1
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Kilner CL, Carrell AA, Wieczynski DJ, Votzke S, DeWitt K, Yammine A, Shaw J, Pelletier DA, Weston DJ, Gibert JP. Temperature and CO 2 interactively drive shifts in the compositional and functional structure of peatland protist communities. GLOBAL CHANGE BIOLOGY 2024; 30:e17203. [PMID: 38433341 DOI: 10.1111/gcb.17203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 03/05/2024]
Abstract
Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long-term whole-ecosystem warming experiment at a boreal peatland to answer how temperature and CO2 jointly influence communities of abundant, diverse, yet poorly understood, non-fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria and fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report large climate-induced, community-wide shifts in the community functional composition of these microbes (size, shape, and metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO2 with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO2 and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO2 levels could alter the structure and function of peatland microbial food webs-a fragile ecosystem that stores upwards of 25% of all terrestrial carbon and is increasingly threatened by human exploitation.
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Affiliation(s)
- Christopher L Kilner
- Department of Biology, Duke University, Durham, North Carolina, USA
- Bird Conservancy of the Rockies, Fort Collins, Colorado, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Samantha Votzke
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Katrina DeWitt
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Andrea Yammine
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jean P Gibert
- Department of Biology, Duke University, Durham, North Carolina, USA
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2
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Gleich SJ, Hu SK, Krinos AI, Caron DA. Protistan community composition and metabolism in the North Pacific Subtropical Gyre: Influences of mesoscale eddies and depth. Environ Microbiol 2024; 26:e16556. [PMID: 38081167 DOI: 10.1111/1462-2920.16556] [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: 08/11/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024]
Abstract
Marine protists and their metabolic activities are intricately tied to the cycling of nutrients and the flow of energy through microbial food webs. Physiochemical changes in the environment, such as those that result from mesoscale eddies, may impact protistan communities, but the effects that such changes have on protists are poorly known. A metatranscriptomic study was conducted to investigate how eddies affected protists at adjacent cyclonic and anticyclonic eddy sites in the oligotrophic ocean at four depths from 25 to 250 m. Eddy polarity impacted protists at all depths sampled, although the effects of eddy polarity were secondary to the impact of depth across the depth range. Eddy-induced vertical shifts in the water column yielded differences in the cyclonic and anticyclonic eddy protistan communities, and these differences were the most pronounced at and just below the deep chlorophyll maximum. An analysis of transcripts associated with protistan nutritional physiology at 150 m revealed that cyclonic eddies may support a more heterotrophic community, while anticyclonic eddies promote a more phototrophic community. The results of this study indicate that eddies alter the metabolism of protists particularly in the lower euphotic zone and may therefore impact carbon export from the euphotic zone.
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Affiliation(s)
- Samantha J Gleich
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Sarah K Hu
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Arianna I Krinos
- MIT-WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, Cambridge and Woods Hole, Cambridge, Massachusetts, USA
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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3
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Charvet S, Bock NA, Kim E, Duhamel S. Transcriptomics reveal a unique phago-mixotrophic response to low nutrient concentrations in the prasinophyte Pterosperma cristatum. ISME COMMUNICATIONS 2024; 4:ycae083. [PMID: 38957873 PMCID: PMC11217555 DOI: 10.1093/ismeco/ycae083] [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: 12/15/2023] [Revised: 05/23/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024]
Abstract
Constitutive mixoplankton-plastid-bearing microbial eukaryotes capable of both phototrophy and phagotrophy-are ubiquitous in marine ecosystems and facilitate carbon transfer to higher trophic levels within aquatic food webs, which supports enhanced sinking carbon flux. However, the regulation of the relative contribution of photosynthesis and prey consumption remains poorly characterized. We investigated the transcriptional dynamics behind this phenotypic plasticity in the prasinophyte green alga Pterosperma cristatum. Based on what is known of other mixoplankton species that cannot grow without photosynthesis (obligate phototrophs), we hypothesized that P. cristatum uses phagotrophy to circumvent the restrictions imposed on photosynthesis by nutrient depletion, to obtain nutrients from ingested prey, and to maintain photosynthetic carbon fixation. We observed an increase in feeding as a response to nutrient depletion, coinciding with an upregulation of expression for genes involved in essential steps of phagocytosis including prey recognition, adhesion and engulfment, transport and maturation of food vacuoles, and digestion. Unexpectedly, genes involved in the photosynthetic electron transfer chain, pigment biosynthesis, and carbon fixation were downregulated as feeding increased, implying an abatement of photosynthesis. Contrary to our original hypothesis, our results therefore suggest that depletion of inorganic nutrients triggered an alteration of trophic behavior from photosynthesis to phagotrophy in P. cristatum. While this behavior distinguishes P. cristatum from other groups of constitutive mixoplankton, its physiological response aligns with recent discoveries from natural microbial communities. These findings indicate that mixoplankton communities in nutrient-limited oceans can regulate photosynthesis against bacterivory based on nutrient availability.
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Affiliation(s)
- Sophie Charvet
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, United States
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, NY 10024, United States
- Department of Biology, School of Natural and Social Sciences, Susquehanna University, Selinsgrove, PA 17870, United States
| | - Nicholas A Bock
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, United States
- Laboratoire d’Océanographie de Villefranche, CNRS and Sorbonne Université, 06230 Villefranche-sur-Mer, France
| | - Eunsoo Kim
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, NY 10024, United States
- Division of EcoScience, Ewha Womans University, Seoul 03760, South Korea
| | - Solange Duhamel
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, United States
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, NY 10024, United States
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, United States
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4
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Alexander H, Hu SK, Krinos AI, Pachiadaki M, Tully BJ, Neely CJ, Reiter T. Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton. mBio 2023; 14:e0167623. [PMID: 37947402 PMCID: PMC10746220 DOI: 10.1128/mbio.01676-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8-2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life.IMPORTANCESingle-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.
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Affiliation(s)
- Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Sarah K. Hu
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Arianna I. Krinos
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, Massachusetts, USA
| | - Maria Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Benjamin J. Tully
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Christopher J. Neely
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Taylor Reiter
- Population Health and Reproduction, University of California, Davis, Davis, California, USA
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5
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Schulz G, Camenzind T, Sánchez-Galindo LM, Schneider D, Scheu S, Krashevska V. Response of protists to nitrogen addition, arbuscular mycorrhizal fungi manipulation, and mesofauna reduction in a tropical montane rainforest in southern Ecuador. J Eukaryot Microbiol 2023; 70:e12996. [PMID: 37577763 DOI: 10.1111/jeu.12996] [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: 03/09/2023] [Revised: 07/10/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023]
Abstract
The tropical Andes are a species-rich and nitrogen-limited system, susceptible to increased nitrogen (N) inputs from the atmosphere. However, our understanding of the impacts of increased N input on belowground systems, in particular on protists and their role in nutrient cycling, remains limited. We explored how increased N affects protists in tropical montane rainforests in Ecuador using high-throughput sequencing (HTS) of environmental DNA from two litter layers. In addition, we manipulated the amount of arbuscular mycorrhizal fungi (AMF) and mesofauna, both playing a significant role in N cycling and interacting in complex ways with protist communities. We found that N strongly affected protist community composition in both layers, while mesofauna reduction had a stronger effect on the lower layer. Changes in concentration of the AMF marker lipid had little effect on protists. In both layers, the addition of N increased phagotrophs and animal parasites and decreased plant parasites, while mixotrophs decreased in the upper layer but increased in the lower layer. In the upper layer with higher AMF concentration, mixotrophs decreased, while in the lower layer, photoautotrophs increased and plant parasites decreased. With reduced mesofauna, phagotrophs increased and animal parasites decreased in both layers, while plant parasites increased only in the upper layer. The findings indicate that to understand the intricate response of protist communities to environmental changes, it is critical to thoroughly analyze these communities across litter and soil layers, and to include HTS.
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Affiliation(s)
- Garvin Schulz
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Laura M Sánchez-Galindo
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Goettingen Genomics Laboratory, University of Göttingen, Göttingen, Germany
| | - Stefan Scheu
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany
| | - Valentyna Krashevska
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
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6
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Nef C, Madoui MA, Pelletier É, Bowler C. Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. PLoS Biol 2022; 20:e3001893. [PMID: 36441816 PMCID: PMC9731442 DOI: 10.1371/journal.pbio.3001893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/08/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data.
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Affiliation(s)
- Charlotte Nef
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Mohammed-Amin Madoui
- Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | - Éric Pelletier
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Metabolic Genomics, Genoscope, Institut de Biologie François-Jacob, CEA, CNRS, Université Evry, Université Paris Saclay, Evry, France
| | - Chris Bowler
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- * E-mail:
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7
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Koppelle S, López-Escardó D, Brussaard CPD, Huisman J, Philippart CJM, Massana R, Wilken S. Mixotrophy in the bloom-forming genus Phaeocystis and other haptophytes. HARMFUL ALGAE 2022; 117:102292. [PMID: 35944956 DOI: 10.1016/j.hal.2022.102292] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 05/13/2023]
Abstract
Phaeocystis is a globally widespread marine phytoplankton genus, best known for its colony-forming species that can form large blooms and odorous foam during bloom decline. In the North Sea, Phaeocystis globosa typically becomes abundant towards the end of the spring bloom, when nutrients are depleted and the share of mixotrophic protists increases. Although mixotrophy is widespread across the eukaryotic tree of life and is also found amongst haptophytes, a mixotrophic nutrition has not yet been demonstrated in Phaeocystis. Here, we sampled two consecutive Phaeocystis globosa spring blooms in the coastal North Sea. In both years, bacterial cells were observed inside 0.6 - 2% of P. globosa cells using double CARD-FISH hybridizations in combination with laser scanning confocal microscopy. Incubation experiments manipulating light and nutrient availability showed a trend towards higher occurrence of intracellular bacteria under P-deplete conditions. Based on counts of bacteria inside P. globosa cells in combination with theoretical values of prey digestion times, maximum ingestion rates of up to 0.08 bacteria cell-1 h-1 were estimated. In addition, a gene-based predictive model was applied to the transcriptome assemblies of seven Phaeocystis strains and 24 other haptophytes to assess their trophic mode. This model predicted a phago-mixotrophic feeding strategy in several (but not all) strains of P. globosa, P. antarctica and other haptophytes that were previously assumed to be autotrophic. The observation of bacterial cells inside P. globosa and the gene-based model predictions strongly suggest that the phago-mixotrophic feeding strategy is widespread among members of the Phaeocystis genus and other haptophytes, and might contribute to their remarkable success to form nuisance blooms under nutrient-limiting conditions.
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Affiliation(s)
- Sebastiaan Koppelle
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands.
| | - David López-Escardó
- Ecology of Marine Microbes, Institut de Ciènces del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Corina P D Brussaard
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands; Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands
| | - Catharina J M Philippart
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands; Department of Physical Geography, Utrecht University, P.O. Box 80115, 3508 TC, Utrecht, The Netherlands
| | - Ramon Massana
- Ecology of Marine Microbes, Institut de Ciènces del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Susanne Wilken
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands.
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8
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Calderini ML, Salmi P, Rigaud C, Peltomaa E, Taipale SJ. Metabolic plasticity of mixotrophic algae is key for their persistence in browning environments. Mol Ecol 2022; 31:4726-4738. [PMID: 35844067 PMCID: PMC9544590 DOI: 10.1111/mec.16619] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Abstract
Light availability is the main regulator of primary production, shaping photosynthetic communities and their production of ecologically important biomolecules. In freshwater ecosystems, increasing dissolved organic carbon (DOC) concentrations, commonly known as browning, leads to lower light availability and the proliferation of mixotrophic phytoplankton. Here, a mixotrophic algal species (Cryptomonas sp.) was grown under five increasing DOC concentrations to uncover the plastic responses behind the success of mixotrophs in browning environments and their effect in the availability of nutritionally important biomolecules. In addition to the browning treatments, phototrophic, heterotrophic and mixotrophic growth conditions were used as controls. Despite reduced light availability, browning did not impair algal growth compared to phototrophic conditions. Comparative transcriptomics showed that genes related to photosynthesis were down‐regulated, whereas phagotrophy gene categories (phagosome, lysosome and endocytosis) were up‐regulated along the browning gradient. Stable isotope analysis of phospholipid fractions validated these results, highlighting that the studied mixotroph increases its reliance on heterotrophic processes with browning. Metabolic pathway reconstruction using transcriptomic data suggests that organic carbon is acquired through phagotrophy and used to provide energy in conjunction with photosynthesis. Although metabolic responses to browning were observed, essential fatty acid content was similar between treatments while sterol content was slightly higher upon browning. Together, our results provide a mechanistic model of how a mixotrophic alga responds to browning and how such responses affect the availability of nutritionally essential biomolecules for higher trophic levels.
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Affiliation(s)
- Marco L Calderini
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Department of Biological and Environmental Science, University of Jyvaskyla, Finland
| | - Pauliina Salmi
- Spectral Imaging Laboratory, Faculty of Information Technology, University of Jyväskylä, Jyväskylä, Finland
| | - Cyril Rigaud
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Elina Peltomaa
- Institute of Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Helsinki, Finland
| | - Sami J Taipale
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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9
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Nef C, Dittami S, Kaas R, Briand E, Noël C, Mairet F, Garnier M. Sharing Vitamin B12 between Bacteria and Microalgae Does Not Systematically Occur: Case Study of the Haptophyte Tisochrysis lutea. Microorganisms 2022; 10:microorganisms10071337. [PMID: 35889056 PMCID: PMC9323062 DOI: 10.3390/microorganisms10071337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 02/01/2023] Open
Abstract
Haptophyte microalgae are key contributors to microbial communities in many environments. It has been proposed recently that members of this group would be virtually all dependent on vitamin B12 (cobalamin), an enzymatic cofactor produced only by some bacteria and archaea. Here, we examined the processes of vitamin B12 acquisition by haptophytes. We tested whether co-cultivating the model species Tisochrysis lutea with B12-producing bacteria in vitamin-deprived conditions would allow the microalga to overcome B12 deprivation. While T. lutea can grow by scavenging vitamin B12 from bacterial extracts, co-culture experiments showed that the algae did not receive B12 from its associated bacteria, despite bacteria/algae ratios supposedly being sufficient to allow enough vitamin production. Since other studies reported mutualistic algae–bacteria interactions for cobalamin, these results question the specificity of such associations. Finally, cultivating T. lutea with a complex bacterial consortium in the absence of the vitamin partially rescued its growth, highlighting the importance of microbial interactions and diversity. This work suggests that direct sharing of vitamin B12 is specific to each species pair and that algae in complex natural communities can acquire it indirectly by other mechanisms (e.g., after bacterial lysis).
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Affiliation(s)
- Charlotte Nef
- Physiologie et Biotechnologie des Algues, IFREMER, Rue de l’Ile d’Yeu, F-44311 Nantes, France;
- Correspondence:
| | - Simon Dittami
- Station Biologique de Roscoff, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne University, F-29680 Roscoff, France;
| | - Raymond Kaas
- Physiologie et Biotechnologie des Algues, IFREMER, Rue de l’Ile d’Yeu, F-44311 Nantes, France;
| | - Enora Briand
- GENALG, PHYTOX, IFREMER, F-44000 Nantes, France; (E.B.); (M.G.)
| | - Cyril Noël
- SEBIMER, IRSI, IFREMER, F-29280 Brest, France;
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10
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González-Olalla JM, Medina-Sánchez JM, Norici A, Carrillo P. Regulation of Phagotrophy by Prey, Low Nutrients, and Low Light in the Mixotrophic Haptophyte Isochrysis galbana. MICROBIAL ECOLOGY 2021; 82:981-993. [PMID: 33661311 DOI: 10.1007/s00248-021-01723-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
Mixotrophy combines autotrophy and phagotrophy in the same cell. However, it is not known to what extent the phagotrophy influences metabolism, cell composition, and growth. In this work, we assess, on the one hand (first test), the role of phagotrophy on the elemental and biochemical composition, cell metabolism, and enzymes related to C, N, and S metabolism of Isochrysis galbana Parke, 1949. On the other hand, we study how a predicted increase of phagotrophy under environmental conditions of low nutrients (second test) and low light (third test) can affect its metabolism and growth. Our results for the first test revealed that bacterivory increased the phosphorous and iron content per cell, accelerating cell division and improving the cell fitness; in addition, the stimulation of some C and N enzymatic routes help to maintain, to some degree, compositional homeostasis. Under nutrient or light scarcity, I. galbana grew more slowly despite greater bacterial consumption, and the activities of key enzymes involved in C, N, and S metabolism changed according to a predominantly phototrophic strategy of nutrition in this alga. Contrary to recent studies, the stimulation of phagotrophy under low nutrient and low irradiance did not imply greater and more efficient C flux.
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Affiliation(s)
- Juan Manuel González-Olalla
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.
- University Institute of Water research, University of Granada, C/Ramón y Cajal, 4, 18071, Granada, Spain.
| | - Juan Manuel Medina-Sánchez
- University Institute of Water research, University of Granada, C/Ramón y Cajal, 4, 18071, Granada, Spain
- Department of Ecology, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, 18071, Granada, Spain
| | - Alessandra Norici
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Presentación Carrillo
- University Institute of Water research, University of Granada, C/Ramón y Cajal, 4, 18071, Granada, Spain
- Department of Ecology, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, 18071, Granada, Spain
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11
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Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean. Nat Microbiol 2021; 6:173-186. [PMID: 33398100 DOI: 10.1038/s41564-020-00814-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 10/13/2020] [Indexed: 01/28/2023]
Abstract
Marine microeukaryotes play a fundamental role in biogeochemical cycling through the transfer of energy to higher trophic levels and vertical carbon transport. Despite their global importance, microeukaryote physiology, nutrient metabolism and contributions to carbon cycling across offshore ecosystems are poorly characterized. Here, we observed the prevalence of dinoflagellates along a 4,600-km meridional transect extending across the central Pacific Ocean, where oligotrophic gyres meet equatorial upwelling waters rich in macronutrients yet low in dissolved iron. A combined multi-omics and geochemical analysis provided a window into dinoflagellate metabolism across the transect, indicating a continuous taxonomic dinoflagellate community that shifted its functional transcriptome and proteome as it extended from the euphotic to the mesopelagic zone. In euphotic waters, multi-omics data suggested that a combination of trophic modes were utilized, while mesopelagic metabolism was marked by cytoskeletal investments and nutrient recycling. Rearrangement in nutrient metabolism was evident in response to variable nitrogen and iron regimes across the gradient, with no associated change in community assemblage. Total dinoflagellate proteins scaled with particulate carbon export, with both elevated in equatorial waters, suggesting a link between dinoflagellate abundance and total carbon flux. Dinoflagellates employ numerous metabolic strategies that enable broad occupation of central Pacific ecosystems and play a dual role in carbon transformation through both photosynthetic fixation in the euphotic zone and remineralization in the mesopelagic zone.
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12
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Massana R, Labarre A, López-Escardó D, Obiol A, Bucchini F, Hackl T, Fischer MG, Vandepoele K, Tikhonenkov DV, Husnik F, Keeling PJ. Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate. ISME JOURNAL 2020; 15:154-167. [PMID: 32920602 PMCID: PMC7852580 DOI: 10.1038/s41396-020-00770-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 11/17/2022]
Abstract
Phagocytosis is a fundamental process in marine ecosystems by which prey organisms are consumed and their biomass incorporated in food webs or remineralized. However, studies searching for the genes underlying this key ecological process in free-living phagocytizing protists are still scarce, in part due to the lack of appropriate ecological models. Our reanalysis of recent molecular datasets revealed that the cultured heterotrophic flagellate Cafeteria burkhardae is widespread in the global oceans, which prompted us to design a transcriptomics study with this species, grown with the cultured flavobacterium Dokdonia sp. We compared the gene expression between exponential and stationary phases, which were complemented with three starvation by dilution phases that appeared as intermediate states. We found distinct expression profiles in each condition and identified 2056 differentially expressed genes between exponential and stationary samples. Upregulated genes at the exponential phase were related to DNA duplication, transcription and translational machinery, protein remodeling, respiration and phagocytosis, whereas upregulated genes in the stationary phase were involved in signal transduction, cell adhesion, and lipid metabolism. We identified a few highly expressed phagocytosis genes, like peptidases and proton pumps, which could be used to target this ecologically relevant process in marine ecosystems.
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Affiliation(s)
- Ramon Massana
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta 37-49, ES-08003, Barcelona, Catalonia, Spain.
| | - Aurelie Labarre
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - David López-Escardó
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Aleix Obiol
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - François Bucchini
- Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Thomas Hackl
- Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | | | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Russia
| | - Filip Husnik
- University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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13
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Livanou E, Barsakis K, Psarra S, Lika K. Modelling the nutritional strategies in mixotrophic nanoflagellates. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2020.109053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Graupner N, Jensen M, Bock C, Marks S, Rahmann S, Beisser D, Boenigk J. Evolution of heterotrophy in chrysophytes as reflected by comparative transcriptomics. FEMS Microbiol Ecol 2019. [PMID: 29518196 PMCID: PMC6019013 DOI: 10.1093/femsec/fiy039] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Shifts in the nutritional mode between phototrophy, mixotrophy and heterotrophy are a widespread phenomenon in the evolution of eukaryotic diversity. The transition between nutritional modes is particularly pronounced in chrysophytes and occurred independently several times through parallel evolution. Thus, chrysophytes provide a unique opportunity for studying the molecular basis of nutritional diversification and of the accompanying pathway reduction and degradation of plastid structures. In order to analyze the succession in switching the nutritional mode from mixotrophy to heterotrophy, we compared the transcriptome of the mixotrophic Poterioochromonas malhamensis with the transcriptomes of three obligate heterotrophic species of Ochromonadales. We used the transcriptome of P. malhamensis as a reference for plastid reduction in the heterotrophic taxa. The analyzed heterotrophic taxa were in different stages of plastid reduction. We investigated the reduction of several photosynthesis related pathways e.g. the xanthophyll cycle, the mevalonate pathway, the shikimate pathway and the tryptophan biosynthesis as well as the reduction of plastid structures and postulate a presumable succession of pathway reduction and degradation of accompanying structures.
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Affiliation(s)
- Nadine Graupner
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany
| | - Manfred Jensen
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany
| | - Christina Bock
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany
| | - Sabina Marks
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, D-45147 Essen, Germany
| | - Daniela Beisser
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany
| | - Jens Boenigk
- Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, D-45141 Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 2, D-45141 Essen, Germany
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15
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Mixotrophy in nanoflagellates across environmental gradients in the ocean. Proc Natl Acad Sci U S A 2019; 116:6211-6220. [PMID: 30760589 DOI: 10.1073/pnas.1814860116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Mixotrophy, the combination of autotrophic and heterotrophic nutrition, is a common trophic strategy among unicellular eukaryotes in the ocean. There are a number of hypotheses about the conditions that select for mixotrophy, and field studies have documented the prevalence of mixotrophy in a range of environments. However, there is currently little evidence for how mixotrophy varies across environmental gradients, and whether empirical patterns support theoretical predictions. Here I synthesize experiments that have quantified the abundance of phototrophic, mixotrophic, and heterotrophic nanoflagellates, to ask whether there are broad patterns in the prevalence of mixotrophy (relative to pure autotrophy and heterotrophy), and to ask whether observed patterns are consistent with a trait-based model of trophic strategies. The data suggest that mixotrophs increase in abundance at lower latitudes, while autotrophs and heterotrophs do not, and that this may be driven by increased light availability. Both mixotrophs and autotrophs increase greatly in productive coastal environments, while heterotrophs increase only slightly. These patterns are consistent with a model of resource competition in which nutrients and carbon can both limit growth and mixotrophs experience a trade-off in allocating biomass to phagotrophy vs. autotrophic functions. Importantly, mixotrophy is selected for under a range of conditions even when mixotrophs experience a penalty for using a generalist trophic strategy, due to the synergy between photosynthetically derived carbon and prey-derived nutrients. For this reason mixotrophy is favored relative to specialist strategies by increased irradiance, while at the same time increased nutrient supply increases the competitive ability of mixotrophs against heterotrophs.
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16
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Zhang L, Lyu K, Wang N, Gu L, Sun Y, Zhu X, Wang J, Huang Y, Yang Z. Transcriptomic Analysis Reveals the Pathways Associated with Resisting and Degrading Microcystin in Ochromonas. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:11102-11113. [PMID: 30176726 DOI: 10.1021/acs.est.8b03106] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Toxic Microcystis bloom is a tough environment problem worldwide. Microcystin is highly toxic and is an easily accumulated secondary metabolite of toxic Microcystis that threatens water safety. Biodegradation of microcystin by protozoan grazing is a promising and efficient biological method, but the mechanism in this process is still unclear. The present study aimed to identify potential pathways involved in resisting and degrading microcystin in flagellates through transcriptomic analyses. A total of 999 unigenes were significantly differentially expressed between treatments with flagellates Ochromonas fed on microcystin-producing Microcystis and microcystin-free Microcystis. These dysregulated genes were strongly associated with translation, carbohydrate metabolism, phagosome, and energy metabolism. Upregulated genes encoding peroxiredoxin, serine/threonine-protein phosphatase, glutathione S-transferase (GST), HSP70, and O-GlcNAc transferase were involved in resisting microcystin. In addition, genes encoding cathepsin and GST and genes related to inducing reactive oxygen species (ROS) were all upregulated, which highly probably linked with degrading microcystin in flagellates. The results of this study provided a better understanding of transcriptomic responses of flagellates to toxic Microcystis as well as highlighted a potential mechanism of biodegrading microcystin by flagellate Ochromonas, which served as a strong theoretical support for control of toxic microalgae by protozoans.
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Affiliation(s)
- Lu Zhang
- Jiangsu Province Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences , Nanjing Normal University , 1 Wenyuan Road , Nanjing 210023 , China
| | - Kai Lyu
- Jiangsu Province Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences , Nanjing Normal University , 1 Wenyuan Road , Nanjing 210023 , China
| | - Na Wang
- Jiangsu Province Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences , Nanjing Normal University , 1 Wenyuan Road , Nanjing 210023 , China
| | - Lei Gu
- Jiangsu Province Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences , Nanjing Normal University , 1 Wenyuan Road , Nanjing 210023 , China
| | - Yunfei Sun
- Jiangsu Province Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences , Nanjing Normal University , 1 Wenyuan Road , Nanjing 210023 , China
| | - Xuexia Zhu
- Jiangsu Province Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences , Nanjing Normal University , 1 Wenyuan Road , Nanjing 210023 , China
| | - Jun Wang
- Jiangsu Province Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences , Nanjing Normal University , 1 Wenyuan Road , Nanjing 210023 , China
| | - Yuan Huang
- Jiangsu Province Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences , Nanjing Normal University , 1 Wenyuan Road , Nanjing 210023 , China
| | - Zhou Yang
- Jiangsu Province Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences , Nanjing Normal University , 1 Wenyuan Road , Nanjing 210023 , China
- Department of Ecology, College of Life Science and Technology , Jinan University , Guangzhou 510632 , China
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17
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Tsuchiya M, Chikaraishi Y, Nomaki H, Sasaki Y, Tame A, Uematsu K, Ohkouchi N. Compound-specific isotope analysis of benthic foraminifer amino acids suggests microhabitat variability in rocky-shore environments. Ecol Evol 2018; 8:8380-8395. [PMID: 30250710 PMCID: PMC6144965 DOI: 10.1002/ece3.4358] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/19/2018] [Accepted: 06/20/2018] [Indexed: 01/13/2023] Open
Abstract
The abundance and biomass of benthic foraminifera are high in intertidal rocky-shore habitats. However, the availability of food to support their high biomass has been poorly studied in these habitats compared to those at seafloor covered by sediments. Previous field and laboratory observations have suggested that there is diversity in the food preferences and modes of life among rocky-shore benthic foraminifera. In this study, we used the stable nitrogen isotopic composition of amino acids to estimate the trophic position, trophic niche, and feeding strategy of individual foraminifera species. We also characterized the configuration and structure of the endobiotic microalgae in foraminifera using transmission electron microscopy, and we identified the origin of endobionts based on nucleotide sequences. Our results demonstrated a large variation in the trophic positions of different foraminifera from the same habitat, a reflection of endobiotic features and the different modes of life and food preferences of the foraminifera. Foraminifera did not rely solely on exogenous food sources. Some species effectively used organic matter derived from endobionts in the cell cytoplasm. The high biomass and species density of benthic foraminifera found in intertidal rocky-shore habitats are thus probably maintained by the use of multiple nitrogen resources and by microhabitat segregation among species as a consequence.
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Affiliation(s)
- Masashi Tsuchiya
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
| | - Yoshito Chikaraishi
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
- Institute of Low Temperature ScienceHokkaido UniversitySapporoJapan
| | - Hidetaka Nomaki
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
| | - Yoko Sasaki
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
| | | | | | - Naohiko Ohkouchi
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
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18
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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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19
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Hu SK, Liu Z, Alexander H, Campbell V, Connell PE, Dyhrman ST, Heidelberg KB, Caron DA. Shifting metabolic priorities among key protistan taxa within and below the euphotic zone. Environ Microbiol 2018; 20:2865-2879. [PMID: 29708635 DOI: 10.1111/1462-2920.14259] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 12/12/2022]
Abstract
A metatranscriptome study targeting the protistan community was conducted off the coast of Southern California, at the San Pedro Ocean Time-series station at the surface, 150 m (oxycline), and 890 m to link putative metabolic patterns to distinct protistan lineages. Comparison of relative transcript abundances revealed depth-related shifts in the nutritional modes of key taxonomic groups. Eukaryotic gene expression in the sunlit surface environment was dominated by phototrophs, such as diatoms and chlorophytes, and high abundances of transcripts associated with synthesis pathways (e.g., photosynthesis, carbon fixation, fatty acid synthesis). Sub-euphotic depths (150 and 890 m) exhibited strong contributions from dinoflagellates and ciliates, and were characterized by transcripts relating to digestion or intracellular nutrient recycling (e.g., breakdown of fatty acids and V-type ATPases). These transcriptional patterns underlie the distinct nutritional modes of ecologically important protistan lineages that drive marine food webs, and provide a framework to investigate trophic dynamics across diverse protistan communities.
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Affiliation(s)
- Sarah K Hu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Zhenfeng Liu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Harriet Alexander
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, USA
| | - Victoria Campbell
- Division Allergy and Infectious Diseases, UW Medicine, Seattle, WA, USA
| | - Paige E Connell
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Sonya T Dyhrman
- Department of Earth and Environmental Sciences, Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA
| | - Karla B Heidelberg
- 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
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20
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Graupner N, Boenigk J, Bock C, Jensen M, Marks S, Rahmann S, Beisser D. Functional and phylogenetic analysis of the core transcriptome of Ochromonadales. METABARCODING AND METAGENOMICS 2017. [DOI: 10.3897/mbmg.1.19862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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21
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Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis. ISME JOURNAL 2017; 11:2022-2034. [PMID: 28524870 PMCID: PMC5563956 DOI: 10.1038/ismej.2017.68] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/20/2017] [Accepted: 04/03/2017] [Indexed: 12/24/2022]
Abstract
Collectively, phagotrophic algae (mixotrophs) form a functional continuum of nutritional modes between autotrophy and heterotrophy, but the specific physiological benefits of mixotrophic nutrition differ among taxa. Ochromonas spp. are ubiquitous chrysophytes that exhibit high nutritional flexibility, although most species generally fall towards the heterotrophic end of the mixotrophy spectrum. We assessed the sources of carbon and nitrogen in Ochromonas sp. strain BG-1 growing mixotrophically via short-term stable isotope probing. An axenic culture was grown in the presence of either heat-killed bacteria enriched with 15N and 13C, or unlabeled heat-killed bacteria and labeled inorganic substrates (13C-bicarbonate and 15N-ammonium). The alga exhibited high growth rates (up to 2 divisions per day) only until heat-killed bacteria were depleted. NanoSIMS and bulk IRMS isotope analyses revealed that Ochromonas obtained 84-99% of its carbon and 88-95% of its nitrogen from consumed bacteria. The chrysophyte assimilated inorganic 13C-carbon and 15N-nitrogen when bacterial abundances were very low, but autotrophic (photosynthetic) activity was insufficient to support net population growth of the alga. Our use of nanoSIMS represents its first application towards the study of a mixotrophic alga, enabling a better understanding and quantitative assessment of carbon and nutrient acquisition by this species.
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22
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Lie AAY, Liu Z, Terrado R, Tatters AO, Heidelberg KB, Caron DA. Effect of light and prey availability on gene expression of the mixotrophic chrysophyte, Ochromonas sp. BMC Genomics 2017; 18:163. [PMID: 28196482 PMCID: PMC5310065 DOI: 10.1186/s12864-017-3549-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/02/2017] [Indexed: 12/21/2022] Open
Abstract
Background Ochromonas is a genus of mixotrophic chrysophytes that is found ubiquitously in many aquatic environments. Species in this genus can be important consumers of bacteria but vary in their ability to perform photosynthesis. We studied the effect of light and bacteria on growth and gene expression of a predominantly phagotrophic Ochromonas species. Axenic cultures of Ochromonas sp. were fed with heat-killed bacteria (HKB) and grown in constant light or darkness. RNA was extracted from cultures in the light or in the dark with HKB present (Light + HKB; Dark + HKB), and in the light after HKB were depleted (Light + depleted HKB). Results There were no significant differences in the growth or bacterial ingestion rates between algae grown in light or dark conditions. The availability of light led to a differential expression of only 8% of genes in the transcriptome. A number of genes associated with photosynthesis, phagotrophy, and tetrapyrrole synthesis was upregulated in the Light + HKB treatment compared to Dark + HKB. Conversely, the comparison between the Light + HKB and Light + depleted HKB treatments revealed that the presence of HKB led to differential expression of 59% of genes, including the majority of genes involved in major carbon and nitrogen metabolic pathways. Genes coding for unidirectional enzymes for the utilization of glucose were upregulated in the presence of HKB, implying increased glycolytic activities during phagotrophy. Algae without HKB upregulated their expression of genes coding for ammonium transporters, implying uptake of inorganic nitrogen from the culture medium when prey were unavailable. Conclusions Transcriptomic results agreed with previous observations that light had minimal effect on the population growth of Ochromonas sp. However, light led to the upregulation of a number of phototrophy- and phagotrophy-related genes, while the availability of bacterial prey led to prominent changes in major carbon and nitrogen metabolic pathways. Our study demonstrated the potential of transcriptomic approaches to improve our understanding of the trophic physiologies of complex mixotrophs, and revealed responses in Ochromonas sp. not apparent from traditional culture studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3549-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alle A Y Lie
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA.
| | - Zhenfeng Liu
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Ramon Terrado
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Avery O Tatters
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Karla B Heidelberg
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
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23
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Beisser D, Graupner N, Bock C, Wodniok S, Grossmann L, Vos M, Sures B, Rahmann S, Boenigk J. Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes. PeerJ 2017; 5:e2832. [PMID: 28097055 PMCID: PMC5228505 DOI: 10.7717/peerj.2832] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/27/2016] [Indexed: 02/02/2023] Open
Abstract
Background Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes. Results We sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae. Conclusions Our study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.
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Affiliation(s)
- Daniela Beisser
- Genome Informatics, University of Duisburg-Essen, Essen, Germany
| | - Nadine Graupner
- Biodiversity, University of Duisburg-Essen, Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Christina Bock
- Biodiversity, University of Duisburg-Essen, Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Sabina Wodniok
- Biodiversity, University of Duisburg-Essen, Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Lars Grossmann
- Biodiversity, University of Duisburg-Essen, Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Matthijs Vos
- Theoretical and Applied Biodiversity, Ruhr-University Bochum, Bochum, Germany
| | - Bernd Sures
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany
| | - Sven Rahmann
- Genome Informatics, University of Duisburg-Essen, Essen, Germany
| | - Jens Boenigk
- Biodiversity, University of Duisburg-Essen, Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
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Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis. PLoS One 2017; 12:e0168183. [PMID: 28056027 PMCID: PMC5215829 DOI: 10.1371/journal.pone.0168183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 11/28/2016] [Indexed: 11/19/2022] Open
Abstract
Aquatic environments are heavily impacted by human activities including climate warming and the introduction of xenobiotics. Due to the application of silver nanoparticles as bactericidal agent the introduction of silver into the environment strongly has increased during the past years. Silver ions affect the primary metabolism of algae, in particular photosynthesis. Mixotrophic algae are an interesting test case as they do not exclusively rely on photosynthesis which may attenuate the harmful effect of silver. In order to study the effect of silver ions on mixotrophs, cultures of the chrysophyte Poterioochromonas malhamensis were treated in a replicate design in light and darkness with silver nitrate at a sub-lethal concentration. At five time points samples were taken for the identification and quantitation of proteins by mass spectrometry. In our analysis, relative quantitative protein mass spectrometry has shown to be a useful tool for functional analyses in conjunction with transcriptome reference sequences. A total of 3,952 proteins in 63 samples were identified and quantified, mapping to 4,829 transcripts of the sequenced and assembled transcriptome. Among them, 720 and 104 proteins performing various cellular functions were differentially expressed after eight days in light versus darkness and after three days of silver treatment, respectively. Specifically pathways of the energy and primary carbon metabolism were differentially affected by light and the utilization of expensive reactions hints to an energy surplus of P. malhamensis under light conditions. The excess energy is not invested in growth, but in the synthesis of storage metabolites. The effects of silver were less explicit, observable especially in the dark treatments where the light effect could not mask coinciding but weaker effects of silver. Photosynthesis, particularly the light harvesting complexes, and several sulphur containing enzymes were affected presumably due to a direct interference with the silver ions, mainly affecting energy supply.
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25
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Caron DA, Alexander H, Allen AE, Archibald JM, Armbrust EV, Bachy C, Bell CJ, Bharti A, Dyhrman ST, Guida SM, Heidelberg KB, Kaye JZ, Metzner J, Smith SR, Worden AZ. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat Rev Microbiol 2016; 15:6-20. [DOI: 10.1038/nrmicro.2016.160] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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