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Ray AE, Tribbia DZ, Cowan DA, Ferrari BC. Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis. Microbiol Mol Biol Rev 2023; 87:e0004823. [PMID: 37914532 PMCID: PMC10732025 DOI: 10.1128/mmbr.00048-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
SUMMARY Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.
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Affiliation(s)
- Angelique E. Ray
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Dana Z. Tribbia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
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2
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Malard LA, Bergk-Pinto B, Layton R, Vogel TM, Larose C, Pearce DA. Snow Microorganisms Colonise Arctic Soils Following Snow Melt. MICROBIAL ECOLOGY 2023; 86:1661-1675. [PMID: 36939866 PMCID: PMC10497451 DOI: 10.1007/s00248-023-02204-y] [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: 05/21/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Arctic soils are constantly subjected to microbial invasion from either airborne, marine, or animal sources, which may impact local microbial communities and ecosystem functioning. However, in winter, Arctic soils are isolated from outside sources other than snow, which is the sole source of microorganisms. Successful colonisation of soil by snow microorganisms depends on the ability to survive and compete of both, the invading and resident community. Using shallow shotgun metagenome sequencing and amplicon sequencing, this study monitored snow and soil microbial communities throughout snow melt to investigate the colonisation process of Arctic soils. Microbial colonisation likely occurred as all the characteristics of successful colonisation were observed. The colonising microorganisms originating from the snow were already adapted to the local environmental conditions and were subsequently subjected to many similar conditions in the Arctic soil. Furthermore, competition-related genes (e.g. motility and virulence) increased in snow samples as the snow melted. Overall, one hundred potentially successful colonisers were identified in the soil and, thus, demonstrated the deposition and growth of snow microorganisms in soils during melt.
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Affiliation(s)
- Lucie A Malard
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-Upon-Tyne, NE1 8ST, UK.
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Benoit Bergk-Pinto
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
- BioIT, TAG (Transversal Activities in Applied Genomics) Sciensano, 1050, Brussels, Belgium
| | - Rose Layton
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - David A Pearce
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-Upon-Tyne, NE1 8ST, UK.
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Dutta A, Connors E, Trinh R, Erazo N, Dasarathy S, Ducklow HW, Steinberg DK, Schofield OM, Bowman JS. Depth drives the distribution of microbial ecological functions in the coastal western Antarctic Peninsula. Front Microbiol 2023; 14:1168507. [PMID: 37275172 PMCID: PMC10232865 DOI: 10.3389/fmicb.2023.1168507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 06/07/2023] Open
Abstract
The Antarctic marine environment is a dynamic ecosystem where microorganisms play an important role in key biogeochemical cycles. Despite the role that microbes play in this ecosystem, little is known about the genetic and metabolic diversity of Antarctic marine microbes. In this study we leveraged DNA samples collected by the Palmer Long Term Ecological Research (LTER) project to sequence shotgun metagenomes of 48 key samples collected across the marine ecosystem of the western Antarctic Peninsula (wAP). We developed an in silico metagenomics pipeline (iMAGine) for processing metagenomic data and constructing metagenome-assembled genomes (MAGs), identifying a diverse genomic repertoire related to the carbon, sulfur, and nitrogen cycles. A novel analytical approach based on gene coverage was used to understand the differences in microbial community functions across depth and region. Our results showed that microbial community functions were partitioned based on depth. Bacterial members harbored diverse genes for carbohydrate transformation, indicating the availability of processes to convert complex carbons into simpler bioavailable forms. We generated 137 dereplicated MAGs giving us a new perspective on the role of prokaryotes in the coastal wAP. In particular, the presence of mixotrophic prokaryotes capable of autotrophic and heterotrophic lifestyles indicated a metabolically flexible community, which we hypothesize enables survival under rapidly changing conditions. Overall, the study identified key microbial community functions and created a valuable sequence library collection for future Antarctic genomics research.
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Affiliation(s)
- Avishek Dutta
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
- Department of Geology, University of Georgia, Athens, GA, United States
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - Elizabeth Connors
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Rebecca Trinh
- Department of Earth and Environmental Sciences, Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
| | - Natalia Erazo
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Srishti Dasarathy
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Hugh W. Ducklow
- Department of Earth and Environmental Sciences, Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
| | - Deborah K. Steinberg
- Department of Biological Science, College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, United States
| | - Oscar M. Schofield
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Jeff S. Bowman
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
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4
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Archer SDJ, Lee KC, Caruso T, Alcami A, Araya JG, Cary SC, Cowan DA, Etchebehere C, Gantsetseg B, Gomez-Silva B, Hartery S, Hogg ID, Kansour MK, Lawrence T, Lee CK, Lee PKH, Leopold M, Leung MHY, Maki T, McKay CP, Al Mailem DM, Ramond JB, Rastrojo A, Šantl-Temkiv T, Sun HJ, Tong X, Vandenbrink B, Warren-Rhodes KA, Pointing SB. Contribution of soil bacteria to the atmosphere across biomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162137. [PMID: 36775167 DOI: 10.1016/j.scitotenv.2023.162137] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/20/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The dispersion of microorganisms through the atmosphere is a continual and essential process that underpins biogeography and ecosystem development and function. Despite the ubiquity of atmospheric microorganisms globally, specific knowledge of the determinants of atmospheric microbial diversity at any given location remains unresolved. Here we describe bacterial diversity in the atmospheric boundary layer and underlying soil at twelve globally distributed locations encompassing all major biomes, and characterise the contribution of local and distant soils to the observed atmospheric community. Across biomes the diversity of bacteria in the atmosphere was negatively correlated with mean annual precipitation but positively correlated to mean annual temperature. We identified distinct non-randomly assembled atmosphere and soil communities from each location, and some broad trends persisted across biomes including the enrichment of desiccation and UV tolerant taxa in the atmospheric community. Source tracking revealed that local soils were more influential than distant soil sources in determining observed diversity in the atmosphere, with more emissive semi-arid and arid biomes contributing most to signatures from distant soil. Our findings highlight complexities in the atmospheric microbiota that are relevant to understanding regional and global ecosystem connectivity.
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Affiliation(s)
- Stephen D J Archer
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Kevin C Lee
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Tancredi Caruso
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Antonio Alcami
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Jonathan G Araya
- Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - S Craig Cary
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Claudia Etchebehere
- Biological Research Institute Clemente Estable, Ministry of Education, Montevideo, Uruguay
| | | | - Benito Gomez-Silva
- Departamento Biomédico and CeBiB, Universidad de Antofagasta, Antofagasta, Chile
| | - Sean Hartery
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand; Canadian High Arctic Research Station, Cambridge Bay, Nunavut, Canada
| | - Mayada K Kansour
- Department of Biological Sciences, Kuwait University, Kuwait City, Kuwait
| | - Timothy Lawrence
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Charles K Lee
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Matthias Leopold
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Australia
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Teruya Maki
- Department of Life Sciences, Kindai University, Osaka, Japan
| | | | - Dina M Al Mailem
- Department of Biological Sciences, Kuwait University, Kuwait City, Kuwait
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa; Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Henry J Sun
- Desert Research Institute, Las Vegas, NV, USA
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Bryan Vandenbrink
- Canadian High Arctic Research Station, Cambridge Bay, Nunavut, Canada
| | | | - Stephen B Pointing
- Yale-NUS College, National University of Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore; Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa, Japan.
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Santos A, Gómez-Espinoza O, Núñez-Montero K, Zárate A, Andreote FD, Pylro VS, Bravo L, Barrientos L. Measuring the effect of climate change in Antarctic microbial communities: toward novel experimental approaches. Curr Opin Biotechnol 2023; 81:102918. [PMID: 36972633 DOI: 10.1016/j.copbio.2023.102918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/05/2023] [Accepted: 02/17/2023] [Indexed: 03/29/2023]
Abstract
The Antarctic continent is undergoing a rapid warming, affecting microbial communities throughout its ecosystems. This continent is a natural laboratory for studying the effect of climate change, however, assessing the microbial communities' responses to environmental changes is challenging from a methodological point of view. We suggest novel experimental designs, including multivariable assessments that apply multiomics methods in combination with continuous environmental data recording and new warming simulation systems. Moreover, we propose that climate change studies in Antarctica should consider three main objectives, including descriptive studies, short-term temporary adaptation studies, and long-term adaptive evolution studies. This will help us to understand and manage the effects of climate change on the Earth.
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Affiliation(s)
- Andrés Santos
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Olman Gómez-Espinoza
- Biotechnology Research Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Kattia Núñez-Montero
- Biotechnology Research Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Ana Zárate
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile
| | - Fernando D Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Victor S Pylro
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | - León Bravo
- Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Leticia Barrientos
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco 4811230, Chile.
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