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Lappan R, Thakar J, Molares Moncayo L, Besser A, Bradley JA, Goordial J, Trembath-Reichert E, Greening C. The atmosphere: a transport medium or an active microbial ecosystem? THE ISME JOURNAL 2024; 18:wrae092. [PMID: 38804464 PMCID: PMC11214262 DOI: 10.1093/ismejo/wrae092] [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: 03/14/2024] [Revised: 05/05/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.
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Affiliation(s)
- Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- School of Earth, Atmosphere & Environment, Monash University, Clayton, Victoria 3800, Australia
- Securing Antarctica’s Environmental Future, Monash University, Clayton, Victoria 3800, Australia
| | - Jordan Thakar
- School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Laura Molares Moncayo
- School of Geography, Queen Mary University of London, London E1 4NS, United Kingdom
- Natural History Museum, London SW7 5BD, United Kingdom
- Aix Marseille University, University of Toulon, CNRS, IRD, MIO, Marseille 13009, France
| | - Alexi Besser
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, United States
| | - James A Bradley
- Aix Marseille University, University of Toulon, CNRS, IRD, MIO, Marseille 13009, France
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Jacqueline Goordial
- School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | | | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Securing Antarctica’s Environmental Future, Monash University, Clayton, Victoria 3800, Australia
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Rahlff J, Esser SP, Plewka J, Heinrichs ME, Soares A, Scarchilli C, Grigioni P, Wex H, Giebel HA, Probst AJ. Marine viruses disperse bidirectionally along the natural water cycle. Nat Commun 2023; 14:6354. [PMID: 37816747 PMCID: PMC10564846 DOI: 10.1038/s41467-023-42125-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
Marine viruses in seawater have frequently been studied, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2% of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols collected at ~2 m height above sea level and rain. Viruses detected in rain and these aerosols showed a significantly higher percent G/C base content compared to marine viruses. CRISPR spacer matches of marine prokaryotes to foreign viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization, adaptations, and dispersal support transmission of viruses along the natural water cycle.
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Affiliation(s)
- Janina Rahlff
- Group for Aquatic Microbial Ecology, Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, 45141, Essen, Germany.
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39231, Kalmar, Sweden.
- Aero-Aquatic Virus Research Group, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743, Jena, Germany.
| | - Sarah P Esser
- Group for Aquatic Microbial Ecology, Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, 45141, Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, 45141, Essen, Germany
| | - Julia Plewka
- Group for Aquatic Microbial Ecology, Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, 45141, Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, 45141, Essen, Germany
| | - Mara Elena Heinrichs
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - André Soares
- Group for Aquatic Microbial Ecology, Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, 45141, Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, 45141, Essen, Germany
| | - Claudio Scarchilli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123, Rome, Italy
| | - Paolo Grigioni
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123, Rome, Italy
| | - Heike Wex
- Atmospheric Microphysics, Leibniz Institute for Tropospheric Research (TROPOS), 04318, Leipzig, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Center for Marine Sensors (ZfMarS), Carl von Ossietzky University of Oldenburg, 26382, Wilhelmshaven, Germany
| | - Alexander J Probst
- Group for Aquatic Microbial Ecology, Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, 45141, Essen, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, 45141, Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, 45141, Essen, Germany
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Amato P, Mathonat F, Nuñez Lopez L, Péguilhan R, Bourhane Z, Rossi F, Vyskocil J, Joly M, Ervens B. The aeromicrobiome: the selective and dynamic outer-layer of the Earth's microbiome. Front Microbiol 2023; 14:1186847. [PMID: 37260685 PMCID: PMC10227452 DOI: 10.3389/fmicb.2023.1186847] [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: 03/15/2023] [Accepted: 04/24/2023] [Indexed: 06/02/2023] Open
Abstract
The atmosphere is an integral component of the Earth's microbiome. Abundance, viability, and diversity of microorganisms circulating in the air are determined by various factors including environmental physical variables and intrinsic and biological properties of microbes, all ranging over large scales. The aeromicrobiome is thus poorly understood and difficult to predict due to the high heterogeneity of the airborne microorganisms and their properties, spatially and temporally. The atmosphere acts as a highly selective dispersion means on large scales for microbial cells, exposing them to a multitude of physical and chemical atmospheric processes. We provide here a brief critical review of the current knowledge and propose future research directions aiming at improving our comprehension of the atmosphere as a biome.
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Affiliation(s)
- Pierre Amato
- Université Clermont Auvergne, CNRS, Institut de Chimie de Clermont-Ferrand (ICCF), Clermont-Ferrand, France
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Rossi F, Péguilhan R, Turgeon N, Veillette M, Baray JL, Deguillaume L, Amato P, Duchaine C. Quantification of antibiotic resistance genes (ARGs) in clouds at a mountain site (puy de Dôme, central France). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161264. [PMID: 36587700 DOI: 10.1016/j.scitotenv.2022.161264] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/19/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
Antibiotic resistance in bacteria is becoming a major sanitary concern worldwide. The extensive use of large quantities of antibiotics to sustain human activity has led to the rapid acquisition and maintenance of antibiotic resistant genes (ARGs) in bacteria and to their spread into the environment. Eventually, these can be disseminated over long distances by atmospheric transport. Here, we assessed the presence of ARGs in clouds as an indicator of long-distance travel potential of antibiotic resistance in the atmosphere. We hypothesized that a variety of ARGs can reach the altitude of clouds mainly located within the free troposphere. Once incorporated in the atmosphere, they are efficiently transported and their respective concentrations should differ depending on the sources and the geographical origin of the air masses. We deployed high-flow rate impingers and collected twelve clouds between September 2019 and October 2021 at the meteorological station of the puy de Dôme summit (1465 m a.s.l., France). Total airborne bacteria concentration was assessed by flow cytometry, and ARGs subtypes of the main families of antibiotic resistance (quinolone, sulfonamide, tetracycline; glycopeptide, aminoglycoside, β-lactamase, macrolide) including one mobile genetic element (transposase) were quantified by qPCR. Our results indicate the presence of 29 different ARGs' subtypes at concentrations ranging from 1.01 × 103 to 1.61 × 104 copies m-3 of air. Clear distinctions could be observed between clouds in air masses transported over marine areas (Atlantic Ocean) and clouds influenced by continental surfaces. Specifically, quinolones (mostly qepA) resistance genes were prevalent in marine clouds (54 % of the total ARGs on average), whereas higher contributions of sulfonamide, tetracycline; glycopeptide, β-lactamase and macrolide were found in continental clouds. This study constitutes the first evidence for the presence of microbial ARGs in clouds at concentrations comparable to other natural environments. This highlights the atmosphere as routes for the dissemination of ARGs at large scale.
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Affiliation(s)
- Florent Rossi
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada
| | - Raphaëlle Péguilhan
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Nathalie Turgeon
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada
| | - Marc Veillette
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada
| | - Jean-Luc Baray
- Université Clermont Auvergne, CNRS, Observatoire de Physique du Globe de Clermont-Ferrand, UAR 833, F-63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique, UMR 6016, F-63000 Clermont-Ferrand, France
| | - Laurent Deguillaume
- Université Clermont Auvergne, CNRS, Observatoire de Physique du Globe de Clermont-Ferrand, UAR 833, F-63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique, UMR 6016, F-63000 Clermont-Ferrand, France
| | - Pierre Amato
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France
| | - Caroline Duchaine
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada.
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Qi J, Ji M, Wang W, Zhang Z, Liu K, Huang Z, Liu Y. Effect of Indian monsoon on the glacial airborne bacteria over the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154980. [PMID: 35378188 DOI: 10.1016/j.scitotenv.2022.154980] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
The glacier of the Tibetan Plateau (TP) is influenced by the Indian monsoon and continental westerlies. Wind flow can carry a variety of bacteria and disperse across the TP. Once these bacteria are colonized to the glacier surface, they could affect the biogeochemical cycle of the glacial ecosystems. However, very few studies have focused on the relationships between these airborne bacteria and atmospheric circulation over glaciers of the TP. Here we studied the diversity, taxonomic composition, and community structure of airborne bacteria on six TP glaciers using 16S rRNA gene sequencing. The results revealed an increase in the airborne bacterial diversity over the glaciers under the effect of the Indian monsoon. Airborne bacteria were dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, while relative abundances of Bacteroidetes and Firmicutes were significantly higher under the influence of the Indian monsoon in the southern and central of the TP, respectively. Moreover, significantly different airborne bacterial community structures were observed over glaciers under the influence of the Indian monsoon, which could be explained by the increased community stochasticity. In addition, the Indian monsoon increases the diversity and relative abundance of potential pathogens, which includes the most notorious bacteria such as Pseudomonas fluorescens, Staphylococcus aureus, and Clostridium butyricum. Our results revealed for the first time that atmospheric circulation influences the composition of airborne bacteria over the glaciers on the TP, this may provide critical insights into the distinct microbial community structure and function in glaciers across the TP.
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Affiliation(s)
- Jing Qi
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; School of Life Sciences, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mukan Ji
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Wenqiang Wang
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; School of Life Sciences, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongwei Huang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
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