Genomes of Microbes Involved in Cycling of Single-Carbon Compounds in Floodplain Sediments

The Science

A multi-institutional team of researchers generated over 1,000 genomes for bacteria and archaea from 0.5- to 1.5-meter-deep sediments from a montane floodplain. Samples from above and below the floodplain water table experienced a range of oxygen availability as the water table fluctuated. Genomes extracted from these samples revealed the presence of microbes capable of producing and consuming methane and other single carbon compounds. The team found microbes with genes for making methane at depths without oxygen and microbes that can consume methane at depths both with and without oxygen.

The Impact

Carbon cycling by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high amounts of organic carbon that can be degraded into simple compounds such as methane or methanol, the fate of which depends on the microbial metabolic capabilities present as well as the water saturation and oxygen availability. By studying the microbes present in floodplain sediments, researchers can determine which pathways of carbon cycling may occur at different depths in the floodplain, which is important for improving the accuracy of carbon cycling and climate models.

Summary

A multi-institutional team of researchers used high-throughput sequencing of total microbial communities to understand the cycling of single-carbon (C1) compounds, particularly methane-cycling, by microorganisms found in the sediments of a montane riparian floodplain. The team generated 1,233 metagenome-assembled genomes (MAGs) from 0.5- to 1.5-m depth below the floodplain surface, capturing the transition between oxygen-containing, unsaturated sediments and oxygen-depleted, saturated sediments in the Slate River floodplain in Crested Butte, Colo.

Genomes of putative methane producers, methane consumers, and other C1 consumers (using compounds such as methanol and methylamines) were recovered. Methane producers were found only in oxygen-depleted depths and originated from three different groups, each with a different pathway for making methane. Putative methane-consuming microorganisms originated from within the Archaea (Candidatus Methanoperedens) in oxygen-depleted depths and from uncultured bacteria (Candidatus Binatia) in depths with oxygen. The genetic potential for C1 consumption was widespread, with over 10% and 19% of MAGs encoding a methanol dehydrogenase or a substrate-specific methyltransferase, respectively. Overall, genomes from Slate River floodplain sediments reveal potential for methane production and consumption in the system and a robust potential for C1 cycling.

Principal Investigator

Anna N. Rasumussen
SLAC National Accelerator Laboratory
[email protected]

Co-Principal Investigator

Chris Francis
Stanford University
[email protected]

Program Manager

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

Funding

Funding for this work was provided by the Earth and Environmental Systems Sciences Division within the U.S. Department of Energy’s Biological and Environmental Research program, through its support of the SLAC Floodplain Hydro-Biogeochemistry Science Focus Area under contract no. DE- AC02-76SF00515.

References