Microbial Community Dynamics Impacting Methane Consumption in Freshwater Lakes

The Science

Decay of plant material in oxygen-limited sediments of lakes and wetlands results in the production of massive amounts of methane (CH4), a potent greenhouse gas. However, only a fraction of the CH4 produced in these environments enters the atmosphere due to the metabolic activities of microbial methanotrophs. Methanotrophs are a class of bacteria capable of consuming CH4 and using it as both a source of carbon and energy to fuel their growth. Understanding even the basic physiology of methanotrophs remains limited, as evidenced by the recent discovery of a new fermentative mode of methanotrophic metabolism in organisms that were previously thought to strictly require oxygen for growth. In a new study by researchers at the University of Washington, experimental microcosms established with lake sediments were used to examine methanotrophic communities and their response to varying levels of oxygen. By tracking community composition through DNA pyrosequencing, the team determined that the methanotroph community features a nonrandom assemblage of organisms, with specific types adapted to either high or low oxygen levels. When the methanotroph community shifted in response to oxygen availability, an array of nonmethanotrophic microbes also changed. Preliminary evidence suggests that these organisms are metabolically partnered with methanotrophs, exchanging nutrients and facilitating methanotrophic processes. These results represent the first detailed examination of microbial community dynamics in a methanotrophic ecosystem and suggest a high degree of complexity in their response to shifting environmental variables. Gain­ing a more sophisticated understanding of microbial community dynamics influencing methano­trophs in natural settings will help to facilitate more accurate predictions of environmental CH4 production and consumption.


Researchers first measured taxonomic compositions of long-term enrichment cultures and determined that, although dominated by Methylococcaceae types, these cultures also contained accompanying types belonging to a limited number of bacterial taxa, methylotrophs and non-methylotrophs. Researchers then followed the short-term community dynamics, in two oxygen tension regimens (150 μM and 15 μM), observing rapid loss of species diversity. In all microcosms, a single type of Methylobacter represented the major methane-oxidizing partner. The accompanying members of the communities revealed different trajectories in response to different oxygen tensions, with Methylotenera species being the early responders to methane stimulus under both conditions. The communities in both conditions were convergent in terms of their assemblage, suggesting selection for specific taxa. These results support prior observations from metagenomics on distribution of carbon from methane among diverse bacterial populations and further suggest that communities are likely responsible for methane cycling, rather than a single type of microbe.

BER Program Manager

Dawn Adin

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Oshkin, I. Y., D. A. C Beck, A. E. Lamb, V. Tchesnokova, G. Benuska, T. L. McTaggart, M. G. Kalyuzhnaya, S. N. Dedysh, M. E. Lidstrom, and L. Chistoserdova. 2014. “Methane-Fed Microbial Microcosms Show Differential Community Dynamics and Pinpoint Taxa Involved in Communal Response,” The ISME Journal, DOI: 10.1038/ismej.2014.203.