Articles | Volume 22, issue 5
https://doi.org/10.5194/bg-22-1257-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-22-1257-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
06 Mar 2025
Research article |
| 06 Mar 2025
| 06 Mar 2025
Clouds influence the functioning of airborne microorganisms
Raphaëlle Péguilhan
Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
now at: Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
Florent Rossi
Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
now at: Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
Muriel Joly
Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Engy Nasr
Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
Bérénice Batut
Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
now at: Institut Français de Bioinformatique, CNRS UAR 3601, France, and Mésocentre Clermont-Auvergne, Université Clermont Auvergne, Aubiere, France
François Enault
Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement (LMGE), 63000 Clermont-Ferrand, France
Barbara Ervens
Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement (LMGE), 63000 Clermont-Ferrand, France
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EGUsphere, https://doi.org/10.5194/egusphere-2025-419, https://doi.org/10.5194/egusphere-2025-419, 2025
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Over the past two decades, the European Geosciences Union (EGU) has demonstrated the success, viability and benefits of interactive open access (OA) publishing with public peer review in its journals, its publishing platform EGUsphere and virtual compilations. The article summarizes the evolution of the EGU/Copernicus publications and of OA publishing with interactive public peer review at large by placing the EGU/Copernicus publications in the context of current and future global open science.
Barbara Ervens, Pierre Amato, Kifle Aregahegn, Muriel Joly, Amina Khaled, Tiphaine Labed-Veydert, Frédéric Mathonat, Leslie Nuñez López, Raphaëlle Péguilhan, and Minghui Zhang
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Atmospheric microorganisms are a small fraction of Earth's microbiome, with bacteria being a significant part. Aerosolized bacteria are airborne for a few days, encountering unique chemical and physical conditions affecting stress levels and survival. We explore chemical and microphysical conditions bacteria encounter, highlighting potential nutrient and oxidant limitations and diverse effects by pollutants, which may ultimately impact the microbiome's role in global ecosystems and biodiversity.
Barbara Ervens, Andrew Rickard, Bernard Aumont, William P. L. Carter, Max McGillen, Abdelwahid Mellouki, John Orlando, Bénédicte Picquet-Varrault, Paul Seakins, William R. Stockwell, Luc Vereecken, and Timothy J. Wallington
Atmos. Chem. Phys., 24, 13317–13339, https://doi.org/10.5194/acp-24-13317-2024, https://doi.org/10.5194/acp-24-13317-2024, 2024
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Chemical mechanisms describe the chemical processes in atmospheric models that are used to describe the changes in the atmospheric composition. Therefore, accurate chemical mechanisms are necessary to predict the evolution of air pollution and climate change. The article describes all steps that are needed to build chemical mechanisms and discusses the advances and needs of experimental and theoretical research activities needed to build reliable chemical mechanisms.
Leslie Nuñez López, Pierre Amato, and Barbara Ervens
Atmos. Chem. Phys., 24, 5181–5198, https://doi.org/10.5194/acp-24-5181-2024, https://doi.org/10.5194/acp-24-5181-2024, 2024
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Living bacteria comprise a small particle fraction in the atmosphere. Our model study shows that atmospheric bacteria in clouds may efficiently biodegrade formic and acetic acids that affect the acidity of rain. We conclude that current atmospheric models underestimate losses of these acids as they only consider chemical processes. We suggest that biodegradation can affect atmospheric concentration not only of formic and acetic acids but also of other volatile, moderately soluble organics.
Maud Leriche, Pierre Tulet, Laurent Deguillaume, Frédéric Burnet, Aurélie Colomb, Agnès Borbon, Corinne Jambert, Valentin Duflot, Stéphan Houdier, Jean-Luc Jaffrezo, Mickaël Vaïtilingom, Pamela Dominutti, Manon Rocco, Camille Mouchel-Vallon, Samira El Gdachi, Maxence Brissy, Maroua Fathalli, Nicolas Maury, Bert Verreyken, Crist Amelynck, Niels Schoon, Valérie Gros, Jean-Marc Pichon, Mickael Ribeiro, Eric Pique, Emmanuel Leclerc, Thierry Bourrianne, Axel Roy, Eric Moulin, Joël Barrie, Jean-Marc Metzger, Guillaume Péris, Christian Guadagno, Chatrapatty Bhugwant, Jean-Mathieu Tibere, Arnaud Tournigand, Evelyn Freney, Karine Sellegri, Anne-Marie Delort, Pierre Amato, Muriel Joly, Jean-Luc Baray, Pascal Renard, Angelica Bianco, Anne Réchou, and Guillaume Payen
Atmos. Chem. Phys., 24, 4129–4155, https://doi.org/10.5194/acp-24-4129-2024, https://doi.org/10.5194/acp-24-4129-2024, 2024
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Aerosol particles in the atmosphere play a key role in climate change and air pollution. A large number of aerosol particles are formed from the oxidation of volatile organic compounds (VOCs and secondary organic aerosols – SOA). An important field campaign was organized on Réunion in March–April 2019 to understand the formation of SOA in a tropical atmosphere mostly influenced by VOCs emitted by forest and in the presence of clouds. This work synthesizes the results of this campaign.
Amina Khaled, Minghui Zhang, and Barbara Ervens
Atmos. Chem. Phys., 22, 1989–2009, https://doi.org/10.5194/acp-22-1989-2022, https://doi.org/10.5194/acp-22-1989-2022, 2022
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Chemical reactions with iron in clouds and aerosol form and cycle reactive oxygen species (ROS). Previous model studies assumed that all cloud droplets (particles) contain iron, while single-particle analyses showed otherwise. By means of a model, we explore the bias in predicted ROS budgets by distributing a given iron mass to either all or only a few droplets (particles). Implications for oxidation potential, radical loss and iron oxidation state are discussed.
Pamela A. Dominutti, Pascal Renard, Mickaël Vaïtilingom, Angelica Bianco, Jean-Luc Baray, Agnès Borbon, Thierry Bourianne, Frédéric Burnet, Aurélie Colomb, Anne-Marie Delort, Valentin Duflot, Stephan Houdier, Jean-Luc Jaffrezo, Muriel Joly, Martin Leremboure, Jean-Marc Metzger, Jean-Marc Pichon, Mickaël Ribeiro, Manon Rocco, Pierre Tulet, Anthony Vella, Maud Leriche, and Laurent Deguillaume
Atmos. Chem. Phys., 22, 505–533, https://doi.org/10.5194/acp-22-505-2022, https://doi.org/10.5194/acp-22-505-2022, 2022
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We present here the results obtained during an intensive field campaign conducted in March to April 2019 in Reunion. Our study integrates a comprehensive chemical and microphysical characterization of cloud water. Our investigations reveal that air mass history and cloud microphysical properties do not fully explain the variability observed in their chemical composition. This highlights the complexity of emission sources, multiphasic exchanges, and transformations in clouds.
Ramon Campos Braga, Barbara Ervens, Daniel Rosenfeld, Meinrat O. Andreae, Jan-David Förster, Daniel Fütterer, Lianet Hernández Pardo, Bruna A. Holanda, Tina Jurkat-Witschas, Ovid O. Krüger, Oliver Lauer, Luiz A. T. Machado, Christopher Pöhlker, Daniel Sauer, Christiane Voigt, Adrian Walser, Manfred Wendisch, Ulrich Pöschl, and Mira L. Pöhlker
Atmos. Chem. Phys., 21, 17513–17528, https://doi.org/10.5194/acp-21-17513-2021, https://doi.org/10.5194/acp-21-17513-2021, 2021
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Interactions of aerosol particles with clouds represent a large uncertainty in estimates of climate change. Properties of aerosol particles control their ability to act as cloud condensation nuclei. Using aerosol measurements in the Amazon, we performed model studies to compare predicted and measured cloud droplet number concentrations at cloud bases. Our results confirm previous estimates of particle hygroscopicity in this region.
Soleil E. Worthy, Anand Kumar, Yu Xi, Jingwei Yun, Jessie Chen, Cuishan Xu, Victoria E. Irish, Pierre Amato, and Allan K. Bertram
Atmos. Chem. Phys., 21, 14631–14648, https://doi.org/10.5194/acp-21-14631-2021, https://doi.org/10.5194/acp-21-14631-2021, 2021
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We studied the effect of (NH4)2SO4 on the immersion freezing of non-mineral dust ice-nucleating substances (INSs) and mineral dusts. (NH4)2SO4 had no effect on the median freezing temperature of 9 of the 10 tested non-mineral dust INSs, slightly decreased that of the other, and increased that of all the mineral dusts. The difference in the response of mineral dust and non-mineral dust INSs to (NH4)2SO4 suggests that they nucleate ice and/or interact with (NH4)2SO4 via different mechanisms.
Ramon Campos Braga, Daniel Rosenfeld, Ovid O. Krüger, Barbara Ervens, Bruna A. Holanda, Manfred Wendisch, Trismono Krisna, Ulrich Pöschl, Meinrat O. Andreae, Christiane Voigt, and Mira L. Pöhlker
Atmos. Chem. Phys., 21, 14079–14088, https://doi.org/10.5194/acp-21-14079-2021, https://doi.org/10.5194/acp-21-14079-2021, 2021
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Quantifying the precipitation within clouds is crucial for our understanding of the Earth's hydrological cycle. Using in situ measurements of cloud and rain properties over the Amazon Basin and Atlantic Ocean, we show here a linear relationship between the effective radius (re) and precipitation water content near the tops of convective clouds for different pollution states and temperature levels. Our results emphasize the role of re to determine both initiation and amount of precipitation.
Mira L. Pöhlker, Minghui Zhang, Ramon Campos Braga, Ovid O. Krüger, Ulrich Pöschl, and Barbara Ervens
Atmos. Chem. Phys., 21, 11723–11740, https://doi.org/10.5194/acp-21-11723-2021, https://doi.org/10.5194/acp-21-11723-2021, 2021
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Clouds cool our atmosphere. The role of small aerosol particles in affecting them represents one of the largest uncertainties in current estimates of climate change. Traditionally it is assumed that cloud droplets only form particles of diameters ~ 100 nm (
accumulation mode). Previous studies suggest that this can also occur in smaller particles (
Aitken mode). Our study provides a general framework to estimate under which aerosol and cloud conditions Aitken mode particles affect clouds.
Minghui Zhang, Amina Khaled, Pierre Amato, Anne-Marie Delort, and Barbara Ervens
Atmos. Chem. Phys., 21, 3699–3724, https://doi.org/10.5194/acp-21-3699-2021, https://doi.org/10.5194/acp-21-3699-2021, 2021
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Although primary biological aerosol particles (PBAPs, bioaerosols) represent a small fraction of total atmospheric aerosol burden, they might affect climate and public health. We summarize which PBAP properties are important to affect their inclusion in clouds and interaction with light and might also affect their residence time and transport in the atmosphere. Our study highlights that not only chemical and physical but also biological processes can modify these physicochemical properties.
Amina Khaled, Minghui Zhang, Pierre Amato, Anne-Marie Delort, and Barbara Ervens
Atmos. Chem. Phys., 21, 3123–3141, https://doi.org/10.5194/acp-21-3123-2021, https://doi.org/10.5194/acp-21-3123-2021, 2021
Saly Jaber, Muriel Joly, Maxence Brissy, Martin Leremboure, Amina Khaled, Barbara Ervens, and Anne-Marie Delort
Biogeosciences, 18, 1067–1080, https://doi.org/10.5194/bg-18-1067-2021, https://doi.org/10.5194/bg-18-1067-2021, 2021
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Our study is of interest to atmospheric scientists and environmental microbiologists, as we show that clouds can be considered a medium where bacteria efficiently degrade and transform amino acids, in competition with chemical processes. As current atmospheric multiphase models are restricted to chemical degradation of organic compounds, our conclusions motivate further model development.
Cited articles
Amato, P., Demeer, F., Melaouhi, A., Fontanella, S., Martin-Biesse, A.-S., Sancelme, M., Laj, P., and Delort, A.-M.: A fate for organic acids, formaldehyde and methanol in cloud water: their biotransformation by micro-organisms, Atmos. Chem. Phys., 7, 4159–4169, https://doi.org/10.5194/acp-7-4159-2007, 2007a.
Amato, P., Parazols, M., Sancelme, M., Laj, P., Mailhot, G., and Delort, A.-M.: Microorganisms isolated from the water phase of tropospheric clouds at the Puy de Dôme: major groups and growth abilities at low temperatures, FEMS Microbiol. Ecol., 59, 242–254, https://doi.org/10.1111/j.1574-6941.2006.00199.x, 2007b.
Amato, P., Joly, M., Schaupp, C., Attard, E., Möhler, O., Morris, C. E., Brunet, Y., and Delort, A.-M.: Survival and ice nucleation activity of bacteria as aerosols in a cloud simulation chamber, Atmos. Chem. Phys., 15, 6455–6465, https://doi.org/10.5194/acp-15-6455-2015, 2015.
Amato, P., Joly, M., Besaury, L., Oudart, A., Taib, N., Moné, A. I., Deguillaume, L., Delort, A.-M., and Debroas, D.: Active microorganisms thrive among extremely diverse communities in cloud water, PloS one, 12, e0182869, https://doi.org/10.1371/journal.pone.0182869, 2017.
Amato, P., Besaury, L., Joly, M., Penaud, B., Deguillaume, L., and Delort, A.-M.: Metatranscriptomic exploration of microbial functioning in clouds, Sci. Rep.-UK, 9, 4383, https://doi.org/10.1038/s41598-019-41032-4, 2019.
Amato, P., Mathonat, F., Nuñez Lopez, L., Péguilhan, R., Bourhane, Z., Rossi, F., Vyskocil, J., Joly, M., and Ervens, B.: The aeromicrobiome: the selective and dynamic outer-layer of the Earth's microbiome, Front. Microbiol., 14, 1186847, https://doi.org/10.3389/fmicb.2023.1186847, 2023.
Baldrian, P., Kolařík, M., Stursová, M., Kopecký, J., Valášková, V., Větrovský, T., Zifčáková, L., Snajdr, J., Rídl, J., Vlček, C., and Voříšková, J.: Active and total microbial communities in forest soil are largely different and highly stratified during decomposition, ISME J., 6, 248–258, https://doi.org/10.1038/ismej.2011.95, 2012.
Baray, J.-L., Deguillaume, L., Colomb, A., Sellegri, K., Freney, E., Rose, C., Van Baelen, J., Pichon, J.-M., Picard, D., Fréville, P., Bouvier, L., Ribeiro, M., Amato, P., Banson, S., Bianco, A., Borbon, A., Bourcier, L., Bras, Y., Brigante, M., Cacault, P., Chauvigné, A., Charbouillot, T., Chaumerliac, N., Delort, A.-M., Delmotte, M., Dupuy, R., Farah, A., Febvre, G., Flossmann, A., Gourbeyre, C., Hervier, C., Hervo, M., Huret, N., Joly, M., Kazan, V., Lopez, M., Mailhot, G., Marinoni, A., Masson, O., Montoux, N., Parazols, M., Peyrin, F., Pointin, Y., Ramonet, M., Rocco, M., Sancelme, M., Sauvage, S., Schmidt, M., Tison, E., Vaïtilingom, M., Villani, P., Wang, M., Yver-Kwok, C., and Laj, P.: Cézeaux-Aulnat-Opme-Puy De Dôme: a multi-site for the long-term survey of the tropospheric composition and climate change, Atmos. Meas. Tech., 13, 3413–3445, https://doi.org/10.5194/amt-13-3413-2020, 2020.
Bianco, A., Voyard, G., Deguillaume, L., Mailhot, G., and Brigante, M.: Improving the characterization of dissolved organic carbon in cloud water: Amino acids and their impact on the oxidant capacity, Sci. Rep.-UK, 6, 37420, https://doi.org/10.1038/srep37420, 2016.
Bianco, A., Deguillaume, L., Vaïtilingom, M., Nicol, E., Baray, J.-L., Chaumerliac, N., and Bridoux, M.: Molecular characterization of cloud water Samples collected at the Puy de Dôme (France) by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Environ. Sci. Technol., 52, 10275–10285, https://doi.org/10.1021/acs.est.8b01964, 2018.
Bianco, A., Deguillaume, L., Chaumerliac, N., Vaïtilingom, M., Wang, M., Delort, A.-M., and Bridoux, M. C.: Effect of endogenous microbiota on the molecular composition of cloud water: a study by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), Sci. Rep.-UK, 9, 7663, https://doi.org/10.1038/s41598-019-44149-8, 2019.
Bowers, R. M., McLetchie, S., Knight, R., and Fierer, N.: Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments, ISME J., 5, 601–612, https://doi.org/10.1038/ismej.2010.167, 2011.
Bowers, R. M., Clements, N., Emerson, J. B., Wiedinmyer, C., Hannigan, M. P., and Fierer, N.: Seasonal variability in bacterial and fungal diversity of the near-surface atmosphere, Environ. Sci. Technol., 47, 12097–12106, https://doi.org/10.1021/es402970s, 2013.
Brown, J. K. M. and Hovmøller, M. S.: Aerial Dispersal of pathogens on the global and continental scales and its impact on plant disease, Science, 297, 537–541, https://doi.org/10.1126/science.1072678, 2002.
Buchfink, B., Xie, C., and Huson, D. H.: Fast and sensitive protein alignment using DIAMOND, Nat. Methods, 12, 59–60, https://doi.org/10.1038/nmeth.3176, 2015.
Burrows, S. M., Butler, T., Jöckel, P., Tost, H., Kerkweg, A., Pöschl, U., and Lawrence, M. G.: Bacteria in the global atmosphere – Part 2: Modeling of emissions and transport between different ecosystems, Atmos. Chem. Phys., 9, 9281–9297, https://doi.org/10.5194/acp-9-9281-2009, 2009.
Camacho-Sanchez, M., Burraco, P., Gomez-Mestre, I., and Leonard, J. A.: Preservation of RNA and DNA from mammal samples under field conditions, Mol. Ecol. Resour., 13, 663–673, https://doi.org/10.1111/1755-0998.12108, 2013.
Chen, L., Hu, M., Huang, L., Hua, Z., Kuang, J., Li, S., and Shu, W.: Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage, ISME J., 9, 1579–1592, https://doi.org/10.1038/ismej.2014.245, 2015.
Chen, Y.-J., Leung, P. M., Wood, J. L., Bay, S. K., Hugenholtz, P., Kessler, A. J., Shelley, G., Waite, D. W., Franks, A. E., Cook, P. L. M., and Greening, C.: Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem, ISME J., 15, 2986–3004, https://doi.org/10.1038/s41396-021-00988-w, 2021.
Chowdhury, N., Marschner, P., and Burns, R.: Response of microbial activity and community structure to decreasing soil osmotic and matric potential, Plant Soil, 344, 241–254, https://doi.org/10.1007/s11104-011-0743-9, 2011.
Cruz, C. N. and Pandis, S. N.: Deliquescence and hygroscopic growth of mixed inorganic–organic atmospheric aerosol, Environ. Sci. Technol., 34, 4313–4319, https://doi.org/10.1021/es9907109, 2000.
Dagan, G., Koren, I., Altaratz, O., and Lehahn, Y.: Shallow convective cloud field lifetime as a key factor for evaluating aerosol effects, iScience, 10, 192–202, https://doi.org/10.1016/j.isci.2018.11.032, 2018.
Dalton, D. A. and Kramer, S.: Nitrogen-fixing bacteria in non-legumes, in: Plant-Associated Bacteria, edited by: Gnanamanickam, S. S., Springer Netherlands, Dordrecht, 105–130, https://doi.org/10.1007/978-1-4020-4538-7_3, 2006.
Deguillaume, L., Charbouillot, T., Joly, M., Vaïtilingom, M., Parazols, M., Marinoni, A., Amato, P., Delort, A.-M., Vinatier, V., Flossmann, A., Chaumerliac, N., Pichon, J. M., Houdier, S., Laj, P., Sellegri, K., Colomb, A., Brigante, M., and Mailhot, G.: Classification of clouds sampled at the puy de Dôme (France) based on 10 yr of monitoring of their physicochemical properties, Atmos. Chem. Phys., 14, 1485–1506, https://doi.org/10.5194/acp-14-1485-2014, 2014.
Dillon, K. P., Correa, F., Judon, C., Sancelme, M., Fennell, D. E., Delort, A.-M., and Amato, P.: Cyanobacteria and algae in clouds and rain in the area of puy de Dôme, Central France, Appl. Environ. Microbiol., https://doi.org/10.1128/AEM.01850-20, 2020.
Ervens, B. and Amato, P.: The global impact of bacterial processes on carbon mass, Atmos. Chem. Phys., 20, 1777–1794, https://doi.org/10.5194/acp-20-1777-2020, 2020.
Ervens, B., Sorooshian, A., Aldhaif, A. M., Shingler, T., Crosbie, E., Ziemba, L., Campuzano-Jost, P., Jimenez, J. L., and Wisthaler, A.: Is there an aerosol signature of chemical cloud processing?, Atmos. Chem. Phys., 18, 16099–16119, https://doi.org/10.5194/acp-18-16099-2018, 2018.
Ervens, B., Amato, P., Aregahegn, K., Joly, M., Khaled, A., Labed-Veydert, T., Mathonat, F., Nuñez López, L., Péguilhan, R., and Zhang, M.: Ideas and perspectives: Microorganisms in the air through the lenses of atmospheric chemistry and microphysics, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2024-2377, 2024.
Feingold, G., Cotton, W. R., Stevens, B., and Frisch, A. S.: The Relationship between Drop In-Cloud Residence Time and Drizzle Production in Numerically Simulated Stratocumulus Clouds, J. Atmos. Sci., 53, 1108–1122, https://doi.org/10.1175/1520-0469(1996)053<1108:TRBDIC>2.0.CO;2, 1996.
Fierer, N., Liu, Z., Rodríguez-Hernández, M., Knight, R., Henn, M., and Hernandez, M. T.: Short-term temporal variability in airborne bacterial and fungal populations, Appl. Environ. Microbiol., 74, 200–207, https://doi.org/10.1128/AEM.01467-07, 2008.
Franzosa, E. A., Morgan, X. C., Segata, N., Waldron, L., Reyes, J., Earl, A. M., Giannoukos, G., Boylan, M. R., Ciulla, D., Gevers, D., Izard, J., Garrett, W. S., Chan, A. T., and Huttenhower, C.: Relating the metatranscriptome and metagenome of the human gut, P. Natl. Acad. Sci. USA, 111, E2329–E2338, https://doi.org/10.1073/pnas.1319284111, 2014.
Fuzzi, S., Mandrioli, P., and Perfetto, A.: Fog droplets – an atmospheric source of secondary biological aerosol particles, Atmos. Environ., 31, 287–290, https://doi.org/10.1016/1352-2310(96)00160-4, 1997.
Gray, D. A., Dugar, G., Gamba, P., Strahl, H., Jonker, M. J., and Hamoen, L. W.: Extreme slow growth as alternative strategy to survive deep starvation in bacteria, Nat. Commun., 10, 890, https://doi.org/10.1038/s41467-019-08719-8, 2019.
Griffiths, E. and Birch, H. F.: Microbiological Changes in Freshly Moistened Soil, Nature, 189, 424–424, https://doi.org/10.1038/189424a0, 1961.
Gusareva, E. S., Acerbi, E., Lau, K. J. X., Luhung, I., Premkrishnan, B. N. V., Kolundžija, S., Purbojati, R. W., Wong, A., Houghton, J. N. I., Miller, D., Gaultier, N. E., Heinle, C. E., Clare, M. E., Vettath, V. K., Kee, C., Lim, S. B. Y., Chénard, C., Phung, W. J., Kushwaha, K. K., Nee, A. P., Putra, A., Panicker, D., Yanqing, K., Hwee, Y. Z., Lohar, S. R., Kuwata, M., Kim, H. L., Yang, L., Uchida, A., Drautz-Moses, D. I., Junqueira, A. C. M., and Schuster, S. C.: Microbial communities in the tropical air ecosystem follow a precise diel cycle, P. Natl. Acad. Sci. USA, 116, 23299–23308, https://doi.org/10.1073/pnas.1908493116, 2019.
Herrmann, H., Schaefer, T., Tilgner, A., Styler, S. A., Weller, C., Teich, M., and Otto, T.: Tropospheric Aqueous-Phase Chemistry: Kinetics, mechanisms, and its coupling to a changing gas phase, Chem. Rev., 115, 4259–4334, https://doi.org/10.1021/cr500447k, 2015.
Hill, K. A., Shepson, P. B., Galbavy, E. S., Anastasio, C., Kourtev, P. S., Konopka, A., and Stirm, B. H.: Processing of atmospheric nitrogen by clouds above a forest environment, J. Geophys. Res., 112, D11301, https://doi.org/10.1029/2006JD008002, 2007.
Hoffmann, L., Günther, G., Li, D., Stein, O., Wu, X., Griessbach, S., Heng, Y., Konopka, P., Müller, R., Vogel, B., and Wright, J. S.: From ERA-Interim to ERA5: the considerable impact of ECMWF's next-generation reanalysis on Lagrangian transport simulations, Atmos. Chem. Phys., 19, 3097–3124, https://doi.org/10.5194/acp-19-3097-2019, 2019.
Jaber, S., Joly, M., Brissy, M., Leremboure, M., Khaled, A., Ervens, B., and Delort, A.-M.: Biotic and abiotic transformation of amino acids in cloud water: experimental studies and atmospheric implications, Biogeosciences, 18, 1067–1080, https://doi.org/10.5194/bg-18-1067-2021, 2021.
Jørgensen, R. N., Jørgensen, B. J., and Nielsen, N. E.: N2O emission immediately after rainfall in a dry stubble field, Soil. Biol. Biochem., 30, 545–546, https://doi.org/10.1016/S0038-0717(97)00144-2, 1998.
Jorth, P., Turner, K. H., Gumus, P., Nizam, N., Buduneli, N., and Whiteley, M.: Metatranscriptomics of the human oral microbiome during health and disease, mBio, 5, e01012-14, https://doi.org/10.1128/mBio.01012-14, 2014.
Jousse, C., Dalle, C., Canet, I., Lagrée, M., Traïkia, M., Lyan, B., Mendes, C., Sancelme, M., Amato, P., and Delort, A.-M.: Metabolomic study of the response to cold shock in a strain of Pseudomonas syringae isolated from cloud water, Metabolomics, 14, 11, https://doi.org/10.1007/s11306-017-1295-7, 2018.
Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M., and Ishiguro-Watanabe, M.: KEGG for taxonomy-based analysis of pathways and genomes, Nucleic Acids Res., 51, D587–D592, https://doi.org/10.1093/nar/gkac963, 2023.
Khaled, A., Zhang, M., Amato, P., Delort, A.-M., and Ervens, B.: Biodegradation by bacteria in clouds: an underestimated sink for some organics in the atmospheric multiphase system, Atmos. Chem. Phys., 21, 3123–3141, https://doi.org/10.5194/acp-21-3123-2021, 2021.
Klein, A. M., Bohannan, B. J. M., Jaffe, D. A., Levin, D. A., and Green, J. L.: Molecular evidence for metabolically active bacteria in the atmosphere, Front. Microbiol., 772, https://doi.org/10.3389/fmicb.2016.00772, 2016.
Koehler, K. A., Kreidenweis, S. M., DeMott, P. J., Prenni, A. J., Carrico, C. M., Ervens, B., and Feingold, G.: Water activity and activation diameters from hygroscopicity data – Part II: Application to organic species, Atmos. Chem. Phys., 6, 795–809, https://doi.org/10.5194/acp-6-795-2006, 2006.
Krumins, V., Mainelis, G., Kerkhof, L. J., and Fennell, D. E.: Substrate-dependent rRNA production in an airborne bacterium, Environ. Sci. Tech. Lett., 1, 376–381, https://doi.org/10.1021/ez500245y, 2014.
Kudla, B., Caddick, M. X., Langdon, T., Martinez-Rossi, N. M., Bennett, C. F., Sibley, S., Davies, R. W., and Arst Jr., H. N.: The regulatory gene areA mediating nitrogen metabolite repression in Aspergillus nidulans. Mutations affecting specificity of gene activation alter a loop residue of a putative zinc finger, EMBO J., 9, 1355, https://doi.org/10.1002/j.1460-2075.1990.tb08250.x, 1990.
Lelieveld, J. and Crutzen, P. J.: Influences of cloud photochemical processes on tropospheric ozone, Nature, 343, 227–233, https://doi.org/10.1038/343227a0, 1990.
Leroch, M., Kleber, A., Silva, E., Coenen, T., Koppenhöfer, D., Shmaryahu, A., Valenzuela, P. D. T., and Hahn, M.: Transcriptome profiling of Botrytis cinerea conidial germination reveals upregulation of infection-related genes during the prepenetration stage, Eukaryot. Cell., 12, 614–626, https://doi.org/10.1128/ec.00295-12, 2013.
Li, C., Jia, S., Rajput, S. A., Qi, D., and Wang, S.: Transcriptional Stages of Conidia Germination and Associated Genes in Aspergillus flavus: An Essential Role for Redox Genes, Toxins, 14, 560, https://doi.org/10.3390/toxins14080560, 2022.
Li, K., Guo, Y., Nizkorodov, S. A., Rudich, Y., Angelaki, M., Wang, X., An, T., Perrier, S., and George, C.: Spontaneous dark formation of OH radicals at the interface of aqueous atmospheric droplets, P. Natl. Acad. Sci. USA, 120, e2220228120, https://doi.org/10.1073/pnas.2220228120, 2023.
Li, W. and Godzik, A.: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, 22, 1658–1659, https://doi.org/10.1093/bioinformatics/btl158, 2006.
Menke, S., Gillingham, M. A. F., Wilhelm, K., and Sommer, S.: Home-made cost effective preservation buffer is a better alternative to commercial preservation methods for microbiome research, Front. Microbiol., 8, 102, https://doi.org/10.3389/fmicb.2017.00102, 2017.
Noguchi, H., Taniguchi, T., and Itoh, T.: MetaGeneAnnotator: Detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes, DNA Res., 15, 387–396, https://doi.org/10.1093/dnares/dsn027, 2008.
Nuñez López, L., Amato, P., and Ervens, B.: Bacteria in clouds biodegrade atmospheric formic and acetic acids, Atmos. Chem. Phys., 24, 5181–5198, https://doi.org/10.5194/acp-24-5181-2024, 2024.
Osherov, N. and May, G. S.: The molecular mechanisms of conidial germination, FEMS Microbiol. Lett., 199, 153–160, https://doi.org/10.1111/j.1574-6968.2001.tb10667.x, 2001.
Péguilhan, R.: Metatranscriptomic analysis of cloud and aerosol samples at puy de Dôme, France, ENA [data set], https://www.ebi.ac.uk/ena/browser/view/PRJEB54740 (last access: 4 March 2025), 2025.
Péguilhan, R., Besaury, L., Rossi, F., Enault, F., Baray, J.-L., Deguillaume, L., and Amato, P.: Rainfalls sprinkle cloud bacterial diversity while scavenging biomass, FEMS Microbiol. Ecol., 97, fiab144, https://doi.org/10.1093/femsec/fiab144, 2021.
Péguilhan, R., Rossi, F., Rué, O., Joly, M., and Amato, P.: Comparative analysis of bacterial diversity in clouds and aerosols, Atmos. Environ., 298, 119635, https://doi.org/10.1016/j.atmosenv.2023.119635, 2023a.
Péguilhan, R., Rossi, F., Rué, O., Joly, M., and Amato, P.: Experimental and methodological framework for the assessment of nucleic acids in airborne microorganisms, bioRxiv [preprint], https://doi.org/10.1101/2023.10.10.561683, 2023b.
Poolman, B. and Glaasker, E.: Regulation of compatible solute accumulation in bacteria, Mol. Microbiol., 29, 397–407, https://doi.org/10.1046/j.1365-2958.1998.00875.x, 1998.
Prass, M., Andreae, M. O., de Araùjo, A. C., Artaxo, P., Ditas, F., Elbert, W., Förster, J.-D., Franco, M. A., Hrabe de Angelis, I., Kesselmeier, J., Klimach, T., Kremper, L. A., Thines, E., Walter, D., Weber, J., Weber, B., Fuchs, B. M., Pöschl, U., and Pöhlker, C.: Bioaerosols in the Amazon rain forest: temporal variations and vertical profiles of Eukarya, Bacteria, and Archaea, Biogeosciences, 18, 4873–4887, https://doi.org/10.5194/bg-18-4873-2021, 2021.
Pruppacher, H. R. and Jaenicke, R.: The processing of water vapor and aerosols by atmospheric clouds, a global estimate, Atmos. Res., 38, 283–295, https://doi.org/10.1016/0169-8095(94)00098-X, 1995.
Renard, P., Bianco, A., Baray, J.-L., Bridoux, M., Delort, A.-M., and Deguillaume, L.: Classification of Clouds Sampled at the Puy de Dôme Station (France) Based on Chemical Measurements and Air Mass History Matrices, Atmosphere-Basel, 11, 732, https://doi.org/10.3390/atmos11070732, 2020.
Renard, P., Brissy, M., Rossi, F., Leremboure, M., Jaber, S., Baray, J.-L., Bianco, A., Delort, A.-M., and Deguillaume, L.: Free amino acid quantification in cloud water at the Puy de Dôme station (France), Atmos. Chem. Phys., 22, 2467–2486, https://doi.org/10.5194/acp-22-2467-2022, 2022.
Rosado-Porto, D., Ratering, S., Moser, G., Deppe, M., Müller, C., and Schnell, S.: Soil metatranscriptome demonstrates a shift in C, N, and S metabolisms of a grassland ecosystem in response to elevated atmospheric CO2, Front. Microbiol., 13, 937021, https://doi.org/10.3389/fmicb.2022.937021, 2022.
Saikh, S. R. and Das, S. K.: Fog-Induced Alteration in Airborne Microbial Community: a Study over Central Indo-Gangetic Plain in India, Appl. Environ. Microb., 89, e01367–22, https://doi.org/10.1128/aem.01367-22, 2023.
Salazar, G., Paoli, L., Alberti, A., Huerta-Cepas, J., Ruscheweyh, H.-J., Cuenca, M., Field, C. M., Coelho, L. P., Cruaud, C., Engelen, S., Gregory, A. C., Labadie, K., Marec, C., Pelletier, E., Royo-Llonch, M., Roux, S., Sánchez, P., Uehara, H., Zayed, A. A., Zeller, G., Carmichael, M., Dimier, C., Ferland, J., Kandels, S., Picheral, M., Pisarev, S., Poulain, J., Acinas, S. G., Babin, M., Bork, P., Boss, E., Bowler, C., Cochrane, G., de Vargas, C., Follows, M., Gorsky, G., Grimsley, N., Guidi, L., Hingamp, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Karp-Boss, L., Karsenti, E., Not, F., Ogata, H., Pesant, S., Poulton, N., Raes, J., Sardet, C., Speich, S., Stemmann, L., Sullivan, M. B., Sunagawa, S., Wincker, P., Acinas, S. G., Babin, M., Bork, P., Bowler, C., de Vargas, C., Guidi, L., Hingamp, P., Iudicone, D., Karp-Boss, L., Karsenti, E., Ogata, H., Pesant, S., Speich, S., Sullivan, M. B., Wincker, P., and Sunagawa, S.: Gene expression changes and community turnover differentially shape the global ocean metatranscriptome, Cell, 179, 1068–1083.e21, https://doi.org/10.1016/j.cell.2019.10.014, 2019.
Šantl-Temkiv, T., Finster, K., Dittmar, T., Hansen, B. M., Thyrhaug, R., Nielsen, N. W., and Karlson, U. G.: Hailstones: A window into the microbial and chemical inventory of a storm cloud, PloS one, 8, e53550, 2013.
Šantl-Temkiv, T., Amato, P., Gosewinkel, U., Thyrhaug, R., Charton, A., Chicot, B., Finster, K., Bratbak, G., and Löndahl, J.: High-flow-rate impinger for the study of concentration, viability, metabolic activity, and ice-nucleation activity of airborne bacteria, Environ. Sci. Technol., https://doi.org/10.1021/acs.est.7b01480, 2017.
Šantl-Temkiv, T., Gosewinkel, U., Starnawski, P., Lever, M., and Finster, K.: Aeolian dispersal of bacteria in southwest Greenland: their sources, abundance, diversity and physiological states, FEMS Microbiol. Ecol., 94, fiy031, https://doi.org/10.1093/femsec/fiy031, 2018.
Šantl-Temkiv, T., Amato, P., Casamayor, E. O., Lee, P. K. H., and Pointing, S. B.: Microbial ecology of the atmosphere, FEMS Microbiol. Rev., 46, fuac009, https://doi.org/10.1093/femsre/fuac009, 2022.
Satinsky, B. M., Zielinski, B. L., Doherty, M., Smith, C. B., Sharma, S., Paul, J. H., Crump, B. C., and Moran, M. A.: The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010, Microbiome, 2, 17, https://doi.org/10.1186/2049-2618-2-17, 2014.
Sattler, B., Puxbaum, H., and Psenner, R.: Bacterial growth in supercooled cloud droplets, Geophys. Res. Lett., 28, 239–242, 2001.
Schostag, M. D., Albers, C. N., Jacobsen, C. S., and Priemé, A.: Low Turnover of Soil Bacterial rRNA at Low Temperatures, Front Microbiol., 11, 962, https://doi.org/10.3389/fmicb.2020.00962, 2020.
Skopp, J., Jawson, M. D., and Doran, J. W.: Steady-State Aerobic Microbial Activity as a Function of Soil Water Content, Soil Sci. Soc. Am. J., 54, 1619–1625, https://doi.org/10.2136/sssaj1990.03615995005400060018x, 1990.
Smith, D. J., Ravichandar, J. D., Jain, S., Griffin, D. W., Yu, H., Tan, Q., Thissen, J., Lusby, T., Nicoll, P., Shedler, S., Martinez, P., Osorio, A., Lechniak, J., Choi, S., Sabino, K., Iverson, K., Chan, L., Jaing, C., and McGrath, J.: Airborne bacteria in Earth's lower stratosphere resemble taxa detected in the troposphere: results from a new NASA aircraft bioaerosol collector (ABC), Front Microbiol., 9, 1752, https://doi.org/10.3389/fmicb.2018.01752, 2018.
Stevenson, A., Cray, J. A., Williams, J. P., Santos, R., Sahay, R., Neuenkirchen, N., McClure, C. D., Grant, I. R., Houghton, J. D., Quinn, J. P., Timson, D. J., Patil, S. V., Singhal, R. S., Antón, J., Dijksterhuis, J., Hocking, A. D., Lievens, B., Rangel, D. E. N., Voytek, M. A., Gunde-Cimerman, N., Oren, A., Timmis, K. N., McGenity, T. J., and Hallsworth, J. E.: Is there a common water-activity limit for the three domains of life?, ISME J., 9, 1333–1351, https://doi.org/10.1038/ismej.2014.219, 2015.
The UniProt Consortium: UniProt: a worldwide hub of protein knowledge, Nucl. Acid. Res., 47, D506–D515, https://doi.org/10.1093/nar/gky1049, 2019.
Tignat-Perrier, R., Dommergue, A., Thollot, A., Magand, O., Amato, P., Joly, M., Sellegri, K., Vogel, T. M., and Larose, C.: Seasonal shift in airborne microbial communities, Sci. Total Environ., 716, 137129, https://doi.org/10.1016/j.scitotenv.2020.137129, 2020.
Tong, H., Hu, Q., Zhu, L., and Dong, X.: Prokaryotic Aquaporins, Cells, 8, 1316, https://doi.org/10.3390/cells8111316, 2019.
Unger, S., Máguas, C., Pereira, J. S., David, T. S., and Werner, C.: The influence of precipitation pulses on soil respiration – Assessing the “Birch effect” by stable carbon isotopes, Soil. Biol. Biochem., 42, 1800–1810, https://doi.org/10.1016/j.soilbio.2010.06.019, 2010.
Vaïtilingom, M., Deguillaume, L., Vinatier, V., Sancelme, M., Amato, P., Chaumerliac, N., and Delort, A.-M.: Potential impact of microbial activity on the oxidant capacity and organic carbon budget in clouds, P. Natl. Acad. Sci. USA, 110, 559–564, https://doi.org/10.1073/pnas.1205743110, 2013.
van Leeuwen, M. R., Krijgsheld, P., Bleichrodt, R., Menke, H., Stam, H., Stark, J., Wösten, H. A. B., and Dijksterhuis, J.: Germination of conidia of Aspergillus niger is accompanied by major changes in RNA profiles, Stud. Mycol., 74, 59–70, https://doi.org/10.3114/sim0009, 2013.
Veses, V., Richards, A., and Gow, N. A.: Vacuoles and fungal biology, Curr. Opin. Microbiol., 11, 503–510, https://doi.org/10.1016/j.mib.2008.09.017, 2008.
Wang, S., Lin, R., Tumukunde, E., Zeng, W., Bao, Q., Wang, S., and Wang, Y.: Glutamine synthetase contributes to the regulation of growth, conidiation, sclerotia development, and resistance to oxidative stress in the fungus Aspergillus flavus, Toxins-Basel, 14, 822, https://doi.org/10.3390/toxins14120822, 2022.
Wirgot, N., Vinatier, V., Deguillaume, L., Sancelme, M., and Delort, A.-M.: H2O2 modulates the energetic metabolism of the cloud microbiome, Atmos. Chem. Phys., 17, 14841–14851, https://doi.org/10.5194/acp-17-14841-2017, 2017.
Wirgot, N., Lagrée, M., Traïkia, M., Besaury, L., Amato, P., Canet, I., Sancelme, M., Jousse, C., Diémé, B., Lyan, B., and Delort, A.-M.: Metabolic modulations of Pseudomonas graminis in response to H2O2 in cloud water, Sci. Rep.-UK, 9, 1–14, https://doi.org/10.1038/s41598-019-49319-2, 2019.
Woo, C. and Yamamoto, N.: Falling bacterial communities from the atmosphere, Environ. Microbiome, 15, 22, https://doi.org/10.1186/s40793-020-00369-4, 2020.
Wood, D. E. and Salzberg, S. L.: Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome Biol., 15, R46, https://doi.org/10.1186/gb-2014-15-3-r46, 2014.
Yang, K., Tian, J., and Keller, N. P.: Post-translational modifications drive secondary metabolite biosynthesis in Aspergillus: a review, Environ. Microbiol., 24, 2857–2881, https://doi.org/10.1111/1462-2920.16034, 2022.
Zhang, Y., Zhao, Z., Dai, M., Jiao, N., and Herndl, G. J.: Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea, Mol. Ecol., 23, 2260–2274, https://doi.org/10.1111/mec.12739, 2014.
Zhang, Y., Thompson, K. N., Huttenhower, C., and Franzosa, E. A.: Statistical approaches for differential expression analysis in metatranscriptomics, Bioinformatics, 37, i34–i41, https://doi.org/10.1093/bioinformatics/btab327, 2021.
Zhou, X., Fornara, D., Ikenaga, M., Akagi, I., Zhang, R., and Jia, Z.: The resilience of microbial community under drying and rewetting cycles of three forest soils, Front Microbiol., 7, 1101, https://doi.org/10.3389/fmicb.2016.01101, 2016.
Short summary
Using comparative metagenomics and metatranscriptomics, we examined the functioning of airborne microorganisms in clouds and a clear atmosphere. Clouds are atmospheric masses where multiple microbial processes are promoted compared with a clear atmosphere. Overrepresented microbial functions of interest include the processing of chemical compounds, biomass production, and regulation of oxidants. This has implications for biogeochemical cycles and microbial ecology.
Using comparative metagenomics and metatranscriptomics, we examined the functioning of airborne...
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