AOML's Ocean Chemistry and Ecosystems Division


December 15, 2014


● Christopher Kelble, along with Michael Schirripa, Mandy Karnauskas and J. Kevin Craig (NMFS), were awarded the Bronze Medal Award "For advancing ecosystem-based management via the first comprehensive Gulf of Mexico Ecosystem Status Report with over 140 ecological indicators" on December 9, 2014 by NOAA Administrator Dr. Kathy Sullivan (Figure 1).

● The AOML Microbiology team has just been awarded the EPA's 2013 Scientific and Technological Achievement Award, Level II for Scientific and Technical Achievement Supporting Implementation of EPA Method 1611 for Rapid Recreational Water Testing. This award arose from their work with the US EPA for multi-laboratory testing and validation of the EPA quantitative PCR methods for environmental detection and enumeration of Enterococcus and Bacteroidales fecal indicator bacteria. This work was conducted over several years in collaboration with EPA, USGS, and several academic partners, and is summarized in the publication Shanks et al., (2012) Inter-Laboratory Comparison of Real-time PCR Methods for Quantification of General Fecal Indicator Bacteria, Environ. Sci. Technol. 46:945-953. The letter from EPA read "I personally commend you on being a co-author for one of the winners in the U.S. Environmental Protection Agency's (EPA) 2013 Scientific and Technological Achievement Award competition for your research publications, Inter-laboratory Comparison of Real-time PCR Methods for Quantification of General Fecal Indicator Bacteria, MPN Estimation of QPCR Target Sequence Recoveries from Whole Cell Calibrator Samples, and Comparison of Enterococcus PCR Analysis Results from Fresh and Marine Waters on Two Real-time Instruments".

● K. Goodwin attended the 2014 CalCofi meeting. A poster (NOAA CalCOFI Genomics Project (NCOG): Microbial 'Omics in the Southern California Bight) was presented which highlighted a new project that implements cutting-edge metagenomic and metatranscriptomic analysis into the 65-year old CalCofi program (Figure 2).

NOAA Corps

● A farewell send-off was held for LT Rachel Kotkowski on Thursday (Dec 11, 2014). She has completed her land assignment at AOML and will be next serving as Operations Officer on the R/V Gordon Gunter out of Pascagula, LA.

December 8, 2014

Ecosystem Restoration, Assessment, and Modeling

● Lindsey Visser, Lauren Valentino, and Dr. Chris Kelble participated in a cruise aboard the R/V Walton Smith last week (Dec. 1-5) focused on surveying water quality in south Florida's coastal waters. They collected samples for nutrients, chlorophyll a, and dissolved inorganic carbon. This was the first cruise to resume sampling water quality in south Florida coastal water after a two-year hiatus due to a lack of funding. These cruises have an additional focus on lower trophic level dynamics downstream from the Shark River on the southwest Florida shelf.

Environmental Microbiology

● Maribeth Gidley was an invited speaker at a Science Cafe on Dec. 10, 2014 at Vizcaya Museum and Gardens. The Science Cafe discussion concerned the impacts of Sea Level Rise and extreme weather events on individuals and communities; Dr. Gidley discussed the public health implications of these events.

Coral Health and Monitoring

● OCED researchers Ian Enochs and Derek Manzello had their abstracts accepted for oral presentations at the 2015 ASLO Aquatic Sciences meeting in Granada, Spain to be held in February. Manzello is also co-author on another oral presentation. All talks listed below. OCED researchers in bold:

Enochs I, Manzello D, Johnston L, Price N, Donham E, Golodziej G, Clark S, Young C. NATURALLY ACIDIFIED CORAL REEFS AT MAUG ATOLL: SIMILARITIES AND DIFFERENCES WITH OTHER HIGH-CO2 SYSTEMS. Session #61, Global climate change: ocean acidification experiments at CO2 vents.

Manzello D, Enochs I, Bruckner A, Renaud P, Kolodziej G, Carlton R, Glynn P. GALÁPAGOS CORAL REEF PERSISTENCE AFTER ENSO WARMING ACROSS AN ACIDIFICATION GRADIENT. Session #61, Global climate change: ocean acidification experiments at CO2 vents.

McGillis W, Langdon C, Martz T, Hsueh D, Loose B, Takeshita Y, Donham E, Price N, Smith J, Manzello D. AN INNOVATIVE APPROACH TO ASSESSING CORAL REEF HEALTH AT SEVEN SITES AROUND THE WORLD. Session #38, Advances in flux measurements in aquatic environments using the eddy correlation technique.

The manuscript entitled "Galápagos Coral Reef Persistence after ENSO Warming Across an Acidification Gradient" was accepted for publication in Geophysical Research Letters. This paper shows that since the 1982-83 El Niño-Southern Oscillation warming event, the persistence of reefs around the Galápagos Islands has differed across an acidification gradient. Reefs disappeared where pH < 8.0 and aragonite saturation state (Ωarag) ≤ 3 and have not recovered, whereas one reef has persisted where pH > 8.0 and Ωarag > 3. These results provide field evidence that the ability of coral reefs to persist with warming declines with acidification and this depressed resilience is likely reduced further by high nutrients. Based on current CO2 emission trajectories, the warming and acidification that eliminated coral reefs from the Galápagos Islands will occur for nearly all reefs by mid-century.

Citation (OCED researchers in bold):

Manzello D, Enochs I, Bruckner A, Renaud P, Kolodziej G, Carlton R, Glynn P. Galápagos Coral Reef Persistence after ENSO Warming Across an Acidification Gradient. Geophysical Research Letters. In press.

November 17, 2014

OCED Outreach

● Thomas Carsey presented the talk Just Beyond the Shore: Observations of Southeast Florida's Coastal Ocean at a meeting of the Key Biscayne Citizen Scientist Project, Key Biscayne, November 12, 2014.

November 10, 2014

OCED Outreach

● Xaymara Serrano (OCED) presented her doctoral research at the 7th NOAA EPP Biennial Education and Science Forum, held at the University of Maryland Eastern Shore (UMES) from October 26-29. The goal of this forum was to showcase results of collaborative research and education projects between scientists and students at NOAA-EPP funded academic institutions and NOAA scientists, and to promote career opportunities for STEM graduates with academic, government and public/private sectors. Xaymara participated in this meeting along with a group of other graduate students and alumni whose graduate research was funded through NOAA's Living Marine Resources Cooperative Science Center (LMRCSC,

Coral Health and Monitoring

● Lew Gramer attended a meeting last week in Honolulu on Coral Reef Resilience, sponsored by the NOAA Coral Reef Conservation Program. Resource managers from Great Barrier Reef Marine Park Authority, US Federal, State, and territorial agencies in the Pacific and the Caribbean joined researchers from NOAA (including OAR, NESDIS, and NMFS) and from the Universities of Hawaii, Miami, Queensland, Virgin Islands, and Plymouth (UK). The goals of the meeting were to share information on incorporating metrics for larval connectivity, stress disturbance exposure, and ecosystem diversity into resilience assessments of reefs, and on how to apply these metrics for more effective resource management in the face of future short-term and long-term environmental change.

November 3, 2014

OCED Outreach

● LTJG Michael Doig and Erica Rule presented information about the NOAA Corps to students at South Broward High School on October 27 (Figure 1).

Coral Health and Monitoring

● Renee Carlton of OCED is participating in Living Oceans Foundation (LOF) Global Reef Expedition (GRE) to the Solomon Islands from October 27 to November 25, 2014 (Figure 2). Renee will collect seawater CO2 data and coral cores for calcification analysis as part of the ongoing collaboration between LOF and OCED to obtain baseline ocean acidification relevant data from remote coral reef locations across the Pacific Ocean. The Solomon Islands lie in the Coral Triangle, which is home to the greatest amount of marine biodiversity on the planet and is thus a priority area for marine conservation. There has been no ocean acidification research conducted in this vital region, making this a first-of-its-kind study. This is the 10th GRE cruise that OCED scientists have participated in since June 2012.

● Last week at Little Cayman Island in the Caribbean, the Central Caribbean Marine Institute (CCMI) finished redeploying their buoy, which is part of the Coral Reef Early Warning System (CREWS) Network. The buoy was first deployed in October of 2013 and needs to be returned to land each year for cleaning, repainting and instrumentation swap-out. The buoy was towed from its deployment site on October 14th and returned to position on October 29th. OCED's Mike Jankulak worked remotely with CCMI personnel to update the buoy's programming and develop procedures for instrument configuration. As of October 31st all data feeds from the buoy to AOML and NDBC had fully resumed. Data can be viewed at

October 27, 2014

Coral Health and Monitoring

●Derek Manzello attended the workshop entitled Prioritizing Coral Restoration Sites hosted by Florida Fish and Wildlife at Nova SE University on October 22-23. This was the first of a 3-part workshop that will generate a spatially-explicit model to highlight the best locations for reef restoration based on both physical and biological factors.

●Renee Carlton, Graham Kolodziej, and Lauren Valentino traveled to the Cheeca Rocks NCRMP sentinel climate change and ocean acidification monitoring site where they collected zooxanthellae samples from 99 colonies of the ESA listed coral Oribicella faveolata over three fixed monitoring sites. Graham Kolodziej, Lauren Valentino, and NOAA Corp officer Mike Doig will return to Cheeca Rocks to collect 100 more samples from three different sites this week. OCED postdoc Dr. Paul Jones will work with Chris Sinigalliano to perform qPCR analysis to identify if certain zooxanthellae clades are associated with recovery of this critically endangered species. Carlton et al. also retrieved a temperature probe from Hens and Chickens Reef, downloaded the data and redeployed the unit. This site has the longest running temperature record for the Florida keys, extending back to 1975. This record was reestablished in Dec 2013 by OCED researchers as part of NCRMP. Research by OCED scientist Derek Manzello has elucidated a significant warming trend in this dataset. The 2014 warm-water bleaching event will be incorporated into this analysis to understand the significance of this recent thermal stress event over the past 40 years.

October 20, 2014

Environmental Microbiology

●The AOML microbiology team joined the FIU Southeast Environmental Research Center this past week to measure and document baseline nutrient and microbiological water quality conditions for a wide range of residential canals in the Florida Keys that are slated for either experimental remediation efforts or to be control canals for these remediation experiments. Chris Sinigalliano, Maribeth Gidley, and student intern Danny Morales spent the past week in the Florida Keys collecting and processing water samples from the experimental remediation and control canals, and will conduct microbial molecular source tracking analysis to establish baseline conditions and to document what improvements, if any, result from the canal water quality remediation efforts. It is hoped that these remediation efforts may led to more general improvement in the regional coastal water quality of the Florida Keys, and to improvement of community infrastructure resiliency in the face of anticipated impacts from climate change and sea level rise.

Coral Health and Monitoring

●The paper entitled Recent decade of growth and calcification of Orbicella faveolata in the Florida Keys: An Inshore-Offshore Comparison authored by OCED scientists Derek Manzello, Ian Enochs, Graham Kolodziej, and Renee Carlton was accepted for publication in Marine Ecology Progress Series. This study shows that calcification rates in this ESA-listed species were higher inshore vs. offshore over the past decade and also showed a marked resilience to both cold and warm-water stress. This fast growth inshore and high resilience to thermal stress is hypothesized to be one of the reasons for why the inshore patch reefs of the Florida Keys have maintained high coral cover relative to the reefs offshore.

October 14, 2014

Coral Health and Monitoring

● The Lao Lao Bay station in Saipan has been destroyed by "super typhoon" Vongfong which passed within 50 nm of the station on October 5th at 18Z and was then estimated at 90 knots of intensity (Category 2) (Figure 1). The islands of Rota, Tinian and Saipan suffered some damage to structures and experienced intermittent power outages but they appear to have escaped anything worse and the Governor's declared state of emergency had been lifted. Vongfong underwent rapid intensification after leaving the CNMI and is estimated to have become the most intense tropical cyclone of 2014 (Category 5). The fiberglass tube snapped close to the waterline (Figure 2) and the upper half, about 20 feet of tube filled with positively buoyant polyurethane foam, has not been found. The station had been offline but locally storing data since July 31st, when its cellular account was terminated. All data produced since July are believed to be unrecoverable. The station had been problematic for quite some time, as it had been difficult getting support for maintenance of the station. See

October 6, 2014

Coral Health and Monitoring

● Graham Kolodziej, Derek Manzello, and Lauren Valentino of OCED conducted coral reef CaCO3 budget surveys off of Miami-Dade and Broward counties on 29-30 Sept and 3 October with the assistance of NOAA Corps officers Mike Doig and Rachel Kotkowski. These surveys are part of the CRCP funded project Coral growth and reef framework persistence of the Florida Reef Tract with accelerating ocean acidification: The SEFCRI region.

Ecosystem Restoration, Assessment, and Modeling

●Geoffrey Cook from OCED and David Enfield and Chunzai Wang from PhOD are co-authors on a manuscript entitled Evidence of climate-driven ecosystem reorganization in the Gulf of Mexico that was submitted to the Proceedings of the National Academy of Science. The manuscript analyzes over 100 indicators in the Gulf of Mexico. The indicators were found to be influenced by two primary factors. The first was the implementation of fishing regulations in the 1970s; the second factor was the influence of the Atlantic Multi-Decadal Oscillation (AMO). The AMO was correlated with everything from the pressures being exerted on the ecosystem to the ecosystem state to the ecosystem services being produced by the ecosystem.

Environmental Microbiology

● Kelly Goodwin participated in the US-EU Marine Working Group on October 1, 2014, held at the French Embassy in Washington DC. The Working Group is comprised of the following sub-groups: Marine Microbial Ecology, Ocean Acidification/Stressors, Ocean Literacy, Ocean Observation Systems, and Aquaculture. These groups are working to implement the 2013 Galway Declaration which calls for collaborative international research on the coupled North Atlantic-Arctic system. Dr. Goodwin helped Gabrine Guiu, the EU co-chair of the Marine Microbial Ecology theme, present a summary of achievements, opportunities, and challenges facing coordinated EU-US marine microbial ecology research.

September 22, 2014

Environmental Microbiology

● Chris Sinigalliano and Maribeth Gidley were invited participants at a special public outreach and education presentation at Key Largo this past Friday, the first of the 2014-2015 "Ocean Life" series. Hosted by Florida International University's School of Environment, Arts and Society and the Friends of the Key Largo Cultural Center, the series features interdisciplinary experts from the region on marine topics that affect the Keys. The primary speaker at this first presentation of the season was Dr. Henry O. Briceño of the FIU Southeast Environmental Research Center on "Keys Canals: Your Backyard Swimming Pool ", which presented collaborative research by SERC and the AOML Microbiology Program on water quality issues in Florida Keys residential canals. This was followed by a public information question and answer session in which Drs. Gidley and Sinigalliano participated.

Coral Health and Monitoring

● Renee Carlton and Derek Manzello traveled to the Cheeca Rocks NOAA NCRMP sentinel climate and acidification monitoring site on 16-17 Sept 2014 where they worked with collaborator, Dr. Brooke Gintert of RSMAS/MGG, to document the ongoing Keys-wide coral bleaching event utilizing high-resolution landscape mosaic imagery. This will be a first of its kind dataset since no previous investigator has utilized this technique to document a coral bleaching event. Bleaching was severe at Cheeca Rocks (Fig. 1). The last major bleaching event to impact the Florida Keys was in 2005. Cheeca Rocks was studied by NCRMP collaborator, Dr. Marilyn Brandt of the University of the Virgin Islands, who upon seeing the recent pictures confirmed that this event was likely far more severe than 2005. Sea temperatures at nearby Molasses Reef were the hottest on record this summer, as well as this past winter (Fig. 2). Cheeca Rocks is one of the few sites that has been resilient to recent stress and maintained high coral cover. AOML coral scientists will be documenting the response of this coral reef to this thermal stress event.

● During the last week in August and the first week in September, Xaymara Serrano also took note of some extensive bleaching in the Keys while collecting coral larvae for her research:

8/29- Emerald reef:
Siderastrea/Millepora/Palythoa - really bleached or dead Agaricia - bleached
Orbicella faveolata/Montastraea cavernosa/Porites astreoides - ok, pale

9/2 Little Grecian Rocks:
Porites furcata - really bleached
Acropora palmata - partially bleached
Orbicella - pale

9/2 Horseshoe reef:
Agaricia/Millepora/Agaricia - really bleached
Siderastrea/Porites astreoides - some pale, some completely bleached
Orbicella - pale, some areas beginning to bleach

Ocean Carbon Cycle Group

● Betty Huss and Kevin Sullivan lead an effort to revamp the ocean carbon cycle group webpage. The concise, informative and visually appealing page of group activities and data holdings can be found at:

● The annual global carbon assessment by the global carbon program (GCP) was released yesterday. A world-wide-web highlight on the first utilization of data-based ocean estimates relying heavily on NOAA ship of opportunity CO2 data to determine flux variability is being created by Erica Rule and Monica Allen (OAR communications).

Synopses of GCP:
The Global Carbon Project's report each year incorporates data from multiple research institutes around the world on carbon dioxide emissions, carbon increase in the atmosphere, and land and ocean sinks for its annual assessment of the Earth's carbon budget. The Global Carbon Budget 2014, led by Prof Le Quéré, Director of the Tyndall Centre at the University of East Anglia, with 59 co-authors from 10 countries and 49 institutions, is published in the "living data" format to provide the highest transparency and traceability in the reporting of this set of key indicators and drivers of climate change. Le Quéré, C., Moriarty, R., Andrew, R.M., Peters, G.P., Ciais, P., Friedlingstein, P., Jones, S.D., Sitch, S., Tans, P., Arneth, A., Boden, T.A., Bopp, L., Bozec, Y., Canadell, J.G., Chevallier, F., Cosca, C.E., Harris, I., Hoppema, M., Houghton, R.A., House, J.I., Jain, A., Johannessen, T., Kato, E., Keeling, R.F., Kitidis, V., Klein Goldewijk, K., Koven, C., Landa, C.S., Landschützer, P., Lenton, A., Lima, I.D., Marland, G., Mathis, J.T., Metzl, N., Nojiri, Y., Olsen, A., Ono, T., Peters, W., Pfeil, B., Poulter, B., Raupach, M.R., Regnier, P., Rödenbeck, C., Saito, S., Salisbury, J.E., Schuster, U., Schwinger, J., Séférian, R., Segschneider, J., Steinhoff, T., Stocker, B.D., Sutton, A.J., Takahashi, T., Tilbrook, B., van der Werf, G.R., Viovy, N., Wang, Y.P., Wanninkhof, R., Wiltshire, A., Zeng, N., 2014. Global carbon budget 2014. Earth Syst. Sci. Data Discuss. 7, 521-610.

Florida Area Coastal Environment

● The FACE team completed their Numeric Nutrient Study cruise for September on the 22nd and 23rd. On board the R/V Hildebrand were Tom Carsey, Maribeth Gidley, Jack Stamates, Joe Bishop, Michael Doig, Rachel Kotkowski, and Lauren Valentino. Day 1 was calm and perfect; day 2 saw plenty of rain and windy weather. A waterspout was seen, as well as a sea turtle of unknown species. In addition to water quality samples, samples for microbiology and dissolved organic carbon were obtained at coral reef sites, inlets, outfalls, and background sites off of Miami-Dade and Broward counties.

September 15, 2014

Environmental Microbiology

● Chris Sinigalliano, Maribeth Gidley, and student intern Daniel Morales represented AOML microbiology research during a special session of Microbiology in the Coastal Zone at the 2014 Southeastern Microbiology Summit, a joint meeting of the Southeastern Branch and the Florida Branch of the American Society for Microbiology, on Sept 5-7, at Ponte Vedra, Florida. Chris Sinigalliano was an invited speaker giving an oral presentation on Urban Coastal Oceanography and NOAA Investigations of Microbial Water Quality Impacts from Coastal Inlets and Treated Wastewater Outfalls in the Southeast Florida Region. Daniel Morales presented a research poster covering summer research by AOML interns entitled Seaweed Wrack as a Potential Environmental Reservoir for Fecal Bacteria at South Florida Recreational Beaches.

● Chris Sinigalliano participated in a special training workshop on Environmental Microbial Genomics and Metagenomics in Walnut Creek, California Sept 7-12, hosted by the US Department of Energy's Joint Genome Institute.

Ocean Acidification

● Ruben van Hooidonk attended a meeting entitled Using Spatial Data and Analysis to Understand the Human Impacts of Ocean Acidification, along with Linwood Pendleton, Lisa Suatoni, Julie Ekstrom, Libby Jewett, Dwight Gledhill, Sarah Cooly, Chris Langdon, at the National Socio-Environmental Synthesis Center (SESYNC) in Annapolis, Maryland, September 9-10, 2014. Using projections of ocean acidification that he and Derek Manzello published (van Hooidonk, et al. 2014), several studies have been conducted to assess the risk and impact of ocean acidification on humans. These studies focussed on the impacts of ocean acidification on commercially important mollusks, fisheries and coastal protection by coral reefs, and should be submitted for publication in the near future.

September 2, 2014

● Renee Carlton, Graham Koldziej, and Derek Manzello installed temperature sensors at four coral reef locations at Biscayne National Park and at the Fowey Rocks lighthouse on 29-Aug-2014. These thermistors will provide in situ temperatures as part of the climate monitoring of the National Coral Reef Monitoring Program (NCRMP) of the Coral Reef Conservation Program (CRCP). During the surveys, extensive coral reef bleaching was observed at all the sites (see Fig. 1 and 2). The bleaching thresholds that were estimated and published for the Florida Reef Tract were exceeded in the past few weeks at Fowey Rocks and Molasses Reef (Fig. 3), thus the bleaching was expected. Sea temperatures at Molasses Reef C-MAN station are currently the warmest that they've ever been since the station's inception in 1988.

August 18, 2014

Coral Health and Monitoring

● The paper entitled Geographic differences in vertical connectivity in the Caribbean coral Montastraea cavernosa despite high levels of horizontal connectivity at shallow depths by X. Serrano, I. B. Baums, K. O'Reilly, T. B. Smith, R. J. Jones, T. L. Shearer, F. L. D. Nunes and A. C. Baker was published in the Journal of Molecular Ecology. In this study, the authors assessed vertical connectivity in 583 coral colonies of M. cavernosa collected from three depth zones (≤10, 15-20 and ≥25 m) at sites in Florida (within the Upper Keys, Lower Keys and Dry Tortugas), Bermuda and the U.S. Virgin Islands. Overall, this is the first work to demonstrate significant genetic differentiation by depth for coral populations in Florida.

August 11, 2014

● Undergraduate Hollings Scholar Daniel Coleman of Tulane University participated in research with mentor Lew Gramer, on periodic summer upwelling events in the northern portion of the Florida reef tract from May through July. Dan and Lew's poster entitled Summer cold-water anomalies on the Florida Reef Tract: Ecologically significant upwelling was presented by Dan at the 2014 NOAA Office of Education's Science and Education Symposium. The poster won the prize for "Best Poster of Session", (along with a $250 cash prize!) and the results of the work are likely to become part of an upcoming manuscript submitted for peer review this Fall.

Ocean Carbon Cycle

● The following paper was published: Rodgers, K.B., Aumont, O., Mikaloff Fletcher, S.E., Plancherel, Y., Bopp, L., de Boyer Montegut, C., Ludicone, D., Keeling, R.F., Madec, G., Wanninkhof, R., 2014. Strong sensitivity of Southern Ocean carbon uptake and nutrient cycling to wind stirring. Biogeosciences 11, 4077-4098.

● The following paper was resubmitted to the Journal of Geophysical Research - Oceans: Kristene McTaggart and Rik Wanninkhof, Antarctic Bottom Water Temperature Changes in the Western South Atlantic from 1989-2014.

● The following white paper was published and received recognition from the CPO/COD program manager, David Legler and Acting OAR director, Craig McLean: Feely, R. A., L. D. Talley, J. L. Bullister, C. A. Carlson, S. C. Doney, R. A. Fine, E. Firing, N. Gruber, D. A. Hansell, G. C. Johnson, R. M. Key, C. Langdon, A. Macdonald, J. T. Mathis, S. Mecking, F. J. Millero, C. W. Mordy, C. L. Sabine, W. M. Smethie, J. H. Swift, A. M. Thurnherr, R. H. Wanninkhof, M. J. Warner (2014): The US Repeat Hydrography CO2/Tracer Program (GO-SHIP): Accomplishments from the first decadal survey. A US CLIVAR and OCB Report, 2014-5, US CLIVAR Project Office, 47 pp. Comments from Craig McLean (US Head of Delegation to the IOC/UNESCO and Assistant Administrator for Research, NOAA): Congratulations to all authors and contributors to this remarkable work. As I represent the US at the Intergovernmental Oceanographic Commission (IOC), I find this global program a remarkable demonstration of coordination and alignment across governments and science institutions. As a NOAA person I am grateful to all collaborators and participants from across all organizations. This is a fine document, easy to read for persons beyond the science community and will bring valuable understanding to the policy community as well. Congratulations to all -- those who stood on deck, worked the samples, analyzed the data, and generated the report.

● Robert Castle met the NOAA ship RONALD H. BROWN in Newport, Oregon to reinstall the pCO2 underway system on the ship.

Ecosystem Restoration, Assessment, and Modeling

● Chris Kelble, chair of the NOAA IEA stering committee, attended the 2014 NOAA IEA Face to Face Meeting and ensuing IEA Steering Committee Meeting on August 5-8 at ESRL in Boulder, Colorado.

Coral Health and Monitoring

● Xaymara Serrano will be in Key Largo from August 8 to September 19 assisting during coral spawning (for the species Acropora cervicornis and Orbicella faveolata) and conducting experiments with newly settled recruits. This work will be done in conjunction with Dr. Margaret Miller from NMFS. The project is designed to assess the effects of increased nutrients and thermal stress on corals during the early life stages.

August 4, 2014

● Derek Manzello won 2nd place in the "Living Seas" category of the 2014 OAR Photo Contest with his photograph of a clownfish in Fiji (Figure 1). The winning photographs are shown in the OAR Weekly Update August 1, 2014.

July 28, 2014

● Pamela Fletcher completed her doctoral degree last week with participation from committee member James Hendee. Her thesis research included results from several NOAA funded projects including the Marine and Estuarine Goal Setting for South Florida project ( and the coral reef and marine resource managers climate information needs assessment project. Pamela received her degree from the University of Florida's Soil and Water Science Department and the title of her thesis is Using participatory decision support to improve coral reef management.

Coral Health and Monitoring

● Renee Carlton, Mike Jankulak, Graham Kolodziej, and Derek Manzello traveled to the Florida Keys to conduct field work on July 21-23. They conducted calcium carbonate budget surveys at the Cheeca Rocks NCRMP class III climate and acidification sentinel site, as well as collected coral cores for growth measurements. Additionally, they downloaded pH data from the Cheeca Rocks acidification buoy to ensure the sensor is working properly.

● Jim Hendee and Karsten Shein (NCDC) participated as mentors in the NSF-funded Research Experience for Undergraduates (REU) program at Little Cayman Research Center (LCRC) July 21 - 26, 2014. Jim spoke of the CREWS Network, the CREWS station at LCRC, how ecological forecasting works, and a bit on the newly proposed (by Kelly Goodwin and Chris Sinigalliano) Coral Microbiome Observing Network (CMON) and about Genomic Observatories (GO). The Director of LCRC, Dr. Carrie Manfrino, is seeking to re-write the LCRC/AOML MOU that has existed in the past for work with the CREWS station to now include AOML/OCED participation in the REU project for next year's students, as well as the proposed CMON/GO project. Other projects may also be included so that AOML has a broad collaboration with LCRC in the future.

July 21, 2014

Ecosystem Restoration, Assessment, and Modeling

● Rik Wanninkhof and Chris Kelble attended the 5th Annual NOAA/NGI Gulf Hypoxia Research Coordination Workshop July 14-16 at the Stennis Space Center (Mississippi). The workshop was designed to advance fisheries ecosystem management in the northern Gulf to inform efforts to assess and predict the potential ecological and socioeconomic effects of diversions and hypoxia. The workshop was designed to 1) provide a forum for strengthening communication and coordination between physical, biological, and socio-economic modelers of Gulf of Mexico hypoxia and Mississippi River diversions, and the users and stakeholders (e.g. Hypoxia Task Force, fisheries managers); 2) validate and refine key fisheries management and habitat conservation needs associated with ecosystem (including socioeconomic) effects of hypoxia and large-scale river diversions in the Gulf of Mexico; and 3) assess adaptive management needs for advancing ecosystem modeling of hypoxia and diversion effects on habitats and living resources in the northern Gulf of Mexico (Figure 1).

● A special volume of Ecological Indicators on Tools to Support Ecosystem Based Management of South Florida's Coastal Resources should be released this week. Chris Kelble is the managing guest editor for this special issue with Peter Ortner and Joseph Boyer also serving as guest editors. Most of the articles in the special volume present results from the Marine and Estuarine Goal Setting for South Florida (MARES) project. MARES had a number of OCED scientists serve as leaders, PIs, and participants, including Chris Kelble, Pamela Fletcher, Geoffrey Cook, Thomas Carsey, Jack Stamates, Jim Hendee, Chris Sinigalliano, Maribeth Gidley, and Michelle Wood. The special volume has the following five articles authored by OCED scientists:

1. The manuscript Using the Integrated Ecosystem Assessment Framework to Build Consensus and Transfer Information to Managers by Pamela Fletcher (SeaGrant/OCEd), Chris Kelble (OCED), William Nuttle, and Gregory Kiker was published in Ecological Indicators. The manuscript investigates how portions of the IEA framework were applied to build consensus on the focal ecosystem components and processes that are characteristic of a sustainable South Florida coastal ecosystem that is producing ecosystem services at the level society desires. Resource managers, researchers, academics, and non-governmental organizations participated in facilitated meetings and contributed to the synthesis of science and a myriad of science communications to transfer information to decision makers and the public. A proof of concept Bayesian Belief Network was developed to explore integrating the results of this assessment into an interactive management scenario evaluation tool. The four-year effort resulted in the development of a research and management coordination network in South Florida that should provide the foundation for implementing ecosystem-based resource management across multiple agencies (Figure 1).

2. The manuscript entitled Towards Marine Ecosystem Based Management in South Florida: Investigating the Connections among Ecosystem Pressures, States, and Services in a Complex Coastal System authored by AOML/CIMAS researchers Geoff Cook, Chris Kelble, and Pamela Fletcher was published in Ecological Indicators. Building upon the integrated conceptual ecosystem models developed during the MARES project, the manuscript explores the relative impact of 12 ecosystem pressures on 11 ecosystem states and 11 ecosystem services in coastal South Florida. The most pervasive pressures were Freshwater Delivery, Temperature Effects of Climate Change, and Impacts of Climate Change on Weather. The most at risk ecosystem states, as determined by cumulative impacts, were Protected Species, Fish and Shellfish, and Coral and Hardbottom Habitats. Similarly, the most at risk ecosystem services are Existence of Natural System, Pristine Wilderness Experience, and Non-extractive Recreation Opportunities (Figure 2). Through this exploration of the interaction among various ecosystem pressures, states, and ecosystem services, an understanding of how ecosystem services are impacted by multiple interacting pressures is derived. In so doing, a tool for resource managers to understand trade-offs and the possible impact on the production of ecosystem services that may occur when considering alternative management strategies is provided.

3. The manuscript Developing Integrated Ecosystem Indices by David Loomis, Peter B. Ortner, Chris Kelble, and Shona Paterson was published in Ecological Indicators. This manuscript investigates the need to develop consistent indicators for both the biophysical and social sciences. This consistency is necessary to allow integration between these indicators and quantify trade-offs among ecosystem services and ecosystem health. To accomplish this integration, the manuscript employs a "recursive relationship" approach that defines (and redefines) variables, indicators, and indices along a sliding hierarchy from measurable parameters to highly aggregated indices (Figure 3).

4. Two manuscripts detailing the selection and justification of waterbird indicators were co-authored by Pamela Fletcher and were published in Ecological Indicators. The first of these manuscripts developed a suite of conceptual models to investigate the niche of different waterbirds and select those that would make appropriate indicators. The second manuscript quantitatively scores the proposed indicators against a suite of pre-defined indicator criteria to justify their selection and proposes appropriate metrics to evaluate the waterbird indicators.

Environmental Microbiology

● Kelly Goodwin kicked off an intensive summer field campaign that will apply NOAA-developed Molecular Source Tracking (MST) markers to beaches in the vicinity of Los Angeles. In addition to MST, the project utilizes traditional and rapid detection of fecal indicator bacteria (FIB) and pathogen analysis in order to evaluate the risks posed by degraded water quality and the efficacy of remediation strategies. The work is part of a Cooperative Research and Development Agreement (CRADA) to support technology transfer.


● The paper entitled Carbon dynamics of Florida Bay: spatiotemporal patterns and biological control by Jia-Zhong Zhang and Charles Fischer was accepted for publication in Environmental Science and Technology. In this study, it was revealed that there are distinct CO2 source and sink regions in the bay and the seasonal variation of the CO2 sink was caused by cyanobacteria bloom. Based on the analysis of multi-year data, this paper provided the first estimate of ocean acidification trends and the annual CO2 fluxes to atmosphere from the bay in 2006-2012.

July 14, 2014

World Ocean Assessment

● Kelly Goodwin, Chris Kelble, and Rik Wanninkhof have been named official U.S. Government lead reviewers of chapters of the first World Ocean Assessment (WOA,, while Jim Hendee, Greg Foltz, Rick Lumpkin, olly Baringer and Gustavo Goni will act as science reviewers of select chapters. This is the first WOA, comprised of 57 chapters, designed to document trends in the state of the marine environment (including socioeconomic aspects). Subsequent WOAs will be generated every five years. The aim of the review process is to ensure technical and policy reviews of the WOA chapters, integrate these reviews with the public reviews received in response to a Federal Register Notice, and write and submit the integrated USG review to the UN Secretariat.

Coastal Oceanography

● Summer AOML student interns Danny Morales and Mishelle Rodriguez joined environmental public health physician Maribeth Gidley, and the crew (Joseph Bishop, LTJG Michael Doig, and Charles Featherstone) of NOAA's research vessel, R/V HILDEBRAND, to help collect water quality samples during this week's FACE-NNCS cruise. Samples collected will be analyzed for nutrients, microbial contaminants and source tracking markers of both coral and human health concern, and samples will be prepared for next-generation-sequencing and microbial community genomic analysis (as part of a NOAA Coral Reef Conservation Program project).

Ecosystem Restoration, Assessment, and Modeling

● The manuscript Population connectivity shifts at high frequency within an open-coast marine protected area network authored by AOML/CIMAS researcher Geoff Cook, and Ed Parnell and Lisa Levin of Scripps Institution of Oceanography was accepted for publication in PLoS ONE. Combining otolith microchemistry with ADCP-derived simulation modeling, the authors reconstructed the population connectivity (via larval dispersal) patterns of damselfish inhabiting a marine protected area (MPA) network along the southern California coastline (Figure 1). For over two years, the study documented self-recruitment at two of six study reefs, one of which is a no-take MPA. On biweekly time scales, we observed directional variability in alongshore current data and saw concomitant shifts in microchemistry-derived larval dispersal trajectories and reef connectivity patterns. As one of the few empirical studies of population connectivity within an open coast MPA network, this work can inform the MPA design process, implementation of ecosystem based management plans, and facilitate conservation decisions.

● The manuscript Quantifying Florida Bay habitat suitability for fishes and invertebrates under climate change scenarios authored by AOML/CIMAS researcher Kelly Kearney, and Mark Butler (Old Dominion University), Robert Glazer (Florida Fish and Wildlife Commission), Christopher Kelble (AOML/OCED), Joe Serafy (NOAA/SEFSC), and Erik Stabenau (National Parks Service) was accepted for publication in Environmental Management. This study uses a combination of hydrological and ecological models to investigate how the suitability of habitat will change in Florida Bay for three key fishery species (Spotted Seatrout, Grey Snapper, and Spiny Lobster) and four common prey species (Mojarra, Rainwater Killifish, Goldspotted Killifish, and Pinfish) under a variety of climate change scenarios. The scenarios investigated included changes in sea level, temperature, rainfall, runoff, and evaporation. Changes in habitat suitability varied in both magnitude and direction across both scenarios and species, but were on average small; suggesting that the estuarine fauna of Florida Bay may not be that vulnerable to climate change (Figure 2).

Environmental Microbiology

● OCED scientists and summer students participated in the Ocean Sampling Day on June 21, the first global simultaneous sampling for microbes in ocean, coastal and Great Lakes waters. Over time, sampling will support international and NOAA missions to provide a snapshot of the diversity of microbes, their functions, and their potential economic benefits. Among other economic applications, microbes have been used for novel medicines, as biofuels, and to consume spilled oil. Organized and led by the European Union's MicroB3 organization, NOAA coordinated twelve sampling sites for Ocean Sampling Day 2014 within U.S. coastal waters. View images of the sample collection process in the following AOML photo gallery.

July 7, 2014


● The Coastal-Marine Automated Network (C-MAN) stations at Sand Key (SANF1) and Pulaski Shoal (PLSF1) were replaced by National Data Buoy Center technicians recently, after extensive outages. With the Long Key (LONF1) and Sombrero Key Light (SMKF1) stations repaired earlier this spring, we now have all five Florida Keys C-MAN stations operational for the first time in a few years. Meteorological sensors are operating for wind speed/direction, air temperature, and pressure at all stations. Dew point temperature and heat index are available for the Long Key and Sombrero Key Light stations, and sea surface temperature is available for the Long Key and Molasses Reef stations. Unfortunately, the ICON station at LaoLao Bay, Saipan, will soon terminate operations due to lack of funds and local maintenance work.

● NSU's Oceanographic Center will be hosting the free Dive In Summer Film Series and presenting the Changing Seas episode entitled Galápagos: Windows into the Future, which featured OCED's Derek Manzello. The film will commence at 6pm on Wednesday, July 9 and will be followed by a panel discussion featuring Dr. Manzello and other Galapagos experts. These screenings are free, but space is limited; anyone interested in attending MUST register in advance at or by calling 954-262-3678. The Changing Seas episode originally aired on local PBS stations on June 25 and can be viewed here:

Environmental Microbiology

● The microbiology team will be conducting a 3-day survey of microbial contamination at recreational beaches throughout the Florida Keys National Marine Sanctuary this week. As part of their summer student intern projects, they will be measuring fecal indicator bacteria, microbial source tracking markers, pathogens, and other microbial contaminants in the sand, seaweed wrack, and near-shore waters of beaches from Key Largo to Key West, basing their field operations out of the Keys Marine Laboratory at Long Key, Florida. Participating are Maribeth Gidley and Chris Sinigalliano, and summer student interns Alejandro de la Cova, Trina Malone, Danny Morales, Mishelle Rodriguez and Camilla Mirow. They will be conducting beach sampling out of the KML facility from July 9 through July 12.