Abstract
SummaryUnderstanding of global methane sources and sinks is a prerequisite for the design of strategies to counteract global warming. Microbial methane oxidation in soils represents the largest biological sink for atmospheric methane. However, still very little is known about the identity, metabolic properties and distribution of the microbial group proposed to be responsible for most of this uptake, the uncultivated upland soil cluster α (USCα). Here, we reconstructed a draft genome of USCα from a combination of targeted cell sorting and metagenomes from forest soil, providing the first insights into its metabolic potential and environmental adaptation strategies. The 16S rRNA gene sequence recovered was distinctive and suggests this crucial group as a new genus within the Beijerinckiaceae, close to Methylocapsa. Application of a fluorescently labelled suicide substrate for the particulate methane monooxygenase enzyme (pMMO) coupled to 16S rRNA fluorescence in situ hybridisation (FISH) allowed for the first time a direct link of the high‐affinity activity of methane oxidation to USCα cells in situ. Analysis of the global biogeography of this group further revealed its presence in previously unrecognized habitats, such as subterranean and volcanic biofilm environments, indicating a potential role of these environments in the biological sink for atmospheric methane.
Highlights
Methane (CH4) is an important greenhouse gas with a current atmospheric concentration of 1.84 p.p.m.v. and a global warming potential (GWP100) 34 times greater than CO2 (Ciais, 2013)
This recovered a preliminary genome bin for upland soil cluster a (USCa), with a dedicated partial 16S ribosomal RNA (rRNA) gene sequence. Based on this partial sequence, a specific PCR forward primer for the USCa 16S rRNA gene was designed. This primer was paired with a universal reverse bacterial 16S rRNA primer to amplify the full 16S rRNA gene sequence of USCa, and Sanger-sequencing of this product resulted in the reconstruction of the full-length 16S rRNA gene sequence for phylogenetic analyses
We applied a combination of metagenomic sequencing, targeted cell sorting and phylogenomic and biogeography analyses to unravel the identity of the atmospheric methane-oxidizing bacteria of the USCa clade from forest soil and connect it to their proposed activity, investigate their genetic potential and re-assess their environmental distribution
Summary
Understanding of global methane sources and sinks is a prerequisite for the design of strategies to counteract global warming. Microbial methane oxidation in soils represents the largest biological sink for atmospheric methane. Still very little is known about the identity, metabolic properties and distribution of the microbial group proposed to be responsible for most of this uptake, the uncultivated upland soil cluster a (USCa). We reconstructed a draft genome of USCa from a combination of targeted cell sorting and metagenomes from forest soil, providing the first insights into its metabolic potential and environmental adaptation strategies. Application of a fluorescently labelled suicide substrate for the particulate methane monooxygenase enzyme (pMMO) coupled to 16S rRNA fluorescence in situ hybridisation (FISH) allowed for the first time a direct link of the high-affinity activity of methane oxidation to USCa cells in situ. Subterranean and volcanic biofilm environments, indicating a potential role of these environments in the biological sink for atmospheric methane
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