Microbes from Phyla Chloroflexi Provide Clues to Carbon Cycling, Respiration in Sediments

Microorganisms within terrestrial aquifer sediments control buried organic carbon turnover, degrade organic contaminants, and impact drinking water quality.

The Science

Through metagenomics, researchers sequenced 86 organisms from the phylum Chloroflexi, representing 15 distinct lineages, to discover the secrets of microbial life within terrestrial aquifer sediment deposits.

These Chloroflexi microbes were found to have metabolic processes involved in plant biomass degradation, which could be useful for biofuels production, as well as a better understanding of the subsurface nitrogen and carbon cycles. Microorganisms in aquifer sediments are responsible for subterranean carbon turnover and the degradation of organic contaminants. Consequently, these microorganisms can heavily impact the quality of underground drinking water. In earlier studies, it was determined that Chloroflexi represent a significant amount of the microbial population in sediments. However, these microbes are poorly understood, as only six of about 30 Chloroflexi classes have been sequenced. For this reason, a team of researchers including scientists from the Department of Energy’s Joint Genome Institute (JGI) conducted a study on the microbial composition of these aquifer sediments to gain a broader knowledge of the metabolic characteristics of Chloroflexi microbes.

The Impact

The researchers were able to reconstruct three near-complete Chloroflexi genomes from the metagenomic data collected at the Integrated Field-Scale Subsurface Research Challenge Site in Colorado as part of a DOE JGI Community Sequencing Program project led by Jill Banfield of the University of California–Berkeley. Metabolic analyses revealed that Chloroflexi can break down plant mass, influence subsurface carbon and nitrogen cycles, and adapt to changing oxygen levels. These traits, the researchers noted, were likely to apply to Chloroflexi in other sediment environments, making these microbes good candidates for mining useful enzymes and pathways for DOE missions of bioenergy and carbon processing as well as for biodegradation.

Principal Investigator

Jill Banfield
University of California–Berkeley

BER Program Manager

Ramana Madupu

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


 Hug, L. A., C. J. Castelle, K. C. Wrighton, B. C. Thomas, I. Sharon, K. R. Frischkorn, K. H. Williams, S. G. Tringe, and J. F. Banfield. 2013. “Community Genomic Analyses Constrain the Distribution of Metabolic Traits Across the Chloroflexi Phylum and Indicate Roles in Sediment Carbon Cycling,” Microbiome 1(22). DOI:10.1186/2049-2618-1-22.