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[Abundance and diversity of methanotrophic Gammaproteobacteria in northern wetlands].

https://arctichealth.org/en/permalink/ahliterature259581
Source
Mikrobiologiia. 2014 Mar-Apr;83(2):204-14
Publication Type
Article
Author
O V Danilova
S N Dedysh
Source
Mikrobiologiia. 2014 Mar-Apr;83(2):204-14
Language
Russian
Publication Type
Article
Keywords
Biodiversity
Fresh Water - microbiology
Gammaproteobacteria - genetics - isolation & purification - metabolism
Hydrogen-Ion Concentration
In Situ Hybridization, Fluorescence
Methane - metabolism
Methylococcaceae - genetics
Methylocystaceae - genetics
Molecular Sequence Data
Oxygenases - genetics
Phylogeny
RNA, Ribosomal, 16S
Russia
Wetlands
Abstract
Numeric abundance, identity and pH preferences of methanotrophic Gammaproteobacteria (type I methanotrophs) inhabiting the northern acidic wetlands were studied. The rates of methane oxidation by peat samples from six-wetlands of European Northern Russia (pH 3.9-4.7) varied from 0.04 to 0.60 µg CH4 g(-1) peat h(-1). The number of cells revealed by hybridization with fluorochrome-labeled probes M84 + M705 specific for type I methanotrophs was 0.05-2.16 x 10(5) cells g(-1) dry peat, i.e. 0.4-12.5% of the total number of methanotrophs and 0.004-0.39% of the total number of bacteria. Analysis of the fragments of the pmoA gene encoding particulate methane monooxygenase revealed predominance of the genus Methylocystis (92% of the clones) in the studied sample of acidic peat, while the proportion of the pmoA sequences of type I methanotrophs was insignificant (8%). PCR amplification of the 16S rRNA gene fragments of type I methanotrophs with TypeIF-Type IR primers had low specificity, since only three sequences out of 53 analyzed belonged to methanotrophs and exhibited 93-99% similarity to those of Methylovulum, Methylomonas, and Methylobacter species. Isolates of type I methanotrophs obtained from peat (strains SH10 and 83A5) were identified as members of the species Methylomonaspaludis and Methylovulum miyakonense, respectively. Only Methylomonaspaludum SH10 was capable of growth in acidic media (pH range for growth 3.8-7.2 with the optimum at pH 5.8-6.2), while Methylovulum miyakonense 83A5 exhibited the typical growth characteristics of neutrophilic methanotrophs (pH range for growth 5.5-8.0 with the optimum at pH 6.5-7.5).
PubMed ID
25423724 View in PubMed
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Microbial Community Composition and Methanotroph Diversity of a Subarctic Wetland in Russia.

https://arctichealth.org/en/permalink/ahliterature289533
Source
Mikrobiologiia. 2016 Sep; 85(5):545-554
Publication Type
Journal Article
Date
Sep-2016
Author
O V Danilova
S E Belova
I V Gagarinova
S N Dedysh
Source
Mikrobiologiia. 2016 Sep; 85(5):545-554
Date
Sep-2016
Language
English
Publication Type
Journal Article
Keywords
Acidobacteria - classification - genetics - isolation & purification - metabolism
Actinobacteria - classification - genetics - isolation & purification - metabolism
Alphaproteobacteria - classification - genetics - isolation & purification - metabolism
Arctic Regions
Bacterial Proteins - genetics - metabolism
Bryophyta - physiology
Gammaproteobacteria - classification - genetics - isolation & purification - metabolism
Gene Expression
Groundwater - microbiology
Lichens - physiology
Methane - chemistry - metabolism
Microbial Consortia - physiology
Oxygenases - genetics - metabolism
Phylogeny
Planctomycetales - classification - genetics - isolation & purification - metabolism
Russia
Verrucomicrobia - classification - genetics - isolation & purification - metabolism
Wetlands
Abstract
This study assessed the microbial diversity, activity, and composition of methane-oxidizing communities of a subarctic wetland in Russia,with mosaic cover of Sphagnum mosses and lichens of the genera Cladonia and Cetraria. Potential methane-oxidizing activity of peat sampled from lichen-dominated wetland sites was higher than that in the sites dominated by Sphagnum mosses. In peat from lichendominated sites, major bacterial groups identified by high-throughput sequencing of the 16S rRNA genes were the Acidobacteria (35.4-41.2% of total 16S rRNA gene reads), Alphaproteobacteria (19.1-24.2%), Gammaproteobacteria (7.9-11.1%), Actinobacteria (5.5-13.2%), Planctomycetes (7.2-9.5%), and Verrucomicrobia (5.1-9.5%). The distinctive feature of this community was high proportion of Subdivision 2 Acidobacteria, which are not char- acteristic for boreal Sphagnum peat bogs. Methanotrophic community composition was determined by mo- lecular analysis of the pmoA gene encoding particulate methane monooxygenase. Most (-80%) of all pmoA gene fragments revealed in peat from lichen-dominated sites belonged to the phylogenetic lineage represented by a microaerobic spiral-shaped methanotroph, "Candidatus Methylospira mobilis." Members of the genus Methylocystis, which are typical inhabitants of boreal Sphagnum peat bogs, represented only a minor group of indigenous methanotrophs. The specific feature of a methanotrophic community in peat from lichen-dominated sites was the presence of uncultivated USCa (Upland Soil Cluster alpha) methanotrophs, which are typical for acidic upland soils showing atmospheric methane oxidation. The methanotrophic community composition in lichen-dominated sites of a tundra wetland, therefore, was markedly different from that in bo- real Sphagnum peat bogs.
PubMed ID
29364602 View in PubMed
Less detail

Microbial Community Composition and Methanotroph Diversity of a Subarctic Wetland in Russia.

https://arctichealth.org/en/permalink/ahliterature289691
Source
Mikrobiologiia. 2016 Sep; 85(5):545-554
Publication Type
Journal Article
Date
Sep-2016
Author
O V Danilova
S E Belova
I V Gagarinova
S N Dedysh
Source
Mikrobiologiia. 2016 Sep; 85(5):545-554
Date
Sep-2016
Language
English
Publication Type
Journal Article
Keywords
Acidobacteria - classification - genetics - isolation & purification - metabolism
Actinobacteria - classification - genetics - isolation & purification - metabolism
Alphaproteobacteria - classification - genetics - isolation & purification - metabolism
Arctic Regions
Bacterial Proteins - genetics - metabolism
Bryophyta - physiology
Gammaproteobacteria - classification - genetics - isolation & purification - metabolism
Gene Expression
Groundwater - microbiology
Lichens - physiology
Methane - chemistry - metabolism
Microbial Consortia - physiology
Oxygenases - genetics - metabolism
Phylogeny
Planctomycetales - classification - genetics - isolation & purification - metabolism
Russia
Verrucomicrobia - classification - genetics - isolation & purification - metabolism
Wetlands
Abstract
This study assessed the microbial diversity, activity, and composition of methane-oxidizing communities of a subarctic wetland in Russia,with mosaic cover of Sphagnum mosses and lichens of the genera Cladonia and Cetraria. Potential methane-oxidizing activity of peat sampled from lichen-dominated wetland sites was higher than that in the sites dominated by Sphagnum mosses. In peat from lichendominated sites, major bacterial groups identified by high-throughput sequencing of the 16S rRNA genes were the Acidobacteria (35.4-41.2% of total 16S rRNA gene reads), Alphaproteobacteria (19.1-24.2%), Gammaproteobacteria (7.9-11.1%), Actinobacteria (5.5-13.2%), Planctomycetes (7.2-9.5%), and Verrucomicrobia (5.1-9.5%). The distinctive feature of this community was high proportion of Subdivision 2 Acidobacteria, which are not char- acteristic for boreal Sphagnum peat bogs. Methanotrophic community composition was determined by mo- lecular analysis of the pmoA gene encoding particulate methane monooxygenase. Most (-80%) of all pmoA gene fragments revealed in peat from lichen-dominated sites belonged to the phylogenetic lineage represented by a microaerobic spiral-shaped methanotroph, "Candidatus Methylospira mobilis." Members of the genus Methylocystis, which are typical inhabitants of boreal Sphagnum peat bogs, represented only a minor group of indigenous methanotrophs. The specific feature of a methanotrophic community in peat from lichen-dominated sites was the presence of uncultivated USCa (Upland Soil Cluster alpha) methanotrophs, which are typical for acidic upland soils showing atmospheric methane oxidation. The methanotrophic community composition in lichen-dominated sites of a tundra wetland, therefore, was markedly different from that in bo- real Sphagnum peat bogs.
PubMed ID
29364602 View in PubMed
Less detail