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Perneel M, Lagaisse R, Mortelmans J, Maere S, Hablützel PI. Seasonal metabolic dynamics of microeukaryotic plankton: a year-long metatranscriptomic study in a temperate sea. mBio 2024:e0038324. [PMID: 38980008 DOI: 10.1128/mbio.00383-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/11/2024] [Indexed: 07/10/2024] Open
Abstract
Seasonal fluctuations profoundly affect marine microeukaryotic plankton composition and metabolism, but accurately tracking these changes has been a long-standing challenge. In this study, we present a year-long metatranscriptomic data set from the Southern Bight of the North Sea, shedding light on the seasonal dynamics in temperate plankton ecosystems. We observe distinct shifts in active plankton species and their metabolic processes in response to seasonal changes. We characterized the metabolic signatures of different seasonal phases in detail, thereby revealing the metabolic versatility of dinoflagellates, the heterotrophic dietary strategy of Phaeocystis during its late-stage blooms, and stark variations in summer and fall diatom abundance and metabolic activity across nearby sampling stations. Our data illuminate the varied contributions of microeukaryotic taxa to biomass production and nutrient cycling at different times of the year and allow delineation of their ecological niches. IMPORTANCE Ecosystem composition and metabolic functions of temperate marine microeukaryote plankton are strongly influenced by seasonal dynamics. Although monitoring of species composition of microeukaryotes has expanded recently, few methods also contain seasonally resolved information on ecosystem functioning. We generated a year-long spatially resolved metatranscriptomic data set to assess seasonal dynamics of microeukaryote species and their associated metabolic functions in the Southern Bight of the North Sea. Our study underscores the potential of metatranscriptomics as a powerful tool for advancing our understanding of marine ecosystem functionality and resilience in response to environmental changes, emphasizing its potential in continuous marine ecosystem monitoring to enhance our ecological understanding of the ocean's eukaryotic microbiome.
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Affiliation(s)
- Michiel Perneel
- Flanders Marine Institute (VLIZ), Ostend, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | | | | | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Pascal I Hablützel
- Flanders Marine Institute (VLIZ), Ostend, Belgium
- Biology Department, Vrije Universiteit Brussel, Brussels, Belgium
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2
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Zhang Z, Zhang Q, Chen B, Yu Y, Wang T, Xu N, Fan X, Penuelas J, Fu Z, Deng Y, Zhu YG, Qian H. Global biogeography of microbes driving ocean ecological status under climate change. Nat Commun 2024; 15:4657. [PMID: 38822036 PMCID: PMC11143227 DOI: 10.1038/s41467-024-49124-0] [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: 10/25/2023] [Accepted: 05/23/2024] [Indexed: 06/02/2024] Open
Abstract
Microbial communities play a crucial role in ocean ecology and global biogeochemical processes. However, understanding the intricate interactions among diversity, taxonomical composition, functional traits, and how these factors respond to climate change remains a significant challenge. Here, we propose seven distinct ecological statuses by systematically considering the diversity, structure, and biogeochemical potential of the ocean microbiome to delineate their biogeography. Anthropogenic climate change is expected to alter the ecological status of the surface ocean by influencing environmental conditions, particularly nutrient and oxygen contents. Our predictive model, which utilizes machine learning, indicates that the ecological status of approximately 32.44% of the surface ocean may undergo changes from the present to the end of this century, assuming no policy interventions. These changes mainly include poleward shifts in the main taxa, increases in photosynthetic carbon fixation and decreases in nutrient metabolism. However, this proportion can decrease significantly with effective control of greenhouse gas emissions. Our study underscores the urgent necessity for implementing policies to mitigate climate change, particularly from an ecological perspective.
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Affiliation(s)
- Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
- College of Chemistry & Chemical Engineering, Shaoxing University, Shaoxing, 312000, PR China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, PR China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
- College of Chemistry & Chemical Engineering, Shaoxing University, Shaoxing, 312000, PR China
| | - Xiaoji Fan
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, PR China
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, 08193, Barcelona, Catalonia, Spain
- CREAF, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Catalonia, Spain
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Ye Deng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, PR China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, PR China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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Novák Vanclová AM, Nef C, Füssy Z, Vancl A, Liu F, Bowler C, Dorrell RG. New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates. EMBO Rep 2024; 25:1859-1885. [PMID: 38499810 PMCID: PMC11014865 DOI: 10.1038/s44319-024-00103-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024] Open
Abstract
Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes that can serve as a model system for plastid symbiogenesis due to their susceptibility to plastid loss and replacement via serial endosymbiosis. Kareniaceae harbor fucoxanthin-pigmented plastids instead of the ancestral peridinin-pigmented ones and support them with a diverse range of nucleus-encoded plastid-targeted proteins originating from the haptophyte endosymbiont, dinoflagellate host, and/or lateral gene transfers (LGT). Here, we present predicted plastid proteomes from seven distantly related kareniaceans in three genera (Karenia, Karlodinium, and Takayama) and analyze their evolutionary patterns using automated tree building and sorting. We project a relatively limited ( ~ 10%) haptophyte signal pointing towards a shared origin in the family Chrysochromulinaceae. Our data establish significant variations in the functional distributions of these signals, emphasizing the importance of micro-evolutionary processes in shaping the chimeric proteomes. Analysis of plastid genome sequences recontextualizes these results by a striking finding the extant kareniacean plastids are in fact not all of the same origin, as two of the studied species (Karlodinium armiger, Takayama helix) possess plastids from different haptophyte orders than the rest.
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Affiliation(s)
- Anna Mg Novák Vanclová
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.
- Institute Jacques Monod, Paris, France.
| | - Charlotte Nef
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Zoltán Füssy
- Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Adél Vancl
- Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Fuhai Liu
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Centre de Recherches Interdisciplinaires, Paris, France
- Tsinghua-UC Berkeley Shenzhen Institute, Shenzhen, China
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Richard G Dorrell
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, Sorbonne Université, Paris, France.
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Carve M, Manning T, Mouradov A, Shimeta J. eDNA metabarcoding reveals biodiversity and depth stratification patterns of dinoflagellate assemblages within the epipelagic zone of the western Coral Sea. BMC Ecol Evol 2024; 24:38. [PMID: 38528460 DOI: 10.1186/s12862-024-02220-7] [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: 08/11/2023] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Dinoflagellates play critical roles in the functioning of marine ecosystems but also may pose a hazard to human and ecosystem health by causing harmful algal blooms (HABs). The Coral Sea is a biodiversity hotspot, but its dinoflagellate assemblages in pelagic waters have not been studied by modern sequencing methods. We used metabarcoding of the 18 S rRNA V4 amplicon to assess the diversity and structure of dinoflagellate assemblages throughout the water column to a depth of 150 m at three stations in the Western Coral Sea. Additionally, at one station we compared metabarcoding with morphological methods to optimise identification and detection of dinoflagellates. RESULTS Stratification of dinoflagellate assemblages was evident in depth-specific relative abundances of taxonomic groups; the greatest difference was between the 5-30 m assemblages and the 130-150 m assemblages. The relative abundance of Dinophyceae (photosynthetic and heterotrophic) decreased with increasing depth, whereas that of Syndiniales (parasitic) increased with increasing depth. The composition of major taxonomic groups was similar among stations. Taxonomic richness and diversity of amplicon sequence variants (ASVs) were similar among depths and stations; however, the abundance of dominant taxa was highest within 0-30 m, and the abundance of rare taxa was highest within 130-150 m, indicating adaptations to specific depth strata. The number of unclassified ASVs at the family and species levels was very high, particularly for Syndinian representatives. CONCLUSIONS Dinoflagellate assemblages in open water of the Coral Sea are highly diverse and taxonomically stratified by depth; patterns of relative abundance along the depth gradient reflect environmental factors and ecological processes. Metabarcoding detects more species richness than does traditional microscopical methods of sample analysis, yet the methods are complementary, with morphological analysis revealing additional richness. The large number of unclassified dinoflagellate-ASVs indicates a need for improved taxonomic reference databases and suggests presence of dinoflagellate-crypto and-morphospecies.
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Affiliation(s)
- Megan Carve
- School of Science, RMIT University, Melbourne, VIC, Australia
| | - Tahnee Manning
- School of Science, RMIT University, Melbourne, VIC, Australia
| | - Aidyn Mouradov
- School of Science, RMIT University, Melbourne, VIC, Australia
| | - Jeff Shimeta
- School of Science, RMIT University, Melbourne, VIC, Australia.
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5
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Kajan K, Fuchs BM, Orlić S. Insight into planktonic protistan and fungal communities across the nutrient-depleted environment of the South Pacific Subtropical Gyre. Microbiol Spectr 2024; 12:e0301623. [PMID: 38334383 PMCID: PMC10913754 DOI: 10.1128/spectrum.03016-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Ocean microorganisms constitute ~70% of the marine biomass, contribute to ~50% of the Earth's primary production, and play a vital role in global biogeochemical cycles. The marine heterotrophic and mixotrophic protistan and fungal communities have often been overlooked mainly due to limitations in morphological species identification. Despite the accumulation of studies on biogeographic patterns observed in microbial communities, our understanding of the abundance and distribution patterns within the microbial community of the largest subtropical gyre, the South Pacific Gyre (SPG), remains incomplete. Here, we investigated the diversity and vertical composition of protistan and fungal communities in the water column of the ultra-oligotrophic SPG. Our results showed apparent differences in protistan community diversity in the photic and aphotic regions. The entire protistan community diversity was significantly affected by temperature, salinity, oxygen, and nutrient concentrations, while the parasitic community diversity was also affected by chlorophyll a concentration. The parasitic protists were assigned to the class Syndiniales accounting for over 98% of the total parasitic protists, exhibiting higher relative sequence abundance along the water depth and displaying consistent patterns among different sampling stations. In contrast to the protistan community, the fungal community along the SPG primarily clustered based on the sampling station and pelagic zones. In particular, our study reveals a significant presence of parasitic protists and functionally diverse fungi in SPG and their potential impact on carbon cycling in the gyre.IMPORTANCEOur findings carry important implications for understanding the distribution patterns of the previously unrecognized occurrence of parasitic protists and functionally diverse fungi in the nutrient-limited South Pacific Gyre. In particular, our study reveals a significant presence of parasitic Syndiniales, predominantly abundant in the upper 300 m of the aphotic zone in the gyre, and a distinct presence of fungal communities in the aphotic zone at the central part of the gyre. These findings strongly suggest that these communities play a substantial role in yet insufficiently described microbial food web. Moreover, our research enhances our understanding of their contribution to the dynamics of the food webs in oligotrophic gyres and is valuable for projecting the ecological consequences of future climate warming.
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Affiliation(s)
- Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
| | - Bernhard M. Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Zagreb, Croatia
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6
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Li H, Chen J, Yu L, Fan G, Li T, Li L, Yuan H, Wang J, Wang C, Li D, Lin S. In situ community transcriptomics illuminates CO 2-fixation potentials and supporting roles of phagotrophy and proton pump in plankton in a subtropical marginal sea. Microbiol Spectr 2024; 12:e0217723. [PMID: 38319114 PMCID: PMC10913738 DOI: 10.1128/spectrum.02177-23] [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: 05/23/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
Lineage-wise physiological activities of plankton communities in the ocean are important but challenging to characterize. Here, we conducted whole-assemblage metatranscriptomic profiling at continental shelf and slope sites in the South China Sea to investigate carbon fixation potential in different lineages. RuBisCO expression, the proxy of Calvin carbon fixation (CCF) potential, was mainly contributed by Bacillariophyta, Chlorophyta, Cyanobacteria, and Haptophyta, which was differentially affected by environmental factors among lineages. CCF potential exhibited positive or negative correlations with phagotrophy gene expression, suggesting phagotrophy possibly enhances or complements CCF. Our data also reveal significant non-Calvin carbon fixation (NCF) potential, as indicated by the active expression of genes in all five currently recognized NCF pathways, mainly contributed by Flavobacteriales, Alteromonadales, and Oceanospirillales. Furthermore, in Flavobacteriales, Alteromonadales, Pelagibacterales, and Rhodobacterales, NCF potential was positively correlated with proton-pump rhodopsin (PPR) expression, suggesting that NCF might be energetically supported by PPR. The novel insights into the lineage-differential potential of carbon fixation, widespread mixotrophy, and PPR as an energy source for NCF lay a methodological and informational foundation for further research to understand carbon fixation and the trophic landscape in the ocean.IMPORTANCEMarine plankton plays an important role in global carbon cycling and climate regulation. Phytoplankton and cyanobacteria fix CO2 to produce organic compounds using solar energy and mainly by the Calvin cycle, whereas autotrophic bacteria and archaea may fix CO2 by non-Calvin cycle carbon fixation pathways. How active individual lineages are in carbon fixation and mixotrophy, and what energy source bacteria may employ in non-Calvin carbon fixation, in a natural plankton assemblage are poorly understood and underexplored. Using metatranscriptomics, we studied carbon fixation in marine plankton with lineage resolution in tropical marginal shelf and slope areas. Based on the sequencing results, we characterized the carbon fixation potential of different lineages and assessed Calvin- and non-Calvin- carbon fixation activities and energy sources. Data revealed a high number of unigenes (4.4 million), lineage-dependent differential potentials of Calvin carbon fixation and responses to environmental conditions, major contributors of non-Calvin carbon fixation, and their potential energy source.
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Affiliation(s)
- Hongfei Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
| | - Jianwei Chen
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, Shandong, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Guangyi Fan
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, Shandong, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, Guangdong, China
| | - Tangcheng Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Huatao Yuan
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Jingtian Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Denghui Li
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, Shandong, China
- Qingdao Innovation Center of Seaweed Biotechnology, Qingdao, Shandong, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
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7
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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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8
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Montuori E, De Luca D, Penna A, Stalberga D, Lauritano C. Alexandrium spp.: From Toxicity to Potential Biotechnological Benefits. Mar Drugs 2023; 22:31. [PMID: 38248656 PMCID: PMC10821459 DOI: 10.3390/md22010031] [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: 11/10/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
Many dinoflagellates of the genus Alexandrium are well known for being responsible for harmful algal blooms (HABs), producing potent toxins that cause damages to other marine organisms, aquaculture, fishery, tourism, as well as induce human intoxications and even death after consumption of contaminated shellfish or fish. In this review, we summarize potential bioprospecting associated to the genus Alexandrium, including which Alexandrium spp. produce metabolites with anticancer, antimicrobial, antiviral, as well as anti-Alzheimer applications. When available, we report their mechanisms of action and targets. We also discuss recent progress on the identification of secondary metabolites with biological properties favorable to human health and aquaculture. Altogether, this information highlights the importance of studying which culturing conditions induce the activation of enzymatic pathways responsible for the synthesis of bioactive metabolites. It also suggests considering and comparing clones collected in different locations for toxin monitoring and marine bioprospecting. This review can be of interest not only for the scientific community, but also for the entire population and industries.
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Affiliation(s)
- Eleonora Montuori
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy;
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy
| | - Daniele De Luca
- Research Infrastructure for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Antonella Penna
- Department of Biomolecular Sciences, University of Urbino, Campus E. Mattei, 61029 Urbino, Italy;
| | - Darta Stalberga
- Department of Biomedical and Clinical Sciences, Division of Clinical Chemistry and Pharmacology, Linköping University, SE-58183 Linköping, Sweden;
| | - Chiara Lauritano
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy
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9
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Browning TJ, Saito MA, Garaba SP, Wang X, Achterberg EP, Moore CM, Engel A, Mcllvin MR, Moran D, Voss D, Zielinski O, Tagliabue A. Persistent equatorial Pacific iron limitation under ENSO forcing. Nature 2023; 621:330-335. [PMID: 37587345 PMCID: PMC10499608 DOI: 10.1038/s41586-023-06439-0] [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: 01/13/2022] [Accepted: 07/14/2023] [Indexed: 08/18/2023]
Abstract
Projected responses of ocean net primary productivity to climate change are highly uncertain1. Models suggest that the climate sensitivity of phytoplankton nutrient limitation in the low-latitude Pacific Ocean plays a crucial role1-3, but this is poorly constrained by observations4. Here we show that changes in physical forcing drove coherent fluctuations in the strength of equatorial Pacific iron limitation through multiple El Niño/Southern Oscillation (ENSO) cycles, but that this was overestimated twofold by a state-of-the-art climate model. Our assessment was enabled by first using a combination of field nutrient-addition experiments, proteomics and above-water hyperspectral radiometry to show that phytoplankton physiological responses to iron limitation led to approximately threefold changes in chlorophyll-normalized phytoplankton fluorescence. We then exploited the >18-year satellite fluorescence record to quantify climate-induced nutrient limitation variability. Such synoptic constraints provide a powerful approach for benchmarking the realism of model projections of net primary productivity to climate changes.
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Affiliation(s)
- Thomas J Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
| | - Mak A Saito
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Shungudzemwoyo P Garaba
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Xuechao Wang
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Eric P Achterberg
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - C Mark Moore
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
| | - Anja Engel
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Dawn Moran
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Daniela Voss
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Oliver Zielinski
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- German Research Center for Artificial Intelligence (DFKI), Oldenburg, Germany
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Warnemünde, Germany
| | - Alessandro Tagliabue
- Department of Earth, Ocean, Ecological Sciences, University of Liverpool, Liverpool, UK
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10
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Browning TJ, Moore CM. Global analysis of ocean phytoplankton nutrient limitation reveals high prevalence of co-limitation. Nat Commun 2023; 14:5014. [PMID: 37591895 PMCID: PMC10435517 DOI: 10.1038/s41467-023-40774-0] [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: 12/02/2022] [Accepted: 08/09/2023] [Indexed: 08/19/2023] Open
Abstract
Nutrient availability limits phytoplankton growth throughout much of the global ocean. Here we synthesize available experimental data to identify three dominant nutrient limitation regimes: nitrogen is limiting in the stratified subtropical gyres and in the summertime Arctic Ocean, iron is most commonly limiting in upwelling regions, and both nutrients are frequently co-limiting in regions in between the nitrogen and iron limited systems. Manganese can be co-limiting with iron in parts of the Southern Ocean, whilst phosphate and cobalt can be co-/serially limiting in some settings. Overall, an analysis of experimental responses showed that phytoplankton net growth can be significantly enhanced through increasing the number of different nutrients supplied, regardless of latitude, temperature, or trophic status, implying surface seawaters are often approaching nutrient co-limitation. Assessments of nutrient deficiency based on seawater nutrient concentrations and nutrient stress diagnosed via molecular biomarkers showed good agreement with experimentally-assessed nutrient limitation, validating conceptual and theoretical links between nutrient stoichiometry and microbial ecophysiology.
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Affiliation(s)
- Thomas J Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24148, Germany.
| | - C Mark Moore
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, SO14 3ZH, UK.
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11
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Shemi A, Ben-Dor S, Rotkopf R, Dym O, Vardi A. Phylogeny and biogeography of the algal DMS-releasing enzyme in the global ocean. ISME COMMUNICATIONS 2023; 3:72. [PMID: 37452148 PMCID: PMC10349084 DOI: 10.1038/s43705-023-00280-2] [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: 02/21/2023] [Revised: 05/27/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Phytoplankton produce the volatile dimethyl sulfide (DMS), an important infochemical mediating microbial interactions, which is also emitted to the atmosphere and affecting the global climate. Albeit the enzymatic source for DMS in eukaryotes was elucidated, namely a DMSP lyase (DL) called Alma1, we still lack basic knowledge regarding its taxonomic distribution. We defined unique sequence motifs which enable the identification of DL homologs (DLHs) in model systems and environmental populations. We used these motifs to predict DLHs in diverse algae by analyzing hundreds of genomic and transcriptomic sequences from model systems under stress conditions and from environmental samples. Our findings show that the DL enzyme is more taxonomically widespread than previously thought, as it is encoded by known algal taxa as haptophytes and dinoflagellates, but also by chlorophytes, pelagophytes and diatoms, which were conventionally considered to lack the DL enzyme. By exploring the Tara Oceans database, we showed that DLHs are widespread across the oceans and are predominantly expressed by dinoflagellates. Certain dinoflagellate DLHs were differentially expressed between the euphotic and mesopelagic zones, suggesting a functional specialization and an involvement in the metabolic plasticity of mixotrophic dinoflagellates. In specific regions as the Southern Ocean, DLH expression by haptophytes and diatoms was correlated with environmental drivers such as nutrient availability. The expanded repertoire of putative DL enzymes from diverse microbial origins and geographic niches suggests new potential players in the marine sulfur cycle and provides a foundation to study the cellular function of the DL enzyme in marine microbes.
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Affiliation(s)
- Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ron Rotkopf
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Orly Dym
- Structural Proteomics Unit, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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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: 6] [Impact Index Per Article: 6.0] [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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Obiol A, López-Escardó D, Salomaki ED, Wiśniewska MM, Forn I, Sà E, Vaqué D, Kolísko M, Massana R. Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory. MICROBIOME 2023; 11:134. [PMID: 37322519 PMCID: PMC10268365 DOI: 10.1186/s40168-023-01571-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Marine heterotrophic flagellates (HF) are dominant bacterivores in the ocean, where they represent the trophic link between bacteria and higher trophic levels and participate in the recycling of inorganic nutrients for regenerated primary production. Studying their activity and function in the ecosystem is challenging since most of the HFs in the ocean are still uncultured. In the present work, we investigated gene expression of natural HF communities during bacterivory in four unamended seawater incubations. RESULTS The most abundant species growing in our incubations belonged to the taxonomic groups MAST-4, MAST-7, Chrysophyceae, and Telonemia. Gene expression dynamics were similar between incubations and could be divided into three states based on microbial counts, each state displaying distinct expression patterns. The analysis of samples where HF growth was highest revealed some highly expressed genes that could be related to bacterivory. Using available genomic and transcriptomic references, we identified 25 species growing in our incubations and used those to compare the expression levels of these specific genes. Video Abstract CONCLUSIONS: Our results indicate that several peptidases, together with some glycoside hydrolases and glycosyltransferases, are more expressed in phagotrophic than in phototrophic species, and thus could be used to infer the process of bacterivory in natural assemblages.
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Affiliation(s)
- Aleix Obiol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain.
| | - David López-Escardó
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Monika M Wiśniewska
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Elisabet Sà
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain.
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14
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Salvato F, Vintila S, Finkel OM, Dangl JL, Kleiner M. Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:977-988. [PMID: 35876747 DOI: 10.1094/mpmi-05-22-0116-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry-based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Fernanda Salvato
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Omri M Finkel
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Jeffery L Dangl
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
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15
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Fu F, Tschitschko B, Hutchins DA, Larsson ME, Baker KG, McInnes A, Kahlke T, Verma A, Murray SA, Doblin MA. Temperature variability interacts with mean temperature to influence the predictability of microbial phenotypes. GLOBAL CHANGE BIOLOGY 2022; 28:5741-5754. [PMID: 35795906 PMCID: PMC9543556 DOI: 10.1111/gcb.16330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/23/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
Despite their relatively high thermal optima (Topt ), tropical taxa may be particularly vulnerable to a rising baseline and increased temperature variation because they live in relatively stable temperatures closer to their Topt . We examined how microbial eukaryotes with differing thermal histories responded to temperature fluctuations of different amplitudes (0 control, ±2, ±4°C) around mean temperatures below or above their Topt . Cosmopolitan dinoflagellates were selected based on their distinct thermal traits and included two species of the same genus (tropical and temperate Coolia spp.), and two strains of the same species maintained at different temperatures for >500 generations (tropical Amphidinium massartii control temperature and high temperature, CT and HT, respectively). There was a universal decline in population growth rate under temperature fluctuations, but strains with narrower thermal niche breadth (temperate Coolia and HT) showed ~10% greater reduction in growth. At suboptimal mean temperatures, cells in the cool phase of the fluctuation stopped dividing, fixed less carbon (C) and had enlarged cell volumes that scaled positively with elemental C, N, and P and C:Chlorophyll-a. However, at a supra-optimal mean temperature, fixed C was directed away from cell division and novel trait combinations developed, leading to greater phenotypic diversity. At the molecular level, heat-shock proteins, and chaperones, in addition to transcripts involving genome rearrangements, were upregulated in CT and HT during the warm phase of the supra-optimal fluctuation (30 ± 4°C), a stress response indicating protection. In contrast, the tropical Coolia species upregulated major energy pathways in the warm phase of its supra-optimal fluctuation (25 ± 4°C), indicating a broadscale shift in metabolism. Our results demonstrate divergent effects between taxa and that temporal variability in environmental conditions interacts with changes in the thermal mean to mediate microbial responses to global change, with implications for biogeochemical cycling.
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Affiliation(s)
- Fei‐Xue Fu
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Bernhard Tschitschko
- Climate Change ClusterUniversity of Technology SydneyUltimoNew South WalesAustralia
- Max Planck Institute for Marine MicrobiologyBremenGermany
| | - David A. Hutchins
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Michaela E. Larsson
- Climate Change ClusterUniversity of Technology SydneyUltimoNew South WalesAustralia
| | - Kirralee G. Baker
- Climate Change ClusterUniversity of Technology SydneyUltimoNew South WalesAustralia
- Institute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
| | - Allison McInnes
- Climate Change ClusterUniversity of Technology SydneyUltimoNew South WalesAustralia
- Centre for Microbiome Research, School of Biomedical SciencesTranslational Research Institute, Queensland University of TechnologyWoolloongabbaQueenslandAustralia
| | - Tim Kahlke
- Climate Change ClusterUniversity of Technology SydneyUltimoNew South WalesAustralia
| | - Arjun Verma
- Climate Change ClusterUniversity of Technology SydneyUltimoNew South WalesAustralia
- School of Life SciencesUniversity of Technology SydneyUltimoNew South WalesAustralia
| | - Shauna A. Murray
- Climate Change ClusterUniversity of Technology SydneyUltimoNew South WalesAustralia
- School of Life SciencesUniversity of Technology SydneyUltimoNew South WalesAustralia
- Sydney Institute of Marine ScienceMosmanNew South WalesAustralia
| | - Martina A. Doblin
- Climate Change ClusterUniversity of Technology SydneyUltimoNew South WalesAustralia
- Sydney Institute of Marine ScienceMosmanNew South WalesAustralia
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16
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Sanchez-Garcia S, Wang H, Wagner-Döbler I. The microbiome of the dinoflagellate Prorocentrum cordatum in laboratory culture and its changes at higher temperatures. Front Microbiol 2022; 13:952238. [PMID: 36246277 PMCID: PMC9555710 DOI: 10.3389/fmicb.2022.952238] [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: 05/24/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
In the ocean, phytoplankton are dependent on communities of bacteria living in the phycosphere, a hot spot of metabolic and genetic exchange. Many types of interactions between phytoplankton and phycosphere bacteria have been shown, but it is unclear if the microbial communities associated with microalgae strains in culture collections are beneficial or harmful to the host strain. Here, we studied the microbial communities associated with four strains of the dinoflagellate Prorocentrum cordatum that had been isolated from distant geographical locations and maintained in culture collection for hundreds of generations. Community composition was determined by 16S rRNA gene amplicon sequencing. The dinoflagellate host strain was the strongest parameter separating communities, while growth phase, lifestyle (particle-attached versus free-living) and temperature had only a modulating effect. Although the strains had been isolated from distant locations in the Atlantic and Pacific Ocean, 14 ASVs were shared among all strains, the most abundant ones being Gilvibacter, Marivita, uncultivated Rhodobacteraceae, Marinobacter, Hyphomonadaceae, Cupriavidus, Variovorax, and Paucibacter. Adaptation to higher temperatures resulted in specific changes in each phycosphere microbiome, including increased abundance of rare community members. We then compared the growth of the four xenic cultures to that of the axenic P. cordatum CCMP1329. At 20°C, growth of the xenic cultures was similar or slower than that of CCMP1329. At 26°C, all four xenic cultures experienced a death phase, while the axenic culture stably remained in the stationary phase. At 30°C, only two of the xenic cultures were able to grow. A shift of dinoflagellate metabolism from autotrophy to mixotrophy and competition between dinoflagellate and bacteria for limiting nutrients, including essential vitamins, may contribute to these differences in growth patterns.
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17
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Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proc Natl Acad Sci U S A 2022; 119:e2200014119. [PMID: 36067300 PMCID: PMC9477243 DOI: 10.1073/pnas.2200014119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.
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18
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Hu R, Liu S, Saleem M, Xiong Z, Zhou Z, Luo Z, Shu L, He Z, Wang C. Environmentally‐induced reconstruction of microbial communities alters particulate carbon flux of deep chlorophyll maxima in the South China sea. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruiwen Hu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Songfeng Liu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Muhammad Saleem
- Department of Biological Sciences Alabama State University Montgomery AL USA
| | - Zhiyao Xiong
- School of Marine Sciences Sun Yat‐sen University Zhuhai
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Longfei Shu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Zhili He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
- College of Agronomy Hunan Agricultural University Changsha China
| | - Cheng Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
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19
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Ward BA, Collins S. Rapid evolution allows coexistence of highly divergent lineages within the same niche. Ecol Lett 2022; 25:1839-1853. [PMID: 35759351 PMCID: PMC9543677 DOI: 10.1111/ele.14061] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/11/2022] [Accepted: 05/30/2022] [Indexed: 01/02/2023]
Abstract
Marine microbial communities are extremely complex and diverse. The number of locally coexisting species often vastly exceeds the number of identifiable niches, and taxonomic composition often appears decoupled from local environmental conditions. This is contrary to the view that environmental conditions should select for a few locally well-adapted species. Here we use an individual-based eco-evolutionary model to show that virtually unlimited taxonomic diversity can be supported in highly evolving assemblages, even in the absence of niche separation. With a steady stream of heritable changes to phenotype, competitive exclusion may be weakened, allowing sustained coexistence of nearly neutral phenotypes with highly divergent lineages. This behaviour is robust even to abrupt environmental perturbations that might be expected to cause strong selection pressure and an associated loss of diversity. We, therefore, suggest that rapid evolution and individual-level variability are key drivers of species coexistence and maintenance of microbial biodiversity.
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Affiliation(s)
- Ben A Ward
- School of Ocean and Earth Science, University of Southampton, Southampton, UK
| | - Sinead Collins
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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20
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Pierella Karlusich JJ, Pelletier E, Zinger L, Lombard F, Zingone A, Colin S, Gasol JM, Dorrell RG, Henry N, Scalco E, Acinas SG, Wincker P, de Vargas C, Bowler C. A robust approach to estimate relative phytoplankton cell abundances from metagenomes. Mol Ecol Resour 2022; 23:16-40. [PMID: 35108459 PMCID: PMC10078663 DOI: 10.1111/1755-0998.13592] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022]
Abstract
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Eric Pelletier
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Fabien Lombard
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), 06230, Villefranche-sur-Mer, France.,Institut Universitaire de France (IUF), Paris, France
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Sébastien Colin
- European Molecular Biology Laboratory, Heidelberg, Germany.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France
| | - Nicolas Henry
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Patrick Wincker
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Colomban de Vargas
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Département de biologie, 75005, Paris, France.,CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
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21
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Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom. THE ISME JOURNAL 2022; 16:569-579. [PMID: 34482372 PMCID: PMC8776772 DOI: 10.1038/s41396-021-01084-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/13/2021] [Accepted: 08/02/2021] [Indexed: 02/07/2023]
Abstract
Production and use of proteins is under strong selection in microbes, but it is unclear how proteome-level traits relate to ecological strategies. We identified and quantified proteomic traits of eukaryotic microbes and bacteria through an Antarctic phytoplankton bloom using in situ metaproteomics. Different taxa, rather than different environmental conditions, formed distinct clusters based on their ribosomal and photosynthetic proteomic proportions, and we propose that these characteristics relate to ecological differences. We defined and used a proteomic proxy for regulatory cost, which showed that SAR11 had the lowest regulatory cost of any taxa we observed at our summertime Southern Ocean study site. Haptophytes had lower regulatory cost than diatoms, which may underpin haptophyte-to-diatom bloom progression in the Ross Sea. We were able to make these proteomic trait inferences by assessing various sources of bias in metaproteomics, providing practical recommendations for researchers in the field. We have quantified several proteomic traits (ribosomal and photosynthetic proteomic proportions, regulatory cost) in eukaryotic and bacterial taxa, which can then be incorporated into trait-based models of microbial communities that reflect resource allocation strategies.
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22
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Disentangling the Ecological Processes Shaping the Latitudinal Pattern of Phytoplankton Communities in the Pacific Ocean. mSystems 2022; 7:e0120321. [PMID: 35089068 PMCID: PMC8725599 DOI: 10.1128/msystems.01203-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Phytoplankton diversity and community compositions vary across spaces and are fundamentally affected by several deterministic (e.g., environmental selection) and stochastic (e.g., ecological drift) processes. How this suite of different processes regulates the biogeography of phytoplankton remains to be comprehensively explored. Using high-throughput sequencing data and null model analysis, we revealed the ecological processes shaping the latitudinal community structure of three major phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) across the Pacific Ocean (70°N, 170°W to 35°S, 170°W). At the basin scale, heterogeneous selection (selection under heterogeneous environmental conditions) dominated the assembly processes of all phytoplankton groups; however, its relative importance varied greatly at the climatic zonal scale, explaining the distinct latitudinal α- and β-diversity among phytoplankton groups. Assembly processes in Synechococcus and haptophyte communities were mainly controlled by physical and nutrient factors, respectively. High temperature drove Synechococcus communities to be more deterministic with higher diversity, while haptophyte communities were less environmentally selected at low latitudes due to their wide niche breadth and mixotrophic lifestyle. Diatom communities were overwhelmingly dominated by the selection process but with low correlation of measured environmental factors to their community compositions. This could be attributed to the high growth rate of diatoms, as indicated by their lower site occupation frequency than predicted in the neutral community model. Our study showed that heterogeneous selection is the main force that shaped the biogeography of three key phytoplankton groups in the Pacific Ocean, with a latitudinal variation of relative importance due to the distinct traits among phytoplankton. IMPORTANCE Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and community compositions varying spatially. How fundamental processes (e.g., selection, dispersal, and drift) regulate their global biogeography remains to be comprehensively explored. In this study, we disentangled the ecological processes of three key phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) along the same latitudinal gradients in the Pacific Ocean. Heterogeneous selection, by promoting species richness and reducing similarity between communities, was the dominant process shaping the communities of each phytoplankton group at the basin scale. However, its relative importance varied greatly among different phytoplankton groups in different climate zones, explaining the uneven latitudinal α- and β-diversity. We also highlight the importance of identifying key factors mediating the relative importance of assembly processes in phytoplankton communities, which will enhance our understanding of their biogeography in the ocean and future patterns under climate changes.
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23
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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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24
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McIlvin MR, Saito MA. Online Nanoflow Two-Dimension Comprehensive Active Modulation Reversed Phase-Reversed Phase Liquid Chromatography High-Resolution Mass Spectrometry for Metaproteomics of Environmental and Microbiome Samples. J Proteome Res 2021; 20:4589-4597. [PMID: 34384028 DOI: 10.1021/acs.jproteome.1c00588] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metaproteomics is a powerful analytical approach that can assess the functional capabilities deployed by microbial communities in both environmental and biomedical microbiome settings. Yet, the mass spectra resulting from these mixed biological communities are challenging to obtain due to the high number of low intensity peak features. The use of multiple dimensions of chromatographic separation prior to mass spectrometry analyses has been applied to proteomics previously but can require increased sampling handling and instrument time. Here, we demonstrate an automated online comprehensive active modulation two-dimensional liquid chromatography method for metaproteome sample analysis. A high pH PLRP-S column was used in the first dimension followed by low pH separation in the second dimension using dual modulating C18 traps and a C18 column. This method increased the number of unique peptides found in ocean metaproteome samples by more than 50% when compared to a one-dimension separation while using the same amount of sample and instrument time.
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Affiliation(s)
- Matthew R McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02563, United States
| | - Mak A Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02563, United States
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25
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Marine plankton metabolisms revealed. Nat Microbiol 2021; 6:147-148. [PMID: 33510437 DOI: 10.1038/s41564-020-00856-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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