Faculty Opinions recommendation of Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing.

ABSTRACTMethylocellaspp. are facultative methanotrophs that grow on methane and multicarbon substrates, such as acetate. Acetate represses transcription of methane monooxygenase ofMethylocella silvestrisin laboratory culture. DNA stable-isotope probing (DNA-SIP) using13C-methane and12C-acetate, carried out withMethylocella-spiked peat soil, showed that acetate also repressed methane oxidation byMethylocellain environmental samples.

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Identification of the Functionally Active Methanotroph Population in a Peat Soil Microcosm by Stable-Isotope Probing

Applied and Environmental Microbiology ◽

10.1128/aem.68.3.1446-1453.2002 ◽

2002 ◽

Vol 68 (3) ◽

pp. 1446-1453 ◽

Cited By ~ 170

Author(s):

Samantha A. Morris ◽

Stefan Radajewski ◽

Toby W. Willison ◽

J. Colin Murrell

Keyword(s):

Stable Isotope ◽

Gradient Centrifugation ◽

Peat Soil ◽

Pcr Amplification ◽

Cesium Chloride ◽

Stable Isotope Probing ◽

Soil Microcosm ◽

16S Rrna Genes ◽

Rrna Genes ◽

Type I

ABSTRACT The active population of low-affinity methanotrophs in a peat soil microcosm was characterized by stable-isotope probing. “Heavy” 13C-labeled DNA, produced after microbial growth on 13CH4, was separated from naturally abundant 12C-DNA by cesium chloride density gradient centrifugation and used as a template for the PCR. Amplification products of 16S rRNA genes and pmoA, mxaF, and mmoX, which encode key enzymes in the CH4 oxidation pathway, were analyzed. Sequences related to extant type I and type II methanotrophs were identified, indicating that these methanotrophs were active in peat exposed to 8% (vol/vol) CH4. The 13C-DNA libraries also contained clones that were related to β-subclass Proteobacteria, suggesting that novel groups of bacteria may also be involved in CH4 cycling in this soil.

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Active viral population dynamics in frozen Arctic peat soil revealed with H218O stable isotope probing metagenomics

10.1101/2021.01.25.428156 ◽

2021 ◽

Author(s):

Gareth Trubl ◽

Jeffrey A. Kimbrel ◽

Jose Liquet-Gonzalez ◽

Erin E. Nuccio ◽

Peter K. Weber ◽

...

Keyword(s):

Stable Isotope ◽

Peat Soil ◽

Stable Isotope Probing ◽

Viral Population ◽

Soil Processes ◽

Carbohydrate Utilization ◽

Bacterial Populations ◽

Viral Ecology ◽

Bacterial Phyla ◽

Winter Conditions

AbstractWinter soil processes are critical to the carbon balance of northern ecosystems, yet the microbial ecology governing biogeochemical cycling in frozen soils is largely unknown. We used stable isotope probing targeted metagenomics to reveal the genomic potential of active microbial populations, with an emphasis on viruses, in soils. Peat soils were incubated under simulated winter conditions (subzero and anoxic) with H218O or natural abundance water for 184 and 370 days. Isotope incorporation revealed 46 active bacterial populations (MAGs; spanning 9 bacterial phyla) and 243 active viral populations (vOTUs). Active hosts were predicted for 33% of the active vOTUs and were some of the most abundant MAGs, having capacity for fermentation and carbohydrate utilization. Additionally, almost one-third of vOTUs carried auxiliary metabolic genes spanning five functional categories, highlighting the potential impact of viruses in microbial biogeochemistry. CO2 production throughout the incubation supports our evidence of microbial activities under winter conditions. Our results revealed a multi-trophic and changing microbial community in tandem with a changing viral community targeting dominant active bacteria consistent with the “kill-the-winner” hypothesis. These data have important implications for low-temperature soil processes in northern peatlands and reveal active host-linked soil viral ecology, with potential multifaceted biogeochemical impacts.

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