AUTHOR=Nadalig Thierry , Greule Markus , Bringel Françoise , Keppler Frank , Vuilleumier Stéphane 

TITLE=Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation

JOURNAL=Frontiers in Microbiology

VOLUME=5

YEAR=2014

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2014.00523

DOI=10.3389/fmicb.2014.00523

ISSN=1664-302X

ABSTRACT=<p>Chloromethane (CH<sub>3</sub>Cl) is produced on earth by a variety of abiotic and biological processes. It is the most important halogenated trace gas in the atmosphere, where it contributes to ozone destruction. Current estimates of the global CH<sub>3</sub>Cl budget are uncertain and suggest that microorganisms might play a more important role in degrading atmospheric CH<sub>3</sub>Cl than previously thought. Its degradation by bacteria has been demonstrated in marine, terrestrial, and phyllospheric environments. Improving our knowledge of these degradation processes and their magnitude is thus highly relevant for a better understanding of the global budget of CH<sub>3</sub>Cl. The <italic>cmu</italic> pathway, for <italic><underline>c</underline></italic>hloro<italic><underline>m</underline></italic>ethane <italic><underline>u</underline></italic>tilisation, is the only microbial pathway for CH<sub>3</sub>Cl degradation elucidated so far, and was characterized in detail in aerobic methylotrophic Alphaproteobacteria. Here, we reveal the potential of using a two-pronged approach involving a combination of comparative genomics and isotopic fractionation during CH<sub>3</sub>Cl degradation to newly address the question of the diversity of chloromethane-degrading bacteria in the environment. Analysis of available bacterial genome sequences reveals that several bacteria not yet known to degrade CH<sub>3</sub>Cl contain part or all of the complement of <italic>cmu</italic> genes required for CH<sub>3</sub>Cl degradation. These organisms, unlike bacteria shown to grow with CH<sub>3</sub>Cl using the <italic>cmu</italic> pathway, are obligate anaerobes. On the other hand, analysis of the complete genome of the chloromethane-degrading bacterium <italic>Leisingera methylohalidivorans</italic> MB2 showed that this bacterium does not contain <italic>cmu</italic> genes. Isotope fractionation experiments with <italic>L. methylohalidivorans</italic> MB2 suggest that the unknown pathway used by this bacterium for growth with CH<sub>3</sub>Cl can be differentiated from the <italic>cmu</italic> pathway. This result opens the prospect that contributions from bacteria with the <italic>cmu</italic> and <italic>Leisingera</italic>-type pathways to the atmospheric CH<sub>3</sub>Cl budget may be teased apart in the future.</p>