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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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Borbee EM, Puspa IA, Restiana E, Setiawan F, Maduppa H, Humphries AT, Lane CE. Surface currents shape protist community structure across the Indo-Pacific. JOURNAL OF PHYCOLOGY 2024. [PMID: 38817114 DOI: 10.1111/jpy.13465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/25/2024] [Accepted: 04/02/2024] [Indexed: 06/01/2024]
Abstract
Biogeographic structure in marine protist communities is shaped by a combination of dispersal potential and environmental selection. High-throughput sequencing and global sampling efforts have helped better resolve the composition and functions of these communities in the world's oceans using both molecular and visual methods. However, molecular barcoding data are critically lacking across the Indo-Pacific, a region widely considered the epicenter of marine biodiversity. To fill this gap, we characterized protist communities in four sampling regions across Indonesia that represent the latitudinal, longitudinal, and human population gradients of the region: Lombok, Wakatobi, Misool, and Waigeo. We show high spatial structuring in marine protist communities across Indonesia, and biotic factors appear to play little role in driving this observed structure. Our results appear to be driven by abiotic factors linked to surface current patterns across the Indo-Pacific as a result of: (1) a choke point in circulation at the Indonesian Throughflow leading to low diatom diversity in Lombok, Wakatobi, and Misool; (2) an increase in nutrient availability at the edge of the Halmahera Eddy in Waigeo, leading to an increase in diatom diversity; and/or (3) seasonal variations in protist communities in line with shifts in velocity of the Indonesian Throughflow. Overall, our results highlight the importance of abiotic factors in shaping protist communities on broad geographic scales over biotic, top-down pressures, such as grazing from higher trophic levels.
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Affiliation(s)
- Erin M Borbee
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Inna Ayu Puspa
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Ester Restiana
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Fahkrizal Setiawan
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Hawis Maduppa
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Austin T Humphries
- Department of Fisheries, Animal, and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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3
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Li S, Luo N, Li C, Mao S, Huang H. Diversity and distribution analysis of eukaryotic communities in the Xiangshan Bay, East China sea by metabarcoding approach. MARINE ENVIRONMENTAL RESEARCH 2024; 197:106451. [PMID: 38492505 DOI: 10.1016/j.marenvres.2024.106451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/04/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Eukaryotic communities play an important role in the coastal ecosystem of Xiangshan Bay, a narrow semi-closed bay famous for fisheries and marine farming. However, information on the diversity and composition of eukaryotic communities in Xiangshan Bay remains unclear. In this study, the metabarcoding approach was utilized to comprehensively investigate the eukaryotic plankton community structure and dominant taxa, particularly eukaryotic microalgae, in the Xiangshan Bay over a period of four months in 2018. The results showed that the three major phyla were Arthropoda, Chlorophyta, and Bacillariophyta. The richness indices revealed that species richness peaked in February and was at its lowest in May. Diversity indices showed that the samples collected in May had the lowest diversity. Centropages was detected in the samples of all months, however, its highest dominance was observed in the samples collected in February. In addition, compared to other months, a greater proportion of eukaryotic microalgae was witnessed in March. The three eukaryotic algae with highest abundances in March were Cyclotella, Prorocentrum, and Thalassiosira. Moreover, high diversity of pico-sized (0.2-2.0 μm) phytoplankton (which are often easily missed by microscopy) was discovered in this study by using metabarcoding approach. This study highlights the strength and significance of the metabarcoding approach to uncover a large number of eukaryotic species which remains undetectable during application of conventional approaches. The findings of this study reveals that the eukaryotic community structure varies noticeably in both time and space throughout sampling period, with temperature being the most important environmental factor influencing these changes. This study lays a solid foundation to understand eukaryotic plankton composition, temporal and spatial dynamics and the distribution mechanism of eukaryotic plankton community in Xiangshan Bay, providing theoretical reference for further studies related to marine ecology.
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Affiliation(s)
- Shuangqing Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Ningjian Luo
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Chuang Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Shuoqian Mao
- Ningbo Institute of Oceanography, Ningbo, 315832, China.
| | - Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
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4
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Pigani E, Mele BH, Campese L, Ser-Giacomi E, Ribera M, Iudicone D, Suweis S. Deviation from neutral species abundance distributions unveils geographical differences in the structure of diatom communities. SCIENCE ADVANCES 2024; 10:eadh0477. [PMID: 38457496 PMCID: PMC10923497 DOI: 10.1126/sciadv.adh0477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/05/2024] [Indexed: 03/10/2024]
Abstract
In recent years, the application of metagenomics techniques has advanced our understanding of plankton communities and their global distribution. Despite this progress, the relationship between the abundance distribution of diatom species and varying marine environmental conditions remains poorly understood. This study, leveraging data from the Tara Oceans expedition, tests the hypothesis that diatoms in sampled stations display a consistent species abundance distribution structure, as though they were sampled from a single ocean-wide metacommunity. Using a neutral sampling theory, we thus develop a framework to estimate the structure and diversity of diatom communities at each sampling station given the shape of the species abundance distribution of the metacommunity and the information of a reference station. Our analysis reveals a substantial temperature gradient in the discrepancies between predicted and observed biodiversity across the sampled stations. These findings challenge the hypothesis of a single neutral metacommunity, indicating that environmental differences substantially influence both the composition and structure of diatom communities.
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Affiliation(s)
- Emanuele Pigani
- Stazione Zoologica Anton Dohrn, 80135 Napoli, Italy
- Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università di Padova, 35131 Padova, Italy
| | | | | | - Enrico Ser-Giacomi
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Samir Suweis
- Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università di Padova, 35131 Padova, Italy
- Istituto Nazionale di Fisica Nucleare, INFN, Sezione di Padova, 35131 Padova, Italy
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5
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Meziti A, Smeti E, Daniilides D, Spatharis S, Tsirtsis G, Kormas KA. Increased contribution of parasites in microbial eukaryotic communities of different Aegean Sea coastal systems. PeerJ 2023; 11:e16655. [PMID: 38144191 PMCID: PMC10740597 DOI: 10.7717/peerj.16655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/21/2023] [Indexed: 12/26/2023] Open
Abstract
Background-Aim Protistan communities have a major contribution to biochemical processes and food webs in coastal ecosystems. However, related studies are scarce and usually limited in specific groups and/or sites. The present study examined the spatial structure of the entire protistan community in seven different gulfs and three different depths in a regional Mediterranean Sea, aiming to define taxa that are important for differences detected in the marine microbial network across the different gulfs studied as well as their trophic interactions. Methods Protistan community structure analysis was based on the diversity of the V2-V3 hypervariable region of the 18S rRNA gene. Operational taxonomic units (OTUs) were identified using a 97% sequence identity threshold and were characterized based on their taxonomy, trophic role, abundance and niche specialization level. The differentially abundant, between gulfs, OTUs were considered for all depths and interactions amongst them were calculated, with statistic and network analysis. Results It was shown that Dinophyceae, Bacillariophyta and Syndiniales were the most abundant groups, prevalent in all sites and depths. Gulfs separation was more striking at surface corroborating with changes in environmental factors, while it was less pronounced in higher depths. The study of differentially abundant, between gulfs, OTUs revealed that the strongest biotic interactions in all depths occurred between parasite species (mainly Syndiniales) and other trophic groups. Most of these species were generalists but not abundant highlighting the importance of rare species in protistan community assemblage. Conclusion Overall this study revealed the emergence of parasites as important contributors in protistan network regulation regardless of depth.
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Affiliation(s)
- Alexandra Meziti
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
| | - Evangelia Smeti
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
- Institute of Marine Biological Resources & Inland Waters, Hellenic Centre for Marine Research, Anavissos, Greece
| | - Daniil Daniilides
- Faculty of Biology, Department of Ecology and Systematics, University of Athens, Athens, Greece
| | - Sofie Spatharis
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - George Tsirtsis
- Department of Marine Sciences, University of the Aegean, Mytilene, Greece
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Milke F, Meyerjürgens J, Simon M. Ecological mechanisms and current systems shape the modular structure of the global oceans' prokaryotic seascape. Nat Commun 2023; 14:6141. [PMID: 37783696 PMCID: PMC10545751 DOI: 10.1038/s41467-023-41909-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 09/24/2023] [Indexed: 10/04/2023] Open
Abstract
Major biogeographic features of the microbial seascape in the oceans have been established and their underlying ecological mechanisms in the (sub)tropical oceans and the Pacific Ocean identified. However, we still lack a unifying understanding of how prokaryotic communities and biogeographic patterns are affected by large-scale current systems in distinct ocean basins and how they are globally shaped in line with ecological mechanisms. Here we show that prokaryotic communities in the epipelagic Pacific and Atlantic Ocean, in the southern Indian Ocean, and the Mediterranean Sea are composed of modules of co-occurring taxa with similar environmental preferences. The relative partitioning of these modules varies along latitudinal and longitudinal gradients and are related to different hydrographic and biotic conditions. Homogeneous selection and dispersal limitation were identified as the major ecological mechanisms shaping these communities and their free-living (FL) and particle-associated (PA) fractions. Large-scale current systems govern the dispersal of prokaryotic modules leading to the highest diversity near subtropical fronts.
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Affiliation(s)
- Felix Milke
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany.
| | - Jens Meyerjürgens
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstraße 231, D-26129, Oldenburg, Germany.
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7
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Martiny JBH, Martiny AC, Brodie E, Chase AB, Rodríguez-Verdugo A, Treseder KK, Allison SD. Investigating the eco-evolutionary response of microbiomes to environmental change. Ecol Lett 2023; 26 Suppl 1:S81-S90. [PMID: 36965002 DOI: 10.1111/ele.14209] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/27/2023]
Abstract
Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.
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Affiliation(s)
- Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, California, USA
| | - Eoin Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, Dallas, Texas, USA
| | | | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, California, USA
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8
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Chaabane S, de Garidel-Thoron T, Giraud X, Schiebel R, Beaugrand G, Brummer GJ, Casajus N, Greco M, Grigoratou M, Howa H, Jonkers L, Kucera M, Kuroyanagi A, Meilland J, Monteiro F, Mortyn G, Almogi-Labin A, Asahi H, Avnaim-Katav S, Bassinot F, Davis CV, Field DB, Hernández-Almeida I, Herut B, Hosie G, Howard W, Jentzen A, Johns DG, Keigwin L, Kitchener J, Kohfeld KE, Lessa DVO, Manno C, Marchant M, Ofstad S, Ortiz JD, Post A, Rigual-Hernandez A, Rillo MC, Robinson K, Sagawa T, Sierro F, Takahashi KT, Torfstein A, Venancio I, Yamasaki M, Ziveri P. The FORCIS database: A global census of planktonic Foraminifera from ocean waters. Sci Data 2023; 10:354. [PMID: 37270659 DOI: 10.1038/s41597-023-02264-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/24/2023] [Indexed: 06/05/2023] Open
Abstract
Planktonic Foraminifera are unique paleo-environmental indicators through their excellent fossil record in ocean sediments. Their distribution and diversity are affected by different environmental factors including anthropogenically forced ocean and climate change. Until now, historical changes in their distribution have not been fully assessed at the global scale. Here we present the FORCIS (Foraminifera Response to Climatic Stress) database on foraminiferal species diversity and distribution in the global ocean from 1910 until 2018 including published and unpublished data. The FORCIS database includes data collected using plankton tows, continuous plankton recorder, sediment traps and plankton pump, and contains ~22,000, ~157,000, ~9,000, ~400 subsamples, respectively (one single plankton aliquot collected within a depth range, time interval, size fraction range, at a single location) from each category. Our database provides a perspective of the distribution patterns of planktonic Foraminifera in the global ocean on large spatial (regional to basin scale, and at the vertical scale), and temporal (seasonal to interdecadal) scales over the past century.
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Affiliation(s)
- Sonia Chaabane
- Aix-Marseille Université, CNRS, IRD, INRAE, CEREGE, Aix-en-Provence, France.
- Department of Climate Geochemistry, Max Planck Institute for Chemistry, Mainz, Germany.
- Fondation pour la recherche sur la biodiversité (FRB-CESAB), Montpellier, France.
| | | | - Xavier Giraud
- Aix-Marseille Université, CNRS, IRD, INRAE, CEREGE, Aix-en-Provence, France
| | - Ralf Schiebel
- Department of Climate Geochemistry, Max Planck Institute for Chemistry, Mainz, Germany
| | - Gregory Beaugrand
- Université Littoral Côte d'Opale, Univ. Lille, CNRS, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, Wimereux, France
| | - Geert-Jan Brummer
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Ocean Systems, Texel, The Netherlands
| | - Nicolas Casajus
- Fondation pour la recherche sur la biodiversité (FRB-CESAB), Montpellier, France
| | - Mattia Greco
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | | | - Hélène Howa
- LPG-BIAF, UMR-CNRS 6112, University of Angers, Angers, France
| | - Lukas Jonkers
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Michal Kucera
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | | | - Julie Meilland
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Fanny Monteiro
- BRIDGE, School of Geographical Sciences, University of Bristol, Bristol, UK
| | - Graham Mortyn
- Universitat Autonoma de Barcelona, ICTA and Dept. of Geography, Barcelona, Spain
| | | | - Hirofumi Asahi
- Fukui Prefectural Satoyama-Satoumi Research Institute, 22-12-1, Torihama, Wakasa, Mikatakaminaka, Fukui, 919-1331, Japan
| | | | - Franck Bassinot
- Laboratoire des Sciences Du Climat et de L'Environnement, Domaine Du CNRS, Gif-sur-Yvette, 91198, France
| | - Catherine V Davis
- Department of Marine, Earth, and Atmospheric Sciences, North Carolina State University, Raleigh, NC, USA
| | - David B Field
- Department of Natural and Computational Sciences, Hawaii Pacific University, Kaneohe, HI, 96744, USA
| | | | - Barak Herut
- Israel Oceanographic & Limnological Research, Haifa, 31080, Israel
| | - Graham Hosie
- SCAR life Sciences. Formerly of the Australian Antarctic Division, Department of the Environment, 203 Channel Highwa, Kingston, Tasmania, 7050, Australia
| | - Will Howard
- Climate Change Institute, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Anna Jentzen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, 24148, Kiel, Germany
| | - David G Johns
- The Marine Biological Association,The Laboratory, Citadel Hill Plymouth, Devon, PL1 2PB, UK
| | - Lloyd Keigwin
- Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - John Kitchener
- Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, 7050, Tasmania, Australia
| | - Karen E Kohfeld
- School of Resource and Environmental Management, Simon Fraser University, Burnaby, Canada
- School of Environmental Science, Simon Fraser University, Vancouver, Canada
| | - Douglas V O Lessa
- Programa de Pós-Graduação em Geoquímica Ambiental, Universidade Federal Fluminense, Niterói, 24.020-141, Rio de Janiero, Brazil
| | - Clara Manno
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB30ET, UK
| | | | - Siri Ofstad
- Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Joseph D Ortiz
- College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, USA
| | - Alexandra Post
- Geoscience Australia, GPO Box 378, Canberra, ACT, 2601, Australia
| | | | - Marina C Rillo
- ICBM, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Wilhelmshaven, Germany
| | | | - Takuya Sagawa
- Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 9201192, Japan
| | - Francisco Sierro
- Departamento de Geología, Universidad de Salamanca, 37008, Salamanca, Spain
| | | | - Adi Torfstein
- The Fredy & Nadine Herrmann Institute of Earth Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Interuniversity Institute for Marine Sciences, Eilat, 88103, Israel
| | - Igor Venancio
- Programa de Geociências (Geoquímica), Universidade Federal Fluminense, Niterói, Brazil
| | - Makoto Yamasaki
- Department of Earth Resource Science, Graduate school of International Resource Sciences, Akita University, 1-1 Tegata-Gakuencho, Akita, 010-8502, Japan
| | - Patrizia Ziveri
- Universitat Autonoma de Barcelona, ICTA and Dept. of Geography, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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9
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Dorrell RG, Kuo A, Füssy Z, Richardson EH, Salamov A, Zarevski N, Freyria NJ, Ibarbalz FM, Jenkins J, Pierella Karlusich JJ, Stecca Steindorff A, Edgar RE, Handley L, Lail K, Lipzen A, Lombard V, McFarlane J, Nef C, Novák Vanclová AM, Peng Y, Plott C, Potvin M, Vieira FRJ, Barry K, de Vargas C, Henrissat B, Pelletier E, Schmutz J, Wincker P, Dacks JB, Bowler C, Grigoriev IV, Lovejoy C. Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae. Life Sci Alliance 2023; 6:6/3/e202201833. [PMID: 36522135 PMCID: PMC9756366 DOI: 10.26508/lsa.202201833] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.
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Affiliation(s)
- Richard G Dorrell
- Institut de Biologie de l'ENS, Département de Biologie, 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
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zoltan Füssy
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Elisabeth H Richardson
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikola Zarevski
- Institut de Biologie de l'ENS, Département de Biologie, 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
| | - Nastasia J Freyria
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Federico M Ibarbalz
- Institut de Biologie de l'ENS, Département de Biologie, 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
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Juan Jose Pierella Karlusich
- Institut de Biologie de l'ENS, Département de Biologie, 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
| | - Andrei Stecca Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robyn E Edgar
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Lori Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - John McFarlane
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Charlotte Nef
- Institut de Biologie de l'ENS, Département de Biologie, 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
| | - Anna Mg Novák Vanclová
- Institut de Biologie de l'ENS, Département de Biologie, 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
| | - Yi Peng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Marianne Potvin
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'ENS, Département de Biologie, 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
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colomban de Vargas
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, Roscoff, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eric Pelletier
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Patrick Wincker
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, 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
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
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10
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Borbee EM, Ayu IP, Carvalho P, Restiana E, Setiawan F, Subhan B, Humphries AT, Madduppa H, Lane CE. Rubble fields shape planktonic protist communities in Indonesia at a local scale. J Eukaryot Microbiol 2023; 70:e12954. [PMID: 36401815 DOI: 10.1111/jeu.12954] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022]
Abstract
The Coral Triangle encompasses nearly 30% of the world's coral reefs and is widely considered the epicenter of marine biodiversity. Destructive fishing practices and natural disturbances common to this region damage reefs leaving behind fields of coral rubble. While the impacts of disturbances in these ecosystems are well documented on metazoans, we have a poor understanding of their impact on microbial communities at the base of the food web. We use metabarcoding to characterize protist community composition in sites of varying fisheries management schemes and benthic profiles across the island of Lombok, Indonesia. Our study shows that rubble coverage and net primary productivity are the strongest explainers of variation in protist communities across Lombok. More specifically, rubble fields are characterized by increases in small heterotrophic protists, including ciliates and cercozoans. In addition to shifts in heterotrophic protist communities, we also observed increases in diatom relative abundance in rubble fields, which corresponded to sites with higher net primary productivity. These results are the first to characterize protist communities in tropical marine rubble fields and provide insight on environmental factors potentially driving these shifts on a local scale.
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Affiliation(s)
- Erin M Borbee
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Inna Puspa Ayu
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Paul Carvalho
- Department of Fisheries, Animal, and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Ester Restiana
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia.,Department of Fisheries, University of Jambi, Jambi, Indonesia
| | - Fahkrizal Setiawan
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Beginer Subhan
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Austin T Humphries
- Department of Fisheries, Animal, and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Hawis Madduppa
- Department of Marine Science and Technology, Institut Pertainian Bogor, Bogor, Indonesia
| | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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11
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Huang H, Xu S, Li S, Wang X, Guo K, Yan R, Xie W, Yin K, Hou S, Jiang H. Diversity and Distribution of Harmful Algal Bloom Species from Seamount to Coastal Waters in the South China Sea. Microbiol Spectr 2023; 11:e0416922. [PMID: 36815795 PMCID: PMC10100961 DOI: 10.1128/spectrum.04169-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/26/2023] [Indexed: 02/24/2023] Open
Abstract
Mount Xianbei is one of the largest shallow seamounts located in the middle of the South China Sea (SCS), which might play a role in shaping the biodiversity of surrounding continental coastal waters, particularly the diversity of phytoplankton species causing frequent harmful algal blooms (HABs) in northern SCS. However, the diversity, composition, and distribution of phytoplankton species in the seamount regions of Xianbei remain largely unexplored. In this study, samples around and outside the seamount regions were collected during a late summer cruise of 2021 to test whether seamounts play a role in HAB species propagation. In total, we identified 19 HAB species across all samples using the ASV-based DNA metabarcoding approach, 6 of which had not been reported previously in the SCS, suggesting a diverse HAB species in the SCS. Specifically, 16 HAB species were found in the seamount region of Xianbei, and 5 of them were also found in the coastal waters, indicating a close connection between seamount and coastal waters. This study was the first attempt to explore HAB species' spatial diversity and vertical distribution in the seamount region of Xianbei at single-nucleotide resolution, which provides a novel explanation for the coastal HAB occurrence in the northern SCS. IMPORTANCE There are a number of seamounts under the water of the South China Sea (SCS). The seamounts might play a role in shaping the biodiversity of surrounding continental coastal waters. However, there is no direct evidence revealing the relationship of the biodiversity of phytoplankton between seamounts and coastal waters in the SCS, especially those species having the potential to form harmful algal blooms (HABs). Some HAB species might proliferate in certain geographic locations, while others may be broadly distributed across oceanic provinces. In this study, we provided a detailed analysis of phytoplankton composition and molecular detection of HAB species from seamount to coastal waters in the SCS, which suggested a strong interaction in the HAB species between the two areas. This finding provides new insights into the diversity and distribution of HABs in seamounts and their role in shaping the composition and the occurrence of HABs in coastal water.
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Affiliation(s)
- Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
| | - Shuaishuai Xu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Shuangqing Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Xinwei Wang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Kangli Guo
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Rongman Yan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei Xie
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Kedong Yin
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shengwei Hou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Haibo Jiang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
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12
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Flegontova O, Flegontov P, Jachníková N, Lukeš J, Horák A. Water masses shape pico-nano eukaryotic communities of the Weddell Sea. Commun Biol 2023; 6:64. [PMID: 36653511 PMCID: PMC9849203 DOI: 10.1038/s42003-023-04452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Polar oceans belong to the most productive and rapidly changing environments, yet our understanding of this fragile ecosystem remains limited. Here we present an analysis of a unique set of DNA metabarcoding samples from the western Weddell Sea sampled throughout the whole water column and across five water masses with different characteristics and different origin. We focus on factors affecting the distribution of planktonic pico-nano eukaryotes and observe an ecological succession of eukaryotic communities as the water masses move away from the surface and as oxygen becomes depleted with time. At the beginning of this succession, in the photic zone, algae, bacteriovores, and predators of small eukaryotes dominate the community, while another community develops as the water sinks deeper, mostly composed of parasitoids (syndinians), mesoplankton predators (radiolarians), and diplonemids. The strongly correlated distribution of syndinians and diplonemids along the depth and oxygen gradients suggests their close ecological link and moves us closer to understanding the biological role of the latter group in the ocean ecosystem.
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Affiliation(s)
- Olga Flegontova
- grid.418338.50000 0001 2255 8513Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic ,grid.412684.d0000 0001 2155 4545Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Pavel Flegontov
- grid.418338.50000 0001 2255 8513Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic ,grid.412684.d0000 0001 2155 4545Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Nikola Jachníková
- grid.14509.390000 0001 2166 4904Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Julius Lukeš
- grid.418338.50000 0001 2255 8513Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic ,grid.14509.390000 0001 2166 4904Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Aleš Horák
- grid.418338.50000 0001 2255 8513Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic ,grid.14509.390000 0001 2166 4904Department of Molecular Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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13
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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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14
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Vaulot D, Sim CWH, Ong D, Teo B, Biwer C, Jamy M, Lopes dos Santos A. metaPR 2 : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Mol Ecol Resour 2022; 22:3188-3201. [PMID: 35762265 PMCID: PMC9796713 DOI: 10.1111/1755-0998.13674] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/26/2022] [Accepted: 06/20/2022] [Indexed: 01/07/2023]
Abstract
In recent years, metabarcoding has become the method of choice for investigating the composition and assembly of microbial eukaryotic communities. The number of environmental data sets published has increased very rapidly. Although unprocessed sequence files are often publicly available, processed data, in particular clustered sequences, are rarely available in a usable format. Clustered sequences are reported as operational taxonomic units (OTUs) with different similarity levels or more recently as amplicon sequence variants (ASVs). This hampers comparative studies between different environments and data sets, for example examining the biogeographical patterns of specific groups/species, as well analysing the genetic microdiversity within these groups. Here, we present a newly-assembled database of processed 18S rRNA metabarcodes that are annotated with the PR2 reference sequence database. This database, called metaPR2 , contains 41 data sets corresponding to more than 4000 samples and 90,000 ASVs. The database, which is accessible through both a web-based interface (https://shiny.metapr2.org) and an R package, should prove very useful to all researchers working on protist diversity in a variety of systems.
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Affiliation(s)
- Daniel Vaulot
- UMR 7144, ECOMAP, CNRSSorbonne Université, Station Biologique de RoscoffRoscoffFrance
| | | | - Denise Ong
- Asian School of the EnvironmentNanyang Technological UniversitySingapore
| | - Bryan Teo
- Asian School of the EnvironmentNanyang Technological UniversitySingapore
| | - Charlie Biwer
- Department of Organismal Biology (Systematic Biology)Uppsala UniversityUppsalaSweden
| | - Mahwash Jamy
- Department of Organismal Biology (Systematic Biology)Uppsala UniversityUppsalaSweden
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15
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Richter DJ, Watteaux R, Vannier T, Leconte J, Frémont P, Reygondeau G, Maillet N, Henry N, Benoit G, Da Silva O, Delmont TO, Fernàndez-Guerra A, Suweis S, Narci R, Berney C, Eveillard D, Gavory F, Guidi L, Labadie K, Mahieu E, Poulain J, Romac S, Roux S, Dimier C, Kandels S, Picheral M, Searson S, Pesant S, Aury JM, Brum JR, Lemaitre C, Pelletier E, Bork P, Sunagawa S, Lombard F, Karp-Boss L, Bowler C, Sullivan MB, Karsenti E, Mariadassou M, Probert I, Peterlongo P, Wincker P, de Vargas C, Ribera d'Alcalà M, Iudicone D, Jaillon O. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. eLife 2022; 11:78129. [PMID: 35920817 PMCID: PMC9348854 DOI: 10.7554/elife.78129] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton. Oceans are brimming with life invisible to our eyes, a myriad of species of bacteria, viruses and other microscopic organisms essential for the health of the planet. These ‘marine plankton’ are unable to swim against currents and should therefore be constantly on the move, yet previous studies have suggested that distinct species of plankton may in fact inhabit different oceanic regions. However, proving this theory has been challenging; collecting plankton is logistically difficult, and it is often impossible to distinguish between species simply by examining them under a microscope. However, within the last decade, a research schooner called Tara has travelled the globe to gather thousands of plankton samples. At the same time, advances in genomics have made it possible to identify species based only on fragments of their DNA sequence. To understand the hidden geography of plankton communities in Earth’s oceans, Richter et al. pored over DNA from the Tara Oceans expedition. This revealed that, despite being unable to resist the flow of water, various planktonic species which live close to the surface manage to occupy distinct, stable provinces shaped by currents. Different sizes of plankton are distributed in different sized provinces, with the smallest organisms tending to inhabit the smallest areas. Comparing DNA similarities and speeds of currents at the ocean surface revealed how these might stretch and mix plankton communities. Plankton play a critical role in the health of the ocean and the chemical cycles of planet Earth. These results could allow deeper investigation by marine modellers, ecologists, and evolutionary biologists. Meanwhile, work is already underway to investigate how climate change might impact this hidden geography.
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Affiliation(s)
- Daniel J Richter
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Romain Watteaux
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,CEA, DAM, DIF, F-91297, Arpajon Cedex, France
| | - Thomas Vannier
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM, Marseille, France
| | - Jade Leconte
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Paul Frémont
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Gabriel Reygondeau
- Changing Ocean Research Unit, Institute for the Oceans and Fisheries, University of British Columbia. Aquatic Ecosystems Research Lab, Vancouver, Canada.,Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Nicolas Maillet
- Institut pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Gaëtan Benoit
- Univ Rennes, CNRS, Inria, IRISA-UMR 6074, Rennes, France
| | - Ophélie Da Silva
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Antonio Fernàndez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Samir Suweis
- Dipartimento di Fisica e Astronomia 'G. Galilei' & CNISM, INFN, Università di Padova, Padova, Italy
| | - Romain Narci
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Cédric Berney
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Damien Eveillard
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Nantes Université, Ecole Centrale Nantes, CNRS, LS2N, Nantes, France
| | - Frederick Gavory
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Lionel Guidi
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | - Karine Labadie
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Eric Mahieu
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, United States
| | - Céline Dimier
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Directors' Research European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Picheral
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | - Sarah Searson
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | | | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, United States.,Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, United States
| | | | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Yonsei Frontier Lab, Yonsei University, Seoul, Republic of Korea.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg, Zurich, Switzerland
| | - Fabien Lombard
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut Universitaire de France (IUF), Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, United States
| | - Chris Bowler
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, United States.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, United States.,Center of Microbiome Science, The Ohio State University, Columbus, United States.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, United States
| | - Eric Karsenti
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Directors' Research European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Ian Probert
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | | | | | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
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16
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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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17
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Milke F, Sanchez-Garcia S, Dlugosch L, McNichol J, Fuhrman J, Simon M, Wagner-Döbler I. Composition and Biogeography of Planktonic Pro- and Eukaryotic Communities in the Atlantic Ocean: Primer Choice Matters. Front Microbiol 2022; 13:895875. [PMID: 35836413 PMCID: PMC9273945 DOI: 10.3389/fmicb.2022.895875] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/18/2022] [Indexed: 01/02/2023] Open
Abstract
Basin-scale biogeographic observations of marine pelagic pro- and eukaryotic communities are necessary to understand forces driving community composition and for providing a baseline to monitor global change. Deep sequencing of rRNA genes provides community composition at high resolution; yet, it is unclear how the choice of primers affects biogeographic patterns. Here, we re-amplified 16S rRNA genes from DNA sampled during R/V Polarstern Cruise ANT28-5 over a latitudinal transect across the Atlantic Ocean from 52°S to 47°N using universal V4-V5 primers and compared the results with those obtained previously with V5-V6 bacteria-specific primers. For validation of our results, we inferred community composition based on 16S rRNA genes of metagenomes from the same stations and single amplified genomes (SAGs) from the Global Ocean Reference Genome (GORG) database. We found that the universal V4-V5 primers retrieved SAR11 clades with similar relative proportions as those found in the GORG database while the V5-V6 primers recovered strongly diverging clade abundances. We confirmed an inverse bell-shaped distance-decay relationship and a latitudinal diversity gradient that did not decline linearly with absolute latitude in the Atlantic Ocean. Patterns were modified by sampling depth, sequencing depth, choice of primers, and abundance filtering. Especially richness patterns were not robust to methodological change. This study offers a detailed picture of the Atlantic Ocean microbiome using a universal set of PCR primers that allow for the conjunction of biogeographical patterns among organisms from different domains of life.
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Affiliation(s)
- Felix Milke
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Selene Sanchez-Garcia
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Leon Dlugosch
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jesse McNichol
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jed Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Meinhard Simon
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Irene Wagner-Döbler
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
- *Correspondence: Irene Wagner-Döbler,
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18
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Dominguez-Huerta G, Zayed AA, Wainaina JM, Guo J, Tian F, Pratama AA, Bolduc B, Mohssen M, Zablocki O, Pelletier E, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Bowler C, Eveillard D, Guidi L, Karsenti E, Kuhn JH, Ogata H, Wincker P, Culley A, Chaffron S, Sullivan MB. Diversity and ecological footprint of Global Ocean RNA viruses. Science 2022; 376:1202-1208. [PMID: 35679415 DOI: 10.1126/science.abn6358] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their ecological impacts from pole to pole. Our analyses revealed four ecological zones, latitudinal and depth diversity patterns, and environmental correlates for RNA viruses. Our findings only partially parallel those of cosampled plankton and show unexpectedly high polar ecological interactions. The influence of RNA viruses on ecosystems appears to be large, as predicted hosts are ecologically important. Moreover, the occurrence of auxiliary metabolic genes indicates that RNA viruses cause reprogramming of diverse host metabolisms, including photosynthesis and carbon cycling, and that RNA virus abundances predict ocean carbon export.
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Affiliation(s)
- Guillermo Dominguez-Huerta
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - James M Wainaina
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Jiarong Guo
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Funing Tian
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Mohamed Mohssen
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA.,The Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Erwan Delage
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000 Nantes, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Corinne da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | | | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Damien Eveillard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000 Nantes, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, F-06230 Villefranche-sur-mer, France
| | - Eric Karsenti
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.,Directors' Research European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Alexander Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Samuel Chaffron
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France.,Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000 Nantes, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, OH 43210, USA.,Center of Microbiome Science, The Ohio State University, Columbus, OH 43210, USA.,The Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA
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19
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Hörstmann C, Buttigieg PL, John U, Raes EJ, Wolf-Gladrow D, Bracher A, Waite AM. Microbial diversity through an oceanographic lens: refining the concept of ocean provinces through trophic-level analysis and productivity-specific length scales. Environ Microbiol 2021; 24:404-419. [PMID: 34766422 DOI: 10.1111/1462-2920.15832] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023]
Abstract
In the marine realm, microorganisms are responsible for the bulk of primary production, thereby sustaining marine life across all trophic levels. Longhurst provinces have distinct microbial fingerprints; however, little is known about how microbial diversity and primary productivity change at finer spatial scales. Here, we sampled the Atlantic Ocean from south to north (~50°S-50°N), every ~0.5° latitude. We conducted measurements of primary productivity, chlorophyll-a and relative abundance of 16S and 18S rRNA genes, alongside analyses of the physicochemical and hydrographic environment. We analysed the diversity of autotrophs, mixotrophs and heterotrophs, and noted distinct patterns among these guilds across provinces with high and low chlorophyll-a conditions. Eukaryotic autotrophs and prokaryotic heterotrophs showed a shared inter-province diversity pattern, distinct from the diversity pattern shared by mixotrophs, cyanobacteria and eukaryotic heterotrophs. Additionally, we calculated samplewise productivity-specific length scales, the potential horizontal displacement of microbial communities by surface currents to an intrinsic biological rate (here, specific primary productivity). This scale provides key context for our trophically disaggregated diversity analysis that we could relate to underlying oceanographic features. We integrate this element to provide more nuanced insights into the mosaic-like nature of microbial provincialism, linking diversity patterns to oceanographic transport through primary production.
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Affiliation(s)
- Cora Hörstmann
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany.,Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, Germany
| | | | - Uwe John
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Eric J Raes
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Dieter Wolf-Gladrow
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany
| | - Astrid Bracher
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany.,Institute of Environmental Physics, University of Bremen, Bremen, Germany
| | - Anya M Waite
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada
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20
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Agatha S, Ganser MH, Santoferrara LF. The importance of type species and their correct identification: A key example from tintinnid ciliates (Alveolata, Ciliophora, Spirotricha). J Eukaryot Microbiol 2021; 68:e12865. [PMID: 34243218 DOI: 10.1111/jeu.12865] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/20/2021] [Accepted: 07/05/2021] [Indexed: 11/30/2022]
Abstract
Types and the corresponding rules in the International Code of Zoological Nomenclature are crucial for taxonomy and are meant to provide nomenclatural stability. In the case of neotypification, especially diligent taxonomic work is required to retain continuity. In the present communication, we first outline the main principles of typification and neotypification. We then discuss a critical case, using a current example from the marine planktonic tintinnid genus Tintinnopsis Stein, 1867 (Alveolata, Ciliophora). This diverse and ubiquitous genus is nonmonophyletic, but its revision and the erection of new related genera is currently prevented by the uncertain affiliation of its type species.
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Affiliation(s)
- Sabine Agatha
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Luciana F Santoferrara
- Department of Ecology and Evolutionary Biology, University of Connecticut at Stamford, Stamford, CT, USA.,Department of Marine Sciences, University of Connecticut at Stamford, Stamford, CT, USA
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