surface ocean carbonate conditions in different oceanic (17 sites), coastal (13 sites), and coral reef (10 sites) regimes. A time of trend emergence (ToE) methodology indicates that the length of sustained observations necessary to detect statistically significant anthropogenic trends in pCO2 varies by marine environment. The ToE estimates range from 8 to 15?years at the open ocean sites, 16 to 41?years at the coastal sites, and 9 to 22?years at the coral reef sites.

● Full Citation: Sutton A, Feely R, Maenner-Jones S, Musielwicz S, Osborne J, Dietrich C, Monacci N, Cross J, Bott R, Kozyr A, Andersson A, Bates N, Cai W-J, Cronin M, De Carlo EH, Hales B, Howden S, Lee C, Manzello DP, McPhaden M, Melendez M, Mickett JB, Newton J, Noakes S, Noh JH, Olafsdottir RS, Salisbury J, Send U, Trull T, Vandemark D, Weller R (2019), Autonomous seawater pCO2 and pH time series from 40 surface buoys and the emergence of anthropogenic trends. Earth System Science Data In Press.

Meetings

● Dr. Rik Wanninkhof is a co-author of a poster to be presented at the annual meeting of ASLO this week. The poster, "Decadal trends of carbonate chemistry variables along the North America east coast," is led by Y.-Y. Xue of the University of Delaware. The research was sponsored by the NOAA Ocean Acidification program (OAP).

Announcements

● Dr. Chris Kelble has been nominated to serve on the Biscayne Bay Task Force for Miami-Dade County. His CV is being submitted with other nominees to the Miami-Dade Clerk of the Board for consideration. There should be a vote on the nominees by the County Commissioners in the end of March and the task force should be enpaneled shortly thereafter.

● Dr. Chris Kelble has also been nominated to serve of the Florida Department of Agriculture science-based Solution task force, https://fdacs-solutiontaskforce.com/. Dr. Kelble was nominated as a result of his work investigating red tide dynamics in 2018 and ongoing collaboration with commercial fishermen to increase monitoring efforts on Florida's west coast.

February 19, 2019

Meetings

● Charline Quenee is attending the Florida Keys National Marine Sanctuary - Sanctuary Advisory Committee meeting in Marathon on February 19, and conducting surveys in Key West and Key Largo on February 20 and 21. The surveys are designed to collect data on stakeholder perception of management for the Sanctuary and form the basis for Charline’s MS degree.

February 11, 2019

Field Work

● Dr. Denis Pierrot is in Charleston, SC to get the underway pCO2 system ready for the start of the season. He will assist in the installation of a Picarro system which will perform atmospheric xCO2 measurements in a comparison exercise with the AOML pCO2 system. Both systems will be tested at sea during a 3-day sea trial Feb.11-13, tentatively.

Visitors

● Dr. Craig McLean (AA for OAR) and Dr. Neil Jacobs (NOAA's Assistant Administrator) will be at AOML Monday from 3-4 PM to say hello and check-in post shutdown. There will be a brief all-hands meeting at 3 PM in the AOML lobby.

February 3, 2019

Welcome Aboard

● Brianna Alanis began her internship today at OCED. Brianna is a student with the Center for Coastal and Marine Ecosystems at the University of Texas-Rio Grande Valley. She is being mentored by Chris Kelble. Brianna is investigating correlations among water quality and primary productivity off of the Shark River with salinity, temperature, and river discharge.

Manuscripts

● The paper "A novel sparse compositional technique reveals microbial perturbations" with co-author Dr. Luke Thompson was accepted for publication inmSystems (American Society for Microbiology). The paper describes a new method for calculating differences between microbiomes and other community datasets. The method, Robust Aitchison PCA, accounts for the sparse compositional nature of microbiome and other ecological datasets. The method has been tested on sponge-associated and human-associated microbial communities, yielding high discriminatory power and salient feature ranking between microbial niches.

Field Work

● Kelly Montenero, Ian Smith, and Brianna Alanis will be conducting the juvenile sportfish survey in Florida Bay from February 5-8. This will be the first dry season survey of this year, because of the government shutdown. The dry season surveys focus on developing a better understanding of trophodynamics through the use of isotope analysis.

AOML GITHUB ORGANIZATION

● Dr. Luke Thompson has created a GitHub organization for AOML: https://github.com/NOAA-AOML. Several of the other NOAA labs have GitHub organizations (pages), which are listed at the main NOAA organization: https://github.com/NOAAGov/NOAA-Affiliated-Projects.

The purpose of a lab-wide GitHub page is to share code across the lab and with the public, especially code that might be reused by others. The organization contains two repositories so far (for microbiome sampling and analysis), but it's just getting started. Anyone at AOML who develops any kind of code (MATLAB, R, Python, FORTRAN, etc.) for any kind of research (hurricanes, ocean chemistry, ecosystems, or physical oceanography) is encouraged to create repositories and host them on the AOML page.

The purpose of a lab-wide GitHub page is to share code across the lab and with the public, especially code that might be reused by others. The organization contains two repositories so far (for microbiome sampling and analysis), but it's just getting started. Anyone at AOML who develops any kind of code (MATLAB, R, Python, FORTRAN, etc.) for any kind of research (hurricanes, ocean chemistry, ecosystems, or physical oceanography) is encouraged to create repositories and host them on the AOML page.

If you're not familiar with GitHub and want to learn how to use it, check out these resources:
✲ What is GitHub?" video: https://www.youtube.com/watch?v=w3jLJU7DT5E"
✲ Nuts and bolts tutorial from Luke: https://github.com/cuttlefishh/python-for-data-analysis/blob/master/lessons/lesson20.md"

To use the AOML GitHub page:
✲ Create yourself a GitHub account that you'll use for NOAA-related work. This is separate from any personal account you might have.
✲ Request to join the NOAA-AOML organization.
✲ Create a code repository on your NOAA GitHub account. See the attached policy document for guidance.
✲ When your repository or "repo" is sufficiently mature, migrate it over to the NOAA-AOML organization.
✲ You or others can suggest changes to the code and issue a "pull request" to have those changes "merged".

The attached document NOAA GitHub Usage Guidelines.pdf provides guidance on NOAA's GitHub policy. If you have questions about how to use GitHub or the AOML GitHub organization, feel free to contact Dr. Luke Thompson (luke.thompson@noaa.gov).

December 17, 2018

Manuscripts

● The manuscript entitled "Role of host genetics and heat tolerant algal symbionts in sustaining populations of the endangered coral Orbicella faveolata in the Florida Keys with ocean warming" authored by OCED scientists Derek Manzello, Ian Enochs, Graham Kolodziej, and Mike Jankulak was accepted for publication in Global Change Biology. During the second year of back-to-back bleaching events in the Florida Keys in 2014 and 2015, OCED scientists characterized key environmental and biological factors associated with bleaching resilience in the threatened reef-building coral Orbicella faveolata. On inshore reefs in the upper Florida Keys, despite significantly higher temperatures, O. faveolata was most abundant, had the highest bleaching resistance, and contained the most corals dominated by heat tolerant algal symbionts, illustrating a causal link between heat tolerance and ecosystem resilience in an era of global change. Our results show that in the Florida Keys, O. faveolata coral-symbiont associations have adapted and/or acclimatized on inshore reefs to conditions up to ~1@deg;C warmer than the offshore sites, providing a potential source of heat tolerant genotypes to help shepherd this ESA listed species through this century.

Manzello DP, Matz M, Enochs IC, Valentino L, Carlton R, Kolodziej G, Serrano X, Towle E, Jankulak M (In press). Role of host genetics and heat tolerant algal symbionts in sustaining populations of the endangered coralOrbicella faveolata in the Florida Keys with ocean warming. Global Change Biology doi: 10.1111/gcb.14545.

Meetings

● Dr. Derek Manzello, Nathan Formel, Dr. Ian Enochs, and Dr. Lew Gramer attended the Reef Futures Conference in Key Largo this week. Manzello and Enochs gave presentations on potential mechanisms of coral resilience and maximizing restoration success. Lew Gramer presented results from a just-completed study (Rosales et al.) relating coral microbiomes to their physical oceanographic habitat in Southeast Florida, some preliminary analysis from an ongoing Omics-funded project on Acroporid disease in the Florida Keys, and a little about planned future work on modeling coral disease dispersal.

● Dr. Luke Thompson will attend the 1st Parasite Microbiome Project Workshop in Clearwater, Florida, from January 10-14, 2019. This workshop, hosted by the Gordon and Betty Moore Foundation, is the kickoff meeting for the Parasite Microbiome Project, which seeks to improve understanding of microbial interactions with parasites. Dr. Thompson will give a presentation about the Earth Microbiome Project, to help inform the transfer of technologies and knowledge gained from previous microbiome projects to improve hypotheses and objectives for the Parasite Microbiome Project.

Field Work

● Kelly Montenero, Ian Smith and Charline Quenee are participating on a South Florida Ecosystem Research cruise on December 17-21 aboard the R/V Walton Smith. This cruise will again be modified to better sample the ongoing HAB event on the southwest Florida shelf.

Project Updates

● AOML/OCED is entering into an agreement with the Reef Check Foundation to deploy Dr. Mana Amorthammarong's sea temperature sensors at coral reef sites around the globe. The project is called the Opuhala Project, named for the Hawaiian goddess of corals and spiny creatures, in which sensors will be deployed at 5m, 10m, and 15m, and at fringing reefs, barrier reefs, and atolls (where appropriate), and will be used to not only track the record of sea temperatures at coral reefs around the globe, but also the condition of the coral reefs where they are being deployed, using the widely utilized Reef Check monitoring protocol. Results and observations from field monitoring will be reported on custom blogs, and the data will be uploaded to the CHAMP Web site using specialized software that Mana has developed. The sea temperatures derived from the Opuhala sensors will also be utilized by Ruben van Hooidonk and colleagues to fine-tune satellite algorithms to better predict sea temperatures under the conditions and locations where the sensors will be deployed. A paper just written on the test deployment off Broward County last year is currently undergoing final edits and will be circulated for internal review soon, before submission to the Bulletin of Marine Science. The results of the first year's study (all of 2019) will be reported at the 14th International Coral Reef Symposium in July, 2020, in Bremen, Germany. Our attorney in OAR, Roxie Allison-Holman, is making sure we are not exporting technology contrary to our deemed export guidelines.

December 10, 2018

Farewell

● Dr. Neda Trifonova is leaving AOML for a position at the University of Aberdeen. Her last day is this Friday, December 14th. We will be going to happy hour on Friday at the RSMAS commons to send her off. Please join us in wishing her the best of luck.

Manuscripts

● Dr. Chris Kelble is a co-author of the essay Effective, Science-Based Fishery Management is Good for Gulf of Mexico's "Bottom Line" - but Evolving Challenges Remain: that was accepted for publication in Fisheries. The article highlights the successes that fisheries management has achieved in the Gulf of Mexico, while also explaining the challenges that remain. It discusses the importance of including environmental conditions to overcome the remaining challenges.

● Dr. Neda Trifonova authored and Dr. Chris Kelble co-authored the manuscript entitled "Predicting ecosystem components in the Gulf of Mexico and their responses to climate variability with a dynamic Bayesian network model" that is accepted for publication in PLoS One. This manuscript uses a data-driven Bayesian network model to predict how the Gulf of Mexico ecosystem will be affected by rising Sea-Surface Temperatures.

Meetings

● Dr. Lew Gramer is speaking at REEF FUTURES 2018 in Ocean Reef Club, Key Largo, during the Wednesday afternoon (Dec. 12th) sessions. He will present results from a just-completed study (Rosales et al.) relating coral microbiomes to their physical oceanographic habitat in Southeast Florida, some preliminary analysis from an ongoing Omics-funded project on Acroporid disease in the Florida Keys, and a little about planned future work on modeling coral disease dispersal.

November 26, 2018

Meetings

● The NOAA Senior Research Council will be meeting in the AOML library on Tuesday and Wednesday, November 27 and 28.

● On Wednesday, November 28 there will be an all hands 'omics meeting with Libby Jewett, the program manager for 'omics. It will take place in the first floor conference room from 1-4pm. All 'omics PIs should plan to attend. Formal presentations are not desired, but you may show a slide or two if it helps communicate your message. Please be prepared to discuss:

   Progress on the milestones and deliverables listed in both FY18 and prior statements of work. Written
   highlights are strongly encouraged, particularly for FY16 and FY17 statements of work.

   Plans and ideas for FY19 and beyond. Keep in mind that only federal employees can be present if you
   wish to discuss pre-decisional specifics.

Field Work

● Ian Smith, Kelly Montenero, Dr. Chris Kelble, and Charline Quenee will be conducting a survey of juvenile sportfish in Florida Bay on November 27-30. This will complete this year's field sampling for the project that assesses and evaluates the impacts of Everglades Restoration Projects on the valuable sportfish populations of Florida Bay.

November 19, 2018

Meetings

● Dr. Ian Enochs gave a presentation to NOAA's Ocean Acidification Working Group on Subsurface Automated Samplers that he developed in collaboration with Nate Formel. Further information on the use and construction of the samplers can be found at https://www.coral.noaa.gov/accrete/sas/.

Review Panels

● Dr. Chris Kelble has been selected to serve as a reviewer for the "Cooperative Institute for the North Atlantic Region" competition that just closed. The proposed CI will serve a critical function at the juncture of the interdependent global and regional observing systems in the North Atlantic Ocean and those of the Northeast U.S. Shelf Large Marine Ecosystem (NEUS LME). In so doing, the Institute will link basin-scale climate observations to ecosystem-scale monitoring, assessments, and decision making. Broad scale climate observations will also be integrated into the Global Ocean Observation System. . The intent of this CI is to expand and improve our ability to collect, deliver, and use ocean information to study the effect of climate change on various spatial scales including regions, LMEs, and the Nation.

Field Work

● Ian Smith, Kelly Montenero, Chris Kelble, and Charline Quenee will be conducting a survey of juvenile sportfish in Florida Bay on November 27-30. This will complete this year's field sampling for the project that assesses and evaluates the impacts of Everglades Restoration Projects on the valuable sportfish populations of Florida Bay.

November 13, 2018

Meetings

● Kelly Montenero will attend the Sanctuary Advisory Committee meeting of Channel Islands National Marine Sanctuary and meet with colleagues there to discuss applying the IEA approach to Sanctuary Condition Reports on November 14-17.

Field Work

● Dr. Denis Pierrot will be taking various samples and test the newly installed pCO2 system on board the M/V Selfoss. Denis will be sailing between Reykjavic, Iceland and Portland, ME on a 10-day transit across the North Atlantic as part of a collaboration with LOCEAN in France and the Marine Institute in Iceland.

Announcements

Climate.gov has published a piece on their homepage on Dr. Ruben van Hooidonk's article "Opposite latitudinal gradients in projected ocean acidification and bleaching impacts on coral reefs". It shows how ocean warming will drive corals to the poles, but ocean acidification works in the opposite direction leaving little space for corals if we don't curb our emissions. It is a feature on the climate.gov homepage:
https://www.climate.gov/news-features/featured-images/no-safe-haven-coral-combined-impacts-warming-and-ocean-acidification

● NOAA's Integrated Ecosystem Assessment Program has just launched it's new website and is requesting your feedback. Our goal with this website is to provide our scientists, management partners, stakeholders, and others with an understanding of what an Integrated Ecosystem Assessment is, where and how they are currently being implemented, and other ecosystem science needed to make informed decisions. As an important partner in our work, we are requesting that you take just a few minutes to review the website and fill out this form. Your feedback will help us improve the quality of the IEA website and allow you to easily find and understand the information you need. We hope to collect all feedback before the end of November. We thank you for your time and look forward to your feedback.
IEA website: https://www.integratedecosystemassessment.noaa.gov/
Review form:
https://docs.google.com/forms/d/e/1FAIpQLSf2jQwxl27oI_AlDtKnZe9JBGZho7arqkPETNnX50e8XsB9rA/viewform?usp=sf_link

November 5, 2018

Meetings

● Dr. Chris Sinigalliano and Dr. Maribeth Gidley from the AOML Environmental Microbiology Program will participate in the Florida Department of Environmental Protection CRCP Water Quality Monitoring Plan review on Thursday November 8, 2018 at the Nova Southeastern University Oceanographic Center. The NOAA-CRCP water quality program has recently concluded 24 months of sampling at Government Cut and the St. Lucie Inlet and 12 months of sampling the seven inlets in between. Thus, it is time to review results and update the monitoring plan, as needed. The participants of this workshop from a range of institutions including FDEP, NOAA-CRCP, NOAA AOML, USGS, NSU, FIU, Broward County, and other federal, state, local, and academic partners will review the last 24 months of this program and provide advice on planing the future coastal water quality monitoring activities of this program in South Florida.

● Dr. Kelly Goodwin will serve on a listening session to solicit stakeholder input regarding implementation of the Department of Commerce 2018-2022 Strategic Plan and NOAA's "blue economy" interests including advancing innovation, strengthening domestic commerce, and increasing U.S. exports. RDML Timothy Gallaudet, PhD, Assistant Secretary of Commerce for Oceans and Atmosphere and Acting Under Secretary of Commerce for Oceans and Atmosphere, will discuss opportunities to improve the efficiency of U.S. ports, promote domestic aquaculture production, and expand exploration of the nation's Exclusive Economic Zone. Open questions from the public will follow a roundtable discussion moderated by Margaret Leinen, Director of Scripps Institution of Oceanography. Dr. Goodwin will join the following panelists: Robert Dooley, Commercial Fishing - Pacific Fisheries Management Council; Don Kent, Hubbs Seaworld Research Institute; Dr. Eric Terrill, Scripps; a representative, Port of San Diego) at the Broadway Pier in San Diego on November 9, 2018.

● On November 6, 2018 while in San Diego for Blue Tech week, Craig McLean (OAR Assistant Administrator and Acting Chief Scientist) and staff met with Kelly Goodwin, Toby Garfield (Acting Deputy Director of SWFSC), and Commander John Crofts at SWFSC. Discussion topics were broad and included recent saildrone missions and progress on the 'omics roadmap, which is due to the NOAA Research Council in the beginning of December.

● On November 8, Luke Thompson will give a webinar for the International Microbiome and Metagenomics Standards Alliance entitled "Standards-enabled metagenomics and metabolomics of Earth's microbial communities".

● Kelly Montenero will give a presentation at the National Marine Sanctuary Research Coordinators meeting on November 8th at Mote Marine Lab on Summerland Key. The presentation discussed collaboration between NOAA's IEA program, the Sanctuary system and the Marine Biodiversity Observation Network.

Manuscripts

● The paper entitled "Why more comparative approaches are required in time-series analyses of coral reef ecosystems" with AOML/OCED co-author Dr. Derek Manzello was accepted for publication in the journal Marine Ecology Progress Series. Using sites in Mo'orea and Panama as examples of resilient reefs that have been studied over 35 years, this paper demonstrates the potential of the comparative approach by exploring different ecological drivers of community resilience at each location. In both cases, coral reef community resilience is associated with strong herbivory, but in Mo'orea, resilience is a product of rapid coral community recovery through sexual recruitment in response to a largely indiscriminate disturbance (Crown-of-Thorns starfish predation), while in Panama, resilience appears to be a product of corals acquiring resistance to a repetitive selective disturbance (bleaching). Based on these trends, a hypothesis-driven conceptual framework is proposed to test for mechanisms driving community resilience. The recent decade of coral reef degradation has brough time-series analyses to the forefront of research on these systems, where they are detecting disturbances that are unique to modern ecological science.

● Edmunds P, Adam T, Baker A, Doo S, Glynn PW, Manzello DP, Silbiger N, Smith T, Fong P (2018) Why more comparative approaches are required in time-series analyses of coral reef ecosystems. Marine Ecology Progress Series. In Press.

● The paper entitled "Functionally profiling metagenomes and metatranscriptomes at species-level resolution" with AOML/OCED co-author Dr. Luke Thompson was accepted for publication in the journal Nature Methods. This paper presents a tool called HUMAnN2, which allows for species-level resolution of functional profiles of metagenomes. For this paper, Luke used HUMAnN2 to profile and reveal patterns in marine metagenomes from depth profiles in the Red Sea, which Luke collected back in 2011.

● Franzosa, E.A., L.J. McIver, G. Rahnavard, L.R. Thompson, M. Schirmer, G. Weingart, K. Schwarzberg-Lipson, R. Knight, J.G. Caporaso, N. Segata, and C. Huttenhower. Functionally profiling metagenomes and metatranscriptomes at species-level resolution. Nature Methods, 15(11):962-968 (doi:10.1038/s41592-018-0176-y) (2018).

Field Work

● Ian Smith will be going out to sample the hypoxic area and red tide off of Charlotte Harbor on November 8 with a commercial fishermen. Ian will investigate whether the sub-surface bloom and hypoxia we first documented on last month's cruise still persist. This will also hopefully be the beginning of a new collaboration with private industry, where we hope to have commercial fisherman collecting data for us routinely when they go out fishing in these areas.

October 29, 2018

Meetings

● On November 8, Dr. Luke Thompson will present a webinar for the International Microbiome and Metagenomics Standards Alliance entitled "Standards-enabled metagenomics and metabolomics of Earth's microbial communities".

● Dr. Leticia Barbero will be in Vienna, Austria from October 29th to November 2nd to participate in a workshop organized by the International Atomic Energy Agency (IAEA) Division of Latin America and the Caribbean, Department of Technical Cooperation. The purpose of the workshop is to design a regional project in the area of marine environment to strengthen capacities in marine and coastal management, including ocean acidification monitoring, for the participating countries.

Field Work

● Dr. Lew Gramer, Dr. Mana Amornthammarong (both CIMAS), and Joe Bishop built 44 low-cost, high-precision thermistor instrument packages. This week, they worked with CIMAS field scientists at SEFSC - Dana Williams, Allan Bright, Annabeth Peterson, and MPS intern Samara Neufeld - to deploy all 44 thermistors together with 12 Tilt Current Meters, at four reef sites stretching across 33 km of the Upper Florida Keys. The deployments were made using a NOAA SEFSC Small boat. The reef sites are reef restoration sites restored by Coral Restoration Foundation with funding from the NOAA Coral Restoration Center and that this project builds on a multi-year collaboration with CRF. These instruments will measure very fine-scale structure in near-bottom sea temperature and ocean currents, to inform analysis of coral outplant transcriptomes and microbiomes to be collected at the sites (Rosales et al. 'Omics 2019).

October 22, 2018

Meetings

● Dr. Catalina Aguilar and Dr. Stephanie Rosales will be attending the "Third Global Invertebrate Alliance Research Conference and Workshop (GIGA III)" in Curacao, October 19-21, GIGA is a collaborative network of scientist studying invertebrate animal genomics. Catalina will give a presentation entitled "Understanding heat stress resistance in Orbicella faveolata from the Florida Keys using gene networks analyses".

● Dr. Maribeth Gidley will be attending the 10th Annual Southeast Florida Regional Climate Leadership Summit in Miami Beach October 24-25th. This summit is held annually on behalf of the Southeast Florida Regional Climate Change Compact, to give the public and local leaders the opportunity to learn more about climate change issues and how they affect Southeast Florida. The Southeast Florida Regional Climate Change Compact, is a partnership between Broward, Miami-Dade, Monroe and Palm Beach counties, to collaborate and coordinate action and resilience policy and action across the four county lines. Maribeth will be participating in a roundtable discussion on the impacts of sea level rise on the health and well-being of coastal communities.

Manuscripts

● Dr. Ruben van hooidonk co-authored a manuscript entitled "Designating spatial priorities for marine biodiversity conservation in the Coral Triangle" that has been accepted in the journal, Frontiers in Marine Science. The paper analyzes current MPAs in the Coral Triangle (CT) to assess if the MPAs are representative of all aspects of biodiversity, including populations, species, and biogenic habitats. It used conservation planning software (Zonation) as a decision-support tool to plan MPAs that would maximize representation of biodiversity features while balancing selection of protected areas based on the likelihood of threats. The results indicate that the average representation of biodiversity features within the existing MPA system is currently about 5%. By increasing MPA coverage from 2% to 10% of the total area of the CT, the average representation of biodiversity features within the MPA system would increase to over 37%. This study demonstrates that the application of design tools, instead of ad hoc approaches, can support the design of a comprehensive MPA network that includes a representative range of biodiversity. https://www.frontiersin.org/articles/10.3389/fmars.2018.00400/abstract

● Asaad, I, CJ Lundquist, MV Erdmann, R Van Hooidonk, MJ Costello. Designating spatial priorities for marine biodiversity conservation in the Coral Triangle. In Press. Frontiers in Marine Science.

Field Work

● Dr. Lew Gramer (CIMAS) will be working with collaborators from NOAA SEFSC to deploy dense networks of innovative oceanographic instruments at four reef sites in the upper Florida Keys. The instruments are measuring near-bottom sea temperature and ocean currents at high spatial resolution as part of an interdisciplinary study on disease transmission and resistance among coral outplants. The year-long study is being undertaken with RSMAS and the Coral Restoration Foundation, and is funded by the NOAA 'Omics Initiative.

Report

● Dr. Ruben van Hooidonk is the second author on the UNESCO report "Impacts of Climate Change on World Heritage Coral Reefs". The report will be published in early September by UNESCO/World Heritage and will be available from the UNESCO website (as the First Assessment). It reports on heat stress in natural World Heritage properties during the third global coral bleaching event which took place on June 2014 through May 2017. It updates the first assessment with high-resolution future projection analysis under the RCP2.6 emissions scenario, in which emissions peak during the current decade (2010-2020) and achieve the limit of well below 2°C by 2100. This updated analysis provides understanding of the implications of meeting the long-term goal of the UNFCCC Paris Agreement for World Heritage-listed coral reefs. Under a CO2 emission business-as-usual scenario (RCP8.5), all 29 World Heritage-listed coral reef properties are expected to experience annual severe bleaching this century, leading to dramatic deterioration in ecological functioning and decline in the quality and quantity of ecosystem services these reefs provide. When emissions follow the RCP2.6 scenario, no World Heritage-listed coral reefs would experience annual severe bleaching this century.

October 09, 2018

Meetings

● Dr. Kristen Harper will be visiting MBARI to develop 18s libraries for the recently completed September CalCOFI cruise.

● Dr. Kelly Goodwin and Dr. Kristen Harper will be attending the US-Norway bilateral on "eDNA analyses - a tool for quantitative assessments of marine ecosystems?" in Tromso, Norway on October 8-11. The workshop goals include establishing guidelines for inter-laboratory reproducibility and producing a white paper on eDNA use in fisheries stock assessments.

Seminar

● John Morris gave a student seminar at RSMAS entitled "Evaluating the response of microboring rates to ocean acidification." His research characterized dissolution rates of Caribbean coral reef frameworks under experimentally manipulated acidification scenarios. The study was conducted in the CIMAS Experimental Reef Lab and was funded by the Ocean Acidification Program.

Congressional Briefing

● Dr. Kelly Goodwin of AOML will join colleagues from NMFS (Cisco Werner) and NOS (Steve Thur) to brief staff from the Senate Appropriations Committee's Subcommittee on Commerce, Justice, Science and Related Agencies on NOAA's 'omics work.

Field Work

● Kelly Montenero, Dr. Chris Kelble, Ian Smith, and others will be participating in a R/V Walton Smith cruise from October 12-19. This is the next in the series of south Florida Ecosystem Restoration research cruises, but will be expanded to help sample the ongoing red tide on the southwest Florida Shelf. The focus will be on quantifying human health and ecosystem impacts from the red tide event with additional funding and collaboration from NOS HAB event response, NMFS/SEFSC, and the State of Florida Fish and Wildlife Research Institute.

October 01, 2018

Seminar

● On October 2, AOML will host Dr. Emily Jones from the Center for Coastal and Marine Ecosystems (CCME) at Florida A&M University. Dr. Jones will be presenting "Exploration of collaborative research topics in coastal ecology" on Tuesday at 10AM in the first floor conference room. Dr. Jones is visiting AOML, because she has to spend 6-12 months at a NOAA facility and wants to explore possible collaborations with AOML. If you would like to meet with Dr. Jones when she is here, please contact Dr. Chris Kelble.

Field Work

● Joe Bishop and Dr. Mana Amornthammarong are traveling with Albert Jones of the Caribbean Community Climate Change Center, and John Halas of Environmental Moorings, Int., to finalize the installation of CREWS buoys in Grenada and St. Vincent and the Grenadines, September 24 - October 2. Once the data are transmitting, they will be available on the CHAMP Portal page at: www.coral.noaa.gov/champportal.

Outreach and Education

● Luke Thompson will teach Python For Data Analysis at the Scripps Institution of Oceanography from October 1 until December 5. You can follow along with the lectures and lessons, respectively, at https://www.youtube.com/channel/UCVZrIrWtcvTzYlrNx7RcDyg and https://github.com/cuttlefishh/python-for-data-analysis.

September 24, 2018

Meetings

● Dr. Denis Pierrot is attending a meeting on biogeochemistry data quality control at PMEL on Monday and Tuesday.

● Dr. Neda Trifonova is presenting at the 10th International Conference on Ecological Informatics in Jena, Germany this week. Her talk is entitled "Investigating climate impacts in the Gulf of Mexico with a dynamic Bayesian model."

● Dr. Jim Hendee visited Dr. Kelly Goodwin at the SWFSC September 20 and toured Weston Solutions (where Kelly helped design and develop their microbiological survey techniques under a CRADA agreement that lasted five years), the J. Craig Venter Institute (JCVI), and Southwest Fisheries Science Center. Jim and Kelly met with post-docs Luke Thompson, Kirsten Harper and Dovi Kacev; and heard updates on their various projects. At JCVI, they had discussions with Andy Allen about his work in diatom genetics and about possibilities in developing a collaborative initiative in aquaculture. John Hyde conducted a tour of the impressive aquaculture and tech tank facilities, and again discussed goals an aquaculture collaborative might achieve. Finally, they met with Toby Garfield, Deputy Director (Acting) of SWFSC, and discussed various subjects, including Dr. Chris Kelble's partnership with him in their EBM projects.

Field Work

● Dr. Denis Pierrot and Kevin Sullivan visited the EIMSKIP MV Selfoss and started the installation of a pCO2 system on the vessel, which transits between Iceland and Portland, Maine.

● The Grenada CREWS station was installed September 26, 2018 by the CREWS Team (minus Jim) at Kahonae Reef. You can see the chronology of the adventure at the CREWS Blog (KRGN1) at: https://krgn1-log.blogspot.com/.

● Joe Bishop and Dr. Mana Amornthammarong are traveling with Albert Jones of the Caribbean Community Climate Change Center, and John Halas of Environmental Moorings, Int., to finalize the installation of CREWS buoys in Grenada and St. Vincent and the Grenadines, September 24 - October 2. Once the data are transmitting, they will be available on the CHAMP Portal page at: www.coral.noaa.gov/champportal.

Outreach and Education

● On September 27th, Dr. Ruben Van Hooidonk will be presenting a talk on the impacts of climate change on coral reefs during a Climate Diplomacy Day. This is an event hosted by the Miami Business School at the University of Miami on the main campus. It is organized by various EU consulates (German, British, Italy and Dutch). During Climate Diplomacy Week (September 24 to 30), EU Delegations, embassies and Consulates General of several EU Member States around the world hold various events to foster dialogue and cooperation on climate change, showcase success stories and inspire further action. Other participants at the University of Miami event include Ben Kirtman, John A. Quelch and Bryan Norcross.

September 17, 2018

Meetings

● Kelly Montenero, Charline Quenee, and Dr. Chris Kelble will be hosting an indicator selection workshop for the Florida Keys National Marine Sanctuary (FKNMS) on September 20. This meeting is co-hosted by FKNMS staff that are collaborating on the CRCP funded Florida Keys IEA. The meeting aims to identify and prioritize data-rich indicators that will be used to assess the status of the FKNMS for ensuing FKNMS condition reports. After the meeting on Friday, Kelly Montenero and Dr. Chris Kelble will be meeting with Sarah Fangman, FKNMS superintendent to update her on the Florida Keys IEA progress and make sure the products we produce will be of use to her and the FKNMS.

Congressional Briefing

● Dr. Kelly Goodwin of AOML will join colleagues from NMFS (Cisco Werner) and NOS (Steve Thur) to brief staff from the Senate Appropriations Committee's Subcommittee on Commerce, Justice, Science and Related Agencies on NOAA's 'omics work.

Outreach and Education

● Dr. Chris Kelble will be attending and presenting at the Florida SeaGrant Biscayne Bay WaterWatch appreciation night on September 19. AOML analyzes the nutrient and chlorophyll-a samples collected by the Biscayne Bay WaterWatch citizen scientists network developed and led by Florida SeaGrant.

Report

● Dr. Ruben van Hooidonk is the second author on the UNESCO report "Impacts of Climate Change on World Heritage Coral Reefs". The report will be published in early September by UNESCO/World Heritage and will be available from the UNESCO website (as the First Assessment). It reports on heat stress in natural World Heritage properties during the third global coral bleaching event which took place on June 2014 through May 2017. It updates the first assessment with high-resolution future projection analysis under the RCP2.6 emissions scenario, in which emissions peak during the current decade (2010-2020) and achieve the limit of well below 2°C by 2100. This updated analysis provides understanding of the implications of meeting the long-term goal of the UNFCCC Paris Agreement for World Heritage-listed coral reefs. Under a CO2 emission business-as-usual scenario (RCP8.5), all 29 World Heritage-listed coral reef properties are expected to experience annual severe bleaching this century, leading to dramatic deterioration in ecological functioning and decline in the quality and quantity of ecosystem services these reefs provide. When emissions follow the RCP2.6 scenario, no World Heritage-listed coral reefs would experience annual severe bleaching this century.

September 10, 2018

Congratulations

● Dr. Rik Wanninkhof was selected for the steering committee of the newly formed International Oceanic Commission (IOC) Working Group on Integrated Ocean Carbon Research. This high-level WG will fill knowledge gaps related to ocean carbon by designing and promoting the implementation of the new generation of integrated ocean carbon research.

Manuscripts

● The 2nd edition of the reference series "World Seas" will be released on September 21. The volume contains a chapter on 'omics: K.D. Goodwin, F. Muller-Karger, G. Canonico. Molecular Approaches for an Operational Marine Biodiversity Observation Network. In World Seas: An Environmental Evaluation, Vol III. Ecological Issues and Environmental Impacts, 2nd edition. C. Sheppard, ed., Academic Press, ISBN: 9780128050521 (2018). Pre-order is available now, with a 15% discount from:
https://www.elsevier.com/books/world-seas-an-environmental-evaluation/sheppard/978-0-12-805052-1.

Field Work

● Dr. Kirsten Harper will be joining the Monterey Bay Research Institute (MBARI) on the Controlled, Agile, and Novel Observing Network (CANON) cruise aboard the R/V Western Flyer on September 6th - 11th. During the CANON cruise, paired CTD and 3G ESP/LRAUV samples ("eAUV") will be collected to compare methods of sampling biodiversity through environmental DNA (eDNA). In addition, Dr. Harper will be collecting eDNA samples on the R/V Reuben Lasker in June 2018 which will be used for the continuation of her project focusing on detecting the diurnal movement of fish species using eDNA. Following the CANON cruise, Dr. Harper will remain at MBARI until September 14th to learn MBARI's protocol for metabarcoding of eDNA samples, and apply this to her own samples when she returns to NOAA.

Meetings

● Dr. Ruben van Hooidonk, Dr. Leticia Barbero and Dr. Rik Wanninkhof attended the Ocean Acidification Research to Product Development Workshop 2018 in Silver Spring on Sept 12-14. The meeting goals were to determine ocean acidification projects that exhibit operational potential or are currently being developed for operational delivery. Participants proposed ways to overcome barriers that currently inhibit operational delivery.

September 4, 2018

Field Work

● The first deployment of an "eAUV" in western Lake Erie will occur on August 27- September 5, 2018. This long-range autonomous underwater vehicle (LRAUV) carrying an integrated 3rd Generation Environmental Sample Processor (3G ESP) will relay concentrations of harmful algae toxin in near-real time and archive samples for genomic analysis. Dr. Kelly Goodwin will travel to GLERL at the end of the mission to help with instrument and sample recovery. Click Here to View the Press Release.

● Dr. Kirsten Harper will be joining the Monterey Bay Research Institute (MBARI) on the Controlled, Agile, and Novel Observing Network (CANON) cruise aboard the R/V Western Flyer on September 6th - 11th. During the CANON cruise, paired CTD and 3G ESP/LRAUV samples ("eAUV") will be collected to compare methods of sampling biodiversity through environmental DNA (eDNA). In addition, Dr. Harper will be collecting eDNA samples on the R/V Reuben Lasker in June 2018 which will be used for the continuation of her project focusing on detecting the diurnal movement of fish species using eDNA. Following the CANON cruise, Dr. Harper will remain at MBARI until September 14th to learn MBARI's protocol for metabarcoding of eDNA samples, and apply this to her own samples when she returns to NOAA.

Meetings

● AOML-SEFSC hosted a science symposium on Wednesday, September 5th, followed by a planning and coordination workshop on Thursday, September 6th. The symposium on Wednesday, September 5th took place from 12:30-5:00 in the AOML first floor conference room. The workshop on Thursday, September 6th took place from 8:30-4:30 in the RSMAS Library.

August 27, 2018

Manuscripts

● The companion papers entitled "Effect of seawater temperature, pH, and nutrients on the distribution and character of low abundance shallow water benthic foraminifera in the Galapagos" and "Shallow water benthic foraminifera of the Galapagos archipelago: ecologically sensitive carbonate producers in an atypical tropical oceanographic setting" with AOML/OCED co-author Dr. Derek Manzello were accepted for publication in the journals PLoS One and Journal of Foraminiferal Research, respectively. Benthic foraminifera, a group of unicellular protists that construct calcium carbonate shells, are sensitive to environmental change, making them indicators of coral reef water quality and health. These studies assessed shallow-water foraminiferal assemblages from 19 locations spanning the Galapagos archipelago. Foram abundances were low, averaging only 0.7% of all sand-sized carbonate grains, yet a total of 161 species in 72 genera were found. The combined impact of the El Nino Southern Oscillation (ENSO) and upwelling from the Equatorial Undercurrent (EUC) were the main drivers impacting foraminiferal abundances and assemblage patterns throughout the archipelago. Repeated ENSO temperature anomalies appear to have predominantly driven down foraminiferal density, while chronically high nutrients and low aragonite saturation and low pH-induced by EUC upwelling and La Nina anomalies likely inhibited post-ENSO recovery. While the Eastern Tropical Pacific does not show the diversity of its western counterpart, Galapagos foraminiferal assemblages revealed a relatively high foraminiferal diversity for the region, as well as evidence in support of earlier reports of high endemism within the archipelago.

● Humphreys AF, Halfar J, Ingle JC, Manzello DP, Reymond CE, Westphal H, Riegl B (2018) Shallow water benthic foraminifera of the Galapagos archipelago: ecologically sensitive carbonate producers in an atypical tropical oceanographic setting. Journal of Foraminiferal Research, In press.

● Humphreys A, Halfar J, Ingle J, Manzello DP, Reymond C, Westphal H, Riegl B (2018) Effect of Seawater Temperature, pH, and Nutrients on the Distribution and Character of Low Abundance Shallow Water Benthic Foraminifera in the Galapagos. PLoS One, In press.

Field Work

● The first deployment of an "eAUV" in western Lake Erie will occur on August 27- September 5, 2018. This long-range autonomous underwater vehicle (LRAUV) carrying an integrated 3rd Generation Environmental Sample Processor (3G ESP) will relay concentrations of harmful algae toxin in near-real time and archive samples for genomic analysis. Dr. Kelly Goodwin will travel to GLERL at the end of the mission to help with instrument and sample recovery. Click Here to View the Press Release.

Outreach and Education

Climate.gov has produced a Featured Image article about the OA Product Suite. Featured Images are articles featuring a compelling photo, map, or data visualization with a long caption that is about 400-500 words and explains the image and what a reader is seeing. It's intended for a wider audience. The purpose of the article is to highlight the OAPS and the efforts we here at NOAA do to protect our oceans and the communities that depend on them from Ocean Acidification. The article shows an animation of surface water pH in the Caribbean Sea and Gulf of Mexico for the year 2015 and the text tells the story of OA, the fact that the oceans take up 30% of all CO2 emitted per year, and what this means for marine life. This product was developed by Dr. Ruben van Hooidonk. The OAPS is a further improvement of the original OAPS developed by Dwight Gledhill and both data and animations can be found here: http://www.coral.noaa.gov/accrete/oaps.html

August 20, 2018

Field Work

● Dr. Jim Hendee, Dr. Mana Ammornthammorang, and Joe Bishop are installing the latest buoy in thenetwork of CREWS buoys this week at Mayreau Gardens. The designation is SVGM1 for St. Vincent and The Grenadines, at Mayreau Gardens, site #1. The depth of the pins is ~58', right next to a drop off. The site gets significant current flow and water exchange from the south and north through tidal currents and the coral cover is significant. The schedule was to unload the ferry Friday night, drilling and buoy hull painting Saturday, buoy assembly and mooring line assembly Monday and Tuesday, buoy attachment Wednesday, review procedures with locals hosts on Thursday, and return to Miami on Friday.

● Ian Smith, Kelly Montenero, and Aly Thompson will be conducting a survey of juvenile sportfish in Florida Bay on August 21-24. This survey is in support of NOAA's efforts to support Everglades Restoration and ensure they benefit coastal ecosystems.

Meetings

● Dr. Luke Thompson will attend the 148th Annual Meeting of the American Fisheries Society (AFS) in Atlantic City, New Jersey from August 19-20. At AFS, he will present a talk in the session "Integration of Genetic Techniques with Quantitative Stock Assessment and Ecological Models for Resolving Fishery Management Issues" entitled "Computational Workflows for Rapid and Customizable Analysis of Amplicon Sequencing Data from Environmental DNA".

August 13, 2018

Congratulations

Dr. Rik Wanninkhof's article, "Relationship between wind speed and gas exchange over the ocean revisited," was included in a special collection celebrating the 15th year of publication of Limnology and Oceanography: Methods.

Manuscripts

● Climatic modulation of surface acidification rates through summertime wind forcing in the Southern Ocean by Liang Xue, Wei-Jun Cai, Taro Takahashi, Libao Gao, Rik Wanninkhof, Meng Wei, Kuiping Li, Lin Feng and Weidong Yu appeared in press today in Nature Communications.

● Spatial and temporal variability of pCO2, carbon fluxes and saturation states on the West Florida Shelf by Robbins, Barbero, Wanninkhof and others was accepted for publication in the Journal of Geophysical Research.

Field Work

● Dr. Chris Sinigalliano and Dr. Maribeth Gidley are in Saipan from July 29 thru August 15 for the 'Omics funded project "Microbial Source Tracking Technology Transition & Microbiome Characterization of LBSP-impacted Saipan coastal water to guide coral management."

● Dr. Jim Hendee, Dr. Mana Ammornthammorang, and Joe Bishop are installing a CREWS buoy in St. Vincent this week and next. These buoys are being paid for by the Caribbean Community Climate Change Centre (5Cs).

● Ian Smith and Aly Thompson will be conducting a survey of juvenile sportfish in Florida Bay on August 21-24. This survey is in support of NOAA's efforts to support Everglades Restoration and ensure they benefit coastal ecosystems.

● Kelly Montenero, Charline Quenee, and Ian Smith will be conducting a survey of South Florida's coastal water quality, including measures of eDNA and coral holobiomes. This cruise will take place on the R/V Walton Smith from August 6-10.

Meetings

● Graham Kolodziej is giving a lecture entitled "Coral reef persistence in dynamic CO2 environments" at the 2018 Galapagos Ocean Acidification School, to be held at the Charles Darwin Research Station in Puerto Ayora, Galapagos, Ecuador from August 19-28, 2018. This course will train participants in different aspects of ocean acidification (OA) research and include both a class room and filed component. The field component includes a research cruise to the Roca Rendonda CO2 vent where participants will conduct OA research. Mr. Kolodziej will demonstrate use of the recently developed subsurface auto-samplers developed by Ian Enochs and Nate Formel, as well as deploy bioerosion monitoring units to cross-compare with the published results by Ian Enochs from CO2 vents in the Mariana Islands and Papua New Guinea. Finally, he will discuss previous OA research on Galapagos coral reefs that has been led by Derek Manzello since 2003.

July 30, 2018

Manuscripts

● The paper entitled "Seasonal variability of carbonate chemistry and decadal changes in waters of a marine sanctuary in the Northwestern Gulf of Mexico" with AOML/OCED co-authors Derek Manzello, Ian Enochs, and Leticia Barbero was accepted for publication in the journal Marine Chemistry. This study reports seasonal water column carbonate chemistry data collected over a three-year period (late 2013 to 2016) at Flower Garden Banks National Marine Sanctuary (FGBNMS) located on the subtropical shelf edge of the northwestern Gulf of Mexico. The FGBNMS hosts the northernmost tropical coral species in the contiguous United States, with over 50% living coral cover. Temperature and salinity both played an important role in controlling the surface water carbonate system dynamics, although temperature was the sole significant factor when there was no flooding. The FGBNMS area acted as a sink for atmospheric CO2 in winter and a CO2 source in summer, while the time-integrated CO2 flux is close to zero. Results from three cruises, i.e., the Gulf of Mexico and East Coast Carbon Project (GOMECC-1) in 2007, the rapid response study, and the Gulf of Mexico Ecosystems and Carbon Cruise (GOMECC-3), revealed decreases in both pH and saturation state with respect to aragonite (Oarag) in subsurface waters (~100-250m) over time. These decreases are larger than those observed in other tropical and subtropical waters. Anthropogenic CO2 contributed 30-41% of the overall DIC increase, while elevated respiration accounted for the rest.

Hu X, Nuttall MF, Wang H, Yao H, Staryk CJ, McCutcheon MM, Eckert RJ, Embresi JA, Johnston M, Hickerson E, Schmahl GP, Manzello DP, Enochs IC, DiMarco S, Barbero L (2018) Seasonal variability of carbonate chemistry and decadal changes in waters of a marine sanctuary in the Northwestern Gulf of Mexico. Marine Chemistry doi:10.1016/j.marchem.2018.07.006.

Field Work

● Dr. Chris Sinigalliano and Dr. Maribeth Gidley travel to Saipan from July 29 thru August 15 for the 'Omics funded project "Microbial Source Tracking Technology Transition & Microbiome Characterization of LBSP-impacted Saipan coastal water to guide coral management."

● Dr. Denis Pierrot will travel to Mar del Plata, Argentina as a mentor of the GOAN Pier2Peer program in order to train researchers on the best practices regarding a newly installed GO pCO2 system. He will be there for a week from Aug. 4th to Aug. 12th.

Education and Outreach

● The Frost Science Museum's Outdoor Explorers Camp visited AOML to learn about ocean acidification and how the ACCRETE lab is using technology to study conditions on coral reef ecosystems. The group was made up of 14 sixth through eighth grade students from Miami-Dade County and four Frost employees. The program at AOML was led by CIMAS Research Associate Nate Formel and Gulliver Preparatory School teacher Alan Piggot. The campers were introduced to the scope of work being done in the Ocean Chemistry and Ecosystem Division (OCED) at AOML and, more specifically, to the concept of ocean acidification and how it is impacting local coral reefs. After a few hands-on labs to help reinforce the main concepts of our changing ocean chemistry, the kids toured the ACCRETE Advanced Manufacturing and Design Lab (AMDL) and Experimental Reef Lab (ERL) to see the technology that OCED and the University of Miami are utilizing to create new and innovative tools for studying conditions on coral reefs.

Frost campers helped the ACCRETE group by participating in labs written as outreach related to a new subsurface automated water sampler developed by Dr. Ian Enochs and Nate Formel over the last year. The final project for the visiting campers, before heading home, was to create their own simplified version of the lab's subsurface automated samplers (SAS). The campers raced each other, completing the circuitry themselves, to finish building the samplers and test them out. At the end of the day the campers left with a souvenir from the AMDL's laser cutter, as well as a greater knowledge of the state of our oceans and what's being done at AOML and CIMAS to study and conserve them. The lesson plans used for the visit were designed for a classroom setting, but proved to be easily adaptable for the enthusiastic Frost students.

July 23, 2018

Notable Events

● Dr. Luke Thompson has been promoted to Assistant Research Professor in the Department of Biological Sciences at the University of Southern Mississippi, which is his university partner with the Northern Gulf Institute. He will continue to report to AOML/OCED and remain stationed at Southwest Fisheries Science Center in La Jolla, California.

Field Work

● Patrick Mears and Charles Featherstone are in their last week of the East Coast Acidification cruise with an expected arrival in Miami on July 29. A four-day delayed departure and a severe strom over the weekend have impacted execution of cruise objectives.

● In late July, Dr. Chris Sinigalliano and Dr. Maribeth Gidley will be traveling to Saipan in the Northern Mariana Islands. This is the final segment of a technology transfer program with CNMI BECQ (The Bureau of Environmental and Coastal Quality) and the Pall Corporation. They will be engaging in water quality work involving molecular source tracking of land based sources of pollution with partners from BECQ and American University. This study was originally funded by CRCP, while the latter part is funded through the AOML Omics initiative.

● Dr. Jim Hendee, Joe Bishop, and Dr. Natchanon Amornthammarong will travel August 13-24 to St. Vincent and the Grenadines for the installation of a CREWS station.

July 16, 2018

Manuscripts

● A manuscript entitled "Ascorbic acid as a reductant for extraction of iron-bound phosphorus in soil samples: a method comparison" co-authored by Dr. Zhang and Dr. Lanning has been accepted for publication in Communication in Soil Science and Plant Analysis.

Field Work

● Charles Featherstone and Patrick Mears are participating in the ECOA-2 research cruise from June 22 to July 29.

July 9, 2018

Manuscripts

● Multiple authors, including Dr. Rik Wanninkhof, have submitted their paper, "The oceanic sink for anthropogenic CO2 from 1994 to 2007" to Science. In the manuscript, they quantify the oceanic sink for anthropogenic CO2 over the period 1994 to 2007 using inorganic carbon observations from the GO-SHIP global repeat hydrography program. AOML and PMEL are major contributors to the international GO-SHIP program .

Field Work

● Kelly Montenero, Charline Quenee, and Ian Smith conducted the juvenile sportfish survey in Florida Bay on July 9-13.

● Alyssa Thompson was in Key West from July 9 - 10 to conduct a hull dive aboard the R/V Gordon Gunter.

● Dr. Maribeth Gidley will be travelling to Galveston, TX on July 12 to assist with the second part of the Beach Exposure And Child HEalth Study (UM BEACHES) project. This study is funded through the Gulf of Mexico Research Initiative with collaborative institutions including the University of Arkansas and the University of Texas, and is intended to assess how child interaction with the beach may increase their risk of exposure to beach contaminants. The Miami portion of the study was successfully completed last week, having taken place on Crandon Beach and Haulover Beach. UM student intern Alexander Richardson, UM HHMI student interns Brandon Rogers and Alexandra Ayala, and Hollings Scholar Anthony Bonacolta were an integral part in making the Miami side of the BEACHES Project a big success.

● Dr. Kirsten Harper and Dr. Kelly Goodwin will be in the field on July 14 collecting San Diego Bay water for analysis of marine turtle eDNA. eDNA sampling will co-occur with routine turtle monitoring. Development of eDNA methods would allow animals to be tracked using the DNA from sloughed or excreted cells and reduce the need for net capture of animals.

● Members of ACCRETE, including Graham Koldziej, Catalina Aguilar, Nate Formel, Liz Dutra, and John Morris, are conducting National Coral Reef Monitoring Plan operations in the Dry Tortugas this week on board the R/V Angari. They will be conducting carbonate budget surveys, trading out instruments, as well as characterizing diel carbonate chemistry dynamics using Subsurface Automatic Samplers (SAS) developed by Dr. Ian Enochs and Nate Formel.

● Dr. Stephanie Rosales and Dr. Lew Gramer of CIMAS did three reef site surveys in the Upper Keys on July 12th with Dr. Dana Williams (SEFSC) and RSMAS students Ben Young and Ana Palacio. The surveys are the first part of a new study funded by the NOAA 'Omics Initiative, to better understand differences in disease resistance among out-planted Acroporid corals, by characterizing the corals' transcriptomes, microbiomes, and their oceanographic habitat.

● Charles Featherstone and Patrick Mears are participating in the ECOA-2 research cruise from June 22 to July 29.

Meetings

● Dr. Chris Kelble will be attending the Integrated Ecosystem Assessment Human Dimensions Working Group meeting July 9-10 in Baton Rouge, LA.

● Dr. Neda Trifonova and Dr. Chris Kelble will be attending the Integrated Ecosystem Assessment Qualitative Network Modeling Working Group meeting July 11-13 in Baton Rouge, LA. Neda and Chris lead this working group that investigates and compares the differences among fuzzy-logic cognitive mapping, Bayesian belief networks and qualitative network modeling to conduct scenario evaluations with conceptual models.

Education and Outreach

● Dr. Maribeth Gidley is an invited speaker at the Frost Museum on July 12 for their Summer Science Camp following the theme of Sustainability and Climate Solutions titled "Keeping it Current - Climate Design Lab." Dr. Gidley's presentation is entitled "Human Health Challenges in the Face of a Changing Climate."

July 2, 2018

Manuscripts

● The manuscript "Climatic modulation of surface acidification rates through summertime wind forcing in the Southern Ocean" by Liang Xue, Wei-Jun Cai, Taro Takahashi, Libao Gao, Rik Wanninkhof, Meng Wei, Kuiping Li, Lin Feng, and Weidong Yu [Paper #NCOMMS-17-11366C] was accepted for publication in Nature Communications.

● OCED scientists published a paper entitled "The influence of diel carbonate chemistry fluctuations on the calcification rate of Acropora cervicornis under present day and future acidification conditions" in the Journal of Experimental Marine Biology and Ecology.

Enochs IC, Manzello DP, Jones PJ, Aguilar C, Cohen K, Valentino L, Chopmeyer S, Koldziej G, Jankulak M, Lirman D (2018). "The influence of diel carbonate chemistry fluctuations on the calcification rate of Acropora cervicornis under present day and future acidification conditions." Journal of Experimental Marine Biology and Ecology, 506: 135-143.

● The manuscript entitled "Advancing Marine Biological Observations and Data Requirements of the Complementary Essential Ocean Variables (EOVs) and Essential Biodiversity Variables (EBVs) Frameworks" was published in Frontiers in Marine Science, section Ocean Observation. This manuscript was authored by Frank Edgar Muller-Karger, Patricia Miloslavich, Nicholas J Bax, Samantha Simmons, Mark John Costello, Isabel Sousa Pinto, Gabrielle Canonico, Woody Turner, Michael Gill, Enrique Montes, Ben Best, Jay Pearlman, Patrick Halpin, Daniel Dunn, Abigail Benson, Corinne Martin, Lauren Weatherdon, Ward Appeltans, Pieter Provoost, Eduardo Klein, Chris Kelble, Robert J. Miller, Francisco Chavez, Katrin Iken, Sanae Chiba, David Obura, Laetitia M. Navarro, Henrique M Pereira, Valerie Allain, Sonia Batten, Lisandro Benedetti-Cecchi, J. Emmett Duffy, Raphael M Kudela, Lisa-Maria Rebelo, Yunne Shin, Gary Geller.

Field Work

● Kelly Montenero, Charline Quenee, and Ian Smith will be conducting the juvenile sportfish survey in Florida Bay July 9-13.

● Charles Featherstone and Patrick Mears are participating in the ECOA-2 research cruise from June 22 to July 29.

IT Security Training

● The FY18 IT Security Awareness Course was announced by the NOAA CIO offic and has set a due date of COB August 31, 2018 for completion of this course. A link to the course can be found at: https://campus.noaasecure.us/index.k2?locRef=1.

June 25, 2018

Manuscripts

● A paper entitled "Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus" with AOML/OCED co-author Dr. Luke Thompson was accepted for publication in The ISME Journal. This is the first study to quantify how the gut microbiome of wild animals is affected by exposure to environmental pollutants. The data show that exposure to environmental radiation is associated with major changes in gut microbial composition, including a shift in the Firmicutes:Bacteroidetes ratio and predicted functional profiles. The paper also pioneers the use of statistical methods that allow robust detection of taxonomic differences in compositional data.

Lavrinienko, A., T. Mappes, E. Tukalenko, T.A. Mousseau, A.P. Meller, R. Knight, J.T. Morton, L.R. Thompson and P.C. Watts. Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus. Accepted, ISME Journal.

Field Work

● Dr. Maribeth Gidley along with student interns Brandon Rogers and Alexandra Ayala will be taking part in the UM BEACHES (Beach Exposure And Child Hralth Study) June 21 through June 29. This study is funded through the Gulf of Mexico Research Initiative with collaborative institutions including the University of Arkansas and the University of Texas, and is intended to assess how child interaction with the beach may increase their risk of exposure to beach contaminants. The first portion of the study will take place on Crandon Beach, with the second half at Haulover Beach.

● Ian Smith, Aly Thompson, and Kelly Montenero will be conducting the South Florida Ecosystem Restoration research cruise aboard the R/V Savannah on June 22-26.

● Charles Featherstone and Patrick Mears are participating in the ECOA-2 research cruise from June 22 to July 29.

Meetings

● Dr. Chris Kelble attended the Integrated Ecosystem Assessment Steering Committee Meeting on June 26-30 in Boulder, CO.

IT Security Training

● The FY18 IT Security Awareness Course was announced late Friday afternoon. by the NOAA CIO office. NOAA has set a due date of COB August 31, 2018 for completion of this course. A link to this course can be found at: https://campus.noaasecure.us/index.k2?locRef=1.

June 18, 2018

Congratulations

● Dr. Jia-Zhong Zhang has been invited to serve as a member of editorial board of Scientific Reports.

Field Work

● Dr. Jim Hendee, Joe Bishop, and Dr. Mana Amornthammarong will be installing an ICON buoy in Grenada from June 11 through June 22.

● Ian Smith, Aly Thompson, and Kelly Montenero will be conducting the South Florida Ecosystem Restoration research cruise aboard the R/V Savannah on June 22-26.

● Charles Featherstone and Patrick Mears will be participating in the ECOA-2 research cruise from June 22 to July 29.

● Dr. Kelly Goodwin, Dr. Chris Sinigalliano, and Dr. Kirsten Harper participated in the 2018 Ocean Sampling Day (OSD). OSD is a global sampling event that was held on June 21, 2018. EU partners will analyze the DNA to gain a global snapshot of the microbial ecology of the earth's oceans. Learn more at: http://www.assembleplus.eu/research/ocean-sampling-day-2018.

Meetings

● Dr. Chris Kelble will be attending the Integrated Ecosystem Assessment Steering Committee Meeting on June 26-30 in Boulder, CO.

June 11, 2018

Publications

● OCED and RSMAS scientists provided input to a climate.gov web article on anthropogenic CO2 uptake in the Atlantic Ocean: https://www.climate.gov/news-features/featured-images/cruises-cut-slice-through-atlantics-carbon-pie.

Summer Interns

● Naja Murphy will be joining OCED as a University of Miami undergraduate summer intern. She will be participating in research to investigate the best methodology for conducting oxygen incubations for primary productivity. In addition, Naja will be participating in field work including the upcoming research cruise on the R/V Savannah.

Field Work

● Dr. Jim Hendee, Joe Bishop, and Dr. Mana Amornthammarong will be installing an ICON buoy in Grenada from June 11 through June 22.

● Ian Smith, Kelly Montenero and Charline Quenee will be in the Florida Bay on June 12-15 to conduct juvenile sportfish and seagrass monitoring.

Meetings

● Dr. Chris Kelble will be attending the Gulf of Mexico Alliance All Hands-Meeting and pre-meeting workshop for the RESTORE Council Monitoring and Assessment Program on June 11-13.

● Dr. Rik Wanninkhof will be attending the SOCCOM annual meeting in Princeton, NJ on June 11-13.

● Dr. Neda Trifonova and Dr. Lew Gramer will attend the 2018 ASLO Summer Meeting in Victoria, British Columbia, June 10-15. Dr. Trifonova will be presenting "Detecting Tipping Points to Improve Gulf of Mexico Restoration and Management" and Dr. Gramer will be presenting "Physical Habitat as a Driver of Coral Reef Microbiome Community Structure: Next-Generation-Sequencing and Oceanography."

● Dr. Chris Kelble will be attending the Integrated Ecosystem Assessment Steering Committee Meeting on June 26-30 in Boulder, CO.

June 4, 2018

Manuscripts

● Dr. Chris Kelble is a co-author on a manuscript accepted for publication in Frontiers in Marine Science. The manuscript entitled "Advancing Marine Biological Observations and Data Requirements of the Complementary Essential Ocean Variables (EOVs) and Essential Biodiversity Variables (EBVs) Frameworks" explores how we can operationalize two frameworks; one being proposed for global biodiversity monitoring and one for ocean monitoring. The manuscripts proposes a hierarchical methodology to meld the two frameworks for the development of ocean biodiversity observational systems.

Frank Edgar Muller-Karger, Patricia Miloslavich, Nicholas J Bax, Samantha Simmons, Mark John Costello, Isabel Sousa Pinto, Gabrielle Canonico, Woody Turner, Michael Gill, Enrique Montes, Ben Best, Jay Pearlman, Patrick Halpin, Daniel Dunn, Abigail Benson, Corinne Martin, Lauren Weatherdon, Ward Appeltans, Pieter Provoost, Eduardo Klein, Chris Kelble, Robert J. Miller, Francisco Chavez, Katrin Iken, Sanae Chiba, David Obura, Laetitia M. Navarro, Henrique M Pereira, Valerie Allain, Sonia Batten, Lisandro Benedetti-Cecchi, J. Emmett Duffy, Raphael M Kudela, Lisa-Maria Rebelo, Yunne Shin, Gary Geller. In Press. Advancing Marine Biological Observations and Data Requirements of the Complementary Essential Ocean Variables (EOVs) and Essential Biodiversity Variables (EBVs) Frameworks. Frontiers in Marine Science.

● The paper entitled "State of corals and coral reefs of the Galapagos Islands (Ecuador): past, present and future" with AOML/OCED's Dr. Derek Manzello as a co-author was accepted for publication in Marine Pollution Bulletin. This discusses the status and trend of coral communities and coral reefs in the Galapagos Islands, focusing on the lack of recovery for all but one coral reef site since the 1982-83 El Nino warming event that led to mass coral bleaching mortality.

Glynn P.W., Feingold J., Baker A., Banks S., Baums I., Cole J., Colgan M., Fong P., Glynn P.J., Manzello D.P., Riegl B., Ruttenberg B., Smith T.B., Vera-Zambrano M. (2018). State of corals and coral reefs of the Galapagos Islands (Ecuador): past, present and future. Marine Pollution Bulletin, In Press.

● An OpEd piece on the need for systematic and sustained plankton observations in ocean observing programs is published in Limnology and Oceanography Bulletin. It was produced by the Scientific Committee for Ocean Research working group SCOR WG-154 “Integration of Plankton-Observing Sensor Systems to Existing Global Sampling Programs (P-OBS, http://www.scor-int.org/SCOR_WGs_WG154.htm.

Boss, E., Waite, A., Muller-Karger, F. , Yamazaki, H., Wanninkhof, R., Uitz, J., Thomalla, S., Sosik, H., Sloyan, B., Richardson, A., Miloslavich, P., Karstensen, J., Gregori, G., Fennel, K., Claustre, H., Cornejo, M., Berman-Frank, I., Batten, S. and Acinas, S. (2018). Beyond Chlorophyll Fluorescence: The Time is Right to Expand Biological Measurements in Ocean Observing Programs. Limnology and Oceanography Bulletin. doi:10.1002/lob.10243.

● Dr. Luke Thompson is co-author on a manuscript accepted for publication inNature Reviews Microbiology. This review discusses the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis, and the integration of multiple omics data sets. Recommendations include replacing operational taxonomic unit-based analyses with new methods that are based on exact sequence variants, how to integrate metagenomic and metabolomic data, and how to deal with compositional data analysis. Many of the issues, including classic issues such as experimental design and research reproducibility, will be relevant to bioinformatics analyses beyond microbiome research.

Knight, R., A. Vrbanac, B.C. Taylor, A. Aksenov, C. Callewaert, J. Debelius, A. Gonzalez, T. Kosciolek, L. McCall, D. McDonald, A.V. Melnik, J.T. Morton, J. Navas, R.A. Quinn, J.G. Sanders, A.D. Swafford, L.R. Thompson, A. Tripathi, Z.Z. Xu, J.R. Zaneveld, Q. Zhu, J.G. Caporaso and P.C. Dorrestein. Best practices for analyzing microbiomes. Nature Reviews Microbiology (2018), DOI: 10.1038/s41579-018-0029-9.

Summer Interns

● A NOAA Hollings Scholar, Anthony Bonacolta, joins OCED this summer. Anthony, a senior from the University of Miami, will be conducting his research for the NOAA Hollings Scholarship Program on the genomic characterization of bacterial biodiversity in South Florida coral reef microbiomes.

● OCED is also joined this summer by University of Miami undergraduate summer intern Alex Richardson, who will be participating in research on molecular microbial source tracking of microbial contaminants from land-based sources of pollution (LBSP) in coastal marine habitats. This includes molecular analysis of environmental sample from across Southeast Florida and from Saipan in the Commonwealth of the Northern Mariana Islands.

Field Work

● On June 7-9, 2018, the National Oceanic and Atmospheric Administration (NOAA) in partnership with the Monterey Bay Aquarium Research Institute (MBARI) will field test an instrument called an Environmental Sample Processor (ESP) that has been installed inside a long-range autonomous underwater vehicle (LRAUV). The instrument provides a mobile platform to autonomously collect samples for 'omic analysis. Two AUVs will be deployed by MBARI's R/V Western Flyer in rendezvous with NOAA's R/V Reuben Lasker during its annual Pelagic Juvenile Rockfish Recruitment and Ecosystem Assessment Survey. The ships will meet at an offshore upwelling front identified by autonomous vehicle and conduct CTD and net tows in coordination with the ESP-equipped AUV ("eAUV"). OCED's Dr. Kirsten Harper will be aboard the Lasker collecting water samples to compare with samples collected by the eAUV. In addition to engagement with the eAUV, she will collect water from CTDs in association with mid water trawls to investigate the environmental DNA (eDNA) signals of selected fish species.

● The R/V Ron Brown will complete the GO-SHIP I07 cruise on June 8 with Dr. Denis Volkov AOML/CIMAS is chief scientist with 26 scientists and students representing 19 institutions. AOML participants include Andy Stefanik, Ian Smith, Chuck Featherstone, Leah Chomiak, and Jay Hooper. Follow their adventures on the cruise blog at https://i07n.wordpress.com/.

Meetings

● Dr. Derek Manzello is an invited speaker at the workshop entitled "Interventions to Increase the Resilience of Coral Reefs" that is being hosted by the National Academy of Sciences on 31 May 2018 at RSMAS. The goal of the workshop is to explore the state of the science, the risks, and the benefits of ecological and genetic interventions with the potential to increase the long-term persistence of coral reefs in environmentally degraded scenarios. The workshop is one component of the information-gathering activities that will inform the deliberations of the National Academies' Committee on Interventions to Increase the Resilience of Coral Reefs. Manzello will present on the current and future trends of climate change and ocean acidification on Caribbean coral reefs. The workshop is open to the public: http://www.dels.nas.edu/Study-In-Progress/Interventions-Increase-Resilience/DELS-OSB-17-01?bname=osb.

● Dr. Chris Kelble will be attending the Gulf of Mexico Alliance All Hands-Meeting and pre-meeting workshop for the RESTORE Council Monitoring and Assessment Program on June 11-13.

● Dr. Derek Manzello is traveling to Cebu, Philippines from 1-11 June 2018 where he will give an oral presentation at the 4th Asia-Pacific Coral Reef Symposium. Dr. Manzello's talk is entitled "East meets West: Identifying the Common Denominators that Drive Coral Bleaching Resistance and Resilience in the Atlantic and Pacific." This talk will highlight the recent research of the Acidification, Climate and Coral Reef Ecosystems Team (ACCRETE) on resilient coral reefs in the Florida Keys and compare/contrast these results with resilient reef sites in Palau, Singapore, and Great Barrier Reef. The goal is to determine if there are common environmental and biological factors associated with reef areas that may be resistant to thermal stress, as well as stimulate discussion for coordinated research between the Atlantic and Pacific Oceans to better understand these trends.

● Dr. Stephanie Rosales will be attending a workshop entitled "Mining Microbial and Viral Genomes and Metagenomes for Biotechnological Applications Using IMG" at the American Society for Microbiology (ASM) meeting on June 7-11. Dr. Rosales will also be presenting a talk on the "The Physical Habitat as a Driver of Microbiome Structure on Urban-impacted Coral Reefs".

● Dr. Neda Trifonova will attend the Effect of Climatre Change on the World's Oceans in Washington DC on June 4-8. Dr. Trifonova will be presenting "Predicting Ecological Responses to Climate Variability with a Dynamic Bayesian Network Model".

May 21, 2018

Announcements

● Joe Bishop, Dr. Natchanon Amornthammarong and Dr. Jim Hendee from OCED, together with Albert Jones, from the Caribbean Community Climate Change Center (5Cs), Dr. Pamela Fletcher from Sea Grant, and John Halas from Environmental Moorings, Inc., installed the third CREWS buoy (in St.Lucia) of Phase 2 in the year-long campaign to install the buoys at five sites in the Caribbean. The station was installed within the Soufriere Marine Management Area on the west side of St. Lucia at latitude 13° 51.5456' N, longitude 61° 04.2784' W. Conversations were conducted with locals in outreach efforts led by the team to discuss the utility of the buoy data, as well as information on the maintenance aspects of the buoy. Mike Jankulak will oversee the posting of the data to a special open-access blog, and Lew Gramer, together with student intern Madison Soden, will oversee the collaboration with St. Lucia researchers in the formulation and elicitation of ecological forecasts. The greater portion of funding is through 5Cs, although funding for information systems and data come from NOAA's Coral Reef Conservation Program, and from OCED's Coral Health and Monitoring Program. Sea Grant is providing salary support for Pamela Fletcher.

Field Work

● The GO-SHIP I07 cruise on the R/V Brown continues with Dr. Denis Volkov AOML/CIMAS as chief scientist and 26 scientists and students representing 19 institutions participating. AOML participants include Andy Stefanik, Ian Smith, Chuck Featherstone, Leah Chomiak, and Jay Hooper. Follow their adventures on the cruise blog at https://i07n.wordpress.com/.

● Chris Kelble, Kelly Montenero, Alyssa Thompson, and Charline Quenee conducted the juvenile sportfish survey in Florida Bay on May 21-24.

Meetings

● Dr. Luke Thompson will give two talks about the Earth Microbiome Project in the San Francisco Bay Area at the end of this month. On May 29 he will speak at the DOE Joint Genome Institute in Walnut Creek about "Lessons from a scientifically crowdsourced microbiome survey". On May 30 he will speak at the Department of Earth Systems at Stanford University about "Investigating the structure of microbial diversity on Earth".

May 15, 2018

Field Work

● Patrick Mears and the R/V Nathaniel Palmer returned to port on May 15th, after conducting GO-SHIP 2018 S04P.

● The GO-SHIP I07 cruise on the R/V Brown continues with Dr. Denis Volkov AOML/CIMAS as chief scientist and 26 scientists and students representing 19 institutions participating. AOML participants include Andy Stefanik, Ian Smith, Chuck Featherstone, Leah Chomiak, and Jay Hooper. Follow their adventures on the cruise blog at https://i07n.wordpress.com/.

● Joe Bishop, Dr. Natchanon Amornthammarong and Dr. Jim Hendee from OCED will join Albert Jones, from the Caribbean Community Climate Change Center (5Cs), Dr. Pamela Fletcher from Sea Grant, and John Halas from Environmental Moorings Inc., to install the third CREWS buoy (in St.Lucia) of Phase 2 in the year-long campaign to install the buoys at five sites in the Caribbean. The installation effort will be May 7 - May 18, and will include installing mooring pins to the bottom, preparing the buoy electronics, and eventual deployment at the final site in Soufriere Marine Management Area on the west side of St. Lucia. Conversations with locals in outreach efforts will be led by Dr. Fletcher to discuss the utility of the buoy data, as well as information on the maintenance aspects of the buoy. Once the data are retrieved at AOML, Mike Jankulak will oversee the posting of the data to a special open-access blog, and Lew Gramer, together with student intern Madison Soden, will oversee the collaboration with St. Lucia researchers and formulation and elicitation of ecological forecasts. The greater portion of funding is through 5Cs, although funding for information systems and data come from NOAA's Coral Reef Conservation Program, and from OCED's Coral Health and Monitoring Program. Sea Grant is providing salary support for Pamela Fletcher.

Meetings

● Dr. Chris Kelble, Shannon Martin, Kelly Montenero, Dr. Neda Trifonova and Charline Quenee hosted a regional meeting for the Gulf of Mexico Integrated Ecosystem Assessment program in Key West May 14th-18th. The last day will be a special session coordinated with the Florida Keys National Marine Sanctuary to determine how the IEA program can benefit the Sanctuary's science needs and decision-making and kick-off the Florida Keys IEA effort funded by CRCP.

May 7, 2018

Bon Voyage

● This is Ben Vandine's last week at AOML! Ben has been an extremely valuable asset to OCED and AOML serving as our field coordinator and AOML's associate director. Ben and his wife are moving onto his next assignment in Woods Hole, MA. Ben will be serving as a co-captain on a 72' fisheries research vessel with the Northeast Fisheries Science Center. ENS Aly Thompson has started taking over Ben's responsibilities with the Small boat Program and other duties in OCED, and she has already proved a valuable asset to AOML field work.

Manuscripts

● The paper entitled "American Gut: an open platform for citizen-science microbiome research" with AOML/OCED author Dr. Luke Thompson was accepted for publication in the journal mSystems and will be published online May 15. This paper shows that a citizen-science, self-selected cohort shipping samples through the mail at room temperature recaptures many known gut microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n=1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.

McDonald, D., E.R. Hyde, J.W. Debelius, J.T. Morton, A. Gonzalez, G. Ackermann, A.A. Aksenov, B. Behsaz, C. Brennan, Y. Chen, L. DeRight-Goldasich, P.C. Dorrestein, R.R. Dunn, A.K. Fahimipourg, J. Gaffney, J.A. Gilbert, G. Gogul, J.L. Green, P. Hugenholtz, G. Humphrey, C. Huttenhower, M.A. Jackson, S. Janssen, D.V. Jeste, L. Jiang, S.T. Kelley, D. Knights, T. Kosciolek, J. Ladau, J. Leach, C. Marotz, D. Meleshko, A.V. Melnik, J.L. Metcalf, H. Mohimani, E. Montassier, J. Navas-Molina, T.T. Nguyen, S. Peddada, P. Pevzner, K.S. Pollard, G. Rahnavard, A. Robbins-Pianka, N. Sangwan, J. Shorenstein, L. Smarr, S. Song, T. Spector, A.D. Swafford, V.G. Thackray, L.R. Thompson, A. Tripathi, Y. Vazquez-Baeza, A. Vrbanac, P. Wischmeyer, E. Wolfe, Q. Zhu, The American Gut Consortium & R. Knight. (2018). American Gut: an open platform for citizen-science microbiome research. mSystems, DOI: 10.1128/mSystems.00031-18.

Fieldwork

● Patrick Mears is still on board the R/V Nathaniel Palmer conducting GO-SHIP 2018 S04P. Last week, they sampled from the Amundsen Sea to the Bellinghausen Sea.

● The GO-SHIP I07 cruise on the R/V Brown continues with Dr. Denis Volkov AOML/CIMAS as chief scientist and 26 scientists and students representing 19 institutions participating. AOML participants include Andy Stefanik, Ian Smith, Chuck Featherstone, Leah Chomiak, and Jay Hooper. Follow their adventures on the cruise blog at https://i07n.wordpress.com/.

Kelly Montenero and Dr. Chris Kelble participated in a south Florida Ecosystem Research Cruise aboard the R/V Walton Smith from April 30 through May 4.

● Joe Bishop, Dr. Natchanon Amornthammarong and Dr. Jim Hendee from OCED will join Albert Jones, from the Caribbean Community Climate Change Center (5Cs), Dr. Pamela Fletcher from Sea Grant, and John Halas from Environmental Moorings Inc., to install the third CREWS buoy (in St.Lucia) of Phase 2 in the year-long campaign to install the buoys at five sites in the Caribbean. The installation effort will be May 7 - May 18, and will include installing mooring pins to the bottom, preparing the buoy electronics, and eventual deployment at the final site in Soufriere Marine Management Area on the west side of St. Lucia. Conversations with locals in outreach efforts will be led by Dr. Fletcher to discuss the utility of the buoy data, as well as information on the maintenance aspects of the buoy. Once the data are retrieved at AOML, Mike Jankulak will oversee the posting of the data to a special open-access blog, and Lew Gramer, together with student intern Madison Soden, will oversee the collaboration with St. Lucia researchers and formulation and elicitation of ecological forecasts. The greater portion of funding is through 5Cs, although funding for information systems and data come from NOAA's Coral Reef Conservation Program, and from OCED's Coral Health and Monitoring Program. Sea Grant is providing salary support for Pamela Fletcher.

Meetings

● Dr. Luke Thompson attended the 20th Genomic Standards Consortium Meeting at UC San Diego, California, from May 2-4. The three-day meeting highlighted the nexus of genomic standards, microbiomes, and advances in metabolomics, immunome, and taxonomy.

AOML, SEFSC & Miami Forecast Office Open House

● School groups: Thursday & Friday 10-2:00 pm.

● General public: Saturday 10-3:00 pm.

● AOML is expecting an estimated 500 students will be visiting our facility on both Thursday and Friday.

Contact Erica Rule if you'd like to volunteer to help ensure student groups and visitors stay together and are guided from location to location on time.

April 30, 2018

Manuscripts

● The paper entitled "Resilience in carbonate production despite three coral bleaching events in five years on an inshore patch reef in the Florida Keys" with AOML/OCED authors Dr. Derek Manzello, Dr. Ian Enochs, and Graham Kolodziej was accepted for publication in the journal Marine Biology. The persistence of coral reef frameworks requires that calcium carbonate (CaCO3) production by corals and other calcifiers outpaces CaCO3 loss via physical, chemical, and biological erosion. Coral bleaching causes declines in CaCO3 production, but this varies with bleaching severity and the species impacted. We conducted census-based CaCO3 budget surveys at Cheeca Rocks, an inshore patch reef in the Florida Keys, annually from 2012-2016 and parameterized the budgets with coral core data collected in 2017. Carbonate production declined after the first year of back-to-back bleaching in 2014, but then increased after 2015 to values greater than the initial surveys in 2012. Cheeca Rocks is an outlier in the Caribbean and Florida Keys in terms of coral cover, carbonate production, and abundance of the coral species Orbicella faveolata, which is threatened under the Endangered Species Act. Given the resilience of this site to repeated bleaching events, it may deserve special management attention.

Large colonies of the ESA-listed coral species Orbicella faveolata during peak bleaching in 2014 and again in 2018, illustrating recovery of Cheeca Rocks. Coral colony in foreground is ~2m in height and likely 100-200 years old.

Manzello DP, Enochs IC, Kolodziej G, Carlton R, Valentino L (2018) Resilience in carbonate production despite three coral bleaching events in five years on an inshore patch reef in the Florida Keys. Marine Biology. In Press.

Fieldwork

● The R/V Ron Brown departed on April 23 for the GO-SHIP I07 cruise with Dr. Denis Volkov, AOML/CIMAS as chief scientist and 26 scientists and students representing 19 institutions participating. AOML participants include Andy Stefanik, Ian Smith, Chuck Featherstone, Leah Chomiak, and Jay Hooper. Follow their adventures on the cruise blog at https://i07n.wordpress.com/.

Kelly Montenero and Dr. Chris Kelble will be participating on a south Florida Ecosystem Research Cruise aboard the R/V Walton Smith from April 30 through May 4.

● Joe Bishop, Dr. Natchanon Amornthammarong and Dr. Jim Hendee from OCED will join Albert Jones, from the Caribbean Community Climate Change Center (5Cs), Dr. Pamela Fletcher from Sea Grant, and John Halas from Environmental Moorings Inc., to install the third CREWS buoy (in St.Lucia) of Phase 2 in the year-long campaign to install the buoys at five sites in the Caribbean. The installation effort will be May 7 - May 18, and will include installing mooring pins to the bottom, preparing the buoy electronics, and eventual deployment at the final site in Soufriere Marine Management Area on the west side of St. Lucia. Conversations with locals in outreach efforts will be led by Dr. Fletcher to discuss the utility of the buoy data, as well as information on the maintenance aspects of the buoy. Once the data are retrieved at AOML, Mike Jankulak will oversee the posting of the data to a special open-access blog, and Lew Gramer, together with student intern Madison Soden, will oversee the collaboration with St. Lucia researchers and formulation and elicitation of ecological forecasts. The greater portion of funding is through 5Cs, although funding for information systems and data come from NOAA's Coral Reef Conservation Program, and from OCED's Coral Health and Monitoring Program. Sea Grant is providing salary support for Pamela Fletcher.

● Patrick Mears is still onboard the USAP icebreaker, Nathaniel B. Palmer conducting GO-SHIP 2018 S04P.

Meetings

● Dr. Kelly Goodwin and Dr. Kirsten Harper will attend a symposium on eDNA hosted by NOAA/NMFS with the Norwegian Institute of Marine Research. The US-Norway bilateral on eDNA will be held at Woods Hole, MA May 1-2, 2018. The meeting will have four main themes: 1) Overview of applications of eDNA in management of fisheries and aquacultures. 2) "eDNAta" - Reviewing existing reference databases. 3) Quantification of biomass based on eDNA: Where are we? How do we proceed? 4) Development of standardized eDNA sampling/analysis protocols. Each session will have talks by both the US and Norwegian participants followed by a roundtable discussion. Dr. Kirsten Harper will be presenting "Progress and future directions of eDNA approaches for population assessment of sea turtles."

April 23, 2018

Field Work

● The R/V Ron Brown is scheduled to start on GO-SHIP cruise I07 on April 23. Dr. Denis Volkov, AOML/CIMAS is the chief scientists and 26 scientists and students representing 19 institutions are participating. The AOML cruise participants are Andy Stefanik, Ian Smith, Chuck Featherstone, Leah Chomiak, and Jay Hooper. Follow their adventures on the IO7N cruise blog at https://i07n.wordpress.com/.

● Dr. Chris Kelble and Kelly Montenero will be participating on a south Florida Ecosystem Research Cruise aboard the R/V Walton Smith from April 30 through May 4.

Announcements

● Dr. Kelly Goodwin will provide an "Oceans Portfolio Priorities Pitch" on 'omics at the next OAR Oceans, Coasts, and Great Lakes Portfolio Meeting on April 23, 2018.

Dr. Luke Thompson has published digital versions of Earth Microbiome Project protocols for sample collection, DNA extraction, and amplicon sequencing to the protocols.io site. This effort supports AOML's contribution to the Global Omics Observatory Network (GLOMICON) by standardizing methods and making them available to the broader research community. The protocols can be found at https://www.protocols.io/groups/earth-microbiome-project/protocols.

● The new coral reef monitoring buoy was successfully installed in St Kitts on 4/16/2018 at Paradise reef and all data is transmitting successfully.

Fieldwork

● Patrick Mears is currently underway toward the ice of Antarctica as part of the GO-SHIP SO4P line in the Southern Ocean onboard the USAP icebreaker, Nathaniel B. Palmer.

April 16, 2018

Outreach and Education

● Last weekend Liz Dutra attended the USA Science & Engineering festival with over 375,000 attendees in Washington D.C. The focus of the festival was to immerse attendees in the world of STEM. Liz currently serves as the Marine Science Education and Outreach Manager for a non-profit called the Big Blue & You. Big Blue & You had an exhibit at the festival where Liz represented our laboratory as a Coral Reef Biologist. At Liz's station, she was teaching attendees all about the pH scale in order to explain the term Ocean Acidification. Liz ran mini pH demonstrations in order to give attendees a true understanding of OA. Liz also spoke about what we do in OCED's coral OA research using several coral skeletons and a coral core. Liz was partnered with an intern from the Coral Restoration Foundation, who was teaching attendees about what CRF does while they participated in an art project. Participants created a woven tapestry that emulated different colors of the ocean. Overall, we had a very well attended exhibit with over 1500-2000 participants. It was truly amazing to represent NOAA/OCED at the largest celebration of STEM in the country.

Fieldwork

● Patrick Mears is currently underway toward the ice of Antarctica as part of the GO-SHIP SO4P line in the Southern Ocean onboard the USAP icebreaker, Nathaniel B. Palmer.

● Albert Jones, from the Caribbean Community Climate Change Center (5Cs), Dr. Pamela Fletcher from Sea Grant, and John Halas from Environmental Moorings, Inc., will join Joe Bishop, Dr. Natchanon Amornthammarong and Dr. Jim Hendee from OCED, to install the second CREWS buoy of Phase 2 in the year-long campaign to install the buoys at five sites in the Caribbean. The installation effort will be April 9 - 22, and will include installing mooring pins to the bottom, preparing the buoy electronics for deployment, eventual deployment at the final site "Anchors Away", at 17° 21' 23" N, 62° 51' 18: W. Conversations with locals in outreach efforts will be led by Dr. Fletcher to discuss the utility of the buoy data, as well as information on the maintenance aspects of the buoy. Once the data are retrieved at AOML, Mike Jankulak will oversee the posting of the data to a special open-access blog, and Lew Gramer, together with student intern Madison Soden, will oversee the collaboration with St. Kitts researchers and formulation and elicitation of ecological forecasts. The greater portion of funding is through 5Cs, although funding for information systems and data come from NOAA's Coral Reef Conservation Program, and from OCED's Coral Health and Monitoring Program. Sea Grant is providing salary support for Pamela Fletcher.

Announcements

● Dr. Kelly Goodwin participated in a brain-storming session hosted by Amazon on April 11, 2018. The meeting focused on ecosystems and fisheries data, including 'omics. Amazon Sustainability and Amazon Web Services (AWS) are working jointly to provide improved access to high-value data through the AWS Public Datasets program (PDS; https://aws.amazon.com/about-aws/whats-new/2008/12/03/public-data-sets-on-aws-now-available/). Amazon is currently identifying data needs for fisheries and partnering with NOAA, through the Big Data Cooperative Research and Development Agreement (CRADA), to explore how NOAA data and AWS's infrastructure may enable further work in this area. One goal of the meeting was to bring together Amazon, NOAA, and key stakeholders to identify current data-related challenges and discuss possible ways to address them.

April 9, 2018

Manuscripts

NOTE: This article is under embargo and should not be publicized anywhere until the embargo is lifted. The manuscript entitled "Loss of coral reef growth capacity to track future increases in sea-level" with OCED co-authors Derek Manzello, Renee Carlton, Ian Enochs, Graham Kolodziej, and Lauren Valentino was accepted for publication in Nature. This paper utilized data collected as part of the National Coral Reef Monitoring Program (NCRMP) and is the result of a collaboration between OCED and Chris Perry of the University of Exeter, UK. This study calculated the vertical growth potential of >200 Tropical Western Atlantic and Indian Ocean reefs and compared it against recent and projected rates of sea-level rise under different Representative Concentration Pathway (RCP) scenarios. It was found that few reefs will have the capacity to track sea-level rise projections under RCP 4.5 scenarios without sustained ecological recovery, whilst under RCP 8.5 most reefs are predicted to experience mean water depth increases >0.5 m by 2100. This has significant socio-economic and policy implications for urbanised tropical coastlines and reef islands as there will be increased flooding risk and coastal damage during storms as the physical buffering capacity of reefs is depressed. Urgent action to mitigate climate, sea-level and future ecological changes are thus needed to limit magnitudes of future reef submergence.

Perry C, Alvarez-Filip L, Graham N, Mumby PJ, Wilson SK, Kench PS, Manzello DP, Morgan K, Slangen ABA, Thompson DP, Januchowski-Hartley F, Smithers SG, Steneck RR, Carlton R, Edinger EE, Enochs IC, Estrada-Saldivar N, Haywood MDE, Kolodziej G, Murphy GN, Perez-Cervantes E, Suchley A, Valentino L, Boenish R, Wilson M, Macdonald C (2018) Loss of coral reef growth capacity to track future increases in sea-level. In Press. Nature.

● The manuscript entitled "Climate Change Threatens the World's Marine Protected Areas" and co-authored by Ruben van Hooidonk was accepted for publication in Nature Climate Change. The manuscript finds that continued business-as-usual emissions (RCP8.5) will likely result in thermal stress exceeding the Community Thermal Safety Margin (CTSM) in tropical MPAs by 2050. Although MPAs are widely-promoted as a means to mitigate the effects of climate change, the opposite perspective is more in line with the scientific reality: without drastic reductions in carbon emissions, ocean warming, acidification, and oxygen depletion in the 21st century will in all likelihood disrupt the composition and functioning of the ecosystems currently protected within the world's MPAs.

U J Bruno, A Bates, C Cacciapaglia, E Pike, S Armstrup, R van Hooidonk, S Henson, R Aronson. Climate Change Threatens the World's Marine Protected Areas. Accepted. Nature Climate Change.

● The manuscript enitled "Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm" with OCED co-author Luke Thompson was accepted for publication in Nature Communications. Airborne microbes from the ocean play important roles in Earth's climate system and human health, yet little is known about factors controlling their transfer from the ocean to the atmosphere. We studied microbiomes of isolated sea spray aerosol (SSA) collected in a unique ocean-atmosphere facility, and demonstrated taxon-specific aerosolization of bacteria and viruses. These trends were conserved within taxonomic orders and classes, and temporal variation in aerosolization was similarly shared by related taxa. We observed enhanced transfer into SSA of Actinobacteria, certain Gammaproteobacteria, and lipid-enveloped viruses; conversely, Flavobacteriia, some Alphaproteobacteria, and Caudovirales were generally under-represented in SSA. Viruses did not transfer to SSA as efficiently as bacteria. The enrichment of mycolic acid-coated Corynebacteriales and lipid-enveloped viruses (inferred from genomic comparisons) suggested that hydrophobic properties increase transport to the sea surface and SSA. The results identify taxa relevant to atmospheric processes and a framework to further elucidate aerosolization mechanisms influencing microbial and viral transport pathways.

Michaud, J.M., L.R. Thompson, D. Kaul, J. Espinoza, R.A. Richter, Z.Z. Xu, C. Lee, K.M. Pham, C.M. Beall, F. Malfatti, F. Azam, R. Knight, K.A. Prather, C.L. Dupont & M.D. Burkart. (2018). Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm. Accepted. Nature Communications.

● The manuscript enitled "Hidden in plain sight: The importance of cryptic interactions in marine plankton" authored by OCED's Dr. Nicole Millette was accepted for publication in Limnology and Oceanography: Letters. Generalizations in foodweb modeling have helped scientists explain and study interactions within the aquatic environment. Established methods focus on quantifying and qualifying these generalizations, but rapid technological advancements in recent years have revealed that our generalizations of interactions may obscure significant processes within the plankton community. We explore a range of interactions within the planktonic foodweb that are "cryptic" because existing methods are biased against them with the intention of highlighting a range of cryptic interactions and the potential impact of overlooking them in future research. We discuss how including these interactions into biogeochemical and foodweb models alters our understanding of the transfer of carbon and other materials from one species/functional group to another and highlight examples of recent models that have incorporated cryptic interactions.

Millette, N, J Grosse, W Johnson, M Jungbluth, E Suter. 2018. Hidden in plain sight: The importance of cryptic interactions in marine plankton. Accepted. Limnology and Oceanography: Letters.

Announcements

● Dr. Kelly Goodwin was appointed to the NOAA Research Council's 'Omics Task Force.

Outreach

● Charline Quenee will take part in the Skype-a-Scientist program on 04/09/18. She will be virtually presenting to a class of 2nd to 5th graders from John P. Faber Elementary in New Jersey about marine science, conservation, and how to get involved in science.

● In collaboration with the Angari foundation, Dr. Ian Enochs recorded narration and voice over in an audio studio at the Miami Animation and Gaming International Complex (MAGIC) at the Wolfson Campus of Miami Dade College. The material will be incorporated into a virtual reality video and learning tool based on the OCED research at Cheeca Rocks and the Experimental Reef Lab.

Fieldwork

● John Morris, Nate Formel, and Dr. Ian Enochs will be traveling to the Grenadines next week to explore a volcanic vent off the island of Mayreau. The project represents a collaboration with Dr. Jim Hendee and Dr. Derek Manzello, aimed at identifying a high-temperature, high-CO2 Caribbean reef system. The team will be testing prototype Subsurface Automatic Sampler (SAS) units, designed and built in house at the OCED Advanced Manufacturing and Design (AMD) lab.

● Patrick Mears is currently underway toward the ice of Antarctica as part of the GO-SHIP SO4P line in the Southern Ocean onboard the USAP icebreaker, Nathaniel B. Palmer.

● Albert Jones, from the Caribbean Community Climate Change Center (5Cs), Dr. Pamela Fletcher from Sea Grant, and John Halas from Environmental Moorings, Inc., will join Joe Bishop, Dr. Natchanon Amornthammarong and Dr. Jim Hendee from OCED, to install the second CREWS buoy of Phase 2 in the year-long campaign to install the buoys at five sites in the Caribbean. The installation effort will be April 9 - 22, and will include installing mooring pins to the bottom, preparing the buoy electronics for deployment, eventual deployment at the final site "Anchors Away", at 17° 21' 23" N, 62° 51' 18: W. Conversations with locals in outreach efforts will be led by Dr. Fletcher to discuss the utility of the buoy data, as well as information on the maintenance aspects of the buoy. Once the data are retrieved at AOML, Mike Jankulak will oversee the posting of the data to a special open-access blog, and Lew Gramer, together with student intern Madison Soden, will oversee the collaboration with St. Kitts researchers and formulation and elicitation of ecological forecasts. The greater portion of funding is through 5Cs, although funding for information systems and data come from NOAA's Coral Reef Conservation Program, and from OCED's Coral Health and Monitoring Program. Sea Grant is providing salary support for Pamela Fletcher.

Research Vessels

● OCED christened the division's new research vessel the R/V GBN1. The name means George Berberian Numero Uno, which is a nickname given to George many decades ago. OCED wanted to recognize George for his more than 40 years of service to AOML starting before AOML was constructed.

Farewell

● Dr. Paul Jones and Dr. Xaymara Serrano left OCED to pursue other ventures last week. Dr. Jones will be working for the South Florida Water Management District and Dr. Serrano will be working for the US Army Corps of Engineers in Jacksonville, FL.

Congratulations

● LT. Benjamin Vandine successfully passed his Master's presentation and examination on Thursday, April 5.

April 2, 2018

Announcements

● On April 3-4, there was a safety inspection of all AOML spaces conducted by visitors from NOAA's Environmental Compliance and Safety Assessment System (NECSAS).

● On April 4, RADM Tim Gallaudet, Acting NOAA Administrator and Assistant Secretary of Commerce for Oceans and Atmosphere and Dr. Neil Jacobs, Assistant Secretary of Commerce for Environmental Observation and Prediction visited AOML.

● Stephanie Rosales received a travel award to attend the American Society for Microbiology in June.

Manuscripts

● A news article has been submitted to Limnology and Oceanography describing the need for biological observations on sustained global ocean observation networks. This is the topic of a new Scientific Committee for Ocean Research (SCOR) working group entitled SCOR WG-154 "Integration of Plankton-Observing Sensor Systems to Existing Global Sampling Programs (P-OBS)".

"Beyond chlorophyll fluorescence: The time is right to expand biological measurements in oceanobserving programs". Emmanuel Boss, Anya Waite, Frank Muller-Karger, Hidekatsu Yamazaki, Rik Wanninkhof, Heidi Sosik, Bernadette Sloyan, Anthony Richardson, Patricia Miloslavich, Johannes Karstensen, Gerald Gregori, Katja Fennel, Herve Claustre, Marcela Cornejo, Ilana Berman-Frank, Sonia Batten, Silvia Acinas. Submitted to Limnology and Oceanography March 31, 2018.

● Dr. Neda Trifonova co-authored a paper entitled "Hidden variables in a Dynamic Bayesian Network identify ecosystem level change" which was published this week in Ecological Informatics. The paper describes the use of a series of Dynamic Bayesian network models fitted with different hidden variable structures to simulate a system that is known to have undergone a major structural change, i.e. the Baltic Sea food web. Dynamic Bayesian networks with hidden variables that can capture unobserved processes, have been proposed as a method to overcome the challenge of scarce data and static modeling approaches in terms of capturing functional changes in ecosystems. The setup of the hidden variables picked up a pattern that agrees with previous research regarding the system dynamics. The results suggest the hidden variable may in fact detect patterns before they can be clearly seen in the observed data, which provides a chance for predicting large-scale ecosystem changes.

Uusitalo, L., Tomczak, M.T., Muller-Karulis, B., Putnis, I., Trifonova, N. and Tucker, A., 2018. Hidden variables in a Dynamic Bayesian Network identify ecosystem level change. Ecological Informatics. doi: 10.1016/j.ecoinf.2018.03.003

Outreach

● Charline Quenee will take part in the Skype-a-Scientist program on 04/09/18. She will be virtually presenting to a class of 2nd to 5th graders from John P. Faber Elementary in New Jersey about marine science, conservation, and how to get involved in science.

Fieldwork

● Patrick Mears is currently underway toward the ice of Antarctica as part of the GO-SHIP SO4P line in the Southern Ocean onboard the USAP icebreaker, Nathaniel B. Palmer.

● Albert Jones, from the Caribbean Community Climate Change Center (5Cs), Dr. Pamela Fletcher from Sea Grant, and John Halas from Environmental Moorings, Inc., will join Joe Bishop, Dr. Natchanon Amornthammarong and Dr. Jim Hendee from OCED, to install the second CREWS buoy of Phase 2 in the year-long campaign to install the buoys at five sites in the Caribbean. The installation effort will be April 9 - 22, and will include installing mooring pins to the bottom, preparing the buoy electronics for deployment, eventual deployment at the final site "Anchors Away", at 17° 21' 23" N, 62° 51' 18: W. Conversations with locals in outreach efforts will be led by Dr. Fletcher to discuss the utility of the buoy data, as well as information on the maintenance aspects of the buoy. Once the data are retrieved at AOML, Mike Jankulak will oversee the posting of the data to a special open-access blog, and Lew Gramer, together with student intern Madison Soden, will oversee the collaboration with St. Kitts researchers and formulation and elicitation of ecological forecasts. The greater portion of funding is through 5Cs, although funding for information systems and data come from NOAA's Coral Reef Conservation Program, and from OCED's Coral Health and Monitoring Program. Sea Grant is providing salary support for Pamela Fletcher.

Research Vessels

● The new research vessel is undergoing sea trials and, if successful, is being picked up from Dusky Marine on April 2. This week the vessel will be getting outfitted with electronics and next week will be the training for potential boat operators.

March 19, 2018

Welcome Aboard

● Kelly Montenero joined OCED this week as a CIMAS employee. She will be working on a new project implementing an integrated ecosystem assessment in the Florida Keys National Marine Sanctuary. In addition she will be helping with other field and laboratory responsibilities. This project aims to identify tipping points that should translate into management targets for the Florida Keys National Marine Sanctuary.

Announcements

● OCED's nutrient Lab recently completed the analysis of nutrient reference seawater samples as part of the 2017-2018 International Inter-Comparison Exercise sponsored by the International Ocean Carbon Coordination Project (IOCCP) and the Japan Agency for Marine-Earth Science and Technology (JAMSTEC). More than 70 nutrient laboratories from 31 countries have participated in the study. During the study, nutrient reference samples of unknown concentration were prepared in Japan and Korea and supplied to participating laboratories for analysis, and the results were then reported back to the organizers. The exercise is part of an effort to develop nutrient reference material in seawater and a globally uniform analytical procedure for analysis of nutrient in seawater samples. By establishing international standards for nutrient comparability, researchers will be able to more accurately document the changes in ocean nutrient concentrations as results of change in natural and anthropogenic forcing in the oceans.

Workshops

● Dr. Chris Sinigalliano and Dr. Maribeth Gidley travelled to Saipan from March 5 - March 21 to conduct the second in a series of special technology transfer workshops on molecular Microbial Source Tracking (MST) for the Bureau of Environmental Coastal Quality (BECQ) of the US territory of the Commonwealth of the Northern Mariana Islands (CNMI). These MST technology transfer workshops are intended to build state-of-the-art MST analytical capability at the CNMI BECQ to help them better protect and manage coral reef habitats and other critical coastal ecosystems. By combining the AOML MST training workshop with the American University stable isotope source tracking study, and the additional EPA support efforts for the BECQ, the NOAA Coral Reef Conservation Program is leveraging the capacity building at the Commonwealth of the Northern Mariana Islands with actual source tracking studies to provide actionable environmental intelligence for marine resource managers while establishing the CNMI BECQ as an on-going regional resource for this type of pollution source tracking technology.

● Dr. Luke Thompson will teach a workshop on microbiome analysis at the University of Oulu in Finland, March 19-21, 2018.

Fieldwork

● Joe Bishop, Dr. Natchanon Amornthammarong and Dr. Jim Hendee from OCED along with Albert Jones from the Caribbean Community Climate Change Center (5Cs), Dr. Pamela Fletcher from Sea Grant, and John Halas from Environmental Moorings, Inc., are in Antigua to install the first CREWS buoy of Phase 2 in the year-long campaign to install the buoys at five sites in the Caribbean. They hope to deploy the mooring today at Monk's Head Reef in Antigua (17.015730o N, 61.872670o W). The team is also undertaking conversations with locals in outreach efforts led by Dr. Fletcher to discuss the utility of the buoy data, as well as information on the maintenance aspects of the buoy. Once the data are retrieved at AOML, Mike Jankulak will oversee the posting of the data to a special open-access blog, and Dr. Lew Gramer together with student intern Madison Soden, will oversee the collaboration with Antigua researchers and formulation and elicitation of ecological forecasts. You can follow the team's trip on their blog at https://mhab1-log.blogspot.com/.

● Patrick Mears is currently underway toward the ice of Antarctica as part of the GO-SHIP SO4P line in the Southern Ocean onboard the USAP icebreaker, Nathaniel B. Palmer.

● Ian Smith, Kelly Montenero, and Charline Quenee conducted a survey of juvenile sportfish and prey fish in Florida Bay on March 23-26. These cruises investigate how disturbances such as seagrass die-offs and hurricanes impact the juvenile sportfish and prey base in Florida Bay. They also have supported the development and continued enhancement of a performance measure that has been transitioned by the US Army Corps of Engineers to assess and evaluate the impacts of Everglades Restoration on Florida Bay.

Meetings

● Dr. Chris Kelble was in Washington DC to attend the NOAA Educational Partnership Program with Minority Serving Institutions 9th Biennial Education and Science Forum on March 18-21. Chris presented AOML's work on coastal resiliency at the meeting and hopes to build partnerships with PIs in the program to increase AOML's EPP internships and partnerships.

● Dr. Libby Jewett, director of the NOAA Ocean Acidification Program (OAP) visited AOML on Thursday March 22 from 6AM to 3 PM. The visit is part of the "bring your [favorite] program manager to work" program meant to provide managers and researchers a venue of informal exchanges and better insights into AOML capabilities and interests in support of ocean acidification research and goals. OAP funds activities in OCED and PhOD at a level of 1.2 M per year.

Small Boats

● Darel McCormick from the NOAA Small Boat Program came out to conduct an inspection on the R/V Cable March 21-23. This is a comprehensive, 3-year inspection that covers life-safety equipment, administration of the small boat program at AOML, the electrical, mechanical, and material condition of the vessel.

March 5, 2018

Workshops

● Dr. Chris Sinigalliano and Dr. Maribeth Gidley travelled to Saipan from March 5 - March 21 to conduct the second in a series of special technology transfer workshops on molecular Microbial Source Tracking (MST) for the Bureau of Environmental Coastal Quality (BECQ) of the US territory of the Commonwealth of the Northern Mariana Islands (CNMI). These MST technology transfer workshops are intended to build state-of-the-art MST analytical capability at the CNMI BECQ to help them better protect and manage coral reef habitats and other critical coastal ecosystems. By combining the AOML MST training workshop with the American University stable isotope source tracking study, and the additional EPA support efforts for the BECQ, the NOAA Coral Reef Conservation Program is leveraging the capacity building at the Commonwealth of the Northern Mariana Islands with actual source tracking studies to provide actionable environmental intelligence for marine resource managers while establishing the CNMI BECQ as an on-going regional resource for this type of pollution source tracking technology.

Fieldwork

● Albert Jones, from the Caribbean Community Climate Change Center (5Cs), Dr. Pamela Fletcher from Sea Grant, and John Halas from Environmental Moorings, Inc., will join Joe Bishop, Dr. Natchanon Amornthammarong and Dr. Jim Hendee from OCED, to install the first CREWS buoy of Phase 2 in the year-long campaign to install the buoys at five sites in the Caribbean. The installation effort will be March 12 - 23rd, and will include installing mooring pins to the bottom, preparing the buoy electronics for deployment, eventual deployment at the final site at Monk's Head Reef in Antigua (17.015730o N, 61.872670o W), and conversations with locals in outreach efforts led by Dr. Fletcher to discuss the utility of the buoy data, as well as information on the maintenance aspects of the buoy. Once the data are retrieved at AOML, Mike Jankulak will oversee the posting of the data to a special open-access blog, and Lew Gramer, together with student intern Madison Soden, will oversee the collaboration with Antigua researchers and formulation and elicitation of ecological forecasts. The greater portion of funding is through 5Cs, although funding for information systems and data come from NOAA's Coral Reef Conservation Program, and from OCED's Coral Health and Monitoring Program. Sea Grant is providing salary support for Pamela Fletcher.

On the left is John Halasm EMI with a local diver from Department of the Environment, Antigua

● Patrick Mears is participating in the GO-SHIP SO4P line in the Southern Ocean onboard the USAP icebreaker, Nathaniel B. Palmer for 67 days at sea as a DIC analyst. The ship departs on March 9.

● Dr. Chris Kelble, Ian Smith, and Charline Quenee will be conducting a survey of south Florida's coastal waters aboard the R/V Savannah for the south Florida Ecosystem Restoration Research Project on March 8-12.

● Ian Smith and Charline Quenee will be conducting a survey of juvenile sportfish and prey fish in Florida Bay in mid-March. These cruises investigate how disturbances such as seagrass die-offs and hurricanes impact the juvenile sportfish and prey base in Florida Bay. They also have supported the development and continued enhancement of a performance measure that has been transitioned by the US Army Corps of Engineers to assess and evaluate the impacts of Everglades Restoration on Florida Bay.

Meetings

● Dr. Rik Wanninkhof, Kevin Sullivan and Dr. Denis Pierrot will attend a pCO2 sensor workshop organized by the Ocean Thematic Centre (OTC) of the European research infrastructure Integrated Carbon Observation System (ICOS), in Bergen, Norway on March 6-9.

Small Boats

● The new Dusky 25' research vessel is scheduled to be delivered to AOML on April 2nd. The vessel is being custom-built for the specific needs of OCED and will serve as a water chemistry and diving platform that is capable of operating in the Florida Keys, the Bahamas, and greater South Florida. The manufacturer has installed a side door for CTD operations, and they are currently installing a 4' fixed dive ladder, a Hardcover T-Top, and a brand-new suite of electronics. If you have any questions on capabilities or future work on this vessel, please contact Dr. Chris Kelble or Ben VanDine.

February 26, 2018

Bon Voyage

● Dr. Xaymara Serrano has accepted a FTE position as the lead Coral / Benthic Biologist of the Environmental Division, US Army Corps of Engineers, with offices in Jacksonville, Florida. This new position will allow Xaymara to learn new skills in marine policy, environmental law and management, as well as use her knowledge and experience working with Florida reefs to help draft recommendations which may help minimize/mitigate ecosystem impacts. Most of the work Xaymara will conduct will be focused on SE Florida reefs so she expects to continue some of her collaborations with OCED scientists such as Drs. Jim Hendee, Chris Sinigalliano, Stephanie Rosales, Lew Gramer, Ruben van Hooidonk, Ian Enochs, and Derek Manzello. Xaymara is expected to begin her new position at the end of April.

Manuscripts

Dr. Ian Enochs and Dr. Derek Mazello co-authored a paper investigating the combined effect of elevated temperature and elevated pCO2 on the growth, survival, condition, and morphology of larvae of the commercially important Florida stone crab, Menippe mercenaria. This study investigated the combined effect of elevated temperature and elevated pCO2 on the growth, survival, condition, and morphology of larvae of the commercially important Florida stone crab, Menippe mercenaria. Elevated pCO2 resulted in a 37% decrease in survivorship relative to the control; however the effect of elevated temperature reduced larval survivorship by 71%. Exposure to both elevated temperature and pCO2 reduced larval survivorship by 80% relative to the control. Although elevated pCO2 could result in a reduction in larval supply, future increases in seawater temperatures are even more likely to threaten the future sustainability of the stone-crab fishery. The paper entitled "Warming and pCO2 effects on Florida stone crab larvae" was accepted for publication in Estuarine, Coastal and Shelf Science.

Dr. Maribeth Gidley and Dr. Chris Sinigalliano co-authored a paper that evaluates long-term databases for impact of management on Fecal Indicator Bacteria (FIB). This was research was undertaken, because beach water monitoring programs identify poor water quality, but often the causes of the degradation are frequently unknown. The findings of this research have important policy implications because the selected beach management practices associated with low levels of FIB can be implemented in other parts of the US and around the world to improve recreational beach water quality. The lead author Elizabeth Kelly worked in our environmental microbiology lab as a doctoral student.

Announcements

● On Wednesday February 21, NOAA divers Dr. Jim Hendee, Dr. Derek Manzello, and LT Ben VanDine conducted 8 hours of dive training, including O2 administration and first aid, and rescue scenarios for divers in the water.

● Dr. Chris Kelble will be helping lead a tour of the Everglades.

Fieldwork

● Patrick Mears will be traveling to Australia this week to participate in the GO-SHIP SO4P line in the Southern Ocean onboard the USAP icebreaker, Nathaniel B. Palmer for 67 days at sea as a DIC analyst. The ship is scheduled to depart on March 9.

February 20, 2018

Welcome Aboard

● Dr. Kirsten J. Harper joined CIMAS this week to work with Dr. Kelly Goodwin on eDNA and eAUV development. Dr. Harper is originally from Glasgow, Scotland. She received an undergraduate degree in Marine and Freshwater Ecology from the University of Glasgow in 2007, a Masters of Research in Marine and Freshwater Ecology and Environmental Management from the University of Glasgow in 2009, and a PhD in Ecology focusing on Invasive Species from the University of Stirling in 2016. She has studied fiddler crabs in Indonesia, monitored nesting sea turtles in Cyprus, worked on coral disease in Tobago, and developed eDNA protocols for sea turtles in San Diego.

Manuscripts

● Dr. Rik Wanninkhof is a co-author on a recently accepted paper that presents a means to assess multiple climate simulations in the Southern Ocean relative to the best available observations and observational products. The paper recommends standardization of observationally-based benchmarks that the modeling community should aspire to meet in order to reduce uncertainties in climate projections, and especially uncertainties related to oceanic heat and carbon uptake. The paper was a product of the US CLIVAR sponsored Southern Ocean Working Group (SOWG). It takes advantage of new observations and understanding that have allowed for progress in the creation of data/model metrics for the Southern Ocean. This is required to address the wide variability in global coupled climate model simulations of the Southern Ocean in response to ongoing anthropogenic trends.

Citation

● Russell, J. L., I. Kamenkovich, C. Bitz, R. Ferrari, S. T. Gille, P. J. Goodman, R. Hallberg, K. Johnson, K. Khazmutdinova, I. Marinov, M. Mazloff, S. Riser, J. L. Sarmiento, K. Speer, L. D. Talley and R. Wanninkhof. "Metrics for Evaluation of the Southern Ocean in Coupled Climate Models and Earth System Models." J. Geophys. Res. Paper #2017JC013461 (2018).

Announcements

● Dr. Pamela Fletcher, UF/IFAS-Florida Sea Grant laboratory liaison is conducting a needs assessment as part of AOML's Coral Reef Early Warning System (CREWS) being led by Dr. James Hendee. Pamela is gathering information from stakeholders who are installing the early warning system monitoring buoys in 2018. The assessment is intended to identify individuals and organizations who will use the CREWS data for regional and local planning in the Caribbean. This project is funded by USAID and is managed by the Caribbean Community Climate Change Centre. NOAA/AOML is providing technical expertise for buoy installation and stakeholder engagement to promote the use of data and information.

● Dr. Goodwin provided a lecture to Scripps Institute of Oceanography course "Graduate Marine Biotechnology" on February 13, 2018 and will provide a lecture for the UC San Diego course "Marine Microbiology" on February 26, 2018.

Meetings

● Dr. Pamela Fletcher, UF/IFAS-Florida Sea Grant laboratory liaison is hosting NOAA/OCM at UF/IFAS in Davie Feb 21 to 22 for the Planning for Meaningful Evaluation training. The training will be attended by academic, governmental and non-governmental participants involved in research and outreach projects. During this training, Pamela will be working with a group of UF colleagues focused on sea level resilience in South Florida. The team is using NOAA data and information in outreach programming and this training will assist in project planning.

● Dr. Kelly Goodwin will present a talk entitled "NOAA cross-line, interagency, and international engagement in 'omics" at the NOAA Research Council meeting in Silver Spring, Maryland on February 20, 2018.

● Dr. Luke Thompson will attend the 'Omic Biomonitoring Workshop at the Max-Planck-Institute for Marine Microbiology in Bremen, Germany, at the Max Planck Institute from February 20-22, 2018. Dr. Thompson will give a talk entitled "Global characterization of microbial taxonomic and functional diversity in the Earth Microbiome Project." Dr. Kelly Goodwin will remotely present a talk entitled "NOAA 'omics research and efforts to transition into management applications and operational observations" at the Workshop on Enhancing Interoperability & Coordination of Long-term 'Omics Observations in Bremen, Germany on February 21, 2018.

February 13, 2018

Meetings

● OCED's Dr. Derek Manzello is attending the Ocean Sciences Meeting in Portland, Oregon where he will give a talk entitled: "Local Adaptation and/or Acclimatization to Suboptimal Environmental Conditions on Inshore Patch Reefs in the Florida Keys Leads to Bleaching Resistance and Resilience."

February 5, 2018

Proposals

● Dr. Chris Kelble is co-PI on a project led by Dr. Jen Rehage at Florida International University that was selected for funding by the National Parks Service's Cooperative Ecosystem Study Initiative. The project entitled "Effects of freshwater inflows and seagrass die-off on recreational fisheries: A trophic & movement ecology approach" will supplement the ongoing juvenile sportfish research in Florida Bay by enabling us to conduct more cruises and more fully process the samples we collect.

Field Work

● Kevin Sullivan and Patrick Mears are traveling to Charleston, South Carolina on February 6-8 to reinstall underway analytical equipment aboard the NOAA Ship Ronald H. Brown as part of the Ship of Opportunity CO2 (SOOP-CO2) program.

Meetings

● Dr. Natchanon Amornthammarong gave an oral presentation on the topic of "Advanced Environmental Technologies" at a meeting of the Thai government at Clearwater Beach, Florida on January 25-28, 2018. He met with the Deputy Prime Minister of Thailand, the Minister of Science and Technology, the Deputy Minister of Education and several other key people from the Thai government. The principal aim of this conference was to provide a forum for exploring strategies for developing human intellectual capital for Thailand 4.0 in the next decade. The conference focused on four key enabling technologies required for Thailand 4.0, namely: smart sensors, energy storages, bio-data science and technology, and water resources management and technology.

● Dr. Rik Wanninkhof will be attending the first meeting of the SCOR Working group on integrating bio-optics and plankton enumeration into established global ocean surveys such as GO-SHIP (P-OBS) on Saturday, Feb. 10 in Portland, Oregon.

● Dr. Rik Wanninkhof and Dr. Denis Pierrot will be leading a workshop on establishing a Global Observing Network for Reference Surface Water pCO2 Observations. The workshop is organized by the the International Ocean Carbon Coordination project (IOCCP). The IOCCP is a joint project of the Scientific Committee on Oceanic Research and Intergovernmental Oceanographic Commission of UNESCO and an affiliate program of the Global Carbon Project. This workshop takes place on Sunday, Feb. 11 in Portland, Oregon.

● Dr. Kelly Goodwin will provide updates about 'omics, including National Microbiome Initiative implementation, to the NOAA Research Council on February 20, 2018, and during a talk to be provided to the AtlantOS/Agriculture and Agri-Food Canada Workshop on Enhancing the Interoperability and Coordination of Long-term Omic Observatories to be held at the Max Planck Institute for Marine Microbiology in Germany during February 21-23, 2018.

January 29, 2018

Awards and Honors

"Ocean acidification enhances the bioerosion of a common coral reef sponge: implications for the persistence of the Florida Reef Tract" by Dr. Ian Enochs, Dr. Derek Manzello, and Graham Kolodziej is the most cited paper published in the Bulletin of Marine Science in the last three years. The paper describes accelerated erosion of reef frameworks by a bioeroding sponge under ocean acidification conditions and models the impacts on coral reef permanence in the Florida Keys. RSMAS Bulletin of Marine Science.

● Two papers by OCED authors were selected by AOML to be put forward as their nominations for the OAR best paper award. Dr. Luke Thompson and Dr. Kelly Goodwin's paper, "A communal catalogue reveals Earth's multiscale microbial diversity," was selected as the AOML nominee for Oceans and Great Lakes and Dr. Ruben van Hooidonk's paper, "Local-scale projections of coral reef futures and implications of the Paris Agreement," was selected as the AOML nominee for Climate.

Citations

Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vazquez-Baeza, Y., Gonzalez, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., Haroon, M. F., Kanbar, J., Zhu, Q., Song, S., Kosciolek, T., Bokulich, N. A., Lefler, J., Brislawn, C. J., Humphrey, G. C., Owens, S. M., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J. A., Clauset, A., Stevens, R. L., Shade, A., Pollard, K. S., Goodwin, K. D., Jansson, J. K., Gilbert, J. A., Knight, R., and The Earth Microbiome Project Consortium. (2017). A communal catalogue reveals Earth's multiscale microbial diversity. Nature, 551(7681), 457-463, doi:10.1038/nature24621.

van Hooidonk, R. J., Maynard, J., and Tamelander, J. (2016). Local-scale projections of coral reef futures and implications of the Paris Agreement. Scientific Reports. (https://www.nature.com/articles/srep39666).

Field Work

● The AOML microbiology team will be conducting field sampling operations next week in the Florida Keys for the Marine Biodiversity Observation Network (MBON) and the Coral Genomic Observing Network (CGON). Dr. Paul Jones, Dr. Maribeth Gidley, and Ben Vandine will be collecting coral tissue samples, reef sediment samples, and reef water samples from six sentinel reefs in the Florida Keys National Marine Sanctuary for microbiome genomic characterization on Jan 30 - Feb 1, 2018.

● Kevin Sullivan and Patrick Mears are traveling to Charleston, South Carolina on February 6-8 to reinstall underway analytical equipment aboard the NOAA Ship Ronald H. Brown as part of the Ship of Opportunity CO2 (SOOP-CO2) program.

Meetings

● Dr. Kelly Goodwin will provide updates about 'omics, including National Microbiome Initiative implementation, to the Interagency Biodiversity Ad Hoc Working Group on January 25, 2018, to the NOAA Research Council on February 20, 2018, and during a talk to be provided to the the AtlantOS/Agriculture and Agri-Food Canada Workshop on Enhancing the Interoperability and Coordination of Long-term Omic Observatories to be held at the Max Planck Institute for Marine Microbiology in Germany during February 21-23, 2018 . She will present "Meta-omics off the US Pacific Coast and Beyond" during the US-Japan Living Marine Resources Bilateral in Hawaii January 29-30, 2018.

● Dr. Chris Kelble is participating in the "Science support to Biscayne National Park: imagining a healthier and more valuable Biscayne Bay, and then making it so" on Monday and Tuesday, January 29-30. The meeting is being hosted at BNP headquarters on Monday and at AOML on Tuesday. It is being put on by the Pew Fellows in collaboration with the Hoover Foundation.

● Dr. Maribeth Gidley has been invited to present a talk on the subject "Current and Future Health Concerns Associated with Rising Seas and a Changing Climate" at the University of Miami's Cooper Fellowship Training Symposium, "Empowering Capable Climate Communicators" on Saturday, February 3, 2018.

Seminar

● Dr. Stephanie Rosales will be giving a seminar on January 31st at 10AM in the first floor conference room at AOML entitled "Investigating the importance of microbial communities in marine mammals and coral reefs using omics."
Abstract: Marine mammals are top predators that are essential for the health and function of our oceans. These top predators are often affected by various factors that can be detrimental to their populations. Therefore, there is a need to evaluate undetermined causes of deaths and to better understand known diseases in marine mammals to mitigate future mortality events. In this talk, she will present some of her dissertation work that looked at a harbor seal mortality event caused by an unknown brain disease and the use of omics techniques to investigate the cause of death. She will also present her research from AOML looking at Southeast Florida Coral Initiative (SEFCRI) coral microbiome data. She will showcase the collaborative effort to correlate coral microbiome community changes to physical oceanographic conditions in four coral reefs sites. This is an effort to establish ideal environmental locations for corals and their microbiomes, which may aid in their survival. Additionally, she will talk about future projects and some of her community involvement efforts.

Updates

● Dr. Stephanie Rosales has started volunteering with Code/Art a Miami-based non-profit organization that aims to teach girls to code with the goal of increasing the number of women in computer science related fields. Stephanie presented at iPrep school which hosts one of Code/Art's after-school clubs. There, she introduced the students to bioinformatics and went through a short microbiome module.

● Dr. Stephanie Rosales, in collaboration with Dr. Ross Cunning and Dr. Michael Schmale at RSMAS, hosted the first bioinformatics meeting on Friday, January 19 to connect scientists from NOAA and RSMAS that are using bioinformatics for their research. If you are interested in participating in these bioinformatics meetings, please contact Stephanie.

● The NOAA Fisheries Southeast Regional Office (SERO) requested the assistance of Dr. Lew Gramer to review the particle tracking and sediment transport models the U.S. Army Corps of Engineers (USACE) is developing for the Port Everglades Navigation Improvement Project. The USACE is developing the models to evaluate impacts to coral and coral reef habitat from the dredging needed to deepen and lengthen the Port's Entrance Channel. Model results will be critical to consultations the USACE will pursue with SERO under the Endangered Species Act and Magnuson-Stevens Fishery Conservation and Management Act. Specially, these consultations will examine the predicted spatial extent and amounts of sediment accumulation on coral and coral reef habitat from the dredging and transport of dredged material during and up to a year after dredging ceases.

January 8, 2018

Meetings

● Dr. Kelly Goodwin will participate in the (virtual) Second Environmental DNA Technical Exchange Workshop January 9-10, 2018.

Visitors

● Dr. Kathy Tedesco, program manager for the OOMD/CPO/OAR sponsored GO-SHIP, XBT, and Ship of opportunity CO2 program will be visiting AOML January 11 and 12.

Outreach

● On Wednesday Jan 10th, Dr. Paul Jones will be giving a lecture at the Smithsonian Marine Station in Fort Pierce as part of their Marine Science in the Morning lecture series. The title of the talk is "Caribbean Cooking: Impacts of warming coastal waters on coral reefs of the Florida Keys and beyond".

Manuscripts

● Dr. Leticia Barbero is a contributing author of Chapter 16, Coastal Oceans and Continental Shelves of the U.S. Global Change Research Program Second State of the Carbon Cycle Report (SOCCR-2). The public comment period was completed January 8. This authoritative report considers relevant carbon-management science perspectives and science-based tools for supporting and informing decisions for North America with emphasis on the USA. SOCCR-2 also provides a status of, and emerging opportunities for, improving measurements, observations, and projections of carbon inventories and fluxes and identifies their uncertainty.

● Dr. Ian Enochs, Dr. Derek Manzello, and Dr. Renee Carlton are co-author of a landmark paper, "Taking the metabolic pulse of the world's coral reefs". It has been accepted for publication in PLOS One.

Citation

● Cyronak T, Andersson A, Langdon C, Albright R, Bates N, Caldeira K, Carlton R, Corredor J, Dunbar R, Enochs I, Erez B, Eyre B, Gattuso J-P, Gledhill D, Kayanne H, Kline D, Koweek D, Lantz C, Lazar B, Manzello DP, McMahon A, Melendez M, Page H, Santos I, Schulz K, Shaw E, Jacobs, Suzuki A, Teneva L, Watanabe A, Yamamoto S. paper, "Taking the metabolic pulse of the world's coral reefs (In Press). PLoS One.