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Microorganisms
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Biology, Diversity, and Ecology of Methanotrophic Bacteria
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Biology, Diversity, and Ecology of Methanotrophic Bacteria

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

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 17118

Special Issue Editors

Dr. Svetlana N. Dedysh

E-Mail Website
Guest Editor
Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117 901 Moscow, Russia
Interests: microbiology of wetlands; acidic peatlands; methanotrophic bacteria; ecology of methanotrophs; planctomycetes; acidobacteria; bacterial systematics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Marina G. Kalyuzhnaya

E-Mail Website
Guest Editor
Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
Interests: single carbon cycling; plant-methanotroph interaction; synthetic methanotrophy; novel methanotrophic traits; symbiosis; methane driven N2-fixation; C1-microbial networks; metagenomics and multi-omics
Special Issues, Collections and Topics in MDPI journals
Prof. Lisa Y. Stein

E-Mail Website
Guest Editor
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
Interests: hypoxic methane oxidation; nitrogen cycling and methanotrophy; value-added products from single-carbon feedstocks; functional genomics; physiological diversity of methanotrophs

Special Issue Information

Dear Colleagues,

Aerobic methanotrophic bacteria are one of the metabolically unique groups of prokaryotes, which play a key role in the global cycling of the potent greenhouse gas methane and other one-carbon compounds. Despite the long history of studying aerobic methanotrophs, these bacteria remain an inexhaustible source of exciting discoveries. These include earlier unknown phenotypes of methanotrophic bacteria, unexpected features of their metabolic organization, and novel aspects of their functioning in the environment. Cultivation-independent studies have revealed the existence of diverse groups of methanotrophs that have not yet been cultured and represent a challenge for further cultivation studies as well as for cultivation-independent -omics approaches. We welcome all kinds of studies covering various aspects of biology, metabolic and taxonomic diversity, ecology and environmental importance of methanotrophic bacteria. Potential topics include but are not limited to the following: novel methanotrophic bacteria; genome-based systematics of methanotrophs; as-yet-unexplored metabolic traits of aerobic methanotrophs and/or synthetic methanotrophy; plant-associated methanotrophs; symbioses and cooperative relationships in native communities; aerobic methanotrophy in extreme environments; ecology and in situ activity of methanotrophic bacteria.

Guest Editors

Dr. Svetlana N. Dedysh
Prof. Marina G. Kalyuzhnaya
Prof. Lisa Y. Stein

 

Keywords

  • Methanotrophic bacteria
  • One-carbon metabolism
  • Genome-based systematics
  • Cultivation
  • Methanotroph ecology

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Published Papers (4 papers)

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13 pages, 3170 KiB  
Article
Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs
by Svetlana E. Belova, Olga V. Danilova, Anastasia A. Ivanova, Alexander Y. Merkel and Svetlana N. Dedysh
Microorganisms 2020, 8(12), 2047; https://doi.org/10.3390/microorganisms8122047 - 21 Dec 2020
Cited by 10 | Viewed by 3254
Abstract
Upland soils of tundra function as a constant sink for atmospheric CH4 but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of −0.4 to −0.6 mg CH4-C m−2 day−1 were determined by [...] Read more.
Upland soils of tundra function as a constant sink for atmospheric CH4 but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of −0.4 to −0.6 mg CH4-C m−2 day−1 were determined by the static chamber method in a mildly acidic upland soil of the lichen-dominated forested tundra, North Siberia, Russia. The maximal CH4 oxidation activity was localized in an organic surface soil layer underlying the lichen cover. Molecular identification of methanotrophic bacteria based on retrieval of the pmoA gene revealed Upland Soil Cluster Alpha (USCα) as the only detectable methanotroph group. Quantification of these pmoA gene fragments by means of specific qPCR assay detected ~107pmoA gene copies g−1 dry soil. The pmoA diversity was represented by seven closely related phylotypes; the most abundant phylotype displayed 97.5% identity to pmoA of Candidatus Methyloaffinis lahnbergensis. Further analysis of prokaryote diversity in this soil did not reveal 16S rRNA gene fragments from well-studied methanotrophs of the order Methylococcales and the family Methylocystaceae. The largest group of reads (~4% of all bacterial 16S rRNA gene fragments) that could potentially belong to methanotrophs was classified as uncultivated Beijerinckiaceae bacteria. These reads displayed 96–100 and 95–98% sequence similarity to 16S rRNA gene of Candidatus Methyloaffinis lahnbergensis and “Methylocapsa gorgona” MG08, respectively, and were represented by eight species-level operational taxonomic units (OTUs), two of which were highly abundant. These identification results characterize subarctic upland soils, which are exposed to atmospheric methane concentrations only, as a unique habitat colonized mostly by USCα methanotrophs. Full article
(This article belongs to the Special Issue Biology, Diversity, and Ecology of Methanotrophic Bacteria)
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18 pages, 4718 KiB  
Article
Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland
by Gi-Yong Jung, Sung-Keun Rhee, Young-Soo Han and So-Jeong Kim
Microorganisms 2020, 8(11), 1719; https://doi.org/10.3390/microorganisms8111719 - 2 Nov 2020
Cited by 24 | Viewed by 4903
Abstract
Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is [...] Read more.
Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate synthesis, and heavy metal resistance. This metabolic versatility of strain B8 might enable its survival in wetland environments. Full article
(This article belongs to the Special Issue Biology, Diversity, and Ecology of Methanotrophic Bacteria)
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19 pages, 6081 KiB  
Article
Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities
by Yue Zheng, Huan Wang, Zheng Yu, Fauzi Haroon, Maria E. Hernández and Ludmila Chistoserdova
Microorganisms 2020, 8(10), 1614; https://doi.org/10.3390/microorganisms8101614 - 20 Oct 2020
Cited by 9 | Viewed by 3313
Abstract
In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting [...] Read more.
In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting that multiple functional guilds feed on methane, likely through guild-to-guild carbon transfer, and potentially through intraguild and intraspecies interactions. We observed that, under two simulated dioxygen partial pressures—low versus high—community trajectories were different, with considerable variability among the replicates. In all microcosms, four major functional guilds were prominently present, representing Methylococcaceae (the true methanotrophs), Methylophilaceae (the nonmethanotrophic methylotrophs), Burkholderiales, and Bacteroidetes. Additional functional guilds were detected in multiple samples, such as members of Opitutae, as well as the predatory species, suggesting additional complexity for methane-oxidizing communities. Metatranscriptomic analysis suggested simultaneous expression of the two alternative types of methanol dehydrogenases in both Methylococcaceae and Methylophilaceae, while high expression of the oxidative/nitrosative stress response genes suggested competition for dioxygen among the community members. The transcriptomic analysis further suggested that Burkholderiales likely feed on acetate that is produced by Methylococcaceae under hypoxic conditions, while Bacteroidetes likely feed on biopolymers produced by both Methylococcaceae and Methylophilaceae. Full article
(This article belongs to the Special Issue Biology, Diversity, and Ecology of Methanotrophic Bacteria)
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18 pages, 3751 KiB  
Article
Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus
by Igor Y. Oshkin, Kirill K. Miroshnikov, Denis S. Grouzdev and Svetlana N. Dedysh
Microorganisms 2020, 8(5), 768; https://doi.org/10.3390/microorganisms8050768 - 20 May 2020
Cited by 17 | Viewed by 4566
Abstract
The Methylocystis and Methylosinus are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing [...] Read more.
The Methylocystis and Methylosinus are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing methane fluxes from soils and wetlands. The original separation of these methanotrophs in two distinct genera was based mainly on their differences in cell morphology. Further comparative studies that explored various single-gene-based phylogenies suggested the monophyletic nature of each of these genera. Current availability of genome sequences from members of the Methylocystis/Methylosinus clade opens the possibility for in-depth comparison of the genomic potentials of these methanotrophs. Here, we report the finished genome sequence of Methylocystis heyeri H2T and compare it to 23 currently available genomes of Methylocystis and Methylosinus species. The phylogenomic analysis confirmed that members of these genera form two separate clades. The Methylocystis/Methylosinus pan-genome core comprised 1173 genes, with the accessory genome containing 4941 and 11,192 genes in the shell and the cloud, respectively. Major differences between the genome-encoded environmental traits of these methanotrophs include a variety of enzymes for methane oxidation and dinitrogen fixation as well as genomic determinants for cell motility and photosynthesis. Full article
(This article belongs to the Special Issue Biology, Diversity, and Ecology of Methanotrophic Bacteria)
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