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Microorganisms
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Microbial Cycling of Atmospheric Trace Gases
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Microbial Cycling of Atmospheric Trace Gases

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 January 2021) | Viewed by 44009

Special Issue Editors

Dr. Marcela Hernández

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Guest Editor
School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
Interests: methanogens in paddy rice soils; carbon monoxide oxidisers in volcanic soils
Dr. Marc G. Dumont

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Guest Editor
School of Biological Sciences, University of Southampton, Southampton, UK
Interests: methanotrophic bacteria; interaction between plants and microorganisms in the rhizosphere
Prof. Dr. Colin Murrell

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Guest Editor
School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
Interests: microbiology of atmospheric trace gases; methanotrophic and methylotrophic bacteria; microbial growth on C1 compounds
Prof. Dr. Terry McGenity

E-Mail Website
Guest Editor
School of Biological Sciences, University of Essex, Colchester, Essex, UK
Interests: carbon cycling; isoprene cycling; bioremediation and pollution microbiology; extremophiles; astrobiology; halophiles

Special Issue Information

Dear Colleagues,

Atmospheric trace gases are those with mixing ratios <1% (10,000 ppmv), and most exist at concentrations below 20 ppmv. Despite their low concentration, many can influence atmospheric chemistry and climate. Terrestrial ecosystems are important controllers of trace gases, but the role of the biosphere in controlling the flux of these gases is still poorly understood. Microorganisms in particular are responsible for both the production and consumption of trace gases. These include gases with relatively high global warming potentials, such as methane and nitrous oxide. The pathways for their production and consumption have been studied for decades, yet new routes for their metabolism are continuously being discovered. Other gases, such as hydrogen and carbon monoxide are less well studied. In addition, the microbial metabolism of biogenic volatile organic compounds (BVOCs) is poorly characterized. Examples of BVOCs are halogenated methanes, methanol, acetone, propanol, acetaldehyde, methylated amines, dimethylsulfide, terpenes, isoprene, gaseous alkanes, alkenes, and aromatics. The Special Issue will present fundamental and applied research on microorganisms, in either pure culture or uncultured within complex communities within the natural environment, which produce or consume atmospheric trace gases. If you wish to submit a manuscript for consideration, please send a document with a tentative title, list of authors, and a short abstract to Dr. Marcela Hernández.

Dr. Marcela Hernandez
Dr. Marc G. Dumont
Prof. Dr. Colin Murrell
Prof. Dr. Terry McGenity
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (13 papers)

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Research

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20 pages, 2985 KiB  
Article
Disproportionate CH4 Sink Strength from an Endemic, Sub-Alpine Australian Soil Microbial Community
by Marshall D. McDaniel, Marcela Hernández, Marc G. Dumont, Lachlan J. Ingram and Mark A. Adams
Microorganisms 2021, 9(3), 606; https://doi.org/10.3390/microorganisms9030606 - 15 Mar 2021
Cited by 2 | Viewed by 2794
Abstract
Soil-to-atmosphere methane (CH4) fluxes are dependent on opposing microbial processes of production and consumption. Here we use a soil–vegetation gradient in an Australian sub-alpine ecosystem to examine links between composition of soil microbial communities, and the fluxes of greenhouse gases they [...] Read more.
Soil-to-atmosphere methane (CH4) fluxes are dependent on opposing microbial processes of production and consumption. Here we use a soil–vegetation gradient in an Australian sub-alpine ecosystem to examine links between composition of soil microbial communities, and the fluxes of greenhouse gases they regulate. For each soil/vegetation type (forest, grassland, and bog), we measured carbon dioxide (CO2) and CH4 fluxes and their production/consumption at 5 cm intervals to a depth of 30 cm. All soils were sources of CO2, ranging from 49 to 93 mg CO2 m−2 h−1. Forest soils were strong net sinks for CH4, at rates of up to −413 µg CH4 m−2 h−1. Grassland soils varied, with some soils acting as sources and some as sinks, but overall averaged −97 µg CH4 m−2 h−1. Bog soils were net sources of CH4 (+340 µg CH4 m−2 h−1). Methanotrophs were dominated by USCα in forest and grassland soils, and Candidatus Methylomirabilis in the bog soils. Methylocystis were also detected at relatively low abundance in all soils. Our study suggests that there is a disproportionately large contribution of these ecosystems to the global soil CH4 sink, which highlights our dependence on soil ecosystem services in remote locations driven by unique populations of soil microbes. It is paramount to explore and understand these remote, hard-to-reach ecosystems to better understand biogeochemical cycles that underpin global sustainability. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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15 pages, 3653 KiB  
Article
A Novel Moderately Thermophilic Facultative Methylotroph within the Class Alphaproteobacteria
by Tajul Islam, Marcela Hernández, Amare Gessesse, J. Colin Murrell and Lise Øvreås
Microorganisms 2021, 9(3), 477; https://doi.org/10.3390/microorganisms9030477 - 25 Feb 2021
Cited by 8 | Viewed by 3253
Abstract
Methylotrophic bacteria (non-methanotrophic methanol oxidizers) consuming reduced carbon compounds containing no carbon–carbon bonds as their sole carbon and energy source have been found in a great variety of environments. Here, we report a unique moderately thermophilic methanol-oxidising bacterium (strain LS7-MT) that grows optimally [...] Read more.
Methylotrophic bacteria (non-methanotrophic methanol oxidizers) consuming reduced carbon compounds containing no carbon–carbon bonds as their sole carbon and energy source have been found in a great variety of environments. Here, we report a unique moderately thermophilic methanol-oxidising bacterium (strain LS7-MT) that grows optimally at 55 °C (with a growth range spanning 30 to 60 °C). The pure isolate was recovered from a methane-utilizing mixed culture enrichment from an alkaline thermal spring in the Ethiopia Rift Valley, and utilized methanol, methylamine, glucose and a variety of multi-carbon compounds. Phylogenetic analysis of the 16S rRNA gene sequences demonstrated that strain LS7-MT represented a new facultatively methylotrophic bacterium within the order Hyphomicrobiales of the class Alphaproteobacteria. This new strain showed 94 to 96% 16S rRNA gene identity to the two methylotroph genera, Methyloceanibacter and Methyloligella. Analysis of the draft genome of strain LS7-MT revealed genes for methanol dehydrogenase, essential for methanol oxidation. Functional and comparative genomics of this new isolate revealed genomic and physiological divergence from extant methylotrophs. Strain LS7-MT contained a complete mxaF gene cluster and xoxF1 encoding the lanthanide-dependent methanol dehydrogenase (XoxF). This is the first report of methanol oxidation at 55 °C by a moderately thermophilic bacterium within the class Alphaproteobacteria. These findings expand our knowledge of methylotrophy by the phylum Proteobacteria in thermal ecosystems and their contribution to global carbon and nitrogen cycles. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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12 pages, 1685 KiB  
Article
Simultaneous Oxidation of Atmospheric Methane, Carbon Monoxide and Hydrogen for Bacterial Growth
by Alexander Tøsdal Tveit, Tilman Schmider, Anne Grethe Hestnes, Matteus Lindgren, Alena Didriksen and Mette Marianne Svenning
Microorganisms 2021, 9(1), 153; https://doi.org/10.3390/microorganisms9010153 - 12 Jan 2021
Cited by 10 | Viewed by 3353
Abstract
The second largest sink for atmospheric methane (CH4) is atmospheric methane oxidizing-bacteria (atmMOB). How atmMOB are able to sustain life on the low CH4 concentrations in air is unknown. Here, we show that during growth, with air as its only [...] Read more.
The second largest sink for atmospheric methane (CH4) is atmospheric methane oxidizing-bacteria (atmMOB). How atmMOB are able to sustain life on the low CH4 concentrations in air is unknown. Here, we show that during growth, with air as its only source for energy and carbon, the recently isolated atmospheric methane-oxidizer Methylocapsa gorgona MG08 (USCα) oxidizes three atmospheric energy sources: CH4, carbon monoxide (CO), and hydrogen (H2) to support growth. The cell-specific CH4 oxidation rate of M. gorgona MG08 was estimated at ~0.7 × 10−18 mol cell−1 h−1, which, together with the oxidation of CO and H2, supplies 0.38 kJ Cmol−1 h−1 during growth in air. This is seven times lower than previously assumed necessary to support bacterial maintenance. We conclude that atmospheric methane-oxidation is supported by a metabolic flexibility that enables the simultaneous harvest of CH4, H2 and CO from air, but the key characteristic of atmospheric CH4 oxidizing bacteria might be very low energy requirements. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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18 pages, 1792 KiB  
Article
Anaerobic Carbon Monoxide Uptake by Microbial Communities in Volcanic Deposits at Different Stages of Successional Development on O-yama Volcano, Miyake-jima, Japan
by Amber N. DePoy, Gary M. King and Hiroyuki Ohta
Microorganisms 2021, 9(1), 12; https://doi.org/10.3390/microorganisms9010012 - 22 Dec 2020
Cited by 4 | Viewed by 2101
Abstract
Research on Kilauea and O-yama Volcanoes has shown that microbial communities and their activities undergo major shifts in response to plant colonization and that molybdenum-dependent CO oxidizers (Mo-COX) and their activities vary with vegetation and deposit age. Results reported here reveal that anaerobic [...] Read more.
Research on Kilauea and O-yama Volcanoes has shown that microbial communities and their activities undergo major shifts in response to plant colonization and that molybdenum-dependent CO oxidizers (Mo-COX) and their activities vary with vegetation and deposit age. Results reported here reveal that anaerobic CO oxidation attributed to nickel-dependent CO oxidizers (Ni-COX) also occurs in volcanic deposits that encompass different developmental stages. Ni-COX at three distinct sites responded rapidly to anoxia and oxidized CO from initial concentrations of about 10 ppm to sub-atmospheric levels. CO was also actively consumed at initial 25% concentrations and 25 °C, and during incubations at 60 °C; however, uptake under the latter conditions was largely confined to an 800-year-old forested site. Analyses of microbial communities based on 16S rRNA gene sequences in treatments with and without 25% CO incubated at 25 °C or 60 °C revealed distinct responses to temperature and CO among the sites and evidence for enrichment of known and potentially novel Ni-COX. The results collectively show that CO uptake by volcanic deposits occurs under a wide range of conditions; that CO oxidizers in volcanic deposits may be more diverse than previously imagined; and that Ni-dependent CO oxidizers might play previously unsuspected roles in microbial succession. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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16 pages, 3149 KiB  
Article
Reconstructing Genomes of Carbon Monoxide Oxidisers in Volcanic Deposits Including Members of the Class Ktedonobacteria
by Marcela Hernández, Blanca Vera-Gargallo, Marcela Calabi-Floody, Gary M. King, Ralf Conrad and Christoph C. Tebbe
Microorganisms 2020, 8(12), 1880; https://doi.org/10.3390/microorganisms8121880 - 27 Nov 2020
Cited by 11 | Viewed by 3746
Abstract
Microorganisms can potentially colonise volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H2) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of [...] Read more.
Microorganisms can potentially colonise volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H2) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of 380, 269 and 63 years, respectively. A total of 19 metagenome-assembled genomes (MAGs) were retrieved from all stages with a higher number observed in the youngest soil (1640: 2 MAGs, 1751: 1 MAG, 1957: 16 MAGs). Genomic similarity indices showed that several MAGs had amino-acid identity (AAI) values >50% to the phyla Actinobacteria, Acidobacteria, Gemmatimonadetes, Proteobacteria and Chloroflexi. Three MAGs from the youngest site (1957) belonged to the class Ktedonobacteria (Chloroflexi). Complete cellular functions of all the MAGs were characterised, including carbon fixation, terpenoid backbone biosynthesis, formate oxidation and CO oxidation. All 19 environmental genomes contained at least one gene encoding a putative carbon monoxide dehydrogenase (CODH). Three MAGs had form I coxL operon (encoding the large subunit CO-dehydrogenase). One of these MAGs (MAG-1957-2.1, Ktedonobacterales) was highly abundant in the youngest soil. MAG-1957-2.1 also contained genes encoding a [NiFe]-hydrogenase and hyp genes encoding accessory enzymes and proteins. Little is known about the Ktedonobacterales through cultivated isolates, but some species can utilise H2 and CO for growth. Our results strongly suggest that the remote volcanic sites in Chile represent a natural habitat for Ktedonobacteria and they may use reduced gases for growth. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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16 pages, 2784 KiB  
Article
Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves
by Nasmille L. Larke-Mejía, Ornella Carrión, Andrew T. Crombie, Terry J. McGenity and J. Colin Murrell
Microorganisms 2020, 8(10), 1557; https://doi.org/10.3390/microorganisms8101557 - 10 Oct 2020
Cited by 14 | Viewed by 2843
Abstract
The volatile secondary metabolite, isoprene, is released by trees to the atmosphere in enormous quantities, where it has important effects on air quality and climate. Oil palm trees, one of the highest isoprene emitters, are increasingly dominating agroforestry over large areas of Asia, [...] Read more.
The volatile secondary metabolite, isoprene, is released by trees to the atmosphere in enormous quantities, where it has important effects on air quality and climate. Oil palm trees, one of the highest isoprene emitters, are increasingly dominating agroforestry over large areas of Asia, with associated uncertainties over their effects on climate. Microbes capable of using isoprene as a source of carbon for growth have been identified in soils and in the tree phyllosphere, and most are members of the Actinobacteria. Here, we used DNA stable isotope probing to identify the isoprene-degrading bacteria associated with oil palm leaves and inhabiting the surrounding soil. Among the most abundant isoprene degraders of the leaf-associated community were members of the Sphingomonadales, although no representatives of this order were previously known to degrade isoprene. Informed by these data, we obtained representatives of the most abundant isoprene degraders in enrichments, including Sphingopyxis strain OPL5 (Sphingomonadales), able to grow on isoprene as the sole source of carbon and energy. Sequencing of the genome of strain OPL5, as well as a novel Gordonia strain, confirmed their pathways of isoprene degradation and broadened our knowledge of the genetic and taxonomic diversity of this important bacterial trait. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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9 pages, 1561 KiB  
Communication
An Unexpectedly Broad Thermal and Salinity-Tolerant Estuarine Methanogen Community
by Lynsay I. Blake, Angela Sherry, Obioma K. Mejeha, Peter Leary, Henry Coombs, Wendy Stone, Ian M. Head and Neil D. Gray
Microorganisms 2020, 8(10), 1467; https://doi.org/10.3390/microorganisms8101467 - 24 Sep 2020
Cited by 4 | Viewed by 2329
Abstract
Moderately thermophilic (Tmax, ~55 °C) methanogens are identified after extended enrichments from temperate, tropical and low-temperature environments. However, thermophilic methanogens with higher growth temperatures (Topt ≥ 60 °C) are only reported from high-temperature environments. A microcosm-based approach was used to [...] Read more.
Moderately thermophilic (Tmax, ~55 °C) methanogens are identified after extended enrichments from temperate, tropical and low-temperature environments. However, thermophilic methanogens with higher growth temperatures (Topt ≥ 60 °C) are only reported from high-temperature environments. A microcosm-based approach was used to measure the rate of methane production and methanogen community structure over a range of temperatures and salinities in sediment from a temperate estuary. We report short-term incubations (<48 h) revealing methanogens with optimal activity reaching 70 °C in a temperate estuary sediment (in situ temperature 4–5 °C). While 30 °C enrichments amended with acetate, H2 or methanol selected for corresponding mesophilic trophic groups, at 60 °C, only hydrogenotrophs (genus Methanothermobacter) were observed. Since these methanogens are not known to be active under in situ temperatures, we conclude constant dispersal from high temperature habitats. The likely provenance of the thermophilic methanogens was studied by enrichments covering a range of temperatures and salinities. These enrichments indicated that the estuarine sediment hosted methanogens encompassing the global activity envelope of most cultured species. We suggest that estuaries are fascinating sink and source environments for microbial function study. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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15 pages, 1755 KiB  
Article
Niche Differentiation of Active Methane-Oxidizing Bacteria in Estuarine Mangrove Forest Soils in Taiwan
by Yo-Jin Shiau, Chiao-Wen Lin, Yuanfeng Cai, Zhongjun Jia, Yu-Te Lin and Chih-Yu Chiu
Microorganisms 2020, 8(8), 1248; https://doi.org/10.3390/microorganisms8081248 - 17 Aug 2020
Cited by 12 | Viewed by 3366
Abstract
Mangrove forests are one of the important ecosystems in tropical coasts because of their high primary production, which they sustain by sequestering a substantial amount of CO2 into plant biomass. These forests often experience various levels of inundation and play an important [...] Read more.
Mangrove forests are one of the important ecosystems in tropical coasts because of their high primary production, which they sustain by sequestering a substantial amount of CO2 into plant biomass. These forests often experience various levels of inundation and play an important role in CH4 emissions, but the taxonomy of methanotrophs in these systems remains poorly understood. In this study, DNA-based stable isotope probing showed significant niche differentiation in active aerobic methanotrophs in response to niche differentiation in upstream and downstream mangrove soils of the Tamsui estuary in northwestern Taiwan, in which salinity levels differ between winter and summer. Methylobacter and Methylomicrobium-like Type I methanotrophs dominated methane-oxidizing communities in the field conditions and were significantly 13C-labeled in both upstream and downstream sites, while Methylobacter were well adapted to high salinity and low temperature. The Type II methanotroph Methylocystis comprised only 10–15% of all the methane oxidizers in the upstream site but less than 5% at the downstream site under field conditions. 13C-DNA levels in Methylocystis were significantly lower than those in Type I methanotrophs, while phylogenetic analysis further revealed the presence of novel methane oxidizers that are phylogenetically distantly related to Type Ia in fresh and incubated soils at a downstream site. These results suggest that Type I methanotrophs display niche differentiation associated with environmental differences between upstream and downstream mangrove soils. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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18 pages, 2469 KiB  
Article
Isoprene Oxidation by the Gram-Negative Model bacterium Variovorax sp. WS11
by Robin A. Dawson, Nasmille L. Larke-Mejía, Andrew T. Crombie, Muhammad Farhan Ul Haque and J. Colin Murrell
Microorganisms 2020, 8(3), 349; https://doi.org/10.3390/microorganisms8030349 - 29 Feb 2020
Cited by 15 | Viewed by 3689
Abstract
Plant-produced isoprene (2-methyl-1,3-butadiene) represents a significant portion of global volatile organic compound production, equaled only by methane. A metabolic pathway for the degradation of isoprene was first described for the Gram-positive bacterium Rhodococcus sp. AD45, and an alternative model organism has yet to [...] Read more.
Plant-produced isoprene (2-methyl-1,3-butadiene) represents a significant portion of global volatile organic compound production, equaled only by methane. A metabolic pathway for the degradation of isoprene was first described for the Gram-positive bacterium Rhodococcus sp. AD45, and an alternative model organism has yet to be characterised. Here, we report the characterisation of a novel Gram-negative isoprene-degrading bacterium, Variovorax sp. WS11. Isoprene metabolism in this bacterium involves a plasmid-encoded iso metabolic gene cluster which differs from that found in Rhodococcus sp. AD45 in terms of organisation and regulation. Expression of iso metabolic genes is significantly upregulated by both isoprene and epoxyisoprene. The enzyme responsible for the initial oxidation of isoprene, isoprene monooxygenase, oxidises a wide range of alkene substrates in a manner which is strongly influenced by the presence of alkyl side-chains and differs from other well-characterised soluble diiron monooxygenases according to its response to alkyne inhibitors. This study presents Variovorax sp. WS11 as both a comparative and contrasting model organism for the study of isoprene metabolism in bacteria, aiding our understanding of the conservation of this biochemical pathway across diverse ecological niches. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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20 pages, 1576 KiB  
Article
Seasonal Changes in Microbial Dissolved Organic Sulfur Transformations in Coastal Waters
by Joanna L Dixon, Frances E Hopkins, John A Stephens and Hendrik Schäfer
Microorganisms 2020, 8(3), 337; https://doi.org/10.3390/microorganisms8030337 - 27 Feb 2020
Cited by 8 | Viewed by 3041
Abstract
The marine trace gas dimethylsulfide (DMS) is the single most important biogenic source of atmospheric sulfur, accounting for up to 80% of global biogenic sulfur emissions. Approximately 300 million tons of DMS are produced annually, but the majority is degraded by microbes in [...] Read more.
The marine trace gas dimethylsulfide (DMS) is the single most important biogenic source of atmospheric sulfur, accounting for up to 80% of global biogenic sulfur emissions. Approximately 300 million tons of DMS are produced annually, but the majority is degraded by microbes in seawater. The DMS precursor dimethylsulfoniopropionate (DMSP) and oxidation product dimethylsulphoxide (DMSO) are also important organic sulfur reservoirs. However, the marine sinks of dissolved DMSO remain unknown. We used a novel combination of stable and radiotracers to determine seasonal changes in multiple dissolved organic sulfur transformation rates to ascertain whether microbial uptake of dissolved DMSO was a significant loss pathway. Surface concentrations of DMS ranged from 0.5 to 17.0 nM with biological consumption rates between 2.4 and 40.8 nM·d−1. DMS produced from the reduction of DMSO was not a significant process. Surface concentrations of total DMSO ranged from 2.3 to 102 nM with biological consumption of dissolved DMSO between 2.9 and 111 nM·d−1. Comparisons between 14C2-DMSO assimilation and dissimilation rates suggest that the majority of dissolved DMSO was respired (>94%). Radiotracer microbial consumption rates suggest that dissimilation of dissolved DMSO to CO2 can be a significant loss pathway in coastal waters, illustrating the significance of bacteria in controlling organic sulfur seawater concentrations. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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Review

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15 pages, 1549 KiB  
Review
Molecular Ecology of Isoprene-Degrading Bacteria
by Ornella Carrión, Terry J. McGenity and J. Colin Murrell
Microorganisms 2020, 8(7), 967; https://doi.org/10.3390/microorganisms8070967 - 27 Jun 2020
Cited by 12 | Viewed by 3095
Abstract
Isoprene is a highly abundant biogenic volatile organic compound (BVOC) that is emitted to the atmosphere in amounts approximating to those of methane. The effects that isoprene has on Earth’s climate are both significant and complex, however, unlike methane, very little is known [...] Read more.
Isoprene is a highly abundant biogenic volatile organic compound (BVOC) that is emitted to the atmosphere in amounts approximating to those of methane. The effects that isoprene has on Earth’s climate are both significant and complex, however, unlike methane, very little is known about the biological degradation of this environmentally important trace gas. Here, we review the mechanisms by which bacteria catabolise isoprene, what is known about the diversity of isoprene degraders in the environment, and the molecular tools currently available to study their ecology. Specifically, we focus on the use of probes based on the gene encoding the α-subunit of isoprene monooxygenase, isoA, and DNA stable-isotope probing (DNA-SIP) alone or in combination with other cultivation-independent techniques to determine the abundance, diversity, and activity of isoprene degraders in the environment. These parameters are essential in order to evaluate how microbes might mitigate the effects of this important but neglected climate-active gas. We also suggest key aspects of isoprene metabolism that require further investigation in order to better understand the global isoprene biogeochemical cycle. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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12 pages, 225 KiB  
Review
Methane Production in Soil Environments—Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation
by Ralf Conrad
Microorganisms 2020, 8(6), 881; https://doi.org/10.3390/microorganisms8060881 - 11 Jun 2020
Cited by 62 | Viewed by 6287
Abstract
Flooding and desiccation of soil environments mainly affect the availability of water and oxygen. While water is necessary for all life, oxygen is required for aerobic microorganisms. In the absence of O2, anaerobic processes such as CH4 production prevail. There [...] Read more.
Flooding and desiccation of soil environments mainly affect the availability of water and oxygen. While water is necessary for all life, oxygen is required for aerobic microorganisms. In the absence of O2, anaerobic processes such as CH4 production prevail. There is a substantial theoretical knowledge of the biogeochemistry and microbiology of processes in the absence of O2. Noteworthy are processes involved in the sequential degradation of organic matter coupled with the sequential reduction of electron acceptors, and, finally, the formation of CH4. These processes follow basic thermodynamic and kinetic principles, but also require the presence of microorganisms as catalysts. Meanwhile, there is a lot of empirical data that combines the observation of process function with the structure of microbial communities. While most of these observations confirmed existing theoretical knowledge, some resulted in new information. One important example was the observation that methanogens, which have been believed to be strictly anaerobic, can tolerate O2 to quite some extent and thus survive desiccation of flooded soil environments amazingly well. Another example is the strong indication of the importance of redox-active soil organic carbon compounds, which may affect the rates and pathways of CH4 production. It is noteworthy that drainage and aeration turns flooded soils, not generally, into sinks for atmospheric CH4, probably due to the peculiarities of the resident methanotrophic bacteria. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)

Other

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8 pages, 546 KiB  
Brief Report
Complete Genome of Isoprene Degrading Nocardioides sp. WS12
by Lisa Gibson, Nasmille L. Larke-Mejía and J. Colin Murrell
Microorganisms 2020, 8(6), 889; https://doi.org/10.3390/microorganisms8060889 - 12 Jun 2020
Cited by 13 | Viewed by 2927
Abstract
Isoprene is a climate-active gas whose wide-spread global production stems mostly from terrestrial plant emissions. The biodegradation of isoprene is carried out by a number of different bacteria from a wide range of environments. This study investigates the genome of a novel isoprene [...] Read more.
Isoprene is a climate-active gas whose wide-spread global production stems mostly from terrestrial plant emissions. The biodegradation of isoprene is carried out by a number of different bacteria from a wide range of environments. This study investigates the genome of a novel isoprene degrading bacterium Nocardioides sp. WS12, isolated from soil associated with Salix alba (Willow), a tree known to produce high amounts of isoprene. The Nocardioides sp. WS12 genome was fully sequenced, revealing the presence of a complete isoprene monooxygenase gene cluster, along with associated isoprene degradation pathway genes. Genes associated with rubber degradation were also present, suggesting that Nocardioides sp. WS12 may also have the capacity to degrade poly-cis-1,4-isoprene. Full article
(This article belongs to the Special Issue Microbial Cycling of Atmospheric Trace Gases)
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