Articles | Volume 15, issue 18
https://doi.org/10.5194/bg-15-5733-2018
© Author(s) 2018. 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-15-5733-2018
© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| Highlight paper
| 
28 Sep 2018
Research article | Highlight paper |
| 28 Sep 2018
| 28 Sep 2018
Potential for phenol biodegradation in cloud waters
Audrey Lallement
Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de
Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Ludovic Besaury
Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de
Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Elise Tixier
Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de
Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Martine Sancelme
Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de
Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Pierre Amato
Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de
Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Virginie Vinatier
Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de
Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Isabelle Canet
Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de
Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Olga V. Polyakova
Lomonosov Moscow State University, Chemistry Department, Leninskie
Gory 1/3, Moscow, 119991, Russia
Viatcheslay B. Artaev
LECO Corporation, 3000 Lakeview Avenue, St. Joseph, Michigan 49085,
USA
Albert T. Lebedev
Lomonosov Moscow State University, Chemistry Department, Leninskie
Gory 1/3, Moscow, 119991, Russia
Laurent Deguillaume
Université Clermont Auvergne, CNRS, Laboratoire de
Météorologie Physique, 63000 Clermont-Ferrand, France
Gilles Mailhot
Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de
Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Anne-Marie Delort
CORRESPONDING AUTHOR
Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de
Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
Related authors
No articles found.
Peng Cheng, Gilles Mailhot, Mohamed Sarakha, Guillaume Voyard, Daniele Scheres Firak, Thomas Schaefer, Hartmut Herrmann, and Marcello Brigante
EGUsphere, https://doi.org/10.5194/egusphere-2025-1744, https://doi.org/10.5194/egusphere-2025-1744, 2025
This preprint is open for discussion and under review for Atmospheric Chemistry and Physics (ACP).
Short summary
Short summary
This study investigates the complexation of Fe(II) and Fe(III) with glutamic acid under cloud water conditions and the effect on Fenton and photo-Fenton reactions, hydroxyl radical formation, and their impact on amino acid oxidation.
Elsa Abs, Christoph Keuschnig, Pierre Amato, Chris Bowler, Eric Capo, Alexander Chase, Luciana Chavez Rodriguez, Abraham Dabengwa, Thomas Dussarrat, Thomas Guzman, Linnea Honeker, Jenni Hultman, Kirsten Küsel, Zhen Li, Anna Mankowski, William Riley, Scott Saleska, and Lisa Wingate
EGUsphere, https://doi.org/10.5194/egusphere-2025-1716, https://doi.org/10.5194/egusphere-2025-1716, 2025
This preprint is open for discussion and under review for Biogeosciences (BG).
Short summary
Short summary
Meta-omics technologies offer new tools to understand how microbial and plant functional diversity shape biogeochemical cycles across ecosystems. This perspective explores how integrating omics data with ecological and modeling approaches can improve our understanding of greenhouse gas fluxes and nutrient dynamics, from soils to clouds, and from the past to the future. We highlight challenges and opportunities for scaling omics insights from local processes to Earth system models.
Raphaëlle Péguilhan, Florent Rossi, Muriel Joly, Engy Nasr, Bérénice Batut, François Enault, Barbara Ervens, and Pierre Amato
Biogeosciences, 22, 1257–1275, https://doi.org/10.5194/bg-22-1257-2025, https://doi.org/10.5194/bg-22-1257-2025, 2025
Short summary
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.
Mickael Vaitilingom, Christophe Bernard, Mickael Ribeiro, Christophe Verhaege, Christophe Gourbeyre, Christophe Berthod, Angelica Bianco, and Laurent Deguillaume
Atmos. Meas. Tech., 18, 1073–1090, https://doi.org/10.5194/amt-18-1073-2025, https://doi.org/10.5194/amt-18-1073-2025, 2025
Short summary
Short summary
The new collector BOOGIE has been designed to sample cloud droplets and evaluated. Computational fluid dynamics simulations are performed to evaluate the sampling efficiency for different droplet sizes. In situ measurements show very good water collection rates and sampling efficiency. BOOGIE is compared to other cloud collectors and the efficiency is comparable, as are the chemical and biological compositions.
Barbara Ervens, Pierre Amato, Kifle Aregahegn, Muriel Joly, Amina Khaled, Tiphaine Labed-Veydert, Frédéric Mathonat, Leslie Nuñez López, Raphaëlle Péguilhan, and Minghui Zhang
Biogeosciences, 22, 243–256, https://doi.org/10.5194/bg-22-243-2025, https://doi.org/10.5194/bg-22-243-2025, 2025
Short summary
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.
Lucas Pailler, Laurent Deguillaume, Hélène Lavanant, Isabelle Schmitz, Marie Hubert, Edith Nicol, Mickaël Ribeiro, Jean-Marc Pichon, Mickaël Vaïtilingom, Pamela Dominutti, Frédéric Burnet, Pierre Tulet, Maud Leriche, and Angelica Bianco
Atmos. Chem. Phys., 24, 5567–5584, https://doi.org/10.5194/acp-24-5567-2024, https://doi.org/10.5194/acp-24-5567-2024, 2024
Short summary
Short summary
The composition of dissolved organic matter of cloud water has been investigated through non-targeted high-resolution mass spectrometry on only a few samples collected in the Northern Hemisphere. In this work, the chemical composition of samples collected at Réunion Island (SH) is investigated and compared to samples collected at Puy de Dôme (NH). Sampling, analysis and data treatment with the same methodology produced a unique dataset for investigating the molecular composition of clouds.
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.
Pascal Renard, Maxence Brissy, Florent Rossi, Martin Leremboure, Saly Jaber, Jean-Luc Baray, Angelica Bianco, Anne-Marie Delort, and Laurent Deguillaume
Atmos. Chem. Phys., 22, 2467–2486, https://doi.org/10.5194/acp-22-2467-2022, https://doi.org/10.5194/acp-22-2467-2022, 2022
Short summary
Short summary
Amino acids (AAs) have been quantified in cloud water collected at the Puy de Dôme station (France). Concentrations and speciation of those compounds are highly variable among the samples. Sources from the sea surface and atmospheric transformations during the air mass transport, mainly in the free troposphere, have been shown to modulate AA levels in cloud water.
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
Short summary
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.
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
Short summary
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.
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
Short summary
Short summary
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.
Valentin Duflot, Pierre Tulet, Olivier Flores, Christelle Barthe, Aurélie Colomb, Laurent Deguillaume, Mickael Vaïtilingom, Anne Perring, Alex Huffman, Mark T. Hernandez, Karine Sellegri, Ellis Robinson, David J. O'Connor, Odessa M. Gomez, Frédéric Burnet, Thierry Bourrianne, Dominique Strasberg, Manon Rocco, Allan K. Bertram, Patrick Chazette, Julien Totems, Jacques Fournel, Pierre Stamenoff, Jean-Marc Metzger, Mathilde Chabasset, Clothilde Rousseau, Eric Bourrianne, Martine Sancelme, Anne-Marie Delort, Rachel E. Wegener, Cedric Chou, and Pablo Elizondo
Atmos. Chem. Phys., 19, 10591–10618, https://doi.org/10.5194/acp-19-10591-2019, https://doi.org/10.5194/acp-19-10591-2019, 2019
Short summary
Short summary
The Forests gAses aeRosols Clouds Exploratory (FARCE) campaign was conducted in March–April 2015 on the tropical island of La Réunion. For the first time, several scientific teams from different disciplines collaborated to provide reference measurements and characterization of La Réunion vegetation, volatile organic compounds (VOCs), biogenic VOCs (BVOCs), (bio)aerosols and composition of clouds, with a strong focus on the Maïdo mount slope area.
Clémence Rose, Nadine Chaumerliac, Laurent Deguillaume, Hélène Perroux, Camille Mouchel-Vallon, Maud Leriche, Luc Patryl, and Patrick Armand
Atmos. Chem. Phys., 18, 2225–2242, https://doi.org/10.5194/acp-18-2225-2018, https://doi.org/10.5194/acp-18-2225-2018, 2018
Short summary
Short summary
A detailed aqueous phase mechanism CLEPS 1.1 is coupled with warm microphysics including activation of aerosol particles into cloud droplets. Simulated aqueous concentrations of carboxylic acids are close to the long-term measurements conducted at Puy de Dôme (France). Sensitivity tests show that formic and acetic acids mainly originate from the gas phase with highly variable aqueous-phase reactivity depending on cloud pH, while C3–C4 carboxylic acids mainly originate from the particulate phase.
Nolwenn Wirgot, Virginie Vinatier, Laurent Deguillaume, Martine Sancelme, and Anne-Marie Delort
Atmos. Chem. Phys., 17, 14841–14851, https://doi.org/10.5194/acp-17-14841-2017, https://doi.org/10.5194/acp-17-14841-2017, 2017
Short summary
Short summary
This article highlights the interactions between H2O2 and microorganisms within the cloud system. Experiments performed in microcosms with bacterial strains isolated from clouds showed that H2O2 strongly impacted the microbial energetic state. The ATP depletion measured in the presence of H2O2 was not due to the loss of cell viability. The strong correlation between ATP and H2O2 based on the analysis of 37 real cloud samples confirmed that H2O2 modulates the metabolism of cloud microorganisms.
Camille Mouchel-Vallon, Laurent Deguillaume, Anne Monod, Hélène Perroux, Clémence Rose, Giovanni Ghigo, Yoann Long, Maud Leriche, Bernard Aumont, Luc Patryl, Patrick Armand, and Nadine Chaumerliac
Geosci. Model Dev., 10, 1339–1362, https://doi.org/10.5194/gmd-10-1339-2017, https://doi.org/10.5194/gmd-10-1339-2017, 2017
Short summary
Short summary
The Cloud Explicit Physico-chemical Scheme (CLEPS 1.0) describes oxidation of water-soluble organic compounds resulting from isoprene oxidation. It is based on structure activity relationships (SARs) (global rate constants and branching ratios for HO• abstraction and addition) and GROMHE SAR (Henry's law constants for undocumented species). It is coupled to the MCM gas phase mechanism and is included in a model using the DSMACC model and KPP to analyze experimental and field data.
C. Barbet, L. Deguillaume, N. Chaumerliac, M. Leriche, A. Berger, E. Freney, A. Colomb, K. Sellegri, L. Patryl, and P. Armand
Atmos. Chem. Phys. Discuss., https://doi.org/10.5194/acpd-15-13395-2015, https://doi.org/10.5194/acpd-15-13395-2015, 2015
Preprint withdrawn
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
Related subject area
Biogeochemistry: Environmental Microbiology
Technical note: Flow cytometry assays for the detection, counting and cell sorting of polyphosphate-accumulating bacteria
Animal burrowing at cold seep ecotones boosts productivity by linking macromolecule turnover with chemosynthesis and nutrient cycling
Clouds influence the functioning of airborne microorganisms
Grazing mortality as a controlling factor in the uncultured non-cyanobacterial diazotroph (Gamma A) around the Kuroshio region
Ideas and perspectives: Microorganisms in the air through the lenses of atmospheric chemistry and microphysics
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
Changes in diazotrophic community structure associated with Kuroshio succession in the northern South China Sea
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
Clémentin Bouquet, Hermine Billard, Cécile C. Bidaud, Jonathan Colombet, Young-Tae Chang, Joan Artigas, Isabelle Batisson, Karim Benzerara, Fériel Skouri-Panet, Elodie Duprat, and Anne-Catherine Lehours
Biogeosciences, 22, 1729–1744, https://doi.org/10.5194/bg-22-1729-2025, https://doi.org/10.5194/bg-22-1729-2025, 2025
Short summary
Short summary
In the context of the ecological sustainability of phosphorus, the ubiquitous presence of polyphosphate-accumulating bacteria in natural environments invites efforts to reveal their unknown roles in the biogeochemical cycle of phosphorus. In this study, we evaluated the potential of combining the staining of intracellular polyphosphate granules and their subsequent detection by flow cytometry for the detection, quantification and cell sorting of polyphosphate-accumulating bacteria.
Maxim Rubin-Blum, Eyal Rahav, Guy Sisma-Ventura, Yana Yudkovski, Zoya Harbuzov, Or M. Bialik, Oded Ezra, Anneleen Foubert, Barak Herut, and Yizhaq Makovsky
Biogeosciences, 22, 1321–1340, https://doi.org/10.5194/bg-22-1321-2025, https://doi.org/10.5194/bg-22-1321-2025, 2025
Short summary
Short summary
Chemotones, transition zones in chemosynthetic ecosystems, alter geochemical cycles and biodiversity. We studied seep chemotones, which are heavily burrowed by ghost shrimp. To investigate if burrowing affects habitat functionality, we surveyed the seafloor with deep-sea vehicles, analyzed sediment, and explored microbial communities in burrows. We found chemosynthetic biofilms, linking them to macromolecule turnover and nutrient cycling. This process may play a crucial role in deep-sea cycles.
Raphaëlle Péguilhan, Florent Rossi, Muriel Joly, Engy Nasr, Bérénice Batut, François Enault, Barbara Ervens, and Pierre Amato
Biogeosciences, 22, 1257–1275, https://doi.org/10.5194/bg-22-1257-2025, https://doi.org/10.5194/bg-22-1257-2025, 2025
Short summary
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.
Takuya Sato, Tamaha Yamaguchi, Kiyotaka Hidaka, Sayaka Sogawa, Takashi Setou, Taketoshi Kodama, Takuhei Shiozaki, and Kazutaka Takahashi
Biogeosciences, 22, 625–639, https://doi.org/10.5194/bg-22-625-2025, https://doi.org/10.5194/bg-22-625-2025, 2025
Short summary
Short summary
Gamma A is a widespread non-cyanobacterial diazotroph that plays a crucial role in marine ecosystems, but its controlling factors are still largely unknown. This study, for the first time, quantified microzooplankton grazing on Gamma A and revealed the 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.
Barbara Ervens, Pierre Amato, Kifle Aregahegn, Muriel Joly, Amina Khaled, Tiphaine Labed-Veydert, Frédéric Mathonat, Leslie Nuñez López, Raphaëlle Péguilhan, and Minghui Zhang
Biogeosciences, 22, 243–256, https://doi.org/10.5194/bg-22-243-2025, https://doi.org/10.5194/bg-22-243-2025, 2025
Short summary
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.
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
Short summary
Short summary
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
Short summary
Short summary
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.
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
Short summary
Short summary
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.
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
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.
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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
Short summary
Short summary
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.
Cited articles
Ajaz, M., Noor, N., Rasool, S. A., and Khan, S. A.: Phenol resistant bacteria
from soil: identification-characterization and genetical studies, Pak. J.
Bot., 36, 415–424, 2004.
Al-Khalid, T. and El-Naas, M. H.: Aerobic biodegradation of phenols: a
comprehensive review, Crit. Rev. Env. Sci.
Tech., 42, 1631–1690, https://doi.org/10.1080/10643389.2011.569872, 2012.
Amann, R. I., Ludwig, W., and Schleifer, K. H.: Phylogenetic identification
and in situ detection of individual microbial cells without cultivation,
Microbiol. Rev., 59, 143–169, 1995.
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, 2017a.
Amato, P., Brisebois, E., Draghi, M., Duchaine, C., Fröhlich-Nowoisky,
J., Huffman, J. A., Mainelis, G., Robine, E., and Thibaudon, M.: Main
biological aerosols, specificities, abundance, and diversity, in:
Microbiology of Aerosols, edited by: Delort, A. and Amato, P., 3–22,
https://doi.org/10.1002/9781119132318.ch1a, 2017b.
Andrews, S.: FastQC: a quality control tool for high throughput sequence
data, Babraham Bioinfomatics, available at:
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (last access:
27 June 2017), 2010.
Atkinson, R., Aschmann, S. M., and Arey, J.: Reactions of OH and
NO3 radicals with phenol, cresols, and 2-nitrophenol at 296±2 K, Environ. Sci. Technol., 26, 1397–1403, https://doi.org/10.1021/es00031a018, 1992.
Auffret, M. D., Yergeau, E., Labbé, D., Fayolle-Guichard, F., and Greer,
C. W.: Importance of Rhodococcus strains in a bacterial consortium
degrading a mixture of hydrocarbons, gasoline, and diesel oil additives
revealed by metatranscriptomic analysis, Appl. Microbiol. Biot., 99,
2419–2430, https://doi.org/10.1007/s00253-014-6159-8, 2015.
Babich, H. and Davis, D. L.: Phenol: a review of environmental and health
risks, Regul. Toxicol. Pharm., 1, 90–109, https://doi.org/10.1016/0273-2300(81)90071-4,
1981.
Bartoli, C., Lamichhane, J. R., Berge, O., Guilbaud, C., Varvaro, L.,
Balestra, G. M., Vinatzer, B. A., and Morris, C. E.: A framework to gauge the
epidemic potential of plant pathogens in environmental reservoirs: the
example of kiwifruit canker, Mol. Plant Pathol., 16, 137–149,
https://doi.org/10.1111/mpp.12167, 2015.
Basha, K. M., Rajendran, A., and Thangavelu, V.: Recent advances in the
biodegradation of phenol: a review, Asian Journal of Experimental Biological
Sciences, 1, 219–234, 2010.
Berge, O., Monteil, C. L., Bartoli, C., Chandeysson, C., Guilbaud, C., Sands,
D. C., and Morris, C. E.: A user's guide to a data base of the diversity of
Pseudomonas syringae and its application to classifying strains in
this phylogenetic complex, PLoS One, 9, e105547, https://doi.org/10.1371/journal.pone.0105547, 2014.
Besaury, L., Amato, P., Sancelme, M., and Delort, A. M.: Draft genome
sequence of Pseudomonas syringae PDD-32b-74, a model strain for
ice-nucleation studies in the atmosphere, Genome Announcements, 5, 28751406,
https://doi.org/10.1128/genomeA.00742-17, 2017a.
Besaury, L., Amato, P., Wirgot, N., Sancelme, M., and Delort, A. M.: Draft
genome sequence of Pseudomonas graminis PDD-13b-3, a model strain
isolated from cloud water, Genome Announcements, 5,
https://doi.org/10.1128/genomeA.00464-17, 2017b.
Brennerova, M. V., Josefiova, J., Brenner, V., Pieper, D. H., and Junca, H.:
Metagenomics reveals diversity and abundance of meta-cleavage pathways in
microbial communities from soil highly contaminated with jet fuel under
air-sparging bioremediation, Environ. Microbiol., 11, 2216–2227,
https://doi.org/10.1111/j.1462-2920.2009.01943.x, 2009.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer,
K., and Madden, T. L.: BLAST+: architecture and applications, BMC
Bioinformatics, 10, 421, https://doi.org/10.1186/1471-2105-10-421, 2009.
Choi, E. J., Jin, H. M., Lee, S. H., Math, R. K., Madsen, E. L., and Jeon, C.
O.: Comparative genomic analysis and BTEX degradation pathways of
Pseudoxanthomonas spadix BD-a59, Appl. Environ. Microbiol., 79,
663–671, https://doi.org/10.1128/AEM.02809-12, 2013.
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.
Delort, A.-M., Vaïtilingom, M., Amato, P., Sancelme, M., Parazols, M.,
Mailhot, G., Laj, P., and Deguillaume, L.: A short overview of the microbial
population in clouds: potential roles in atmospheric chemistry and nucleation
processes, Atmos. Res., 98, 249–260, https://doi.org/10.1016/j.atmosres.2010.07.004,
2010.
Delort, A. M., Vaïtilingom, M., Joly, M., Amato, P., Wirgot, N.,
Lallement, A., Sancelme, M., Matulova, M., and Deguillaume, L.: Clouds: a
transient and stressing habitat for microorganisms, in: Microbial Ecology of
Extreme Environments, edited by: Chénard, C. and Lauro, F. M., 215–245,
Springer International Publishing, https://doi.org/10.1007/978-3-319-51686-8_10, 2017.
Der Yang, R. and Humphrey, A. E.: Dynamic and steady state studies of phenol
biodegradation in pure and mixed cultures, Biotechnol. Bioeng., 17,
1211–1235, https://doi.org/10.1002/bit.260170809, 1975.
Duan, W., Meng, F., Cui, H., Lin, Y., Wang, G., and Wu, J.: Ecotoxicity of
phenol and cresols to aquatic organisms: a review, Ecotox. Environ. Safe.,
157, 441–456, https://doi.org/10.1016/j.ecoenv.2018.03.089, 2018.
Erhan, E., Yer, E., Akay, G., Keskinler, B., and Keskinler, D.: Phenol
degradation in a fixed-bed bioreactor using micro-cellular
polymer-immobilized Pseudomonas syringae, J. Chem. Technol.
Biotechnol., 79, 195–206, https://doi.org/10.1002/jctb.938, 2004.
Fang, H., Cai, L., Yu, Y., and Zhang, T.: Metagenomic analysis reveals the
prevalence of biodegradation genes for organic pollutants in activated
sludge, Bioresource Technol., 129, 209–218,
https://doi.org/10.1016/j.biortech.2012.11.054, 2013.
Gami, A. A., Shukor, M. Y., Khalil, K. A., Dahalan, F. A., Khalid, A., and
Ahmad, S. A.: Phenol and its toxicity, Journal of Environmental Microbiology
and Toxicology, 2, 11–24, 2014.
Gilardoni, S., Massoli, P., Paglione, M., Giulianelli, L., Carbone, C.,
Rinaldi, M., Decesari, S., Sandrini, S., Costabile, F., Gobbi, G. P.,
Pietrogrande, M. C., Visentin, M., Scotto, F., Fuzzi, S., and Facchini, M.
C.: Direct observation of aqueous secondary organic aerosol from
biomass-burning emissions, P. Natl. Acad. Sci. USA, 113, 10013–10018,
https://doi.org/10.1073/pnas.1602212113, 2016.
Grosjean, D.: Atmospheric fate of toxic aromatic compounds, Sci. Total
Environ., 100, 367–414, https://doi.org/10.1016/0048-9697(91)90386-S, 1991.
Harrison, M. A. J., Cape, J. N., and Heal, M. R.: Experimentally determined
Henry's law coefficients of phenol, 2-methylphenol and 2-nitrophenol in the
temperature range 281–302 K, Atmos. Environ., 36, 1843–1851,
https://doi.org/10.1016/S1352-2310(02)00137-1, 2002.
Harrison, M. A. J., Barra, S., Borghesi, D., Vione, D., Arsene, C., and
Olariu, R. I.: Nitrated phenols in the atmosphere: a review, Atmos. Environ.,
39, 231–248, https://doi.org/10.1016/j.atmosenv.2004.09.044, 2005.
Heal, M. R., Pilling, M. J., Titcombe, P. E., and Whitaker, B. J.: Mass
accommodation of aniline, phenol and toluene on aqueous droplets, Geophys.
Res. Lett., 22, 3043–3046, https://doi.org/10.1029/95GL02944, 1995.
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, 1–16,
https://doi.org/10.1029/2006JD008002, 2007.
Jadeja, N. B., More, R. P., Purohit, H. J., and Kapley, A.: Metagenomic
analysis of oxygenases from activated sludge, Bioresource Technol., 165,
250–256, https://doi.org/10.1016/j.biortech.2014.02.045, 2014.
Joly, M., Attard, E., Sancelme, M., Deguillaume, L., Guilbaud, C., Morris, C.
E., Amato, P., and Delort, A.-M.: Ice nucleation activity of bacteria
isolated from cloud water, Atmos. Environ., 70, 392–400,
https://doi.org/10.1016/j.atmosenv.2013.01.027, 2013.
Kafilzadeh, F., Farhangdoost, M.-S., and Tahery, Y.: Isolation and
identification of phenol degrading bacteria from Lake Parishan and their
growth kinetic assay, Afr. J. Biotechnol., 9, 6721–6726, 2010.
Kumar, A., Kumar, S., and Kumar, S.: Biodegradation kinetics of phenol and
catechol using Pseudomonas putida MTCC 1194, Biochem. Eng. J., 22,
151–159, https://doi.org/10.1016/j.bej.2004.09.006, 2005.
Lallement, A., Besaury, L., Eyheraguibel, B., Amato, P., Sancelme, M.,
Mailhot, G., and Delort, A. M.: Draft genome sequence of Rhodococcus enclensis 23b-28, a model strain isolated from cloud water, Genome
Announcements, 5, 29074669, https://doi.org/10.1128/genomeA.01199-17, 2017.
Langmead, B. and Salzberg, S. L.: Fast gapped-read alignment with Bowtie 2,
Nature Methods, 9, 357–359, https://doi.org/10.1038/nmeth.1923, 2012.
Lebedev, A. T., Polyakova, O. V., Mazur, D. M., and Artaev, V. B.: The
benefits of high resolution mass spectrometry in environmental analysis,
Analyst, 138, 6946–6953, https://doi.org/10.1039/C3AN01237A, 2013.
Lebedev, A. T., Polyakova, O. V., Mazur, D. M., Artaev, V. B., Canet, I.,
Lallement, A., Vaïtilingom, M., Deguillaume, L., and Delort, A.-M.:
Detection of semi-volatile compounds in cloud waters by GC × GC-TOF-MS. Evidence of phenols and phthalates as priority pollutants,
Environ. Pollut., 241, 616–625, https://doi.org/10.1016/j.envpol.2018.05.089, 2018.
Leinonen, R., Nardone, F., Zhu, W., and Apweiler, R.: UniSave: the UniProtKB
sequence/annotation version database, Bioinformatics, 22, 1284–1285,
https://doi.org/10.1093/bioinformatics/btl105, 2006.
Li, H.: Aligning sequence reads, clone sequences and assembly contigs with
BWA-MEM, arXiv preprint arXiv:1303.3997, available at: https://arxiv.org/pdf/1303.3997.pdf (last access: 5 September 2018), 2013.
Lober, C. W.: Chemexfoliation – indications and cautions, J. Am. Acad.
Dermatol., 17, 109–112, https://doi.org/10.1016/S0190-9622(87)70181-9, 1987.
Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G., and
Neufeld, J. D.: PANDAseq: paired-end assembler for illumina sequences, BMC
Bioinformatics, 13, 31, https://doi.org/10.1186/1471-2105-13-31, 2012.
Michalowicz, J. and Duda, W.: Phenols transformations in the environment and
living organisms, Current Topics in Biophysics, 30, 24–36, 2007.
Mishra, V. K. and Kumar, N.: Microbial degradation of phenol: a review,
Journal of Water Pollution and Purification Research, 4, 17–22, 2017.
Molin, G. and Nilsson, I.: Degradation of phenol by Pseudomonas putida ATCC 11172 in continuous culture at different ratios of biofilm
surface to culture volume, Appl. Environ. Microbiol., 50, 946–950, 1985.
Morris, C. E., Sands, D. C., Vinatzer, B. A., Glaux, C., Guilbaud, C.,
Buffiere, A., Yan, S., Dominguez, H., and Thompson, B. M.: The life history
of the plant pathogen Pseudomonas syringae is linked to the water
cycle, ISME J., 2, 321–334, https://doi.org/10.1038/ismej.2007.113, 2008.
Olariu, R. I.: Atmospheric oxidation of selected aromatic hydrocarbons,
Doctoral Thesis, Bergische Universitat Gesamthochschule Wuppertal, Wuppertal,
2001.
Olariu, R. I., Klotz, B., Barnes, I., Becker, K. H., and Mocanu, R.: FT–IR
study of the ring-retaining products from the reaction of OH radicals with
phenol, o-, m-, and p-cresol, Atmos. Environ., 36, 3685–3697,
https://doi.org/10.1016/S1352-2310(02)00202-9, 2002.
Padmanabhan, P., Padmanabhan, S., DeRito, C., Gray, A., Gannon, D., Snape, J.
R., Tsai, C. S., Park, W., Jeon, C., and Madsen, E. L.: Respiration of
13C-labeled substrates added to soil in the field and subsequent
16S rRNA gene analysis of 13C-labeled soil DNA, Appl. Environ.
Microbiol., 69, 1614–1622, https://doi.org/10.1128/AEM.69.3.1614-1622.2003, 2003.
Rayne, S., Forest, K., and Friesen, K. J.: Mechanistic aspects regarding the
direct aqueous environmental photochemistry of phenol and its simple
halogenated derivatives. A review, Environ. Int., 35, 425–437,
https://doi.org/10.1016/j.envint.2008.09.004, 2009.
Reasoner, D. J. and Geldreich, E. E.: A new medium for the enumeration and
subculture of bacteria from potable water, Appl. Environ. Microb., 49, 1–7,
1985.
Renard, P., Canet, I., Sancelme, M., Wirgot, N., Deguillaume, L., and Delort,
A.-M.: Screening of cloud microorganisms isolated at the Puy de Dôme
(France) station for the production of biosurfactants, Atmos. Chem. Phys.,
16, 12347–12358, https://doi.org/10.5194/acp-16-12347-2016, 2016.
Rubio, M. A., Lissi, E., Herrera, N., Pérez, V., and Fuentes, N.: Phenol
and nitrophenols in the air and dew waters of Santiago de Chile, Chemosphere,
86, 1035–1039, https://doi.org/10.1016/j.chemosphere.2011.11.046, 2012.
Sandhu, A., Halverson, L. J., and Beattie, G. A.: Bacterial degradation of
airborne phenol in the phyllosphere, Environ. Microbiol., 9, 383–392,
https://doi.org/10.1111/j.1462-2920.2006.01149.x, 2007.
Sandhu, A., Halverson, L. J., and Beattie, G. A.: Identification and genetic
characterization of phenol-degrading bacteria from leaf microbial
communities, Microb. Ecol., 57, 276–285, https://doi.org/10.1007/s00248-008-9473-9,
2009.
Sattler, B., Puxbaum, H., and Psenner, R.: Bacterial growth in supercooled
cloud droplets, Geophys. Res. Lett., 28, 239–242, https://doi.org/10.1029/2000GL011684,
2001.
Schauer, J. J., Kleeman, M. J., Cass, G. R., and Simoneit, B. R. T.:
Measurement of emissions from air pollution sources. 3.
C1-C29 organic compounds from fireplace combustion of
wood, Environ. Sci. Technol., 35, 1716–1728, https://doi.org/10.1021/es001331e, 2001.
Schmieder, R. and Edwards, R.: Quality control and preprocessing of
metagenomic datasets, Bioinformatics, 27, 863–864,
https://doi.org/10.1093/bioinformatics/btr026, 2011.
Schummer, C., Groff, C., Al Chami, J., Jaber, F., and Millet, M.: Analysis of
phenols and nitrophenols in rainwater collected simultaneously on an urban
and rural site in east of France, Sci. Total Environ., 407, 5637–5643,
https://doi.org/10.1016/j.scitotenv.2009.06.051, 2009.
Sharma, N., Tanksale, H., Kapley, A., and Purohit, H. J.: Mining the
metagenome of activated biomass of an industrial wastewater treatment plant
by a novel method, Indian J. Microbiol., 52, 538–543,
https://doi.org/10.1007/s12088-012-0263-1, 2012.
Silva, C. C., Hayden, H., Sawbridge, T., Mele, P., De Paula, S. O., Silva, L.
C. F., Vidigal, P. M. P., Vicentini, R., Sousa, M. P., Torres, A. P. R.,
Santiago, V. M. J., and Oliveira, V. M.: Identification of genes and pathways
related to phenol degradation in metagenomic libraries from petroleum
refinery wastewater, PLoS One, 8, e61811, https://doi.org/10.1371/journal.pone.0061811,
2013.
Sridevi, V., Chandana Lakshmi, M. V. V., Manasa, M., and Sravani, M.:
Metabolic pathways for the biodegradation of phenol, International Journal of
Engineering Science and Advanced Technology, 2, 695–705, 2012.
Sturaro, A., Rella, R., Parvoli, G., and Ferrara, D.: Long-term phenol,
cresols and BTEX monitoring in urban air, Environ. Monit. Assess., 164,
93–100, https://doi.org/10.1007/s10661-009-0877-x, 2010.
Suenaga, H., Koyama, Y., Miyakoshi, M., Miyazaki, R., Yano, H., Sota, M.,
Ohtsubo, Y., Tsuda, M., and Miyazaki, K.: Novel organization of aromatic
degradation pathway genes in a microbial community as revealed by metagenomic
analysis, ISME J., 3, 1335–1348, https://doi.org/10.1038/ismej.2009.76, 2009.
Sun, Y. L., Zhang, Q., Anastasio, C., and Sun, J.: Insights into secondary
organic aerosol formed via aqueous-phase reactions of phenolic compounds
based on high resolution mass spectrometry, Atmos. Chem. Phys., 10,
4809–4822, https://doi.org/10.5194/acp-10-4809-2010, 2010.
Tao, Y., Fishman, A., Bentley, W. E., and Wood, T. K.: Oxidation of benzene
to phenol, catechol, and 1, 2, 3-trihydroxybenzene by toluene 4-monooxygenase
of Pseudomonas mendocina KR1 and toluene 3-monooxygenase of
Ralstonia pickettii PKO1, Appl. Environ. Microbiol., 70, 3814–3820,
https://doi.org/10.1128/AEM.70.7.3814-3820.2004, 2004.
Tian, M., Du, D., Zhou, W., Zeng, X., and Cheng, G.: Phenol degradation and
genotypic analysis of dioxygenase genes in bacteria isolated from sediments,
Braz. J. Microbiol., 48, 305–313, https://doi.org/10.1016/j.bjm.2016.12.002, 2017.
Vaïtilingom, M., Amato, P., Sancelme, M., Laj, P., Leriche, M., and
Delort, A.-M.: Contribution of microbial activity to carbon chemistry in
clouds, Appl. Environ. Microbiol., 76, 23–29, https://doi.org/10.1128/AEM.01127-09,
2010.
Vaïtilingom, M., Attard, E., Gaiani, N., Sancelme, M., Deguillaume, L.,
Flossmann, A. I., Amato, P., and Delort, A.-M.: Long-term features of cloud
microbiology at the puy de Dôme (France), Atmos. Environ., 56, 88–100,
https://doi.org/10.1016/j.atmosenv.2012.03.072, 2012.
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.
Vione, D., Barra, S., de Gennaro, G., de Rienzo, M., Gilardoni, S., Perrone,
M. G., and Pozzoli, L.: Polycyclic aromatic hydrocarbons in the atmosphere:
monitoring, sources, sinks and fate. II: sinks and fate, Ann. Chim. Banner,
94, 257–268, https://doi.org/10.1002/adic.200490031, 2004.
Volkamer, R., Klotz, B., Barnes, I., Imamura, T., Wirtz, K., Washida, N.,
Heinz Becker, K., and Platt, U.: OH-initiated oxidation of benzene Part I.
Phenol formation under atmospheric conditions, Phys. Chem. Chem. Phys., 4,
1598–1610, https://doi.org/10.1039/B108747A, 2002.
Zhai, A.: Determination of phenols in drinking water with agilent bond elut
plexa SPE and HPLC, Agilent, available at:
https://www.agilent.com/cs/library/applications/5990-9730EN.pdf (last
access: 10 October 2017), 2012.
Short summary
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.
The main objective of this work was to evaluate the potential degradation of phenol, a highly...
Altmetrics
Final-revised paper
Preprint