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Kong Y, Zhang R, Blain S, Obernosterer I. Seasonal dynamics in microbial trace metals transporters during phytoplankton blooms in the Southern Ocean. Environ Microbiol 2024; 26:e16695. [PMID: 39367538 DOI: 10.1111/1462-2920.16695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/26/2024] [Indexed: 10/06/2024]
Abstract
Trace metals are required as cofactors in metalloproteins that are essential in microbial metabolism and growth. The microbial requirements of diverse metals and the capabilities of prokaryotic taxa to acquire these metals remain poorly understood. We present here results from metagenomic observations over an entire productive season in the region off Kerguelen Island (Indian Sector of the Southern Ocean). We observed seasonal patterns in the abundance of prokaryotic transporters of seven trace elements (zinc [Zn], manganese [Mn], nickel [Ni], molybdenum [Mo], tungsten [W], copper [Cu] and cobalt [Co]) and the consecutive spring and summer phytoplankton blooms were strong drivers of these temporal trends. Taxonomic affiliation of the functional genes revealed that Rhodobacteraceae had a broad repertoire of trace metal transporters (Mn, Zn, Ni, W and Mo) and a more restricted set was observed for other prokaryotic groups, such as Flavobacteriaceae (Zn), Nitrincolaceae (Ni and W) and Thioglobaceae (Mo). The prevalence of trace metal transporters within a prokaryotic group, as determined on the family level, was overall confirmed in representative metagenome-assembled genomes. We discuss the potential involvement of prokaryotic groups in processes related to organic matter utilisation that require these metals and the consequences on carbon and trace metal cycling in surface waters of the Southern Ocean.
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Affiliation(s)
- Yanhui Kong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- Laboratoire d'Océanographie Microbienne, LOMIC, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Rui Zhang
- Laboratoire d'Océanographie Microbienne, LOMIC, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Stéphane Blain
- Laboratoire d'Océanographie Microbienne, LOMIC, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Ingrid Obernosterer
- Laboratoire d'Océanographie Microbienne, LOMIC, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
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2
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Cohen NR, Krinos AI, Kell RM, Chmiel RJ, Moran DM, McIlvin MR, Lopez PZ, Barth AJ, Stone JP, Alanis BA, Chan EW, Breier JA, Jakuba MV, Johnson R, Alexander H, Saito MA. Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling. Nat Commun 2024; 15:7325. [PMID: 39183190 PMCID: PMC11345423 DOI: 10.1038/s41467-024-51583-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 08/13/2024] [Indexed: 08/27/2024] Open
Abstract
Microeukaryotes are key contributors to marine carbon cycling. Their physiology, ecology, and interactions with the chemical environment are poorly understood in offshore ecosystems, and especially in the deep ocean. Using the Autonomous Underwater Vehicle Clio, microbial communities along a 1050 km transect in the western North Atlantic Ocean were surveyed at 10-200 m vertical depth increments to capture metabolic signatures spanning oligotrophic, continental margin, and productive coastal ecosystems. Microeukaryotes were examined using a paired metatranscriptomic and metaproteomic approach. Here we show a diverse surface assemblage consisting of stramenopiles, dinoflagellates and ciliates represented in both the transcript and protein fractions, with foraminifera, radiolaria, picozoa, and discoba proteins enriched at >200 m, and fungal proteins emerging in waters >3000 m. In the broad microeukaryote community, nitrogen stress biomarkers were found at coastal sites, with phosphorus stress biomarkers offshore. This multi-omics dataset broadens our understanding of how microeukaryotic taxa and their functional processes are structured along environmental gradients of temperature, light, and nutrients.
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Affiliation(s)
- Natalie R Cohen
- University of Georgia Skidaway Institute of Oceanography, Savannah, GA, 31411, USA.
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, 02543, USA.
| | - Arianna I Krinos
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, 02543, USA
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, Cambridge, MA, 02543, USA
| | - Riss M Kell
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, 02543, USA
- Gloucester Marine Genomics Institute, Gloucester, MA, 01930, USA
| | - Rebecca J Chmiel
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, 02543, USA
| | - Dawn M Moran
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, 02543, USA
| | - Matthew R McIlvin
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, 02543, USA
| | - Paloma Z Lopez
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, 02543, USA
- Bermuda Institute of Ocean Sciences, St. George's, GE, 01, Bermuda
| | | | | | | | - Eric W Chan
- University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - John A Breier
- University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - Michael V Jakuba
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, 02543, USA
| | - Rod Johnson
- Bermuda Institute of Ocean Sciences, St. George's, GE, 01, Bermuda
- Arizona State University, Tempe, AZ, USA
| | - Harriet Alexander
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, 02543, USA
| | - Mak A Saito
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, 02543, USA.
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3
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Cheng S, Meng F, Wang Y, Zhang J, Zhang L. The potential linkage between sediment oxygen demand and microbes and its contribution to the dissolved oxygen depletion in the Gan River. Front Microbiol 2024; 15:1413447. [PMID: 39144217 PMCID: PMC11322766 DOI: 10.3389/fmicb.2024.1413447] [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: 04/07/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024] Open
Abstract
The role of sediment oxygen demand (SOD) in causing dissolved oxygen (DO) depletion is widely acknowledged, with previous studies mainly focusing on chemical and biological SOD separately. However, the relationship between the putative functions of sediment microbes and SOD, and their impact on DO depletion in overlying water, remains unclear. In this study, DO depletion was observed in the downstream of the Gan River during the summer. Sediments were sampled from three downstream sites (YZ, Down1, and Down2) and one upstream site (CK) as a control. Aquatic physicochemical parameters and SOD levels were measured, and microbial functions were inferred from taxonomic genes through analyses of the 16S rRNA gene. The results showed that DO depletion sites exhibited a higher SOD rate compared to CK. The microbial community structure was influenced by the spatial variation of Proteobacteria, Chloroflexi, and Bacteroidota, with total organic carbon (TOC) content acting as a significant environmental driver. A negative correlation was observed between microbial diversity and DO concentration (p < 0.05). Aerobic microbes were more abundant in DO depletion sites, particularly Proteobacteria. Microbes involved in various biogeochemical cycles, such as carbon (methane oxidation, methanotrophs, and methylotrophs), nitrogen (nitrification and denitrification), sulfur (sulfide and sulfur compound oxidation), and manganese cycles (manganese oxidation), exhibited higher abundance in DO depletion sites, except for the iron cycle (iron oxidation). These processes were negatively correlated with DO concentration and positively with SOD (p < 0.05). Overall, the results highlight that aerobic bacteria's metabolic processes consume oxygen, increasing the SOD rate and contributing to DO depletion in the overlying water. Additionally, the study underscores the importance of targeting the removal of in situ microbial molecular mechanisms associated with toxic H2S and CH4 to support reoxygenation efforts in rehabilitating DO depletion sites in the Gan River, aiding in identifying factors controlling DO consumption and offering practical value for the river's restoration and management.
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Affiliation(s)
- Shoutao Cheng
- Country School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Fansheng Meng
- Research Center of Environmental Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yeyao Wang
- Country School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
- China National Environmental Monitoring Center, Beijing, China
| | - Jiasheng Zhang
- Research Center of Environmental Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Lingsong Zhang
- Research Center of Environmental Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing, China
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Liu Z, Cao F, Wan J, Chen X, Kong B, Li D, Zhang XH, Jiang Y, Shi X. Stable microbial community diversity across large-scale Antarctic water masses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174559. [PMID: 38992373 DOI: 10.1016/j.scitotenv.2024.174559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
The distinctive environmental attributes of the Southern Ocean underscore the indispensability of microorganisms in this region. We analyzed 208 samples obtained from four separate layers (Surface, Deep Chlorophyll Maximum, Middle, and Bottom) in the neighboring seas of the Antarctic Peninsula and the Cosmonaut Sea to explore variations in microbial composition, interactions and community assembly processes. The results demonstrated noteworthy distinctions in alpha and beta diversity across diverse communities, with the increase in water depth, a gradual rise in community diversity was observed. In particular, the co-occurrence network analysis exposed pronounced microbial interactions within the same water mass, which are notably stronger than those observed between different water masses. Co-occurrence network complexity was higher in the surface water mass than in the bottom water mass. Yet, the surface water mass exhibited greater network stability. Moreover, in the phylogenetic-based β-nearest taxon distance analyses, deterministic processes were identified as the primary factors influencing community assembly in Antarctic microorganisms. This study contributes to exploring diversity and assembly processes under the complex hydrological conditions of Antarctica.
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Affiliation(s)
- Zhengang Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Furong Cao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jiyuan Wan
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Bin Kong
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Dong Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Xiaochong Shi
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Manck LE, Coale TH, Stephens BM, Forsch KO, Aluwihare LI, Dupont CL, Allen AE, Barbeau KA. Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron. THE ISME JOURNAL 2024; 18:wrae061. [PMID: 38624181 PMCID: PMC11069385 DOI: 10.1093/ismejo/wrae061] [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: 03/05/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.
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Affiliation(s)
- Lauren E Manck
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Flathead Lake Biological Station, University of Montana, Polson, MT 59860, United States
| | - Tyler H Coale
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, United States
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, United States
| | - Brandon M Stephens
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Institute of Oceanography, National Taiwan University, Taipei, 106, Taiwan
| | - Kiefer O Forsch
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
| | - Lihini I Aluwihare
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
| | - Christopher L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, United States
- Department of Human Health, J. Craig Venter Institute, La Jolla, CA 92037, United States
- Department of Synthetic Biology, J. Craig Venter Institute, La Jolla, CA 92037, United States
| | - Andrew E Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, United States
| | - Katherine A Barbeau
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
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Zhang R, Debeljak P, Blain S, Obernosterer I. Seasonal shifts in Fe-acquisition strategies in Southern Ocean microbial communities revealed by metagenomics and autonomous sampling. Environ Microbiol 2023; 25:1816-1829. [PMID: 37157891 DOI: 10.1111/1462-2920.16397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
Iron (Fe) governs the cycling of organic carbon in large parts of the Southern Ocean. The strategies of diverse microbes to acquire the different chemical forms of Fe under seasonally changing organic carbon regimes remain, however, poorly understood. Here, we report high-resolution seasonal metagenomic observations from the region off Kerguelen Island (Indian Sector of the Southern Ocean) where natural Fe-fertilization induces consecutive spring and summer phytoplankton blooms. Our data illustrate pronounced, but distinct seasonal patterns in the abundance of genes implicated in the transport of different forms of Fe and organic substrates, of siderophore biosynthesis and carbohydrate-active enzymes. The seasonal dynamics suggest a temporal decoupling in the prokaryotic requirements of Fe and organic carbon during the spring phytoplankton bloom and a concerted access to these resources after the summer bloom. Taxonomic assignments revealed differences in the prokaryotic groups harbouring genes of a given Fe-related category and pronounced seasonal successions were observed. Using MAGs we could decipher the respective Fe- and organic substrate-related genes of individual taxa assigned to abundant groups. The ecological strategies related to Fe-acquisition provide insights on how this element could shape microbial community composition with potential implications on organic matter transformations in the Southern Ocean.
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Affiliation(s)
- Rui Zhang
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
| | - Pavla Debeljak
- Sorbonne Université, Muséum National d'Histoire, Naturelle, CNRS, EPHE, Université des Antilles, Institut de Systématique, Evolution, Biodiversité (ISYEB), Paris, France
- SupBiotech, Villejuif, France
| | - Stephane Blain
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
| | - Ingrid Obernosterer
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
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7
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Debeljak P, Bayer B, Sun Y, Herndl GJ, Obernosterer I. Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean. MICROBIOME 2023; 11:187. [PMID: 37596690 PMCID: PMC10439609 DOI: 10.1186/s40168-023-01600-3] [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: 01/13/2023] [Accepted: 06/16/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe under varying environmental settings remain poorly studied. Here, we used a combination of metatranscriptomics and metaproteomics to identify prokaryotic membrane transporters for organic substrates and Fe in naturally iron-fertilized and high-nutrient, low-chlorophyll waters of the Southern Ocean during spring and late summer. RESULTS Pronounced differences in membrane transporter profiles between seasons were observed at both sites, both at the transcript and protein level. When specific compound classes were considered, the two approaches revealed different patterns. At the transcript level, seasonal patterns were only observed for subsets of genes belonging to each transporter category. At the protein level, membrane transporters of organic compounds were relatively more abundant in spring as compared to summer, while the opposite pattern was observed for Fe transporters. These observations suggest an enhanced requirement for organic C in early spring and for Fe in late summer. Mapping transcripts and proteins to 50 metagenomic-assembled genomes revealed distinct taxon-specific seasonal differences pointing to potentially opportunistic clades, such as Pseudomonadales and Nitrincolaceae, and groups with a more restricted repertoire of expressed transporters, such as Alphaproteobacteria and Flavobacteriaceae. CONCLUSION The combined investigations of C and Fe membrane transporters suggest seasonal changes in the microbial requirements of these elements under different productivity regimes. The taxon-specific acquisition strategies of different forms of C and Fe illustrate how diverse microbes could shape transcript and protein expression profiles at the community level at different seasons. Our results on the C- and Fe-related metabolic capabilities of microbial taxa provide new insights into their potential role in the cycling of C and Fe under varying nutrient regimes in the Southern Ocean. Video Abstract.
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Affiliation(s)
- Pavla Debeljak
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France.
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria.
- SupBiotech, Villejuif, France.
| | - Barbara Bayer
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
| | - Ying Sun
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
- Department of Marine Microbiology and Biogeochemistry, NIOZ (Royal Netherlands Institute for Sea Research), Den Burg, 1790 AB, The Netherlands
- Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, Vienna, 1030, Austria
| | - Ingrid Obernosterer
- Laboratoire d'Océanographie Microbienne (LOMIC), CNRS, Sorbonne Université, Banyuls/Mer, F-66650, France
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Pinhassi J, Farnelid H, García SM, Teira E, Galand PE, Obernosterer I, Quince C, Vila-Costa M, Gasol JM, Lundin D, Andersson AF, Labrenz M, Riemann L. Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters. Front Microbiol 2022; 13:869093. [PMID: 36532459 PMCID: PMC9751014 DOI: 10.3389/fmicb.2022.869093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 11/11/2022] [Indexed: 10/31/2024] Open
Abstract
Coastal ecosystems deteriorate globally due to human-induced stress factors, like nutrient loading and pollution. Bacteria are critical to marine ecosystems, e.g., by regulating nutrient cycles, synthesizing vitamins, or degrading pollutants, thereby providing essential ecosystem services ultimately affecting economic activities. Yet, until now bacteria are overlooked both as mediators and indicators of ecosystem health, mainly due to methodological limitations in assessing bacterial ecosystem functions. However, these limitations are largely overcome by the advances in molecular biology and bioinformatics methods for characterizing the genetics that underlie functional traits of key bacterial populations - "key" in providing important ecosystem services, being abundant, or by possessing high metabolic rates. It is therefore timely to analyze and define the functional responses of bacteria to human-induced effects on coastal ecosystem health. We posit that categorizing the responses of key marine bacterial populations to changes in environmental conditions through modern microbial oceanography methods will allow establishing the nascent field of genetic counselling for our coastal waters. This requires systematic field studies of linkages between functional traits of key bacterial populations and their ecosystem functions in coastal seas, complemented with systematic experimental analyses of the responses to different stressors. Research and training in environmental management along with dissemination of results and dialogue with societal actors are equally important to ensure the role of bacteria is understood as fundamentally important for coastal ecosystems. Using the responses of microorganisms as a tool to develop genetic counselling for coastal ecosystems can ultimately allow for integrating bacteria as indicators of environmental change.
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Affiliation(s)
- Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Hanna Farnelid
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Sandra Martínez García
- Departamento de Ecoloxía e Bioloxía Animal, Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain
| | - Eva Teira
- Departamento de Ecoloxía e Bioloxía Animal, Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain
| | - Pierre E. Galand
- CNRS, Laboratoire d’Ecogéochimie des Environnements Benthiques (LECOB), Sorbonne Université, Banyuls-sur-Mer, France
| | - Ingrid Obernosterer
- CNRS, Laboratoire d’Océanographie Microbienne (LOMIC), Sorbonne Université, Banyuls-sur-Mer, France
| | | | | | | | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Anders F. Andersson
- Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Lasse Riemann
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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Dinasquet J, Landa M, Obernosterer I. SAR11 clade microdiversity and activity during the early spring blooms off Kerguelen Island, Southern Ocean. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:907-916. [PMID: 36028477 DOI: 10.1111/1758-2229.13117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/10/2022] [Indexed: 05/17/2023]
Abstract
The ecology of the SAR11 clade, the most abundant bacterial group in the ocean, has been intensively studied in temperate and tropical regions, but its distribution remains largely unexplored in the Southern Ocean. Through amplicon sequencing of the 16S rRNA gene, we assessed the contribution of the SAR11 clade to bacterial community composition in the naturally iron fertilized region off Kerguelen Island. We investigated the upper 300 m at seven sites located in early spring phytoplankton blooms and at one high-nutrient low-chlorophyll site. Despite pronounced vertical patterns of the bacterioplankton assemblages, the SAR11 clade had high relative abundances at all depths and sites, averaging 40% (±15%) of the total community relative abundance. Micro-autoradiography combined with CARD-FISH further revealed that the clade had an overall stable contribution (45%-60% in surface waters) to bacterial biomass production (determined by 3 H-leucine incorporation) during different early bloom stages. The spatio-temporal partitioning of some of the SAR11 subclades suggests a niche specificity and periodic selection of different subclades in response to the fluctuating extreme conditions of the Southern Ocean. These observations improve our understanding of the ecology of the SAR11 clade and its implications in biogeochemical cycles in the rapidly changing Southern Ocean.
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Affiliation(s)
- Julie Dinasquet
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
- Marine Biology Research Division and Climate, Atmospheric Science & Physical Oceanography Department, Scripps Institution of Oceanography, San Diego, California, USA
| | - Marine Landa
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
- Sorbonne Université/Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Ingrid Obernosterer
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
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