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Bains W, Petkowski JJ, Seager S. Venus' Atmospheric Chemistry and Cloud Characteristics Are Compatible with Venusian Life. ASTROBIOLOGY 2024; 24:371-385. [PMID: 37306952 DOI: 10.1089/ast.2022.0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Venus is Earth's sister planet, with similar mass and density but an uninhabitably hot surface, an atmosphere with a water activity 50-100 times lower than anywhere on Earths' surface, and clouds believed to be made of concentrated sulfuric acid. These features have been taken to imply that the chances of finding life on Venus are vanishingly small, with several authors describing Venus' clouds as "uninhabitable," and that apparent signs of life there must therefore be abiotic, or artefactual. In this article, we argue that although many features of Venus can rule out the possibility that Earth life could live there, none rule out the possibility of all life based on what we know of the physical principle of life on Earth. Specifically, there is abundant energy, the energy requirements for retaining water and capturing hydrogen atoms to build biomass are not excessive, defenses against sulfuric acid are conceivable and have terrestrial precedent, and the speculative possibility that life uses concentrated sulfuric acid as a solvent instead of water remains. Metals are likely to be available in limited supply, and the radiation environment is benign. The clouds can support a biomass that could readily be detectable by future astrobiology-focused space missions from its impact on the atmosphere. Although we consider the prospects for finding life on Venus to be speculative, they are not absent. The scientific reward from finding life in such an un-Earthlike environment justifies considering how observations and missions should be designed to be capable of detecting life if it is there.
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Affiliation(s)
- William Bains
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- School of Physics and Astronomy, Cardiff University, Cardiff, United Kingdom
| | - Janusz J Petkowski
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- JJ Scientific, Warsaw, Poland
| | - Sara Seager
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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2
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Seager MD, Seager S, Bains W, Petkowski JJ. Stability of 20 Biogenic Amino Acids in Concentrated Sulfuric Acid: Implications for the Habitability of Venus' Clouds. ASTROBIOLOGY 2024; 24:386-396. [PMID: 38498680 PMCID: PMC11035925 DOI: 10.1089/ast.2023.0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 01/01/2024] [Indexed: 03/20/2024]
Abstract
Scientists have long speculated about the potential habitability of Venus, not at the 700K surface, but in the cloud layers located at 48-60 km altitudes, where temperatures match those found on Earth's surface. However, the prevailing belief has been that Venus' clouds cannot support life due to the cloud chemical composition of concentrated sulfuric acid-a highly aggressive solvent. In this work, we study 20 biogenic amino acids at the range of Venus' cloud sulfuric acid concentrations (81% and 98% w/w, the rest water) and temperatures. We find 19 of the biogenic amino acids we tested are either unreactive (13 in 98% w/w and 12 in 81% w/w) or chemically modified in the side chain only, after 4 weeks. Our major finding, therefore, is that the amino acid backbone remains intact in concentrated sulfuric acid. These findings significantly broaden the range of biologically relevant molecules that could be components of a biochemistry based on a concentrated sulfuric acid solvent.
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Affiliation(s)
- Maxwell D. Seager
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
- Nanoplanet Consulting, Concord, Massachusetts, USA
| | - Sara Seager
- Nanoplanet Consulting, Concord, Massachusetts, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - William Bains
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- School of Physics & Astronomy, Cardiff University, Cardiff, United Kingdom
- Rufus Scientific, Royston, United Kingdom
| | - Janusz J. Petkowski
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Faculty of Environmental Engineering, Wroclaw University of Science and Technology, Wroclaw, Poland
- JJ Scientific, Warsaw, Poland
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3
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Tastassa AC, Sharaby Y, Lang-Yona N. Aeromicrobiology: A global review of the cycling and relationships of bioaerosols with the atmosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168478. [PMID: 37967625 DOI: 10.1016/j.scitotenv.2023.168478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/31/2023] [Accepted: 11/08/2023] [Indexed: 11/17/2023]
Abstract
Airborne microorganisms and biological matter (bioaerosols) play a key role in global biogeochemical cycling, human and crop health trends, and climate patterns. Their presence in the atmosphere is controlled by three main stages: emission, transport, and deposition. Aerial survival rates of bioaerosols are increased through adaptations such as ultra-violet radiation and desiccation resistance or association with particulate matter. Current research into modern concerns such as climate change, global gene transfer, and pathogenicity often neglects to consider atmospheric involvement. This comprehensive review outlines the transpiring of bioaerosols across taxa in the atmosphere, with significant focus on their interactions with environmental elements including abiotic factors (e.g., atmospheric composition, water cycle, and pollution) and events (e.g., dust storms, hurricanes, and wildfires). The aim of this review is to increase understanding and shed light on needed research regarding the interplay between global atmospheric phenomena and the aeromicrobiome. The abundantly documented bacteria and fungi are discussed in context of their cycling and human health impacts. Gaps in knowledge regarding airborne viral community, the challenges and importance of studying their composition, concentrations and survival in the air are addressed, along with understudied plant pathogenic oomycetes, and archaea cycling. Key methodologies in sampling, collection, and processing are described to provide an up-to-date picture of ameliorations in the field. We propose optimization to microbiological methods, commonly used in soil and water analysis, that adjust them to the context of aerobiology, along with other directions towards novel and necessary advancements. This review offers new perspectives into aeromicrobiology and calls for advancements in global-scale bioremediation, insights into ecology, climate change impacts, and pathogenicity transmittance.
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Affiliation(s)
- Ariel C Tastassa
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, 3200003 Haifa, Israel
| | - Yehonatan Sharaby
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, 3200003 Haifa, Israel
| | - Naama Lang-Yona
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, 3200003 Haifa, Israel.
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4
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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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5
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Heinrichs ME, Piedade GJ, Popa O, Sommers P, Trubl G, Weissenbach J, Rahlff J. Breaking the Ice: A Review of Phages in Polar Ecosystems. Methods Mol Biol 2024; 2738:31-71. [PMID: 37966591 DOI: 10.1007/978-1-0716-3549-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.
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Affiliation(s)
- Mara Elena Heinrichs
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Gonçalo J Piedade
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Ovidiu Popa
- Institute of Quantitative and Theoretical Biology Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | | | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Julia Weissenbach
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Janina Rahlff
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
- Aero-Aquatic Virus Research Group, Friedrich Schiller University Jena, Jena, Germany.
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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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7
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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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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: 7] [Impact Index Per Article: 7.0] [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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9
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Comparison of Atmospheric and Lithospheric Culturable Bacterial Communities from Two Dissimilar Active Volcanic Sites, Surtsey Island and Fimmvörðuháls Mountain in Iceland. Microorganisms 2023; 11:microorganisms11030665. [PMID: 36985243 PMCID: PMC10057085 DOI: 10.3390/microorganisms11030665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023] Open
Abstract
Surface microbes are aerosolized into the atmosphere by wind and events such as dust storms and volcanic eruptions. Before they reach their deposition site, they experience stressful atmospheric conditions which preclude the successful dispersal of a large fraction of cells. In this study, our objectives were to assess and compare the atmospheric and lithospheric bacterial cultivable diversity of two geographically different Icelandic volcanic sites: the island Surtsey and the Fimmvörðuháls mountain, to predict the origin of the culturable microbes from these sites, and to select airborne candidates for further investigation. Using a combination of MALDI Biotyper analysis and partial 16S rRNA gene sequencing, a total of 1162 strains were identified, belonging to 72 species affiliated to 40 genera with potentially 26 new species. The most prevalent phyla identified were Proteobacteria and Actinobacteria. Statistical analysis showed significant differences between atmospheric and lithospheric microbial communities, with distinct communities in Surtsey’s air. By combining the air mass back trajectories and the analysis of the closest representative species of our isolates, we concluded that 85% of our isolates came from the surrounding environments and only 15% from long distances. The taxonomic proportions of the isolates were reflected by the site’s nature and location.
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10
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Jroundi F, Povedano-Priego C, Pinel-Cabello M, Descostes M, Grizard P, Purevsan B, Merroun ML. Evidence of microbial activity in a uranium roll-front deposit: Unlocking their potential role as bioenhancers of the ore genesis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160636. [PMID: 36464038 DOI: 10.1016/j.scitotenv.2022.160636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Uranium (U) roll-front deposits constitute a valuable source for an economical extraction by in situ recovery (ISR) mining. Such technology may induce changes in the subsurface microbiota, raising questions about the way their activities could build a functional ecosystem in such extreme environments (i.e.: oligotrophy and high SO4 concentration and salinity). Additionally, more information is needed to dissipate the doubts about the microbial role in the genesis of such U orebodies. A U roll-front deposit hosted in an aquifer driven system (in Zoovch Ovoo, Mongolia), intended for mining by acid ISR, was previously explored and showed to be governed by a complex bacterial diversity, linked to the redox zonation and the geochemical conditions. Here for the first time, transcriptional activities of microorganisms living in such U ore deposits are determined and their metabolic capabilities allocated in the three redox-inherited compartments, naturally defined by the roll-front system. Several genes encoding for crucial metabolic pathways demonstrated a strong biological role controlling the subsurface cycling of many elements including nitrate, sulfate, metals and radionuclides (e.g.: uranium), through oxidation-reduction reactions. Interestingly, the discovered transcriptional behaviour gives important insights into the good microbial adaptation to the geochemical conditions and their active contribution to the stabilization of the U ore deposits. Overall, evidences on the importance of these microbial metabolic activities in the aquifer system are discussed that may clarify the doubts on the microbial role in the genesis of low-temperature U roll-front deposits, along the Zoovch Ovoo mine.
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Affiliation(s)
- Fadwa Jroundi
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
| | - Cristina Povedano-Priego
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - María Pinel-Cabello
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - Michael Descostes
- ORANO Mining, 125 Avenue de Paris, 92330 Châtillon, France; Centre de Géosciences, MINES ParisTech, PSL University, 35 rue St Honoré, 77300 Fontainebleau, France
| | - Pierre Grizard
- ORANO Mining, 125 Avenue de Paris, 92330 Châtillon, France
| | - Bayaarma Purevsan
- Badrakh Energy LLC, Jamyan Gun Avenue - 9, Sukhbaatar district, 1st khoroo, UB-14240, Mongolia
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
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11
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Dillon KP, Krumins V, Deshpande A, Kerkhof LJ, Mainelis G, Fennell DE. Characterization and DNA Stable-Isotope Probing of Methanotrophic Bioaerosols. Microbiol Spectr 2022; 10:e0342122. [PMID: 36409096 PMCID: PMC9769660 DOI: 10.1128/spectrum.03421-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/15/2022] [Indexed: 11/23/2022] Open
Abstract
The growth and activity of bacteria have been extensively studied in nearly every environment on Earth, but there have been limited studies focusing on the air. Suspended bacteria (outside of water droplets) may stay in the atmosphere for time frames that could allow for growth on volatile compounds, including the potent greenhouse gas methane. We investigated the ability of aerosolized methanotrophic bacteria to grow on methane in the airborne state in rotating gas-phase bioreactors. The physical half-life of the aerial bacterium-sized particles was 3 days. To assess the potential for airborne growth, gas-phase bioreactors containing the aerosolized cultures were amended with 1,500 ppmv 13CH4 or 12CH4. Three of seven experiments demonstrated 13C incorporation into DNA, indicating growth in air. Bacteria associated with the genera Methylocystis and Methylocaldum were detected in 13C-DNA fractions, thus indicating that they were synthesizing new DNA, suggesting growth in air. We conclude that methanotrophs outside of water droplets in the air can potentially grow under certain conditions. Based on our data, humidity seems to be a major limitation to bacterial growth in air. Furthermore, low biomass levels can pose problems for detecting 13C-DNA synthesis in our experimental system. IMPORTANCE Currently, the cellular activities of bacteria in the airborne state outside of water droplets have not been heavily studied. Evidence suggests that these airborne bacteria produce ribosomes and metabolize gaseous compounds. Despite having a potentially important impact on atmospheric chemistry, the ability of bacteria in the air to metabolize substrates such as methane is not well understood. Demonstrating that bacteria in the air can metabolize and grow on substrates will expand knowledge about the potential activities and functions of the atmospheric microbiome. This study provides evidence for DNA synthesis and, ultimately, growth of airborne methanotrophs.
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Affiliation(s)
- Kevin P. Dillon
- Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Aishwarya Deshpande
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Lee J. Kerkhof
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Gediminas Mainelis
- Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Donna E. Fennell
- Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA
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12
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How Well Do We Handle the Sample Preparation, FT-ICR Mass Spectrometry Analysis, and Data Treatment of Atmospheric Waters? MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227796. [PMID: 36431897 PMCID: PMC9692371 DOI: 10.3390/molecules27227796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
FT-ICR MS (Fourier-transform ion cyclotron resonance mass spectrometry) analysis has shown great potential to aid in the understanding of the extremely high molecular diversity of cloud water samples. The main goal of this work was to determine the differences in terms of formula assignment for analytical (i.e., measurement replicates) and experimental replicates of a given cloud water sample. The experimental replicates, obtained by solid phase extraction, were also compared to the results obtained for freeze-dried samples to evaluate whether the presence of salts interferes with the analysis. Two S/N ratios, generally adopted for atmospheric samples, were evaluated, and three different algorithms were used for assignment: DataAnalysis 5.3 (Bruker), Composer (Sierra Analytics), and MFAssignR (Chemical Advanced Resolution Methods Lab). In contrast to other works, we wanted to treat this comparison from the point of view of users, who usually must deal with a simple list of m/z ratios and intensity with limited access to the mass spectrum characteristics. The aim of this study was to establish a methodology for the treatment of atmospheric aqueous samples in light of the comparison of three different software programs, to enhance the possibility of data comparison within samples.
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13
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de Lorenzo V. Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210395. [PMID: 35757882 PMCID: PMC9234819 DOI: 10.1098/rstb.2021.0395] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems. This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain
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14
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George PBL, Rossi F, St-Germain MW, Amato P, Badard T, Bergeron MG, Boissinot M, Charette SJ, Coleman BL, Corbeil J, Culley AI, Gaucher ML, Girard M, Godbout S, Kirychuk SP, Marette A, McGeer A, O’Shaughnessy PT, Parmley EJ, Simard S, Reid-Smith RJ, Topp E, Trudel L, Yao M, Brassard P, Delort AM, Larios AD, Létourneau V, Paquet VE, Pedneau MH, Pic É, Thompson B, Veillette M, Thaler M, Scapino I, Lebeuf M, Baghdadi M, Castillo Toro A, Cayouette AB, Dubois MJ, Durocher AF, Girard SB, Diaz AKC, Khalloufi A, Leclerc S, Lemieux J, Maldonado MP, Pilon G, Murphy CP, Notling CA, Ofori-Darko D, Provencher J, Richer-Fortin A, Turgeon N, Duchaine C. Antimicrobial Resistance in the Environment: Towards Elucidating the Roles of Bioaerosols in Transmission and Detection of Antibacterial Resistance Genes. Antibiotics (Basel) 2022; 11:974. [PMID: 35884228 PMCID: PMC9312183 DOI: 10.3390/antibiotics11070974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/15/2022] [Indexed: 02/01/2023] Open
Abstract
Antimicrobial resistance (AMR) is continuing to grow across the world. Though often thought of as a mostly public health issue, AMR is also a major agricultural and environmental problem. As such, many researchers refer to it as the preeminent One Health issue. Aerial transport of antimicrobial-resistant bacteria via bioaerosols is still poorly understood. Recent work has highlighted the presence of antibiotic resistance genes in bioaerosols. Emissions of AMR bacteria and genes have been detected from various sources, including wastewater treatment plants, hospitals, and agricultural practices; however, their impacts on the broader environment are poorly understood. Contextualizing the roles of bioaerosols in the dissemination of AMR necessitates a multidisciplinary approach. Environmental factors, industrial and medical practices, as well as ecological principles influence the aerial dissemination of resistant bacteria. This article introduces an ongoing project assessing the presence and fate of AMR in bioaerosols across Canada. Its various sub-studies include the assessment of the emissions of antibiotic resistance genes from many agricultural practices, their long-distance transport, new integrative methods of assessment, and the creation of dissemination models over short and long distances. Results from sub-studies are beginning to be published. Consequently, this paper explains the background behind the development of the various sub-studies and highlight their shared aspects.
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Affiliation(s)
- Paul B. L. George
- Département de Médecine Moléculaire, Université Laval, Quebec City, QC G1V 0A6, Canada; (P.B.L.G.); (J.C.); (I.S.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
| | - Florent Rossi
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Chimie de Clermont-Ferrand, SIGMA Clermont, CNRS, Université Clermont-Auvergne, 63178 Clermont-Ferrand, France; (P.A.); (A.-M.D.)
| | - Magali-Wen St-Germain
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand, SIGMA Clermont, CNRS, Université Clermont-Auvergne, 63178 Clermont-Ferrand, France; (P.A.); (A.-M.D.)
| | - Thierry Badard
- Centre de Recherche en Données et Intelligence Géospatiales (CRDIG), Quebec City, QC G1V 0A6, Canada;
| | - Michel G. Bergeron
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec-Université Laval, Axe Maladies Infectieuses et Immunitaires, Quebec City, QC G1V 4G2, Canada; (M.G.B.); (M.B.); (É.P.)
| | - Maurice Boissinot
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec-Université Laval, Axe Maladies Infectieuses et Immunitaires, Quebec City, QC G1V 4G2, Canada; (M.G.B.); (M.B.); (É.P.)
| | - Steve J. Charette
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Brenda L. Coleman
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; (B.L.C.); (A.M.)
| | - Jacques Corbeil
- Département de Médecine Moléculaire, Université Laval, Quebec City, QC G1V 0A6, Canada; (P.B.L.G.); (J.C.); (I.S.)
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec-Université Laval, Axe Maladies Infectieuses et Immunitaires, Quebec City, QC G1V 4G2, Canada; (M.G.B.); (M.B.); (É.P.)
| | - Alexander I. Culley
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Marie-Lou Gaucher
- Research Chair in Meat Safety, Département de Pathologie et Microbiologie, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | | | - Stéphane Godbout
- Institut de Recherche et de Développement en Agroenvironnement (IRDA), Quebec City, QC G1P 3W8, Canada; (S.G.); (A.D.L.); (A.K.C.D.)
- Département des Sols et de Génie Agroalimentaire, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Shelley P. Kirychuk
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada; (S.P.K.); (B.T.); (A.C.T.); (C.A.N.)
| | - André Marette
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
- Institut sur la Nutrition et les Aliments Fonctionnels, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Allison McGeer
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; (B.L.C.); (A.M.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Patrick T. O’Shaughnessy
- Department of Occupational and Environmental Health, The University of Iowa, Iowa City, IA 52246, USA;
| | - E. Jane Parmley
- Canadian Wildlife Health Cooperative, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Population Medicine, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.J.R.-S.); (M.P.M.)
| | - Serge Simard
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Richard J. Reid-Smith
- Department of Population Medicine, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.J.R.-S.); (M.P.M.)
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada; (C.P.M.); (D.O.-D.)
| | - Edward Topp
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3, Canada;
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Luc Trudel
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
| | - Maosheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China;
| | - Patrick Brassard
- Département des Sols et de Génie Agroalimentaire, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Anne-Marie Delort
- Institut de Chimie de Clermont-Ferrand, SIGMA Clermont, CNRS, Université Clermont-Auvergne, 63178 Clermont-Ferrand, France; (P.A.); (A.-M.D.)
| | - Araceli D. Larios
- Institut de Recherche et de Développement en Agroenvironnement (IRDA), Quebec City, QC G1P 3W8, Canada; (S.G.); (A.D.L.); (A.K.C.D.)
- Tecnológico Nacional de México/ITS de Perote, Perote 91270, Mexico
| | - Valérie Létourneau
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Valérie E. Paquet
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Marie-Hélène Pedneau
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Émilie Pic
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec-Université Laval, Axe Maladies Infectieuses et Immunitaires, Quebec City, QC G1V 4G2, Canada; (M.G.B.); (M.B.); (É.P.)
| | - Brooke Thompson
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada; (S.P.K.); (B.T.); (A.C.T.); (C.A.N.)
| | - Marc Veillette
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Mary Thaler
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Ilaria Scapino
- Département de Médecine Moléculaire, Université Laval, Quebec City, QC G1V 0A6, Canada; (P.B.L.G.); (J.C.); (I.S.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Maria Lebeuf
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Mahsa Baghdadi
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Alejandra Castillo Toro
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada; (S.P.K.); (B.T.); (A.C.T.); (C.A.N.)
| | - Amélia Bélanger Cayouette
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Marie-Julie Dubois
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
- Institut sur la Nutrition et les Aliments Fonctionnels, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Alicia F. Durocher
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Sarah B. Girard
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Andrea Katherín Carranza Diaz
- Institut de Recherche et de Développement en Agroenvironnement (IRDA), Quebec City, QC G1P 3W8, Canada; (S.G.); (A.D.L.); (A.K.C.D.)
- Département des Sols et de Génie Agroalimentaire, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Asmaâ Khalloufi
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Research Chair in Meat Safety, Département de Pathologie et Microbiologie, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | - Samantha Leclerc
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Joanie Lemieux
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec-Université Laval, Axe Maladies Infectieuses et Immunitaires, Quebec City, QC G1V 4G2, Canada; (M.G.B.); (M.B.); (É.P.)
| | - Manuel Pérez Maldonado
- Department of Population Medicine, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.J.R.-S.); (M.P.M.)
| | - Geneviève Pilon
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Colleen P. Murphy
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada; (C.P.M.); (D.O.-D.)
| | - Charly A. Notling
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada; (S.P.K.); (B.T.); (A.C.T.); (C.A.N.)
| | - Daniel Ofori-Darko
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada; (C.P.M.); (D.O.-D.)
| | - Juliette Provencher
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Annabelle Richer-Fortin
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Nathalie Turgeon
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Caroline Duchaine
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
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15
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González AG, Bianco A, Boutorh J, Cheize M, Mailhot G, Delort AM, Planquette H, Chaumerliac N, Deguillaume L, Sarthou G. Influence of strong iron-binding ligands on cloud water oxidant capacity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154642. [PMID: 35306063 DOI: 10.1016/j.scitotenv.2022.154642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/09/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Iron (Fe) plays a dual role in atmospheric chemistry: it is involved in chemical and photochemical reactivity and serves as a micronutrient for microorganisms that have recently been shown to produce strong organic ligands. These ligands control the reactivity, mobility, solubility and speciation of Fe, which have a potential impact on Fe bioavailability and cloud water oxidant capacity. In this work, the concentrations of Fe-binding ligands and the conditional stability constants were experimentally measured for the first time by Competitive Ligand Exchange-Adsorptive Cathodic Stripping Voltammetry (CLE-ACSV) technique in cloud water samples collected at puy de Dôme (France). The conditional stability constants, which indicate the strength of the Fe-ligand complexes, are higher than those considered until now in cloud chemistry (mainly Fe-oxalate). To understand the effect of Fe complexation on cloud water reactivity, we used the CLEPS cloud chemistry model. According to the model results, we found that Fe complexation impacts the hydroxyl radical formation rate: contrary to our expectations, Fe complexation by natural organic ligands led to an increase in hydroxyl radical production. These findings have important impacts on cloud chemistry and the global iron cycle.
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Affiliation(s)
- Aridane G González
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Spain; CNRS, Univ Brest, IRD, Ifremer, LEMAR, F-29280 Plouzane, France.
| | - Angelica Bianco
- Laboratoire de Météorologie Physique, UMR 6016, CNRS, Université Clermont Auvergne, 63178 Aubière, France.
| | - Julia Boutorh
- CNRS, Univ Brest, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
| | - Marie Cheize
- CNRS, Univ Brest, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
| | - Gilles Mailhot
- CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Anne-Marie Delort
- CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | | | - Nadine Chaumerliac
- Laboratoire de Météorologie Physique, UMR 6016, CNRS, Université Clermont Auvergne, 63178 Aubière, France
| | - Laurent Deguillaume
- Laboratoire de Météorologie Physique, UMR 6016, CNRS, Université Clermont Auvergne, 63178 Aubière, France; Observatoire de Physique du Globe de Clermont-Ferrand, UAR 833, CNRS, Université Clermont Auvergne, 63178 Aubière, France
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16
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Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests. Proc Natl Acad Sci U S A 2022; 119:e2118852119. [PMID: 35727987 PMCID: PMC9245616 DOI: 10.1073/pnas.2118852119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Advances in DNA sequencing have provided an unprecedented view of the complex microbial communities that populate global ecosystems. We present a metatranscriptomic analysis of samples from the boreal forest—the largest terrestrial carbon store—capturing the seasonally resolved transcriptomes of Norway spruce roots and more than 350 root-associated fungal species. Our findings link the functional response of host-trees to increased nutrient availability, with profound perturbations in the fungal community. Notably, we observed an exchange in prevalence and host-coordination of specialist ectomycorrhizal species critical for enzymatic cycling of recalcitrant carbon, to metabolically versatile species with resilient melanized cell walls. This research unites kingdom-spanning taxonomic and functional details of the boreal root microbiome, contributing a missing perspective toward modeling global carbon cycling. Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.
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17
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Sasaki S, Yamagishi A, Yoshimura Y, Enya K, Miyakawa A, Ohno S, Fujita K, Usui T, Limaye S. In situ bio/chemical characterization of Venus cloud particles using Life-signature Detection Microscope for Venus (Venus LDM). Can J Microbiol 2022; 68:413-425. [PMID: 35235433 DOI: 10.1139/cjm-2021-0140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Much of the information about the size and shape of aerosols forming haze and the cloud layer of Venus is obtained from indirect inferences from nephelometers on probes and from analysis of the variation of polarization with the phase angle and the glory feature from images of Venus. Microscopic imaging of Venus' aerosols has been advocated recently. Direct measurements from a fluorescence microscope can provide information on the morphology, density, and biochemical characteristics of the particles; thus, the fluorescence microscope is attractive for the in situ particle characterization of Venus' cloud layer. Fluorescence imaging of Venus' cloud particles presents several challenges due to the sulfuric acid composition and the corrosive effects. In this article, we identify the challenges and describe our approach to overcoming them for a fluorescence microscope based on an in situ bio/chemical and physical characterization instrument for use in the clouds of Venus from a suitable aerial platform. We report that a pH adjustment using alkali was effective for obtaining fluorescence images, and that fluorescence attenuation was observed after the adjustment, even when the acidophile suspension in the concentrated sulfuric acid was used as a sample.
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Affiliation(s)
- Satoshi Sasaki
- Tokyo University of Technology, 13097, Hachioji, Japan, 192-0914;
| | - Akihiko Yamagishi
- Tokyo University of Pharmacy and Life Sciences, 13115, Hachioji, Tokyo, Japan;
| | | | - Keigo Enya
- JAXA, 13557, Sagamihara, Kanagawa, Japan;
| | - Atsuo Miyakawa
- Tokyo University of Pharmacy and Life Sciences, 13115, Hachioji, Tokyo, Japan;
| | - Sohsuke Ohno
- Chiba Institute of Technology, 12829, Chiba, Chiba, Japan;
| | | | | | - Sanjay Limaye
- University of Wisconsin-Madison, 5228, Madison, Wisconsin, United States;
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18
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Šantl-Temkiv T, Amato P, Casamayor EO, Lee PKH, Pointing SB. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6524182. [PMID: 35137064 PMCID: PMC9249623 DOI: 10.1093/femsre/fuac009] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/31/2022] [Accepted: 02/06/2022] [Indexed: 11/30/2022] Open
Abstract
The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.
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Affiliation(s)
- Tina Šantl-Temkiv
- Department of Biology, Aarhus University, DK-8000 Aarhus, Denmark
- Stellar Astrophysics Centre, Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus, Denmark
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand, SIGMA Clermont, CNRS, Université Clermont Auvergne, 63178, Clermont-Ferrand, France
| | - Emilio O Casamayor
- Centre for Advanced Studies of Blanes, Spanish Council for Research (CSIC), 17300, Blanes, Spain
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Stephen B Pointing
- Corresponding author: Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore 138527. Tel: +65 6601 1000; E-mail:
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19
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Alsante AN, Thornton DCO, Brooks SD. Ocean Aerobiology. Front Microbiol 2021; 12:764178. [PMID: 34777320 PMCID: PMC8586456 DOI: 10.3389/fmicb.2021.764178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022] Open
Abstract
Ocean aerobiology is defined here as the study of biological particles of marine origin, including living organisms, present in the atmosphere and their role in ecological, biogeochemical, and climate processes. Hundreds of trillions of microorganisms are exchanged between ocean and atmosphere daily. Within a few days, tropospheric transport potentially disperses microorganisms over continents and between oceans. There is a need to better identify and quantify marine aerobiota, characterize the time spans and distances of marine microorganisms’ atmospheric transport, and determine whether microorganisms acclimate to atmospheric conditions and remain viable, or even grow. Exploring the atmosphere as a microbial habitat is fundamental for understanding the consequences of dispersal and will expand our knowledge of biodiversity, biogeography, and ecosystem connectivity across different marine environments. Marine organic matter is chemically transformed in the atmosphere, including remineralization back to CO2. The magnitude of these transformations is insignificant in the context of the annual marine carbon cycle, but may be a significant sink for marine recalcitrant organic matter over long (∼104 years) timescales. In addition, organic matter in sea spray aerosol plays a significant role in the Earth’s radiative budget by scattering solar radiation, and indirectly by affecting cloud properties. Marine organic matter is generally a poor source of cloud condensation nuclei (CCN), but a significant source of ice nucleating particles (INPs), affecting the formation of mixed-phase and ice clouds. This review will show that marine biogenic aerosol plays an impactful, but poorly constrained, role in marine ecosystems, biogeochemical processes, and the Earth’s climate system. Further work is needed to characterize the connectivity and feedbacks between the atmosphere and ocean ecosystems in order to integrate this complexity into Earth System models, facilitating future climate and biogeochemical predictions.
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Affiliation(s)
- Alyssa N Alsante
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Daniel C O Thornton
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Sarah D Brooks
- Department of Atmospheric Sciences, Texas A&M University, College Station, TX, United States
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20
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Péguilhan R, Besaury L, Rossi F, Enault F, Baray JL, Deguillaume L, Amato P. Rainfalls sprinkle cloud bacterial diversity while scavenging biomass. FEMS Microbiol Ecol 2021; 97:6420242. [PMID: 34734249 DOI: 10.1093/femsec/fiab144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/27/2021] [Indexed: 11/15/2022] Open
Abstract
Bacteria circulate in the atmosphere, through clouds and precipitation to surface ecosystems. Here, we conducted a coordinated study of bacteria assemblages in clouds and precipitation at two sites distant of ∼800 m in elevation in a rural vegetated area around puy de Dôme Mountain, France, and analysed them in regard to meteorological, chemical and air masses' history data. In both clouds and precipitation, bacteria generally associated with vegetation or soil dominated. Elevated ATP-to-cell ratio in clouds compared with precipitation suggested a higher proportion of viable cells and/or specific biological processes. The increase of bacterial cell concentration from clouds to precipitation indicated strong below-cloud scavenging. Using ions as tracers, we derive that 0.2 to 25.5% of the 1.1 × 107 to 6.6 × 108 bacteria cell/m2/h1 deposited with precipitation originated from the source clouds. Yet, the relative species richness decreased with the proportion of inputs from clouds, pointing them as sources of distant microbial diversity. Biodiversity profiles, thus, differed between clouds and precipitation in relation with distant/local influencing sources, and potentially with bacterial phenotypic traits. Notably Undibacterium, Bacillus and Staphylococcus were more represented in clouds, while epiphytic bacteria such as Massilia, Sphingomonas, Rhodococcus and Pseudomonas were enriched in precipitation.
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Affiliation(s)
- Raphaëlle Péguilhan
- Université Clermont Auvergne, CNRS, SIGMA Clermont , ICCF, F-63000 CLERMONT-FERRAND, France
| | - Ludovic Besaury
- Université Clermont Auvergne, CNRS, SIGMA Clermont , ICCF, F-63000 CLERMONT-FERRAND, France
| | - Florent Rossi
- Université Clermont Auvergne, CNRS, SIGMA Clermont , ICCF, F-63000 CLERMONT-FERRAND, France
| | - François Enault
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, F-63000 CLERMONT-FERRAND, France
| | - Jean-Luc Baray
- Université Clermont Auvergne, CNRS, Observatoire de Physique du Globe de Clermont-Ferrand , UMS 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 , UMS 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
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21
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Miaow K, Lacap-Bugler D, Buckley HL. Identifying optimal bioinformatics protocols for aerosol microbial community data. PeerJ 2021; 9:e12065. [PMID: 34703658 PMCID: PMC8487624 DOI: 10.7717/peerj.12065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/05/2021] [Indexed: 11/20/2022] Open
Abstract
Microbes are fundamental to Earth’s ecosystems, thus understanding ecosystem connectivity through microbial dispersal is key to predicting future ecosystem changes in a warming world. However, aerial microbial dispersal remains poorly understood. Few studies have been performed on bioaerosols (microorganisms and biological fragments suspended in the atmosphere), despite them harboring pathogens and allergens. Most environmental microbes grow poorly in culture, therefore molecular approaches are required to characterize aerial diversity. Bioinformatic tools are needed for processing the next generation sequencing (NGS) data generated from these molecular approaches; however, there are numerous options and choices in the process. These choices can markedly affect key aspects of the data output including relative abundances, diversity, and taxonomy. Bioaerosol samples have relatively little DNA, and often contain novel and proportionally high levels of contaminant organisms, that are difficult to identify. Therefore, bioinformatics choices are of crucial importance. A bioaerosol dataset for bacteria and fungi based on the 16S rRNA gene (16S) and internal transcribed spacer (ITS) DNA sequencing from parks in the metropolitan area of Auckland, Aotearoa New Zealand was used to develop a process for determining the bioinformatics pipeline that would maximize the data amount and quality generated. Two popular tools (Dada2 and USEARCH) were compared for amplicon sequence variant (ASV) inference and generation of an ASV table. A scorecard was created and used to assess multiple outputs and make systematic choices about the most suitable option. The read number and ASVs were assessed, alpha diversity was calculated (Hill numbers), beta diversity (Bray–Curtis distances), differential abundance by site and consistency of ASVs were considered. USEARCH was selected, due to higher consistency in ASVs identified and greater read counts. Taxonomic assignment is highly dependent on the taxonomic database used. Two popular taxonomy databases were compared in terms of number and confidence of assignments, and a combined approach developed that uses information in both databases to maximize the number and confidence of taxonomic assignments. This approach increased the assignment rate by 12–15%, depending on amplicon and the overall assignment was 77% for bacteria and 47% for fungi. Assessment of decontamination using “decontam” and “microDecon” was performed, based on review of ASVs identified as contaminants by each and consideration of the probability of them being legitimate members of the bioaerosol community. For this example, “microDecon’s” subtraction approach for removing background contamination was selected. This study demonstrates a systematic approach to determining the optimal bioinformatics pipeline using a multi-criteria scorecard for microbial bioaerosol data. Example code in the R environment for this data processing pipeline is provided.
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Affiliation(s)
- Katie Miaow
- School of Science, Auckland University of Technology, Auckland, Auckland, New Zealand
| | | | - Hannah L Buckley
- School of Science, Auckland University of Technology, Auckland, Auckland, New Zealand
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22
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Seager S, Petkowski JJ, Gao P, Bains W, Bryan NC, Ranjan S, Greaves J. The Venusian Lower Atmosphere Haze as a Depot for Desiccated Microbial Life: A Proposed Life Cycle for Persistence of the Venusian Aerial Biosphere. ASTROBIOLOGY 2021; 21:1206-1223. [PMID: 32787733 DOI: 10.1089/ast.2020.2244] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We revisit the hypothesis that there is life in the venusian clouds to propose a life cycle that resolves the conundrum of how life can persist aloft for hundreds of millions to billions of years. Most discussions of an aerial biosphere in the venusian atmosphere temperate layers never address whether the life-small microbial-type particles-is free floating or confined to the liquid environment inside cloud droplets. We argue that life must reside inside liquid droplets such that it will be protected from a fatal net loss of liquid to the atmosphere, an unavoidable problem for any free-floating microbial life forms. However, the droplet habitat poses a lifetime limitation: Droplets inexorably grow (over a few months) to large enough sizes that are forced by gravity to settle downward to hotter, uninhabitable layers of the venusian atmosphere. (Droplet fragmentation-which would reduce particle size-does not occur in venusian atmosphere conditions.) We propose for the first time that the only way life can survive indefinitely is with a life cycle that involves microbial life drying out as liquid droplets evaporate during settling, with the small desiccated "spores" halting at, and partially populating, the venusian atmosphere stagnant lower haze layer (33-48 km altitude). We, thus, call the venusian lower haze layer a "depot" for desiccated microbial life. The spores eventually return to the cloud layer by upward diffusion caused by mixing induced by gravity waves, act as cloud condensation nuclei, and rehydrate for a continued life cycle. We also review the challenges for life in the extremely harsh conditions of the venusian atmosphere, refuting the notion that the "habitable" cloud layer has an analogy in any terrestrial environment.
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Affiliation(s)
- Sara Seager
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Janusz J Petkowski
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Peter Gao
- Department of Astronomy, University of California at Berkeley, California, USA
| | - William Bains
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Noelle C Bryan
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sukrit Ranjan
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jane Greaves
- School of Physics and Astronomy, Cardiff University, Cardiff, United Kingdom
- Institute of Astronomy, Cambridge University, Cambridge, United Kingdom
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23
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Izenberg NR, Gentry DM, Smith DJ, Gilmore MS, Grinspoon DH, Bullock MA, Boston PJ, Słowik GP. The Venus Life Equation. ASTROBIOLOGY 2021; 21:1305-1315. [PMID: 33512272 DOI: 10.1089/ast.2020.2326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Ancient Venus and Earth may have been similar in crucial ways for the development of life, such as liquid water oceans, land-ocean interfaces, favorable chemical ingredients, and energy pathways. If life ever developed on, or was transported to, early Venus from elsewhere, it might have thrived, expanded, and then survived the changes that have led to an inhospitable surface on Venus today. The Venus cloud layer may provide a refugium for extant life that persisted from an earlier more habitable surface environment. We introduce the Venus Life Equation (VLE)-a theory and evidence-based approach to calculate the probability of extant life on Venus, L, using three primary factors of life: Origination, Robustness, and Continuity, or L = O · R · C. We evaluate each of these factors using our current understanding of Earth and Venus environmental conditions from the Archean to the present. We find that the probability of origination of life on Venus would be similar to that of Earth, and argue that the other factors should be nonzero, comparable with other promising astrobiological targets in the solar system. The VLE also identifies poorly understood aspects of Venus that can be addressed by direct observations with future exploration missions.
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Affiliation(s)
- Noam R Izenberg
- Earth and Environmental Sciences Department, Johns Hopkins University Applied Physics Laboratory (JHUAPL), Laurel, Maryland, USA
| | - Diana M Gentry
- NASA Ames Research Center, Moffett Field, California, USA
| | - David J Smith
- NASA Ames Research Center, Moffett Field, California, USA
| | - Martha S Gilmore
- Earth and Environmental Sciences Department, Wesleyan University, Middletown, Connecticut, USA
| | | | | | | | - Grzegorz P Słowik
- Institute of Materials and Biomedical Engineering, Faculty of Mechanical Engineering, University of Zielona Góra, Zielona Góra, Poland
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Limaye SS, Mogul R, Baines KH, Bullock MA, Cockell C, Cutts JA, Gentry DM, Grinspoon DH, Head JW, Jessup KL, Kompanichenko V, Lee YJ, Mathies R, Milojevic T, Pertzborn RA, Rothschild L, Sasaki S, Schulze-Makuch D, Smith DJ, Way MJ. Venus, an Astrobiology Target. ASTROBIOLOGY 2021; 21:1163-1185. [PMID: 33970019 DOI: 10.1089/ast.2020.2268] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We present a case for the exploration of Venus as an astrobiology target-(1) investigations focused on the likelihood that liquid water existed on the surface in the past, leading to the potential for the origin and evolution of life, (2) investigations into the potential for habitable zones within Venus' present-day clouds and Venus-like exo atmospheres, (3) theoretical investigations into how active aerobiology may impact the radiative energy balance of Venus' clouds and Venus-like atmospheres, and (4) application of these investigative approaches toward better understanding the atmospheric dynamics and habitability of exoplanets. The proximity of Venus to Earth, guidance for exoplanet habitability investigations, and access to the potential cloud habitable layer and surface for prolonged in situ extended measurements together make the planet a very attractive target for near term astrobiological exploration.
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Affiliation(s)
- Sanjay S Limaye
- Space Science and Engineering Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Rakesh Mogul
- Chemistry and Biochemistry Department, Cal Poly Pomona, Pomona, California, USA
| | - Kevin H Baines
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - Charles Cockell
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, Scotland
| | - James A Cutts
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Diana M Gentry
- NASA Ames Research Center, Moffett Field, California, USA
| | | | - James W Head
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, Rhode Island, USA
| | | | - Vladimir Kompanichenko
- Institute for Complex Analysis of Regional Problems, Russian Academy of Sciences, Birobidzhan, Russia
| | - Yeon Joo Lee
- Zentrum für Astronomie und Astrophysik, Technical University of Berlin, Berlin, Germany
| | - Richard Mathies
- Chemistry Department and Space Sciences Lab, University of California, Berkeley, Berkeley, California, USA
| | - Tetyana Milojevic
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Rosalyn A Pertzborn
- Space Science and Engineering Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Satoshi Sasaki
- School of Health Sciences, Tokyo University of Technology, Hachioji, Japan
| | - Dirk Schulze-Makuch
- Center for Astronomy and Astrophysics (ZAA), Technische Universität Berlin, Berlin, Germany
- German Research Centre for Geosciences (GFZ), Potsdam, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
| | - David J Smith
- NASA Ames Research Center, Moffett Field, California, USA
| | - Michael J Way
- NASA Goddard Institute for Space Studies, New York, New York, USA
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Zhang Y, Thompson KN, Branck T, Yan Yan, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci 2021; 4:279-311. [PMID: 34465175 DOI: 10.1146/annurev-biodatasci-031121-103035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.
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Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Tobyn Branck
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Yan
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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Possibilities for an Aerial Biosphere in Temperate Sub Neptune-Sized Exoplanet Atmospheres. UNIVERSE 2021. [DOI: 10.3390/universe7060172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The search for signs of life through the detection of exoplanet atmosphere biosignature gases is gaining momentum. Yet, only a handful of rocky exoplanet atmospheres are suitable for observation with planned next-generation telescopes. To broaden prospects, we describe the possibilities for an aerial, liquid water cloud-based biosphere in the atmospheres of sub Neptune-sized temperate exoplanets, those receiving Earth-like irradiation from their host stars. One such planet is known (K2-18b) and other candidates are being followed up. Sub Neptunes are common and easier to study observationally than rocky exoplanets because of their larger sizes, lower densities, and extended atmospheres or envelopes. Yet, sub Neptunes lack any solid surface as we know it, so it is worthwhile considering whether their atmospheres can support an aerial biosphere. We review, synthesize, and build upon existing research. Passive microbial-like life particles must persist aloft in a region with liquid water clouds for long enough to metabolize, reproduce, and spread before downward transport to lower altitudes that may be too hot for life of any kind to survive. Dynamical studies are needed to flesh out quantitative details of life particle residence times. A sub Neptune would need to be a part of a planetary system with an unstable asteroid belt in order for meteoritic material to provide nutrients, though life would also need to efficiently reuse and recycle metals. The origin of life may be the most severe limiting challenge. Regardless of the uncertainties, we can keep an open mind to the search for biosignature gases as a part of general observational studies of sub Neptune exoplanets.
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Schulze-Makuch D. The Case (or Not) for Life in the Venusian Clouds. Life (Basel) 2021; 11:255. [PMID: 33804625 PMCID: PMC8003671 DOI: 10.3390/life11030255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 01/04/2023] Open
Abstract
The possible detection of the biomarker of phosphine as reported by Greaves et al. in the Venusian atmosphere stirred much excitement in the astrobiology community. While many in the community are adamant that the environmental conditions in the Venusian atmosphere are too extreme for life to exist, others point to the claimed detection of a convincing biomarker, the conjecture that early Venus was doubtlessly habitable, and any Venusian life might have adapted by natural selection to the harsh conditions in the Venusian clouds after the surface became uninhabitable. Here, I first briefly characterize the environmental conditions in the lower Venusian atmosphere and outline what challenges a biosphere would face to thrive there, and how some of these obstacles for life could possibly have been overcome. Then, I discuss the significance of the possible detection of phosphine and what it means (and does not mean) and provide an assessment on whether life may exist in the temperate cloud layer of the Venusian atmosphere or not.
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Affiliation(s)
- Dirk Schulze-Makuch
- Astrobiology Research Group, Center for Astronomy and Astrophysics (ZAA), Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany; ; Tel.: +49-30-314-23736
- German Research Centre for Geosciences (GFZ), Section Geomicrobiology, 14473 Potsdam, Germany
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, (IGB), 12587 Stechlin, Germany
- School of the Environment, Washington State University, Pullman, WA 99163, USA
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Rai S, Singh DK, Kumar A. Microbial, environmental and anthropogenic factors influencing the indoor microbiome of the built environment. J Basic Microbiol 2021; 61:267-292. [PMID: 33522603 DOI: 10.1002/jobm.202000575] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/03/2021] [Accepted: 01/10/2021] [Indexed: 12/25/2022]
Abstract
A built environment is a human-made environment providing surroundings for human occupancy, activities, and settlement. It is supposed to safeguard humans from all undesirable and harmful pollutants; however, indoor concentrations of some pollutants are much greater than that of the outdoors. Bioaerosols infiltrate from the outdoors in addition to many indoor sources of bioaerosols including the use of various chemicals as well as activities like cooking, smoking, cleaning, or even normal movement. They are also associated with a number of serious health concerns. Various ecological factors associated with the generation, the persistence as well as the dispersal of these microbial components of indoor bioaerosols, are discussed in this review, that have not been considered all together till now. The factors like microbial taxa, environmental factors, and anthropogenic activities (human occupancy, activities, and impact of urbanization) are addressed in the review. Effects of both indoor environmental factors like architectural design, lighting, ventilation, temperature, humidity, indoor/outdoor ratio, particulate matter, indoor chemistry as well as outdoor environmental factors like geography, seasons, and meteorology on the microbial concentrations have been discussed. Efforts are underway to design selective pressures for microbes to create a healthy symbiotic built microbiome as the "right" indoor microbiome is a "healthy" indoor microbiome.
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Affiliation(s)
- Sandhya Rai
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Dileep K Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Amod Kumar
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi, India
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Niu M, Zhou F, Yang Y, Sun Y, Zhu T, Shen F. Abundance and composition of airborne archaea during springtime mixed dust and haze periods in Beijing, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 752:141641. [PMID: 32892037 DOI: 10.1016/j.scitotenv.2020.141641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/09/2020] [Accepted: 08/09/2020] [Indexed: 05/21/2023]
Abstract
Archaea have an important role in the elemental biogeochemical cycle and human health. However, characteristics of airborne archaea affected by anthropogenic and natural processes are unclear. In this study, we investigated the abundance, structures, influencing factors and assembly processes of the archaeal communities in the air samples collected from Beijing in springtime using quantitative polymerase chain reaction (qPCR), high-throughput sequencing technology and statistical analysis. The concentrations of airborne archaea ranged from 101 to 103 copies m-3 (455 ± 211 copies m-3), accounting for 0.67% of the total prokaryote (sum of archaea and bacteria). An increase in airborne archaea was seen when the air quality shifted from clean to slightly polluted conditions. Sandstorm dust imported a large number of archaea to the local atmosphere. Euryarchaeota, Thaumarchaeota and Crenarchaeota were the dominant phyla, revealing the primary role of soil in releasing archaea to the ambient environment. Dispersal-related neutral processes play an important role in shaping the structure of airborne archaeal assembly. Of all phyla, methanogenic Euryarchaeota were most abundant in the air parcels come from the south of Beijing. Air masses from the west of Beijing, which brought sandstorm to Beijing, carried large amounts of ammonia oxidizing archaea Nitrososphaera. The results demonstrate the importance of air mass sources and local weather conditions in shaping the local airborne archaea community.
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Affiliation(s)
- Mutong Niu
- School of Space and Environment, Beihang University, Beijing 102206, China.
| | - Feng Zhou
- School of Space and Environment, Beihang University, Beijing 102206, China.
| | - Yi Yang
- School of Space and Environment, Beihang University, Beijing 102206, China.
| | - Ye Sun
- School of Space and Environment, Beihang University, Beijing 102206, China.
| | - Tianle Zhu
- School of Space and Environment, Beihang University, Beijing 102206, China.
| | - Fangxia Shen
- School of Space and Environment, Beihang University, Beijing 102206, China.
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Cyanobacteria and Algae in Clouds and Rain in the Area of puy de Dôme, Central France. Appl Environ Microbiol 2020; 87:AEM.01850-20. [PMID: 33097513 DOI: 10.1128/aem.01850-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/10/2020] [Indexed: 01/04/2023] Open
Abstract
The atmosphere contains diverse living microbes, of which the heterotrophic community has been the best studied. Microbes with other trophic modes, such as photoautotrophy, have received much less attention. In this study, culture-independent and dependent methods were used to examine the presence and diversity of oxygenic photoautotrophic microbes in clouds and rain collected at or around puy de Dôme Mountain, central France. Cloud water was collected from the summit of puy de Dôme (1,465 m above sea level [a.s.l.]) for cultivation and metagenomic analysis. Cyanobacteria, diatoms, green algae, and other oxygenic photoautotrophs were found to be recurrent members of clouds, while green algae affiliated with the Chlorellaceae were successfully cultured from three different clouds. Additionally, rain samples were collected below the mountain from Opme meteorological station (680 m a.s.l.). The abundance of chlorophyll a-containing cells and the diversity of cyanobacteria and green algae in rain were assessed by flow cytometry and amplicon sequencing. The corresponding downward flux of chlorophyll a-containing organisms to the ground, entering surface ecosystems with rain, varied with time and was estimated to be between ∼1 and >300 cells cm-2 day-1 during the sampling period. Besides abundant pollen from Pinales and Rosales, cyanobacteria of the Chroococcidiopsidales and green algae of the Trebouxiales were dominant in rain samples. Certain members of these taxa are known to be ubiquitous and stress tolerant and could use the atmosphere for dispersal. Overall, our results indicate that the atmosphere carries diverse, viable oxygenic photoautotrophic microbes and acts as a dispersal vector for this microbial guild.IMPORTANCE Information regarding the diversity and abundance of oxygenic photoautotrophs in the atmosphere is limited. More information from diverse locations is needed. These airborne organisms could have important impacts upon atmospheric processes and on the ecosystems they enter after deposition. Oxygenic photoautotrophic microbes are integral to ecosystem functioning, and some have the potential to affect human health. A better understanding of the diversity and the movements of these aeolian dispersed organisms is needed to understand their ecology, as well as how they could affect ecosystems and human health.
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Abstract
Most definitions of life assume that, at a minimum, life is a physical form of matter distinct from its environment at a lower state of entropy than its surroundings, using energy from the environment for internal maintenance and activity, and capable of autonomous reproduction. These assumptions cover all of life as we know it, though more exotic entities can be envisioned, including organic forms with novel biochemistries, dynamic inorganic matter, and self-replicating machines. The probability that any particular form of life will be found on another planetary body depends on the nature and history of that alien world. So the biospheres would likely be very different on a rocky planet with an ice-covered global ocean, a barren planet devoid of surface liquid, a frigid world with abundant liquid hydrocarbons, on a rogue planet independent of a host star, on a tidally locked planet, on super-Earths, or in long-lived clouds in dense atmospheres. While life at least in microbial form is probably pervasive if rare throughout the Universe, and technologically advanced life is likely much rarer, the chance that an alternative form of life, though not intelligent life, could exist and be detected within our Solar System is a distinct possibility.
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Baltrus DA. Bacterial dispersal and biogeography as underappreciated influences on phytobiomes. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:37-46. [PMID: 32278259 DOI: 10.1016/j.pbi.2020.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 06/11/2023]
Abstract
Bacterial strains are not distributed evenly throughout the environment. Here I explore how differential distribution and dispersal patterns of bacteria could affect interactions and coevolutionary dynamics with plants, and highlight ways that variation could be taken advantage of to develop robust and effective microbial consortia to inoculate crops. Questions about biogeographical patterns in viruses, fungi, and other eukaryotes are equally as prevalent and important for agriculture, and are in some cases more thoroughly explored. For simplicity as well as to bring attention to bacterial biogeography and dispersal in the context of plant interactions, I focus solely on bacterial patterns and questions for this article. The next few years will no doubt bring great advances in our understanding of dispersal capabilities and population dynamics for many plant-associated bacteria, and one of the next looming challenges will be learning to harvest this diversity in ways that can benefit agriculture.
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Affiliation(s)
- David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson AZ, USA; School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson AZ, USA.
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33
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Classification of Clouds Sampled at the Puy de Dôme Station (France) Based on Chemical Measurements and Air Mass History Matrices. ATMOSPHERE 2020. [DOI: 10.3390/atmos11070732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A statistical analysis of 295 cloud samples collected at the Puy de Dôme station in France (PUY), covering the period 2001–2018, was conducted using principal component analysis (PCA), agglomerative hierarchical clustering (AHC), and partial least squares (PLS) regression. Our model classified the cloud water samples on the basis of their chemical concentrations and of the dynamical history of their air masses estimated with back-trajectory calculations. The statistical analysis split our dataset into two sets, i.e., the first set characterized by westerly air masses and marine characteristics, with high concentrations of sea salts and the second set having air masses originating from the northeastern sector and the “continental” zone, with high concentrations of potentially anthropogenic ions. It appears from our dataset that the influence of cloud microphysics remains minor at PUY as compared with the impact of the air mass history, i.e., physicochemical processes, such as multiphase reactivity.
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Lang-Yona N, Öztürk F, Gat D, Aktürk M, Dikmen E, Zarmpas P, Tsagkaraki M, Mihalopoulos N, Birgül A, Kurt-Karakuş PB, Rudich Y. Links between airborne microbiome, meteorology, and chemical composition in northwestern Turkey. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 725:138227. [PMID: 32302827 DOI: 10.1016/j.scitotenv.2020.138227] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 05/28/2023]
Abstract
The composition of atmospheric aerosols is dynamic and influenced by their emission sources, organic and inorganic composition, transport pathways, chemical and physical processes, microorganisms' content and more. Characterization of such factors can improve the ability to evaluate air quality and health risks under different atmospheric scenarios. Here we investigate the microbial composition of the atmospheric particulate matter (<10 μm; PM10), sampled in Bolu, Turkey, and the linkage to the chemical composition changes, and different environmental factors. We show distinct differences between aerosol composition of different sources and air-mass transport patterns, sampled in July-August 2017 and in February 2018. The summer samples had a typical northern component air mass trajectories and higher local wind speed. They were characterized by high PM10 levels, marine and mineral dust tracers and high relative abundance of Ascomycota, suggesting long-range transport of the particles from remote sources. In contrast, samples collected in February were characterized by a dominant contribution of southern air masses, and low wind speed. They had low PM10 values, higher relative abundance of antibiotic resistance genes and anthropogenic ions related to local industries and farming, suggesting a dominance of local sources. With the microbiome analyses reported here for the first time for this region, we show good agreement between airborne microbial composition, aerosol mass load, chemistry, and meteorology. These results allow better air quality evaluation and prediction capabilities.
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Affiliation(s)
- Naama Lang-Yona
- Plant and Environmental Science Department, Weizmann Institute for Science, Rehovot, Israel.
| | - Fatma Öztürk
- Environmental Engineering Department, Bolu Abant İzzet Baysal University, Golkoy Campus, 14030 Bolu, Turkey.
| | - Daniella Gat
- Earth and Planetary Science Department, Weizmann Institute for Science, Rehovot, Israel
| | - Merve Aktürk
- Environmental Engineering Department, Bolu Abant İzzet Baysal University, Golkoy Campus, 14030 Bolu, Turkey
| | - Emre Dikmen
- Environmental Engineering Department, Bolu Abant İzzet Baysal University, Golkoy Campus, 14030 Bolu, Turkey
| | - Pavlos Zarmpas
- Department of Chemistry, University of Crete, P.O. Box 2208, 71003, Voutes, Heraklion, Greece
| | - Maria Tsagkaraki
- Department of Chemistry, University of Crete, P.O. Box 2208, 71003, Voutes, Heraklion, Greece
| | - Nikolaos Mihalopoulos
- Department of Chemistry, University of Crete, P.O. Box 2208, 71003, Voutes, Heraklion, Greece
| | - Aşkın Birgül
- Department of Environmental Engineering, Bursa Technical University, 16310 Bursa, Turkey
| | | | - Yinon Rudich
- Earth and Planetary Science Department, Weizmann Institute for Science, Rehovot, Israel.
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Tignat-Perrier R, Dommergue A, Thollot A, Magand O, Amato P, Joly M, Sellegri K, Vogel TM, Larose C. Seasonal shift in airborne microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:137129. [PMID: 32044476 DOI: 10.1016/j.scitotenv.2020.137129] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 05/23/2023]
Abstract
Microorganisms are ubiquitous in the atmosphere. Global investigations on the geographical and temporal distribution of airborne microbial communities are critical for identifying the sources and the factors shaping airborne communities. At mid-latitude sites, a seasonal shift in both the concentration and diversity of airborne microbial communities has been systematically observed in the planetary boundary layer. While the factors suspected of affecting this seasonal change were hypothesized (e.g., changes in the surface conditions, meteorological parameters and global air circulation), our understanding on how these factors influence the temporal variation of airborne microbial communities, especially at the microbial taxon level, remains limited. Here, we investigated the distribution of both airborne bacterial and fungal communities on a weekly basis over more than one year at the mid-latitude and continental site of puy de Dôme (France; +1465 m altitude above sea level). The seasonal shift in microbial community structure was likely correlated to the seasonal changes in the characteristics of puy de Dôme's landscape (croplands and natural vegetation). The airborne microbial taxa that were the most affected by seasonal changes trended differently throughout the seasons in relation with their trophic mode. In addition, the windy and variable local meteorological conditions found at puy de Dôme were likely responsible for the intraseasonal variability observed in the composition of airborne microbial communities.
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Affiliation(s)
- Romie Tignat-Perrier
- Institut des Géosciences de l'Environnement, Université Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France; Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France.
| | - Aurélien Dommergue
- Institut des Géosciences de l'Environnement, Université Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Alban Thollot
- Institut des Géosciences de l'Environnement, Université Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Olivier Magand
- Institut des Géosciences de l'Environnement, Université Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand, CNRS UMR 6096 Université Clermont Auvergne-Sigma, Clermont-Ferrand, France
| | - Muriel Joly
- Institut de Chimie de Clermont-Ferrand, CNRS UMR 6096 Université Clermont Auvergne-Sigma, Clermont-Ferrand, France
| | - Karine Sellegri
- Institut de Chimie de Clermont-Ferrand, CNRS UMR 6096 Université Clermont Auvergne-Sigma, Clermont-Ferrand, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France
| | - Catherine Larose
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France
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Uritskiy G, Tisza MJ, Gelsinger DR, Munn A, Taylor J, DiRuggiero J. Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community. Environ Microbiol 2020; 23:3401-3417. [DOI: 10.1111/1462-2920.15023] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/12/2020] [Indexed: 02/03/2023]
Affiliation(s)
- Gherman Uritskiy
- Department of Biology Johns Hopkins University Baltimore MD 21218 USA
| | - Michael J. Tisza
- Department of Biology Johns Hopkins University Baltimore MD 21218 USA
- Laboratory of Cellular Oncology NCI, NIH Bethesda MD 20892‐4263 USA
| | | | - Adam Munn
- Department of Biology Johns Hopkins University Baltimore MD 21218 USA
| | - James Taylor
- Department of Biology Johns Hopkins University Baltimore MD 21218 USA
- Department of Computer Science Johns Hopkins University Baltimore MD 21218 USA
| | - Jocelyne DiRuggiero
- Department of Biology Johns Hopkins University Baltimore MD 21218 USA
- Department of Earth and Planetary Sciences Johns Hopkins University Baltimore MD 21218 USA
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Metabolic modulations of Pseudomonas graminis in response to H 2O 2 in cloud water. Sci Rep 2019; 9:12799. [PMID: 31488860 PMCID: PMC6728378 DOI: 10.1038/s41598-019-49319-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/26/2019] [Indexed: 12/26/2022] Open
Abstract
In cloud water, microorganisms are exposed to very strong stresses especially related to the presence of reactive oxygen species including H2O2 and radicals, which are the driving force of cloud chemistry. In order to understand how the bacterium Pseudomonas graminis isolated from cloud water respond to this oxidative stress, it was incubated in microcosms containing a synthetic solution of cloud water in the presence or in the absence of H2O2. P. graminis metabolome was examined by LC-MS and NMR after 50 min and after 24 hours of incubation. After 50 min, the cells were metabolizing H2O2 while this compound was still present in the medium, and it was completely biodegraded after 24 hours. Cells exposed to H2O2 had a distinct metabolome as compared to unexposed cells, revealing modulations of certain metabolic pathways in response to oxidative stress. These data indicated that the regulations observed mainly involved carbohydrate, glutathione, energy, lipid, peptides and amino-acids metabolisms. When cells had detoxified H2O2 from the medium, their metabolome was not distinguishable anymore from unexposed cells, highlighting the capacity of resilience of this bacterium. This work illustrates the interactions existing between the cloud microbial metabolome and cloud chemistry.
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