Assimilation of acetate by the putative atmospheric methane oxidizers belonging to the USC[alpha] clade

Abstract

Forest soils are a major biological sink for atmospheric methane, yet the identity and physiology of the microorganisms responsible for this process remain unclear. Although members of the upland soil cluster ? (USC?) are assumed to represent methanotrophic bacteria adapted to the oxidation of the trace level of methane in the atmosphere and to be an important sink of this greenhouse gas, so far they have resisted isolation. In particular, the question of whether the atmospheric methane oxidizers are able to obtain all their energy and carbon solely from atmospheric methane still waits to be answered. In this study, we performed stable-isotope probing (SIP) of RNA and DNA to investigate the assimilation of (13) C-methane and (13) C-acetate by USC? in an acidic forest soil. RNA-SIP showed that pmoA mRNA of USC? was not labelled by (13) C of supplemented (13) C methane, although catalysed reporter deposition - fluorescence in situ hybridization (CARD-FISH) targeting pmoA mRNA of USC? detected its expression in the incubated soil. In contrast, incorporation of (13) C-acetate into USC?pmoA mRNA was observed. USC?pmoA genes were not labelled, indicating that they had not grown during the incubation. Our results indicate that the contribution of alternative carbon sources, such as acetate, to the metabolism of the putative atmospheric methane oxidizers in upland forest soils might be substantial.

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ORCID for Marc Dumont: orcid.org/0000-0002-7347-8668

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