Articles | Volume 22, issue 1
https://doi.org/10.5194/bg-22-243-2025
© 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-22-243-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Ideas and perspectives
| 
13 Jan 2025
Ideas and perspectives |
| 13 Jan 2025
| 13 Jan 2025
Ideas and perspectives: Microorganisms in the air through the lenses of atmospheric chemistry and microphysics
Institute of Chemistry Clermont-Ferrand, Université Clermont Auvergne, CNRS, 63000 Clermont-Ferrand, France
Pierre Amato
Institute of Chemistry Clermont-Ferrand, Université Clermont Auvergne, CNRS, 63000 Clermont-Ferrand, France
Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, CNRS, 63000 Clermont-Ferrand, France
Kifle Aregahegn
Institute of Chemistry Clermont-Ferrand, Université Clermont Auvergne, CNRS, 63000 Clermont-Ferrand, France
now at: Department of Chemistry, York University, Toronto, ON, Canada
Muriel Joly
Institute of Chemistry Clermont-Ferrand, Université Clermont Auvergne, CNRS, 63000 Clermont-Ferrand, France
Amina Khaled
Institute of Chemistry Clermont-Ferrand, Université Clermont Auvergne, CNRS, 63000 Clermont-Ferrand, France
Tiphaine Labed-Veydert
Institute of Chemistry Clermont-Ferrand, Université Clermont Auvergne, CNRS, 63000 Clermont-Ferrand, France
Frédéric Mathonat
Institute of Chemistry Clermont-Ferrand, Université Clermont Auvergne, CNRS, 63000 Clermont-Ferrand, France
Leslie Nuñez López
Institute of Chemistry Clermont-Ferrand, Université Clermont Auvergne, CNRS, 63000 Clermont-Ferrand, France
Raphaëlle Péguilhan
Institute of Chemistry Clermont-Ferrand, Université Clermont Auvergne, CNRS, 63000 Clermont-Ferrand, France
now at: Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
Minghui Zhang
Institute of Chemistry Clermont-Ferrand, Université Clermont Auvergne, CNRS, 63000 Clermont-Ferrand, France
now at: Minerva Research Group, Max Planck Institute for Chemistry, 55128 Mainz, Germany
Related authors
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
Short summary
Short summary
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.
Raphaëlle Péguilhan, Florent Rossi, Muriel Joly, Engy Nasr, Bérénice Batut, François Enault, Barbara Ervens, and Pierre Amato
EGUsphere, https://doi.org/10.5194/egusphere-2024-2338, https://doi.org/10.5194/egusphere-2024-2338, 2024
Short summary
Short summary
Using comparative metagenomics/metatranscriptomics, we examined the functioning of airborne microorganisms in clouds and clear atmosphere; clouds are atmospheric volumes where multiple microbial processes are promoted compared with clear atmosphere; Overrepresented microbial functions of interest include the processing of chemical compounds, biomass production and the regulation of oxidants; - this has implications for biogeochemical cycles and microbial ecology.
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
Short summary
Short summary
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.
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
Short summary
Short summary
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.
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
Short summary
Short summary
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.
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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.
Saly Jaber, Audrey Lallement, Martine Sancelme, Martin Leremboure, Gilles Mailhot, Barbara Ervens, and Anne-Marie Delort
Atmos. Chem. Phys., 20, 4987–4997, https://doi.org/10.5194/acp-20-4987-2020, https://doi.org/10.5194/acp-20-4987-2020, 2020
Short summary
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Current atmospheric multiphase models do not include biotransformations of organic compounds by bacteria, although many previous studies of our and other research groups have shown microbial activity in cloud water. The current lab/model study shows that for water-soluble aromatic compounds, biodegradation by bacteria may be as efficient as chemical reactions in cloud water.
Barbara Ervens and Pierre Amato
Atmos. Chem. Phys., 20, 1777–1794, https://doi.org/10.5194/acp-20-1777-2020, https://doi.org/10.5194/acp-20-1777-2020, 2020
Short summary
Short summary
Bacteria in the atmosphere are important due to their potential adverse health effects and as initiators of ice cloud formation. Observational studies suggest that bacterial cells grow and multiply in clouds and also consume organic compounds.
We estimate the role of microbial processes in the atmosphere for (i) the increase in biological aerosol mass by cell growth and multiplication and (ii) the sink strength of organics in clouds as a loss process in addition to chemical reactions.
Barbara Ervens, Armin Sorooshian, Abdulmonam M. Aldhaif, Taylor Shingler, Ewan Crosbie, Luke Ziemba, Pedro Campuzano-Jost, Jose L. Jimenez, and Armin Wisthaler
Atmos. Chem. Phys., 18, 16099–16119, https://doi.org/10.5194/acp-18-16099-2018, https://doi.org/10.5194/acp-18-16099-2018, 2018
Short summary
Short summary
The paper presents a new framework that can be used to identify emission scenarios in which aerosol populations are most likely modified by chemical processes in clouds. We show that in neither very polluted nor in very clean air masses is this the case. Only if the ratio of possible aerosol mass precursors (sulfur dioxide, some organics) and preexisting aerosol mass is sufficiently high will aerosol particles show substantially modified physicochemical properties upon cloud processing.
B. Ervens, P. Renard, S. Tlili, S. Ravier, J.-L. Clément, and A. Monod
Atmos. Chem. Phys., 15, 9109–9127, https://doi.org/10.5194/acp-15-9109-2015, https://doi.org/10.5194/acp-15-9109-2015, 2015
Short summary
Short summary
A detailed chemical mechanism is developed based on laboratory studies that predicts the formation of high molecular weight compounds in the aqueous phase of atmospheric aerosol particles. Model simulations using this mechanism for atmospheric conditions show that these pathways are likely not a substantial source of particle mass, unless unidentified precursors for these compounds exist that were not taken into account so far and/or the solubility of oxygen in aerosol water is overestimated.
B. Yuan, P. R. Veres, C. Warneke, J. M. Roberts, J. B. Gilman, A. Koss, P. M. Edwards, M. Graus, W. C. Kuster, S.-M. Li, R. J. Wild, S. S. Brown, W. P. Dubé, B. M. Lerner, E. J. Williams, J. E. Johnson, P. K. Quinn, T. S. Bates, B. Lefer, P. L. Hayes, J. L. Jimenez, R. J. Weber, R. Zamora, B. Ervens, D. B. Millet, B. Rappenglück, and J. A. de Gouw
Atmos. Chem. Phys., 15, 1975–1993, https://doi.org/10.5194/acp-15-1975-2015, https://doi.org/10.5194/acp-15-1975-2015, 2015
Short summary
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In this work, secondary formation of formic acid at an urban site and a site in an oil and gas production region is studied. We investigated various gas phase formation pathways of formic acid, including those recently proposed, using a box model. The contributions from aerosol-related processes, fog events and air-snow exchange to formic acid are also quantified.
B. Ervens, Y. Wang, J. Eagar, W. R. Leaitch, A. M. Macdonald, K. T. Valsaraj, and P. Herckes
Atmos. Chem. Phys., 13, 5117–5135, https://doi.org/10.5194/acp-13-5117-2013, https://doi.org/10.5194/acp-13-5117-2013, 2013
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
Short summary
Short summary
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.
Raphaëlle Péguilhan, Florent Rossi, Muriel Joly, Engy Nasr, Bérénice Batut, François Enault, Barbara Ervens, and Pierre Amato
EGUsphere, https://doi.org/10.5194/egusphere-2024-2338, https://doi.org/10.5194/egusphere-2024-2338, 2024
Short summary
Short summary
Using comparative metagenomics/metatranscriptomics, we examined the functioning of airborne microorganisms in clouds and clear atmosphere; clouds are atmospheric volumes where multiple microbial processes are promoted compared with clear atmosphere; Overrepresented microbial functions of interest include the processing of chemical compounds, biomass production and the regulation of oxidants; - this has implications for biogeochemical cycles and microbial ecology.
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
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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
Short summary
Short summary
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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Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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.
Jean-Luc Baray, Laurent Deguillaume, Aurélie Colomb, Karine Sellegri, Evelyn Freney, Clémence Rose, Joël Van Baelen, Jean-Marc Pichon, David Picard, Patrick Fréville, Laëtitia Bouvier, Mickaël Ribeiro, Pierre Amato, Sandra Banson, Angelica Bianco, Agnès Borbon, Lauréline Bourcier, Yannick Bras, Marcello Brigante, Philippe Cacault, Aurélien Chauvigné, Tiffany Charbouillot, Nadine Chaumerliac, Anne-Marie Delort, Marc Delmotte, Régis Dupuy, Antoine Farah, Guy Febvre, Andrea Flossmann, Christophe Gourbeyre, Claude Hervier, Maxime Hervo, Nathalie Huret, Muriel Joly, Victor Kazan, Morgan Lopez, Gilles Mailhot, Angela Marinoni, Olivier Masson, Nadège Montoux, Marius Parazols, Frédéric Peyrin, Yves Pointin, Michel Ramonet, Manon Rocco, Martine Sancelme, Stéphane Sauvage, Martina Schmidt, Emmanuel Tison, Mickaël Vaïtilingom, Paolo Villani, Miao Wang, Camille Yver-Kwok, and Paolo Laj
Atmos. Meas. Tech., 13, 3413–3445, https://doi.org/10.5194/amt-13-3413-2020, https://doi.org/10.5194/amt-13-3413-2020, 2020
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CO-PDD (Cézeaux-Aulnat-Opme-puy de Dôme) is a fully instrumented platform for atmospheric research. The four sites located at different altitudes from 330 to 1465 m around Clermont-Ferrand (France) host in situ and remote sensing instruments to measure atmospheric composition, including long-term trends and variability, to study interconnected processes (microphysical, chemical, biological, chemical, and dynamical) and to provide a reference point for climate models.
Saly Jaber, Audrey Lallement, Martine Sancelme, Martin Leremboure, Gilles Mailhot, Barbara Ervens, and Anne-Marie Delort
Atmos. Chem. Phys., 20, 4987–4997, https://doi.org/10.5194/acp-20-4987-2020, https://doi.org/10.5194/acp-20-4987-2020, 2020
Short summary
Short summary
Current atmospheric multiphase models do not include biotransformations of organic compounds by bacteria, although many previous studies of our and other research groups have shown microbial activity in cloud water. The current lab/model study shows that for water-soluble aromatic compounds, biodegradation by bacteria may be as efficient as chemical reactions in cloud water.
Barbara Ervens and Pierre Amato
Atmos. Chem. Phys., 20, 1777–1794, https://doi.org/10.5194/acp-20-1777-2020, https://doi.org/10.5194/acp-20-1777-2020, 2020
Short summary
Short summary
Bacteria in the atmosphere are important due to their potential adverse health effects and as initiators of ice cloud formation. Observational studies suggest that bacterial cells grow and multiply in clouds and also consume organic compounds.
We estimate the role of microbial processes in the atmosphere for (i) the increase in biological aerosol mass by cell growth and multiplication and (ii) the sink strength of organics in clouds as a loss process in addition to chemical reactions.
Barbara Ervens, Armin Sorooshian, Abdulmonam M. Aldhaif, Taylor Shingler, Ewan Crosbie, Luke Ziemba, Pedro Campuzano-Jost, Jose L. Jimenez, and Armin Wisthaler
Atmos. Chem. Phys., 18, 16099–16119, https://doi.org/10.5194/acp-18-16099-2018, https://doi.org/10.5194/acp-18-16099-2018, 2018
Short summary
Short summary
The paper presents a new framework that can be used to identify emission scenarios in which aerosol populations are most likely modified by chemical processes in clouds. We show that in neither very polluted nor in very clean air masses is this the case. Only if the ratio of possible aerosol mass precursors (sulfur dioxide, some organics) and preexisting aerosol mass is sufficiently high will aerosol particles show substantially modified physicochemical properties upon cloud processing.
Audrey Lallement, Ludovic Besaury, Elise Tixier, Martine Sancelme, Pierre Amato, Virginie Vinatier, Isabelle Canet, Olga V. Polyakova, Viatcheslay B. Artaev, Albert T. Lebedev, Laurent Deguillaume, Gilles Mailhot, and Anne-Marie Delort
Biogeosciences, 15, 5733–5744, https://doi.org/10.5194/bg-15-5733-2018, https://doi.org/10.5194/bg-15-5733-2018, 2018
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The main objective of this work was to evaluate the potential degradation of phenol, a highly toxic pollutant, by cloud microorganisms. Phenol concentrations measured on five cloud samples collected at the PUY station in France were from 0.15 to 0.74 µg L−1. Metatranscriptomic analysis suggested that phenol could be biodegraded directly in clouds, likely by Gammaproteobacteria. A large screening showed that 93 % of 145 bacterial strains isolated from clouds were able to degrade phenol.
Laura González Palacios, Pablo Corral Arroyo, Kifle Z. Aregahegn, Sarah S. Steimer, Thorsten Bartels-Rausch, Barbara Nozière, Christian George, Markus Ammann, and Rainer Volkamer
Atmos. Chem. Phys., 16, 11823–11836, https://doi.org/10.5194/acp-16-11823-2016, https://doi.org/10.5194/acp-16-11823-2016, 2016
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The sources of radicals at aerosol surfaces are highly uncertain. Here we investigate the HO2 radical production from the UV irradiation of imidazole-2-carboxaldehyde (IC) in bulk aqueous films containing IC and citric acid, as well as IC in ammonium sulfate aerosols. We find that IC is an efficient photosensitizer that forms HO2 radicals from H-donor chemistry. IC is a proxy species for brown carbon in atmospheric aerosols.
B. Ervens, P. Renard, S. Tlili, S. Ravier, J.-L. Clément, and A. Monod
Atmos. Chem. Phys., 15, 9109–9127, https://doi.org/10.5194/acp-15-9109-2015, https://doi.org/10.5194/acp-15-9109-2015, 2015
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A detailed chemical mechanism is developed based on laboratory studies that predicts the formation of high molecular weight compounds in the aqueous phase of atmospheric aerosol particles. Model simulations using this mechanism for atmospheric conditions show that these pathways are likely not a substantial source of particle mass, unless unidentified precursors for these compounds exist that were not taken into account so far and/or the solubility of oxygen in aerosol water is overestimated.
P. Amato, M. Joly, C. Schaupp, E. Attard, O. Möhler, C. E. Morris, Y. Brunet, and A.-M. Delort
Atmos. Chem. Phys., 15, 6455–6465, https://doi.org/10.5194/acp-15-6455-2015, https://doi.org/10.5194/acp-15-6455-2015, 2015
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Mortality rate of typical bacterial aerosols (Pseudomonas species) was determined in a cloud simulation chamber. Ice nucleation activity remained unchanged for several hours in aerosolized cells, whether they were viable or not. Cloud increased the specific removal of ice nucleation active cells by precipitation. Survival was negatively impacted by the presence of cloud and by sulfates.
B. Yuan, P. R. Veres, C. Warneke, J. M. Roberts, J. B. Gilman, A. Koss, P. M. Edwards, M. Graus, W. C. Kuster, S.-M. Li, R. J. Wild, S. S. Brown, W. P. Dubé, B. M. Lerner, E. J. Williams, J. E. Johnson, P. K. Quinn, T. S. Bates, B. Lefer, P. L. Hayes, J. L. Jimenez, R. J. Weber, R. Zamora, B. Ervens, D. B. Millet, B. Rappenglück, and J. A. de Gouw
Atmos. Chem. Phys., 15, 1975–1993, https://doi.org/10.5194/acp-15-1975-2015, https://doi.org/10.5194/acp-15-1975-2015, 2015
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In this work, secondary formation of formic acid at an urban site and a site in an oil and gas production region is studied. We investigated various gas phase formation pathways of formic acid, including those recently proposed, using a box model. The contributions from aerosol-related processes, fog events and air-snow exchange to formic acid are also quantified.
M. Joly, P. Amato, L. Deguillaume, M. Monier, C. Hoose, and A.-M. Delort
Atmos. Chem. Phys., 14, 8185–8195, https://doi.org/10.5194/acp-14-8185-2014, https://doi.org/10.5194/acp-14-8185-2014, 2014
L. Deguillaume, T. Charbouillot, M. Joly, M. Vaïtilingom, M. Parazols, A. Marinoni, P. Amato, A.-M. Delort, V. Vinatier, A. Flossmann, N. Chaumerliac, J. M. Pichon, S. Houdier, P. Laj, K. Sellegri, A. Colomb, M. Brigante, and G. Mailhot
Atmos. Chem. Phys., 14, 1485–1506, https://doi.org/10.5194/acp-14-1485-2014, https://doi.org/10.5194/acp-14-1485-2014, 2014
B. Ervens, Y. Wang, J. Eagar, W. R. Leaitch, A. M. Macdonald, K. T. Valsaraj, and P. Herckes
Atmos. Chem. Phys., 13, 5117–5135, https://doi.org/10.5194/acp-13-5117-2013, https://doi.org/10.5194/acp-13-5117-2013, 2013
Related subject area
Biogeochemistry: Environmental Microbiology
Clouds influence the functioning of airborne microorganisms
Effects of surface water interactions with karst groundwater on microbial biomass, metabolism, and production
Overview: Global change effects on terrestrial biogeochemistry at the plant–soil interface
Grazing mortality as a controlling factor in the uncultured non-cyanobacterial diazotroph (Gamma A) around the Kuroshio region
Changes in diazotrophic community structure associated with Kuroshio succession in the northern South China Sea
Animal burrowing at cold seep ecotones boosts productivity by linking macromolecule turnover with chemosynthesis and nutrient cycling
Technical note: A comparison of methods for estimating coccolith mass
Fractionation of stable carbon isotopes during formate consumption in anoxic rice paddy soils and lake sediments
Characteristics of bacterial and fungal communities and their associations with sugar compounds in atmospheric aerosols at a rural site in northern China
Responses of globally important phytoplankton species to olivine dissolution products and implications for carbon dioxide removal via ocean alkalinity enhancement
Differentiation of cognate bacterial communities in thermokarst landscapes: implications for ecological consequences of permafrost degradation
A multi-phase biogeochemical model for mitigating earthquake-induced liquefaction via microbially induced desaturation and calcium carbonate precipitation
Phosphorus regulates ectomycorrhizal fungi biomass production in a Norway spruce forest
Reallocation of elemental content and macromolecules in the coccolithophore Emiliania huxleyi to acclimate to climate change
Abrasion of sedimentary rocks as a source of hydrogen peroxide and nutrients to subglacial ecosystems
Nitrous oxide (N2O) synthesis by the freshwater cyanobacterium Microcystis aeruginosa
Interdisciplinary strategy to assess the impact of meteorological variables on the biochemical composition of the rain and the dynamics of a small eutrophic lake under rain forcing
Depth-related patterns in microbial community responses to complex organic matter in the western North Atlantic Ocean
Assessing the influence of ocean alkalinity enhancement on a coastal phytoplankton community
Eddy-enhanced primary production sustains heterotrophic microbial activities in the Eastern Tropical North Atlantic
Composition and niche-specific characteristics of microbial consortia colonizing Marsberg copper mine in the Rhenish Massif
Diversity and assembly processes of microbial eukaryotic communities in Fildes Peninsula Lakes (West Antarctica)
Nitrophobic ectomycorrhizal fungi are associated with enhanced hydrophobicity of soil organic matter in a Norway spruce forest
Physiological control on carbon isotope fractionation in marine phytoplankton
Implementation of mycorrhizal mechanisms into soil carbon model improves the prediction of long-term processes of plant litter decomposition
Impact of dust addition on the microbial food web under present and future conditions of pH and temperature
Fractionation of stable carbon isotopes during acetate consumption by methanogenic and sulfidogenic microbial communities in rice paddy soils and lake sediments
Hydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific Ocean
Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin
Disturbance triggers non-linear microbe–environment feedbacks
Hydrographic fronts shape productivity, nitrogen fixation, and microbial community composition in the southern Indian Ocean and the Southern Ocean
Microbial and geo-archaeological records reveal the growth rate, origin and composition of desert rock surface communities
Metagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret iron-rich methanic sediments
Spatiotemporal patterns of N2 fixation in coastal waters derived from rate measurements and remote sensing
Biotic and abiotic transformation of amino acids in cloud water: experimental studies and atmospheric implications
Potential bioavailability of organic matter from atmospheric particles to marine heterotrophic bacteria
Microbial functional signature in the atmospheric boundary layer
New insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystem
Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics
Reviews and syntheses: Bacterial bioluminescence – ecology and impact in the biological carbon pump
Salinity-dependent algae uptake and subsequent carbon and nitrogen metabolisms of two intertidal foraminifera (Ammonia tepida and Haynesina germanica)
On giant shoulders: how a seamount affects the microbial community composition of seawater and sponges
Spatial variations in sedimentary N-transformation rates in the North Sea (German Bight)
Patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge
Co-occurrence of Fe and P stress in natural populations of the marine diazotroph Trichodesmium
Senescence as the main driver of iodide release from a diverse range of marine phytoplankton
Reviews and syntheses: Biological weathering and its consequences at different spatial levels – from nanoscale to global scale
Deep-sea sponge grounds as nutrient sinks: denitrification is common in boreo-Arctic sponges
Inducing the attachment of cable bacteria on oxidizing electrodes
Bacterial degradation activity in the eastern tropical South Pacific oxygen minimum zone
Raphaëlle Péguilhan, Florent Rossi, Muriel Joly, Engy Nasr, Bérénice Batut, François Enault, Barbara Ervens, and Pierre Amato
EGUsphere, https://doi.org/10.5194/egusphere-2024-2338, https://doi.org/10.5194/egusphere-2024-2338, 2024
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Using comparative metagenomics/metatranscriptomics, we examined the functioning of airborne microorganisms in clouds and clear atmosphere; clouds are atmospheric volumes where multiple microbial processes are promoted compared with clear atmosphere; Overrepresented microbial functions of interest include the processing of chemical compounds, biomass production and the regulation of oxidants; - this has implications for biogeochemical cycles and microbial ecology.
Adrian Barry-Sosa, Madison K. Flint, Justin C. Ellena, Jonathan B. Martin, and Brent C. Christner
Biogeosciences, 21, 3965–3984, https://doi.org/10.5194/bg-21-3965-2024, https://doi.org/10.5194/bg-21-3965-2024, 2024
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This study examined springs in north central Florida focusing on how interactions between the surface and subsurface affected the properties of groundwater microbes. We found that microbes reproduced at rates that greatly exceed those documented for any other aquifer. Although the groundwater discharged to spring runs contains low concentrations of nutrients, our results indicate that microbes have access to sources of energy and produce new cells at rates similar to surface waterbodies.
Lucia Fuchslueger, Emily Francesca Solly, Alberto Canarini, and Albert Carles Brangarí
Biogeosciences, 21, 3959–3964, https://doi.org/10.5194/bg-21-3959-2024, https://doi.org/10.5194/bg-21-3959-2024, 2024
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This overview of the special issue “Global change effects on terrestrial biogeochemistry at the plant–soil interface” features empirical, conceptual and modelling-based studies and outlines key findings on plant responses to elevated CO2; soil organism responses to warming; impacts on soil organic carbon, nitrogen and mineral nutrient cycling; and water level changes affecting greenhouse gas emissions, from the Arctic to the tropics, which are crucial for deciphering feedbacks to global change.
Takuya Sato, Tamaha Yamaguchi, Kiyotaka Hidataka, Sayaka Sogawa, Takashi Setou, Taketoshi Kodama, Takuhei Shiozaki, and Kazutaka Takahashi
EGUsphere, https://doi.org/10.5194/egusphere-2024-1294, https://doi.org/10.5194/egusphere-2024-1294, 2024
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Gamma A is a widespread non-cyanobacterial diazotroph and plays a crucial role for marine ecosystems, but its controlling factors are still largely unknown. This study, for the first time, quantified microzooplankton grazing on Gamma A and revealed significance of grazing pressure on Gamma A distribution around the Kuroshio region. It highlights the importance of top-down controls on Gamma A abundance and the associated nitrogen cycle.
Han Zhang, Guangming Mai, Weicheng Luo, Meng Chen, Ran Duan, and Tuo Shi
Biogeosciences, 21, 2529–2546, https://doi.org/10.5194/bg-21-2529-2024, https://doi.org/10.5194/bg-21-2529-2024, 2024
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We report taxon-specific biogeography of N2-fixing microbes (diazotrophs) driven by Kuroshio intrusion (Kl) into the South China Sea. We show that the composition and distribution of distinct diazotrophic taxa shift with Kl-induced variations in physicochemical parameters of seawater and that Kl shapes diazotrophic community primarily as a stochastic process. This study thus has implications for the distribution of diazotrophs in a future warming ocean, as Kls are projected to intensify.
Maxim Rubin-Blum, Eyal Rahav, Guy Sisma-Ventura, Yana Yudkovski, Zoya Harbozov, Or Bialik, Oded Ezra, Anneleen Foubert, Barak Herut, and Yizhaq Makovsky
EGUsphere, https://doi.org/10.5194/egusphere-2024-1285, https://doi.org/10.5194/egusphere-2024-1285, 2024
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Geochemical cycles and biodiversity are altered at transition zones of chemosynthetic ecosystems, chemotones. We asked if burrowing alters the functionality of these habitats. We surveyed the seafloor, analyzed sediment properties, and explored microbial communities in ghost shrimp burrows. We made an exciting discovery of chemosynthetic biofilms, linking them to macromolecule turnover and nutrient cycling, using metagenomics. This phenomenon may play an important role in biogeochemical cycles.
Celina Rebeca Valença, Luc Beaufort, Gustaaf Marinus Hallegraeff, and Marius Nils Müller
Biogeosciences, 21, 1601–1611, https://doi.org/10.5194/bg-21-1601-2024, https://doi.org/10.5194/bg-21-1601-2024, 2024
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Coccolithophores contribute to the global carbon cycle and their calcite structures (coccoliths) are used as a palaeoproxy to understand past oceanographic conditions. Here, we compared three frequently used methods to estimate coccolith mass from the model species Emiliania huxleyi and the results allow for a high level of comparability between the methods, facilitating future comparisons and consolidation of mass changes observed from ecophysiological and biogeochemical studies.
Ralf Conrad and Peter Claus
Biogeosciences, 21, 1161–1172, https://doi.org/10.5194/bg-21-1161-2024, https://doi.org/10.5194/bg-21-1161-2024, 2024
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Knowledge of carbon isotope fractionation is important for the assessment of the pathways involved in the degradation of organic matter. Formate is an important intermediate during this process. It was mainly converted to carbon dioxide and acetate both in the presence and absence of sulfate. Methane was only a minor product and was mainly formed from the acetate. The acetate was depleted in the heavy carbon atom relative to formate, while the carbon dioxide was enriched.
Mutong Niu, Shu Huang, Wei Hu, Yajie Wang, Wanyun Xu, Wan Wei, Qiang Zhang, Zihan Wang, Donghuan Zhang, Rui Jin, Libin Wu, Junjun Deng, Fangxia Shen, and Pingqing Fu
Biogeosciences, 20, 4915–4930, https://doi.org/10.5194/bg-20-4915-2023, https://doi.org/10.5194/bg-20-4915-2023, 2023
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Sugar compounds in air can trace the source of bioaerosols that affect public health and climate. In rural north China, we observed increased fungal activity at night and less variable bacterial community diversity. Certain night-increasing sugar compounds were more closely related to fungi than bacteria. The fungal community greatly influenced sugar compounds, while bacteria played a limited role. Caution is advised when using sugar compounds to trace airborne microbes, particularly bacteria.
David A. Hutchins, Fei-Xue Fu, Shun-Chung Yang, Seth G. John, Stephen J. Romaniello, M. Grace Andrews, and Nathan G. Walworth
Biogeosciences, 20, 4669–4682, https://doi.org/10.5194/bg-20-4669-2023, https://doi.org/10.5194/bg-20-4669-2023, 2023
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Applications of the mineral olivine are a promising means to capture carbon dioxide via coastal enhanced weathering, but little is known about the impacts on important marine phytoplankton. We examined the effects of olivine dissolution products on species from three major phytoplankton groups: diatoms, coccolithophores, and cyanobacteria. Growth and productivity were generally either unaffected or stimulated, suggesting the effects of olivine on key phytoplankton are negligible or positive.
Ze Ren, Shudan Ye, Hongxuan Li, Xilei Huang, and Luyao Chen
Biogeosciences, 20, 4241–4258, https://doi.org/10.5194/bg-20-4241-2023, https://doi.org/10.5194/bg-20-4241-2023, 2023
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Permafrost thaw initiates thermokarst landscape formation, resulting in distinct new habitats, including degraded permafrost soil, thermokarst lake sediments, and lake water. These distinct habitats harbored differentiated bacterial communities that originated from the same source, differing in diversity, assembly mechanisms, and environmental influences. The results imply ecological consequences of permafrost degradation in the face of further climate change.
Caitlyn A. Hall, Andre van Turnhout, Edward Kavazanjian Jr., Leon A. van Paassen, and Bruce Rittmann
Biogeosciences, 20, 2903–2917, https://doi.org/10.5194/bg-20-2903-2023, https://doi.org/10.5194/bg-20-2903-2023, 2023
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Earthquake-induced soil liquefaction poses a significant global threat. Microbially induced desaturation and precipitation (MIDP) via denitrification is a potentially sustainable, non-disruptive bacteria-driven ground improvement technique under existing structures. We developed a next-generation biogeochemical model to understand and predict the behavior of MIDP in the natural environment to design field-based hazard mitigation treatments.
Juan Pablo Almeida, Lorenzo Menichetti, Alf Ekblad, Nicholas P. Rosenstock, and Håkan Wallander
Biogeosciences, 20, 1443–1458, https://doi.org/10.5194/bg-20-1443-2023, https://doi.org/10.5194/bg-20-1443-2023, 2023
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In forests, trees allocate a significant amount of carbon belowground to support mycorrhizal symbiosis. In northern forests nitrogen normally regulates this allocation and consequently mycorrhizal fungi growth. In this study we demonstrate that in a conifer forest from Sweden, fungal growth is regulated by phosphorus instead of nitrogen. This is probably due to an increase in nitrogen deposition to soils caused by decades of human pollution that has altered the ecosystem nutrient regime.
Yong Zhang, Yong Zhang, Shuai Ma, Hanbing Chen, Jiabing Li, Zhengke Li, Kui Xu, Ruiping Huang, Hong Zhang, Yonghe Han, and Jun Sun
Biogeosciences, 20, 1299–1312, https://doi.org/10.5194/bg-20-1299-2023, https://doi.org/10.5194/bg-20-1299-2023, 2023
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We found that increasing light intensity compensates for the negative effects of low phosphorus (P) availability on cellular protein and nitrogen contents. Reduced P availability, increasing light intensity, and ocean acidification act synergistically to increase cellular contents of carbohydrate and POC and the allocation of POC to carbohydrate. These regulation mechanisms in Emiliania huxleyi could provide vital information for evaluating carbon cycle in marine ecosystems under global change.
Beatriz Gill-Olivas, Jon Telling, Mark Skidmore, and Martyn Tranter
Biogeosciences, 20, 929–943, https://doi.org/10.5194/bg-20-929-2023, https://doi.org/10.5194/bg-20-929-2023, 2023
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Microbial ecosystems have been found in all subglacial environments sampled to date. Yet, little is known of the sources of energy and nutrients that sustain these microbial populations. This study shows that crushing of sedimentary rocks, which contain organic carbon, carbonate and sulfide minerals, along with previously weathered silicate minerals, produces a range of compounds and nutrients which can be utilised by the diverse suite of microbes that inhabit glacier beds.
Federico Fabisik, Benoit Guieysse, Jonathan Procter, and Maxence Plouviez
Biogeosciences, 20, 687–693, https://doi.org/10.5194/bg-20-687-2023, https://doi.org/10.5194/bg-20-687-2023, 2023
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We show, for the first time, that pure cultures of the cyanobacterium Microcystis aeruginosa can synthesize the potent greenhouse gas N2O using nitrite as substrate. Our findings have broad environmental implications because M. aeruginosa is globally found in freshwater ecosystems and is often the dominant species found in algae blooms. Further research is now needed to determine the occurrence and significance of N2O emissions from ecosystems rich with M. aeruginosa.
Fanny Noirmain, Jean-Luc Baray, Frédéric Tridon, Philippe Cacault, Hermine Billard, Guillaume Voyard, Joël Van Baelen, and Delphine Latour
Biogeosciences, 19, 5729–5749, https://doi.org/10.5194/bg-19-5729-2022, https://doi.org/10.5194/bg-19-5729-2022, 2022
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We present a study linking rain, meteorology, and mountain lake phytoplankton dynamics on the basis of a case study at Aydat (France) in September 2020. The air mass origin mainly influences the rain chemical composition, which depends on the type of rain, convective or stratiform. Our results also highlighted a non-negligible presence of photosynthetic cells in rainwater. The impact of the atmospheric forcing on the lake could play a key role in phytoplankton dynamics in the temperate zone.
Sarah A. Brown, John Paul Balmonte, Adrienne Hoarfrost, Sherif Ghobrial, and Carol Arnosti
Biogeosciences, 19, 5617–5631, https://doi.org/10.5194/bg-19-5617-2022, https://doi.org/10.5194/bg-19-5617-2022, 2022
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Bacteria use extracellular enzymes to cut large organic matter to sizes small enough for uptake. We compared the enzymatic response of surface, mid-water, and deep-ocean bacteria to complex natural substrates. Bacteria in surface and mid-depth waters produced a much wider range of enzymes than those in the deep ocean and may therefore consume a broader range of organic matter. The extent to which organic matter is recycled by bacteria depends in part on its residence time at different depths.
Aaron Ferderer, Zanna Chase, Fraser Kennedy, Kai G. Schulz, and Lennart T. Bach
Biogeosciences, 19, 5375–5399, https://doi.org/10.5194/bg-19-5375-2022, https://doi.org/10.5194/bg-19-5375-2022, 2022
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Ocean alkalinity enhancement has the capacity to remove vast quantities of carbon from the atmosphere, but its effect on marine ecosystems is largely unknown. We assessed the effect of increased alkalinity on a coastal phytoplankton community when seawater was equilibrated and not equilibrated with atmospheric CO2. We found that the phytoplankton community was moderately affected by increased alkalinity and equilibration with atmospheric CO2 had little influence on this effect.
Quentin Devresse, Kevin W. Becker, Arne Bendinger, Johannes Hahn, and Anja Engel
Biogeosciences, 19, 5199–5219, https://doi.org/10.5194/bg-19-5199-2022, https://doi.org/10.5194/bg-19-5199-2022, 2022
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Eddies are ubiquitous in the ocean and alter physical, chemical, and biological processes. However, how they affect organic carbon production and consumption is largely unknown. Here we show how an eddy triggers a cascade effect on biomass production and metabolic activities of phyto- and bacterioplankton. Our results may contribute to the improvement of biogeochemical models used to estimate carbon fluxes in the ocean.
Sania Arif, Heiko Nacke, Elias Schliekmann, Andreas Reimer, Gernot Arp, and Michael Hoppert
Biogeosciences, 19, 4883–4902, https://doi.org/10.5194/bg-19-4883-2022, https://doi.org/10.5194/bg-19-4883-2022, 2022
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The natural enrichment of Chloroflexi (Ktedonobacteria) at the Kilianstollen Marsberg copper mine rocks being exposed to the acidic sulfate-rich leachate led to an investigation of eight metagenomically assembled genomes (MAGs) involved in copper and other transition heavy metal resistance in addition to low pH resistance and aromatic compounds degradation. The present study offers functional insights about a novel cold-adapted Ktedonobacteria MAG extremophily along with other phyla MAGs.
Chunmei Zhang, Huirong Li, Yinxin Zeng, Haitao Ding, Bin Wang, Yangjie Li, Zhongqiang Ji, Yonghong Bi, and Wei Luo
Biogeosciences, 19, 4639–4654, https://doi.org/10.5194/bg-19-4639-2022, https://doi.org/10.5194/bg-19-4639-2022, 2022
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The unique microbial eukaryotic community structure and lower diversity have been demonstrated in five freshwater lakes of the Fildes Peninsula, Antarctica. Stochastic processes and biotic co-occurrence patterns were shown to be important in shaping microbial eukaryotic communities in the area. Our study provides a better understanding of the dynamic patterns and ecological assembly processes of microbial eukaryotic communities in Antarctic oligotrophic lakes (Fildes Peninsula).
Juan Pablo Almeida, Nicholas P. Rosenstock, Susanne K. Woche, Georg Guggenberger, and Håkan Wallander
Biogeosciences, 19, 3713–3726, https://doi.org/10.5194/bg-19-3713-2022, https://doi.org/10.5194/bg-19-3713-2022, 2022
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Fungi living in symbiosis with tree roots can accumulate belowground, forming special tissues than can repel water. We measured the water repellency of organic material incubated belowground and correlated it with fungal growth. We found a positive association between water repellency and root symbiotic fungi. These results are important because an increase in soil water repellency can reduce the release of CO2 from soils into the atmosphere and mitigate the effects of greenhouse gasses.
Karen M. Brandenburg, Björn Rost, Dedmer B. Van de Waal, Mirja Hoins, and Appy Sluijs
Biogeosciences, 19, 3305–3315, https://doi.org/10.5194/bg-19-3305-2022, https://doi.org/10.5194/bg-19-3305-2022, 2022
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Reconstructions of past CO2 concentrations rely on proxy estimates, with one line of proxies relying on the CO2-dependence of stable carbon isotope fractionation in marine phytoplankton. Culturing experiments provide insights into which processes may impact this. We found, however, that the methods with which these culturing experiments are performed also influence 13C fractionation. Caution should therefore be taken when extrapolating results from these experiments to proxy applications.
Weilin Huang, Peter M. van Bodegom, Toni Viskari, Jari Liski, and Nadejda A. Soudzilovskaia
Biogeosciences, 19, 1469–1490, https://doi.org/10.5194/bg-19-1469-2022, https://doi.org/10.5194/bg-19-1469-2022, 2022
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This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the mediation of plant litter decomposition. We present a model based on litter chemical quality which precludes a conclusive examination of mycorrhizal impacts on soil C. It improves long-term decomposition predictions and advances our understanding of litter decomposition dynamics. It creates a benchmark in quantitatively examining the impacts of plant–microbe interactions on soil C dynamics.
Julie Dinasquet, Estelle Bigeard, Frédéric Gazeau, Farooq Azam, Cécile Guieu, Emilio Marañón, Céline Ridame, France Van Wambeke, Ingrid Obernosterer, and Anne-Claire Baudoux
Biogeosciences, 19, 1303–1319, https://doi.org/10.5194/bg-19-1303-2022, https://doi.org/10.5194/bg-19-1303-2022, 2022
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Saharan dust deposition of nutrients and trace metals is crucial to microbes in the Mediterranean Sea. Here, we tested the response of microbial and viral communities to simulated dust deposition under present and future conditions of temperature and pH. Overall, the effect of the deposition was dependent on the initial microbial assemblage, and future conditions will intensify microbial responses. We observed effects on trophic interactions, cascading all the way down to viral processes.
Ralf Conrad, Pengfei Liu, and Peter Claus
Biogeosciences, 18, 6533–6546, https://doi.org/10.5194/bg-18-6533-2021, https://doi.org/10.5194/bg-18-6533-2021, 2021
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Acetate is an important intermediate during the anaerobic degradation of organic matter. It is consumed by methanogenic and sulfidogenic microorganisms accompanied by stable carbon isotope fractionation. We determined isotope fractionation under different conditions in two paddy soils and two lake sediments and also determined the composition of the microbial communities. Despite a relatively wide range of experimental conditions, the range of fractionation factors was quite moderate.
Natalie R. Cohen, Abigail E. Noble, Dawn M. Moran, Matthew R. McIlvin, Tyler J. Goepfert, Nicholas J. Hawco, Christopher R. German, Tristan J. Horner, Carl H. Lamborg, John P. McCrow, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 18, 5397–5422, https://doi.org/10.5194/bg-18-5397-2021, https://doi.org/10.5194/bg-18-5397-2021, 2021
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A previous study documented an intense hydrothermal plume in the South Pacific Ocean; however, the iron release associated with this plume and the impact on microbiology were unclear. We describe metal concentrations associated with multiple hydrothermal plumes in this region and protein signatures of plume-influenced microbes. Our findings demonstrate that resources released from these systems can be transported away from their source and may alter the physiology of surrounding microbes.
Sabyasachi Bhattacharya, Tarunendu Mapder, Svetlana Fernandes, Chayan Roy, Jagannath Sarkar, Moidu Jameela Rameez, Subhrangshu Mandal, Abhijit Sar, Amit Kumar Chakraborty, Nibendu Mondal, Sumit Chatterjee, Bomba Dam, Aditya Peketi, Ranadhir Chakraborty, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 18, 5203–5222, https://doi.org/10.5194/bg-18-5203-2021, https://doi.org/10.5194/bg-18-5203-2021, 2021
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Physicochemical determinants of microbiome architecture across continental shelves–slopes are unknown, so we explored the geomicrobiology along 3 m sediment horizons of seasonal (shallow coastal) and perennial (deep sea) hypoxic zones of the Arabian Sea. Nature, concentration, and fate of the organic matter delivered to the sea floor were found to shape the microbiome across the western Indian margin, under direct–indirect influence of sedimentation rate and water column O2 level.
Aditi Sengupta, Sarah J. Fansler, Rosalie K. Chu, Robert E. Danczak, Vanessa A. Garayburu-Caruso, Lupita Renteria, Hyun-Seob Song, Jason Toyoda, Jacqueline Hager, and James C. Stegen
Biogeosciences, 18, 4773–4789, https://doi.org/10.5194/bg-18-4773-2021, https://doi.org/10.5194/bg-18-4773-2021, 2021
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Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
Cora Hörstmann, Eric J. Raes, Pier Luigi Buttigieg, Claire Lo Monaco, Uwe John, and Anya M. Waite
Biogeosciences, 18, 3733–3749, https://doi.org/10.5194/bg-18-3733-2021, https://doi.org/10.5194/bg-18-3733-2021, 2021
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Microbes are the main drivers of productivity and nutrient cycling in the ocean. We present a combined approach assessing C and N uptake and microbial community diversity across ecological provinces in the Southern Ocean and southern Indian Ocean. Provinces showed distinct genetic fingerprints, but microbial activity varied gradually across regions, correlating with nutrient concentrations. Our study advances the biogeographic understanding of microbial diversity across C and N uptake regimes.
Nimrod Wieler, Tali Erickson Gini, Osnat Gillor, and Roey Angel
Biogeosciences, 18, 3331–3342, https://doi.org/10.5194/bg-18-3331-2021, https://doi.org/10.5194/bg-18-3331-2021, 2021
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Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands. BRCs play a crucial role in arid environments because of the limited activity of plants and soil. Nevertheless, BRC development rates have never been dated. Here we integrated archaeological, microbiological and geological methods to provide a first estimation of the growth rate of BRCs under natural conditions. This can serve as an affordable dating tool in archaeological sites in arid regions.
Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, and Orit Sivan
Biogeosciences, 18, 2091–2106, https://doi.org/10.5194/bg-18-2091-2021, https://doi.org/10.5194/bg-18-2091-2021, 2021
Mindaugas Zilius, Irma Vybernaite-Lubiene, Diana Vaiciute, Donata Overlingė, Evelina Grinienė, Anastasija Zaiko, Stefano Bonaglia, Iris Liskow, Maren Voss, Agneta Andersson, Sonia Brugel, Tobia Politi, and Paul A. Bukaveckas
Biogeosciences, 18, 1857–1871, https://doi.org/10.5194/bg-18-1857-2021, https://doi.org/10.5194/bg-18-1857-2021, 2021
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In fresh and brackish waters, algal blooms are often dominated by cyanobacteria, which have the ability to utilize atmospheric nitrogen. Cyanobacteria are also unusual in that they float to the surface and are dispersed by wind-driven currents. Their patchy and dynamic distribution makes it difficult to track their abundance and quantify their effects on nutrient cycling. We used remote sensing to map the distribution of cyanobacteria in a large Baltic lagoon and quantify their contributions.
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.
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285, https://doi.org/10.5194/bg-17-6271-2020, https://doi.org/10.5194/bg-17-6271-2020, 2020
Romie Tignat-Perrier, Aurélien Dommergue, Alban Thollot, Olivier Magand, Timothy M. Vogel, and Catherine Larose
Biogeosciences, 17, 6081–6095, https://doi.org/10.5194/bg-17-6081-2020, https://doi.org/10.5194/bg-17-6081-2020, 2020
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The adverse atmospheric environmental conditions do not appear suited for microbial life. We conducted the first global comparative metagenomic analysis to find out if airborne microbial communities might be selected by their ability to resist these adverse conditions. The relatively higher concentration of fungi led to the observation of higher proportions of stress-related functions in air. Fungi might likely resist and survive atmospheric physical stress better than bacteria.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032, https://doi.org/10.5194/bg-17-6017-2020, https://doi.org/10.5194/bg-17-6017-2020, 2020
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Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Anna-Neva Visser, Scott D. Wankel, Pascal A. Niklaus, James M. Byrne, Andreas A. Kappler, and Moritz F. Lehmann
Biogeosciences, 17, 4355–4374, https://doi.org/10.5194/bg-17-4355-2020, https://doi.org/10.5194/bg-17-4355-2020, 2020
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This study focuses on the chemical reaction between Fe(II) and nitrite, which has been reported to produce high levels of the greenhouse gas N2O. We investigated the extent to which dead biomass and Fe(II) minerals might enhance this reaction. Here, nitrite reduction was highest when both additives were present but less pronounced if only Fe(II) minerals were added. Both reaction systems show distinct differences, rather low N2O levels, and indicated the abiotic production of N2.
Lisa Tanet, Séverine Martini, Laurie Casalot, and Christian Tamburini
Biogeosciences, 17, 3757–3778, https://doi.org/10.5194/bg-17-3757-2020, https://doi.org/10.5194/bg-17-3757-2020, 2020
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Bioluminescent bacteria, the most abundant light-emitting organisms in the ocean, can be free-living, be symbiotic or colonize organic particles. This review suggests that they act as a visual target and may indirectly influence the sequestration of biogenic carbon in oceans by increasing the attraction rate for consumers. We summarize the instrumentation available to quantify this impact in future studies and propose synthetic figures integrating these ecological and biogeochemical concepts.
Michael Lintner, Bianca Biedrawa, Julia Wukovits, Wolfgang Wanek, and Petra Heinz
Biogeosciences, 17, 3723–3732, https://doi.org/10.5194/bg-17-3723-2020, https://doi.org/10.5194/bg-17-3723-2020, 2020
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Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changing salinity in the German Wadden Sea immediately influences the foraminiferal community. It seems that A. tepida is better adapted to salinity fluctuations than H. germanica.
Kathrin Busch, Ulrike Hanz, Furu Mienis, Benjamin Mueller, Andre Franke, Emyr Martyn Roberts, Hans Tore Rapp, and Ute Hentschel
Biogeosciences, 17, 3471–3486, https://doi.org/10.5194/bg-17-3471-2020, https://doi.org/10.5194/bg-17-3471-2020, 2020
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Seamounts are globally abundant submarine structures that offer great potential to study the impacts and interactions of environmental gradients at a single geographic location. In an exemplary way, we describe potential mechanisms by which a seamount can affect the structure of pelagic and benthic (sponge-)associated microbial communities. We conclude that the geology, physical oceanography, biogeochemistry, and microbiology of seamounts are even more closely linked than currently appreciated.
Alexander Bratek, Justus E. E. van
Beusekom, Andreas Neumann, Tina Sanders, Jana Friedrich, Kay-Christian Emeis, and Kirstin Dähnke
Biogeosciences, 17, 2839–2851, https://doi.org/10.5194/bg-17-2839-2020, https://doi.org/10.5194/bg-17-2839-2020, 2020
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The following paper highlights the importance of benthic N-transformation rates in different sediment types in the southern North Sea as a source of fixed nitrogen for primary producers and also as a sink of fixed nitrogen. Sedimentary fluxes of dissolved inorganic nitrogen support ∼7 to 59 % of the average annual primary production. Semi-permeable and permeable sediments contribute ∼68 % of the total benthic N2 production rates, counteracting eutrophication in the southern North Sea.
Sabine Haalboom, David M. Price, Furu Mienis, Judith D. L. van Bleijswijk, Henko C. de Stigter, Harry J. Witte, Gert-Jan Reichart, and Gerard C. A. Duineveld
Biogeosciences, 17, 2499–2519, https://doi.org/10.5194/bg-17-2499-2020, https://doi.org/10.5194/bg-17-2499-2020, 2020
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Mineral mining in deep-sea hydrothermal settings will lead to the formation of plumes of fine-grained, chemically reactive, suspended matter. Understanding how natural hydrothermal plumes evolve as they disperse from their source, and how they affect their surrounding environment, may help in characterising the behaviour of the diluted part of mining plumes. The natural plume provided a heterogeneous, geochemically enriched habitat conducive to the development of a distinct microbial ecology.
Noelle A. Held, Eric A. Webb, Matthew M. McIlvin, David A. Hutchins, Natalie R. Cohen, Dawn M. Moran, Korinna Kunde, Maeve C. Lohan, Claire Mahaffey, E. Malcolm S. Woodward, and Mak A. Saito
Biogeosciences, 17, 2537–2551, https://doi.org/10.5194/bg-17-2537-2020, https://doi.org/10.5194/bg-17-2537-2020, 2020
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Trichodesmium is a globally important marine nitrogen fixer that stimulates primary production in the surface ocean. We surveyed metaproteomes of Trichodesmium populations across the North Atlantic and other oceans, and we found that they experience simultaneous phosphate and iron stress because of the biophysical limits of nutrient uptake. Importantly, nitrogenase was most abundant during co-stress, indicating the potential importance of this phenotype to global nitrogen and carbon cycling.
Helmke Hepach, Claire Hughes, Karen Hogg, Susannah Collings, and Rosie Chance
Biogeosciences, 17, 2453–2471, https://doi.org/10.5194/bg-17-2453-2020, https://doi.org/10.5194/bg-17-2453-2020, 2020
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Tropospheric iodine takes part in numerous atmospheric chemical cycles, including tropospheric ozone destruction and aerosol formation. Due to its significance for atmospheric processes, it is crucial to constrain its sources and sinks. This paper aims at investigating and understanding features of biogenic iodate-to-iodide reduction in microalgal monocultures. We find that phytoplankton senescence may play a crucial role in the release of iodide to the marine environment.
Roger D. Finlay, Shahid Mahmood, Nicholas Rosenstock, Emile B. Bolou-Bi, Stephan J. Köhler, Zaenab Fahad, Anna Rosling, Håkan Wallander, Salim Belyazid, Kevin Bishop, and Bin Lian
Biogeosciences, 17, 1507–1533, https://doi.org/10.5194/bg-17-1507-2020, https://doi.org/10.5194/bg-17-1507-2020, 2020
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Effects of biological activity on mineral weathering operate at scales ranging from short-term, microscopic interactions to global, evolutionary timescale processes. Microorganisms have had well-documented effects at large spatio-temporal scales, but to establish the quantitative significance of microscopic measurements for field-scale processes, higher-resolution studies of liquid chemistry at local weathering sites and improved upscaling to soil-scale dissolution rates are still required.
Christine Rooks, James Kar-Hei Fang, Pål Tore Mørkved, Rui Zhao, Hans Tore Rapp, Joana R. Xavier, and Friederike Hoffmann
Biogeosciences, 17, 1231–1245, https://doi.org/10.5194/bg-17-1231-2020, https://doi.org/10.5194/bg-17-1231-2020, 2020
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Sponge grounds are known as nutrient sources, providing nitrate and ammonium to the ocean. We found that they also can do the opposite: in six species from Arctic and North Atlantic sponge grounds, we measured high rates of denitrification, which remove these nutrients from the sea. Rates were highest when the sponge tissue got low in oxygen, which happens when sponges stop pumping because of stress. Sponge grounds may become nutrient sinks when exposed to stress.
Cheng Li, Clare E. Reimers, and Yvan Alleau
Biogeosciences, 17, 597–607, https://doi.org/10.5194/bg-17-597-2020, https://doi.org/10.5194/bg-17-597-2020, 2020
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Novel filamentous cable bacteria that grow in the top layer of intertidal mudflat sediment were attracted to electrodes poised at a positive electrical potential. Several diverse morphologies of Desulfobulbaceae filaments, cells, and colonies were observed on the electrode surface. These observations provide information to suggest conditions that will induce cable bacteria to perform electron donation to an electrode, informing future experiments that culture cable bacteria outside of sediment.
Marie Maßmig, Jan Lüdke, Gerd Krahmann, and Anja Engel
Biogeosciences, 17, 215–230, https://doi.org/10.5194/bg-17-215-2020, https://doi.org/10.5194/bg-17-215-2020, 2020
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Little is known about the rates of bacterial element cycling in oxygen minimum zones (OMZs). We measured bacterial production and rates of extracellular hydrolytic enzymes at various in situ oxygen concentrations in the OMZ off Peru. Our field data show unhampered bacterial activity at low oxygen concentrations. Meanwhile bacterial degradation of organic matter substantially contributed to the formation of the OMZ.
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Short summary
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.
Atmospheric microorganisms are a small fraction of Earth's microbiome, with bacteria being a...
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