1
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Dong K, Wang Y, Zhang W, Li Q. Prevalence and Preferred Niche of Small Eukaryotes with Mixotrophic Potentials in the Global Ocean. Microorganisms 2024; 12:750. [PMID: 38674694 PMCID: PMC11051772 DOI: 10.3390/microorganisms12040750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/23/2024] [Accepted: 03/24/2024] [Indexed: 04/28/2024] Open
Abstract
Unicellular eukaryotes that are capable of phago-mixotrophy in the ocean compete for inorganic nutrients and light with autotrophs, and for bacterial prey with heterotrophs. In this study, we ask what the overall prevalence of eukaryotic mixotrophs in the vast open ocean is, and how the availability of inorganic nutrients, light, and prey affects their relative success. We utilized the Tara Oceans eukaryotic 18S rRNA gene and environmental context variables dataset to conduct a large-scale field analysis. We also performed isolate-based culture experiments to verify growth and nutritional resource relationships for representative mixotrophic taxa. The field analysis suggested that the overall prevalence of mixotrophs were negatively correlated with nutrient concentrations and positively associated with light availability. Concentrations of heterotrophic bacteria as a single variable also presented a positive correlation with mixotrophic prevalence, but to a lesser extent. On the other hand, the culture experiments demonstrated a taxa-specific relationship between mixotrophic growth and nutrition resources, i.e., the growth of one group was significantly dependent on light availability, while the other group was less affected by light when they received sufficient prey. Both groups were capable of growing efficiently with low inorganic nutrients when receiving sufficient prey and light. Therefore, our field analysis and culture experiments both suggest that phago-mixotrophy for ocean eukaryotes is seemingly an efficient strategy to compensate for nutrient deficiency but unnecessary to compensate for light scarcity. This study collectively revealed a close relationship between abiotic and biotic nutritional resources and the prevalence of trophic strategies, shedding light on the importance of light and nutrients for determining the competitive success of mixotrophs versus autotrophic and heterotrophic eukaryotes in the ocean.
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Affiliation(s)
- Kaiyi Dong
- School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Ying Wang
- School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Wenjing Zhang
- School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Qian Li
- School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
- Key Laboratory of Polar Ecosystem and Climate Change, Shanghai Jiao Tong University, Ministry of Education, 1954 Huashan Road, Shanghai 200030, China
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2
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Dobbertin da Costa M, Gast RJ, Millette NC. Temporal and spatial variability of constitutive mixotroph abundance and proportion. FEMS Microbiol Ecol 2024; 100:fiae015. [PMID: 38308512 PMCID: PMC10939395 DOI: 10.1093/femsec/fiae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/19/2023] [Accepted: 02/01/2024] [Indexed: 02/04/2024] Open
Abstract
Mixotrophic plankton can comprise a substantial portion of the plankton community compared to phytoplankton and zooplankton. However, there is a gap in the understanding of conditions that influence mixotroph prevalence and activity in situ because current methods often over- or underestimate mixotroph abundance. A labeled prey-tracer method was utilized to identify active mixotrophs present at two locations in a temperate estuary over a year. The tracer method was combined with light microscopy data to estimate active mixotroph abundance and proportion. This study estimated that actively grazing mixotrophic taxa were more abundant in the spring and autumn compared to summer. Dinoflagellates typically dominated the mixotrophic taxa except during autumn at the low salinity location when cryptophytes dominated. Further analysis suggested that active mixotroph abundances might not be only regulated by environmental conditions favorable to mixotrophy but, instead, environmental conditions favorable to different mixotrophs utilization of phagotrophy. By focusing on mixotrophic taxa that were identified to be actively grazing at time of sampling, this study provided a more nuanced estimation of mixotroph abundance, increasing the understanding of how mixotrophic abundance and proportion in situ are influenced by the planktonic community composition and environmental factors.
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Affiliation(s)
- Marcella Dobbertin da Costa
- Virginia Institute of Marine Science, William & Mary, 1370 Greate Rd., Gloucester Point, VA 23062, United States
| | - Rebecca J Gast
- Woods Hole Oceanographic Institution, 266 Woods Hole Rd, MS #32, Woods Hole, MA 02543, United States
| | - Nicole C Millette
- Virginia Institute of Marine Science, William & Mary, 1370 Greate Rd., Gloucester Point, VA 23062, United States
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3
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Weiner AKM, Sehein T, Cote-L’Heureux A, Sleith RS, Greco M, Malekshahi C, Ryan-Embry C, Ostriker N, Katz LA. Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes. Evolution 2023; 77:2472-2483. [PMID: 37672006 PMCID: PMC10629589 DOI: 10.1093/evolut/qpad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/13/2023] [Accepted: 09/05/2023] [Indexed: 09/07/2023]
Abstract
The enormous population sizes and wide biogeographical distribution of many microbial eukaryotes set the expectation of high levels of intraspecific genetic variation. However, studies investigating protist populations remain scarce, mostly due to limited 'omics data. Instead, most genetics studies of microeukaryotes have thus far relied on single loci, which can be misleading and do not easily allow for detection of recombination, a hallmark of sexual reproduction. Here, we analyze >40 genes from 72 single-cell transcriptomes from two morphospecies-Hyalosphenia papilio and Hyalosphenia elegans-of testate amoebae (Arcellinida, Amoebozoa) to assess genetic diversity in samples collected over four years from New England bogs. We confirm the existence of cryptic species based on our multilocus dataset, which provides evidence of recombination within and high levels of divergence between the cryptic species. At the same time, total levels of genetic diversity within cryptic species are low, suggesting that these abundant organisms have small effective population sizes, perhaps due to extinction and repopulation events coupled with efficient modes of dispersal. This study is one of the first to investigate population genetics in uncultivable heterotrophic protists using transcriptomics data and contributes towards understanding cryptic species of nonmodel microeukaryotes.
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Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bergen, Norway
| | - Taylor Sehein
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Robin S Sleith
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Mattia Greco
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Clara Malekshahi
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Chase Ryan-Embry
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Naomi Ostriker
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, MA, United States
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4
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Millette NC, Gast RJ, Luo JY, Moeller HV, Stamieszkin K, Andersen KH, Brownlee EF, Cohen NR, Duhamel S, Dutkiewicz S, Glibert PM, Johnson MD, Leles SG, Maloney AE, Mcmanus GB, Poulton N, Princiotta SD, Sanders RW, Wilken S. Mixoplankton and mixotrophy: future research priorities. JOURNAL OF PLANKTON RESEARCH 2023; 45:576-596. [PMID: 37483910 PMCID: PMC10361813 DOI: 10.1093/plankt/fbad020] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/14/2023] [Indexed: 07/25/2023]
Abstract
Phago-mixotrophy, the combination of photoautotrophy and phagotrophy in mixoplankton, organisms that can combine both trophic strategies, have gained increasing attention over the past decade. It is now recognized that a substantial number of protistan plankton species engage in phago-mixotrophy to obtain nutrients for growth and reproduction under a range of environmental conditions. Unfortunately, our current understanding of mixoplankton in aquatic systems significantly lags behind our understanding of zooplankton and phytoplankton, limiting our ability to fully comprehend the role of mixoplankton (and phago-mixotrophy) in the plankton food web and biogeochemical cycling. Here, we put forward five research directions that we believe will lead to major advancement in the field: (i) evolution: understanding mixotrophy in the context of the evolutionary transition from phagotrophy to photoautotrophy; (ii) traits and trade-offs: identifying the key traits and trade-offs constraining mixotrophic metabolisms; (iii) biogeography: large-scale patterns of mixoplankton distribution; (iv) biogeochemistry and trophic transfer: understanding mixoplankton as conduits of nutrients and energy; and (v) in situ methods: improving the identification of in situ mixoplankton and their phago-mixotrophic activity.
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Affiliation(s)
| | - Rebecca J Gast
- Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Jessica Y Luo
- NOAA Geophysical Fluid Dynamics Laboratory, 201 Forrestal Rd., Princeton, NJ 08540, USA
| | - Holly V Moeller
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, 1120 Noble Hall, Santa Barbara, CA 93106, USA
| | - Karen Stamieszkin
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr., East Boothbay, ME 04544, USA
| | - Ken H Andersen
- Center for Ocean Life, Natl. Inst. of Aquatic Resources, Technical University of Denmark, Kemitorvet, Bygning 202, Kongens Lyngby 2840, Denmark
| | - Emily F Brownlee
- Department of Biology, St. Mary’s College of Maryland, 18952 E. Fisher Road, St. Mary’s City, MD 20686, USA
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, 10 Ocean Science Circle, Savannah, GA 31411, USA
| | - Solange Duhamel
- Department of Molecular and Cellular Biology, The University of Arizona, 1007 E Lowell Street, Tucson, AZ 85721, USA
| | - Stephanie Dutkiewicz
- Center for Global Change Science, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02874, USA
| | - Patricia M Glibert
- Horn Point Laboratory, University of Maryland Center for Environmental Science, 2020 Horns Point Rd, Cambridge, MD 21613, USA
| | - Matthew D Johnson
- Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Suzana G Leles
- Department of Marine and Environmental Biology, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
| | - Ashley E Maloney
- Geosciences Department, Princeton University, Guyot Hall, Princeton, NJ 08544, USA
| | - George B Mcmanus
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd., Groton, CT 06340, USA
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr., East Boothbay, ME 04544, USA
| | - Sarah D Princiotta
- Biology Department, Pennsylvania State University, Schuylkill Campus, 200 University Drive, Schuylkill Haven, PA 17972, USA
| | - Robert W Sanders
- Department of Biology, Temple University, 1900 N. 12th St., Philadelphia, PA 19122, USA
| | - Susanne Wilken
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
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5
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Kong H, Yang EJ, Jiao N, Lee Y, Jung J, Cho KH, Moon JK, Kim JH, Xu D. RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162608. [PMID: 36871742 DOI: 10.1016/j.scitotenv.2023.162608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The Arctic Ocean (AO) has a harsh environment characterized by low temperatures, extensive ice coverage, and periodic freezing and melting of sea ice, which has provided diverse habitats for microorganisms. Prior studies primarily focused on microeukaryote communities in the upper water or sea ice based on environmental DNA, leaving the composition of active microeukaryotes in the diverse AO environments largely unknown. This study provided a vertical assessment of microeukaryote communities in the AO from snow and ice to sea water at a depth of 1670 m using high-throughput sequencing of co-extracted DNA and RNA. RNA extracts depicted microeukaryote community structure and intergroup correlations more accurately and responded more sensitively to environmental conditions than those derived from DNA. Using RNA:DNA ratios as a proxy for relative activity of major taxonomic groups, the metabolic activities of major microeukaryote groups were determined along depth. Analysis of co-occurrence networks showed that parasitism between Syndiniales and dinoflagellates/ciliates in the deep ocean may be significant. This study increased our knowledge of the diversity of active microeukaryote communities and highlighted the importance of using RNA-based sequencing over DNA-based sequencing to examine the relationship between microeukaryote assemblages and the responses of microeukaryotes to environmental variables in the AO.
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Affiliation(s)
- Hejun Kong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Kyoung-Ho Cho
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jong-Kuk Moon
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jee-Hoon Kim
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.
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6
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Edwards KF, Li Q, McBeain KA, Schvarcz CR, Steward GF. Trophic strategies explain the ocean niches of small eukaryotic phytoplankton. Proc Biol Sci 2023; 290:20222021. [PMID: 36695036 PMCID: PMC9874276 DOI: 10.1098/rspb.2022.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A large fraction of marine primary production is performed by diverse small protists, and many of these phytoplankton are phagotrophic mixotrophs that vary widely in their capacity to consume bacterial prey. Prior analyses suggest that mixotrophic protists as a group vary in importance across ocean environments, but the mechanisms leading to broad functional diversity among mixotrophs, and the biogeochemical consequences of this, are less clear. Here we use isolates from seven major taxa to demonstrate a tradeoff between phototrophic performance (growth in the absence of prey) and phagotrophic performance (clearance rate when consuming Prochlorococcus). We then show that trophic strategy along the autotrophy-mixotrophy spectrum correlates strongly with global niche differences, across depths and across gradients of stratification and chlorophyll a. A model of competition shows that community shifts can be explained by greater fitness of faster-grazing mixotrophs when nutrients are scarce and light is plentiful. Our results illustrate how basic physiological constraints and principles of resource competition can organize complexity in the surface ocean ecosystem.
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Affiliation(s)
- Kyle F. Edwards
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
| | - Qian Li
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA,Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA,School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan Rd, Shanghai Shi, Xuhui Qu 200240, China
| | - Kelsey A. McBeain
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
| | - Christopher R. Schvarcz
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA,Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
| | - Grieg F. Steward
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA,Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology (SOEST), University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
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7
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Endo H, Umezawa Y, Takeda S, Suzuki K. Haptophyte communities along the Kuroshio current reveal their geographical sources and ecological traits. Mol Ecol 2023; 32:110-123. [PMID: 36221794 DOI: 10.1111/mec.16734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 12/29/2022]
Abstract
Haptophytes are one of the most ecologically successful phytoplankton groups in the modern ocean and tend to maintain balanced and stable communities across various environments. However, little is known about the mechanisms that enable community stability and ecological success. To reveal the community characteristics and interactions among haptophytes, we conducted comprehensive observations from the upstream to downstream regions of the Kuroshio Current. Haptophyte abundance and taxonomy were assessed using quantitative polymerase chain reaction and metabarcoding of 18S rRNA sequences, respectively. The haptophyte community structure changed abruptly at sites on the shelf-slope of the East China Sea, indicating the strong influence of shelf waters with high phytoplankton biomass on downstream communities. Correlation network analysis combined with the phylogeny suggested that haptophytes can coexist with their close relatives, possibly owing to their nutritional flexibility, thereby escaping from resource competition. Consistently, some noncalcifying haptophyte genera with high mixotrophic capacities such as Chrysochromulina constituted a major component of the co-occurrence network, whereas coccolithophores such as Emiliania/Gephyrocapsa were rarely observed. Our study findings suggest that noncalcifying haptophytes play crucial roles in community diversity and stability, and in sustaining the food web structure in the Kuroshio ecosystems.
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Affiliation(s)
- Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Yu Umezawa
- Department of Environmental Science on Biosphere, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Shigenobu Takeda
- Faculty of Environmental Earth Science, Hokkaido University, Hokkaido, Sapporo, Japan
| | - Koji Suzuki
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
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8
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Koppelle S, López-Escardó D, Brussaard CPD, Huisman J, Philippart CJM, Massana R, Wilken S. Mixotrophy in the bloom-forming genus Phaeocystis and other haptophytes. HARMFUL ALGAE 2022; 117:102292. [PMID: 35944956 DOI: 10.1016/j.hal.2022.102292] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 05/13/2023]
Abstract
Phaeocystis is a globally widespread marine phytoplankton genus, best known for its colony-forming species that can form large blooms and odorous foam during bloom decline. In the North Sea, Phaeocystis globosa typically becomes abundant towards the end of the spring bloom, when nutrients are depleted and the share of mixotrophic protists increases. Although mixotrophy is widespread across the eukaryotic tree of life and is also found amongst haptophytes, a mixotrophic nutrition has not yet been demonstrated in Phaeocystis. Here, we sampled two consecutive Phaeocystis globosa spring blooms in the coastal North Sea. In both years, bacterial cells were observed inside 0.6 - 2% of P. globosa cells using double CARD-FISH hybridizations in combination with laser scanning confocal microscopy. Incubation experiments manipulating light and nutrient availability showed a trend towards higher occurrence of intracellular bacteria under P-deplete conditions. Based on counts of bacteria inside P. globosa cells in combination with theoretical values of prey digestion times, maximum ingestion rates of up to 0.08 bacteria cell-1 h-1 were estimated. In addition, a gene-based predictive model was applied to the transcriptome assemblies of seven Phaeocystis strains and 24 other haptophytes to assess their trophic mode. This model predicted a phago-mixotrophic feeding strategy in several (but not all) strains of P. globosa, P. antarctica and other haptophytes that were previously assumed to be autotrophic. The observation of bacterial cells inside P. globosa and the gene-based model predictions strongly suggest that the phago-mixotrophic feeding strategy is widespread among members of the Phaeocystis genus and other haptophytes, and might contribute to their remarkable success to form nuisance blooms under nutrient-limiting conditions.
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Affiliation(s)
- Sebastiaan Koppelle
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands.
| | - David López-Escardó
- Ecology of Marine Microbes, Institut de Ciènces del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Corina P D Brussaard
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands; Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands
| | - Catharina J M Philippart
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands; Department of Physical Geography, Utrecht University, P.O. Box 80115, 3508 TC, Utrecht, The Netherlands
| | - Ramon Massana
- Ecology of Marine Microbes, Institut de Ciènces del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Susanne Wilken
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands.
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9
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MacNeil L, Desai DK, Costa M, LaRoche J. Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf. Sci Rep 2022; 12:13078. [PMID: 35906469 PMCID: PMC9338326 DOI: 10.1038/s41598-022-17313-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
The planktonic diversity throughout the oceans is vital to ecosystem functioning and linked to environmental change. Plankton monitoring tools have advanced considerably with high-throughput in-situ digital cameras and genomic sequencing, opening new challenges for high-frequency observations of community composition, structure, and species discovery. Here, we combine multi-marker metabarcoding based on nuclear 18S (V4) and plastidial 16S (V4–V5) rRNA gene amplicons with a digital in-line holographic microscope to provide a synoptic diversity survey of eukaryotic plankton along the Newfoundland Shelf (Canada) during the winter transition phase of the North Atlantic bloom phenomenon. Metabarcoding revealed a rich eukaryotic diversity unidentifiable in the imaging samples, confirming the presence of ecologically important saprophytic protists which were unclassifiable in matching images, and detecting important groups unobserved or taxonomically unresolved during similar sequencing campaigns in the Northwest Atlantic Ocean. In turn, imaging analysis provided quantitative observations of widely prevalent plankton from every trophic level. Despite contrasting plankton compositions portrayed by each sampling method, both capture broad spatial differences between the northern and southern sectors of the Newfoundland Shelf and suggest complementary estimations of important features in eukaryotic assemblages. Future tasks will involve standardizing digital imaging and metabarcoding for wider use and consistent, comparable ocean observations.
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Affiliation(s)
- Liam MacNeil
- Biology Department, Dalhousie University, 1355 Oxford St, Halifax, NS, B3H 4J1, Canada. .,GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany.
| | - Dhwani K Desai
- Biology Department, Dalhousie University, 1355 Oxford St, Halifax, NS, B3H 4J1, Canada.,Department of Biology and Pharmacology, Dalhousie University, 5850 College St, Halifax, NS, B3H 4R2, Canada
| | - Maycira Costa
- Department of Geography, University of Victoria, STN CSC, PO Box 1700, Victoria, BC, V8W2Y2, Canada
| | - Julie LaRoche
- Biology Department, Dalhousie University, 1355 Oxford St, Halifax, NS, B3H 4J1, Canada.
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10
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Grattepanche JD, Jeffrey WH, Gast RJ, Sanders RW. Diversity of Microbial Eukaryotes Along the West Antarctic Peninsula in Austral Spring. Front Microbiol 2022; 13:844856. [PMID: 35651490 PMCID: PMC9149413 DOI: 10.3389/fmicb.2022.844856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
During a cruise from October to November 2019, along the West Antarctic Peninsula, between 64.32 and 68.37°S, we assessed the diversity and composition of the active microbial eukaryotic community within three size fractions: micro- (> 20 μm), nano- (20-5 μm), and pico-size fractions (5-0.2 μm). The communities and the environmental parameters displayed latitudinal gradients, and we observed a strong similarity in the microbial eukaryotic communities as well as the environmental parameters between the sub-surface and the deep chlorophyll maximum (DCM) depths. Chlorophyll concentrations were low, and the mixed layer was shallow for most of the 17 stations sampled. The richness of the microplankton was higher in Marguerite Bay (our southernmost stations), compared to more northern stations, while the diversity for the nano- and pico-plankton was relatively stable across latitude. The microplankton communities were dominated by autotrophs, mostly diatoms, while mixotrophs (phototrophs-consuming bacteria and kleptoplastidic ciliates, mostly alveolates, and cryptophytes) were the most abundant and active members of the nano- and picoplankton communities. While phototrophy was the dominant trophic mode, heterotrophy (mixotrophy, phagotrophy, and parasitism) tended to increase southward. The samples from Marguerite Bay showed a distinct community with a high diversity of nanoplankton predators, including spirotrich ciliates, and dinoflagellates, while cryptophytes were observed elsewhere. Some lineages were significantly related-either positively or negatively-to ice coverage (e.g., positive for Pelagophyceae, negative for Spirotrichea) and temperature (e.g., positive for Cryptophyceae, negative for Spirotrichea). This suggests that climate changes will have a strong impact on the microbial eukaryotic community.
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Affiliation(s)
| | - Wade H. Jeffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL, United States
| | - Rebecca J. Gast
- Department of Biology, Woods Hole Oceanographic Institution, Pensacola, MA, United States
| | - Robert W. Sanders
- Department of Biology, Temple University, Philadelphia, PA, United States
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11
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Cohen NR. Mixotrophic plankton foraging behaviour linked to carbon export. Nat Commun 2022; 13:1302. [PMID: 35288547 PMCID: PMC8921202 DOI: 10.1038/s41467-022-28868-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/04/2022] [Indexed: 11/21/2022] Open
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12
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The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics. Proc Natl Acad Sci U S A 2022; 119:2100916119. [PMID: 35145022 PMCID: PMC8851463 DOI: 10.1073/pnas.2100916119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 12/25/2022] Open
Abstract
Mixotrophy is a ubiquitous nutritional strategy in marine ecosystems. Although our understanding of the distribution and abundance of mixotrophic plankton has improved significantly, the functional roles of mixotrophs are difficult to pinpoint, as mixotroph nutritional strategies are flexible and form a continuum between heterotrophy and phototrophy. We developed a machine learning–based method to assess the nutritional strategies of in situ planktonic populations based on metatranscriptomic profiles. We demonstrate that mixotrophic populations play varying functional roles along physicochemical gradients in the North Pacific Ocean, revealing a degree of physiological plasticity unique to aquatic mixotrophs. Our results highlight mechanisms that may dictate the flow of biogeochemical elements and ecology of the North Pacific Ocean, one of Earth's largest biogeographical provinces. Intricate networks of single-celled eukaryotes (protists) dominate carbon flow in the ocean. Their growth, demise, and interactions with other microorganisms drive the fluxes of biogeochemical elements through marine ecosystems. Mixotrophic protists are capable of both photosynthesis and ingestion of prey and are dominant components of open-ocean planktonic communities. Yet the role of mixotrophs in elemental cycling is obscured by their capacity to act as primary producers or heterotrophic consumers depending on factors that remain largely uncharacterized. Here, we develop and apply a machine learning model that predicts the in situ trophic mode of aquatic protists based on their patterns of gene expression. This approach leverages a public collection of protist transcriptomes as a training set to identify a subset of gene families whose transcriptional profiles predict trophic mode. We applied our model to nearly 100 metatranscriptomes obtained during two oceanographic cruises in the North Pacific and found community-level and population-specific evidence that abundant open-ocean mixotrophic populations shift their predominant mode of nutrient and carbon acquisition in response to natural gradients in nutrient supply and sea surface temperature. Metatranscriptomic data from ship-board incubation experiments revealed that abundant mixotrophic prymnesiophytes from the oligotrophic North Pacific subtropical gyre rapidly remodeled their transcriptome to enhance photosynthesis when supplied with limiting nutrients. Coupling this approach with experiments designed to reveal the mechanisms driving mixotroph physiology provides an avenue toward understanding the ecology of mixotrophy in the natural environment.
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13
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Zonation of protistan plankton in a productive area of the Patagonian shelf: Potential implications for the anchovy distribution. FOOD WEBS 2021. [DOI: 10.1016/j.fooweb.2021.e00211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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Modeling mixoplankton along the biogeochemical gradient of the Southern North Sea. Ecol Modell 2021; 459:109690. [PMID: 34732971 PMCID: PMC8507435 DOI: 10.1016/j.ecolmodel.2021.109690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/22/2022]
Abstract
The ecological importance of mixoplankton within marine protist communities is slowly being recognized. However, most aquatic ecosystem models do not include formulations to model a complete protist community consisting of phytoplankton, protozooplankton and mixoplankton. We introduce PROTIST, a new module for the aquatic ecosystem modelling software Delft3D-WAQ that can model a protist community consisting of two types of phytoplankton (diatoms and green algae), two types of mixoplankton (constitutive mixoplankton and non-constitutive mixoplankton) and protozooplankton. We employed PROTIST to further explore the hypothesis that the biogeochemical gradient of inorganic nutrient and suspended sediment concentrations drives the observed occurrence of constitutive mixoplankton in the Dutch Southern North Sea. To explore this hypothesis, we used 11 1D-vertical aquatic ecosystem models that mimic the abiotic conditions of 11 routine monitoring locations in the Dutch Southern North Sea. Our models result in plausible trophic compositions across the biogeochemical gradient as compared to in-situ data. A sensitivity analysis showed that the dissolved inorganic phosphate and silica concentrations drive the occurrence of constitutive mixoplankton in the Dutch Southern North Sea. A model to simulate the protist community including mixoplankton is introduced. The model was tested in 1D-V models along a biogeochemical gradient. Modelled mixoplankton are more sensitive to nutrients than to light.
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15
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Groussman RD, Coesel SN, Durham BP, Armbrust EV. Diel-Regulated Transcriptional Cascades of Microbial Eukaryotes in the North Pacific Subtropical Gyre. Front Microbiol 2021; 12:682651. [PMID: 34659137 PMCID: PMC8511712 DOI: 10.3389/fmicb.2021.682651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
Open-ocean surface waters host a diverse community of single-celled eukaryotic plankton (protists) consisting of phototrophs, heterotrophs, and mixotrophs. The productivity and biomass of these organisms oscillate over diel cycles, and yet the underlying transcriptional processes are known for few members of the community. Here, we examined a 4-day diel time series of transcriptional abundance profiles for the protist community (0.2-100 μm in cell size) in the North Pacific Subtropical Gyre near Station ALOHA. De novo assembly of poly-A+ selected metatranscriptomes yielded over 30 million contigs with taxonomic and functional annotations assigned to 54 and 25% of translated contigs, respectively. The completeness of the resulting environmental eukaryotic taxonomic bins was assessed, and 48 genera were further evaluated for diel patterns in transcript abundances. These environmental transcriptome bins maintained reproducible temporal partitioning of total gene family abundances, with haptophyte and ochrophyte genera generally showing the greatest diel partitioning of their transcriptomes. The haptophyte Phaeocystis demonstrated the highest proportion of transcript diel periodicity, while most other protists had intermediate levels of periodicity regardless of their trophic status. Dinoflagellates, except for the parasitoid genus Amoebophrya, exhibit the fewest diel oscillations of transcript abundances. Diel-regulated gene families were enriched in key metabolic pathways; photosynthesis, carbon fixation, and fatty acid biosynthesis gene families had peak times concentrated around dawn, while gene families involved in protein turnover (proteasome and protein processing) are most active during the high intensity daylight hours. TCA cycle, oxidative phosphorylation and fatty acid degradation predominantly peaked near dusk. We identified temporal pathway enrichments unique to certain taxa, including assimilatory sulfate reduction at dawn in dictyophytes and signaling pathways at early evening in haptophytes, pointing to possible taxon-specific channels of carbon and nutrients through the microbial community. These results illustrate the synchrony of transcriptional regulation to the diel cycle and how the protist community of the North Pacific Subtropical Gyre structures their transcriptomes to guide the daily flux of matter and energy through the gyre ecosystem.
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Affiliation(s)
- Ryan D. Groussman
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Sacha N. Coesel
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Bryndan P. Durham
- School of Oceanography, University of Washington, Seattle, WA, United States
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
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16
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Decelle J, Veronesi G, LeKieffre C, Gallet B, Chevalier F, Stryhanyuk H, Marro S, Ravanel S, Tucoulou R, Schieber N, Finazzi G, Schwab Y, Musat N. Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae. Environ Microbiol 2021; 23:6569-6586. [PMID: 34499794 DOI: 10.1111/1462-2920.15766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/27/2021] [Accepted: 09/05/2021] [Indexed: 11/28/2022]
Abstract
Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium). We showed that this symbiosis is very dynamic whereby symbionts interact with different host cells via extracellular vesicles within the colony. 3D electron microscopy revealed that the photosynthetic apparatus of the microalgae was more voluminous in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were stored in the symbiotic microalga in starch granules and purine crystals respectively. Nitrogen was also allocated to the algal nucleolus. In the host, low 13 C transfer was detected in the Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (c. 40 ppm) and twofold higher in the host, whereas copper concentration increased in symbionts and was detected in the host cell and extracellular vesicles. Sulfur concentration was around two times higher in symbionts (chromatin and pyrenoid) than their host. This study improves our understanding on the functioning of this oceanic photosymbiosis and paves the way for more studies to further assess its biogeochemical significance.
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Affiliation(s)
- Johan Decelle
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France.,Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Giulia Veronesi
- CNRS, Laboratoire de Chimie et Biologie des Métaux (LCBM), UMR 5249 CNRS-CEA-UGA, F-38054, Grenoble, France.,CEA, LCBM, F-38054, Grenoble, France.,Université Grenoble Alpes, LCBM, F-38054, Grenoble, France.,ESRF, The European Synchrotron, 71, Avenue des Martyrs, 38043, Grenoble, France
| | | | - Benoit Gallet
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Fabien Chevalier
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sophie Marro
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), UMR 7093, Observatoire Océanologique, 06230, Villefranche-sur-Mer, France
| | - Stéphane Ravanel
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France
| | - Rémi Tucoulou
- ESRF, The European Synchrotron, 71, Avenue des Martyrs, 38043, Grenoble, France
| | - Nicole Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Giovanni Finazzi
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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17
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Faure E, Ayata SD, Bittner L. Towards omics-based predictions of planktonic functional composition from environmental data. Nat Commun 2021; 12:4361. [PMID: 34272373 PMCID: PMC8285379 DOI: 10.1038/s41467-021-24547-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Marine microbes play a crucial role in climate regulation, biogeochemical cycles, and trophic networks. Unprecedented amounts of data on planktonic communities were recently collected, sparking a need for innovative data-driven methodologies to quantify and predict their ecosystemic functions. We reanalyze 885 marine metagenome-assembled genomes through a network-based approach and detect 233,756 protein functional clusters, from which 15% are functionally unannotated. We investigate all clusters' distributions across the global ocean through machine learning, identifying biogeographical provinces as the best predictors of protein functional clusters' abundance. The abundances of 14,585 clusters are predictable from the environmental context, including 1347 functionally unannotated clusters. We analyze the biogeography of these 14,585 clusters, identifying the Mediterranean Sea as an outlier in terms of protein functional clusters composition. Applicable to any set of sequences, our approach constitutes a step towards quantitative predictions of functional composition from the environmental context.
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Affiliation(s)
- Emile Faure
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.
| | - Sakina-Dorothée Ayata
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- Institut Universitaire de France, Paris, France
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18
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Weiner AKM, Katz LA. Epigenetics as Driver of Adaptation and Diversification in Microbial Eukaryotes. Front Genet 2021; 12:642220. [PMID: 33796133 PMCID: PMC8007921 DOI: 10.3389/fgene.2021.642220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States
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19
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Schneider LK, Anestis K, Mansour J, Anschütz AA, Gypens N, Hansen PJ, John U, Klemm K, Martin JL, Medic N, Not F, Stolte W. A dataset on trophic modes of aquatic protists. Biodivers Data J 2020; 8:e56648. [PMID: 33177947 PMCID: PMC7599203 DOI: 10.3897/bdj.8.e56648] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/08/2020] [Indexed: 11/12/2022] Open
Abstract
Background An important functional trait of organisms is their trophic mode. It determines their position within food webs, as well as their function within an ecosystem. For the better part of the 20th century, aquatic protist communities were thought to consist mainly of producers (phytoplankton) and consumers (protozooplankton). Phytoplankton cover their energy requirements through photosynthesis (phototrophy), while protozooplankton graze on prey and organic particles (phagotrophy). However, over the past decades, it was shown that another trophic group (mixoplankton) comprise a notable part of aquatic protist communities. Mixoplankton employ a third trophic mode by combining phototrophy and phagotrophy (mixotrophy). Due to the historical dichotomy, it is not straightforward to gain adequate and correct information on the trophic mode of aquatic protists. Long hours of literature research or expert knowledge are needed to correctly assign trophic modes. Additionally, aquatic protists also have a long history of undergoing taxonomic changes which make it difficult to compare past and present literature. While WoRMS, the World Register of Marine Species, keeps track of the taxonomic changes and assigns each species a unique AphiaID that can be linked to its various historic and present taxonomic hierarchy, there is currently no machine-readable database to query aquatic protists for their trophic modes. New information This paper describes a dataset that was submitted to WoRMS and links aquatic protist taxa, with a focus on marine taxa, to their AphiaID and their trophic mode. The bulk of the data used for this dataset stems from (routine) monitoring stations in the North Sea and the Baltic Sea. The data were augmented and checked against state-of-the-art knowledge on mixoplankton taxa by consulting literature and experts. Thus, this dataset provides a first attempt to make the trophic mode of aquatic protists easily accessible in both a human- and machine-readable format.
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Affiliation(s)
- Lisa K Schneider
- Deltares, Delft, Netherlands Deltares Delft Netherlands.,Université Libre de Bruxelles, Bruxelles, Belgium Université Libre de Bruxelles Bruxelles Belgium
| | - Konstantinos Anestis
- Alfred-Wegener-Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany Alfred-Wegener-Institute Helmholtz Center for Polar and Marine Research Bremerhaven Germany
| | - Joost Mansour
- Sorbonne University, CNRS, Roscoff, France Sorbonne University, CNRS Roscoff France
| | - Anna A Anschütz
- School of Earth and Ocean Sciences, Cardiff University, Cardiff, United Kingdom School of Earth and Ocean Sciences, Cardiff University Cardiff United Kingdom.,Université Libre de Bruxelles, Bruxelles, Belgium Université Libre de Bruxelles Bruxelles Belgium
| | - Nathalie Gypens
- Université Libre de Bruxelles, Bruxelles, Belgium Université Libre de Bruxelles Bruxelles Belgium
| | - Per J Hansen
- Marine Biological Laboratory, University of Copenhagen, Copenhagen, Denmark Marine Biological Laboratory, University of Copenhagen Copenhagen Denmark
| | - Uwe John
- Alfred-Wegener-Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany Alfred-Wegener-Institute Helmholtz Center for Polar and Marine Research Bremerhaven Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany Helmholtz Institute for Functional Marine Biodiversity Oldenburg Germany
| | - Kerstin Klemm
- Alfred-Wegener-Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany Alfred-Wegener-Institute Helmholtz Center for Polar and Marine Research Bremerhaven Germany
| | - Jon Lapeya Martin
- Université Libre de Bruxelles, Bruxelles, Belgium Université Libre de Bruxelles Bruxelles Belgium
| | - Nikola Medic
- Marine Biological Laboratory, University of Copenhagen, Copenhagen, Denmark Marine Biological Laboratory, University of Copenhagen Copenhagen Denmark
| | | | - Willem Stolte
- Deltares, Delft, Netherlands Deltares Delft Netherlands
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20
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Caveats on the use of rotenone to estimate mixotrophic grazing in the oceans. Sci Rep 2020; 10:3899. [PMID: 32127594 PMCID: PMC7054392 DOI: 10.1038/s41598-020-60764-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/13/2020] [Indexed: 11/25/2022] Open
Abstract
Phagotrophic mixotrophs (mixoplankton) are now widely recognised as important members of food webs, but their role in the functioning of food webs is not yet fully understood. This is due to the lack of a well-established technique to estimate mixotrophic grazing. An immediate step in this direction would be the development of a method that separates mixotrophic from heterotrophic grazing that can be routinely incorporated into the common techniques used to measure microplankton herbivory (e.g., the dilution technique). This idea was explored by the addition of rotenone, an inhibitor of the respiratory electron chain that has been widely used to selectively eliminate metazoans, both in the field and in the laboratory. Accordingly, rotenone was added to auto-, mixo-, and heterotrophic protist cultures in increasing concentrations (ca. 24 h). The results showed that mixotrophs survived better than heterotrophs at low concentrations of rotenone. Nevertheless, their predation was more affected, rendering rotenone unusable as a heterotrophic grazing deterrent. Additionally, it was found that rotenone had a differential effect depending on the growth phase of an autotrophic culture. Altogether, these results suggest that previous uses of rotenone in the field may have disrupted the planktonic food web.
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21
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Abstract
Photosynthesis evolved in the ocean more than 2 billion years ago and is now performed by a wide range of evolutionarily distinct organisms, including both prokaryotes and eukaryotes. Our appreciation of their abundance, distributions, and contributions to primary production in the ocean has been increasing since they were first discovered in the seventeenth century and has now been enhanced by data emerging from the Tara Oceans project, which performed a comprehensive worldwide sampling of plankton in the upper layers of the ocean between 2009 and 2013. Largely using recent data from Tara Oceans, here we review the geographic distributions of phytoplankton in the global ocean and their diversity, abundance, and standing stock biomass. We also discuss how omics-based information can be incorporated into studies of photosynthesis in the ocean and show the likely importance of mixotrophs and photosymbionts.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
| | - Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
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22
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Dumack K, Fiore‐Donno AM, Bass D, Bonkowski M. Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria). Mol Ecol Resour 2019; 20:398-403. [DOI: 10.1111/1755-0998.13112] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Kenneth Dumack
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
| | - Anna Maria Fiore‐Donno
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
| | - David Bass
- Centre for Environment Fisheries and Aquaculture Science (Cefas) Weymouth UK
- Department of Life Sciences The Natural History Museum London UK
| | - Michael Bonkowski
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
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23
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Marked changes in diversity and relative activity of picoeukaryotes with depth in the world ocean. ISME JOURNAL 2019; 14:437-449. [PMID: 31645670 PMCID: PMC6976695 DOI: 10.1038/s41396-019-0506-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/10/2019] [Accepted: 08/02/2019] [Indexed: 12/20/2022]
Abstract
Microbial eukaryotes are key components of the ocean plankton. Yet, our understanding of their community composition and activity in different water layers of the ocean is limited, particularly for picoeukaryotes (0.2–3 µm cell size). Here, we examined the picoeukaryotic communities inhabiting different vertical zones of the tropical and subtropical global ocean: surface, deep chlorophyll maximum, mesopelagic (including the deep scattering layer and oxygen minimum zones), and bathypelagic. Communities were analysed by high-tthroughput sequencing of the 18S rRNA gene (V4 region) as represented by DNA (community structure) and RNA (metabolism), followed by delineation of Operational Taxonomic Units (OTUs) at 99% similarity. We found a stratification of the picoeukaryotic communities along the water column, with assemblages corresponding to the sunlit and dark ocean. Specific taxonomic groups either increased (e.g., Chrysophyceae or Bicosoecida) or decreased (e.g., Dinoflagellata or MAST-3) in abundance with depth. We used the rRNA:rDNA ratio of each OTU as a proxy of metabolic activity. The highest relative activity was found in the mesopelagic layer for most taxonomic groups, and the lowest in the bathypelagic. Altogether, we characterize the change in community structure and metabolic activity of picoeukaryotes with depth in the global ocean, suggesting a hotspot of activity in the mesopelagic.
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24
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