1
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Zhang H, Wang N, Zhang D, Wang F, Xu S, Ding X, Xie Y, Tian J, Li B, Cui Z, Jiang T. Composition and temporal dynamics of the phytoplankton community in Laizhou Bay revealed by microscopic observation and rbcL gene sequencing. MARINE ENVIRONMENTAL RESEARCH 2024; 202:106734. [PMID: 39244953 DOI: 10.1016/j.marenvres.2024.106734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/15/2024] [Accepted: 09/02/2024] [Indexed: 09/10/2024]
Abstract
Laizhou Bay, a major breeding ground for economic marine organisms in the northern waters of China, is facing rapid environmental degradation. In this study, field surveys in this area were conducted in the spring, summer, and autumn of 2020. Microscopic observation and RuBisCO large subunit (rbcL) gene analysis were employed to understand the community structure and temporal dynamics of phytoplankton. The phytoplankton community structures detected by the two methods showed significant differences. Microscopic observation revealed the dominance of dinoflagellates in spring that shifted to the dominance of diatoms in summer and autumn. However, rbcL gene sequencing consistently identified diatoms as dominant throughout all three seasons, with their relative abundance showing an increasing trend. Conversely, the relative abundance of the second- and third-most abundant taxa, namely, haptophytes and ochrophytes, decreased as the seasons transitioned. rbcL gene sequencing annotated more species than microscopy. It could detect haptophytes and cryptophytes, which were overlooked by microscopy. In addition, rbcL gene sequencing detected a remarkable amount of Thalassiosira profunda, which was previously unidentified in this sea area. However, it appeared to underestimate the contribution of dinoflagellates considerably, with most taxa being only identified through microscopic identification. The two methods jointly identified 28 harmful algal bloom taxa with similar detection quantities but substantial differences in species composition. Phytoplankton communities were influenced by temperature, salinity, and nutrients. The results of this work suggest that a combination of multiple techniques is necessary for a comprehensive understanding of phytoplankton.
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Affiliation(s)
- Huihui Zhang
- School of Oceanography, Yantai University, Yantai, 264005, China
| | - Nan Wang
- School of Oceanography, Yantai University, Yantai, 264005, China
| | - Di Zhang
- School of Oceanography, Yantai University, Yantai, 264005, China
| | - Fei Wang
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, China
| | - Shiji Xu
- Yantai Ocean Center, Ministry of Natural Resources, Yantai, 264006, China
| | - Xiaokun Ding
- School of Oceanography, Yantai University, Yantai, 264005, China
| | - Yixuan Xie
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Jinghuan Tian
- School of Oceanography, Yantai University, Yantai, 264005, China
| | - Bin Li
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, China
| | - Zhengguo Cui
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
| | - Tao Jiang
- School of Oceanography, Yantai University, Yantai, 264005, China.
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2
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Mak EWK, Turk‐Kubo KA, Caron DA, Harbeitner RC, Magasin JD, Coale TH, Hagino K, Takano Y, Nishimura T, Adachi M, Zehr JP. Phagotrophy in the nitrogen-fixing haptophyte Braarudosphaera bigelowii. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13312. [PMID: 39049182 PMCID: PMC11269211 DOI: 10.1111/1758-2229.13312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 06/26/2024] [Indexed: 07/27/2024]
Abstract
Biological nitrogen fixation provides fixed nitrogen for microbes living in the oligotrophic open ocean. UCYN-A2, the previously known symbiont of Braarudosphaera bigelowii, now believed to be an early-stage B. bigelowii organelle that exchanges fixed nitrogen for fixed carbon, is globally distributed. Indirect evidence suggested that B. bigelowii might be a mixotrophic (phagotrophic) phototrophic flagellate. The goal of this study was to determine if B. bigelowii can graze on bacteria using several independent approaches. The results showed that B. bigelowii grazed on co-occurring bacteria at a rate of 5-7 cells/h/B. bigelowii and that the overall grazing rate was significantly higher at nighttime than at daytime. Bacterial abundance changes, assessed with 16S rRNA gene amplicon sequencing analysis, may have indicated preferential grazing by B. bigelowii on specific bacterial genotypes. In addition, Lysotracker™ staining of B. bigelowii suggested digestive activity inside B. bigelowii. Carbon and nitrogen fixation measurements revealed that the carbon demand of B. bigelowii could not be fulfilled by photosynthesis alone, implying supplementation by heterotrophy. These independent lines of evidence together revealed that B. bigelowii engages in phagotrophy, which, beyond serving as a supplementary source of carbon and energy, may also facilitate the indirect assimilation of inorganic nutrients.
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Affiliation(s)
| | | | - David A. Caron
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | | | | | - Tyler H. Coale
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
| | - Kyoko Hagino
- Marine Core Research InstituteKochi UniversityNankokuJapan
| | | | - Tomohiro Nishimura
- Faculty of Agriculture and Marine ScienceKochi UniversityNankokuJapan
- Fisheries Technology Institute, Japan Fisheries Research and Education AgencyHiroshimaJapan
| | - Masao Adachi
- Faculty of Agriculture and Marine ScienceKochi UniversityNankokuJapan
| | - Jonathan P. Zehr
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
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3
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Edwards KF, Rii YM, Li Q, Peoples LM, Church MJ, Steward GF. Trophic strategies of picoeukaryotic phytoplankton vary over time and with depth in the North Pacific Subtropical Gyre. Environ Microbiol 2024; 26:e16689. [PMID: 39168489 DOI: 10.1111/1462-2920.16689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 07/26/2024] [Indexed: 08/23/2024]
Abstract
In oligotrophic oceans, the smallest eukaryotic phytoplankton are both significant primary producers and predators of abundant bacteria such as Prochlorococcus. However, the drivers and consequences of community dynamics among these diverse protists are not well understood. Here, we investigated how trophic strategies along the autotrophy-mixotrophy spectrum vary in importance over time and across depths at Station ALOHA in the North Pacific Subtropical Gyre. We combined picoeukaryote community composition from a 28-month time-series with traits of diverse phytoplankton isolates from the same location, to examine trophic strategies across 13 operational taxonomic units and 8 taxonomic classes. We found that autotrophs and slower-grazing mixotrophs tended to prevail deeper in the photic zone, while the most voracious mixotrophs were relatively abundant near the surface. Within the mixed layer, there was greater phagotrophy when conditions were most stratified and when Chl a concentrations were lowest, although the greatest temporal variation in trophic strategy occurred at intermediate depths (45-100 m). Dynamics at this site are consistent with previously described spatial patterns of trophic strategies. The success of relatively phagotrophic phytoplankton at shallower depths in the most stratified waters suggests that phagotrophy is a competitive strategy for acquiring nutrients when energy from light is plentiful.
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Affiliation(s)
- Kyle F Edwards
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| | - Yoshimi M Rii
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, USA
| | - Qian Li
- School of Oceanography, Shanghai Jiao Tong University, Shanghai Shi, China
| | - Logan M Peoples
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Matthew J Church
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Grieg F Steward
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, and Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
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4
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Cornejo-Castillo FM, Inomura K, Zehr JP, Follows MJ. Metabolic trade-offs constrain the cell size ratio in a nitrogen-fixing symbiosis. Cell 2024; 187:1762-1768.e9. [PMID: 38471501 DOI: 10.1016/j.cell.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 10/06/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Biological dinitrogen (N2) fixation is a key metabolic process exclusively performed by prokaryotes, some of which are symbiotic with eukaryotes. Species of the marine haptophyte algae Braarudosphaera bigelowii harbor the N2-fixing endosymbiotic cyanobacteria UCYN-A, which might be evolving organelle-like characteristics. We found that the size ratio between UCYN-A and their hosts is strikingly conserved across sublineages/species, which is consistent with the size relationships of organelles in this symbiosis and other species. Metabolic modeling showed that this size relationship maximizes the coordinated growth rate based on trade-offs between resource acquisition and exchange. Our findings show that the size relationships of N2-fixing endosymbionts and organelles in unicellular eukaryotes are constrained by predictable metabolic underpinnings and that UCYN-A is, in many regards, functioning like a hypothetical N2-fixing organelle (or nitroplast).
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Affiliation(s)
- Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona 08003, Spain; Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA.
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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5
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Beckett SJ, Demory D, Coenen AR, Casey JR, Dugenne M, Follett CL, Connell P, Carlson MCG, Hu SK, Wilson ST, Muratore D, Rodriguez-Gonzalez RA, Peng S, Becker KW, Mende DR, Armbrust EV, Caron DA, Lindell D, White AE, Ribalet F, Weitz JS. Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre. Nat Commun 2024; 15:2105. [PMID: 38453897 PMCID: PMC10920773 DOI: 10.1038/s41467-024-46165-3] [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: 05/15/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
Photosynthesis fuels primary production at the base of marine food webs. Yet, in many surface ocean ecosystems, diel-driven primary production is tightly coupled to daily loss. This tight coupling raises the question: which top-down drivers predominate in maintaining persistently stable picocyanobacterial populations over longer time scales? Motivated by high-frequency surface water measurements taken in the North Pacific Subtropical Gyre (NPSG), we developed multitrophic models to investigate bottom-up and top-down mechanisms underlying the balanced control of Prochlorococcus populations. We find that incorporating photosynthetic growth with viral- and predator-induced mortality is sufficient to recapitulate daily oscillations of Prochlorococcus abundances with baseline community abundances. In doing so, we infer that grazers in this environment function as the predominant top-down factor despite high standing viral particle densities. The model-data fits also reveal the ecological relevance of light-dependent viral traits and non-canonical factors to cellular loss. Finally, we leverage sensitivity analyses to demonstrate how variation in life history traits across distinct oceanic contexts, including variation in viral adsorption and grazer clearance rates, can transform the quantitative and even qualitative importance of top-down controls in shaping Prochlorococcus population dynamics.
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Affiliation(s)
- Stephen J Beckett
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Biology, University of Maryland, College Park, MD, USA.
| | - David Demory
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Sorbonne Université, CNRS, USR 3579, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France.
| | - Ashley R Coenen
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - John R Casey
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Mathilde Dugenne
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Sorbonne Université, CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer (LOV), Villefranche-sur-Mer, France
| | - Christopher L Follett
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Paige Connell
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Biology Department, San Diego Mesa College, San Diego, CA, USA
| | - Michael C G Carlson
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Sarah K Hu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Oceanography, Texas A&M University, College Station, TX, USA
| | - Samuel T Wilson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Muratore
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Santa Fe Institute, Santa Fe, NM, USA
| | | | - Shengyun Peng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Adobe, San Jose, CA, USA
| | - Kevin W Becker
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | | | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Debbie Lindell
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Angelicque E White
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - François Ribalet
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Biology, University of Maryland, College Park, MD, USA.
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA.
- Institut de Biologie, École Normale Supérieure, Paris, France.
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6
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Cai L, Li H, Deng J, Zhou R, Zeng Q. Biological interactions with Prochlorococcus: implications for the marine carbon cycle. Trends Microbiol 2024; 32:280-291. [PMID: 37722980 DOI: 10.1016/j.tim.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023]
Abstract
The unicellular picocyanobacterium Prochlorococcus is the most abundant photoautotroph and contributes substantially to global CO2 fixation. In the vast euphotic zones of the open ocean, Prochlorococcus converts CO2 into organic compounds and supports diverse organisms, forming an intricate network of interactions that regulate the magnitude of carbon cycling and storage in the ocean. An understanding of the biological interactions with Prochlorococcus is critical for accurately estimating the contributions of Prochlorococcus and interacting organisms to the marine carbon cycle. This review synthesizes the primary production contributed by Prochlorococcus in the global ocean. We outline recent progress on the interactions of Prochlorococcus with heterotrophic bacteria, phages, and grazers that multifacetedly determine Prochlorococcus carbon production and fate. We discuss that climate change might affect the biological interactions with Prochlorococcus and thus the marine carbon cycle.
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Affiliation(s)
- Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Haofu Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China
| | - Junwei Deng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ruiqian Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China; Center for Ocean Research in Hong Kong and Macau, The Hong Kong University of Science and Technology, Hong Kong, China.
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7
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Thompson AW, Nyerges G, Lamberson KM, Sutherland KR. Ubiquitous filter feeders shape open ocean microbial community structure and function. PNAS NEXUS 2024; 3:pgae091. [PMID: 38505693 PMCID: PMC10949910 DOI: 10.1093/pnasnexus/pgae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/13/2024] [Indexed: 03/21/2024]
Abstract
The mechanism of mortality plays a large role in how microorganisms in the open ocean contribute to global energy and nutrient cycling. Salps are ubiquitous pelagic tunicates that are a well-known mortality source for large phototrophic microorganisms in coastal and high-latitude systems, but their impact on the immense populations of smaller prokaryotes in the tropical and subtropical open ocean gyres is not well quantified. We used robustly quantitative techniques to measure salp clearance and enrichment of specific microbial functional groups in the North Pacific Subtropical Gyre, one of the largest ecosystems on Earth. We discovered that salps are a previously unknown predator of the globally abundant nitrogen fixer Crocosphaera; thus, salps restrain new nitrogen delivery to the marine ecosystem. We show that the ocean's two numerically dominant cells, Prochlorococcus and SAR11, are not consumed by salps, which offers a new explanation for the dominance of small cells in open ocean systems. We also identified a double bonus for Prochlorococcus, wherein it not only escapes salp predation but the salps also remove one of its major mixotrophic predators, the prymnesiophyte Chrysochromulina. When we modeled the interaction between salp mesh and particles, we found that cell size alone could not account for these prey selection patterns. Instead, the results suggest that alternative mechanisms, such as surface property, shape, nutritional quality, or even prey behavior, determine which microbial cells are consumed by salps. Together, these results identify salps as a major factor in shaping the structure, function, and ecology of open ocean microbial communities.
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Affiliation(s)
- Anne W Thompson
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Györgyi Nyerges
- Department of Biology, Pacific University, Forest Grove, OR 97116, USA
| | - Kylee M Lamberson
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
| | - Kelly R Sutherland
- Oregon Institute of Marine Biology, University of Oregon, Eugene, OR 97403, USA
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8
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Safonov P, Berdieva M, Nassonova E, Skarlato S, Pozdnyakov I. The first arctic strain of Rhizochromulina: Morphology, ultrastructure, and position in the evolutionary tree of the order Rhizochromulinales (Heterokontophyta, Dictyochophyceae). Eur J Protistol 2024; 92:126050. [PMID: 38150922 DOI: 10.1016/j.ejop.2023.126050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 12/29/2023]
Abstract
Rhizochromulina marina is a unicellular amoeboid alga capable of forming flagellate cells; it is a single validly named species in the genus. Besides, there are numerous environmental sequences and undescribed strains designated as Rhizochromulina sp. or R. marina. The biogeography of the genus is understudied: rhizochromulines from the Indian, Southern, and Arctic Oceans are unknown. Here, we present the description of Rhizochromulina sp. B44, which was for the first time isolated from an arctic habitat. Biofilms of this microalga grow at the bottom of a culture vessel, where neighbouring amoeboid cells form associations through a common network of pseudopodia, i.e. meroplasmodia. Pseudopodia branch, anastomose mainly during meroplasmodia formation, and are supported by microtubules that arise from the perinuclear zone. Actin filaments are localized in the cytoplasm and can be revealed only near the bases of pseudopodia. We succeeded in inducing the transformation of amoeboid cells into flagellates using a prolonged agitation of cultures. Morphological and molecular analyses revealed that the studied strain is most closely related to the type strain of R. marina. At the same time, 18S rDNA sequences of early branching-off rhizochromulinids differ significantly from Rhizochromulina sp. B44, suggesting a high divergence at the genus level.
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Affiliation(s)
- Pavel Safonov
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia.
| | - Mariia Berdieva
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia
| | - Elena Nassonova
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia; Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Sergei Skarlato
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia
| | - Ilya Pozdnyakov
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia
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9
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Yue Y, Liu C, Xu B, Wang Y, Lv Q, Zhou Z, Li R, Kowalchuk GA, Jousset A, Shen Q, Xiong W. Rhizosphere shapes the associations between protistan predators and bacteria within microbiomes through the deterministic selection on bacterial communities. Environ Microbiol 2023; 25:3623-3629. [PMID: 37849426 DOI: 10.1111/1462-2920.16528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
The assembly of bacterial communities in the rhizosphere is well-documented and plays a crucial role in supporting plant performance. However, we have limited knowledge of how plant rhizosphere determines the assembly of protistan predators and whether the potential associations between protistan predators and bacterial communities shift due to rhizosphere selection. To address this, we examined bacterial and protistan taxa from 443 agricultural soil samples including bulk and rhizosphere soils. Our results presented distinct patterns of bacteria and protistan predators in rhizosphere microbiome assembly. Community assembly of protistan predators was determined by a stochastic process in the rhizosphere and the diversity of protistan predators was reduced in the rhizosphere compared to bulk soils, these may be attributed to the indirect impacts from the altered bacterial communities that showed deterministic process assembly in the rhizosphere. Interestingly, we observed that the plant rhizosphere facilitates more close interrelationships between protistan predators and bacterial communities, which might promote a healthy rhizosphere microbial community for plant growth. Overall, our findings indicate that the potential predator-prey relationships within the microbiome, mediated by plant rhizosphere, might contribute to plant performance in agricultural ecosystems.
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Affiliation(s)
- Yang Yue
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Chen Liu
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Boting Xu
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yijin Wang
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qihui Lv
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zeyuan Zhou
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Rong Li
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Alexandre Jousset
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Wu Xiong
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
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10
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Robicheau BM, Tolman J, Desai D, LaRoche J. Microevolutionary patterns in ecotypes of the symbiotic cyanobacterium UCYN-A revealed from a Northwest Atlantic coastal time series. SCIENCE ADVANCES 2023; 9:eadh9768. [PMID: 37774025 PMCID: PMC10541017 DOI: 10.1126/sciadv.adh9768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/28/2023] [Indexed: 10/01/2023]
Abstract
UCYN-A is a globally important nitrogen-fixing symbiotic microbe often found in colder regions and coastal areas where nitrogen fixation has been overlooked. We present a 3-year coastal Northwest Atlantic time series of UCYN-A by integrating oceanographic data with weekly nifH and16S rRNA gene sequencing and quantitative PCR assays for UCYN-A ecotypes. High UCYN-A relative abundances dominated by A1 to A4 ecotypes reoccurred annually in the coastal Northwest Atlantic. Although UCYN-A was detected every summer/fall, the ability to observe separate ecotypes may be highly dependent on sampling time given intense interannual and weekly variability of ecotype-specific occurrences. Additionally, much of UCYN-A's rarer diversity was populated by short-lived neutral mutational variants, therefore providing insight into UCYN-A's microevolutionary patterns. For instance, rare ASVs exhibited community composition restructuring annually, while also sharing a common connection to a dominant ASV within each ecotype. Our study provides additional perspectives for interpreting UCYN-A intraspecific diversity and underscores the need for high-resolution datasets when deciphering spatiotemporal ecologies within UCYN-A.
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Affiliation(s)
- Brent M. Robicheau
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Integrated Microbiome Resource, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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11
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Ban H, Sato S, Yoshikawa S, Yamada K, Nakamura Y, Ichinomiya M, Sato N, Blanc-Mathieu R, Endo H, Kuwata A, Ogata H. Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs. Commun Biol 2023; 6:697. [PMID: 37420035 PMCID: PMC10328945 DOI: 10.1038/s42003-023-05002-x] [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: 10/13/2022] [Accepted: 05/31/2023] [Indexed: 07/09/2023] Open
Abstract
The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.
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Affiliation(s)
- Hiroki Ban
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Shinya Sato
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Shinya Yoshikawa
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Kazumasa Yamada
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Yoji Nakamura
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Mutsuo Ichinomiya
- Prefectural University of Kumamoto, 3-1-100 Tsukide, Kumamoto, 862-8502, Japan
| | - Naoki Sato
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Akira Kuwata
- Shiogama field station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama-cho, Shiogama, Miyagi, Japan.
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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12
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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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13
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Mayers KMJ, Kuhlisch C, Basso JTR, Saltvedt MR, Buchan A, Sandaa RA. Grazing on Marine Viruses and Its Biogeochemical Implications. mBio 2023; 14:e0192121. [PMID: 36715508 PMCID: PMC9973340 DOI: 10.1128/mbio.01921-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Viruses are the most abundant biological entities in the ocean and show great diversity in terms of size, host specificity, and infection cycle. Lytic viruses induce host cell lysis to release their progeny and thereby redirect nutrients from higher to lower trophic levels. Studies continue to show that marine viruses can be ingested by nonhost organisms. However, not much is known about the role of viral particles as a nutrient source and whether they possess a nutritional value to the grazing organisms. This review seeks to assess the elemental composition and biogeochemical relevance of marine viruses, including roseophages, which are a highly abundant group of bacteriophages in the marine environment. We place a particular emphasis on the phylum Nucleocytoviricota (NCV) (formerly known as nucleocytoplasmic large DNA viruses [NCLDVs]), which comprises some of the largest viral particles in the marine plankton that are well in the size range of prey for marine grazers. Many NCVs contain lipid membranes in their capsid that are rich carbon and energy sources, which further increases their nutritional value. Marine viruses may thus be an important nutritional component of the marine plankton, which can be reintegrated into the classical food web by nonhost organism grazing, a process that we coin the "viral sweep." Possibilities for future research to resolve this process are highlighted and discussed in light of current technological advancements.
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Affiliation(s)
- Kyle M. J. Mayers
- Environment and Climate Division, NORCE Norwegian Research Centre, Bergen, Norway
| | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jonelle T. R. Basso
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
| | | | - Alison Buchan
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA
| | - Ruth-Anne Sandaa
- Department of Microbiology, University of Bergen, Bergen, Norway
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14
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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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15
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Thompson AW, Sweeney CP, Sutherland KR. Selective and differential feeding on marine prokaryotes by mucous mesh feeders. Environ Microbiol 2023; 25:880-893. [PMID: 36594240 DOI: 10.1111/1462-2920.16334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Microbial mortality impacts the structure of food webs, carbon flow, and the interactions that create dynamic patterns of abundance across gradients in space and time in diverse ecosystems. In the oceans, estimates of microbial mortality by viruses, protists, and small zooplankton do not account fully for observations of loss, suggesting the existence of underappreciated mortality sources. We examined how ubiquitous mucous mesh feeders (i.e. gelatinous zooplankton) could contribute to microbial mortality in the open ocean. We coupled capture of live animals by blue-water diving to sequence-based approaches to measure the enrichment and selectivity of feeding by two coexisting mucous grazer taxa (pteropods and salps) on numerically dominant marine prokaryotes. We show that mucous mesh grazers consume a variety of marine prokaryotes and select between coexisting lineages and similar cell sizes. We show that Prochlorococcus may evade filtration more than other cells and that planktonic archaea are consumed by macrozooplanktonic grazers. Discovery of these feeding relationships identifies a new source of mortality for Earth's dominant marine microbes and alters our understanding of how top-down processes shape microbial community and function.
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Affiliation(s)
- Anne W Thompson
- Department of Biology, Portland State University, Portland, Oregon, USA
| | - Carey P Sweeney
- Department of Biology, Portland State University, Portland, Oregon, USA
| | - Kelly R Sutherland
- Oregon Institute of Marine Biology, University of Oregon, Eugene, Oregon, USA
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16
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Broad phylogenetic and functional diversity among mixotrophic consumers of Prochlorococcus. THE ISME JOURNAL 2022; 16:1557-1569. [PMID: 35145244 PMCID: PMC9122939 DOI: 10.1038/s41396-022-01204-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 11/26/2022]
Abstract
Small eukaryotic phytoplankton are major contributors to global primary production and marine biogeochemical cycles. Many taxa are thought to be mixotrophic, but quantitative studies of phagotrophy exist for very few. In addition, little is known about consumers of Prochlorococcus, the abundant cyanobacterium at the base of oligotrophic ocean food webs. Here we describe thirty-nine new phytoplankton isolates from the North Pacific Subtropical Gyre (Station ALOHA), all flagellates ~2–5 µm diameter, and we quantify their ability to graze Prochlorococcus. The mixotrophs are from diverse classes (dictyochophytes, haptophytes, chrysophytes, bolidophytes, a dinoflagellate, and a chlorarachniophyte), many from previously uncultured clades. Grazing ability varied substantially, with specific clearance rate (volume cleared per body volume) varying over ten-fold across isolates and six-fold across genera. Slower grazers tended to create more biovolume per prey biovolume consumed. Using qPCR we found that the haptophyte Chrysochromulina was most abundant among the isolated mixotrophs at Station ALOHA, with 76–250 cells mL−1 across depths in the upper euphotic zone (5–100 m). Our results show that within a single ecosystem the phototrophs that ingest bacteria come from many branches of the eukaryotic tree, and are functionally diverse, indicating a broad range of strategies along the spectrum from phototrophy to phagotrophy.
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17
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Potvin M, Rautio M, Lovejoy C. Freshwater Microbial Eukaryotic Core Communities, Open-Water and Under-Ice Specialists in Southern Victoria Island Lakes (Ekaluktutiak, NU, Canada). Front Microbiol 2022; 12:786094. [PMID: 35222298 PMCID: PMC8873588 DOI: 10.3389/fmicb.2021.786094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Across much of the Arctic, lakes and ponds dominate the landscape. Starting in late September, the lakes are covered in ice, with ice persisting well into June or early July. In summer, the lakes are highly productive, supporting waterfowl and fish populations. However, little is known about the diversity and ecology of microscopic life in the lakes that influence biogeochemical cycles and contribute to ecosystem services. Even less is known about the prevalence of species that are characteristic of the seasons or whether some species persist year-round under both ice cover and summer open-water conditions. To begin to address these knowledge gaps, we sampled 10 morphometrically diverse lakes in the region of Ekaluktutiak (Cambridge Bay), on southern Victoria Island (NU, Canada). We focused on Greiner Lake, the lakes connected to it, isolated ponds, and two nearby larger lakes outside the Greiner watershed. The largest lakes sampled were Tahiryuaq (Ferguson Lake) and the nearby Spawning Lake, which support commercial sea-run Arctic char (Salvelinus alpinus) fisheries. Samples for nucleic acids were collected from the lakes along with limnological metadata. Microbial eukaryotes were identified with high-throughput amplicon sequencing targeting the V4 region of the 18S rRNA gene. Ciliates, dinoflagellates, chrysophytes, and cryptophytes dominated the lake assemblages. A Bray–Curtis dissimilarity matrix separated communities into under-ice and open-water clusters, with additional separation by superficial lake area. In all, 133 operational taxonomic units (OTUs) occurred either in all under-ice or all open-water samples and were considered “core” microbial species or ecotypes. These were further characterized as seasonal indicators. Ten of the OTUs were characteristic of all lakes and all seasons sampled. Eight of these were cryptophytes, suggesting diverse functional capacity within the lineage. The core open-water indicators were mostly chrysophytes, with a few ciliates and uncharacterized Cercozoa, suggesting that summer communities are mixotrophic with contributions by heterotrophic taxa. The core under-ice indicators included a dozen ciliates along with chrysophytes, cryptomonads, and dinoflagellates, indicating a more heterotrophic community augmented by mixotrophic taxa in winter.
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Affiliation(s)
- Marianne Potvin
- Département de Biologie, Québec Océan, and Institut Intégrative et des Systèmes (IBIS), Université Laval, Quebec, QC, Canada
| | - Milla Rautio
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
- Groupe de Recherche Interuniversitaire de Limnologie (GRIL), Montreal, QC, Canada
- Center D’Études Nordiques (CEN), Quebec, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Québec Océan, and Institut Intégrative et des Systèmes (IBIS), Université Laval, Quebec, QC, Canada
- *Correspondence: Connie Lovejoy,
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18
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Sun P, Liao Y, Wang Y, Yang EJ, Jiao N, Lee Y, Jung J, Cho KH, Moon JK, Xu D. Contrasting Community Composition and Co-Occurrence Relationships of the Active Pico-Sized Haptophytes in the Surface and Subsurface Chlorophyll Maximum Layers of the Arctic Ocean in Summer. Microorganisms 2022; 10:248. [PMID: 35208705 PMCID: PMC8877492 DOI: 10.3390/microorganisms10020248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/10/2022] Open
Abstract
Haptophytes (Hacrobia: Haptophyta), which can perform phototrophic, phagotrophic, or mixotrophic nutritional modes, are critical for element cycling in a variety of aquatic ecosystems. However, their diversity, particularly in the changing Arctic Ocean (AO), remains largely unknown. In the present study, the biodiversity, community composition, and co-occurrence networks of pico-sized haptophytes in the surface water and subsurface chlorophyll maximum (SCM) layer of the AO were explored. Our results found higher alpha diversity estimates in the surface water compared with in the SCM based on high-throughput sequencing of haptophyte specific 18S rRNA. The community composition of the surface water was significantly different from that of the SCM, and water temperature was identified as the primary factor shaping the community compositions. Prymnesiales (mostly Chrysochromulina), uncultured Prymnesiophyceae, and Phaeocystis dominated the surface water communities, whereas Phaeocystis dominated the SCM communities, followed by Chrysochromulina, uncultured Prymnesiophyceae, and the remaining taxa. The communities of the surface water and SCM layer developed relatively independent modules in the metacommunity network. Nodes in the surface water were more closely connected to one another than those in the SCM. Network stability analysis revealed that surface water networks were more stable than SCM networks. These findings suggest that SCM communities are more susceptible to environmental fluctuations than those in surface water and that future global changes (e.g., global warming) may profoundly influence the development, persistence, and service of SCM in the AO.
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Affiliation(s)
- Ping Sun
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Yuyu Liao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Kyoung-Ho Cho
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Jong-Kuk Moon
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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19
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Microbial Plankton Community Structure and Function Responses to Vitamin B 12 and B 1 Amendments in an Upwelling System. Appl Environ Microbiol 2021; 87:e0152521. [PMID: 34495690 PMCID: PMC8552899 DOI: 10.1128/aem.01525-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
B vitamins are essential cofactors for practically all living organisms on Earth and are produced by a selection of microorganisms. An imbalance between high demand and limited production, in concert with abiotic processes, may explain the low availability of these vitamins in marine systems. Natural microbial communities from surface shelf water in the productive area off northwestern Spain were enclosed in mesocosms in winter, spring, and summer 2016. In order to explore the impact of B-vitamin availability on microbial community composition (16S and 18S rRNA gene sequence analysis) and bacterial function (metatranscriptomics analysis) in different seasons, enrichment experiments were conducted with seawater from the mesocosms. Our findings revealed that significant increases in phytoplankton or prokaryote biomass associated with vitamin B12 and/or B1 amendments were not accompanied by significant changes in community composition, suggesting that most of the microbial taxa benefited from the external B-vitamin supply. Metatranscriptome analysis suggested that many bacteria were potential consumers of vitamins B12 and B1, although the relative abundance of reads related to synthesis was ca. 3.6-fold higher than that related to uptake. Alteromonadales and Oceanospirillales accounted for important portions of vitamin B1 and B12 synthesis gene transcription, despite accounting for only minor portions of the bacterial community. Flavobacteriales appeared to be involved mostly in vitamin B12 and B1 uptake, and Pelagibacterales expressed genes involved in vitamin B1 uptake. Interestingly, the relative expression of vitamin B12 and B1 synthesis genes among bacteria strongly increased upon inorganic nutrient amendment. Collectively, these findings suggest that upwelling events intermittently occurring during spring and summer in productive ecosystems may ensure an adequate production of these cofactors to sustain high levels of phytoplankton growth and biomass. IMPORTANCE B vitamins are essential growth factors for practically all living organisms on Earth that are produced by a selection of microorganisms. An imbalance between high demand and limited production may explain the low concentration of these compounds in marine systems. In order to explore the impact of B-vitamin availability on bacteria and algae in the coastal waters off northwestern Spain, six experiments were conducted with natural surface water enclosed in winter, spring, and summer. Our findings revealed that increases in phytoplankton or bacterial growth associated with B12 and/or B1 amendments were not accompanied by significant changes in community composition, suggesting that most microorganisms benefited from the B-vitamin supply. Our analyses confirmed the role of many bacteria as consumers of vitamins B12 and B1, although the relative abundance of genes related to synthesis was ca. 3.6-fold higher than that related to uptake. Interestingly, prokaryote expression of B12 and B1 synthesis genes strongly increased when inorganic nutrients were added. Collectively, these findings suggest that upwelling of cold and nutrient-rich waters occurring during spring and summer in this coastal area may ensure an adequate production of B vitamins to sustain high levels of algae growth and biomass.
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20
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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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21
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Sandaa RA, Saltvedt MR, Dahle H, Wang H, Våge S, Blanc-Mathieu R, Steen IH, Grimsley N, Edvardsen B, Ogata H, Lawrence J. Adaptive evolution of viruses infecting marine microalgae (haptophytes), from acute infections to stable coexistence. Biol Rev Camb Philos Soc 2021; 97:179-194. [PMID: 34514703 DOI: 10.1111/brv.12795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022]
Abstract
Collectively known as phytoplankton, photosynthetic microbes form the base of the marine food web, and account for up to half of the primary production on Earth. Haptophytes are key components of this phytoplankton community, playing important roles both as primary producers and as mixotrophs that graze on bacteria and protists. Viruses influence the ecology and diversity of phytoplankton in the ocean, with the majority of microalgae-virus interactions described as 'boom and bust' dynamics, which are characteristic of acute virus-host systems. Most haptophytes are, however, part of highly diverse communities and occur at low densities, decreasing their chance of being infected by viruses with high host specificity. Viruses infecting these microalgae have been isolated in the laboratory, and there are several characteristics that distinguish them from acute viruses infecting bloom-forming haptophytes. Herein we synthesise what is known of viruses infecting haptophyte hosts in the ocean, discuss the adaptive evolution of haptophyte-infecting viruses -from those that cause acute infections to those that stably coexist with their host - and identify traits of importance for successful survival in the ocean.
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Affiliation(s)
- Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Marius R Saltvedt
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Haina Wang
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Selina Våge
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Romain Blanc-Mathieu
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Université Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, Postbox 7803, N-5020, Bergen, Norway
| | - Nigel Grimsley
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Bente Edvardsen
- Department of Biosciences, University of Oslo, Postbox 1066, N-0316, Oslo, Norway
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Janice Lawrence
- Biology Department, University of New Brunswick, PO Box 4400, Fredericton, NB, E3B 5A3, Canada
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22
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Dutkiewicz S, Boyd PW, Riebesell U. Exploring biogeochemical and ecological redundancy in phytoplankton communities in the global ocean. GLOBAL CHANGE BIOLOGY 2021; 27:1196-1213. [PMID: 33342048 PMCID: PMC7986797 DOI: 10.1111/gcb.15493] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 06/01/2023]
Abstract
Climate-change-induced alterations of oceanic conditions will lead to the ecological niches of some marine phytoplankton species disappearing, at least regionally. How will such losses affect the ecosystem and the coupled biogeochemical cycles? Here, we couch this question in terms of ecological redundancy (will other species be able to fill the ecological roles of the extinct species) and biogeochemical redundancy (can other species replace their biogeochemical roles). Prior laboratory and field studies point to a spectrum in the degree of redundancy. We use a global three-dimensional computer model with diverse planktonic communities to explore these questions further. The model includes 35 phytoplankton types that differ in size, biogeochemical function and trophic strategy. We run two series of experiments in which single phytoplankton types are either partially or fully eliminated. The niches of the targeted types were not completely reoccupied, often with a reduction in the transfer of matter from autotrophs to heterotrophs. Primary production was often decreased, but sometimes increased due to reduction in grazing pressure. Complex trophic interactions (such as a decrease in the stocks of a predator's grazer) led to unexpected reshuffling of the community structure. Alterations in resource utilization may cause impacts beyond the regions where the type went extinct. Our results suggest a lack of redundancy, especially in the 'knock on' effects on higher trophic levels. Redundancy appeared lowest for types on the edges of trait space (e.g. smallest) or with unique competitive strategies. Though highly idealized, our modelling findings suggest that the results from laboratory or field studies often do not adequately capture the ramifications of functional redundancy. The modelled, often counterintuitive, responses-via complex food web interactions and bottom-up versus top-down controls-indicate that changes in planktonic community will be key determinants of future ocean global change ecology and biogeochemistry.
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Affiliation(s)
- Stephanie Dutkiewicz
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Global Change ScienceMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Philip W. Boyd
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobartTas.Australia
| | - Ulf Riebesell
- GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
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23
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Farnelid H, Turk‐Kubo K, Zehr JP. Cell sorting reveals few novel prokaryote and photosynthetic picoeukaryote associations in the oligotrophic ocean. Environ Microbiol 2021; 23:1469-1480. [PMID: 33295132 PMCID: PMC8048811 DOI: 10.1111/1462-2920.15351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/04/2020] [Indexed: 11/28/2022]
Abstract
Close associations between single-celled marine organisms can have a central role in biogeochemical processes and are of great interest for understanding the evolution of organisms. The global significance of such associations raises the question of whether unidentified associations are yet to be discovered. In this study, fluorescence-activated cell sorted photosynthetic picoeukayote (PPE) populations and single cells were analysed by sequencing of 16S rRNA genes in the oligotrophic North Pacific Subtropical Gyre. Samples were collected during two cruises, spanning depths near the deep chlorophyll maximum, where the abundance of PPEs was highest. The association between the widespread and significant nitrogen (N2 )-fixing cyanobacterium, UCYN-A and its prymnesiophyte host was prevalent in both population and single-cell sorts. Several bacterial sequences, affiliating with previously described symbiotic taxa were detected but their detection was rare and not well replicated, precluding identification of novel tightly linked species-specific associations. Similarly, no enrichment of dominant seawater taxa such as Prochlorococcus, SAR11 or Synechococcus was observed suggesting that these were not systematically ingested by the PPE in this study. The results indicate that apart from the UCYN-A symbiosis, similar tight species-specific associations with PPEs are unusual in the oligotrophic ocean.
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Affiliation(s)
- Hanna Farnelid
- Ocean Sciences DepartmentUniversity of CaliforniaSanta CruzCAUSA
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS)Linnaeus UniversityKalmarSweden
| | - Kendra Turk‐Kubo
- Ocean Sciences DepartmentUniversity of CaliforniaSanta CruzCAUSA
| | - Jonathan P. Zehr
- Ocean Sciences DepartmentUniversity of CaliforniaSanta CruzCAUSA
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24
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Zheng Q, Lin W, Wang Y, Xu D, Liu Y, Jiao N. Top-down controls on nutrient cycling and population dynamics in a model estuarine photoautotroph-heterotroph co-culture system. Mol Ecol 2020; 30:592-607. [PMID: 33226689 DOI: 10.1111/mec.15750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/05/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022]
Abstract
Viral lysis and protistan grazing are thought to be the major processes leading to microbial mortality in aquatic environments and thus regulate community diversity and biogeochemical cycling characteristics. Here, we studied nutrient cycling and bacterial responses to cyanophage-mediated photoautotroph lysis and ciliate predation in a model Synechococcus-heterotroph co-culture system. Both viral lysis and Euplotes grazing facilitated the transformation of organic carbon from biomass to dissolved organic matter with convention efficiencies of 20%-26%. The accumulation of ammonium after the addition of phages and ciliates suggested the importance of recycled NH4 + occurred in the interactions between Synechococcus growth and heterotrophic bacterial metabolism of photosynthate. The slower efficiency of P mineralization compared to N (primarily ammonium) indicated that P-containing organic matter was primarily integrated into bacterial biomass rather than being remineralized into inorganic phosphate under C-rich conditions. In the cyanophage addition treatment, both Fluviicola and Alteromonas exhibited rapid positive responses to Synechococcus lysing, while Marivita exhibited an apparent negative response. Further, the addition of Euplotes altered the incubation system from a Synechococcus-driven phycosphere to a ciliate-remodelled zoosphere that primarily constituted grazing-resistant bacteria and Euplotes symbionts. Top-down controls increased co-culture system diversity and resulted in a preference for free-living lifestyles of dominant populations, which was accompanied by the transfer of matter and energy. Our results indicate top-down control was particularly important for organic matter redistribution and inorganic nutrient regeneration between photoautotrophs and heterotrophs, and altered bacterial lifestyles. This study consequently sheds light on marine biogeochemical cycling and the interaction networks within these dynamic ecosystems.
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Affiliation(s)
- Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Wenxin Lin
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Dapeng Xu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Yanting Liu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People's Republic of China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
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25
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Mars Brisbin M, Conover AE, Mitarai S. Influence of Regional Oceanography and Hydrothermal Activity on Protist Diversity and Community Structure in the Okinawa Trough. MICROBIAL ECOLOGY 2020; 80:746-761. [PMID: 32948905 DOI: 10.1007/s00248-020-01583-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
Microbial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but the relative importance of factors shaping protist diversity, such as environmental selection and dispersal, remains difficult to parse. Water masses of a back-arc basin with hydrothermal activity provide a unique opportunity for studying the effects of dispersal and environmental selection on protist communities. In this study, we used metabarcoding to characterize protist communities in the Okinawa Trough, a back-arc spreading basin containing at least twenty-five active hydrothermal vent fields. Water was sampled from four depths at fourteen stations spanning the length of the Okinawa Trough, including three sites influenced by nearby hydrothermal vent sites. While significant differences in community structure reflecting water depth were present, protist communities were mostly homogeneous horizontally. Protist communities in the bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.
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Affiliation(s)
- Margaret Mars Brisbin
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0412, Japan.
| | - Asa E Conover
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0412, Japan
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0412, Japan
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26
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Choi CJ, Jimenez V, Needham DM, Poirier C, Bachy C, Alexander H, Wilken S, Chavez FP, Sudek S, Giovannoni SJ, Worden AZ. Seasonal and Geographical Transitions in Eukaryotic Phytoplankton Community Structure in the Atlantic and Pacific Oceans. Front Microbiol 2020; 11:542372. [PMID: 33101224 PMCID: PMC7554337 DOI: 10.3389/fmicb.2020.542372] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Much is known about how broad eukaryotic phytoplankton groups vary according to nutrient availability in marine ecosystems. However, genus- and species-level dynamics are generally unknown, although important given that adaptation and acclimation processes differentiate at these levels. We examined phytoplankton communities across seasonal cycles in the North Atlantic (BATS) and under different trophic conditions in the eastern North Pacific (ENP), using phylogenetic classification of plastid-encoded 16S rRNA amplicon sequence variants (ASVs) and other methodologies, including flow cytometric cell sorting. Prasinophytes dominated eukaryotic phytoplankton amplicons during the nutrient-rich deep-mixing winter period at BATS. During stratification (‘summer’) uncultured dictyochophytes formed ∼35 ± 10% of all surface plastid amplicons and dominated those from stramenopile algae, whereas diatoms showed only minor, ephemeral contributions over the entire year. Uncultured dictyochophytes also comprised a major fraction of plastid amplicons in the oligotrophic ENP. Phylogenetic reconstructions of near-full length 16S rRNA sequences established 11 uncultured Dictyochophyte Environmental Clades (DEC). DEC-I and DEC-VI dominated surface dictyochophytes under stratification at BATS and in the ENP, and DEC-IV was also important in the latter. Additionally, although less common at BATS, Florenciella-related clades (FC) were prominent at depth in the ENP. In both ecosystems, pelagophytes contributed notably at depth, with PEC-VIII (Pelagophyte Environmental Clade) and (cultured) Pelagomonas calceolata being most important. Q-PCR confirmed the near absence of P. calceolata at the surface of the same oligotrophic sites where it reached ∼1,500 18S rRNA gene copies ml–1 at the DCM. To further characterize phytoplankton present in our samples, we performed staining and at-sea single-cell sorting experiments. Sequencing results from these indicated several uncultured dictyochophyte clades are comprised of predatory mixotrophs. From an evolutionary perspective, these cells showed both conserved and unique features in the chloroplast genome. In ENP metatranscriptomes we observed high expression of multiple chloroplast genes as well as expression of a selfish element (group II intron) in the psaA gene. Comparative analyses across the Pacific and Atlantic sites support the conclusion that predatory dictyochophytes thrive under low nutrient conditions. The observations that several uncultured dictyochophyte lineages are seemingly capable of photosynthesis and predation, raises questions about potential shifts in phytoplankton trophic roles associated with seasonality and long-term ocean change.
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Affiliation(s)
- Chang Jae Choi
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Valeria Jimenez
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - David M Needham
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Camille Poirier
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Charles Bachy
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Harriet Alexander
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Susanne Wilken
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Francisco P Chavez
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Stephen J Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
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27
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Unusual marine cyanobacteria/haptophyte symbiosis relies on N 2 fixation even in N-rich environments. ISME JOURNAL 2020; 14:2395-2406. [PMID: 32523086 PMCID: PMC7490277 DOI: 10.1038/s41396-020-0691-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/11/2020] [Accepted: 05/27/2020] [Indexed: 12/22/2022]
Abstract
The microbial fixation of N2 is the largest source of biologically available nitrogen (N) to the oceans. However, it is the most energetically expensive N-acquisition process and is believed inhibited when less energetically expensive forms, like dissolved inorganic N (DIN), are available. Curiously, the cosmopolitan N2-fixing UCYN-A/haptophyte symbiosis grows in DIN-replete waters, but the sensitivity of their N2 fixation to DIN is unknown. We used stable isotope incubations, catalyzed reporter deposition fluorescence in-situ hybridization (CARD-FISH), and nanoscale secondary ion mass spectrometry (nanoSIMS), to investigate the N source used by the haptophyte host and sensitivity of UCYN-A N2 fixation in DIN-replete waters. We demonstrate that under our experimental conditions, the haptophyte hosts of two UCYN-A sublineages do not assimilate nitrate (NO3−) and meet little of their N demands via ammonium (NH4+) uptake. Instead the UCYN-A/haptophyte symbiosis relies on UCYN-A N2 fixation to supply large portions of the haptophyte’s N requirements, even under DIN-replete conditions. Furthermore, UCYN-A N2 fixation rates, and haptophyte host carbon fixation rates, were at times stimulated by NO3− additions in N-limited waters suggesting a link between the activities of the bulk phytoplankton assemblage and the UCYN-A/haptophyte symbiosis. The results suggest N2 fixation may be an evolutionarily viable strategy for diazotroph–eukaryote symbioses, even in N-rich coastal or high latitude waters.
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28
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Wilken S, Yung CCM, Hamilton M, Hoadley K, Nzongo J, Eckmann C, Corrochano-Luque M, Poirier C, Worden AZ. The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190090. [PMID: 31587652 PMCID: PMC6792458 DOI: 10.1098/rstb.2019.0090] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2019] [Indexed: 12/16/2022] Open
Abstract
Photosynthesis in eukaryotes first arose through phagocytotic processes wherein an engulfed cyanobacterium was not digested, but instead became a permanent organelle. Other photosynthetic lineages then arose when eukaryotic cells engulfed other already photosynthetic eukaryotic cells. Some of the resulting lineages subsequently lost their ability for phagocytosis, while many others maintained the ability to do both processes. These mixotrophic taxa have more complicated ecological roles, in that they are both primary producers and consumers that can shift more towards producing the organic matter that forms the base of aquatic food chains, or towards respiring and releasing CO2. We still have much to learn about which taxa are predatory mixotrophs as well as about the physiological consequences of this lifestyle, in part, because much of the diversity of unicellular eukaryotes in aquatic ecosystems remains uncultured. Here, we discuss existing methods for studying predatory mixotrophs, their individual biases, and how single-cell approaches can enhance knowledge of these important taxa. The question remains what the gold standard should be for assigning a mixotrophic status to ill-characterized or uncultured taxa-a status that dictates how organisms are incorporated into carbon cycle models and how their ecosystem roles may shift in future lakes and oceans. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Susanne Wilken
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090GE Amsterdam, Noord-Holland, The Netherlands
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Charmaine C. M. Yung
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24148 Kiel, Schleswig-Holstein, Germany
| | - Maria Hamilton
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Division of Physical and Biological Sciences, UC Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kenneth Hoadley
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24148 Kiel, Schleswig-Holstein, Germany
| | - Juliana Nzongo
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Division of Physical and Biological Sciences, UC Santa Cruz, Santa Cruz, CA 95064, USA
| | - Charlotte Eckmann
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Division of Physical and Biological Sciences, UC Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Camille Poirier
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24148 Kiel, Schleswig-Holstein, Germany
| | - Alexandra Z. Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24148 Kiel, Schleswig-Holstein, Germany
- Division of Physical and Biological Sciences, UC Santa Cruz, Santa Cruz, CA 95064, USA
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29
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Sebastián M, Gasol JM. Visualization is crucial for understanding microbial processes in the ocean. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190083. [PMID: 31587650 PMCID: PMC6792457 DOI: 10.1098/rstb.2019.0083] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2019] [Indexed: 12/17/2022] Open
Abstract
Recent developments in community and single-cell genomic approaches have provided an unprecedented amount of information on the ecology of microbes in the aquatic environment. However, linkages between each specific microbe's identity and their in situ level of activity (be it growth, division or just metabolic activity) are much more scarce. The ultimate goal of marine microbial ecology is to understand how the environment determines the types of different microbes in nature, their function, morphology and cell-to-cell interactions and to do so we should gather three levels of information, the genomic (including identity), the functional (activity or growth), and the morphological, and for as many individual cells as possible. We present a brief overview of methodologies applied to address single-cell activity in marine prokaryotes, together with a discussion of the difficulties in identifying and categorizing activity and growth. We then provide and discuss some examples showing how visualization has been pivotal for challenging established paradigms and for understanding the role of microbes in the environment, unveiling processes and interactions that otherwise would have been overlooked. We conclude by stating that more effort should be directed towards integrating visualization in future approaches if we want to gain a comprehensive insight into how microbes contribute to the functioning of ecosystems. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Marta Sebastián
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria (ULPGC), Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, Western Australia, Australia
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30
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Chan YF, Chiang KP, Ku Y, Gong GC. Abiotic and Biotic Factors Affecting the Ingestion Rates of Mixotrophic Nanoflagellates (Haptophyta). MICROBIAL ECOLOGY 2019; 77:607-615. [PMID: 30187089 DOI: 10.1007/s00248-018-1249-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
Mixotrophic haptophytes comprise one of several important groups of mixotrophic nanoflagellates in the pelagic environment. This study aimed to investigate if phagotrophy in mixotrophic haptophytes is regulated by light or other factors in the surface (SE) and bottom (BE) of the euphotic zone in the subtropical northwestern Pacific Ocean. We estimated the rates of bacterial ingestion by haptophytes using fluorescently labeled bacteria (FLBs) and fluorescence in situ hybridization. Haptophyte diversity and abundance were also investigated in the same sampling area. The annual mean abundance of haptophytes was 419 ± 85.6 cells mL-1 in both SE and BE. Cells 3-5 μm in size were the dominant group in all haptophytes and accounted for majority of bacteria standing stock removed by haptophytes (53%). Most haptophyte ingestion rates (IRs) were not significantly different between the two layers (average SE ingestion rate: 12.5 ± 2.29 bac Hap-1 h-1; BE: 14.7 ± 3.03 bac Hap-1 h-1). Furthermore, the haptophyte IRs were negatively correlated with nitrate concentrations in the SE and positively correlated with bacterial abundances in the BE, which accounts for the significantly high IRs in August 2012 and 2013. These findings imply that mixotrophic haptophytes in this region had different factors affecting phagotrophy to adapt to the ambient light intensity alterations between SE and BE.
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Affiliation(s)
- Ya-Fan Chan
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Kuo-Ping Chiang
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 202-24, Taiwan.
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 202-24, Taiwan.
| | - Yun Ku
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 202-24, Taiwan
| | - Gwo-Ching Gong
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 202-24, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 202-24, Taiwan
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31
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Otwell AE, López García de Lomana A, Gibbons SM, Orellana MV, Baliga NS. Systems biology approaches towards predictive microbial ecology. Environ Microbiol 2018; 20:4197-4209. [DOI: 10.1111/1462-2920.14378] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 01/17/2023]
Affiliation(s)
| | | | - Sean M. Gibbons
- Institute for Systems Biology Seattle WA USA
- eScience Institute, University of Washington Seattle WA USA
- Molecular and Cellular Biology Program University of Washington Seattle WA USA
| | - Mónica V. Orellana
- Institute for Systems Biology Seattle WA USA
- Polar Science Center Applied Physics Lab, University of Washington Seattle WA
| | - Nitin S. Baliga
- Institute for Systems Biology Seattle WA USA
- Molecular and Cellular Biology Program University of Washington Seattle WA USA
- Departments of Biology and Microbiology University of Washington Seattle WA USA
- Lawrence Berkeley National Lab Berkeley CA USA
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32
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Mangot JF, Forn I, Obiol A, Massana R. Constant abundances of ubiquitous uncultured protists in the open sea assessed by automated microscopy. Environ Microbiol 2018; 20:3876-3889. [PMID: 30209866 DOI: 10.1111/1462-2920.14408] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/06/2018] [Accepted: 09/08/2018] [Indexed: 11/28/2022]
Abstract
Protists have fundamental ecological roles in marine environments and their diversity is being increasingly explored, yet little is known about the quantitative importance of specific taxa in these ecosystems. Here we optimized a newly developed automated system of image acquisition and image analysis to enumerate minute uncultured cells of different sizes targeted by fluorescence in situ hybridization. The automated counting routine was highly reproducible, well correlated with manual counts, and was then applied on surface and deep chlorophyll maximum samples from the Malaspina 2010 circumnavigation. The three targeted uncultured taxa (MAST-4, MAST-7 and MAST-1C) were found in virtually all samples from several ocean basins (Atlantic, Indian and Pacific) in fairly constant cell abundances, following typical lognormal distributions. Their global abundances averaged 49, 23 and 7 cells ml-1 , respectively, and altogether the three groups accounted for about 10%-20% of heterotrophic picoeukaryotes. Our innovative high-throughput cell counting routine allows for the first time a direct assessment of the biogeographic distribution of small protists (< 5 μm) and shows the ubiquity in sunlit oceans of three bacterivorous taxa, suggesting their key roles in marine ecosystems.
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Affiliation(s)
- Jean-François Mangot
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), E-08003 Barcelona, Catalonia, Spain
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), E-08003 Barcelona, Catalonia, Spain
| | - Aleix Obiol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), E-08003 Barcelona, Catalonia, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), E-08003 Barcelona, Catalonia, Spain
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33
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Wilhelm RC, Hanson BT, Chandra S, Madsen E. Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater. Environ Microbiol 2018; 20:3543-3559. [PMID: 30051558 DOI: 10.1111/1462-2920.14309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022]
Abstract
Earlier research on the biogeochemical factors affecting natural attenuation in coal-tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field-based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single-cell imaging and shotgun metagenomics now provide cultivation-independent tools for their study. We tracked carbon from 13 C-labelled naphthalene through microbial populations in contaminated surface sediments over 6 days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant-based trophic web. Contaminant-exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome-assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.
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Affiliation(s)
- Roland C Wilhelm
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Buck T Hanson
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Subhash Chandra
- Cornell SIMS Laboratory, Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Eugene Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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34
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Anderson R, Charvet S, Hansen PJ. Mixotrophy in Chlorophytes and Haptophytes-Effect of Irradiance, Macronutrient, Micronutrient and Vitamin Limitation. Front Microbiol 2018; 9:1704. [PMID: 30108563 PMCID: PMC6080504 DOI: 10.3389/fmicb.2018.01704] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/09/2018] [Indexed: 01/16/2023] Open
Abstract
Chlorophytes and haptophytes are key contributors to global phytoplankton biomass and productivity. Mixotrophic bacterivory has been detected for both groups, but a shortage of studies with cultured representatives hinders a consistent picture of the ecological relevance and regulation of this trophic strategy. Here, the growth, primary production, fraction of feeding cells (acidotropic probes) and bacterivory rates (surrogate prey) are tested for two species of the chlorophyte genus Nephroselmis and the haptophyte Isochrysis galbana under contrasting regimes of light (high vs. low) and nutrients (non-limited and macronutrient-, micronutrient- and vitamin-limited), at low bacterial concentrations (<107 bacteria mL-1). All three species were obligate phototrophs, unable to compensate for low light conditions through feeding. Under nutrient limitation, N. rotunda and I. galbana fed, but growth ceased or was significantly lower than in the control. Thus, mixotrophic bacterivory could be a survival rather than a growth strategy for certain species. In contrast, nutrient-limited N. pyriformis achieved growth rates equivalent to the control through feeding. This strikingly differs with the classical view of chlorophytes as primarily non-feeders and indicates mixotrophic bacterivory can be a significant trophic strategy for green algae, even at the low bacterial concentrations found in oligotrophic open oceans.
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Affiliation(s)
- Ruth Anderson
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Sophie Charvet
- Leibniz Institute for Baltic Sea Research Warnemuende, Rostock, Germany.,Biology and Paleo Environment, Lamont-Doherty Earth Observatory, Columbia University, New York, NY, United States
| | - Per J Hansen
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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35
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Orsi WD, Wilken S, Del Campo J, Heger T, James E, Richards TA, Keeling PJ, Worden AZ, Santoro AE. Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing. Environ Microbiol 2018; 20:815-827. [PMID: 29215213 DOI: 10.1111/1462-2920.14018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/26/2017] [Accepted: 11/26/2017] [Indexed: 11/29/2022]
Abstract
Photosynthetic picoeukaryotes contribute a significant fraction of primary production in the upper ocean. Micromonas pusilla is an ecologically relevant photosynthetic picoeukaryote, abundantly and widely distributed in marine waters. Grazing by protists may control the abundance of picoeukaryotes such as M. pusilla, but the diversity of the responsible grazers is poorly understood. To identify protists consuming photosynthetic picoeukaryotes in a productive North Pacific Ocean region, we amended seawater with living 15 N, 13 C-labelled M. pusilla cells in a 24-h replicated bottle experiment. DNA stable isotope probing, combined with high-throughput sequencing of V4 hypervariable regions from 18S rRNA gene amplicons (Tag-SIP), identified 19 operational taxonomic units (OTUs) of microbial eukaryotes that consumed M. pusilla. These OTUs were distantly related to cultured taxa within the dinoflagellates, ciliates, stramenopiles (MAST-1C and MAST-3 clades) and Telonema flagellates, thus, far known only from their environmental 18S rRNA gene sequences. Our discovery of eukaryotic prey consumption by MAST cells confirms that their trophic role in marine microbial food webs includes grazing upon picoeukaryotes. Our study provides new experimental evidence directly linking the genetic identity of diverse uncultivated microbial eukaryotes to the consumption of picoeukaryotic phytoplankton in the upper ocean.
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Affiliation(s)
- William D Orsi
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA
| | - Susanne Wilken
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Javier Del Campo
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thierry Heger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Erick James
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas A Richards
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Alyson E Santoro
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA
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36
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Marie D, Le Gall F, Edern R, Gourvil P, Vaulot D. Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry. JOURNAL OF PHYCOLOGY 2017; 53:271-282. [PMID: 27878810 DOI: 10.1111/jpy.12495] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/30/2016] [Indexed: 06/06/2023]
Abstract
Flow cytometry provides a tool to physically sort single algal cells in order to obtain clonal cultures. During sorting, cells are submitted to physical stress factors such as high fluidic pressure, exposure to the laser beam, electrostatic charges, deflection through high voltage fields, and collisions with container surfaces. All of these can damage the cells of interest and success rates for initiation of cultures from flow-sorted cells are generally very low. We found that the addition of bovine serum albumin in the culture medium into which cells were sorted drastically improved the success of initiation of pico- and nano-eukaryotic phytoplankton strains. Adding a mixture of antibiotics (Penicillin, Neomycin, Streptomycin) to the medium in order to slow down bacterial growth further improved culture development. This approach was successfully used to isolate taxonomically diverse strains, including novel taxa, from a fresh sample obtained in the English Channel and from enrichment cultures established during an Atlantic meridional transect cruise. We anticipate that these improvements will be useful to clone or purify existing cultures and to isolate novel cultures from oceanic samples.
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Affiliation(s)
- Dominique Marie
- UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, Sorbonne Universités, Roscoff, France
| | - Florence Le Gall
- UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, Sorbonne Universités, Roscoff, France
| | - Roseline Edern
- UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, Sorbonne Universités, Roscoff, France
| | - Priscillia Gourvil
- UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, Sorbonne Universités, Roscoff, France
| | - Daniel Vaulot
- UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, Sorbonne Universités, Roscoff, France
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37
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Selosse MA, Charpin M, Not F. Mixotrophy everywhere on land and in water: thegrand écarthypothesis. Ecol Lett 2016; 20:246-263. [DOI: 10.1111/ele.12714] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/22/2016] [Accepted: 11/13/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Marc-André Selosse
- Institut de Systématique, Évolution; Biodiversité (ISYEB - UMR 7205 - CNRS; MNHN; UPMC; EPHE); Muséum national d'Histoire naturelle; Sorbonne Universités; 57 rue Cuvier CP50 75005 Paris France
- Department of Plant Taxonomy and Nature Conservation; University of Gdansk; Wita Stwosza 59 80-308 Gdansk Poland
| | - Marie Charpin
- Université Blaise Pascal; Clermont-Ferrand; CNRS Laboratoire micro-organismes: Génome et Environnement; UMR 6023 1 Impasse Amélie Murat 63178 Aubière France
| | - Fabrice Not
- Sorbonne Universités; UPMC Université Paris 06; CNRS; Laboratoire Adaptation et Diversité en Milieu Marin UMR7144; Station Biologique de Roscoff; 29680 Roscoff France
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38
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Fischer R, Giebel HA, Hillebrand H, Ptacnik R. Importance of mixotrophic bacterivory can be predicted by light and loss rates. OIKOS 2016. [DOI: 10.1111/oik.03539] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert Fischer
- Inst. of Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg; Schleusenstraße 1 DE-26382 Wilhelmshaven Germany
| | - Helge-Ansgar Giebel
- Inst. of Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg; Schleusenstraße 1 DE-26382 Wilhelmshaven Germany
| | - Helmut Hillebrand
- Inst. of Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg; Schleusenstraße 1 DE-26382 Wilhelmshaven Germany
| | - Robert Ptacnik
- WasserCluster Lunz - Biologische Station GmbH; Lunz am See Austria
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39
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Moustaka-Gouni M, Kormas KA, Scotti M, Vardaka E, Sommer U. Warming and Acidification Effects on Planktonic Heterotrophic Pico- and Nanoflagellates in a Mesocosm Experiment. Protist 2016; 167:389-410. [DOI: 10.1016/j.protis.2016.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 01/16/2023]
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40
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Edgcomb VP. Marine protist associations and environmental impacts across trophic levels in the twilight zone and below. Curr Opin Microbiol 2016; 31:169-175. [PMID: 27092409 DOI: 10.1016/j.mib.2016.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 11/28/2022]
Abstract
Marine protists are integral to marine food webs and exhibit complex relationships with other microbial taxa. Phagotrophic protists contribute significantly to carbon turnover in the sunlit ocean and evidence suggests grazing in the dark ocean can be significant as well. New in situ sampling technologies hold great promise for more accurately accessing these impacts. The molecular signatures of parasitic protists comprise significant fractions of many high-throughput sequencing datasets, suggesting a major role in controlling populations of their host(s). The prokaryotic symbionts of free-living protists can be numerous, and, particularly in low-oxygen to anoxic marine habitats, their collective metabolisms may contribute significantly to biogeochemical cycling. This short review addresses principally planktonic communities in the mesopelagic and bathypelagic dark ocean.
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Affiliation(s)
- V P Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, USA.
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41
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Egge ES, Johannessen TV, Andersen T, Eikrem W, Bittner L, Larsen A, Sandaa RA, Edvardsen B. Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing. Mol Ecol 2015; 24:3026-42. [PMID: 25893259 PMCID: PMC4692090 DOI: 10.1111/mec.13160] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 02/06/2015] [Accepted: 02/13/2015] [Indexed: 11/28/2022]
Abstract
Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2 years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September–October (autumn) and lowest in April–May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3–5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters.
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Affiliation(s)
| | - Torill Vik Johannessen
- Marine Microbiology, Department of Biology, University of Bergen, PO Box 7803, 5006, Bergen, Norway
| | - Tom Andersen
- Department of Biosciences, University of Oslo, PO Box 1066, 0316, Oslo, Norway
| | - Wenche Eikrem
- Department of Biosciences, University of Oslo, PO Box 1066, 0316, Oslo, Norway.,Norwegian Institute for Water Research, Gaustadalléen 21, 0349, Oslo, Norway
| | - Lucie Bittner
- CNRS FR3631, Institut de Biologie Paris-Seine, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005, Paris, France
| | - Aud Larsen
- Uni Research Environment, Thormøhlensgate 49b, N-5006, Bergen, Norway.,Hjort Centre for Marine Ecosystem Dynamics, N-5006, Bergen, Norway
| | - Ruth-Anne Sandaa
- Marine Microbiology, Department of Biology, University of Bergen, PO Box 7803, 5006, Bergen, Norway
| | - Bente Edvardsen
- Department of Biosciences, University of Oslo, PO Box 1066, 0316, Oslo, Norway
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42
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Duret MT, Pachiadaki MG, Stewart FJ, Sarode N, Christaki U, Monchy S, Srivastava A, Edgcomb VP. Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone. FEMS Microbiol Ecol 2015; 91:fiv037. [DOI: 10.1093/femsec/fiv037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2015] [Indexed: 11/14/2022] Open
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43
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Worden AZ, Follows MJ, Giovannoni SJ, Wilken S, Zimmerman AE, Keeling PJ. Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes. Science 2015; 347:1257594. [DOI: 10.1126/science.1257594] [Citation(s) in RCA: 439] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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44
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45
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Egge ES, Eikrem W, Edvardsen B. Deep-branching novel lineages and high diversity of haptophytes in the Skagerrak (Norway) uncovered by 454 pyrosequencing. J Eukaryot Microbiol 2014; 62:121-40. [PMID: 25099994 PMCID: PMC4344818 DOI: 10.1111/jeu.12157] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 01/14/2023]
Abstract
Microalgae in the division Haptophyta may be difficult to identify to species by microscopy because they are small and fragile. Here, we used high-throughput sequencing to explore the diversity of haptophytes in outer Oslofjorden, Skagerrak, and supplemented this with electron microscopy. Nano- and picoplanktonic subsurface samples were collected monthly for 2 yr, and the haptophytes were targeted by amplification of RNA/cDNA with Haptophyta-specific 18S ribosomal DNA V4 primers. Pyrosequencing revealed higher species richness of haptophytes than previously observed in the Skagerrak by microscopy. From ca. 400,000 reads we obtained 156 haptophyte operational taxonomic units (OTUs) after rigorous filtering and 99.5% clustering. The majority (84%) of the OTUs matched environmental sequences not linked to a morphological species, most of which were affiliated with the order Prymnesiales. Phylogenetic analyses including Oslofjorden OTUs and available cultured and environmental haptophyte sequences showed that several of the OTUs matched sequences forming deep-branching lineages, potentially representing novel haptophyte classes. Pyrosequencing also retrieved cultured species not previously reported by microscopy in the Skagerrak. Electron microscopy revealed species not yet genetically characterised and some potentially novel taxa. This study contributes to linking genotype to phenotype within this ubiquitous and ecologically important protist group, and reveals great, unknown diversity.
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Affiliation(s)
- Elianne S Egge
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316, Oslo, Norway
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46
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Edgcomb VP, Pachiadaki M. Ciliates along Oxyclines of Permanently Stratified Marine Water Columns. J Eukaryot Microbiol 2014; 61:434-45. [DOI: 10.1111/jeu.12122] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 02/28/2014] [Accepted: 02/28/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Virginia P. Edgcomb
- Department of Geology and Geophysics; Woods Hole Oceanographic Institution; Woods Hole Massachusetts 02543
| | - Maria Pachiadaki
- Department of Geology and Geophysics; Woods Hole Oceanographic Institution; Woods Hole Massachusetts 02543
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47
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Faster growth of the major prokaryotic versus eukaryotic CO2 fixers in the oligotrophic ocean. Nat Commun 2014; 5:3776. [PMID: 24777140 PMCID: PMC4015317 DOI: 10.1038/ncomms4776] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 04/01/2014] [Indexed: 01/10/2023] Open
Abstract
Because maintenance of non-scalable cellular components—membranes and chromosomes—requires an increasing fraction of energy as cell size decreases, miniaturization comes at a considerable energetic cost for a phytoplanktonic cell. Consequently, if eukaryotes can use their superior energetic resources to acquire nutrients with more or even similar efficiency compared with prokaryotes, larger unicellular eukaryotes should be able to achieve higher growth rates than smaller cyanobacteria. Here, to test this hypothesis, we directly compare the intrinsic growth rates of phototrophic prokaryotes and eukaryotes from the equatorial to temperate South Atlantic using an original flow cytometric 14CO2-tracer approach. At the ocean basin scale, cyanobacteria double their biomass twice as frequently as the picoeukaryotes indicating that the prokaryotes are faster growing CO2 fixers, better adapted to phototrophic living in the oligotrophic open ocean—the most extensive biome on Earth. After the energetically superior eukaryotes had evolved, prokaryotes appeared to lose control over biological CO2 fixation in all major biomes on Earth. Here the author shows that in the oligotrophic ocean, the most extensive biome on Earth, the prokaryotes fix CO2 twice as fast as eukaryotes.
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Hartmann M, Zubkov MV, Scanlan DJ, Lepère C. In situ interactions between photosynthetic picoeukaryotes and bacterioplankton in the Atlantic Ocean: evidence for mixotrophy. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:835-40. [PMID: 24249292 DOI: 10.1111/1758-2229.12084] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 06/20/2013] [Accepted: 06/22/2013] [Indexed: 05/25/2023]
Abstract
Heterotrophic bacterioplankton, cyanobacteria and phototrophic picoeukaryotes (< 5 μm in size) numerically dominate planktonic oceanic communities. While feeding on bacterioplankton is often attributed to aplastidic protists, recent evidence suggests that phototrophic picoeukaryotes could be important bacterivores. Here, we present direct visual evidence from the surface mixed layer of the Atlantic Ocean that bacterioplankton are internalized by phototrophic picoeukaryotes. In situ interactions of phototrophic picoeukaryotes and bacterioplankton (specifically Prochlorococcus cyanobacteria and the SAR11 clade) were investigated using a combination of flow cytometric cell sorting and dual tyramide signal amplification fluorescence in situ hybridization. Using this method, we observed plastidic Prymnesiophyceae and Chrysophyceae cells containing Prochlorococcus, and to a lesser extent SAR11 cells. These microscopic observations of in situ microbial trophic interactions demonstrate the frequency and likely selectivity of phototrophic picoeukaryote bacterivory in the surface mixed layer of both the North and South Atlantic subtropical gyres and adjacent equatorial region, broadening our views on the ecological role of the smallest oceanic plastidic protists.
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Affiliation(s)
- Manuela Hartmann
- Ocean Biogeochemistry and Ecosystems Research Group, National Oceanography Centre, Southampton, SO14 3ZH, UK
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Chow CET, Kim DY, Sachdeva R, Caron DA, Fuhrman JA. Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists. ISME JOURNAL 2013; 8:816-29. [PMID: 24196323 DOI: 10.1038/ismej.2013.199] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 09/10/2013] [Accepted: 09/26/2013] [Indexed: 01/25/2023]
Abstract
Characterizing ecological relationships between viruses, bacteria and protists in the ocean are critical to understanding ecosystem function, yet these relationships are infrequently investigated together. We evaluated these relationships through microbial association network analysis of samples collected approximately monthly from March 2008 to January 2011 in the surface ocean (0-5 m) at the San Pedro Ocean Time series station. Bacterial, T4-like myoviral and protistan communities were described by Automated Ribosomal Intergenic Spacer Analysis and terminal restriction fragment length polymorphism of the gene encoding the major capsid protein (g23) and 18S ribosomal DNA, respectively. Concurrent shifts in community structure suggested similar timing of responses to environmental and biological parameters. We linked T4-like myoviral, bacterial and protistan operational taxonomic units by local similarity correlations, which were then visualized as association networks. Network links (correlations) potentially represent synergistic and antagonistic relationships such as viral lysis, grazing, competition or other interactions. We found that virus-bacteria relationships were more cross-linked than protist-bacteria relationships, suggestive of increased taxonomic specificity in virus-bacteria relationships. We also found that 80% of bacterial-protist and 74% of bacterial-viral correlations were positive, with the latter suggesting that at monthly and seasonal timescales, viruses may be following their hosts more often than controlling host abundance.
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Affiliation(s)
- Cheryl-Emiliane T Chow
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Diane Y Kim
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Rohan Sachdeva
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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Acosta F, Ngugi DK, Stingl U. Diversity of picoeukaryotes at an oligotrophic site off the Northeastern Red Sea Coast. AQUATIC BIOSYSTEMS 2013; 9:16. [PMID: 23962380 PMCID: PMC3766091 DOI: 10.1186/2046-9063-9-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 08/07/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Picoeukaryotes are protists ≤ 3 μm composed of a wide diversity of taxonomic groups. They are an important constituent of the ocean's microbiota and perform essential ecological roles in marine nutrient and carbon cycles. Despite their importance, the true extent of their diversity has only recently been uncovered by molecular surveys that resulted in the discovery of a substantial number of previously unknown groups. No study on picoeukaryote diversity has been conducted so far in the main Red Sea basin-a unique marine environment characterized by oligotrophic conditions, high levels of irradiance, high salinity and increased water temperature. RESULTS We sampled surface waters off the coast of the northeastern Red Sea and analyzed the picoeukaryotic diversity using Sanger-based clone libraries of the 18S rRNA gene in order to produce high quality, nearly full-length sequences. The community captured by our approach was dominated by three main phyla, the alveolates, stramenopiles and chlorophytes; members of Radiolaria, Cercozoa and Haptophyta were also found, albeit in low abundances. Photosynthetic organisms were especially diverse and abundant in the sample, confirming the importance of picophytoplankton for primary production in the basin as well as indicating the existence of numerous ecological micro-niches for this trophic level in the upper euphotic zone. Heterotrophic organisms were mostly composed of the presumably parasitic Marine Alveolates (MALV) and the presumably bacterivorous Marine Stramenopiles (MAST) groups. A small number of sequences that did not cluster closely with known clades were also found, especially in the MALV-II group, some of which could potentially belong to novel clades. CONCLUSIONS This study provides the first snapshot of the picoeukaryotic diversity present in surface waters of the Red Sea, hence setting the stage for large-scale surveying and characterization of the eukaryotic diversity in the entire basin. Our results indicate that the picoeukaryotic community in the northern Red Sea, despite its unique physiochemical conditions (i.e. increased temperatures, increased salinity, and high UV irradiance) does not differ vastly from its counterparts in other oligotrophic marine habitats.
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Affiliation(s)
- Francisco Acosta
- Red Sea Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - David Kamanda Ngugi
- Red Sea Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Ulrich Stingl
- Red Sea Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
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