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Vipindas PV, Jabir T, Venkatachalam S, Yang EJ, Jain A, Krishnan KP. Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean. Extremophiles 2023; 27:24. [PMID: 37668803 DOI: 10.1007/s00792-023-01310-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/21/2023] [Indexed: 09/06/2023]
Abstract
Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.
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Affiliation(s)
- Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India.
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Eun Jin Yang
- Division of Ocean Sciences, Korea Polar Research Institute, 26 Songdo-dong, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Anand Jain
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
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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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Changes in salinity and temperature drive marine bacterial communities’ structure at Potter Cove, Antarctica. Polar Biol 2019. [DOI: 10.1007/s00300-019-02590-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Espínola F, Dionisi HM, Borglin S, Brislawn CJ, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lozada M. Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. MICROBIAL ECOLOGY 2018; 75:123-139. [PMID: 28702706 DOI: 10.1007/s00248-017-1028-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.
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Affiliation(s)
- Fernando Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Sharon Borglin
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Walter P Mac Cormack
- Instituto Nanobiotec, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Instituto Antártico Argentino, Buenos Aires, Argentina
| | - JoLynn Carroll
- Akvaplan-niva, Fram-High North Research Centre for Climate and the Environment, and ARCEx-Research Centre for Arctic Petroleum Exploration, Department of Geosciences, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina.
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Abele D, Vazquez S, Buma AGJ, Hernandez E, Quiroga C, Held C, Frickenhaus S, Harms L, Lopez JL, Helmke E, Mac Cormack WP. Pelagic and benthic communities of the Antarctic ecosystem of Potter Cove: Genomics and ecological implications. Mar Genomics 2017; 33:1-11. [PMID: 28479280 DOI: 10.1016/j.margen.2017.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 05/02/2017] [Accepted: 05/02/2017] [Indexed: 12/12/2022]
Abstract
Molecular technologies are more frequently applied in Antarctic ecosystem research and the growing amount of sequence-based information available in databases adds a new dimension to understanding the response of Antarctic organisms and communities to environmental change. We apply molecular techniques, including fingerprinting, and amplicon and metagenome sequencing, to understand biodiversity and phylogeography to resolve adaptive processes in an Antarctic coastal ecosystem from microbial to macrobenthic organisms and communities. Interpretation of the molecular data is not only achieved by their combination with classical methods (pigment analyses or microscopy), but furthermore by combining molecular with environmental data (e.g., sediment characteristics, biogeochemistry or oceanography) in space and over time. The studies form part of a long-term ecosystem investigation in Potter Cove on King-George Island, Antarctica, in which we follow the effects of rapid retreat of the local glacier on the cove ecosystem. We formulate and encourage new approaches to integrate molecular tools into Antarctic ecosystem research, environmental conservation actions, and polar ocean observatories.
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Affiliation(s)
- D Abele
- Dept. Biosciences, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27470 Bremerhaven, Germany.
| | - S Vazquez
- Universidad de Buenos Aires, CONICET, Instituto de Nanobiotecnología (NANOBIOTEC), Junín 954, 1113 Buenos Aires, Argentina
| | - A G J Buma
- Dept. Ocean Ecosystems, Energy and Sustainability Research Groningen, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - E Hernandez
- Instituto Antártico Argentino (IAA), 25 de Mayo 1143, 1650 San Martin, Buenos Aires, Argentina
| | - C Quiroga
- Universidad de Buenos Aires, CONICET, Instituto de Medicina y Parasitologia Medica (IMPaM), Paraguay 2155 P.12, 1121 Buenos Aires, Argentina
| | - C Held
- Dept. Biosciences, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27470 Bremerhaven, Germany
| | - S Frickenhaus
- Dept. Biosciences, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27470 Bremerhaven, Germany
| | - L Harms
- Dept. Biosciences, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27470 Bremerhaven, Germany
| | - J L Lopez
- Universidad de Buenos Aires, Catedra de Virologia, Junín 954, 1113 Buenos Aires, Argentina
| | - E Helmke
- Dept. Biosciences, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27470 Bremerhaven, Germany
| | - W P Mac Cormack
- Instituto Antártico Argentino (IAA), 25 de Mayo 1143, 1650 San Martin, Buenos Aires, Argentina
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Learman DR, Henson MW, Thrash JC, Temperton B, Brannock PM, Santos SR, Mahon AR, Halanych KM. Biogeochemical and Microbial Variation across 5500 km of Antarctic Surface Sediment Implicates Organic Matter as a Driver of Benthic Community Structure. Front Microbiol 2016; 7:284. [PMID: 27047451 PMCID: PMC4803750 DOI: 10.3389/fmicb.2016.00284] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/22/2016] [Indexed: 02/01/2023] Open
Abstract
Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that is underexplored with regards to biodiversity. Although pelagic microbial communities in the Southern Ocean and coastal Antarctic waters have been well-studied, there are fewer investigations of benthic communities and most have a focused geographic range. We sampled surface sediment from 24 sites across a 5500 km region of Western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities and sediment geochemistry. Sequencing of the 16S and 18S rRNA genes showed microbial communities in sediments from the Antarctic Peninsula (AP) and Western Antarctica (WA), including the Ross, Amundsen, and Bellingshausen Seas, could be distinguished by correlations with organic matter concentrations and stable isotope fractionation (total organic carbon; TOC, total nitrogen; TN, and δ13C). Overall, samples from the AP were higher in nutrient content (TOC, TN, and NH4+) and communities in these samples had higher relative abundances of operational taxonomic units (OTUs) classified as the diatom, Chaetoceros, a marine cercozoan, and four OTUs classified as Flammeovirgaceae or Flavobacteria. As these OTUs were strongly correlated with TOC, the data suggests the diatoms could be a source of organic matter and the Bacteroidetes and cercozoan are grazers that consume the organic matter. Additionally, samples from WA have lower nutrients and were dominated by Thaumarchaeota, which could be related to their known ability to thrive as lithotrophs. This study documents the largest analysis of benthic microbial communities to date in the Southern Ocean, representing almost half the continental shoreline of Antarctica, and documents trophic interactions and coupling of pelagic and benthic communities. Our results indicate potential modifications in carbon sequestration processes related to change in community composition, identifying a prospective mechanism that links climate change to carbon availability.
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Affiliation(s)
- Deric R Learman
- Department of Biology, Institute for Great Lakes Research, Central Michigan University Mt. Pleasant, MI, USA
| | - Michael W Henson
- Department of Biological Sciences, Louisiana State University Baton Rouge, LA, USA
| | - J Cameron Thrash
- Department of Biological Sciences, Louisiana State University Baton Rouge, LA, USA
| | - Ben Temperton
- Department of Biosciences, University of Exeter Exeter, UK
| | - Pamela M Brannock
- Department of Biological Sciences, Auburn University Auburn, AL, USA
| | - Scott R Santos
- Department of Biological Sciences, Auburn University Auburn, AL, USA
| | - Andrew R Mahon
- Department of Biology, Institute for Great Lakes Research, Central Michigan University Mt. Pleasant, MI, USA
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