AOML's Ocean Chemistry and Ecosystems Division

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.