1
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Nelson DR, Mystikou A, Jaiswal A, Rad-Menendez C, Preston MJ, De Boever F, El Assal DC, Daakour S, Lomas MW, Twizere JC, Green DH, Ratcliff WC, Salehi-Ashtiani K. Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity. Mol Plant 2024:S1674-2052(24)00084-4. [PMID: 38614077 DOI: 10.1016/j.molp.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/31/2024] [Accepted: 03/08/2024] [Indexed: 04/15/2024]
Abstract
Macroalgae are multicellular, aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering, which are directly linked to their multicellularity phenotypes. However, their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain uncharacterized. In this study, we sequenced 110 macroalgal genomes from diverse climates and phyla, and identified key genomic features that distinguish them from their microalgal relatives. Genes for cell adhesion, extracellular matrix formation, cell polarity, transport, and cell differentiation distinguish macroalgae from microalgae across all three major phyla, constituting conserved and unique gene sets supporting multicellular processes. Adhesome genes show phylum- and climate-specific expansions that may facilitate niche adaptation. Collectively, our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.
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Affiliation(s)
- David R Nelson
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Alexandra Mystikou
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE; Biotechnology Research Center, Technology Innovation Institute, PO Box 9639, Masdar City, Abu Dhabi, UAE.
| | - Ashish Jaiswal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Cecilia Rad-Menendez
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - Michael J Preston
- National Center for Marine Algae and Microbiota, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Frederik De Boever
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - Diana C El Assal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Michael W Lomas
- National Center for Marine Algae and Microbiota, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jean-Claude Twizere
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
| | - David H Green
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kourosh Salehi-Ashtiani
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE.
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2
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Lomas MW, Neeley AR, Vandermeulen R, Mannino A, Thomas C, Novak MG, Freeman SA. Phytoplankton optical fingerprint libraries for development of phytoplankton ocean color satellite products. Sci Data 2024; 11:168. [PMID: 38310126 DOI: 10.1038/s41597-024-03001-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/25/2024] [Indexed: 02/05/2024] Open
Abstract
Phytoplankton respond to physical and hydrographic forcing on time and space scales up to and including those relevant to climate change. Quantifying changes in phytoplankton communities over these scales is essential for predicting ocean food resources, occurrences of harmful algal blooms, and carbon and other elemental cycles, among other predictions. However, one of the best tools for quantifying phytoplankton communities across relevant time and space scales, ocean color sensors, is constrained by its own spectral capabilities and availability of adequately vetted and relevant optical models. To address this later shortcoming, greater than fifty strains of phytoplankton, from a range of taxonomic lineages, geographic locations, and time in culture, alone and in mixtures, were grown to exponential and/or stationary phase for determination of hyperspectral UV-VIS absorption coefficients, multi-angle and multi-spectral backscatter coefficients, volume scattering functions, particle size distributions, pigment content, and fluorescence. The aim of this publication is to share these measurements to expedite their utilization in the development of new optical models for the next generation of ocean color satellites.
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Affiliation(s)
- Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA.
| | - Aimee R Neeley
- NASA Goddard Space Flight Center/Science Systems and Applications Inc., Greenbelt, Maryland, 20771, USA
| | - Ryan Vandermeulen
- NASA Goddard Space Flight Center/Science Systems and Applications Inc., Greenbelt, Maryland, 20771, USA
- NOAA National Marine Fisheries Service, Silver Spring, Maryland, 20910, USA
| | - Antonio Mannino
- NASA Goddard Space Flight Center, Greenbelt, Maryland, 20771, USA
| | - Crystal Thomas
- NASA Goddard Space Flight Center/Science Systems and Applications Inc., Greenbelt, Maryland, 20771, USA
| | - Michael G Novak
- NASA Goddard Space Flight Center/Science Systems and Applications Inc., Greenbelt, Maryland, 20771, USA
- Institute of Carbon Cycles, Helmholtz-Zentrum Hereon, Geesthacht, Germany
| | - Scott A Freeman
- NASA Goddard Space Flight Center/Science Systems and Applications Inc., Greenbelt, Maryland, 20771, USA
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3
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Russo L, Bellardini D, Steinberg DK, Congestri R, Lomas MW, D'Alelio D. Long-term oscillations in the normalized biomass-size spectrum reveal the impact of oligotrophication on zooplankton trophic structure in the North Atlantic Subtropical Gyre. Mar Environ Res 2024; 193:106295. [PMID: 38118377 DOI: 10.1016/j.marenvres.2023.106295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023]
Abstract
Ocean warming of the North Atlantic Subtropical Gyre (NASG) induced oligotrophication and a decrease in integrated net primary production during the 2010s, potentially affecting higher trophic levels. We analyzed long-term records (1994-2019) of daytime and nighttime zooplankton biomass in five size classes from the NASG. Daytime biomass decreased in the three largest size classes during the 2010s, while decrease in nighttime biomass was less evident due to the relative stability in diel vertical migrator biomass. We used the normalized biomass size spectrum (NBSS) to estimate the relative transfer efficiency between trophic levels. The steepness of the NBSS slope at the end of the time series increased by 14% (daytime) and 24% (nighttime) from the maximum observed annual average values (2011 and 2009, respectively). This suggests oligotrophication during the 2010s led to a significant reduction in the transfer of biomass across trophic levels, with negative impacts on the NASG planktonic food web.
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Affiliation(s)
- Luca Russo
- Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca scientifica 1, 00133, Rome, Italy.
| | - Daniele Bellardini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy; DiSTAV, Department of Earth, Environment and Life Sciences, University of Genoa, Corso Europa 26, 16132, Genoa, Italy.
| | - Deborah K Steinberg
- Coastal & Ocean Processes Section, Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA, 23062, USA.
| | - Roberta Congestri
- Laboratory of Biology of Algae, Department of Biology, University of Rome 'Tor Vergata', Via Cracovia 1, 00133, Rome, Italy.
| | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA.
| | - Domenico D'Alelio
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133, Palermo, Italy.
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4
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Pearson HC, Savoca MS, Costa DP, Lomas MW, Molina R, Pershing AJ, Smith CR, Villaseñor-Derbez JC, Wing SR, Roman J. Whales in the carbon cycle: can recovery remove carbon dioxide? Trends Ecol Evol 2023; 38:238-249. [PMID: 36528413 DOI: 10.1016/j.tree.2022.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/04/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022]
Abstract
The great whales (baleen and sperm whales), through their massive size and wide distribution, influence ecosystem and carbon dynamics. Whales directly store carbon in their biomass and contribute to carbon export through sinking carcasses. Whale excreta may stimulate phytoplankton growth and capture atmospheric CO2; such indirect pathways represent the greatest potential for whale-carbon sequestration but are poorly understood. We quantify the carbon values of whales while recognizing the numerous ecosystem, cultural, and moral motivations to protect them. We also propose a framework to quantify the economic value of whale carbon as populations change over time. Finally, we suggest research to address key unknowns (e.g., bioavailability of whale-derived nutrients to phytoplankton, species- and region-specific variability in whale carbon contributions).
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Affiliation(s)
- Heidi C Pearson
- Department of Natural Sciences, University of Alaska Southeast, Juneau, AK, USA.
| | - Matthew S Savoca
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Daniel P Costa
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Renato Molina
- Rosenstiel School of Marine, Atmospheric, and Earth Science and Miami Herbert Business School, University of Miami, Miami, FL, USA
| | | | - Craig R Smith
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Juan Carlos Villaseñor-Derbez
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA; Bren School of Environmental Science & Management, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Stephen R Wing
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Joe Roman
- Gund Institute for Environment, University of Vermont, Burlington, VT, USA
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5
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Neeley AR, Lomas MW, Mannino A, Thomas C, Vandermeulen R. Impact of Growth Phase, Pigment Adaptation, and Climate Change Conditions on the Cellular Pigment and Carbon Content of Fifty-One Phytoplankton Isolates. J Phycol 2022; 58:669-690. [PMID: 35844156 DOI: 10.1111/jpy.13279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Owing to their importance in aquatic ecosystems, the demand for models that estimate phytoplankton biomass and community composition in the global ocean has increased over the last decade. Moreover, the impacts of climate change, including elevated carbon dioxide (CO2 ), increased stratification, and warmer sea surface temperatures, will likely shape phytoplankton community composition in the global ocean. Chemotaxonomic methods are useful for modeling phytoplankton community composition from marker pigments normalized to chlorophyll a (Chl a). However, photosynthetic pigments, particularly Chl a, are sensitive to nutrient and light conditions. Cellular carbon is less sensitive, so using carbon biomass instead may provide an alternative approach. To this end, cellular pigment and carbon concentrations were measured in 51 strains of globally relevant, cultured phytoplankton. Pigment-to-Chl a and pigment-to-carbon ratios were computed for each strain. For 25 strains, measurements were taken during two growth phases. While some differences between growth phases were observed, they did not exceed within-class differences. Multiple strains of Amphidinium carterae, Ditylum brightwellii and Heterosigma akashiwo were measured to determine whether time in culture influenced pigment and carbon composition. No appreciable trends in cellular pigment or carbon content were observed. Lastly, the potential impact of climate change conditions on the pigment ratios was assessed using a multistressor experiment that included increased mean light, temperature, and elevated pCO2 on three species: Thalassiosira oceanica, Ostreococcus lucimarinus, and Synechococcus. The largest differences were observed in the pigment-to-carbon ratios, while the marker pigments largely covaried with Chl a. The implications of these observations to chemotaxonomic applications are discussed.
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Affiliation(s)
- Aimee R Neeley
- NASA Goddard Space Flight Center/Science Systems and Applications Inc., Greenbelt, Maryland, 20771, USA
| | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, Bigelow Institute of Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Antonio Mannino
- NASA Goddard Space Flight Center, Greenbelt, Maryland, 20771, USA
| | - Crystal Thomas
- NASA Goddard Space Flight Center/Science Systems and Applications Inc., Greenbelt, Maryland, 20771, USA
| | - Ryan Vandermeulen
- NASA Goddard Space Flight Center/Science Systems and Applications Inc., Greenbelt, Maryland, 20771, USA
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6
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Lomas MW, Bates NR, Johnson RJ, Steinberg DK, Tanioka T. Adaptive carbon export response to warming in the Sargasso Sea. Nat Commun 2022; 13:1211. [PMID: 35260567 PMCID: PMC8904855 DOI: 10.1038/s41467-022-28842-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
Abstract
Ocean ecosystem models predict that warming and increased surface ocean stratification will trigger a series of ecosystem events, reducing the biological export of particulate carbon to the ocean interior. We present a nearly three-decade time series from the open ocean that documents a biological response to ocean warming and nutrient reductions wherein particulate carbon export is maintained, counter to expectations. Carbon export is maintained through a combination of phytoplankton community change to favor cyanobacteria with high cellular carbon-to-phosphorus ratios and enhanced shallow phosphorus recycling leading to increased nutrient use efficiency. These results suggest that surface ocean ecosystems may be more responsive and adapt more rapidly to changes in the hydrographic system than is currently envisioned in earth ecosystem models, with positive consequences for ocean carbon uptake. The ability of the ocean’s biota to sequester carbon is thought to be negatively affected by climate change. Here the authors use time-series data in the Sargasso Sea to show that biotic processes can buffer against these negative impacts.
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Affiliation(s)
- Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
| | - Nicholas R Bates
- Bermuda Institute for Ocean Sciences, St. Georges, Bermuda.,Department of Ocean and Earth Science, University of Southampton, Southampton, UK
| | | | - Deborah K Steinberg
- Virginia Institute of Marine Science, William & Mary, Gloucester Pt., Virginia, VA, USA
| | - Tatsuro Tanioka
- Department of Earth System Science, University of California, Irvine, CA, USA
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7
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Nelson DR, Hazzouri KM, Lauersen KJ, Jaiswal A, Chaiboonchoe A, Mystikou A, Fu W, Daakour S, Dohai B, Alzahmi A, Nobles D, Hurd M, Sexton J, Preston MJ, Blanchette J, Lomas MW, Amiri KMA, Salehi-Ashtiani K. Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution. Cell Host Microbe 2021; 29:250-266.e8. [PMID: 33434515 DOI: 10.1016/j.chom.2020.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/08/2020] [Accepted: 11/18/2020] [Indexed: 01/08/2023]
Abstract
Being integral primary producers in diverse ecosystems, microalgal genomes could be mined for ecological insights, but representative genome sequences are lacking for many phyla. We cultured and sequenced 107 microalgae species from 11 different phyla indigenous to varied geographies and climates. This collection was used to resolve genomic differences between saltwater and freshwater microalgae. Freshwater species showed domain-centric ontology enrichment for nuclear and nuclear membrane functions, while saltwater species were enriched in organellar and cellular membrane functions. Further, marine species contained significantly more viral families in their genomes (p = 8e-4). Sequences from Chlorovirus, Coccolithovirus, Pandoravirus, Marseillevirus, Tupanvirus, and other viruses were found integrated into the genomes of algal from marine environments. These viral-origin sequences were found to be expressed and code for a wide variety of functions. Together, this study comprehensively defines the expanse of protein-coding and viral elements in microalgal genomes and posits a unified adaptive strategy for algal halotolerance.
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Affiliation(s)
- David R Nelson
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Khaled M Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Al Ain, Abu Dhabi, UAE; Biology Department, College of Science, UAE University, Al Ain, Abu Dhabi, UAE
| | - Kyle J Lauersen
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Ashish Jaiswal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Alexandra Mystikou
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Weiqi Fu
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Bushra Dohai
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Amnah Alzahmi
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - David Nobles
- UTEX Culture Collection of Algae at the University of Texas at Austin, Austin, TX, USA
| | - Mark Hurd
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Julie Sexton
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Michael J Preston
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Joan Blanchette
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Michael W Lomas
- National Center for Marine Algae and Microbiota, East Boothbay, ME, USA
| | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Al Ain, Abu Dhabi, UAE; Biology Department, College of Science, UAE University, Al Ain, Abu Dhabi, UAE
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE; Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
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8
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Lange PK, Jeremy Werdell P, Erickson ZK, Dall'Olmo G, Brewin RJW, Zubkov MV, Tarran GA, Bouman HA, Slade WH, Craig SE, Poulton NJ, Bracher A, Lomas MW, Cetinić I. Radiometric approach for the detection of picophytoplankton assemblages across oceanic fronts. Opt Express 2020; 28:25682-25705. [PMID: 32906854 DOI: 10.1364/oe.398127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Cell abundances of Prochlorococcus, Synechococcus, and autotrophic picoeukaryotes were estimated in surface waters using principal component analysis (PCA) of hyperspectral and multispectral remote-sensing reflectance data. This involved the development of models that employed multilinear correlations between cell abundances across the Atlantic Ocean and a combination of PCA scores and sea surface temperatures. The models retrieve high Prochlorococcus abundances in the Equatorial Convergence Zone and show their numerical dominance in oceanic gyres, with decreases in Prochlorococcus abundances towards temperate waters where Synechococcus flourishes, and an emergence of picoeukaryotes in temperate waters. Fine-scale in-situ sampling across ocean fronts provided a large dynamic range of measurements for the training dataset, which resulted in the successful detection of fine-scale Synechococcus patches. Satellite implementation of the models showed good performance (R2 > 0.50) when validated against in-situ data from six Atlantic Meridional Transect cruises. The improved relative performance of the hyperspectral models highlights the importance of future high spectral resolution satellite instruments, such as the NASA PACE mission's Ocean Color Instrument, to extend our spatiotemporal knowledge about ecologically relevant phytoplankton assemblages.
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9
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Garcia CA, Hagstrom GI, Larkin AA, Ustick LJ, Levin SA, Lomas MW, Martiny AC. Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190254. [PMID: 32200740 PMCID: PMC7133529 DOI: 10.1098/rstb.2019.0254] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2020] [Indexed: 01/09/2023] Open
Abstract
Linking 'omics measurements with biogeochemical cycles is a widespread challenge in microbial community ecology. Here, we propose applying genomic adaptation as 'biosensors' for microbial investments to overcome nutrient stress. We then integrate this genomic information with a trait-based model to predict regional shifts in the elemental composition of marine plankton communities. We evaluated this approach using metagenomic and particulate organic matter samples from the Atlantic, Indian and Pacific Oceans. We find that our genome-based trait model significantly improves our prediction of particulate C : P (carbon : phosphorus) across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen and phosphorus stress. In many ecosystems, it can be very challenging to quantify microbial stress. Thus, a carefully calibrated genomic approach could become a widespread tool for understanding microbial responses to environmental changes and the biogeochemical outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Catherine A. Garcia
- Department of Earth System Science, University of California, Irvine, CA 92697, USA
| | - George I. Hagstrom
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alyse A. Larkin
- Department of Earth System Science, University of California, Irvine, CA 92697, USA
| | - Lucas J. Ustick
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Simon A. Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michael W. Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - Adam C. Martiny
- Department of Earth System Science, University of California, Irvine, CA 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
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10
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D'Alelio D, Rampone S, Cusano LM, Morfino V, Russo L, Sanseverino N, Cloern JE, Lomas MW. Machine learning identifies a strong association between warming and reduced primary productivity in an oligotrophic ocean gyre. Sci Rep 2020; 10:3287. [PMID: 32098970 PMCID: PMC7042350 DOI: 10.1038/s41598-020-59989-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 02/06/2020] [Indexed: 12/20/2022] Open
Abstract
Phytoplankton play key roles in the oceans by regulating global biogeochemical cycles and production in marine food webs. Global warming is thought to affect phytoplankton production both directly, by impacting their photosynthetic metabolism, and indirectly by modifying the physical environment in which they grow. In this respect, the Bermuda Atlantic Time-series Study (BATS) in the Sargasso Sea (North Atlantic gyre) provides a unique opportunity to explore effects of warming on phytoplankton production across the vast oligotrophic ocean regions because it is one of the few multidecadal records of measured net primary productivity (NPP). We analysed the time series of phytoplankton primary productivity at BATS site using machine learning techniques (ML) to show that increased water temperature over a 27-year period (1990–2016), and the consequent weakening of vertical mixing in the upper ocean, induced a negative feedback on phytoplankton productivity by reducing the availability of essential resources, nitrogen and light. The unbalanced availability of these resources with warming, coupled with ecological changes at the community level, is expected to intensify the oligotrophic state of open-ocean regions that are far from land-based nutrient sources.
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Affiliation(s)
- Domenico D'Alelio
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121, Naples, Italy.
| | - Salvatore Rampone
- Università degli Studi del Sannio, Via Delle Puglie 76, I-82100, Benevento, Italy
| | - Luigi Maria Cusano
- Università degli Studi del Sannio, Via Delle Puglie 76, I-82100, Benevento, Italy
| | - Valerio Morfino
- Università degli Studi del Sannio, Via Delle Puglie 76, I-82100, Benevento, Italy
| | - Luca Russo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121, Naples, Italy
| | - Nadia Sanseverino
- Università degli Studi del Sannio, Via Delle Puglie 76, I-82100, Benevento, Italy
| | - James E Cloern
- United States Geological Survey (emeritus), Menlo Park, CA, USA
| | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
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11
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Martiny AC, Lomas MW, Fu W, Boyd PW, Chen YLL, Cutter GA, Ellwood MJ, Furuya K, Hashihama F, Kanda J, Karl DM, Kodama T, Li QP, Ma J, Moutin T, Woodward EMS, Moore JK. Biogeochemical controls of surface ocean phosphate. Sci Adv 2019; 5:eaax0341. [PMID: 31489372 PMCID: PMC6713502 DOI: 10.1126/sciadv.aax0341] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/18/2019] [Indexed: 05/26/2023]
Abstract
Surface ocean phosphate is commonly below the standard analytical detection limits, leading to an incomplete picture of the global variation and biogeochemical role of phosphate. A global compilation of phosphate measured using high-sensitivity methods revealed several previously unrecognized low-phosphate areas and clear regional differences. Both observational climatologies and Earth system models (ESMs) systematically overestimated surface phosphate. Furthermore, ESMs misrepresented the relationships between phosphate, phytoplankton biomass, and primary productivity. Atmospheric iron input and nitrogen fixation are known important controls on surface phosphate, but model simulations showed that differences in the iron-to-macronutrient ratio in the vertical nutrient supply and surface lateral transport are additional drivers of phosphate concentrations. Our study demonstrates the importance of accurately quantifying nutrients for understanding the regulation of ocean ecosystems and biogeochemistry now and under future climate conditions.
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Affiliation(s)
- Adam C. Martiny
- Department of Earth System Science, University of California, Irvine, Irvine, CA 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Michael W. Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - Weiwei Fu
- Department of Earth System Science, University of California, Irvine, Irvine, CA 92697, USA
| | - Philip W. Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Yuh-ling L. Chen
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Gregory A. Cutter
- Department of Ocean, Earth, and Atmospheric Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Michael J. Ellwood
- Research School of Earth Sciences, Australian National University, Canberra, ACT 2601, Australia
| | - Ken Furuya
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Fuminori Hashihama
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Jota Kanda
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - David M. Karl
- Daniel K. Inouye Center for Microbial Oceanography, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Taketoshi Kodama
- Japan Sea National Fisheries Research Institute, Japan Fisheries Research and Education Agency, 1-5939-22, Suido-cho, Chuo, Niigata, Japan
| | - Qian P. Li
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People’s Republic of China
| | - Jian Ma
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361102, People’s Republic of China
| | - Thierry Moutin
- Aix Marseille Université, CNRS, Université de Toulon, IRD, OSU Pythéas, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille, France
| | | | - J. Keith Moore
- Department of Earth System Science, University of California, Irvine, Irvine, CA 92697, USA
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12
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13
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Garcia CA, Baer SE, Garcia NS, Rauschenberg S, Twining BS, Lomas MW, Martiny AC. Nutrient supply controls particulate elemental concentrations and ratios in the low latitude eastern Indian Ocean. Nat Commun 2018; 9:4868. [PMID: 30451846 PMCID: PMC6242840 DOI: 10.1038/s41467-018-06892-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 09/14/2018] [Indexed: 11/17/2022] Open
Abstract
Variation in ocean C:N:P of particulate organic matter (POM) has led to competing hypotheses for the underlying drivers. Each hypothesis predicts C:N:P equally well due to regional co-variance in environmental conditions and biodiversity. The Indian Ocean offers a unique positive temperature and nutrient supply relationship to test these hypotheses. Here we show how elemental concentrations and ratios vary over daily and regional scales. POM concentrations were lowest in the southern gyre, elevated across the equator, and peaked in the Bay of Bengal. Elemental ratios were highest in the gyre, but approached Redfield proportions northwards. As Prochlorococcus dominated the phytoplankton community, biodiversity changes could not explain the elemental variation. Instead, our data supports the nutrient supply hypothesis. Finally, gyre dissolved iron concentrations suggest extensive iron stress, leading to depressed ratios compared to other gyres. We propose a model whereby differences in iron supply and N2-fixation influence C:N:P levels across ocean gyres.
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Affiliation(s)
- Catherine A Garcia
- Department of Earth System Science, University of California at Irvine, Irvine, CA, 92617, USA
| | - Steven E Baer
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
- Maine Maritime Academy, Castine, ME, 04420, USA
| | - Nathan S Garcia
- Department of Earth System Science, University of California at Irvine, Irvine, CA, 92617, USA
| | - Sara Rauschenberg
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | | | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Adam C Martiny
- Department of Earth System Science, University of California at Irvine, Irvine, CA, 92617, USA.
- Department of Ecology and Evolution, University of California at Irvine, Irvine, CA, 92617, USA.
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14
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Garcia NS, Sexton J, Riggins T, Brown J, Lomas MW, Martiny AC. High Variability in Cellular Stoichiometry of Carbon, Nitrogen, and Phosphorus Within Classes of Marine Eukaryotic Phytoplankton Under Sufficient Nutrient Conditions. Front Microbiol 2018; 9:543. [PMID: 29636735 PMCID: PMC5880891 DOI: 10.3389/fmicb.2018.00543] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/09/2018] [Indexed: 11/17/2022] Open
Abstract
Current hypotheses suggest that cellular elemental stoichiometry of marine eukaryotic phytoplankton such as the ratios of cellular carbon:nitrogen:phosphorus (C:N:P) vary between phylogenetic groups. To investigate how phylogenetic structure, cell volume, growth rate, and temperature interact to affect the cellular elemental stoichiometry of marine eukaryotic phytoplankton, we examined the C:N:P composition in 30 isolates across 7 classes of marine phytoplankton that were grown with a sufficient supply of nutrients and nitrate as the nitrogen source. The isolates covered a wide range in cell volume (5 orders of magnitude), growth rate (<0.01–0.9 d−1), and habitat temperature (2–24°C). Our analysis indicates that C:N:P is highly variable, with statistical model residuals accounting for over half of the total variance and no relationship between phylogeny and elemental stoichiometry. Furthermore, our data indicated that variability in C:P, N:P, and C:N within Bacillariophyceae (diatoms) was as high as that among all of the isolates that we examined. In addition, a linear statistical model identified a positive relationship between diatom cell volume and C:P and N:P. Among all of the isolates that we examined, the statistical model identified temperature as a significant factor, consistent with the temperature-dependent translation efficiency model, but temperature only explained 5% of the total statistical model variance. While some of our results support data from previous field studies, the high variability of elemental ratios within Bacillariophyceae contradicts previous work that suggests that this cosmopolitan group of microalgae has consistently low C:P and N:P ratios in comparison with other groups.
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Affiliation(s)
- Nathan S Garcia
- Department of Earth System Science, University of California, Irvine, Irvine, CA, United States
| | - Julie Sexton
- Bigelow Laboratory for Ocean Sciences, National Center for Marine Algae and Microbiota, East Boothbay, ME, United States
| | - Tracey Riggins
- Bigelow Laboratory for Ocean Sciences, National Center for Marine Algae and Microbiota, East Boothbay, ME, United States
| | - Jeff Brown
- Bigelow Laboratory for Ocean Sciences, National Center for Marine Algae and Microbiota, East Boothbay, ME, United States
| | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, National Center for Marine Algae and Microbiota, East Boothbay, ME, United States
| | - Adam C Martiny
- Department of Earth System Science, University of California, Irvine, Irvine, CA, United States.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
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15
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Wan XS, Sheng HX, Dai M, Zhang Y, Shi D, Trull TW, Zhu Y, Lomas MW, Kao SJ. Ambient nitrate switches the ammonium consumption pathway in the euphotic ocean. Nat Commun 2018; 9:915. [PMID: 29500422 PMCID: PMC5834513 DOI: 10.1038/s41467-018-03363-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/08/2018] [Indexed: 12/03/2022] Open
Abstract
Phytoplankton assimilation and microbial oxidation of ammonium are two critical conversion pathways in the marine nitrogen cycle. The underlying regulatory mechanisms of these two competing processes remain unclear. Here we show that ambient nitrate acts as a key variable to bifurcate ammonium flow through assimilation or oxidation, and the depth of the nitracline represents a robust spatial boundary between ammonium assimilators and oxidizers in the stratified ocean. Profiles of ammonium utilization show that phytoplankton assemblages in nitrate-depleted regimes have higher ammonium affinity than nitrifiers. In nitrate replete conditions, by contrast, phytoplankton reduce their ammonium reliance and thus enhance the success of nitrifiers. This finding helps to explain existing discrepancies in the understanding of light inhibition of surface nitrification in the global ocean, and provides further insights into the spatial linkages between oceanic nitrification and new production. The underlying regulatory mechanisms of phytoplankton assimilation and microbial oxidation of ammonium in the surface ocean are unclear. Here, using isotope labeling experiments, the authors show that ambient nitrate is a key variable bifurcating ammonium flow through assimilation or oxidation.
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Affiliation(s)
- Xianhui Sean Wan
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Hua-Xia Sheng
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Dalin Shi
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Thomas W Trull
- Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, and CSIRO Oceans and Atmosphere, Hobart, 7001, Australia
| | - Yifan Zhu
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China.
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16
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McCluskey K, Barker KB, Barton HA, Boundy-Mills K, Brown DR, Coddington JA, Cook K, Desmeth P, Geiser D, Glaeser JA, Greene S, Kang S, Lomas MW, Melcher U, Miller SE, Nobles DR, Owens KJ, Reichman JH, da Silva M, Wertz J, Whitworth C, Smith D. The U.S. Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing. mBio 2017; 8:e00982-17. [PMID: 28811341 PMCID: PMC5559631 DOI: 10.1128/mbio.00982-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The U.S. Culture Collection Network held a meeting to share information about how culture collections are responding to the requirements of the recently enacted Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity (CBD). The meeting included representatives of many culture collections and other biological collections, the U.S. Department of State, U.S. Department of Agriculture, Secretariat of the CBD, interested scientific societies, and collection groups, including Scientific Collections International and the Global Genome Biodiversity Network. The participants learned about the policies of the United States and other countries regarding access to genetic resources, the definition of genetic resources, and the status of historical materials and genetic sequence information. Key topics included what constitutes access and how the CBD Access and Benefit-Sharing Clearing-House can help guide researchers through the process of obtaining Prior Informed Consent on Mutually Agreed Terms. U.S. scientists and their international collaborators are required to follow the regulations of other countries when working with microbes originally isolated outside the United States, and the local regulations required by the Nagoya Protocol vary by the country of origin of the genetic resource. Managers of diverse living collections in the United States described their holdings and their efforts to provide access to genetic resources. This meeting laid the foundation for cooperation in establishing a set of standard operating procedures for U.S. and international culture collections in response to the Nagoya Protocol.
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Affiliation(s)
- Kevin McCluskey
- Fungal Genetic Stock Center, Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Katharine B Barker
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Hazel A Barton
- Department of Biology, University of Akron, Akron, Ohio, USA
| | - Kyria Boundy-Mills
- Phaff Yeast Culture Collection, Food Science, University of California, Davis, Davis, California, USA
| | - Daniel R Brown
- Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Kevin Cook
- Bloomington Drosophila Stock Center, Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - David Geiser
- The Fusarium Research Center, Penn State University, State College, Pennsylvania, USA
| | - Jessie A Glaeser
- U.S. Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, Wisconsin, USA
| | - Stephanie Greene
- USDA National Laboratory for Genetic Resources Preservation, Fort Collins, Colorado, USA
| | - Seogchan Kang
- Penn State University, State College, Pennsylvania, USA
| | - Michael W Lomas
- National Center for Marine Algae and Microbiota, East Boothbay Harbor, Maine, USA
| | | | | | | | | | | | | | - John Wertz
- E. coli Stock Center, Yale University, New Haven, Connecticut, USA
| | - Cale Whitworth
- Bloomington Drosophila Stock Center, Department of Biology, Indiana University Bloomington, Indiana, USA
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17
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Baer SE, Lomas MW, Terpis KX, Mouginot C, Martiny AC. Stoichiometry of Prochlorococcus, Synechococcus
, and small eukaryotic populations in the western North Atlantic Ocean. Environ Microbiol 2017; 19:1568-1583. [DOI: 10.1111/1462-2920.13672] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Steven E. Baer
- Bigelow Laboratory for Ocean Sciences; East Boothbay ME 04544 USA
| | - Michael W. Lomas
- Bigelow Laboratory for Ocean Sciences; East Boothbay ME 04544 USA
| | | | - Céline Mouginot
- Department of Earth System Science; University of California, Irvine; Irvine CA 92697 USA
| | - Adam C. Martiny
- Department of Earth System Science; University of California, Irvine; Irvine CA 92697 USA
- Department of Ecology and Evolutionary Biology; University of California, Irvine; Irvine CA 92697 USA
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18
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Abstract
The surface waters of oligotrophic oceans have chronically low phosphate (Pi) concentrations, which renders dissolved organic phosphorus (DOP) an important nutrient source. In the subtropical North Atlantic, cyanobacteria are often numerically dominant, but picoeukaryotes can dominate autotrophic biomass and productivity making them important contributors to the ocean carbon cycle. Despite their importance, little is known regarding the metabolic response of picoeukaryotes to changes in phosphorus (P) source and availability. To understand the molecular mechanisms that regulate P utilization in oligotrophic environments, we evaluated transcriptomes of the picoeukaryote Micromonas pusilla grown under Pi-replete and -deficient conditions, with an additional investigation of growth on DOP in replete conditions. Genes that function in sulfolipid substitution and Pi uptake increased in expression with Pi-deficiency, suggesting cells were reallocating cellular P and increasing P acquisition capabilities. Pi-deficient M. pusilla cells also increased alkaline phosphatase activity and reduced their cellular P content. Cells grown with DOP were able to maintain relatively high growth rates, however the transcriptomic response was more similar to the Pi-deficient response than that seen in cells grown under Pi-replete conditions. The results demonstrate that not all P sources are the same for growth; while M. pusilla, a model picoeukaryote, may grow well on DOP, the metabolic demand is greater than growth on Pi. These findings provide insight into the cellular strategies which may be used to support growth in a stratified future ocean predicted to favor picoeukaryotes.
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Affiliation(s)
- LeAnn P. Whitney
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
- * E-mail:
| | - Michael W. Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
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19
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Kretz CB, Bell DW, Lomas DA, Lomas MW, Martiny AC. Influence of growth rate on the physiological response of marine Synechococcus to phosphate limitation. Front Microbiol 2015; 6:85. [PMID: 25717321 PMCID: PMC4324148 DOI: 10.3389/fmicb.2015.00085] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 01/22/2015] [Indexed: 11/13/2022] Open
Abstract
Phosphate (P) is an important nutrient potentially limiting for primary productivity, yet, we currently know little about the relationship between growth rate and physiological response to P limitation in abundant marine Cyanobacteria. Thus, the aim of this research was to determine how variation in growth rate affected the physiology of marine Synechococcus WH8102 and CC9311 when growing under high N:P conditions. Experiments were carried out in chemostats with a media input N:P of 441 and we estimated the half saturation concentration for growth under P limiting conditions (K s,p ) and cellular C:N:P ratios. The K s,p values were the lowest measured for any phytoplankton and on par with ambient P concentrations in oligotrophic regions. We also observed that both strains were able draw down P below 3 nM. Both K s,p and drawdown concentration were lower for the open ocean vs. coastal Synechococcus strain, which may be linked to differences in P acquisition genes in these strains. Cellular C:P and N:P ratios were significantly higher in relation to the Redfield ratio for both Synechococcus strains but we saw no difference in these ratios among growth rates or strains. These results demonstrate that Synechococcus can proliferate under very low P conditions and also that genetically different strains have unique physiological responses to P limitation.
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Affiliation(s)
- Cécilia B Kretz
- Department of Ecology and Evolutionary Biology, University of California Irvine Irvine, CA, USA
| | - Doug W Bell
- Marine Science Program, School of Earth, Ocean and Environment, University of South Carolina Columbia, SC, USA
| | - Debra A Lomas
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
| | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine Irvine, CA, USA ; Department of Earth System Science, University of California Irvine Irvine, CA, USA
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20
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McCluskey K, Bates S, Boundy-Mills K, Broggiato A, Cova A, Desmeth P, DebRoy C, Fravel D, Garrity G, Gasco MDMJ, Joseph L, Lindner D, Lomas MW, Morton J, Nobles D, Turner J, Ward T, Wertz J, Wiest A, Geiser D. Meeting report: 2nd workshop of the United States culture collection network (May 19–21, 2014, State College, PA, USA). Stand Genomic Sci 2014. [PMCID: PMC4286144 DOI: 10.1186/1944-3277-9-27] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Martiny AC, Vrugt JA, Lomas MW. Concentrations and ratios of particulate organic carbon, nitrogen, and phosphorus in the global ocean. Sci Data 2014; 1:140048. [PMID: 25977799 PMCID: PMC4421931 DOI: 10.1038/sdata.2014.48] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/27/2014] [Indexed: 11/08/2022] Open
Abstract
Knowledge of concentrations and elemental ratios of suspended particles are important for understanding many biogeochemical processes in the ocean. These include patterns of phytoplankton nutrient limitation as well as linkages between the cycles of carbon and nitrogen or phosphorus. To further enable studies of ocean biogeochemistry, we here present a global dataset consisting of 100,605 total measurements of particulate organic carbon, nitrogen, or phosphorus analyzed as part of 70 cruises or time-series. The data are globally distributed and represent all major ocean regions as well as different depths in the water column. The global median C:P, N:P, and C:N ratios are 163, 22, and 6.6, respectively, but the data also includes extensive variation between samples from different regions. Thus, this compilation will hopefully assist in a wide range of future studies of ocean elemental ratios.
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Affiliation(s)
- Adam C Martiny
- Department of Earth System Science, University of California, Irvine, California 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - Jasper A Vrugt
- Department of Earth System Science, University of California, Irvine, California 92697, USA
- Department of Civil and Environmental Engineering, University of California, Irvine, California 92697, USA
| | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA
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22
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Choi HY, Stewart GM, Lomas MW, Kelly RP, Moran SB. Linking the distribution of (210)Po and (210)Pb with plankton community along Line P, Northeast Subarctic Pacific. J Environ Radioact 2014; 138:390-401. [PMID: 24629375 DOI: 10.1016/j.jenvrad.2014.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 02/17/2014] [Accepted: 02/17/2014] [Indexed: 06/03/2023]
Abstract
Depth profiles of (210)Po and (210)Pb activity and phytoplankton and zooplankton abundance were collected during two cruises along the Canadian time-series Line P in the Northeast Subarctic Pacific (ranging from 48o39 N to 50o00 N and 126o40 W to 145o00 W) in August 2010 and February 2011 to evaluate connections between the planktonic community and distributions of these radionuclides in the upper 500 m of the water column. Statistical analysis indicates that (210)Po is more effectively removed from the surface ocean when large (>0.1 mg ind(-1) dry wt) zooplankton dominate, and is less effectively scavenged when the picoplankton Synechococcus is present at high concentrations (>1 × 10(5) cells ml(-1)). While the zooplankton field data are consistent with previous lab studies and field observations, the phytoplankton results seem to conflict with recent evidence that small cells may contribute significantly to export in other oligotrophic regions. Differences in ecosystem mechanisms between the Subarctic Pacific and other oligotrophic systems that limit the contribution of small cells to sinking flux remain to be identified.
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Affiliation(s)
- Hiu Yan Choi
- Queens College and Graduate Center, City University of New York, 65-30 Kissena Blvd., Flushing, NY 11367, USA
| | - Gillian M Stewart
- Queens College and Graduate Center, City University of New York, 65-30 Kissena Blvd., Flushing, NY 11367, USA.
| | - Michael W Lomas
- Bermuda Institute of Ocean Sciences, 17 Biological Station, Ferry Reach, St George's GE 01, Bermuda
| | - Roger P Kelly
- Graduate School of Oceanography, University of Rhode Island, South Ferry Road, Narragansett, RI 02882, USA
| | - S Bradley Moran
- Graduate School of Oceanography, University of Rhode Island, South Ferry Road, Narragansett, RI 02882, USA
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23
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Mackey KRM, Buck KN, Casey JR, Cid A, Lomas MW, Sohrin Y, Paytan A. Phytoplankton responses to atmospheric metal deposition in the coastal and open-ocean Sargasso Sea. Front Microbiol 2012; 3:359. [PMID: 23181057 PMCID: PMC3470407 DOI: 10.3389/fmicb.2012.00359] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 09/20/2012] [Indexed: 11/22/2022] Open
Abstract
This study investigated the impact of atmospheric metal deposition on natural phytoplankton communities at open-ocean and coastal sites in the Sargasso Sea during the spring bloom. Locally collected aerosols with different metal contents were added to natural phytoplankton assemblages from each site, and changes in nitrate, dissolved metal concentration, and phytoplankton abundance and carbon content were monitored. Addition of aerosol doubled the concentrations of cadmium (Cd), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), and nickel (Ni) in the incubation water. Over the 3-day experiments, greater drawdown of dissolved metals occurred in the open ocean water, whereas little metal drawdown occurred in the coastal water. Two populations of picoeukaryotic algae and Synechococcus grew in response to aerosol additions in both experiments. Particulate organic carbon increased and was most sensitive to changes in picoeukaryote abundance. Phytoplankton community composition differed depending on the chemistry of the aerosol added. Enrichment with aerosol that had higher metal content led to a 10-fold increase in Synechococcus abundance in the oceanic experiment but not in the coastal experiment. Enrichment of aerosol-derived Co, Mn, and Ni were particularly enhanced in the oceanic experiment, suggesting the Synechococcus population may have been fertilized by these aerosol metals. Cu-binding ligand concentrations were in excess of dissolved Cu in both experiments, and increased with aerosol additions. Bioavailable free hydrated Cu(2+) concentrations were below toxicity thresholds throughout both experiments. These experiments show (1) atmospheric deposition contributes biologically important metals to seawater, (2) these metals are consumed over time scales commensurate with cell growth, and (3) growth responses can differ between distinct Synechococcus or eukaryotic algal populations despite their relatively close geographic proximity and taxonomic similarity.
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Affiliation(s)
- Katherine R. M. Mackey
- Institute for Marine Science, University of California at Santa CruzSanta Cruz, CA, USA
- Woods Hole Oceanographic InstitutionWoods Hole, MA, USA
- Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MA, USA
| | | | - John R. Casey
- Bermuda Institute of Ocean Sciences, St George’sBermuda
- University of Hawaii at ManoaHonolulu, HI, USA
| | - Abigail Cid
- Institute for Chemical Research, Kyoto University, UjiKyoto, Japan
| | | | - Yoshiki Sohrin
- Institute for Chemical Research, Kyoto University, UjiKyoto, Japan
| | - Adina Paytan
- Institute for Marine Science, University of California at Santa CruzSanta Cruz, CA, USA
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24
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Mackey KRM, Roberts K, Lomas MW, Saito MA, Post AF, Paytan A. Enhanced solubility and ecological impact of atmospheric phosphorus deposition upon extended seawater exposure. Environ Sci Technol 2012; 46:10438-10446. [PMID: 22574853 DOI: 10.1021/es3007996] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Atmospheric P solubility affects the amount of P available for phytoplankton in the surface ocean, yet our understanding of the timing and extent of atmospheric P solubility is based on short-term leaching experiments where conditions may differ substantially from the surface ocean. We conducted longer- term dissolution experiments of atmospheric aerosols in filtered seawater, and found up to 9-fold greater dissolution of P after 72 h compared to instantaneous leaching. Samples rich in anthropogenic materials released dissolved inorganic P (DIP) faster than mineral dust. To gauge the effect of biota on the fate of atmospheric P, we conducted field incubations with aerosol samples collected in the Sargasso Sea and Red Sea. In the Sargasso Sea phytoplankton were not P limited, and biological activity enhanced DIP release from aerosols, and aerosols induced biological mineralization of dissolved organic P in seawater, leading to DIP accumulation. However, in the Red Sea where phytoplankton were colimited by P and N, soluble P was rapidly consumed by phytoplankton following aerosol enrichment. Our results suggest that atmospheric P dissolution could continue over multiple days once reaching the surface ocean, and that previous estimates of atmospheric P deposition may underestimate the contribution from this source.
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Affiliation(s)
- Katherine R M Mackey
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States.
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Parsons RJ, Breitbart M, Lomas MW, Carlson CA. Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea. ISME J 2011; 6:273-84. [PMID: 21833038 DOI: 10.1038/ismej.2011.101] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There are an estimated 10(30) virioplankton in the world oceans, the majority of which are phages (viruses that infect bacteria). Marine phages encompass enormous genetic diversity, affect biogeochemical cycling of elements, and partially control aspects of prokaryotic production and diversity. Despite their importance, there is a paucity of data describing virioplankton distributions over time and depth in oceanic systems. A decade of high-resolution time-series data collected from the upper 300 m in the northwestern Sargasso Sea revealed recurring temporal and vertical patterns of virioplankton abundance in unprecedented detail. An annual virioplankton maximum developed between 60 and 100 m during periods of summer stratification and eroded during winter convective mixing. The timing and vertical positioning of this seasonal pattern was related to variability in water column stability and the dynamics of specific picophytoplankton and heterotrophic bacterioplankton lineages. Between 60 and 100 m, virioplankton abundance was negatively correlated to the dominant heterotrophic bacterioplankton lineage SAR11, as well as the less abundant picophytoplankton, Synechococcus. In contrast, virioplankton abundance was positively correlated to the dominant picophytoplankton lineage Prochlorococcus, and the less abundant alpha-proteobacteria, Rhodobacteraceae. Seasonally, virioplankton abundances were highly synchronous with Prochlorococcus distributions and the virioplankton to Prochlorococcus ratio remained remarkably constant during periods of water column stratification. The data suggest that a significant fraction of viruses in the mid-euphotic zone of the subtropical gyres may be cyanophages and patterns in their abundance are largely determined by Prochlorococcus dynamics in response to water column stability. This high-resolution, decadal survey of virioplankton abundance provides insight into the possible controls of virioplankton dynamics in the open ocean.
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Stewart G, Moran SB, Lomas MW, Kelly RP. Direct comparison of 210Po, 234Th and POC particle-size distributions and export fluxes at the Bermuda Atlantic Time-series Study (BATS) site. J Environ Radioact 2011; 102:479-489. [PMID: 21055851 DOI: 10.1016/j.jenvrad.2010.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 09/17/2010] [Accepted: 09/28/2010] [Indexed: 05/30/2023]
Abstract
Particle-reactive, naturally occurring radionuclides are useful tracers of the sinking flux of organic matter from the surface to the deep ocean. Since the Joint Global Ocean Flux Study (JGOFS) began in 1987, the disequilibrium between (234)Th and its parent (238)U has become widely used as a technique to measure particle export fluxes from surface ocean waters. Another radionuclide pair, (210)Po and (210)Pb, can be used for the same purpose but has not been as widely adopted due to difficulty with accurately constraining the (210)Po/(210)Pb radiochemical balance in the ocean and because of the more time-consuming radiochemical procedures. Direct comparison of particle flux estimated in different ocean regions using these short-lived radionuclides is important in evaluating their utility and accuracy as tracers of particle flux. In this paper, we present paired (234)Th/(238)U and (210)Po/(210)Pb data from oligotrophic surface waters of the subtropical Northwest Atlantic and discuss their advantages and limitations. Vertical profiles of total and particle size-fractionated (210)Po and (234)Th activities, together with particulate organic carbon (POC) concentrations, were measured during three seasons at the Bermuda Atlantic Time-series Study (BATS) site. Both (210)Po and (234)Th reasonably predict sinking POC flux caught in sediment traps, and each tracer provides unique information about the magnitude and efficiency of the ocean's biological pump.
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Longnecker K, Lomas MW, Van Mooy BAS. Abundance and diversity of heterotrophic bacterial cells assimilating phosphate in the subtropical North Atlantic Ocean. Environ Microbiol 2011; 12:2773-82. [PMID: 20545744 DOI: 10.1111/j.1462-2920.2010.02247.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microorganisms play key roles in the cycles of carbon and nutrients in the ocean, and identifying the extent to which specific taxa contribute to these cycles will establish their ecological function. We examined the use of (33)P-phosphate to identify heterotrophic bacteria actively involved in the cycling of phosphate, an essential inorganic nutrient. Seawater from the sub-tropical North Atlantic Ocean was incubated with (33)P-phosphate and analysed by microautoradiography to determine the proportion and diversity of the bacterial community-assimilating phosphate. Complementary incubations using (3)H-leucine and (3)H-thymidine were also conducted. We found that a higher proportion of total heterotrophic bacterial cells in surface water samples assimilated phosphate compared with leucine or thymidine. Bacteria from all of the phylogenetic groups we identified by CARD-FISH were able to assimilate phosphate, although the abundances of cells within each group did not scale directly with the number found to assimilate phosphate. Furthermore, a significantly higher proportion of Alphaproteobacteria, Gammaproteobacteria and Cytophaga-like cells assimilated phosphate compared with leucine or thymidine. Our results suggest that a greater proportion of bacterial cells in surface waters are actively participating in the biogeochemical cycling of phosphorus, and possibly other elements, than is currently estimated through the use of (3)H-leucine or (3)H-thymidine.
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Affiliation(s)
- Krista Longnecker
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543, USA
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Abstract
An important goal of marine biogeochemists is to quantify the rates at which elements cycle through the ocean's diverse microbial assemblage, as well as to determine how these rates vary in time and space. The traditional view that phytoplankton are producers and bacteria are consumers has been found to be overly simplistic, and environmental metagenomics is discovering new and important microbial metabolisms at an accelerating rate. Many nutritional strategies previously attributed to one microorganism or functional group are also or instead carried out by other groups. To tease apart which organism is doing what will require new analytical approaches. Flow cytometry, when combined with other techniques, has great potential for expanding our understanding of microbial interactions because groups can be distinguished optically, sorted, and then collected for subsequent analyses. Herein, we review the advances in our understanding of marine biogeochemistry that have arisen from the use of flow cytometry.
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Affiliation(s)
- Michael W Lomas
- Bermuda Institute of Ocean Sciences, Ferry Reach, St. George's GE01, Bermuda.
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Sigler MF, Harvey HR, Ashjian J, Lomas MW, Napp JM, Stabeno PJ, Van Pelt TI. How Does Climate Change Affect the Bering Sea Ecosystem? ACTA ACUST UNITED AC 2010. [DOI: 10.1029/2010eo480001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Van Mooy BAS, Fredricks HF, Pedler BE, Dyhrman ST, Karl DM, Koblížek M, Lomas MW, Mincer TJ, Moore LR, Moutin T, Rappé MS, Webb EA. Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity. Nature 2009; 458:69-72. [PMID: 19182781 DOI: 10.1038/nature07659] [Citation(s) in RCA: 345] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 03/05/2009] [Accepted: 11/20/2008] [Indexed: 11/09/2022]
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Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004; 304:66-74. [PMID: 15001713 DOI: 10.1126/science.1093857] [Citation(s) in RCA: 2428] [Impact Index Per Article: 121.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We have applied "whole-genome shotgun sequencing" to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.
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Affiliation(s)
- J Craig Venter
- Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA.
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Glibert PM, Magnien R, Lomas MW, Alexander J, Fan C, Haramoto E, Trice M, Kana TM. Harmful Algal Blooms in the Chesapeake and Coastal Bays of Maryland, USA: Comparison of 1997, 1998, and 1999 Events. ACTA ACUST UNITED AC 2001. [DOI: 10.2307/1353178] [Citation(s) in RCA: 173] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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