Moran Mary Ann

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Moran

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Mary Ann

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0000-0002-0702-8167

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Towards integrating evolution, metabolism, and climate change studies of marine ecosystems

(Elsevier, 2019-07-24) Baltar, Federico ; Bayer, Barbara ; Bednarsek, Nina ; Deppeler, Stacy ; Escribano, Ruben ; Gonzalez, Carolina E. ; Hansman, Roberta L. ; Mishra, Rajani Kanta ; Moran, Mary Ann ; Repeta, Daniel J. ; Robinson, Carol ; Sintes, Eva ; Tamburini, Christian ; Valentin, Luis E. ; Herndl, Gerhard J.

Global environmental changes are challenging the structure and functioning of ecosystems. However, a mechanistic understanding of how global environmental changes will affect ecosystems is still lacking. The complex and interacting biological and physical processes spanning vast temporal and spatial scales that constitute an ecosystem make this a formidable problem. A unifying framework based on ecological theory, that considers fundamental and realized niches, combined with metabolic, evolutionary, and climate change studies, is needed to provide the mechanistic understanding required to evaluate and forecast the future of marine communities, ecosystems, and their services.
Bacterial biogeography across the Amazon river-ocean continuum

(Frontiers Media, 2017-05-23) Doherty, Mary ; Yager, Patricia L. ; Moran, Mary Ann ; Coles, Victoria J. ; Fortunato, Caroline S. ; Krusche, Alex V. ; Medeiros, Patricia M. ; Payet, Jérôme P. ; Richey, Jeffrey E. ; Satinsky, Brandon ; Sawakuchi, Henrique O. ; Ward, Nicholas D. ; Crump, Byron C.

Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and >2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.
Environmental data from Niskin bottle sampling during the Fall 2016 ESP deployment in Monterey Bay, CA

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-04-17) Moran, Mary Ann ; Kiene, Ronald

Environmental data from Niskin bottle sampling during the Fall 2016 ESP deployment in Monterey Bay, CA. Samples were taken using Niskin bottles that collected seawater at the same depth and location of the Environmental Sample Processor deployed at Station M0 (36.835 N, 121.901W). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/756413
Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-01-14) Moran, Mary Ann

Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study. This dataset contains the processed, QC'ed, normalized sequence data. The full raw data file is deposited in the NCBI BioProject database under accession PRJNA381627. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/719970
Pulse Amplitude Modulation (PAM) fluorometry readings from microcosm experiments from samples collected by R/V E.O. Wilson in the Gulf of Mexico, Alabama (En-Gen DMSP Cycling project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-11-01) Moran, Mary Ann ; Kiene, Ronald ; Whitman, William

Fv:Fm ratios from control and experimental microcosms from the Dauphin Island Cubitainer Experiment (DICE) measured using a Pulse Amplitude Modulation (PAM) fluorometer. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/3873
Transcriptome data for bacteria collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-07-20) Moran, Mary Ann

Transcriptome data for bacteria Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, Polaribacter dokdonensis MED152, and Dokdonia MED134 collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture. The sequence data description for PRHNA448168 is at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA448168. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/818765
Fourier transform ion cyclotron resonance mass spectrometer (FT-ICRMS) data from seasonal collections, Doboy Sound, Sapelo Island, GA, July and October 2014

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-12-09) Moran, Mary Ann ; Medeiros, Patricia M

Dissolved organic matter (DOM) from field and incubation collections of Doboy Sounds estuarine waters near Sapelo Island, GA in July and October 2014 was analyzed for chemical composition. Analysis of the dissolved organic matter pool retrieved by solid-phase extraction (PPL resin) was analyzed to determine chemical formulas (by Fourier transform ion cyclotron resonance mass spectrometry, FT-ICR MS). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/735751
Environmental data from CTD during the Fall 2016 ESP deployment in Monterey Bay, CA

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-04-17) Moran, Mary Ann

Environmental data from CTD during the Fall 2016 ESP deployment in Monterey Bay, CA. The CTD was moored next to the Environmental Sample Processor (ESP) and sampled seawater ~ every 2.5 minutes while the ESP was filtering seawater. The ESP was located near Station M0 (36.835 N, 121.901W). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/756376
Bacterial production in microcosm experiments from samples collected by R/V E.O. Wilson in the Gulf of Mexico, Alabama (En-Gen DMSP Cycling project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-11-01) Moran, Mary Ann ; Kiene, Ronald ; Whitman, William

Bacterial production measurements from control and experimental microcosms from the Dauphin Island Cubitainer Experiment (DICE). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/3872
Experimental results: summary of microcosm data from Dauphin Island Cubitainer Experiment (DICE) from samples collected by R/V E.O. Wilson in the Gulf of Mexico, Alabama (En-Gen DMSP Cycling project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-11-01) Moran, Mary Ann ; Kiene, Ronald ; Whitman, William

Summary of parameters measured in experimental and control microcosms as part of the Dauphin Island Cubitainer Experiment (DICE). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/3857
Deciphering ocean carbon in a changing world

( 2016-01-13) Moran, Mary Ann ; Kujawinski, Elizabeth B. ; Stubbins, Aron ; Fatland, Rob ; Aluwihare, Lihini I. ; Buchan, Alison ; Crump, Byron C. ; Dorrestein, Pieter C. ; Dyhrman, Sonya T. ; Hess, Nancy J. ; Howe, Bill ; Longnecker, Krista ; Medeiros, Patricia M. ; Niggemann, Jutta ; Obernosterer, Ingrid ; Repeta, Daniel J. ; Waldbauer, Jacob R.

Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) : illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

(Public Library of Science, 2014-06-24) Keeling, Patrick J. ; Burki, Fabien ; Wilcox, Heather M. ; Allam, Bassem ; Allen, Eric E. ; Amaral-Zettler, Linda A. ; Armbrust, E. Virginia ; Archibald, John M. ; Bharti, Arvind K. ; Bell, Callum J. ; Beszteri, Bank ; Bidle, Kay D. ; Cameron, Connor T. ; Campbell, Lisa ; Caron, David A. ; Cattolico, Rose Ann ; Collier, Jackie L. ; Coyne, Kathryn J. ; Davy, Simon K. ; Deschamps, Phillipe ; Dyhrman, Sonya T. ; Edvardsen, Bente ; Gates, Ruth D. ; Gobler, Christopher J. ; Greenwood, Spencer J. ; Guida, Stephanie M. ; Jacobi, Jennifer L. ; Jakobsen, Kjetill S. ; James, Erick R. ; Jenkins, Bethany D. ; John, Uwe ; Johnson, Matthew D. ; Juhl, Andrew R. ; Kamp, Anja ; Katz, Laura A. ; Kiene, Ronald P. ; Kudryavtsev, Alexander N. ; Leander, Brian S. ; Lin, Senjie ; Lovejoy, Connie ; Lynn, Denis ; Marchetti, Adrian ; McManus, George ; Nedelcu, Aurora M. ; Menden-Deuer, Susanne ; Miceli, Cristina ; Mock, Thomas ; Montresor, Marina ; Moran, Mary Ann ; Murray, Shauna A. ; Nadathur, Govind ; Nagai, Satoshi ; Ngam, Peter B. ; Palenik, Brian ; Pawlowski, Jan ; Petroni, Giulio ; Piganeau, Gwenael ; Posewitz, Matthew C. ; Rengefors, Karin ; Romano, Giovanna ; Rumpho, Mary E. ; Rynearson, Tatiana A. ; Schilling, Kelly B. ; Schroeder, Declan C. ; Simpson, Alastair G. B. ; Slamovits, Claudio H. ; Smith, David R. ; Smith, G. Jason ; Smith, Sarah R. ; Sosik, Heidi M. ; Stief, Peter ; Theriot, Edward ; Twary, Scott N. ; Umale, Pooja E. ; Vaulot, Daniel ; Wawrik, Boris ; Wheeler, Glen L. ; Wilson, William H. ; Xu, Yan ; Zingone, Adriana ; Worden, Alexandra Z.

Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.
Environmental, biochemical and genetic drivers of DMSP degradation and DMS production in the Sargasso Sea

( 2011-10) Levine, Naomi M. ; Varaljay, Vanessa A. ; Toole, Dierdre A. ; Dacey, John W. H. ; Doney, Scott C. ; Moran, Mary Ann

Dimethylsulfide (DMS) is a climatically relevant trace gas produced and cycled by the surface ocean food web. Mechanisms driving intraannual variability in DMS production and dimethylsulfoniopropionate (DMSP) degradation in open-ocean, oligotrophic regions were investigated during a 10 month time-series at the Bermuda Atlantic Time-series Study site in the Sargasso Sea. Abundance and transcription of bacterial DMSP degradation genes, DMSP lyase enzyme activity, and DMS and DMSP concentrations, consumption rates, and production rates were quantified over time and depth. This interdisciplinary dataset was used to test current hypotheses of the role of light and carbon supply in regulating upper-ocean sulfur cycling. Findings supported UV-A dependent phytoplankton DMS production. Bacterial DMSP degraders may also contribute significantly to DMS production when temperatures are elevated and UV-A dose is moderate, but may favor DMSP demethylation under low UV-A doses. Three groups of bacterial DMSP degraders with distinct intraannual variability were identified and niche differentiation was indicated. The combination of genetic and biochemical data suggest a modified ‘bacterial switch’ hypothesis where the prevalence of different bacterial DMSP degradation pathways is regulated by a complex set of factors including carbon supply, temperature, and UV-A dose.
Cryptic carbon and sulfur cycling between surface ocean plankton

( 2014-12) Durham, Bryndan P. ; Sharma, Shalabh ; Luo, Haiwei ; Smith, Christa B. ; Amin, Shady A. ; Bender, Sara J. ; Dearth, Stephen P. ; Van Mooy, Benjamin A. S. ; Campagna, Shawn R. ; Kujawinski, Elizabeth B. ; Armbrust, E. Virginia ; Moran, Mary Ann

About half the carbon fixed by phytoplankton in the ocean is taken up and metabolized by marine bacteria, a transfer that is mediated through the seawater dissolved organic carbon (DOC) pool. The chemical complexity of marine DOC, along with a poor understanding of which compounds form the basis of trophic interactions between bacteria and phytoplankton, have impeded efforts to identify key currencies of this carbon cycle link. Here, we used transcriptional patterns in a bacterial-diatom model system based on vitamin B12 auxotrophy as a sensitive assay for metabolite exchange between marine plankton. The most highly upregulated genes (up to 374-fold) by a marine Roseobacter clade bacterium when co-cultured with the diatom Thalassiosira pseudonana were those encoding the transport and catabolism of 2,3- dihydroxypropane-1-sulfonate (DHPS). This compound has no currently recognized role in the marine microbial food web. As the genes for DHPS catabolism have limited distribution among bacterial taxa, T. pseudonana may use this novel sulfonate for targeted feeding of beneficial associates. Indeed, DHPS was both a major component of the T. pseudonana cytosol and an abundant microbial metabolite in a diatom bloom in the eastern North Pacific Ocean. Moreover, transcript analysis of the North Pacific samples provided evidence of DHPS catabolism by Roseobacter populations. Other such biogeochemically important metabolites may be common in the ocean but difficult to discriminate against the complex chemical background of seawater. Bacterial transformation of this diatom-derived sulfonate represents a new and likely sizeable link in both the marine carbon and sulfur cycles.
Quantification of amine- and alcohol-containing metabolites in saline samples using pre-extraction benzoyl chloride derivatization and ultrahigh performance liquid chromatography tandem mass spectrometry (UHPLC MS/MS)

(American Chemical Society, 2021-03-10) Widner, Brittany ; Kido Soule, Melissa C. ; Ferrer-González, Frank Xavier ; Moran, Mary Ann ; Kujawinski, Elizabeth B.

Dissolved metabolites serve as nutrition, energy, and chemical signals for microbial systems. However, the full scope and magnitude of these processes in marine systems are unknown, largely due to insufficient methods, including poor extraction of small, polar compounds using common solid-phase extraction resins. Here, we utilized pre-extraction derivatization and ultrahigh performance liquid chromatography electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) to detect and quantify targeted dissolved metabolites in seawater and saline culture media. Metabolites were derivatized with benzoyl chloride by their primary and secondary amine and alcohol functionalities and quantified using stable isotope-labeled internal standards (SIL-ISs) produced from 13C6-labeled benzoyl chloride. We optimized derivatization, extraction, and sample preparation for field and culture samples and evaluated matrix-derived biases. We have optimized this quantitative method for 73 common metabolites, of which 50 cannot be quantified without derivatization due to low extraction efficiencies. Of the 73 metabolites, 66 were identified in either culture media or seawater and 45 of those were quantified. This derivatization method is sensitive (detection limits = pM to nM), rapid (∼5 min per sample), and high throughput.
Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy

(Springer Nature, 2020-10-23) Ferrer-González, Frank Xavier ; Widner, Brittany ; Holderman, Nicole R. ; Glushka, John ; Edison, Arthur S. ; Kujawinski, Elizabeth B. ; Moran, Mary Ann

The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-d-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.
The global proteome of replete laboratory cultures of Ruergeria pomeroyi DSS-3

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-06-15) Saito, Mak A. ; Moran, Mary Ann

This dataset represents the global proteome of replete laboratory cultures of Ruergeria pomeroyi DSS-3 (collected in triplicate). This dataset is an initial examination of the proteome allocation of this heterotrophic bacteria and will contribute to C-CoMP's efforts that are focused on understanding the physiology of model marine bacteria. A total of 2341 proteins were identified in DSS-3. The Moran laboratory at University of Georgia grew and prepared the cultures and the Saito laboratory at Woods Hole Oceanographic Institution conducted the proteomics analyses. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/875600
The global proteome of replete laboratory cultures of Alteromonas macleodii MIT1002

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2022-06-15) Saito, Mak A. ; Moran, Mary Ann

This dataset represents the global proteome of replete laboratory cultures of Alteromonas macleodii MIT1002 (collected in triplicate). This dataset is an initial examination of the proteome allocation of this heterotrophic bacteria and will contribute to C-CoMP's efforts that are focused on understanding the physiology of model marine bacteria. A total of 2075 proteins were identified in MIT1002. The Moran laboratory at University of Georgia grew and prepared the cultures and the Saito laboratory at Woods Hole Oceanographic Institution conducted the proteomics analyses. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/875612
Metagenomic, metatranscriptomic, and single cell sequencing data from a Environmental Sample Processor deployment in Monterey Bay, CA from 2016.

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-04-01) Moran, Mary Ann

These metagenomic and metatranscriptomic time-series data cover a 52-day period in the fall of 2016 during an intense bloom of the dinoflagellate Akashiwo sanguinea in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes, 82 metatranscriptomes, and 88 16S rRNA amplicon libraries that capture the functions and taxonomy the bacterial and archaeal community. In addition, 88 18S rRNA amplicon libraries describe the taxonomy of the eukaryotic community during the bloom. Microbial cells were collected at station M0 using the moored autonomous robotic Environmental Sample Processor (ESP) instrument and preserved with RNAlater in the instrument until retrieval. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/753343
Environmental data from Niskin bottle sampling during the Fall 2016 ESP deployment in Monterey Bay, CA

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-11-08) Moran, Mary Ann ; Kiene, Ronald

Environmental data from Niskin bottle sampling during the Fall 2016 ESP deployment in Monterey Bay, CA. Samples were taken using Niskin bottles that collected seawater at the same depth and location of the Environmental Sample Processor deployed at Station M0 (36.835 N, 121.901W). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/756413

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