1
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King NG, Wilmes SB, Browett SS, Healey A, McDevitt AD, McKeown NJ, Roche R, Skujina I, Smale DA, Thorpe JM, Malham S. Seasonal development of a tidal mixing front drives shifts in community structure and diversity of bacterioplankton. Mol Ecol 2023; 32:5201-5210. [PMID: 37555658 DOI: 10.1111/mec.17097] [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: 04/19/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/10/2023]
Abstract
Bacterioplankton underpin biogeochemical cycles and an improved understanding of the patterns and drivers of variability in their distribution is needed to determine their wider functioning and importance. Sharp environmental gradients and dispersal barriers associated with ocean fronts are emerging as key determinants of bacterioplankton biodiversity patterns. We examined how the development of the Celtic Sea Front (CF), a tidal mixing front on the Northwest European Shelf affects bacterioplankton communities. We performed 16S-rRNA metabarcoding on 60 seawater samples collected from three depths (surface, 20 m and seafloor), across two research cruises (May and September 2018), encompassing the intra-annual range of the CF intensity. Communities above the thermocline of stratified frontal waters were clearly differentiated and less diverse than those below the thermocline and communities in the well-mixed waters of the Irish Sea. This effect was much more pronounced in September, when the CF was at its peak intensity. The stratified zone likely represents a stressful environment for bacterioplankton due to a combination of high temperatures and low nutrients, which fewer taxa can tolerate. Much of the observed variation was driven by Synechococcus spp. (cyanobacteria), which were more abundant within the stratified zone and are known to thrive in warm oligotrophic waters. Synechococcus spp. are key contributors to global primary productivity and carbon cycling and, as such, variability driven by the CF is likely to influence regional biogeochemical processes. However, further studies are required to explicitly link shifts in community structure to function and quantify their wider importance to pelagic ecosystems.
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Affiliation(s)
- Nathan G King
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, UK
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, UK
| | - Sophie-B Wilmes
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, UK
| | - Samuel S Browett
- Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, UK
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Amy Healey
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Allan D McDevitt
- Department of Natural Resources and Environment, Atlantic Technological University, Galway, Ireland
| | - Niall J McKeown
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ronan Roche
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, UK
| | - Ilze Skujina
- Department of Life Sciences, Aberystwyth University, Aberystwyth, UK
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Dan A Smale
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, UK
| | - Jamie M Thorpe
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, UK
| | - Shelagh Malham
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, UK
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2
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Maturana-Martínez C, Iriarte JL, Ha SY, Lee B, Ahn IY, Vernet M, Cape M, Fernández C, González HE, Galand PE. Biogeography of Southern Ocean Active Prokaryotic Communities Over a Large Spatial Scale. Front Microbiol 2022; 13:862812. [PMID: 35592001 PMCID: PMC9111744 DOI: 10.3389/fmicb.2022.862812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/18/2022] [Indexed: 12/04/2022] Open
Abstract
The activity of marine microorganisms depends on community composition, yet, in some oceans, less is known about the environmental and ecological processes that structure their distribution. The objective of this study was to test the effect of geographical distance and environmental parameters on prokaryotic community structure in the Southern Ocean (SO). We described the total (16S rRNA gene) and the active fraction (16S rRNA-based) of surface microbial communities over a ~6,500 km longitudinal transect in the SO. We found that the community composition of the total fraction was different from the active fraction across the zones investigated. In addition, higher α-diversity and stronger species turnover were displayed in the active community compared to the total community. Oceanospirillales, Alteromonadales, Rhodobacterales, and Flavobacteriales dominated the composition of the bacterioplankton communities; however, there were marked differences at the order level. Temperature, salinity, silicic acid, particulate organic nitrogen, and particulate organic carbon correlated with the composition of bacterioplankton communities. A strong distance–decay pattern between closer and distant communities was observed. We hypothesize that it was related to the different oceanic fronts present in the Antarctic Circumpolar Current. Our findings contribute to a better understanding of the complex arrangement that shapes the structure of bacterioplankton communities in the SO.
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Affiliation(s)
- Claudia Maturana-Martínez
- Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) and Universidad Austral de Chile, Valdivia, Chile.,Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, Banyuls-sur-Mer, France
| | - José Luis Iriarte
- Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) and Universidad Austral de Chile, Valdivia, Chile
| | - Sun-Yong Ha
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Boyeon Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - In-Young Ahn
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Maria Vernet
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Mattias Cape
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Camila Fernández
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Humberto E González
- Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) and Universidad Austral de Chile, Valdivia, Chile
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, Banyuls-sur-Mer, France
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3
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Sun P, Wang Y, Huang X, Huang B, Wang L. Water masses and their associated temperature and cross-domain biotic factors co-shape upwelling microbial communities. WATER RESEARCH 2022; 215:118274. [PMID: 35298994 DOI: 10.1016/j.watres.2022.118274] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Disentangling the drivers and mechanisms that shape microbial communities in a river-influenced coastal upwelling system requires considering a hydrologic dimension that can drive both deterministic and stochastic community assembly by generating hydrological heterogeneity and dispersal events. Additionally, ubiquitous and complex microbial interactions can play a significant role in community structuring. However, how the hydrology, biotic, and abiotic factors collectively shape microbial distribution in the hydrologically complicated river plume-upwelling coupling system remains unknown. Through underway sampling and daily observations, we employed 16S and 18S ribosomal RNA sequencing to disentangle drivers and mechanisms shaping the protist-bacteria microbiota in a river-influenced coastal upwelling system. Our findings indicate that the composition of microbial communities was water mass specific. Collectively, water mass, local water chemistry (mostly temperature) and biotic interaction (mostly cross-domain biotic interaction) shaped the protistan-bacterial communities. In comparison to protists, bacteria were more influenced by abiotic factors such as temperature than by cross-domain biotic factors, implying a stronger coupling of geochemical cycles. Both deterministic and stochastic processes had an effect on the distribution of microbial communities, but deterministic processes were more important for bacteria and were especially pronounced for upwelling communities. The co-occurrence network revealed strong associations between the protistan assemblages Orchrophyta and Ciliophora and the bacterial assemblages Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which may reflect predation and mutualism interactions. Overall, this study emphasizes the importance of taking water masses, temperature and domains of life into account when seeking to understand the drivers and assemblies of protist-bacteria microbiome dynamics in coastal upwelling systems, which is especially true given the complex and dynamic nature of the coastal ecosystem.
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Affiliation(s)
- Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen 361102, China; Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China.
| | - Ying Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen 361102, China
| | - Xin Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen 361102, China
| | - Bangqin Huang
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.
| | - Lei Wang
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
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Liu S, Sun Y, Shi F, Liu Y, Wang F, Dong S, Li M. Composition and Diversity of Soil Microbial Community Associated With Land Use Types in the Agro-Pastoral Area in the Upper Yellow River Basin. FRONTIERS IN PLANT SCIENCE 2022; 13:819661. [PMID: 35548288 PMCID: PMC9082682 DOI: 10.3389/fpls.2022.819661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
The microorganisms of soil are sensitive to their living microenvironment, and their community structure and function will change with the environmental conditions. In the agro-pastoral area on the Qinghai-Tibet Plateau, revealing the diversity of the soil microbial communities and its response to different soil physicochemical properties and environmental factors are important for ecosystem management. The microbial (bacteria and archaea) community composition and diversity under different land use types (cultivated land, grazing grassland and planted forest) were analyzed by 16S rRNA (V4 region) method in a typical agro-pastoral region in the upper Yellow River basin. Also, the soil nutrients were studied and correlated with the microbial community. The results showed that the soil nutrient contents in grassland were low, but the available nutrients were relatively high. There was a great spatial variability under different distances to the river. The microbial community diversity was lower in the grassland than the cultivated land and forest land closer to the river. For all land uses, the dominant phyla of soil microorganisms included Proteobacteria, Actinobacteria, and Bacteroidetes, while the abundance of Clostridia was significantly higher than that of the other groups, indicating that Clostridia dominated the Firmicutes and affected soil microbial community composition. The linear discriminant analysis (LDA) effect size (LefSe) analysis showed different biomarkers were more abundant in grassland than other land use types, suggesting that the structure and diversity of soil microorganisms in grassland were significantly different compared with cultivated land and forest land. The distance-based redundancy analysis (db-RDA) results showed that the total phosphorus (TP) and calcium (Ca) were the key environmental factors affecting the diversity and abundance of the soil microbial community in cultivated land and forestland, respectively. However, the microbial diversity in grassland was more related to spatial distance of the river. These results provided a theoretical basis for the changes in the composition, structure, and function of soil microbial communities in agro-pastoral areas.
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Affiliation(s)
- Shiliang Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yongxiu Sun
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Fangning Shi
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yixuan Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Fangfang Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Shikui Dong
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Mingqi Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
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5
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Oceanographic setting influences the prokaryotic community and metabolome in deep-sea sponges. Sci Rep 2022; 12:3356. [PMID: 35233042 PMCID: PMC8888554 DOI: 10.1038/s41598-022-07292-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/16/2022] [Indexed: 11/09/2022] Open
Abstract
Marine sponges (phylum Porifera) are leading organisms for the discovery of bioactive compounds from nature. Their often rich and species-specific microbiota is hypothesised to be producing many of these compounds. Yet, environmental influences on the sponge-associated microbiota and bioactive compound production remain elusive. Here, we investigated the changes of microbiota and metabolomes in sponges along a depth range of 1232 m. Using 16S rRNA gene amplicon sequencing and untargeted metabolomics, we assessed prokaryotic and chemical diversities in three deep-sea sponge species: Geodia barretti, Stryphnus fortis, and Weberella bursa. Both prokaryotic communities and metabolome varied significantly with depth, which we hypothesized to be the effect of different water masses. Up to 35.5% of microbial ASVs (amplicon sequence variants) showed significant changes with depth while phylum-level composition of host microbiome remained unchanged. The metabolome varied with depth, with relative quantities of known bioactive compounds increasing or decreasing strongly. Other metabolites varying with depth were compatible solutes regulating osmolarity of the cells. Correlations between prokaryotic community and the bioactive compounds in G. barretti suggested members of Acidobacteria, Proteobacteria, Chloroflexi, or an unclassified prokaryote as potential producers.
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Abstract
Microbial communities associated with deep-sea animals are critical to the establishment of novel biological communities in unusual environments. Over the past few decades, rapid exploration of the deep sea has enabled the discovery of novel microbial communities, some of which form symbiotic relationships with animal hosts. Symbiosis in the deep sea changes host physiology, behavior, ecology, and evolution over time and space. Symbiont diversity within a host is often aligned with diverse metabolic pathways that broaden the environmental niche for the animal host. In this review, we focus on microbiomes and obligate symbionts found in different deep-sea habitats and how they facilitate survival of the organisms that live in these environments. In addition, we discuss factors that govern microbiome diversity, host specificity, and biogeography in the deep sea. Finally, we highlight the current limitations of microbiome research and draw a road map for future directions to advance our knowledge of microbiomes in the deep sea. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Eslam O Osman
- Biology Department, Eberly College, Pennsylvania State University, State College, Pennsylvania, USA; .,Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Biology Lab, Zoology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Alexis M Weinnig
- Biology Department, Temple University, Philadelphia, Pennsylvania, USA
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7
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Sun P, Zhang S, Wang Y, Huang B. Biogeographic Role of the Kuroshio Current Intrusion in the Microzooplankton Community in the Boundary Zone of the Northern South China Sea. Microorganisms 2021; 9:1104. [PMID: 34065542 PMCID: PMC8161332 DOI: 10.3390/microorganisms9051104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022] Open
Abstract
Kuroshio Current intrusion (KCI) has significant impacts on the oceanographic conditions and ecological processes of the Pacific-Asian marginal seas. Little is known to which extent and how, specifically, the microzooplankton community can be influenced through the intrusion. Here, we focused on ciliates that often dominated the microzooplankton community and investigated their communities using high-throughput sequencing of 18S rRNA gene transcripts in the northern South China Sea (NSCS), where the Kuroshio Current (KC) intrudes frequently. We first applied an isopycnal mixing model to assess the fractional contribution of the KC to the NSCS. The ciliate community presented a provincial distribution pattern corresponding to more and less Kuroshio-influenced stations. Structural equation modeling revealed a significant impact of the KCI on the community, while environmental variables had a marginal impact. KCI-sensitive OTUs were taxonomically diverse but mainly belonged to classes Spirotrichea and Phyllopharyngea, suggesting the existence of core ciliates responding to the KCI. KCI-sensitive OTUs were grouped into two network modules that showed contrasting abundance behavior with the KC fraction gradient, reflecting differential niches (i.e., winner and loser) in the ciliate community during the Kuroshio intrusion scenarios. Our study showed that the Kuroshio intrusion, rather than environmental control, was particularly detrimental to the oligotrophic microzooplankton community.
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Affiliation(s)
- Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Silu Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
| | - Ying Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
| | - Bangqin Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
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8
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Phoma BS, Makhalanyane TP. Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands. MICROBIAL ECOLOGY 2021; 81:396-409. [PMID: 32935183 DOI: 10.1007/s00248-020-01589-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.
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Affiliation(s)
- Boitumelo Sandra Phoma
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
- Marine Microbiomics Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Thulani Peter Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria, 0028, South Africa.
- Marine Microbiomics Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa.
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9
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Pajares S, Varona-Cordero F, Hernández-Becerril DU. Spatial Distribution Patterns of Bacterioplankton in the Oxygen Minimum Zone of the Tropical Mexican Pacific. MICROBIAL ECOLOGY 2020; 80:519-536. [PMID: 32415330 DOI: 10.1007/s00248-020-01508-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 03/23/2020] [Indexed: 05/16/2023]
Abstract
Microbial communities within oxygen minimum zones (OMZs) are crucial drivers of marine biogeochemical cycles; however, we still lack an understanding of how these communities are distributed across an OMZ. We explored vertical (from 5 to 500 m depth) and horizontal (coast to open ocean) distribution of bacterioplankton and its relationships with the main oceanographic conditions in three transects of the tropical Mexican Pacific OMZ. The distribution of the microbial diversity and the main clades changed along the transition from oxygen-rich surface water to the OMZ core, demonstrating the sensitivity of key bacterial groups to deoxygenation. The euphotic zone was dominated by Synechococcales, followed by Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales, whereas the OMZ core was dominated by SAR11, followed by SAR406, SAR324, SAR202, UBA10353 marine group, Thiomicrospirales and Nitrospinales. The marked environmental gradients along the water column also supported a high potential for niche partitioning among OMZ microorganisms. Additionally, in the OMZ core, bacterial assemblages from the same water mass were more similar to each other than those from another water mass. There were also important differences between coastal and open-ocean communities: Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales were more abundant in coastal areas, while Synechococcales, SAR406, SAR324, SAR202, UBA10353 marine group, and Thiomicrospirales were more abundant in the open ocean. Our results suggest a biogeographic structure of the bacterioplankton in this OMZ region, with limited community mixing across water masses, except in upwelling events, and little dispersion of the community by currents in the euphotic zone.
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Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Institute of Marine Sciences and Limnology, National Autonomous University of Mexico, Mexico City, Mexico.
| | - Francisco Varona-Cordero
- Unidad Académica de Ecología y Biodiversidad Acuática, Institute of Marine Sciences and Limnology, National Autonomous University of Mexico, Mexico City, Mexico
| | - David Uriel Hernández-Becerril
- Unidad Académica de Ecología y Biodiversidad Acuática, Institute of Marine Sciences and Limnology, National Autonomous University of Mexico, Mexico City, Mexico
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10
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Bagnaro A, Baltar F, Brownstein G, Lee WG, Morales SE, Pritchard DW, Hepburn CD. Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems - focus on the pelagic environment. ENVIRONMENTAL MICROBIOME 2020; 15:16. [PMID: 33902717 PMCID: PMC8066478 DOI: 10.1186/s40793-020-00363-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 07/18/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND One of the central objectives of microbial ecology is to study the distribution of microbial communities and their association with their environments. Biogeographical studies have partitioned the oceans into provinces and regions, but the identification of their boundaries remains challenging, hindering our ability to study transition zones (i.e. ecotones) and microbial ecosystem heterogeneity. Fuzzy clustering is a promising method to do so, as it creates overlapping sets of clusters. The outputs of these analyses thus appear both structured (into clusters) and gradual (due to the overlaps), which aligns with the inherent continuity of the pelagic environment, and solves the issue of defining ecosystem boundaries. RESULTS We show the suitability of applying fuzzy clustering to address the patchiness of microbial ecosystems, integrating environmental (Sea Surface Temperature, Salinity) and bacterioplankton data (Operational Taxonomic Units (OTUs) based on 16S rRNA gene) collected during six cruises over 1.5 years from the subtropical frontal zone off New Zealand. The technique was able to precisely identify ecological heterogeneity, distinguishing both the patches and the transitions between them. In particular we show that the subtropical front is a distinct, albeit transient, microbial ecosystem. Each water mass harboured a specific microbial community, and the characteristics of their ecotones matched the characteristics of the environmental transitions, highlighting that environmental mixing lead to community mixing. Further explorations into the OTU community compositions revealed that, although only a small proportion of the OTUs explained community variance, their associations with given water mass were consistent through time. CONCLUSION We demonstrate recurrent associations between microbial communities and dynamic oceanic features. Fuzzy clusters can be applied to any ecosystem (terrestrial, human, marine, etc) to solve uncertainties regarding the position of microbial ecological boundaries and to refine the relation between the distribution of microorganisms and their environment.
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Affiliation(s)
- Antoine Bagnaro
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand.
| | - Federico Baltar
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
- NIWA, University of Otago, Dunedin, New Zealand
- Department of Functional & Evolutionary Ecology, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | | | - William G Lee
- Manaaki Whenua, Landcare Research, Dunedin, New Zealand
| | - Sergio E Morales
- Department of Microbiology & Immunology, University of Otago, Dunedin, New Zealand
| | - Daniel W Pritchard
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
- Te Ao Tūroa, Te Rūnanga o Ngāi Tahu, Dunedin, New Zealand
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11
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Sun P, Wang Y, Laws E, Huang B. Water mass-driven spatial effects and environmental heterogeneity shape microeukaryote biogeography in a subtropical, hydrographically complex ocean system - A case study of ciliates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135753. [PMID: 31836222 DOI: 10.1016/j.scitotenv.2019.135753] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/21/2019] [Accepted: 11/24/2019] [Indexed: 06/10/2023]
Abstract
The relative importance of geographic distance and depth in shaping microeukaryote community composition on a regional scale remains unclear, especially how that composition is related to the movement of water masses. Here, we collected 156 water samples across the Taiwan Strait, which is characterized by complex topography and dynamic circulation, to investigate the composition of the ciliate community with high-throughput sequencing of the 18S rRNA gene transcript. Ciliate alpha diversity exhibited strong correlations with water chemistry, food abundance, and geographic distance; approximately 50% of the variance of the diversity could be explained by dissolved oxygen concentrations, chlorophyll a concentrations, bacterial abundance, and latitude. The sampling sites could be divided into three provinces based on the compositions of the ciliate communities, which exhibited a distinctly nonuniform spatial distribution pattern on a regional scale (587 km). Geographic distance, environmental conditions, and depth were identified as principal determinants of the ciliate community within the Strait. Geographic distance was the most influential factor. The effect of geographic distance seems to mainly reflect the movement of water masses that strongly constrain dispersal and contribute to environmental heterogeneity that accounts for 86.0% and 5.5%, respectively, of community variance across the Strait. Overall, this study revealed that ciliate biogeography as a function of depth and environmental gradients is linked on a regional scale to the water masses that the ciliates inhabit. This result expands our knowledge of the drivers of microeukaryote community composition across regions within which there are water mass movements and strong spatial and environmental gradients.
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Affiliation(s)
- Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China.
| | - Ying Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Edward Laws
- Department of Environmental Sciences, School of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Bangqin Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
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Linse K, Copley JT, Connelly DP, Larter RD, Pearce DA, Polunin NVC, Rogers AD, Chen C, Clarke A, Glover AG, Graham AGC, Huvenne VAI, Marsh L, Reid WDK, Roterman CN, Sweeting CJ, Zwirglmaier K, Tyler PA. Fauna of the Kemp Caldera and its upper bathyal hydrothermal vents (South Sandwich Arc, Antarctica). ROYAL SOCIETY OPEN SCIENCE 2019; 6:191501. [PMID: 31827872 PMCID: PMC6894572 DOI: 10.1098/rsos.191501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/23/2019] [Indexed: 05/24/2023]
Abstract
Faunal assemblages at hydrothermal vents associated with island-arc volcanism are less well known than those at vents on mid-ocean ridges and back-arc spreading centres. This study characterizes chemosynthetic biotopes at active hydrothermal vents discovered at the Kemp Caldera in the South Sandwich Arc. The caldera hosts sulfur and anhydrite vent chimneys in 1375-1487 m depth, which emit sulfide-rich fluids with temperatures up to 212°C, and the microbial community of water samples in the buoyant plume rising from the vents was dominated by sulfur-oxidizing Gammaproteobacteria. A total of 12 macro- and megafaunal taxa depending on hydrothermal activity were collected in these biotopes, of which seven species were known from the East Scotia Ridge (ESR) vents and three species from vents outside the Southern Ocean. Faunal assemblages were dominated by large vesicomyid clams, actinostolid anemones, Sericosura sea spiders and lepetodrilid and cocculinid limpets, but several taxa abundant at nearby ESR hydrothermal vents were rare such as the stalked barnacle Neolepas scotiaensis. Multivariate analysis of fauna at Kemp Caldera and vents in neighbouring areas indicated that the Kemp Caldera is most similar to vent fields in the previously established Southern Ocean vent biogeographic province, showing that the species composition at island-arc hydrothermal vents can be distinct from nearby seafloor-spreading systems. δ 13C and δ 15N isotope values of megafaunal species analysed from the Kemp Caldera were similar to those of the same or related species at other vent fields, but none of the fauna sampled at Kemp Caldera had δ 13C values, indicating nutritional dependence on Epsilonproteobacteria, unlike fauna at other island-arc hydrothermal vents.
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Affiliation(s)
- Katrin Linse
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Jonathan T. Copley
- Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton SO14 3ZH, UK
| | | | - Robert D. Larter
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - David A. Pearce
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Nick V. C. Polunin
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building, Newcastle upon Tyne NE1 7RU, UK
| | - Alex D. Rogers
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Kanagawa Pref. Japan
| | - Andrew Clarke
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Adrian G. Glover
- Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | | | | | - Leigh Marsh
- Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton SO14 3ZH, UK
| | - William D. K. Reid
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building, Newcastle upon Tyne NE1 7RU, UK
| | - C. Nicolai Roterman
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Christopher J. Sweeting
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building, Newcastle upon Tyne NE1 7RU, UK
| | - Katrin Zwirglmaier
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Paul A. Tyler
- Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton SO14 3ZH, UK
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13
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Zorz J, Willis C, Comeau AM, Langille MGI, Johnson CL, Li WKW, LaRoche J. Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean. Front Microbiol 2019; 10:281. [PMID: 30846975 PMCID: PMC6393369 DOI: 10.3389/fmicb.2019.00281] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/04/2019] [Indexed: 11/29/2022] Open
Abstract
The fundamental role of bacteria in global biogeochemical cycles warrants a thorough understanding of the factors controlling bacterial community structure. In this study, the integrated effect of seasonal differences and spatial distribution on bacterial community structure and diversity were investigated at the regional scale. We conducted a comprehensive bacterial survey, with 451 samples of the Scotian Shelf sector of the Northwest Atlantic Ocean during spring and fall of 2014 and 2016, to analyze the effects of physicochemical gradients on bacterial community structure. Throughout the region, Pelagibacteraceae and Rhodobacteraceae were the most common in the free-living fraction, while Flavobacteriia and Deltaproteobacteria were more abundant in the particle-associated fraction. Overall, there was strong covariation of the microbial community diversity from the two size fractions. This relationship existed despite the statistically significant difference in community structure between the free-living and particle-associated size fractions. In both size fractions, distribution patterns of bacterial taxa, and species within taxa, displayed temporal and spatial preferences. Distinct bacterial assemblages specific to season and depth in the water column were identified. These distinct assemblages, consistent for both 2014 and 2016, suggested replicable patterns in microbial communities for spring and fall in this region. Over all sites, temperature and oxygen values were highly correlated with community similarity, and salinity and oxygen values were the most strongly positively- and negatively correlated with alpha diversity, respectively. However, the strengths of these correlations depended on the depth and season sampled. The bathymetry of the Scotian Shelf, the abrupt shelf break to the Scotian Slope and the major ocean currents dominating in the region led to the formation of distinct on-shelf and off-shelf bacterial communities both in spring and fall. The highest species richness was observed at the shelf break, where water masses from the two major currents meet. Our study establishes the baseline for assessing future changes in the bacterial community of the Scotian Shelf waters, a rapidly changing sector of the Atlantic Ocean.
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Affiliation(s)
- Jackie Zorz
- Department of Biology, Dalhousie University, Halifax, NS, Canada.,Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Ciara Willis
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - André M Comeau
- CGEB-Integrated Microbiome Resource, Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Morgan G I Langille
- CGEB-Integrated Microbiome Resource, Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Catherine L Johnson
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - William K W Li
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, NS, Canada
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14
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Easson CG, Lopez JV. Depth-Dependent Environmental Drivers of Microbial Plankton Community Structure in the Northern Gulf of Mexico. Front Microbiol 2019; 9:3175. [PMID: 30662434 PMCID: PMC6328475 DOI: 10.3389/fmicb.2018.03175] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/07/2018] [Indexed: 02/01/2023] Open
Abstract
The Gulf of Mexico (GoM) is a dynamic marine ecosystem influenced by multiple natural and anthropogenic processes and inputs, such as the intrusion of warm oligotrophic water via the Loop Current, freshwater and nutrient input by the Mississippi River, and hydrocarbon inputs via natural seeps and industrial spills. Microbial plankton communities are important to pelagic food webs including in the GoM but understanding the drivers of the natural dynamics of these passively distributed microorganisms can be challenging in such a large and heterogeneous system. As part of the DEEPEND consortium, we applied high throughput 16S rRNA sequencing to investigate the spatial and temporal dynamics of pelagic microbial plankton related to several environmental conditions during two offshore cruises in 2015. Our results show dramatic community shifts across depths, especially between photic and aphotic zones. Though we only have two time points within a single year, observed temporal shifts in microbial plankton communities were restricted to the seasonally influenced epipelagic zone (0-200 m), and appear mainly driven by changes in temperature. Environmental selection in microbial plankton communities was depth-specific, with variables such as turbidity, salinity, and abundance of photosynthetic taxa strongly correlating with community structure in the epipelagic zone, while variables such as oxygen and specific nutrient concentrations were correlated with community structure at deeper depths.
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Affiliation(s)
- Cole G. Easson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Jose V. Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, United States
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15
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Phoma S, Vikram S, Jansson JK, Ansorge IJ, Cowan DA, Van de Peer Y, Makhalanyane TP. Agulhas Current properties shape microbial community diversity and potential functionality. Sci Rep 2018; 8:10542. [PMID: 30002454 PMCID: PMC6043601 DOI: 10.1038/s41598-018-28939-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/28/2018] [Indexed: 11/21/2022] Open
Abstract
Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas Current system and the Subtropical Front in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for OMZ communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulfur cycling capacity in the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas Current system, particularly depth-related parameters, substantially influence microbial community structure. In addition, the capacity for biogeochemical cycling of nitrogen and sulfur is linked primarily to the dominant Gammaproteobacteria taxa, whereas ecologically rare taxa drive carbon cycling.
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Affiliation(s)
- Sandra Phoma
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, P.O. Box 999, Richland, WA, USA
| | - Isabelle J Ansorge
- Department of Oceanography and Marine Research Institute (Ma-Re), University of Cape Town, Rondebosch, 7701, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Yves Van de Peer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
- VIB Centre for Plant Systems Biology, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa.
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16
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Müller O, Wilson B, Paulsen ML, Rumińska A, Armo HR, Bratbak G, Øvreås L. Spatiotemporal Dynamics of Ammonia-Oxidizing Thaumarchaeota in Distinct Arctic Water Masses. Front Microbiol 2018; 9:24. [PMID: 29410658 PMCID: PMC5787140 DOI: 10.3389/fmicb.2018.00024] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/08/2018] [Indexed: 12/01/2022] Open
Abstract
One of the most abundant archaeal groups on Earth is the Thaumarchaeota. They are recognized as major contributors to marine ammonia oxidation, a crucial step in the biogeochemical cycling of nitrogen. Their universal success is attributed to a high genomic flexibility and niche adaptability. Based on differences in the gene coding for ammonia monooxygenase subunit A (amoA), two different ecotypes with distinct distribution patterns in the water column have been identified. We used high-throughput sequencing of 16S rRNA genes combined with archaeal amoA functional gene clone libraries to investigate which environmental factors are driving the distribution of Thaumarchaeota ecotypes in the Atlantic gateway to the Arctic Ocean through an annual cycle in 2014. We observed the characteristic vertical pattern of Thaumarchaeota abundance with high values in the mesopelagic (>200 m) water throughout the entire year, but also in the epipelagic (<200 m) water during the dark winter months (January, March and November). The Thaumarchaeota community was dominated by three OTUs which on average comprised 76% ± 11 and varied in relative abundance according to water mass characteristics and not to depth or ammonium concentration, as suggested in previous studies. The ratios of the abundance of the different OTU types were similar to that of the functional amoA water cluster types. Together, this suggests a strong selection of ecotypes within different water masses, supporting the general idea of water mass characteristics as an important factor in defining microbial community structure. If indeed, as suggested in this study, Thaumarchaeota population dynamics are controlled by a set of factors, described here as water mass characteristics and not just depth alone, then changes in water mass flow will inevitably affect the distribution of the different ecotypes.
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Affiliation(s)
- Oliver Müller
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Bryan Wilson
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Maria L Paulsen
- Department of Microbiology, University of Bergen, Bergen, Norway
| | | | - Hilde R Armo
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Gunnar Bratbak
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Lise Øvreås
- Department of Microbiology, University of Bergen, Bergen, Norway.,University Center in Svalbard (UNIS), Longyearbyen, Norway
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