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Varliero G, Lebre PH, Adams B, Chown SL, Convey P, Dennis PG, Fan D, Ferrari B, Frey B, Hogg ID, Hopkins DW, Kong W, Makhalanyane T, Matcher G, Newsham KK, Stevens MI, Weigh KV, Cowan DA. Biogeographic survey of soil bacterial communities across Antarctica. Microbiome 2024; 12:9. [PMID: 38212738 PMCID: PMC10785390 DOI: 10.1186/s40168-023-01719-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/11/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs. RESULTS Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs. CONCLUSIONS Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.
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Affiliation(s)
- Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Pedro H Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
| | - Byron Adams
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT, 84602, USA
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Clayton, VA, 3800, Australia
| | - Peter Convey
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park, 2006, South Africa
- Biodiversity of Antarctic and Sub-Antarctic Ecosystems (BASE), Santiago, Chile
| | - Paul G Dennis
- School of the Environment, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Dandan Fan
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Belinda Ferrari
- School of Biotechnology and Biomolecular Sciences, University of NSW, Sydney, NSW, 2052, Australia
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - David W Hopkins
- SRUC - Scotland's Rural College, West Mains Road, Edinburgh, EH9 3JG, Scotland, UK
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Thulani Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Gwynneth Matcher
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Kevin K Newsham
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Mark I Stevens
- Securing Antarctica's Environmental Future, Earth and Biological Sciences, South Australian Museum, Adelaide, SA, 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Katherine V Weigh
- School of the Environment, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa.
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Feng M, Varliero G, Qi W, Stierli B, Edwards A, Robinson S, van der Heijden MGA, Frey B. Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential. Environ Microbiol 2023; 25:3116-3138. [PMID: 37688461 DOI: 10.1111/1462-2920.16497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.
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Affiliation(s)
- Maomao Feng
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics SIB, Geneva, Switzerland
| | - Beat Stierli
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Serina Robinson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Plant-Soil Interactions, Agroscope, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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Tarnowski MJ, Varliero G, Scown J, Phelps E, Gorochowski TE. Soil as a transdisciplinary research catalyst: from bioprospecting to biorespecting. R Soc Open Sci 2023; 10:230963. [PMID: 38026022 PMCID: PMC10646459 DOI: 10.1098/rsos.230963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The vast microbial biodiversity of soils is beginning to be observed and understood by applying modern DNA sequencing techniques. However, ensuring this potentially valuable information is used in a fair and equitable way remains a challenge. Here, we present a public engagement project that explores this topic through collaborative research of soil microbiomes at six urban locations using nanopore-based DNA sequencing. The project brought together researchers from the disciplines of synthetic biology, environmental humanities and microbial ecology, as well as school students aged 14-16 years old, to gain a broader understanding of views on the use of data from the environment. Discussions led to the transformation of 'bioprospecting', a metaphor with extractive connotations which is often used to frame environmental DNA sequencing studies, towards a more collaborative approach-'biorespecting'. This shift in terminology acknowledges that genetic information contained in soil arises as a result of entire ecosystems, including the people involved in its creation. Therefore, any use of sequence information should be accountable to the ecosystems from which it arose. As knowledge can arise from ecosystems and communities, science and technology should acknowledge this link and reciprocate with care and benefit-sharing to help improve the wellbeing of future generations.
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Affiliation(s)
- Matthew J. Tarnowski
- School of Biological Science, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biosciences, Geography and Physics, Swansea University, Swansea SA2 8PP, UK
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Jim Scown
- Humanities and Social Sciences, University of Exeter, Cornwall TR10 9FE, UK
| | - Emily Phelps
- School of Biological Science, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Thomas E. Gorochowski
- School of Biological Science, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
- BrisEngBio, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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Mashamaite L, Lebre PH, Varliero G, Maphosa S, Ortiz M, Hogg ID, Cowan DA. Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient. Front Microbiol 2023; 14:1203216. [PMID: 37555066 PMCID: PMC10406297 DOI: 10.3389/fmicb.2023.1203216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
INTRODUCTION The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica. METHODS We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons. RESULTS AND DISCUSSION Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.
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Affiliation(s)
- Lefentse Mashamaite
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Pedro H. Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Silindile Maphosa
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Max Ortiz
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Clemson University Genomics & Bioinformatics Facility, Clemson University, Clemson, SC, United States
| | - Ian D. Hogg
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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Varliero G, Lebre PH, Stevens MI, Czechowski P, Makhalanyane T, Cowan DA. The use of different 16S rRNA gene variable regions in biogeographical studies. Environ Microbiol Rep 2023; 15:216-228. [PMID: 36810880 PMCID: PMC10464692 DOI: 10.1111/1758-2229.13145] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/23/2023] [Indexed: 05/06/2023]
Abstract
16S rRNA gene amplicon sequencing is routinely used in environmental surveys to identify microbial diversity and composition of the samples of interest. The dominant sequencing technology of the past decade (Illumina) is based on the sequencing of 16S rRNA hypervariable regions. Online sequence data repositories, which represent an invaluable resource for investigating microbial distributional patterns across spatial, environmental or temporal scales, contain amplicon datasets from diverse 16S rRNA gene variable regions. However, the utility of these sequence datasets is potentially reduced by the use of different 16S rRNA gene amplified regions. By comparing 10 Antarctic soil samples sequenced for five different 16S rRNA amplicons, we explore whether sequence data derived from diverse 16S rRNA variable regions can be validly used as a resource for biogeographical studies. Patterns of shared and unique taxa differed among samples as a result of variable taxonomic resolutions of the assessed 16S rRNA variable regions. However, our analyses also suggest that the use of multi-primer datasets for biogeographical studies of the domain Bacteria is a valid approach to explore bacterial biogeographical patterns due to the preservation of bacterial taxonomic and diversity patterns across different variable region datasets. We deem composite datasets useful for biogeographical studies.
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Affiliation(s)
- Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and GenomicsUniversity of PretoriaPretoriaSouth Africa
| | - Pedro H. Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and GenomicsUniversity of PretoriaPretoriaSouth Africa
| | - Mark I. Stevens
- Securing Antarctica's Environmental FutureEarth & Biological Sciences, South Australian MuseumAdelaideAustralia
- School of Biological SciencesUniversity of AdelaideAdelaideAustralia
| | - Paul Czechowski
- Helmholtz Institute for Metabolic, Obesity and Vascular Research Leipzig (HI‐MAG)LeipzigGermany
| | - Thulani Makhalanyane
- Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
| | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and GenomicsUniversity of PretoriaPretoriaSouth Africa
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Varliero G, Lebre PH, Frey B, Fountain AG, Anesio AM, Cowan DA. Glacial Water: A Dynamic Microbial Medium. Microorganisms 2023; 11:1153. [PMID: 37317127 DOI: 10.3390/microorganisms11051153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial communities and nutrient dynamics in glaciers and ice sheets continuously change as the hydrological conditions within and on the ice change. Glaciers and ice sheets can be considered bioreactors as microbiomes transform nutrients that enter these icy systems and alter the meltwater chemistry. Global warming is increasing meltwater discharge, affecting nutrient and cell export, and altering proglacial systems. In this review, we integrate the current understanding of glacial hydrology, microbial activity, and nutrient and carbon dynamics to highlight their interdependence and variability on daily and seasonal time scales, as well as their impact on proglacial environments.
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Affiliation(s)
- Gilda Varliero
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Andrew G Fountain
- Departments of Geology and Geography, Portland State University, Portland, OR 97212, USA
| | - Alexandre M Anesio
- Department of Environmental Science, iClimate, Aarhus University, DK-4000 Roskilde, Denmark
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
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Cowan DA, Lebre PH, Amon C, Becker RW, Boga HI, Boulangé A, Chiyaka TL, Coetzee T, de Jager PC, Dikinya O, Eckardt F, Greve M, Harris MA, Hopkins DW, Houngnandan HB, Houngnandan P, Jordaan K, Kaimoyo E, Kambura AK, Kamgan-Nkuekam G, Makhalanyane TP, Maggs-Kölling G, Marais E, Mondlane H, Nghalipo E, Olivier BW, Ortiz M, Pertierra LR, Ramond JB, Seely M, Sithole-Niang I, Valverde A, Varliero G, Vikram S, Wall DH, Zeze A. Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes. Microbiome 2022; 10:131. [PMID: 35996183 PMCID: PMC9396824 DOI: 10.1186/s40168-022-01297-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/15/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents. RESULTS The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation. CONCLUSION This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.
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Affiliation(s)
- D A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - P H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Cer Amon
- Institut National Polytechnique Houphouet-Boigny, Cote d'Ivoire, Yamoussoukro, South Africa
| | - R W Becker
- Biodiversity Research Centre, Department of Agriculture and Natural Resources Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - H I Boga
- Taita Taveta University, Voi, Kenya
| | - A Boulangé
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
- UMR InterTryp, CIRAD-IRD, 34398, Montpellier, France
| | - T L Chiyaka
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - T Coetzee
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - P C de Jager
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - O Dikinya
- Department of Environmental Science, University of Botswana, Gaborone, Botswana
| | - F Eckardt
- Department of Geography, University of Cape Town, Cape Town, South Africa
| | - M Greve
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - M A Harris
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - D W Hopkins
- Scotland's Rural College, Edinburgh, EH9 3JG, UK
| | - H B Houngnandan
- Université Nationale d'Agriculture, Porto-Novo, Benin (Laboratoire de Microbiologie Des Sols Et d'Ecologie Microbienne), Porto-Novo, Benin
| | - P Houngnandan
- Université Nationale d'Agriculture, Porto-Novo, Benin (Laboratoire de Microbiologie Des Sols Et d'Ecologie Microbienne), Porto-Novo, Benin
| | - K Jordaan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Departamento de Genética Molecular Y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - E Kaimoyo
- University of Zambia, Lusaka, Zambia
| | | | - G Kamgan-Nkuekam
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - T P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - E Marais
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | - H Mondlane
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - E Nghalipo
- Biodiversity Research Centre, Department of Agriculture and Natural Resources Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - B W Olivier
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - M Ortiz
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - L R Pertierra
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - J-B Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Departamento de Genética Molecular Y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - M Seely
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | - I Sithole-Niang
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - A Valverde
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - G Varliero
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - S Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - D H Wall
- Department of Biology, Colorado State University, Fort Collins, USA
| | - A Zeze
- Institut National Polytechnique Houphouet-Boigny, Cote d'Ivoire, Yamoussoukro, South Africa
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Frey B, Varliero G, Qi W, Stierli B, Walthert L, Brunner I. Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling. Front Microbiol 2022; 13:828977. [PMID: 35300488 PMCID: PMC8921678 DOI: 10.3389/fmicb.2022.828977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5–10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the “dark matter” of the soil.
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Affiliation(s)
- Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Gilda Varliero
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland.,Centre for Microbial Ecology and Genomics, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Weihong Qi
- Functional Genomics Center Zurich (FGCZ), ETH Zürich/University of Zurich, Zurich, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Lorenz Walthert
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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Varliero G, Rafiq M, Singh S, Summerfield A, Sgouridis F, Cowan DA, Barker G. Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost. FEMS Microbiol Ecol 2021; 97:fiab127. [PMID: 34468725 PMCID: PMC8445667 DOI: 10.1093/femsec/fiab127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022] Open
Abstract
Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.
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Affiliation(s)
- Gilda Varliero
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences 2 Building, Private Bag X20, Hatfield 0028, South Africa
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Airport Road, Baleli, Quetta, Balochistan, Pakistan
- School of Geographical Sciences, University of Bristol, Wills Memorial Building, Bristol BS8 1RL, United Kingdom
| | - Swati Singh
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
- School of Chemistry, University of Bristol, Cantock's Cl, Bristol BS8 1TS, United Kingdom
| | - Annabel Summerfield
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
| | - Fotis Sgouridis
- School of Geographical Sciences, University of Bristol, Wills Memorial Building, Bristol BS8 1RL, United Kingdom
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences 2 Building, Private Bag X20, Hatfield 0028, South Africa
| | - Gary Barker
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
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10
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Varliero G, Anesio AM, Barker GLA. A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems. Front Microbiol 2021; 12:627437. [PMID: 34621246 PMCID: PMC8491546 DOI: 10.3389/fmicb.2021.627437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
The Arctic environment is particularly affected by global warming, and a clear trend of the ice retreat is observed worldwide. In proglacial systems, the newly exposed terrain represents different environmental and nutrient conditions compared to later soil stages. Therefore, proglacial systems show several environmental gradients along the soil succession where microorganisms are active protagonists of the soil and carbon pool formation through nitrogen fixation and rock weathering. We studied the microbial succession of three Arctic proglacial systems located in Svalbard (Midtre Lovénbreen), Sweden (Storglaciären), and Greenland (foreland close to Kangerlussuaq). We analyzed 65 whole shotgun metagenomic soil samples for a total of more than 400 Gb of sequencing data. Microbial succession showed common trends typical of proglacial systems with increasing diversity observed along the forefield chronosequence. Microbial trends were explained by the distance from the ice edge in the Midtre Lovénbreen and Storglaciären forefields and by total nitrogen (TN) and total organic carbon (TOC) in the Greenland proglacial system. Furthermore, we focused specifically on genes associated with nitrogen fixation and biotic rock weathering processes, such as nitrogenase genes, obcA genes, and genes involved in cyanide and siderophore synthesis and transport. Whereas we confirmed the presence of these genes in known nitrogen-fixing and/or rock weathering organisms (e.g., Nostoc, Burkholderia), in this study, we also detected organisms that, even if often found in soil and proglacial systems, have never been related to nitrogen-fixing or rock weathering processes before (e.g., Fimbriiglobus, Streptomyces). The different genera showed different gene trends within and among the studied systems, indicating a community constituted by a plurality of organisms involved in nitrogen fixation and biotic rock weathering, and where the latter were driven by different organisms at different soil succession stages.
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Affiliation(s)
- Gilda Varliero
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Gary L. A. Barker
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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11
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Bosch J, Varliero G, Hallsworth JE, Dallas TD, Hopkins D, Frey B, Kong W, Lebre P, Makhalanyane TP, Cowan DA. Microbial anhydrobiosis. Environ Microbiol 2021; 23:6377-6390. [PMID: 34347349 DOI: 10.1111/1462-2920.15699] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 12/28/2022]
Abstract
The loss of cellular water (desiccation) and the resulting low cytosolic water activity are major stress factors for life. Numerous prokaryotic and eukaryotic taxa have evolved molecular and physiological adaptions to periods of low water availability or water-limited environments that occur across the terrestrial Earth. The changes within cells during the processes of desiccation and rehydration, from the activation (and inactivation) of biosynthetic pathways to the accumulation of compatible solutes, have been studied in considerable detail. However, relatively little is known on the metabolic status of organisms in the desiccated state; that is, in the sometimes extended periods between the drying and rewetting phases. During these periods, which can extend beyond decades and which we term 'anhydrobiosis', organismal survival could be dependent on a continued supply of energy to maintain the basal metabolic processes necessary for critical functions such as macromolecular repair. Here, we review the state of knowledge relating to the function of microorganisms during the anhydrobiotic state, highlighting substantial gaps in our understanding of qualitative and quantitative aspects of molecular and biochemical processes in desiccated cells.
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Affiliation(s)
- Jason Bosch
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Gilda Varliero
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Tiffany D Dallas
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | | | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Pedro Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
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12
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Varliero G, Wray J, Malandain C, Barker G. PhyloPrimer: a taxon-specific oligonucleotide design platform. PeerJ 2021; 9:e11120. [PMID: 33986979 PMCID: PMC8098674 DOI: 10.7717/peerj.11120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/25/2021] [Indexed: 11/26/2022] Open
Abstract
Many environmental and biomedical biomonitoring and detection studies aim to explore the presence of specific organisms or gene functionalities in microbiome samples. In such cases, when the study hypotheses can be answered with the exploration of a small number of genes, a targeted PCR-approach is appropriate. However, due to the complexity of environmental microbial communities, the design of specific primers is challenging and can lead to non-specific results. We designed PhyloPrimer, the first user-friendly platform to semi-automate the design of taxon-specific oligos (i.e., PCR primers) for a gene of interest. The main strength of PhyloPrimer is the ability to retrieve and align GenBank gene sequences matching the user’s input, and to explore their relationships through an online dynamic tree. PhyloPrimer then designs oligos specific to the gene sequences selected from the tree and uses the tree non-selected sequences to look for and maximize oligo differences between targeted and non-targeted sequences, therefore increasing oligo taxon-specificity (positive/negative consensus approach). Designed oligos are then checked for the presence of secondary structure with the nearest-neighbor (NN) calculation and the presence of off-target matches with in silico PCR tests, also processing oligos with degenerate bases. Whilst the main function of PhyloPrimer is the design of taxon-specific oligos (down to the species level), the software can also be used for designing oligos to target a gene without any taxonomic specificity, for designing oligos from preselected sequences and for checking predesigned oligos. We validated the pipeline on four commercially available microbial mock communities using PhyloPrimer to design genus- and species-specific primers for the detection of Streptococcus species in the mock communities. The software performed well on these mock microbial communities and can be found at https://www.cerealsdb.uk.net/cerealgenomics/phyloprimer.
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Affiliation(s)
- Gilda Varliero
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Jared Wray
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Gary Barker
- School of Biological Sciences, University of Bristol, Bristol, UK
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13
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Nash MV, Anesio AM, Barker G, Tranter M, Varliero G, Eloe-Fadrosh EA, Nielsen T, Turpin-Jelfs T, Benning LG, Sánchez-Baracaldo P. Metagenomic insights into diazotrophic communities across Arctic glacier forefields. FEMS Microbiol Ecol 2019; 94:5036517. [PMID: 29901729 PMCID: PMC6054269 DOI: 10.1093/femsec/fiy114] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 06/11/2018] [Indexed: 11/30/2022] Open
Abstract
Microbial nitrogen fixation is crucial for building labile nitrogen stocks and facilitating higher plant colonisation in oligotrophic glacier forefield soils. Here, the diazotrophic bacterial community structure across four Arctic glacier forefields was investigated using metagenomic analysis. In total, 70 soil metagenomes were used for taxonomic interpretation based on 185 nitrogenase (nif) sequences, extracted from assembled contigs. The low number of recovered genes highlights the need for deeper sequencing in some diverse samples, to uncover the complete microbial populations. A key group of forefield diazotrophs, found throughout the forefields, was identified using a nifH phylogeny, associated with nifH Cluster I and III. Sequences related most closely to groups including Alphaproteobacteria, Betaproteobacteria, Cyanobacteria and Firmicutes. Using multiple nif genes in a Last Common Ancestor analysis revealed a diverse range of diazotrophs across the forefields. Key organisms identified across the forefields included Nostoc, Geobacter, Polaromonas and Frankia. Nitrogen fixers that are symbiotic with plants were also identified, through the presence of root associated diazotrophs, which fix nitrogen in return for reduced carbon. Additional nitrogen fixers identified in forefield soils were metabolically diverse, including fermentative and sulphur cycling bacteria, halophiles and anaerobes.
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Affiliation(s)
- Maisie V Nash
- School of Geographical Sciences, University of Bristol, UK
| | | | - Gary Barker
- School of Life Sciences, University of Bristol, UK
| | - Martyn Tranter
- School of Geographical Sciences, University of Bristol, UK
| | | | | | - Torben Nielsen
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, US
| | | | - Liane G Benning
- GFZ German Research Centre for Geosciences, Telegrafenenberg, 14473 Potsdam, Germany.,School of Earth and Environment, University of Leeds, LS2 9JT, Leeds, UK.,Department of Earth Sciences, Free University of Berlin, Malteserstr, 74-100, Building A, 12249, Berlin, Germany
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Varliero G, Bienhold C, Schmid F, Boetius A, Molari M. Microbial Diversity and Connectivity in Deep-Sea Sediments of the South Atlantic Polar Front. Front Microbiol 2019; 10:665. [PMID: 31024475 PMCID: PMC6465420 DOI: 10.3389/fmicb.2019.00665] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/18/2019] [Indexed: 11/16/2022] Open
Abstract
Ultraslow spreading ridges account for one-third of the global mid-ocean ridges. Their impact on the diversity and connectivity of benthic deep-sea microbial assemblages is poorly understood, especially for hydrothermally inactive, magma-starved ridges. We investigated bacterial and archaeal diversity in sediments collected from an amagmatic segment (10°–17°E) of the Southwest Indian Ridge (SWIR) and in the adjacent northern and southern abyssal zones of similar water depths within one biogeochemical province of the Indian Ocean. Microbial diversity was determined by 16S ribosomal RNA (rRNA) gene sequencing. Our results show significant differences in microbial communities between stations outside and inside the SWIR, which were mostly explained by environmental selection. Community similarity correlated significantly with differences in chlorophyll a content and with the presence of upward porewater fluxes carrying reduced compounds (e.g., ammonia and sulfide), suggesting that trophic resource availability is a main driver for changes in microbial community composition. At the stations in the SWIR axial valley (3,655–4,448 m water depth), microbial communities were enriched in bacterial and archaeal taxa common in organic matter-rich subsurface sediments (e.g., SEEP-SRB1, Dehalococcoida, Atribacteria, and Woesearchaeota) and chemosynthetic environments (mainly Helicobacteraceae). The abyssal stations outside the SWIR communities (3,760–4,869 m water depth) were dominated by OM1 clade, JTB255, Planctomycetaceae, and Rhodospirillaceae. We conclude that ultraslow spreading ridges create a unique environmental setting in sedimented segments without distinct hydrothermal activity, and play an important role in shaping microbial communities and promoting diversity, but also in connectivity among deep-sea habitats.
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Affiliation(s)
- Gilda Varliero
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Christina Bienhold
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,HGF-MPG Joint Research Group on Deep Sea Ecology and Technology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Florian Schmid
- Helmholtz Centre for Ocean Research Kiel, GEOMAR, Kiel, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,HGF-MPG Joint Research Group on Deep Sea Ecology and Technology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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