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Cagri Ozturk R, Feyzioglu AM, Capkin E, Yildiz I, Altinok I. Effects of environmental parameters on spatial and temporal distribution of marine microbial communities in the southern Black Sea. MARINE ENVIRONMENTAL RESEARCH 2024; 195:106344. [PMID: 38232435 DOI: 10.1016/j.marenvres.2024.106344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 12/27/2023] [Accepted: 01/07/2024] [Indexed: 01/19/2024]
Abstract
The Black Sea is a unique environment with strong and permanent vertical stratification, with a thin layer of oxic zone above and a permanent anoxic zone below. Few high-throughput genomic surveys have been conducted to examine microbiota in the Black Sea. Yet, there is no study on the seasonal and vertical variation in microbial community compositions, driving forces and mechanisms of community assembly. In this study, seasonal, vertical, and spatial microbial assemblages were studied in terms of diversity, abundance, and community structure using 16S rRNA metabarcoding. 16S rRNA metabarcoding confirmed seasonal changes in microbial communities and the presence of distinct microbial groups among different water layers. Taxa belonging to Cyanobiaceae contributed a large fraction of the total biomass and were the most abundant autotrophic bacteria found across the whole water column, including hydrogen sulfide-containing anoxic zone. Temperature, salinity, water density, conductivity, light, chlorophyll-a, O2, NO3, NH3, PO4, Si, and H2S had a significant influence on the vertical bacterial community assemblages. The copper mine discharge system at 180 m did not affect microbial community structure and composition. Temperature seemed to be a primary factor in the variance between shallow depths. In conclusion, the lack of light, low dissolved oxygen levels, and low temperature do not restrict microbial diversity, as proven by the higher diversity observed in deeper zones. Wastewater in Black Sea region may be discharged into the Black Sea to depth of 180 m or deeper without impacting microbial ecology.
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Affiliation(s)
- Rafet Cagri Ozturk
- Department of Fisheries Technology Engineering, Faculty of Marine Sciences, Karadeniz Technical University, 61530, Trabzon, Türkiye; Aquatic Animal Health and Molecular Genetics (AQUANETIC) Lab, Department of Chemistry C Block, 61080, Ortahisar, Trabzon, Türkiye.
| | - Ali Muzaffer Feyzioglu
- Department of Marine Science and Technology, Faculty of Marine Science, Karadeniz Technical University, 61530, Trabzon, Türkiye.
| | - Erol Capkin
- Department of Fisheries Technology Engineering, Faculty of Marine Sciences, Karadeniz Technical University, 61530, Trabzon, Türkiye.
| | - Ilknur Yildiz
- Institute of Marine Sciences and Technology, Karadeniz Technical University, 61080, Trabzon, Türkiye.
| | - Ilhan Altinok
- Department of Fisheries Technology Engineering, Faculty of Marine Sciences, Karadeniz Technical University, 61530, Trabzon, Türkiye; Aquatic Animal Health and Molecular Genetics (AQUANETIC) Lab, Department of Chemistry C Block, 61080, Ortahisar, Trabzon, Türkiye; Institute of Marine Sciences and Technology, Karadeniz Technical University, 61080, Trabzon, Türkiye.
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2
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Pradhoshini KP, Santhanabharathi B, Priyadharshini M, Ahmed MS, Murugan K, Sivaperumal P, Alam L, Duong VH, Musthafa MS. Microbial consortium and impact of industrial mining on the Natural High Background Radiation Area (NHBRA), India - Characteristic role of primordial radionuclides in influencing the community structure and extremophiles pattern. ENVIRONMENTAL RESEARCH 2024; 244:118000. [PMID: 38128601 DOI: 10.1016/j.envres.2023.118000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 11/26/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023]
Abstract
The present investigation is the first of its kind which aims to study the characteristics of microbial consortium inhabiting one of the natural high background radiation areas of the world, Chavara Coast in Kerala, India. The composition of the microbial community and their structural changes were evaluated under the natural circumstances with exorbitant presence of radionuclides in the sediments and after the radionuclide's recession due to mining effects. For this purpose, the concentration of radionuclides, heavy metals, net radioactivity estimation via gross alpha and beta emitters and other physiochemical characteristics were assessed in the sediments throughout the estuarine stretch. According to the results, the radionuclides had a significant effect in shaping the community structure and composition, as confirmed by the bacterial heterogeneity achieved between the samples. The results indicate that high radioactivity in the background environment reduced the abundance and growth of normal microbial fauna and favoured only the growth of certain extremophiles belonging to families of Piscirickettsiacea, Rhodobacteriacea and Thermodesulfovibrionaceae, which were able to tolerate and adapt towards the ionizing radiation present in the environment. In contrast, communities from Comamondacea, Sphingomonadacea, Moraxellacea and Erythrobacteracea were present in the sediments collected from industrial outlet, reinforcing the potent role of radionuclides in governing the community pattern of microbes present in the natural environment. The study confirms the presence of these novel and unidentified bacterial communities and further opens the possibility of utilizing their usefulness in future prospects.
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Affiliation(s)
- Kumara Perumal Pradhoshini
- Unit of Research in Radiation Biology & Environmental Radioactivity (URRBER), P.G & Research Department of Zoology, The New College (Autonomous), Affiliated to University of Madras, Chennai, Tamil Nadu, 600 014, India; Institute for Environment and Development (LESTARI), Research Centre for Sustainability Science and Governance (SGK), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Bharathi Santhanabharathi
- Unit of Research in Radiation Biology & Environmental Radioactivity (URRBER), P.G & Research Department of Zoology, The New College (Autonomous), Affiliated to University of Madras, Chennai, Tamil Nadu, 600 014, India
| | - Marckasagayam Priyadharshini
- Unit of Research in Radiation Biology & Environmental Radioactivity (URRBER), P.G & Research Department of Zoology, The New College (Autonomous), Affiliated to University of Madras, Chennai, Tamil Nadu, 600 014, India
| | - Munawar Suhail Ahmed
- Unit of Research in Radiation Biology & Environmental Radioactivity (URRBER), P.G & Research Department of Zoology, The New College (Autonomous), Affiliated to University of Madras, Chennai, Tamil Nadu, 600 014, India
| | - Karuvelan Murugan
- Department of Microbiology, Vels Institute of Science, Technology and Advanced Sciences (VISTAS), Pallavaram, Chennai, Tamilnadu, 600117, India
| | - Pitchiah Sivaperumal
- Marine Biomedical Research Lab & Environmental Toxicology Unit, Cellular and Molecular Research Centre, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamilnadu, 600077, India
| | - Lubna Alam
- Fisheries Economics Research Unit, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, Canada
| | - Van-Hao Duong
- VNU School of Interdisciplinary Studies, Vietnam National University, Hanoi, Viet Nam
| | - Mohamed Saiyad Musthafa
- Unit of Research in Radiation Biology & Environmental Radioactivity (URRBER), P.G & Research Department of Zoology, The New College (Autonomous), Affiliated to University of Madras, Chennai, Tamil Nadu, 600 014, India; Institute for Environment and Development (LESTARI), Research Centre for Sustainability Science and Governance (SGK), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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3
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Bendia AG, Moreira JCF, Ferreira JCN, Romano RG, Ferreira IGC, Franco DC, Evangelista H, Montone RC, Pellizari VH. Insights into Antarctic microbiomes: diversity patterns for terrestrial and marine habitats. AN ACAD BRAS CIENC 2023; 95:e20211442. [PMID: 37820122 DOI: 10.1590/0001-3765202320211442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 08/27/2022] [Indexed: 10/13/2023] Open
Abstract
Microorganisms in Antarctica are recognized for having crucial roles in ecosystems functioning and biogeochemical cycles. To explore the diversity and composition of microbial communities through different terrestrial and marine Antarctic habitats, we analyze 16S rRNA sequence datasets from fumarole and marine sediments, soil, snow and seawater environments. We obtained measures of alpha- and beta-diversities, as well as we have identified the core microbiome and the indicator microbial taxa of a particular habitat. Our results showed a unique microbial community structure according to each habitat, including specific taxa composing each microbiome. Marine sediments harbored the highest microbial diversity among the analyzed habitats. In the fumarole sediments, the core microbiome was composed mainly of thermophiles and hyperthermophilic Archaea, while in the majority of soil samples Archaea was absent. In the seawater samples, the core microbiome was mainly composed by cultured and uncultured orders usually identified on Antarctic pelagic ecosystems. Snow samples exhibited common taxa previously described for habitats of the Antarctic Peninsula, which suggests long-distance dispersal processes occurring from the Peninsula to the Continent. This study contributes as a baseline for further efforts on evaluating the microbial responses to environmental conditions and future changes.
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Affiliation(s)
- Amanda G Bendia
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Julio Cezar F Moreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Juliana C N Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Renato G Romano
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Ivan G C Ferreira
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Diego C Franco
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Heitor Evangelista
- Universidade do Estado do Rio de Janeiro (UERJ), Instituto de Biologia Roberto Alcantara Gomes, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
| | - Rosalinda C Montone
- Universidade de São Paulo (USP), Departamento de Oceanografia Física, Química e Geológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
| | - Vivian Helena Pellizari
- Universidade de São Paulo (USP), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Cidade Universitária, Praça do Oceanográfico, 191, 05508-900 São Paulo, SP, Brazil
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Baloza M, Henkel S, Kasten S, Holtappels M, Molari M. The Impact of Sea Ice Cover on Microbial Communities in Antarctic Shelf Sediments. Microorganisms 2023; 11:1572. [PMID: 37375074 DOI: 10.3390/microorganisms11061572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/30/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The area around the Antarctic Peninsula (AP) is facing rapid climatic and environmental changes, with so far unknown impacts on the benthic microbial communities of the continental shelves. In this study, we investigated the impact of contrasting sea ice cover on microbial community compositions in surface sediments from five stations along the eastern shelf of the AP using 16S ribosomal RNA (rRNA) gene sequencing. Redox conditions in sediments with long ice-free periods are characterized by a prevailing ferruginous zone, whereas a comparatively broad upper oxic zone is present at the heavily ice-covered station. Low ice cover stations were highly dominated by microbial communities of Desulfobacterota (mostly Sva1033, Desulfobacteria, and Desulfobulbia), Myxococcota, and Sva0485, whereas Gammaproteobacteria, Alphaproteobacteria, Bacteroidota, and NB1-j prevail at the heavy ice cover station. In the ferruginous zone, Sva1033 was the dominant member of Desulfuromonadales for all stations and, along with eleven other taxa, showed significant positive correlations with dissolved Fe concentrations, suggesting a significant role in iron reduction or an ecological relationship with iron reducers. Our results indicate that sea ice cover and its effect on organic carbon fluxes are the major drivers for changes in benthic microbial communities, favoring potential iron reducers at stations with increased organic matter fluxes.
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Affiliation(s)
- Marwa Baloza
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Faculty 2 Biology/Chemistry, University of Bremen, Leobener Str., 28359 Bremen, Germany
| | - Susann Henkel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Sabine Kasten
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Str., 28359 Bremen, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Moritz Holtappels
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Massimiliano Molari
- HGF-MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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5
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Doytchinov VV, Dimov SG. Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach. LIFE (BASEL, SWITZERLAND) 2022; 12:life12060916. [PMID: 35743947 PMCID: PMC9228076 DOI: 10.3390/life12060916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.
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6
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Zhu D, Sethupathy S, Gao L, Nawaz MZ, Zhang W, Jiang J, Sun J. Microbial diversity and community structure in deep-sea sediments of South Indian Ocean. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45793-45807. [PMID: 35152353 DOI: 10.1007/s11356-022-19157-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
Microbial communities composed of bacteria, archaea and fungi play a pivotal role in driving the biogeochemical cycles in the marine ecosystem. Despite the vastness of the South Indian Ocean, only a few studies reported the simultaneous analysis of bacterial, archaeal and fungal diversity therein, particularly archaeal and fungal communities in deep-sea environments received less attention previously. In this study, microbial diversity, community composition and dynamics in microbial community structure in eight deep-sea sediment samples collected from different sites at varying depths of the South Indian Ocean were explored using Next-Generation Sequencing. In total, 21 bacterial phyla representing 541 OTUs were identified from the eight samples, where phylum Proteobacteria was found as the most abundant bacterial phylum in five out of eight samples. Firmicutes and Chloroflexi were the dominant phyla in the rest of the three samples. In the case of archaea, uncultured species belonging to the phyla Thaumarchaeota and Euryarchaeota were the abundant taxa in all the samples. Similarly, Ascomycota and Basidiomycota were the most abundant fungal phyla present therein. In all the eight samples studied here, about 10-58% and 19-26% OTUs in archaeal and fungal communities were mapped to unclassified taxa respectively, suggesting the lack of representation in databases. Co-occurrence network analysis further revealed that bacterial communities tend to be more dynamic than archaeal and fungal communities. This study provides interesting insights into the microbial diversity, community composition and dynamics in microbial community structure in the deep-sea sediments of the South Indian Ocean.
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Affiliation(s)
- Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| | - Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Lu Gao
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Muhammad Zohaib Nawaz
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
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Fonseca VG, Kirse A, Giebner H, Vause BJ, Drago T, Power DM, Peck LS, Clark MS. Metabarcoding the Antarctic Peninsula biodiversity using a multi-gene approach. ISME COMMUNICATIONS 2022; 2:37. [PMID: 37938273 PMCID: PMC9723778 DOI: 10.1038/s43705-022-00118-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 07/04/2023]
Abstract
Marine sediment communities are major contributors to biogeochemical cycling and benthic ecosystem functioning, but they are poorly described, particularly in remote regions such as Antarctica. We analysed patterns and drivers of diversity in metazoan and prokaryotic benthic communities of the Antarctic Peninsula with metabarcoding approaches. Our results show that the combined use of mitochondrial Cox1, and 16S and 18S rRNA gene regions recovered more phyla, from metazoan to non-metazoan groups, and allowed correlation of possible interactions between kingdoms. This higher level of detection revealed dominance by the arthropods and not nematodes in the Antarctic benthos and further eukaryotic diversity was dominated by benthic protists: the world's largest reservoir of marine diversity. The bacterial family Woeseiaceae was described for the first time in Antarctic sediments. Almost 50% of bacteria and 70% metazoan taxa were unique to each sampled site (high alpha diversity) and harboured unique features for local adaptation (niche-driven). The main abiotic drivers measured, shaping community structure were sediment organic matter, water content and mud. Biotic factors included the nematodes and the highly abundant bacterial fraction, placing protists as a possible bridge for between kingdom interactions. Meiofauna are proposed as sentinels for identifying anthropogenic-induced changes in Antarctic marine sediments.
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Affiliation(s)
- V G Fonseca
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, UK.
| | - A Kirse
- Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany
| | - H Giebner
- Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany
| | - B J Vause
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - T Drago
- Portuguese Institute for Sea and Atmosphere (IPMA), Tavira, Portugal
- Institute Dom Luiz (IDL), University of Lisbon, Lisbon, Portugal
| | - D M Power
- Centre of Marine Sciences (CCMAR), Faro, Portugal
| | - L S Peck
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - M S Clark
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
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Local Environmental Conditions Promote High Turnover Diversity of Benthic Deep-Sea Fungi in the Ross Sea (Antarctica). J Fungi (Basel) 2022; 8:jof8010065. [PMID: 35050005 PMCID: PMC8781733 DOI: 10.3390/jof8010065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/16/2022] Open
Abstract
Fungi are a ubiquitous component of marine systems, but their quantitative relevance, biodiversity and ecological role in benthic deep-sea ecosystems remain largely unexplored. In this study, we investigated fungal abundance, diversity and assemblage composition in two benthic deep-sea sites of the Ross Sea (Southern Ocean, Antarctica), characterized by different environmental conditions (i.e., temperature, salinity, trophic availability). Our results indicate that fungal abundance (estimated as the number of 18S rDNA copies g−1) varied by almost one order of magnitude between the two benthic sites, consistently with changes in sediment characteristics and trophic availability. The highest fungal richness (in terms of Amplicon Sequence Variants−ASVs) was encountered in the sediments characterized by the highest organic matter content, indicating potential control of trophic availability on fungal diversity. The composition of fungal assemblages was highly diverse between sites and within each site (similarity less than 10%), suggesting that differences in environmental and ecological characteristics occurring even at a small spatial scale can promote high turnover diversity. Overall, this study provides new insights on the factors influencing the abundance and diversity of benthic deep-sea fungi inhabiting the Ross Sea, and also paves the way for a better understanding of the potential responses of benthic deep-sea fungi inhabiting Antarctic ecosystems in light of current and future climate changes.
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Purser A, Hehemann L, Boehringer L, Tippenhauer S, Wege M, Bornemann H, Pineda-Metz SEA, Flintrop CM, Koch F, Hellmer HH, Burkhardt-Holm P, Janout M, Werner E, Glemser B, Balaguer J, Rogge A, Holtappels M, Wenzhoefer F. A vast icefish breeding colony discovered in the Antarctic. Curr Biol 2022; 32:842-850.e4. [PMID: 35030328 DOI: 10.1016/j.cub.2021.12.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/15/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
A breeding colony of notothenioid icefish (Neopagetopsis ionah, Nybelin 1947) of globally unprecedented extent has been discovered in the southern Weddell Sea, Antarctica. The colony was estimated to cover at least ∼240 km2 of the eastern flank of the Filchner Trough, comprised of fish nests at a density of 0.26 nests per square meter, representing an estimated total of ∼60 million active nests and associated fish biomass of >60,000 tonnes. The majority of nests were each occupied by 1 adult fish guarding 1,735 eggs (±433 SD). Bottom water temperatures measured across the nesting colony were up to 2°C warmer than the surrounding bottom waters, indicating a spatial correlation between the modified Warm Deep Water (mWDW) upflow onto the Weddell Shelf and the active nesting area. Historical and concurrently collected seal movement data indicate that this concentrated fish biomass may be utilized by predators such as Weddell seals (Leptonychotes weddellii, Lesson 1826). Numerous degraded fish carcasses within and near the nesting colony suggest that, in death as well as life, these fish provide input for local food webs and influence local biogeochemical processing. To our knowledge, the area surveyed harbors the most spatially expansive continuous fish breeding colony discovered to date globally at any depth, as well as an exceptionally high Antarctic seafloor biomass. This discovery provides support for the establishment of a regional marine protected area in the Southern Ocean under the Convention on the Conservation of Antarctic Marine Living Resources (CCAMLR) umbrella. VIDEO ABSTRACT.
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Affiliation(s)
- Autun Purser
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany.
| | - Laura Hehemann
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Lilian Boehringer
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany; Universität Bremen (Fachbereich 2, Biologie/Chemie), 28334 Bremen, Germany
| | - Sandra Tippenhauer
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Mia Wege
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany; Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, South Africa
| | - Horst Bornemann
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Santiago E A Pineda-Metz
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Clara M Flintrop
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Florian Koch
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Hartmut H Hellmer
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Patricia Burkhardt-Holm
- Programme Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland
| | - Markus Janout
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Ellen Werner
- HafenCity University Hamburg, Henning-Voscherau-Platz 1, 20457 Hamburg, Germany
| | - Barbara Glemser
- Universität Bremen (Fachbereich 2, Biologie/Chemie), 28334 Bremen, Germany; Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Jenna Balaguer
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Andreas Rogge
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany; Institute for Ecosystem Research, Kiel University, Kiel, Germany
| | - Moritz Holtappels
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Frank Wenzhoefer
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany; Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany; Department of Biology, University of Southern Denmark, HADAL and Nordcee, 5230 Odense M, Denmark
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10
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Garber AI, Zehnpfennig JR, Sheik CS, Henson MW, Ramírez GA, Mahon AR, Halanych KM, Learman DR. Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy. mSphere 2021; 6:e0077021. [PMID: 34817234 PMCID: PMC8612310 DOI: 10.1128/msphere.00770-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/10/2021] [Indexed: 11/30/2022] Open
Abstract
The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.
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Affiliation(s)
- Arkadiy I. Garber
- Biodesign Center for Mechanisms for Evolution, Arizona State University, Tempe, Arizona, USA
| | | | - Cody S. Sheik
- Biology Department and Large Lakes Observatory, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Michael W. Henson
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Gustavo A. Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
- Department of Marine Biology, Haifa University, Haifa, Israel
| | - Andrew R. Mahon
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Kenneth M. Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Deric R. Learman
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
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11
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Currie AA, Marshall AJ, Lohrer AM, Cummings VJ, Seabrook S, Cary SC. Sea Ice Dynamics Drive Benthic Microbial Communities in McMurdo Sound, Antarctica. Front Microbiol 2021; 12:745915. [PMID: 34777294 PMCID: PMC8581541 DOI: 10.3389/fmicb.2021.745915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/29/2021] [Indexed: 01/04/2023] Open
Abstract
Climate change is driving dramatic variability in sea ice dynamics, a key driver in polar marine ecosystems. Projected changes in Antarctica suggest that regional warming will force dramatic shifts in sea ice thickness and persistence, altering sea ice-associated primary production and deposition to the seafloor. To improve our understanding of the impacts of sea ice change on benthic ecosystems, we directly compared the benthic microbial communities underlying first-year sea ice (FYI) and multi-year sea ice (MYI). Using two tractable coastal habitats in McMurdo Sound, Antarctica, where FYI (Cape Evans) and MYI (New Harbour) prevail, we show that the structure and composition of the benthic microbial communities reflect the legacy of sea ice dynamics. At Cape Evans, an enrichment of known heterotrophic algal polysaccharide degrading taxa (e.g., Flavobacteriaceae, unclassified Gammaproteobacteria, and Rubritaleaceae) and sulfate-reducing bacteria (e.g., Desulfocapsaceae) correlated with comparatively higher chlorophyll a (14.2±0.8μgg-1) and total organic carbon content (0.33%±0.04), reflecting increased productivity and seafloor deposition beneath FYI. Conversely, at New Harbour, an enrichment of known archaeal (e.g., Nitrosopumilaceae) and bacterial (e.g., Woeseiaceae and Nitrospiraceae) chemoautotrophs was common in sediments with considerably lower chlorophyll a (1.0±0.24μgg-1) and total organic carbon content (0.17%±0.01), reflecting restricted productivity beneath MYI. We also report evidence of a submarine discharge of sub-permafrost brine from Taylor Valley into New Harbour. By comparing our two study sites, we show that under current climate-warming scenarios, changes to sea ice productivity and seafloor deposition are likely to initiate major shifts in benthic microbial communities, with heterotrophic organic matter degradation processes becoming increasingly important. This study provides the first assessment of how legacy sea ice conditions influence benthic microbial communities in Antarctica, contributing insight into sea ice-benthic coupling and ecosystem functioning in a polar environment.
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Affiliation(s)
- Ashleigh A Currie
- School of Science, University of Waikato, Hamilton, New Zealand.,Environmental Research Institute, International Centre for Terrestrial Antarctic Research, Hamilton, New Zealand
| | - Alexis J Marshall
- School of Science, University of Waikato, Hamilton, New Zealand.,Environmental Research Institute, International Centre for Terrestrial Antarctic Research, Hamilton, New Zealand
| | - Andrew M Lohrer
- National Institute of Water and Atmosphere, Hamilton, New Zealand
| | - Vonda J Cummings
- National Institute of Water and Atmosphere, Wellington, New Zealand
| | - Sarah Seabrook
- National Institute of Water and Atmosphere, Wellington, New Zealand
| | - S Craig Cary
- School of Science, University of Waikato, Hamilton, New Zealand.,Environmental Research Institute, International Centre for Terrestrial Antarctic Research, Hamilton, New Zealand
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12
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Zárate A, Dorador C, Valdés J, Molina V, Icaza G, Pacheco AS, Castillo A. Benthic microbial diversity trends in response to heavy metals in an oxygen-deficient eutrophic bay of the Humboldt current system offshore the Atacama Desert. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117281. [PMID: 33992902 DOI: 10.1016/j.envpol.2021.117281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/25/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Mejillones Bay is a coastal ecosystem situated in an oxygen-deficient upwelling area impacted by mining activities in the coastal desert region of northern Chile, where conspicuous microbial life develops in the sediments. Herein, heavy metal (loid)s (HMs) such as Cu, Pb, As, Zn, Al, Fe, Cd, Mo, Ni and V as well as benthic microbial communities were studied using spectrometry and iTag-16 S rRNA sequencing. Samples were taken from two contrasting sedimentary localities in the Bay named Punta Rieles (PR) and Punta Chacaya (PC) within 10-50 m water-depth gradient. PR sediments were organic matter rich (21.1% of TOM at 50 m) and overlaid with low-oxygen waters (<0.06 ml O2/L bottom layer) compared with PC. In general, HMs like Al, Ni, Cd, As and Pb tended to increase in concentration with depth in PR, while the opposite pattern was observed in PC. In addition, PR presented a higher number of unique families (72) compared to PC (35). Among the top ten microbial families, Desulfobulbaceae (4.6% vs. 3.2%), Flavobacteriaceae (2.8% vs. 2.3%) and Anaerolineaceae (3.3% vs. 2.3%) dominated in PR, meanwhile Actinomarinales_Unclassified (8.1% vs. 4.2%) and Sandaracinaceae (4.4% vs. 2.0%) were more abundant in PC. Multivariate analyses confirmed that water depth-related variation was a good proxy for oxygen conditions and metal concentrations, explaining the structure of benthic microbial assemblages. Cd, Ni, As and Pb showed uniformly positive associations with communities that represented the keystone taxa in the co-occurrence network, including Anaerolineaceae, Thiotrichaceae, Desulfobulbaceae, Desulfarculaceae and Bacteroidales_unclassified communities. Collectively, these findings provide new insights for establishing the ecological interconnections of benthic microorganisms in response to metal contamination in a coastal upwelling environment.
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Affiliation(s)
- Ana Zárate
- Doctorado en Ciencias Aplicadas Mención Sistemas Marinos Costeros, Universidad de Antofagasta, Antofagasta, Chile; Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile; Humedales Del Caribe Colombiano, Universidad Del Atlántico, Barranquilla, Colombia.
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile; Departamento de Biotecnología, Facultad de Ciencias Del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Jorge Valdés
- Laboratorio de Sedimentología y Paleoambientes, Instituto de Ciencias Naturales A. von Humboldt, Facultad de Ciencias Del Mar y de Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Verónica Molina
- Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile; HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | - Aldo S Pacheco
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Alexis Castillo
- Centro de Investigación y Estudios Avanzados Del Maule. Vicerrectoría de Investigación de Investigación y Posgrado. Universidad Católica Del Maule, Campus San Miguel. Talca, Chile
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13
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Lai D, Hedlund BP, Xie W, Liu J, Phelps TJ, Zhang C, Wang P. Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments. Front Microbiol 2020; 11:572017. [PMID: 33224115 PMCID: PMC7674655 DOI: 10.3389/fmicb.2020.572017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Archaea are widespread in marine sediments and play important roles in the cycling of sedimentary organic carbon. However, factors controlling the distribution of archaea in marine sediments are not well understood. Here we investigated benthic archaeal communities over glacial-interglacial cycles in the northern South China Sea and evaluated their responses to sediment organic matter sources and inter-species interactions. Archaea in sediments deposited during the interglacial period Marine Isotope Stage (MIS) 1 (Holocene) were significantly different from those in sediments deposited in MIS 2 and MIS 3 of the Last Glacial Period when terrestrial input to the South China Sea was enhanced based on analysis of the long-chain n-alkane C31. The absolute archaeal 16S rRNA gene abundance in subsurface sediments was highest in MIS 2, coincident with high sedimentation rates and high concentrations of total organic carbon. Soil Crenarchaeotic Group (SCG; Nitrososphaerales) species, the most abundant ammonia-oxidizing archaea in soils, increased dramatically during MIS 2, likely reflecting transport of terrestrial archaea during glacial periods with high sedimentation rates. Co-occurrence network analyses indicated significant association of SCG archaea with benthic deep-sea microbes such as Bathyarchaeota and Thermoprofundales in MIS 2 and MIS 3, suggesting potential interactions among these archaeal groups. Meanwhile, Thermoprofundales abundance was positively correlated with total organic carbon (TOC), along with n-alkane C31 and sedimentation rate, indicating that Thermoprofundales may be particularly important in processing of organic carbon in deep-sea sediments. Collectively, these results demonstrate that the composition of heterotrophic benthic archaea in the South China Sea may be influenced by terrestrial organic input in tune with glacial-interglacial cycles, suggesting a plausible link between global climate change and microbial population dynamics in deep-sea marine sediments.
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Affiliation(s)
- Dengxun Lai
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China.,School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jingjing Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Tommy J Phelps
- Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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14
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Bacterioplankton reveal years-long retention of Atlantic deep-ocean water by the Tropic Seamount. Sci Rep 2020; 10:4715. [PMID: 32170218 PMCID: PMC7069937 DOI: 10.1038/s41598-020-61417-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 02/24/2020] [Indexed: 12/12/2022] Open
Abstract
Seamounts, often rising hundreds of metres above surrounding seafloor, obstruct the flow of deep-ocean water. While the retention of deep-water by seamounts is predicted from ocean circulation models, its empirical validation has been hampered by large scale and slow rate of the interaction. To overcome these limitations we use the growth of planktonic bacteria to assess the retention time of deep-ocean water by a seamount. The selected Tropic Seamount in the North-Eastern Atlantic is representative for the majority of isolated seamounts, which do not affect the surface ocean waters. We prove deep-water is retained by the seamount by measuring 2.4× higher bacterial concentrations in the seamount-associated or 'sheath'-water than in deep-ocean water unaffected by seamounts. Genomic analyses of flow-sorted, dominant sheath-water bacteria confirm their planktonic origin, whilst proteomic analyses of the sheath-water bacteria, isotopically labelled in situ, indicate their slow growth. According to our radiotracer experiments, it takes the sheath-water bacterioplankton 1.5 years to double their concentration. Therefore, the seamount should retain the deep-ocean water for 1.8 years for the deep-ocean bacterioplankton to grow to the 2.4× higher concentration in the sheath-water. We propose that turbulent mixing of the seamount sheath-water stimulates bacterioplankton growth by increasing cell encounter rate with ambient dissolved organic molecules.
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15
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Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities. ISME JOURNAL 2020; 14:1042-1056. [PMID: 31988474 PMCID: PMC7082342 DOI: 10.1038/s41396-020-0588-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 12/18/2019] [Accepted: 01/15/2020] [Indexed: 11/09/2022]
Abstract
Surveys of 16S rRNA gene sequences derived from marine sediments have indicated that a widely distributed group of Gammaproteobacteria, named “JTB255-Marine Benthic Group” (now the candidate order Woeseiales), accounts for 1–22% of the retrieved sequences. Despite their ubiquity in seafloor communities, little is known about their distribution and specific ecological niches in the deep sea, which constitutes the largest biome globally. Here, we characterized the phylogeny, environmental distribution patterns, abundance, and metabolic potential of Woeseiales bacteria with a focus on representatives from the deep sea. From a phylogenetic analysis of publicly available 16S rRNA gene sequences (≥1400 bp, n = 994), we identified lineages of Woeseiales with greater prevalence in the deep sea than in coastal environments, a pattern corroborated by the distribution of 16S oligotypes recovered from 28 globally distributed sediment samples. Cell counts revealed that Woeseiales bacteria accounted for 5 ± 2% of all microbial cells in deep-sea surface sediments at 23 globally distributed sites. Comparative analyses of a genome, metagenome bins, and single-cell genomes suggested that members of the corresponding clades are likely to grow on proteinaceous matter, potentially derived from detrital cell membranes, cell walls, and other organic remnants in marine sediments.
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16
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Li AZ, Han XB, Zhang MX, Zhou Y, Chen M, Yao Q, Zhu HH. Culture-Dependent and -Independent Analyses Reveal the Diversity, Structure, and Assembly Mechanism of Benthic Bacterial Community in the Ross Sea, Antarctica. Front Microbiol 2019; 10:2523. [PMID: 31787942 PMCID: PMC6856632 DOI: 10.3389/fmicb.2019.02523] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/21/2019] [Indexed: 11/22/2022] Open
Abstract
The benthic bacterial community in Antarctic continental shelf ecosystems are not well-documented. We collected 13 surface sediments from the Ross Sea, a biological hotspot in high-latitude maritime Antarctica undergoing rapid climate change and possible microflora shift, and aimed to study the diversity, structure and assembly mechanism of benthic bacterial community using both culture-dependent and -independent approaches. High-throughput sequencing of 16S rRNA gene amplicons revealed 370 OTUs distributed in 21 phyla and 284 genera. The bacterial community was dominated by Bacteroidetes, Gamma- and Alphaproteobacteria, and constituted by a compact, conserved and positively-correlated group of anaerobes and other competitive aerobic chemoheterotrophs. Null-model test based on βNTI and RCBray indicated that stochastic processes, including dispersal limitation and undominated fractions, were the main forces driving community assembly. On the other hand, environmental factors, mainly temperature, organic matter and chlorophyll, were significantly correlated with bacterial richness, diversity and community structure. Moreover, metabolic and physiological features of the prokaryotic taxa were mapped to evaluate the adaptive mechanisms and functional composition of the benthic bacterial community. Our study is helpful to understand the structural and functional aspects, as well as the ecological and biogeochemical role of the benthic bacterial community in the Ross Sea.
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Affiliation(s)
- An-Zhang Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xi-Bin Han
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Ming-Xia Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yang Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meng Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qing Yao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Grass Science, Guangdong Engineering Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Hong-Hui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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17
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Overholt WA, Schwing P, Raz KM, Hastings D, Hollander DJ, Kostka JE. The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills. Environ Microbiol 2019; 21:4316-4329. [PMID: 31469487 DOI: 10.1111/1462-2920.14794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/20/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022]
Abstract
The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in > 700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Furthermore, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after 2 years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover, deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies.
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Affiliation(s)
- Will A Overholt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Patrick Schwing
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Kala M Raz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - David Hastings
- Department of Marine Science, Eckerd College, St. Petersburg, FL, USA
| | - David J Hollander
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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18
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Peoples LM, Grammatopoulou E, Pombrol M, Xu X, Osuntokun O, Blanton J, Allen EE, Nunnally CC, Drazen JC, Mayor DJ, Bartlett DH. Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches. Front Microbiol 2019; 10:347. [PMID: 30930856 PMCID: PMC6428765 DOI: 10.3389/fmicb.2019.00347] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/11/2019] [Indexed: 11/13/2022] Open
Abstract
Hadal ocean sediments, found at sites deeper than 6,000 m water depth, are thought to contain microbial communities distinct from those at shallower depths due to high hydrostatic pressures and higher abundances of organic matter. These communities may also differ from one other as a result of geographical isolation. Here we compare microbial community composition in surficial sediments of two hadal environments—the Mariana and Kermadec trenches—to evaluate microbial biogeography at hadal depths. Sediment microbial consortia were distinct between trenches, with higher relative sequence abundances of taxa previously correlated with organic matter degradation present in the Kermadec Trench. In contrast, the Mariana Trench, and deeper sediments in both trenches, were enriched in taxa predicted to break down recalcitrant material and contained other uncharacterized lineages. At the 97% similarity level, sequence-abundant taxa were not trench-specific and were related to those found in other hadal and abyssal habitats, indicating potential connectivity between geographically isolated sediments. Despite the diversity of microorganisms identified using culture-independent techniques, most isolates obtained under in situ pressures were related to previously identified piezophiles. Members related to these same taxa also became dominant community members when native sediments were incubated under static, long-term, unamended high-pressure conditions. Our results support the hypothesis that there is connectivity between sediment microbial populations inhabiting the Mariana and Kermadec trenches while showing that both whole communities and specific microbial lineages vary between trench of collection and sediment horizon depth. This in situ biodiversity is largely missed when incubating samples within pressure vessels and highlights the need for revised protocols for high-pressure incubations.
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Affiliation(s)
- Logan M Peoples
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Eleanna Grammatopoulou
- Oceanlab, The Institute of Biological and Environmental Sciences, King's College, The University of Aberdeen, Aberdeen, United Kingdom
| | - Michelle Pombrol
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Xiaoxiong Xu
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Oladayo Osuntokun
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Jessica Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Clifton C Nunnally
- Louisiana Universities Marine Consortium (LUMCON), Chauvin, LA, United States
| | - Jeffrey C Drazen
- Department of Oceanography, University of Hawai'i at Ma-noa, Honolulu, HI, United States
| | - Daniel J Mayor
- Oceanlab, The Institute of Biological and Environmental Sciences, King's College, The University of Aberdeen, Aberdeen, United Kingdom.,National Oceanography Centre, University of Southampton Waterfront Campus European Way, Southampton, United Kingdom
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
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19
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Bowman JS. Identification of Microbial Dark Matter in Antarctic Environments. Front Microbiol 2018; 9:3165. [PMID: 30619224 PMCID: PMC6305705 DOI: 10.3389/fmicb.2018.03165] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022] Open
Abstract
Numerous studies have applied molecular techniques to understand the diversity, evolution, and ecological function of Antarctic bacteria and archaea. One common technique is sequencing of the 16S rRNA gene, which produces a nearly quantitative profile of community membership. However, the utility of this and similar approaches is limited by what is known about the evolution, physiology, and ecology of surveyed taxa. When representative genomes are available in public databases some of this information can be gleaned from genomic studies, and automated pipelines exist to carry out this task. Here the paprica metabolic inference pipeline was used to assess how well Antarctic microbial communities are represented by the available completed genomes. The NCBI's Sequence Read Archive (SRA) was searched for Antarctic datasets that used one of the Illumina platforms to sequence the 16S rRNA gene. These data were quality controlled and denoised to identify unique reads, then analyzed with paprica to determine the degree of overlap with the closest phylogenetic neighbor with a completely sequenced genome. While some unique reads had perfect mapping to 16S rRNA genes from completed genomes, the mean percent overlap for all mapped reads was 86.6%. When samples were grouped by environment, some environments appeared more or less well represented by the available genomes. For the domain Bacteria, seawater was particularly poorly represented with a mean overlap of 80.2%, while for the domain Archaea glacial ice was particularly poorly represented with an overlap of only 48.0% for a single sample. These findings suggest that a considerable effort is needed to improve the representation of Antarctic microbes in genome sequence databases.
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Affiliation(s)
- Jeff S. Bowman
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
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20
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Halanych KM, Mahon AR. Challenging Dogma Concerning Biogeographic Patterns of Antarctica and the Southern Ocean. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-121415-032139] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antarctica is enormous, cold, remote, and particularly sensitive to climate change. Most biological research below 60°S has focused on the isolated nature of the biota and how organisms have adapted to the cold and ice. However, biogeographic patterns in Antarctica and the Southern Ocean, and the processes explaining how those patterns came about, still await adequate explanation. Both terrestrial and marine organisms have been influenced by climatic change (e.g., glaciation), physical phenomena (e.g., oceanic currents), and/or potential barriers to gene flow (e.g., steep thermal gradients). Whereas the Antarctic region contains diverse and complex marine communities, terrestrial systems tend to be comparatively simple with limited diversity. Here, we challenge the current dogma used to explain the diversity and biogeographic patterns present in the Antarctic. We assert that relatively modern processes within the last few million years, rather than geo-logical events that occurred in the Eocene and Miocene, account for present patterns of biodiversity in the region. Additionally, reproductive life history stages appear to have little influence in structuring genetic patterns in the Antarctic, as currents and glacial patterns are noted to be more important drivers of organismal patterns of distribution. Finally, we highlight the need for additional sampling, high-throughput genomic approaches, and broad, multinational cooperation for addressing outstanding questions of Antarctic biogeography and biodiversity.
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Affiliation(s)
- Kenneth M. Halanych
- Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Andrew R. Mahon
- Department of Biology, Central Michigan University, Mount Pleasant, Michigan 48859, USA
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21
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Wassan JT, Wang H, Browne F, Zheng H. A Comprehensive Study on Predicting Functional Role of Metagenomes Using Machine Learning Methods. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 16:751-763. [PMID: 30040657 DOI: 10.1109/tcbb.2018.2858808] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
"Metagenomics" is the study of genomic sequences obtained directly from environmental microbial communities with the aim to linking their structures with functional roles. The field has been aided in the unprecedented advancement through high-throughput omics data sequencing. The outcome of sequencing are biologically rich data sets. Metagenomic data consisting of microbial spe-cies which outnumber microbial samples, lead to the "curse of dimensionality". Hence the focus in metagenomics studies has moved towards developing efficient computational models using Machine Learning (ML), reducing the computational cost. In this paper, we comprehensively assessed various ML approaches to classifying high-dimensional human microbiota effectively into their functional phenotypes. We propose the application of embedded feature selection methods, namely, Extreme Gradient Boost-ing and Penalized Logistic Regression to determine important species. The resultant feature set enhanced the performance of one of the most popular state-of-the-art methods, Random Forest (RF) over metagenomic studies. Experimental results indicate that the proposed method achieved best results in terms of accuracy, area under Receiver Operating Characteristic curve (ROC-AUC) and major improvement in processing time. It outperformed other feature selection methods of filters or wrappers over RF and classifiers such as Support Vector Machine (SVM), Extreme Learning Machine (ELM), and -Nearest Neighbors (-NN).
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22
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Qiao Y, Liu J, Zhao M, Zhang XH. Sediment Depth-Dependent Spatial Variations of Bacterial Communities in Mud Deposits of the Eastern China Marginal Seas. Front Microbiol 2018; 9:1128. [PMID: 29904376 PMCID: PMC5990616 DOI: 10.3389/fmicb.2018.01128] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/14/2018] [Indexed: 12/17/2022] Open
Abstract
The mud sediments of the eastern China marginal seas (ECMS) are deposited under different hydrodynamic conditions with different organic matter sources. These events have been demonstrated to exert significant influences on microbial communities and biogeochemical processes in surface sediments. However, the extent to which such effects occur in subsurface microbial communities remains unclear. In this study, both horizontal and vertical (five sites, each for eight layers) distributions of bacterial abundance and community composition in mud deposits of the South Yellow Sea (SYS) and East China Sea (ECS) were investigated by quantitative PCR and Illumina sequencing of the 16S rRNA gene. Both bacterial abundance and diversity were higher in the ECS than in the SYS, and tended to be higher in up than in deep layers. Proteobacteria (JTB255 marine benthic group), Acidobacteria and Bacteroidetes were dominant in the upper layers, whereas Lactococcus, Pseudomonas, and Dehalococcoidia were enriched in the deep layers. The bacterial communities in surface and subsurface sediments showed different inter-taxa relationships, indicating contrasting co-occurrence patterns. The bacterial communities in the upper layer samples clustered in accordance with mud zones, whereas those in the deep layer samples of all sites tended to cluster together. TOC δ13C and TON δ15N significantly affected the bacterial community composition, suggesting that the abundance and composition of organic matter played critical roles in shaping of sedimentary bacterial communities. This study provides novel insights into the distribution of subsurface bacterial communities in mud deposits of the ECMS, and provides clues for understanding the biogeochemical cycles in this area.
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Affiliation(s)
- Yanlu Qiao
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiwen Liu
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Meixun Zhao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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23
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Bendia AG, Signori CN, Franco DC, Duarte RTD, Bohannan BJM, Pellizari VH. A Mosaic of Geothermal and Marine Features Shapes Microbial Community Structure on Deception Island Volcano, Antarctica. Front Microbiol 2018; 9:899. [PMID: 29867810 PMCID: PMC5949364 DOI: 10.3389/fmicb.2018.00899] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 04/18/2018] [Indexed: 11/13/2022] Open
Abstract
Active volcanoes in Antarctica contrast with their predominantly cold surroundings, resulting in environmental conditions capable of selecting for versatile and extremely diverse microbial communities. This is especially true on Deception Island, where geothermal, marine, and polar environments combine to create an extraordinary range of environmental conditions. Our main goal in this study was to understand how microbial community structure is shaped by gradients of temperature, salinity, and geochemistry in polar marine volcanoes. Thereby, we collected surface sediment samples associated with fumaroles and glaciers at two sites on Deception, with temperatures ranging from 0 to 98°C. Sequencing of the 16S rRNA gene was performed to assess the composition and diversity of Bacteria and Archaea. Our results revealed that Deception harbors a combination of taxonomic groups commonly found both in cold and geothermal environments of continental Antarctica, and also groups normally identified at deep and shallow-sea hydrothermal vents, such as hyperthermophilic archaea. We observed a clear separation in microbial community structure across environmental gradients, suggesting that microbial community structure is strongly niche driven on Deception. Bacterial community structure was significantly associated with temperature, pH, salinity, and chemical composition; in contrast, archaeal community structure was strongly associated only with temperature. Our work suggests that Deception represents a peculiar "open-air" laboratory to elucidate central questions regarding molecular adaptability, microbial evolution, and biogeography of extremophiles in polar regions.
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Affiliation(s)
- Amanda G Bendia
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil
| | - Camila N Signori
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil
| | - Diego C Franco
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil
| | - Rubens T D Duarte
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Vivian H Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil
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24
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Jansen J, Hill NA, Dunstan PK, McKinlay J, Sumner MD, Post AL, Eléaume MP, Armand LK, Warnock JP, Galton-Fenzi BK, Johnson CR. Abundance and richness of key Antarctic seafloor fauna correlates with modelled food availability. Nat Ecol Evol 2017; 2:71-80. [DOI: 10.1038/s41559-017-0392-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 10/20/2017] [Indexed: 11/09/2022]
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25
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Hoffmann K, Hassenrück C, Salman-Carvalho V, Holtappels M, Bienhold C. Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments. Front Microbiol 2017; 8:266. [PMID: 28286496 PMCID: PMC5323390 DOI: 10.3389/fmicb.2017.00266] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/07/2017] [Indexed: 12/14/2022] Open
Abstract
Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae, and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae, and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor, an important feedback mechanism to be considered in future climate change scenarios.
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Affiliation(s)
- Katy Hoffmann
- HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany; Biosciences, HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und MeeresforschungBremerhaven, Germany
| | - Christiane Hassenrück
- HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Verena Salman-Carvalho
- HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany; Biosciences, HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und MeeresforschungBremerhaven, Germany
| | - Moritz Holtappels
- Biosciences, Bentho-Pelagic Processes, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung Bremerhaven, Germany
| | - Christina Bienhold
- HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany; Biosciences, HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und MeeresforschungBremerhaven, Germany
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26
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Franco DC, Signori CN, Duarte RTD, Nakayama CR, Campos LS, Pellizari VH. High Prevalence of Gammaproteobacteria in the Sediments of Admiralty Bay and North Bransfield Basin, Northwestern Antarctic Peninsula. Front Microbiol 2017; 8:153. [PMID: 28210255 PMCID: PMC5288382 DOI: 10.3389/fmicb.2017.00153] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/20/2017] [Indexed: 11/15/2022] Open
Abstract
Microorganisms dominate most Antarctic marine ecosystems, in terms of biomass and taxonomic diversity, and play crucial role in ecosystem functioning due to their high metabolic plasticity. Admiralty Bay is the largest bay on King George Island (South Shetland Islands, Antarctic Peninsula) and a combination of hydro-oceanographic characteristics (bathymetry, sea ice and glacier melting, seasonal entrance of water masses, turbidity, vertical fluxes) create conditions favoring organic carbon deposition on the seafloor and microbial activities. We sampled surface sediments from 15 sites across Admiralty Bay (100–502 m total depth) and the adjacent North Bransfield Basin (693–1147 m), and used the amplicon 454-sequencing of 16S rRNA gene tags to compare the bacterial composition, diversity, and microbial community structure across environmental parameters (sediment grain size, pigments and organic nutrients) between the two areas. Marine sediments had a high abundance of heterotrophic Gammaproteobacteria (92.4% and 83.8% inside and outside the bay, respectively), followed by Alphaproteobacteria (2.5 and 5.5%), Firmicutes (1.5 and 1.6%), Bacteroidetes (1.1 and 1.7%), Deltaproteobacteria (0.8 and 2.5%) and Actinobacteria (0.7 and 1.3%). Differences in alpha-diversity and bacterial community structure were found between the two areas, reflecting the physical and chemical differences in the sediments, and the organic matter input.
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Affiliation(s)
- Diego C Franco
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo São Paulo, Brazil
| | - Camila N Signori
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo São Paulo, Brazil
| | - Rubens T D Duarte
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina Florianópolis, Brazil
| | - Cristina R Nakayama
- Departamento de Ciências Ambientais, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo Diadema, Brazil
| | - Lúcia S Campos
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
| | - Vivian H Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo São Paulo, Brazil
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