Widespread soil bacterium that oxidizes atmospheric methane

Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8515-8524. doi: 10.1073/pnas.1817812116. Epub 2019 Apr 8.

Abstract

The global atmospheric level of methane (CH4), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH4 from the atmosphere, but so far, bacteria that can grow on atmospheric CH4 have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH4 [1.86 parts per million volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH4 oxidation experiments and 13C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH4 aerobically and assimilates carbon from both CH4 and CO2 Its estimated specific affinity for CH4 (a0 s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for Methylocapsa acidiphila and Methylocapsa aurea, close relatives with a lower specific affinity for CH4, suggesting that the ability to utilize atmospheric CH4 for growth is more widespread than previously believed. The closed genome of M. gorgona MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH4 and CO2, and CO2 fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH4 oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).

Keywords: USC alpha; filter cultivation; isolate; methane; trace gases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / metabolism
  • Beijerinckiaceae* / classification
  • Beijerinckiaceae* / enzymology
  • Beijerinckiaceae* / genetics
  • Beijerinckiaceae* / physiology
  • Greenhouse Gases / metabolism*
  • Methane / metabolism*
  • Oxidation-Reduction
  • Oxygenases / metabolism
  • Soil Microbiology

Substances

  • Bacterial Proteins
  • Greenhouse Gases
  • Oxygenases
  • methane monooxygenase
  • Methane

Associated data

  • GENBANK/CP024846