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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] [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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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] [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. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:216-228. [PMID: 36810880 PMCID: PMC10464692 DOI: 10.1111/1758-2229.13145] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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Rzoska-Smith E, Stelzer R, Monterio M, Cary SC, Williamson A. DNA repair enzymes of the Antarctic Dry Valley metagenome. Front Microbiol 2023; 14:1156817. [PMID: 37125210 PMCID: PMC10140301 DOI: 10.3389/fmicb.2023.1156817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Microbiota inhabiting the Dry Valleys of Antarctica are subjected to multiple stressors that can damage deoxyribonucleic acid (DNA) such as desiccation, high ultraviolet light (UV) and multiple freeze-thaw cycles. To identify novel or highly-divergent DNA-processing enzymes that may enable effective DNA repair, we have sequenced metagenomes from 30 sample-sites which are part of the most extensive Antarctic biodiversity survey undertaken to date. We then used these to construct wide-ranging sequence similarity networks from protein-coding sequences and identified candidate genes involved in specialized repair processes including unique nucleases as well as a diverse range of adenosine triphosphate (ATP) -dependent DNA ligases implicated in stationary-phase DNA repair processes. In one of the first direct investigations of enzyme function from these unique samples, we have heterologously expressed and assayed a number of these enzymes, providing insight into the mechanisms that may enable resident microbes to survive these threats to their genomic integrity.
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Affiliation(s)
- Elizabeth Rzoska-Smith
- Proteins and Microbes Laboratory, School of Science, University of Waikato, Hamilton, New Zealand
| | - Ronja Stelzer
- Proteins and Microbes Laboratory, School of Science, University of Waikato, Hamilton, New Zealand
| | - Maria Monterio
- Thermophile Research Unit, School of Science, University of Waikato, Hamilton, New Zealand
| | - Stephen C. Cary
- Thermophile Research Unit, School of Science, University of Waikato, Hamilton, New Zealand
| | - Adele Williamson
- Proteins and Microbes Laboratory, School of Science, University of Waikato, Hamilton, New Zealand
- *Correspondence: Adele Williamson,
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Jackson AC, Jorna J, Chaston JM, Adams BJ. Glacial Legacies: Microbial Communities of Antarctic Refugia. BIOLOGY 2022; 11:biology11101440. [PMID: 36290344 PMCID: PMC9598129 DOI: 10.3390/biology11101440] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
In the cold deserts of the McMurdo Dry Valleys (MDV) the suitability of soil for microbial life is determined by both contemporary processes and legacy effects. Climatic changes and accompanying glacial activity have caused local extinctions and lasting geochemical changes to parts of these soil ecosystems over several million years, while areas of refugia may have escaped these disturbances and existed under relatively stable conditions. This study describes the impact of historical glacial and lacustrine disturbance events on microbial communities across the MDV to investigate how this divergent disturbance history influenced the structuring of microbial communities across this otherwise very stable ecosystem. Soil bacterial communities from 17 sites representing either putative refugia or sites disturbed during the Last Glacial Maximum (LGM) (22-17 kya) were characterized using 16 S metabarcoding. Regardless of geographic distance, several putative refugia sites at elevations above 600 m displayed highly similar microbial communities. At a regional scale, community composition was found to be influenced by elevation and geographic proximity more so than soil geochemical properties. These results suggest that despite the extreme conditions, diverse microbial communities exist in these putative refugia that have presumably remained undisturbed at least through the LGM. We suggest that similarities in microbial communities can be interpreted as evidence for historical climate legacies on an ecosystem-wide scale.
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Affiliation(s)
- Abigail C. Jackson
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
- Correspondence: (A.C.J.); (J.J.)
| | - Jesse Jorna
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
- Correspondence: (A.C.J.); (J.J.)
| | - John M. Chaston
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Byron J. Adams
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
- Monte L. Bean Museum, Brigham Young University, Provo, UT 84602, USA
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Jiang X, Van Horn DJ, Okie JG, Buelow HN, Schwartz E, Colman DR, Feeser KL, Takacs-Vesbach CD. Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient. Extremophiles 2022; 26:15. [PMID: 35296937 DOI: 10.1007/s00792-022-01262-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/10/2022] [Indexed: 02/01/2023]
Abstract
Extremophiles exist among all three domains of life; however, physiological mechanisms for surviving harsh environmental conditions differ among Bacteria, Archaea and Eukarya. Consequently, we expect that domain-specific variation of diversity and community assembly patterns exist along environmental gradients in extreme environments. We investigated inter-domain community compositional differences along a high-elevation salinity gradient in the McMurdo Dry Valleys, Antarctica. Conductivity for 24 soil samples collected along the gradient ranged widely from 50 to 8355 µS cm-1. Taxonomic richness varied among domains, with a total of 359 bacterial, 2 archaeal, 56 fungal, and 69 non-fungal eukaryotic operational taxonomic units (OTUs). Richness for bacteria, archaea, fungi, and non-fungal eukaryotes declined with increasing conductivity (all P < 0.05). Principal coordinate ordination analysis (PCoA) revealed significant (ANOSIM R = 0.97) groupings of low/high salinity bacterial OTUs, while OTUs from other domains were not significantly clustered. Bacterial beta diversity was unimodally distributed along the gradient and had a nested structure driven by species losses, whereas in fungi and non-fungal eukaryotes beta diversity declined monotonically without strong evidence of nestedness. Thus, while increased salinity acts as a stressor in all domains, the mechanisms driving community assembly along the gradient differ substantially between the domains.
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Affiliation(s)
- Xiaoben Jiang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - David J Van Horn
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jordan G Okie
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - Heather N Buelow
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Daniel R Colman
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kelli L Feeser
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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Fuentes B, Choque A, Gómez F, Alarcón J, Castro-Nallar E, Arenas F, Contreras D, Mörchen R, Amelung W, Knief C, Moradi G, Klumpp E, Saavedra CP, Prietzel J, Klysubun W, Remonsellez F, Bol R. Influence of Physical-Chemical Soil Parameters on Microbiota Composition and Diversity in a Deep Hyperarid Core of the Atacama Desert. Front Microbiol 2022; 12:794743. [PMID: 35197940 PMCID: PMC8859261 DOI: 10.3389/fmicb.2021.794743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/24/2021] [Indexed: 01/04/2023] Open
Abstract
The extreme environmental conditions and lack of water on the soil surface in hyperarid deserts hamper microbial life, allowing only highly specialized microbial communities to the establish colonies and survive. Until now, the microbial communities that inhabit or have inhabited soils of hyperarid environments at greater depths have been poorly studied. We analyzed for the first time the variation in microbial communities down to a depth of 3.4 m in one of the driest places of the world, the hyperarid Yungay region in the Atacama Desert, and we related it to changes in soil physico-chemical characteristics. We found that the moisture content changed from 2 to 11% with depth and enabled the differentiation of three depth intervals: (i) surface zone A (0–60 cm), (ii) intermediate zone B (60–220 cm), and (iii) deep zone C (220–340 cm). Each zone showed further specific physicochemical and mineralogical features. Likewise, some bacterial phyla were unique in each zone, i.e., members of the taxa Deinococcota, Halobacterota, and Latescibacterota in zone A; Crenarchaeota, Fusobacteriota, and Deltaproteobacterium Sva0485 in zone B; and Fervidibacteria and Campilobacterota in zone C, which indicates taxon-specific preferences in deep soil habitats. Differences in the microbiota between the zones were rather abrupt, which is concomitant with abrupt changes in the physical-chemical parameters. Overall, moisture content, total carbon (TC), pH, and electric conductivity (EC) were most predictive of microbial richness and diversity, while total sulfur (TS) and total phosphorous (TP) contents were additionally predictive of community composition. We also found statistically significant associations between taxa and soil properties, most of which involved moisture and TC contents. Our findings show that under-explored habitats for microbial survival and existence may prevail at greater soil depths near water or within water-bearing layers, a valuable substantiation also for the ongoing search for biosignatures on other planets, such as Mars.
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Affiliation(s)
- Bárbara Fuentes
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
| | - Alessandra Choque
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Francisco Gómez
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
| | - Jaime Alarcón
- Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
| | - Franko Arenas
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Daniel Contreras
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Ramona Mörchen
- Institute of Crop Science and Resource Conservation, Soil Science and Soil Ecology, University of Bonn, Bonn, Germany
| | - Wulf Amelung
- Institute of Crop Science and Resource Conservation, Soil Science and Soil Ecology, University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation, Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Ghazal Moradi
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Erwin Klumpp
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Jörg Prietzel
- Wissenschaftszentum Weihenstephan, Technical University München, Freising, Germany
| | - Wantana Klysubun
- Synchrotron Light Research Institute, Nakhon Ratchasima, Thailand
| | - Francisco Remonsellez
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto-CEITSAZA, Universidad Católica del Norte, Antofagasta, Chile
- *Correspondence: Francisco Remonsellez,
| | - Roland Bol
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
- School of Natural Sciences, Environment Centre Wales, Bangor University, Bangor, United Kingdom
- Roland Bol,
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Monteiro MR, Marshall AJ, Hawes I, Lee CK, McDonald IR, Cary SC. Geochemically Defined Space-for-Time Transects Successfully Capture Microbial Dynamics Along Lacustrine Chronosequences in a Polar Desert. Front Microbiol 2022; 12:783767. [PMID: 35173689 PMCID: PMC8841834 DOI: 10.3389/fmicb.2021.783767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/15/2021] [Indexed: 11/15/2022] Open
Abstract
The space-for-time substitution approach provides a valuable empirical assessment to infer temporal effects of disturbance from spatial gradients. Applied to predict the response of different ecosystems under current climate change scenarios, it remains poorly tested in microbial ecology studies, partly due to the trophic complexity of the ecosystems typically studied. The McMurdo Dry Valleys (MDV) of Antarctica represent a trophically simple polar desert projected to experience drastic changes in water availability under current climate change scenarios. We used this ideal model system to develop and validate a microbial space-for-time sampling approach, using the variation of geochemical profiles that follow alterations in water availability and reflect past changes in the system. Our framework measured soil electrical conductivity, pH, and water activity in situ to geochemically define 17 space-for-time transects from the shores of four dynamic and two static Dry Valley lakes. We identified microbial taxa that are consistently responsive to changes in wetness in the soils and reliably associated with long-term dry or wet edaphic conditions. Comparisons between transects defined at static (open-basin) and dynamic (closed-basin) lakes highlighted the capacity for geochemically defined space-for-time gradients to identify lasting deterministic impacts of historical changes in water presence on the structure and diversity of extant microbial communities. We highlight the potential for geochemically defined space-for-time transects to resolve legacy impacts of environmental change when used in conjunction with static and dynamic scenarios, and to inform future environmental scenarios through changes in the microbial community structure, composition, and diversity.
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Affiliation(s)
- Maria R. Monteiro
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Alexis J. Marshall
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Ian Hawes
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Charles K. Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Ian R. McDonald
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Stephen Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
- *Correspondence: Stephen Craig Cary,
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Krucon T, Dziewit L, Drewniak L. Insight Into Ecology, Metabolic Potential, and the Taxonomic Composition of Bacterial Communities in the Periodic Water Pond on King George Island (Antarctica). Front Microbiol 2021; 12:708607. [PMID: 34690951 PMCID: PMC8531505 DOI: 10.3389/fmicb.2021.708607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
Polar regions contain a wide variety of lentic ecosystems. These include periodic ponds that have a significant impact on carbon and nitrogen cycling in polar environments. This study was conducted to assess the taxonomic and metabolic diversity of bacteria found in Antarctic pond affected by penguins and sea elephants and to define their role in ongoing processes. Metabolic assays showed that of the 168 tested heterotrophic bacteria present in the Antarctic periodic pond, 96% are able to degrade lipids, 30% cellulose, 26% proteins, and 26% starch. The taxonomic classification of the obtained isolates differs from that based on the composition of the 16S rRNA relative abundances in the studied pond. The dominant Actinobacteria constituting 45% of isolates represents a low proportion of the community, around 4%. With the addition of run-off, the proportions of inhabiting bacteria changed, including a significant decrease in the abundance of Cyanobacteria, from 2.38 to 0.33%, increase of Firmicutes from 9.32 to 19.18%, and a decreasing richness (Chao1 index from 1299 to 889) and diversity (Shannon index from 4.73 to 4.20). Comparative studies of communities found in different Antarctic environments indicate a great role for penguins in shaping bacterial populations.
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Affiliation(s)
- Tomasz Krucon
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Drewniak
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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10
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Solon AJ, Mastrangelo C, Vimercati L, Sommers P, Darcy JL, Gendron EMS, Porazinska DL, Schmidt SK. Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, Antarctica. Front Microbiol 2021; 12:654135. [PMID: 34177836 PMCID: PMC8222675 DOI: 10.3389/fmicb.2021.654135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
Cold, dry, and nutrient-poor, the McMurdo Dry Valleys of Antarctica are among the most extreme terrestrial environments on Earth. Numerous studies have described microbial communities of low elevation soils and streams below glaciers, while less is known about microbial communities in higher elevation soils above glaciers. We characterized microbial life in four landscape features (habitats) of a mountain in Taylor Valley. These habitats varied significantly in soil moisture and include moist soils of a (1) lateral glacial moraine, (2) gully that terminates at the moraine, and very dry soils on (3) a southeastern slope and (4) dry sites near the gully. Using rRNA gene PCR amplicon sequencing of Bacteria and Archaea (16S SSU) and eukaryotes (18S SSU), we found that all habitat types harbored significantly different bacterial and eukaryotic communities and that these differences were most apparent when comparing habitats that had macroscopically visible soil crusts (gully and moraine) to habitats with no visible crusts (near gully and slope). These differences were driven by a relative predominance of Actinobacteria and a Colpodella sp. in non-crust habitats, and by phototrophic bacteria and eukaryotes (e.g., a moss) and predators (e.g., tardigrades) in habitats with biological soil crusts (gully and moraine). The gully and moraine also had significantly higher 16S and 18S ESV richness than the other two habitat types. We further found that many of the phototrophic bacteria and eukaryotes of the gully and moraine share high sequence identity with phototrophs from moist and wet areas elsewhere in the Dry Valleys and other cold desert ecosystems. These include a Moss (Bryum sp.), several algae (e.g., a Chlorococcum sp.) and cyanobacteria (e.g., Nostoc and Phormidium spp.). Overall, the results reported here broaden the diversity of habitat types that have been studied in the Dry Valleys of Antarctica and suggest future avenues of research to more definitively understand the biogeography and factors controlling microbial diversity in this unique ecosystem.
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Affiliation(s)
- Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Claire Mastrangelo
- School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado-Anschutz Medical Campus, Denver, CO, United States
| | - Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - S K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
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11
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Ortiz M, Bosch J, Coclet C, Johnson J, Lebre P, Salawu-Rotimi A, Vikram S, Makhalanyane T, Cowan D. Microbial Nitrogen Cycling in Antarctic Soils. Microorganisms 2020; 8:E1442. [PMID: 32967081 PMCID: PMC7564152 DOI: 10.3390/microorganisms8091442] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 01/19/2023] Open
Abstract
The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more "hospitable" maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa; (M.O.); (J.B.); (C.C.); (J.J.); (P.L.); (A.S.-R.); (S.V.); (T.M.)
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12
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Cary C, Cowan DA, McMinn A, Häggblom MM. Editorial: Thematic issue on polar and alpine microbiology. FEMS Microbiol Ecol 2020; 96:5875089. [PMID: 32697840 DOI: 10.1093/femsec/fiaa136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/12/2022] Open
Affiliation(s)
- Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato - Te Whare Wānanga o Waikato, Hamilton 3240, New Zealand
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Hatfield 0028, Pretoria, South Africa
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, College of Science and Engineering, University of Tasmania, Battery Point, Tasmania, Australia
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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