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Canals O, Corell J, Villarino E, Chust G, Aylagas E, Mendibil I, Michell CT, González-Gordillo JI, Irigoien X, Rodríguez-Ezpeleta N. Global mesozooplankton communities show lower connectivity in deep oceanic layers. Mol Ecol 2024; 33:e17286. [PMID: 38287749 DOI: 10.1111/mec.17286] [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: 03/31/2023] [Revised: 10/06/2023] [Accepted: 12/22/2023] [Indexed: 01/31/2024]
Abstract
Mesozooplankton is a key component of the ocean, regulating global processes such as the carbon pump, and ensuring energy transfer from lower to higher trophic levels. Yet, knowledge on mesozooplankton diversity, distribution and connectivity at global scale is still fragmented. To fill this gap, we applied DNA metabarcoding to mesozooplankton samples collected during the Malaspina-2010 circumnavigation expedition across the Atlantic, Indian and Pacific oceans from the surface to bathypelagic depths. We highlight the still scarce knowledge on global mesozooplankton diversity and identify the Indian Ocean and the deep sea as the oceanic regions with the highest proportion of hidden diversity. We report no consistent alpha-diversity patterns for mesozooplankton at a global scale, neither across vertical nor horizontal gradients. However, beta-diversity analysis suggests horizontal and vertical structuring of mesozooplankton communities mostly attributed to turnover and reveals an increase in mesozooplankton beta-diversity with depth, indicating reduced connectivity at deeper layers. Additionally, we identify a water mass type-mediated structuring of mesozooplankton bathypelagic communities instead of an oceanic basin-mediated as observed at upper layers. This suggests limited dispersal at deep ocean layers, most likely due to weaker currents and lower mixing of water mass types, thus reinforcing the importance of oceanic currents and barriers to dispersal in shaping global plankton communities.
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Affiliation(s)
- Oriol Canals
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Jon Corell
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Ernesto Villarino
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Guillem Chust
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Eva Aylagas
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Iñaki Mendibil
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Craig T Michell
- Biological and Environmental Science and Engineering Division, Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Juan Ignacio González-Gordillo
- Área de Ecología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Campus de Excelencia Internacional del Mar, Puerto Real, Spain
| | - Xabier Irigoien
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
| | - Naiara Rodríguez-Ezpeleta
- AZTI Marine Research Division, Basque Research and Technology Alliance (BRTA), Sukarrieta, Bizkaia, Spain
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2
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Jiao Y, Yang S, Bao W. Biogeographic patterns and community assembly mechanisms of bacterial community in the upper seawater of seamounts and non-seamounts in the Eastern Indian Ocean. Appl Environ Microbiol 2024; 90:e0142424. [PMID: 39150264 PMCID: PMC11409715 DOI: 10.1128/aem.01424-24] [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: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024] Open
Abstract
Seamounts are widespread underwater topographic features in the ocean that exert an influential role in shaping the microbial biogeographic distribution. Nevertheless, research on the differences in microbial biogeographic distribution between seamount and non-seamount upper water column is still lacking, particularly in the Indian Ocean where studies are limited. In the present study, a total of 45 seawater samples were collected from the water column (5-200 m) of seamounts (HS) and non-seamounts (E87 transect) regions in the Eastern Indian Ocean (EIO) for the analysis of microbial biogeographic patterns and community assembly processes. The results indicated that bacterial community diversity did not differ significantly between the HS and E87 transect regions; however, the community composition was significantly different. Additionally, bacterial community diversity, composition, as well as structure were more affected by depth than by region. Community diversity tended to increase with depth in E87 transect region, while it tended to decrease in HS region. A distance decay analysis also demonstrated that bacterial communities were more influenced by environmental and depth distances than geographic distances. In the assembly of bacterial communities on HS and E87 transect regions, as well as at different depths, stochastic processes, particularly dispersal limitation, were found to be predominant. These findings enhance our comprehension of bacterial community characteristics in the upper seawater of seamounts and non-seamounts regions in the EIO and offer insights into the assembly processes shaping microbial communities at varying depths. IMPORTANCE By comparing the bacterial diversity, composition, and structure in the upper seawater of seamount and non-seamount areas, we provide valuable insights into the influential role of seamounts in shaping microbial biogeography. The finding that the depth had a more significant impact on bacterial community characteristics than region underscores the importance of considering vertical stratification when examining microbial distributions. Moreover, the dominance of stochastic processes, particularly dispersal limitation, in governing community assembly across both seamount and non-seamount areas offers critical implications for the mechanisms underlying microbial biogeographic patterns in these dynamic ocean environments. This study expands the current knowledge and lays the groundwork for further investigations into the complex interactions between oceanographic features, environmental gradients, and microbial community dynamics in the Indian Ocean.
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Affiliation(s)
- Yaqian Jiao
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
| | - Shanshan Yang
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
| | - Wenya Bao
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
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3
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Chen J, Jia Y, Sun Y, Liu K, Zhou C, Liu C, Li D, Liu G, Zhang C, Yang T, Huang L, Zhuang Y, Wang D, Xu D, Zhong Q, Guo Y, Li A, Seim I, Jiang L, Wang L, Lee SMY, Liu Y, Wang D, Zhang G, Liu S, Wei X, Yue Z, Zheng S, Shen X, Wang S, Qi C, Chen J, Ye C, Zhao F, Wang J, Fan J, Li B, Sun J, Jia X, Xia Z, Zhang H, Liu J, Zheng Y, Liu X, Wang J, Yang H, Kristiansen K, Xu X, Mock T, Li S, Zhang W, Fan G. Global marine microbial diversity and its potential in bioprospecting. Nature 2024; 633:371-379. [PMID: 39232160 PMCID: PMC11390488 DOI: 10.1038/s41586-024-07891-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems1,2. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications3,4. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.
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Affiliation(s)
- Jianwei Chen
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ying Sun
- BGI Research, Qingdao, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
| | - Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Chuan Liu
- BGI Research, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Chengsong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Yunyun Zhuang
- Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | | | | | - Yang Guo
- BGI Research, Qingdao, China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | - Inge Seim
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Simon Ming Yuen Lee
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yujing Liu
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | - Guoqiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Xiaofeng Wei
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Shanmin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Sen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chen Qi
- BGI Research, Shenzhen, China
| | - Jing Chen
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | - Chen Ye
- BGI Research, Shenzhen, China
| | | | | | - Jie Fan
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | | | - Xiaodong Jia
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, China
| | - Zhangyong Xia
- Department of Neurology, The Second People's Hospital of Liaocheng, Liaocheng, China
| | - He Zhang
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Xin Liu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Karsten Kristiansen
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xun Xu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
| | - Wenwei Zhang
- BGI Research, Shenzhen, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
| | - Guangyi Fan
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
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Schickele A, Debeljak P, Ayata SD, Bittner L, Pelletier E, Guidi L, Irisson JO. The genomic potential of photosynthesis in piconanoplankton is functionally redundant but taxonomically structured at a global scale. SCIENCE ADVANCES 2024; 10:eadl0534. [PMID: 39151014 PMCID: PMC11328907 DOI: 10.1126/sciadv.adl0534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 07/11/2024] [Indexed: 08/18/2024]
Abstract
Carbon fixation is a key metabolic function shaping marine life, but the underlying taxonomic and functional diversity involved is only partially understood. Using metagenomic resources targeted at marine piconanoplankton, we provide a reproducible machine learning framework to derive the potential biogeography of genomic functions through the multi-output regression of gene read counts on environmental climatologies. Leveraging the Marine Atlas of Tara Oceans Unigenes, we investigate the genomic potential of primary production in the global ocean. The latter is performed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) and is often associated with carbon concentration mechanisms in piconanoplankton, major marine unicellular photosynthetic organisms. We show that the genomic potential supporting C4 enzymes and RUBISCO exhibits strong functional redundancy and important affinity toward tropical oligotrophic waters. This redundancy is taxonomically structured by the dominance of Mamiellophyceae and Prymnesiophyceae in mid and high latitudes. These findings enhance our understanding of the relationship between functional and taxonomic diversity of microorganisms and environmental drivers of key biogeochemical cycles.
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Affiliation(s)
- Alexandre Schickele
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230 Villefranche-sur-Mer, France
| | - Pavla Debeljak
- Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS, EPHE, Université des Antilles, Institut de Systématique, Evolution, Biodiversité (ISYEB), F-75005, Paris, France
- SupBiotech, Villejuif, France
| | - Sakina-Dorothée Ayata
- Sorbonne Université, CNRS, IRD, MNHN, Laboratoire d'Océanographie et du Climat, Institut Pierre Simon Laplace, LOCEAN-IPSL, F-75005 Paris, France
- Institut Universitaire de France, Paris, France
| | - Lucie Bittner
- Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS, EPHE, Université des Antilles, Institut de Systématique, Evolution, Biodiversité (ISYEB), F-75005, Paris, France
- Institut Universitaire de France, Paris, France
| | - Eric Pelletier
- Metabolic Genomics, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université d'Evry, Université Paris Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Lionel Guidi
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230 Villefranche-sur-Mer, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Jean-Olivier Irisson
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230 Villefranche-sur-Mer, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
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Filander ZN, Sink KJ, Kitahara MV, Cairns SD, Lombard AT. Diversity patterns of the South African azooxanthellate scleractinians (Cnidaria: Anthozoa), with considerations of environmental correlates. PLoS One 2024; 19:e0296188. [PMID: 39116158 PMCID: PMC11309500 DOI: 10.1371/journal.pone.0296188] [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: 06/06/2023] [Accepted: 12/05/2023] [Indexed: 08/10/2024] Open
Abstract
Azooxanthellate scleractinian corals, a group of species that lack a symbiotic relationship with dinoflagellates, are influenced by environmental variables at various scales. As the global commitment to sustainably manage ocean ecosystems and resources rises, there is a growing need to describe biodiversity trends in previously unsampled areas. Benthic invertebrate research in South Africa is a developing field, and many taxa in deep water environments remain inadequately characterized. Recently, the South African azooxanthellate scleractinian fauna was taxonomically reviewed, but their distributional correlations with physical parameters have not been studied. Here we aim to understand the biodiversity gradients of the South African azooxanthellate coral fauna by analysing the environmental correlates of museum samples. The associated coordinate data were georeferenced and depth obtained from a national bathymetric dataset, prior to undertaking a multivariate analysis. This analysis encompassed several steps, including the grouping of the longitude and depth data (environmental data), identifying families characteristic of the group variability, and examining the correlation of the associated data with the biological data. Additionally, the analysis involved quantifying diversity patterns along the environmental gradients. Overall, our results confirmed two longitudinal groups (eastern margin [Group A] vs southern and western margin [Group B]) and 11 depth categories represented within two bathymetric zones (shallow [50-200 m] and deep [300-1000 m]). Caryophylliids, flabellids, and dendrophylliids contributed the most towards distinguishing longitudinal and depth gradients. Both abiotic variable (longitudinal and depth) partially explained coral distribution patterns, with depth being highly correlated to the species variation observed. Data limitations within our data set resulted to unexplained variance, however, despite these limitations, the study demonstrates that historical museum samples provide a valuable data source that can fill research sampling gaps and help improve the understanding of biodiversity patterns of the coral fauna in under sampled marine ecosystems.
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Affiliation(s)
- Zoleka N. Filander
- Biodiversity and Coastal Research, Oceans and Coasts, Department of Forestry, Fisheries and Environment, Cape Town, South Africa
- Zoology Department, Nelson Mandela University, Gqeberha, South Africa
| | - Kerry J. Sink
- South African National Biodiversity Institute, Cape Town, South Africa
- Institute for Coastal and Marine Research, Nelson Mandela University, Gqeberha, South Africa
| | - Marcelo V. Kitahara
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, Brazil
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, United States of America
| | - Stephen D. Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, United States of America
| | - Amanda T. Lombard
- Institute for Coastal and Marine Research, Nelson Mandela University, Gqeberha, South Africa
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6
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Zavadska D, Henry N, Auladell A, Berney C, Richter DJ. Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes. PLoS One 2024; 19:e0303697. [PMID: 38843225 PMCID: PMC11156365 DOI: 10.1371/journal.pone.0303697] [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: 11/28/2023] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Two common approaches to study the composition of environmental protist communities are metabarcoding and metagenomics. Raw metabarcoding data are usually processed into Operational Taxonomic Units (OTUs) or amplicon sequence variants (ASVs) through clustering or denoising approaches, respectively. Analogous approaches are used to assemble metagenomic reads into metagenome-assembled genomes (MAGs). Understanding the correspondence between the data produced by these two approaches can help to integrate information between the datasets and to explain how metabarcoding OTUs and MAGs are related with the underlying biological entities they are hypothesised to represent. MAGs do not contain the commonly used barcoding loci, therefore sequence homology approaches cannot be used to match OTUs and MAGs. We made an attempt to match V9 metabarcoding OTUs from the 18S rRNA gene (V9 OTUs) and MAGs from the Tara Oceans expedition based on the correspondence of their relative abundances across the same set of samples. We evaluated several metrics for detecting correspondence between features in these two datasets and developed controls to filter artefacts of data structure and processing. After selecting the best-performing metrics, ranking the V9 OTU/MAG matches by their proportionality/correlation coefficients and applying a set of selection criteria, we identified candidate matches between V9 OTUs and MAGs. In some cases, V9 OTUs and MAGs could be matched with a one-to-one correspondence, implying that they likely represent the same underlying biological entity. More generally, matches we observed could be classified into 4 scenarios: one V9 OTU matches many MAGs; many V9 OTUs match many MAGs; many V9 OTUs match one MAG; one V9 OTU matches one MAG. Notably, we found some instances in which different OTU-MAG matches from the same taxonomic group were not classified in the same scenario, with all four scenarios possible even within the same taxonomic group, illustrating that factors beyond taxonomic lineage influence the relationship between OTUs and MAGs. Overall, each scenario produces a different interpretation of V9 OTUs, MAGs and how they compare in terms of the genomic and ecological diversity they represent.
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Affiliation(s)
- Daryna Zavadska
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Nicolas Henry
- CNRS, FR2424, ABiMS, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Adrià Auladell
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Cédric Berney
- CNRS, UMR7144, AD2M, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Daniel J. Richter
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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Rolland J, Boutin R, Eveillard D, Delahaye B. Datascape: exploring heterogeneous dataspace. Sci Rep 2024; 14:7041. [PMID: 38580694 PMCID: PMC10997776 DOI: 10.1038/s41598-024-52493-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/19/2024] [Indexed: 04/07/2024] Open
Abstract
Data science is a powerful field for gaining insights, comparing, and predicting behaviors from datasets. However, the diversity of methods and hypotheses needed to abstract a dataset exhibits a lack of genericity. Moreover, the shape of a dataset, which structures its contained information and uncertainties, is rarely considered. Inspired by state-of-the-art manifold learning and hull estimations algorithms, we propose a novel framework, the datascape, that leverages topology and graph theory to abstract heterogeneous datasets. Built upon the combination of a nearest neighbor graph, a set of convex hulls, and a metric distance that respects the shape of the data, the datascape allows exploration of the dataset's underlying space. We show that the datascape can uncover underlying functions from simulated datasets, build predictive algorithms with performance close to state-of-the-art algorithms, and reveal insightful geodesic paths between points. It demonstrates versatility through ecological, medical, and simulated data use cases.
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Affiliation(s)
- Jakez Rolland
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44322, Nantes, France.
- Bio Logbook, 44200, Nantes, France.
| | | | - Damien Eveillard
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44322, Nantes, France
| | - Benoit Delahaye
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44322, Nantes, France
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8
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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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9
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González-Pech RA, Li VY, Garcia V, Boville E, Mammone M, Kitano H, Ritchie KB, Medina M. The Evolution, Assembly, and Dynamics of Marine Holobionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:443-466. [PMID: 37552896 DOI: 10.1146/annurev-marine-022123-104345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The holobiont concept (i.e., multiple living beings in close symbiosis with one another and functioning as a unit) is revolutionizing our understanding of biology, especially in marine systems. The earliest marine holobiont was likely a syntrophic partnership of at least two prokaryotic members. Since then, symbiosis has enabled marine organisms to conquer all ocean habitats through the formation of holobionts with a wide spectrum of complexities. However, most scientific inquiries have focused on isolated organisms and their adaptations to specific environments. In this review, we attempt to illustrate why a holobiont perspective-specifically, the study of how numerous organisms form a discrete ecological unit through symbiosis-will be a more impactful strategy to advance our understanding of the ecology and evolution of marine life. We argue that this approach is instrumental in addressing the threats to marine biodiversity posed by the current global environmental crisis.
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Affiliation(s)
- Raúl A González-Pech
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vivian Y Li
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vanessa Garcia
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Elizabeth Boville
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Marta Mammone
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | | | - Kim B Ritchie
- Department of Natural Sciences, University of South Carolina, Beaufort, South Carolina, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
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10
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Li Y, Kan J, Liu F, Lian K, Liang Y, Shao H, McMinn A, Wang H, Wang M. Depth shapes microbiome assembly and network stability in the Mariana Trench. Microbiol Spectr 2024; 12:e0211023. [PMID: 38084983 PMCID: PMC10783068 DOI: 10.1128/spectrum.02110-23] [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: 05/19/2023] [Accepted: 11/08/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Exploring microbial interactions and their stability/resilience from the surface to the hadal ocean is critical for further understanding of the microbiome structure and ecosystem function in the Mariana Trench. Vertical gradients did not destabilize microbial communities after long-term evolution and adaption. The uniform niche breadth, diversity, community complexity, and stability of microbiomes in both upper bathypelagic and hadal waters suggest the consistent roles of microbiomes in elemental cycling and adaptive strategies to overcome extreme environmental conditions. Compared with microeukaryotes, bacteria and archaea play a pivotal role in shaping the stability of the hadal microbiome. The consistent co-occurrence stability of microbiomes across vertical gradients was observed in the Mariana Trench. These results illuminate a key principle of microbiomes inhabiting the deepest trench: although distinct microbial communities occupy specific habitats, the interactions within microbial communities remain consistently stable from the upper bathypelagic to the hadal waters.
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Affiliation(s)
- Yi Li
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, Pennsylvania, USA
| | - Feilong Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Kaiyue Lian
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
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11
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Deutschmann IM, Delage E, Giner CR, Sebastián M, Poulain J, Arístegui J, Duarte CM, Acinas SG, Massana R, Gasol JM, Eveillard D, Chaffron S, Logares R. Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean. Nat Commun 2024; 15:126. [PMID: 38168083 PMCID: PMC10762198 DOI: 10.1038/s41467-023-44550-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: 04/10/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change.
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Affiliation(s)
| | - Erwan Delage
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | | | | | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Javier Arístegui
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - Carlos M Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | | | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Damien Eveillard
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Samuel Chaffron
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain.
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12
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Tamayo-Leiva J, Alcorta J, Sepúlveda F, Fuentes-Alburquenque S, Arroyo JI, González-Pastor JE, Díez B. Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton. ISME COMMUNICATIONS 2024; 4:ycae059. [PMID: 38770060 PMCID: PMC11104534 DOI: 10.1093/ismeco/ycae059] [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: 04/03/2024] [Revised: 04/13/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024]
Abstract
Mobile genetic elements (MGEs), collectively referred to as the "mobilome", can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g. protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.
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Affiliation(s)
- Javier Tamayo-Leiva
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile
| | - Jaime Alcorta
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
| | - Felipe Sepúlveda
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
| | - Sebastián Fuentes-Alburquenque
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O’Higgins, Santiago, Chile
- Departamento de Matemáticas y Ciencias de la Ingeniería, Facultad de Ingeniería, Ciencia y Tecnología, Universidad Bernardo O’Higgins, Santiago, Chile
| | - José Ignacio Arroyo
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- The Santa Fe Institute, Santa Fe, NM 87131, United States
- Centro de Modelamiento Matemático, Universidad de Chile, IRL 2807 CNRS Beauchef 851, Santiago, Chile
| | - José Eduardo González-Pastor
- Department of Molecular Evolution, Centro de Astrobiología (CAB), CSIC-INTA. Carretera de Ajalvir km 4, Torrejón de Ardoz 28850 Madrid, Spain
| | - Beatriz Díez
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
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13
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Junger PC, Sarmento H, Giner CR, Mestre M, Sebastián M, Morán XAG, Arístegui J, Agustí S, Duarte CM, Acinas SG, Massana R, Gasol JM, Logares R. Global biogeography of the smallest plankton across ocean depths. SCIENCE ADVANCES 2023; 9:eadg9763. [PMID: 37939185 PMCID: PMC10631730 DOI: 10.1126/sciadv.adg9763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Tiny ocean plankton (picoplankton) are fundamental for the functioning of the biosphere, but the ecological mechanisms shaping their biogeography were partially understood. Comprehending whether these microorganisms are structured by niche versus neutral processes is relevant in the context of global change. We investigate the ecological processes (selection, dispersal, and drift) structuring global-ocean picoplanktonic communities inhabiting the epipelagic (0 to 200 meters), mesopelagic (200 to 1000 meters), and bathypelagic (1000 to 4000 meters) zones. We found that selection decreased, while dispersal limitation increased with depth, possibly due to differences in habitat heterogeneity and dispersal barriers such as water masses and bottom topography. Picoplankton β-diversity positively correlated with environmental heterogeneity and water mass variability, but this relationship tended to be weaker for eukaryotes than for prokaryotes. Community patterns were more pronounced in the Mediterranean Sea, probably because of its cross-basin environmental heterogeneity and deep-water isolation. We conclude that different combinations of ecological mechanisms shape the biogeography of the ocean microbiome across depths.
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Affiliation(s)
- Pedro C. Junger
- Department of Hydrobiology, Universidade Federal de São Carlos (UFSCar), São Carlos, SP 13565-905, Brazil
- Programa de Pós-Graduação em Ecologia e Recursos Naturais, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos (UFSCar), São Carlos, SP 13565-905, Brazil
| | - Hugo Sarmento
- Department of Hydrobiology, Universidade Federal de São Carlos (UFSCar), São Carlos, SP 13565-905, Brazil
| | - Caterina R. Giner
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
| | - Mireia Mestre
- Centro COPAS-COASTAL, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Marta Sebastián
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
| | - Xosé Anxelu G. Morán
- Centro Oceanográfico de Gijón/Xixón (IEO, CSIC), Gijón/Xixón, Asturias 33212, Spain
| | - Javier Arístegui
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria 35214, Spain
| | - Susana Agustí
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Carlos M. Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Silvia G. Acinas
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
| | - Ramon Massana
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya 08003, Spain
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14
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Caccavo JA, Frémont P, Jaillon O, Gehlen M. Climate genomics-Geoscientists, ecologists, and geneticists must reinforce their collaborations to confront climate change. GLOBAL CHANGE BIOLOGY 2023; 29:5999-6001. [PMID: 37665245 DOI: 10.1111/gcb.16924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023]
Abstract
Geoscientists and ecologists alike must confront the impact of climate change on ecosystems and the services they provide. In the marine realm, major changes are projected in net primary and export production, with significant repercussions on food security, carbon storage, and climate system feedbacks. However, these projections do not include the potential for rapid linear evolution to facilitate adaptation to environmental change. Climate genomics confronts this challenge by assessing the vulnerability of ecosystem services to climate change. Because DNA is the primary biological repository of detectable environmentally selected mutations (showing evidence of change before impacts arise in morphological or metabolic patterns), genomics provides a window into selection in response to climate change, while also recording neutral processes deriving from stochastic mechanisms (Lowe et al., Trends in Ecology & Evolution, 2017; 32:141-152). Due to the revolution afforded by sequencing technology developments, genomics can now meet ecologists and climate scientists in a cross-disciplinary space fertile for collaborations. Collaboration between geoscientists, ecologists, and geneticists must be reinforced in order to combine modeling and genomics approaches at every scale to improve our understanding and the management of ecosystems under climate change. To this end, we present advances in climate genomics from plankton to larger vertebrates, stressing the interactions between modeling and genomics, and identifying future work needed to develop and expand the field of climate genomics.
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Affiliation(s)
- Jilda Alicia Caccavo
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
- Laboratoire d'Océanographie et du Climat Expérimentations et Approches Numériques, LOCEAN/IPSL, UPMC-CNRS-IRD-MNHN, Sorbonne Université, Paris, France
| | - Paul Frémont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
- Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
- Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Marion Gehlen
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
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15
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Namsaraev Z, Kozlova A, Tuzov F, Krylova A, Izotova A, Makarov I, Bezgreshnov A, Melnikova A, Trofimova A, Kuzmin D, Patrushev M, Toshchakov S. Biogeographic Analysis Suggests Two Types of Planktonic Prokaryote Communities in the Barents Sea. BIOLOGY 2023; 12:1310. [PMID: 37887020 PMCID: PMC10604488 DOI: 10.3390/biology12101310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023]
Abstract
The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied the diversity of prokaryotic communities using 16S metabarcoding in the western and northeastern parts of the Barents Sea along the Kola Section and the section from Novaya Zemlya to Franz Joseph Land. The hypothesis-independent clustering method revealed the existence of two distinct types of communities. The most common prokaryotic taxa were shared between two types of communities, but their relative abundance was different. It was found that the geographic location of the sampling sites explained more than 30% of the difference between communities, while no statistically significant correlation between environmental parameters and community composition was found. The representatives of the Psychrobacter, Sulfitobacter and Polaribacter genera were dominant in samples from both types of communities. The first type of community was also dominated by members of Halomonas, Pseudoalteromonas, Planococcaceae and an unclassified representative of the Alteromonadaceae family. The second type of community also had a significant proportion of Nitrincolaceae, SAR92, SAR11 Clade I, NS9, Cryomorphaceae and SUP05 representatives. The origin of these communities can be explained by the influence of environmental factors or by the different origins of water masses. This research highlights the importance of studying biogeographic patterns in the Barents Sea in comparison with those in the North Atlantic and Arctic Ocean prokaryote communities.
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Affiliation(s)
- Zorigto Namsaraev
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Aleksandra Kozlova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Fedor Tuzov
- Department of Oceanology, Faculty of Geography, Lomonosov Moscow State University, 119991 Moscow, Russia
- All-Russian Research Institute for Civil Defense and Emergencies, 121352 Moscow, Russia
| | - Anastasia Krylova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Anna Izotova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | | | - Andrei Bezgreshnov
- Arctic and Antarctic Research Institute, 199397 Saint Petersburg, Russia
| | - Anna Melnikova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Anna Trofimova
- Department of Geography and Hydrometeorology, Higher School of Natural Sciences and Technologies, Northern (Arctic) Federal University, 163002 Arkhangelsk, Russia
| | - Denis Kuzmin
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Maksim Patrushev
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Stepan Toshchakov
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
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16
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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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17
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Kaneko H, Endo H, Henry N, Berney C, Mahé F, Poulain J, Labadie K, Beluche O, El Hourany R, Chaffron S, Wincker P, Nakamura R, Karp-Boss L, Boss E, Bowler C, de Vargas C, Tomii K, Ogata H. Predicting global distributions of eukaryotic plankton communities from satellite data. ISME COMMUNICATIONS 2023; 3:101. [PMID: 37740029 PMCID: PMC10517053 DOI: 10.1038/s43705-023-00308-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their biogeography using global satellite observations. Six plankton community types were identified from a co-occurrence network inferred using a novel rDNA 18 S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to construct a model that predicted these community types from satellite data. The model showed an overall 67% accuracy in the prediction of the community types. The prediction using 17 satellite-derived parameters showed better performance than that using only temperature and/or the concentration of chlorophyll a. The constructed model predicted the global spatiotemporal distribution of community types over 19 years. The predicted distributions exhibited strong seasonal changes in community types in the subarctic-subtropical boundary regions, which were consistent with previous field observations. The model also identified the long-term trends in the distribution of community types, which suggested responses to ocean warming.
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Affiliation(s)
- Hiroto Kaneko
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Nicolas Henry
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016, Paris, France
| | - Cédric Berney
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29680, Roscoff, France
| | - Frédéric Mahé
- CIRAD, UMR PHIM, F-34398, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Odette Beluche
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Roy El Hourany
- Univ. Littoral Côte d'Opale, Univ. Lille, CNRS, IRD, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F 62930, Wimereux, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Samuel Chaffron
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016, Paris, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Ryosuke Nakamura
- Digital Architecture Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, 04469, ME, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29680, Roscoff, France
| | - Kentaro Tomii
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
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18
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Hunter P. Scratching the ocean surface: Researchers want to better understand the nature and dynamics of the abundant life living on and in the ocean's surface layers. EMBO Rep 2023; 24:e57928. [PMID: 37589208 PMCID: PMC10481654 DOI: 10.15252/embr.202357928] [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: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/18/2023] Open
Abstract
Accelerating efforts to understand neuston, mysterious communities of organisms that reside on or near the ocean surface.
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19
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Rigonato J, Budinich M, Murillo AA, Brandão MC, Pierella Karlusich JJ, Soviadan YD, Gregory AC, Endo H, Kokoszka F, Vik D, Henry N, Frémont P, Labadie K, Zayed AA, Dimier C, Picheral M, Searson S, Poulain J, Kandels S, Pesant S, Karsenti E, Bork P, Bowler C, de Vargas C, Eveillard D, Gehlen M, Iudicone D, Lombard F, Ogata H, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Chaffron S, Jaillon O. Ocean-wide comparisons of mesopelagic planktonic community structures. ISME COMMUNICATIONS 2023; 3:83. [PMID: 37596349 PMCID: PMC10439195 DOI: 10.1038/s43705-023-00279-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 08/20/2023]
Abstract
For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO3- and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.
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Affiliation(s)
- Janaina Rigonato
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
| | - Marko Budinich
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680, Roscoff, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Alejandro A Murillo
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Manoela C Brandão
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Juan J Pierella Karlusich
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Yawouvi Dodji Soviadan
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Ann C Gregory
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Florian Kokoszka
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Dean Vik
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
| | - Nicolas Henry
- 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, AD2M, UMR 7144, 29680, Roscoff, France
| | - Paul Frémont
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
| | - Céline Dimier
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Marc Picheral
- 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, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Sarah Searson
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
- Directors' Research European Molecular Biology Laboratory Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - 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
| | - Eric Karsenti
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- Directors' Research European Molecular Biology Laboratory Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- 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, AD2M, UMR 7144, 29680, Roscoff, France
| | - Damien Eveillard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Marion Gehlen
- Institut Pierre Simon Laplace, Laboratoire des Sciences du Climat et de l'Environnement, CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette cedex, France
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Fabien Lombard
- 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, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Lars Stemmann
- 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, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, 43214, USA
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
- Department of Biology; Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, 8093, Switzerland
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Samuel Chaffron
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France.
- 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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20
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Ren L, Song X, Wu C, Li G, Zhang X, Xia X, Xiang C, Han BP, Jeppesen E, Wu QL. Biogeographical and Biodiversity Patterns of Marine Planktonic Bacteria Spanning from the South China Sea across the Gulf of Bengal to the Northern Arabian Sea. Microbiol Spectr 2023; 11:e0039823. [PMID: 37098981 PMCID: PMC10269852 DOI: 10.1128/spectrum.00398-23] [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: 01/28/2023] [Accepted: 04/05/2023] [Indexed: 04/27/2023] Open
Abstract
Understanding the biogeographical and biodiversity patterns of bacterial communities is essential in unraveling their responses to future environmental changes. However, the relationships between marine planktonic bacterial biodiversity and seawater chlorophyll a are largely understudied. Here, we used high-throughput sequencing to study the biodiversity patterns of marine planktonic bacteria across a broad chlorophyll a gradient spanning from the South China Sea across the Gulf of Bengal to the northern Arabian Sea. We found that the biogeographical patterns of marine planktonic bacteria complied with the scenario of homogeneous selection, with chlorophyll a concentration being the key environmental selecting variable of bacteria taxa. The relative abundance of Prochlorococcus, the SAR11 clade, the SAR116 clade, and the SAR86 clade significantly decreased in habitats with high chlorophyll a concentrations (>0.5 μg/L). Free-living bacteria (FLB) and particle-associated bacteria (PAB) displayed contrasting alpha diversity and chlorophyll a relationships with a positive linear correlation for FLB but a negative correlation for PAB. We further found that PAB had a narrower niche breadth of chlorophyll a than did FLB, with far fewer bacterial taxa being favored at higher chlorophyll a concentrations. Higher chlorophyll a concentrations were linked to the enhanced stochastic drift and reduced beta diversity of PAB but to the weakened homogeneous selection, enhanced dispersal limitation, and increased beta diversity of FLB. Taken together, our findings might broaden our knowledge about the biogeography of marine planktonic bacteria and advance the understanding of bacterial roles in predicting ecosystem functioning under future environmental changes that are derived from eutrophication. IMPORTANCE One of the long-standing interests of biogeography is to explore diversity patterns and uncover their underlying mechanisms. Despite intensive studies on the responses of eukaryotic communities to chlorophyll a concentrations, we know little about how changes in seawater chlorophyll a concentrations affect free-living bacteria (FLB) and particle-associated bacteria (PAB) diversity patterns in natural systems. Our biogeography study demonstrated that marine FLB and PAB displayed contrasting diversity and chlorophyll a relationships and exhibited completely different assembly mechanisms. Our findings broaden our knowledge about the biogeographical and biodiversity patterns of marine planktonic bacteria in nature systems and suggest that PAB and FLB should be considered independently in predicting marine ecosystem functioning under future frequent eutrophication.
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Affiliation(s)
- Lijuan Ren
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Key Laboratory of Science and Technology on Operational Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xingyu Song
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Key Laboratory of Science and Technology on Operational Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Chuangfeng Wu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Key Laboratory of Science and Technology on Operational Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xiufeng Zhang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Key Laboratory of Science and Technology on Operational Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Chenhui Xiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Key Laboratory of Science and Technology on Operational Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Erik Jeppesen
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
- Department of Bioscience, Aarhus University, Silkeborg, Denmark
- Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara, Turkey
| | - Qinglong L. Wu
- Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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21
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Tartaglione L, Loeffler CR, Miele V, Varriale F, Varra M, Monti M, Varone A, Bodi D, Spielmeyer A, Capellacci S, Penna A, Dell'Aversano C. Dereplication of Gambierdiscusbalechii extract by LC-HRMS and in vitro assay: First description of a putative ciguatoxin and confirmation of 44-methylgambierone. CHEMOSPHERE 2023; 319:137940. [PMID: 36702405 DOI: 10.1016/j.chemosphere.2023.137940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
Marine toxins have a significant impact on seafood resources and human health. Up to date, mainly based on bioassays results, two genera of toxic microalgae, Gambierdiscus and Fukuyoa have been hypothesized to produce a suite of biologically active compounds, including maitotoxins (MTXs) and ciguatoxins (CTXs) with the latter causing ciguatera poisoning (CP) in humans. The global ubiquity of these microalgae and their ability to produce (un-)known bioactive compounds, necessitates strategies for screening, identifying, and reducing the number of target algal species and compounds selected for structural elucidation. To accomplish this task, a dereplication process is necessary to screen and profile algal extracts, identify target compounds, and support the discovery of novel bioactive chemotypes. Herein, a dereplication strategy was applied to a crude extract of a G. balechii culture to investigate for bioactive compounds with relevance to CP using liquid chromatography-high resolution mass spectrometry, in vitro cell-based bioassay, and a combination thereof via a bioassay-guided micro-fractionation. Three biologically active fractions exhibiting CTX-like and MTX-like toxicity were identified. A naturally incurred fish extract (Sphyraena barracuda) was used for confirmation where standards were unavailable. Using this approach, a putative I/C-CTX congener in G. balechii was identified for the first time, 44-methylgambierone was confirmed at 8.6 pg cell-1, and MTX-like compounds were purported. This investigative approach can be applied towards other harmful algal species of interest. The identification of a microalgal species herein, G. balechii (VGO920) which was found capable of producing a putative I/C-CTX in culture is an impactful advancement for global CP research. The large-scale culturing of G. balechii could be used as a source of I/C-CTX reference material not yet commercially available, thus, fulfilling an analytical gap that currently hampers the routine determination of CTXs in various environmental and human health-relevant matrices.
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Affiliation(s)
- Luciana Tartaglione
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy.
| | - Christopher R Loeffler
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy; Institute for Endocrinology and Experimental Oncology "G. Salvatore," National Research Council, Via P. Castellino 111, 80131, Naples, Italy; German Federal Institute for Risk Assessment, Department Safety in the Food Chain, National Reference Laboratory of Marine Biotoxins, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Valentina Miele
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | - Fabio Varriale
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | - Michela Varra
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | - Marcello Monti
- Institute for Endocrinology and Experimental Oncology "G. Salvatore," National Research Council, Via P. Castellino 111, 80131, Naples, Italy
| | - Alessia Varone
- Institute for Endocrinology and Experimental Oncology "G. Salvatore," National Research Council, Via P. Castellino 111, 80131, Naples, Italy
| | - Dorina Bodi
- German Federal Institute for Risk Assessment, Department Safety in the Food Chain, National Reference Laboratory of Marine Biotoxins, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Astrid Spielmeyer
- German Federal Institute for Risk Assessment, Department Safety in the Food Chain, National Reference Laboratory of Marine Biotoxins, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Samuela Capellacci
- Department of Biomolecular Sciences, University of Urbino, Campus E. Mattei, Urbino, Italy
| | - Antonella Penna
- Department of Biomolecular Sciences, University of Urbino, Campus E. Mattei, Urbino, Italy
| | - Carmela Dell'Aversano
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy; NBFC, National Biodiversity Future Center, Palermo, 90133, Italy
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22
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Almagro-Moreno S, Martinez-Urtaza J, Pukatzki S. Vibrio Infections and the Twenty-First Century. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:1-16. [PMID: 36792868 DOI: 10.1007/978-3-031-22997-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The Vibrionaceae is a highly diverse family of aquatic bacteria. Some members of this ubiquitous group can cause a variety of diseases in humans ranging from cholera caused by Vibrio cholerae, severe septicemia caused by Vibrio vulnificus, to acute gastroenteritis by Vibrio parahaemolyticus. Planet Earth is experiencing unprecedented changes of planetary scale associated with climate change. These environmental perturbations paired with overpopulation and pollution are increasing the distribution of pathogenic Vibrios and exacerbating the risk of causing infections. In this chapter, we discuss various aspects of Vibrio infections within the context of the twenty-first century with a major emphasis on the aforementioned pathogenic species. Overall, we believe that the twenty-first century is posed to be both one full of challenges due to the rise of these pathogens, and also a catalyst for innovative and groundbreaking discoveries.
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Affiliation(s)
- Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA. .,National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA.
| | - Jaime Martinez-Urtaza
- Department de Genetica I de Microbiologia, Facultat de Biociencies, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Stefan Pukatzki
- Department of Biology, The City College of New York, New York, NY, USA
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23
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Frémont P, Gehlen M, Jaillon O. Plankton biogeography in the 21st century and impacts of climate change: advances through genomics. C R Biol 2023; 346:13-24. [PMID: 37254792 DOI: 10.5802/crbiol.107] [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: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 06/01/2023]
Abstract
This article summarizes recent advances in our knowledge of plankton biogeography obtained by genomic approaches and the impacts of global warming on it. Large-scale comparison of the genomic content of samples of different plankton size fractions revealed a partitioning of the oceans into genomic provinces and the impact of major oceanic currents on them. By defining ecological niches, these provinces are extrapolated to all oceans, with the exception of the Arctic Ocean. By the end of the 21st century, a major restructuring of these provinces is projected in response to a high emission greenhouse gas scenario over 50% of the surface of the studied oceans. Such a restructuring could lead to a decrease in export production by 4%. Finally, obtaining assembled sequences of a large number of plankton genomes defining this biogeography has allowed to better characterize the genomic content of the provinces and to identify the species structuring them. These genomes similarly enabled a better description of potential future changes of plankton communities under climate change.
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24
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Shao Q, Sun D, Fang C, Feng Y, Wang C. Microbial food webs share similar biogeographic patterns and driving mechanisms with depths in oligotrophic tropical western Pacific Ocean. Front Microbiol 2023; 14:1098264. [PMID: 36778869 PMCID: PMC9909095 DOI: 10.3389/fmicb.2023.1098264] [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: 11/14/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
Microbial food web (MFW) dominates the energy flow in oligotrophic tropical open ocean pelagic ecosystems. Understanding biogeographic patterns and driving mechanisms of key components of the MFW is one of the central topics in current marine ecology. Investigations were conducted along an 1,100-km horizontal gradient and in the full-water column vertical gradient of the oligotrophic tropical western Pacific Ocean. High-throughput sequencing and association networking methods were used to analyze the community structure and interspecies interactions of MFW. The structure of MFW significantly differed with depths, but not across horizontal gradients. Bacteria and microeukaryotes were interconnected and had more predominantly positive and negative linkages in the aphotic layers. Key components of MFW exhibited similar biogeographic patterns and driving mechanisms. Geographic distance exerted minimal effects on the distribution patterns of the microbial food web, while environmental factors played more important roles, especially for temperature and inorganic nutrients. Stochastic processes were more important in the microbial food webs of the 5-200 m layer than the >500 m layer, and drift explained the majority of stochastic processes. Moreover, only a weak but not significant driving force for North Equatorial Current on the east-west connectivity of the microbial food web was found in the upper layers. This knowledge is a critical fundamental data for future planning of marine protected areas targeting the protection of tuna fishing in the western Pacific Ocean.
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Affiliation(s)
- Qianwen Shao
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China,Ningbo Institute of Oceanography, Ningbo, China
| | - Dong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China,*Correspondence: Dong Sun, ✉
| | - Chen Fang
- College of Oceanography, Hohai University, Nanjing, China
| | - Yunzhi Feng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Chunsheng Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China,School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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