Newly Identified Archaea Involved in Anaerobic Carbon Cycling


Archaea, a domain of single-celled microorganisms, represent a significant fraction of Earth’s biodiversity, yet much less is known about Archaea than bacteria. One reason for this lack of knowledge is relatively poor genome sampling, which has limited accuracy for the Archaeal phylogenetic tree. To obtain a better understanding of the diversity and physiological functions of members of the Archaea domain, a team of scientists from the University of California, Berkeley, The Ohio State University, Columbia University, Lawrence Berkeley National Laboratory, the Department of Energy’s (DOE) Joint Genome Institute, Pacific Northwest National Laboratory, and DOE Environmental Molecular Sciences Laboratory used genome-resolved metagenomics analyses to investigate the diversity, genome sizes, metabolic capabilities, and potential environmental niches of Archaea from the Rifle, Colorado, uranium mill tailings site. The team used DOE JGI to sequence DNA from Rifle sediment and groundwater samples, and they not only identified new sequences for more than 150 Archaea but were able to reconstruct the complete genomes of two Archaea that were demonstrated to be representative of two different phyla. Transcriptomic studies conducted using EMSL capabilities on one of these microbes demonstrate that they have small genomes and limited metabolic capabilities; however, these metabolic capabilities are associated with carbon and hydrogen metabolism. These results suggest that these Archaea are either symbionts or parasites that depend on other organisms for some of their metabolic requirements. This research approximately doubled the known genomic diversity of Archaea, reconstructed the first complete genomes for Archaea using cultivation-independent methods, and enabled an extensive revision of the Archaeal tree of life. In addition, these findings can be incorporated into genome-resolved ecosystem models to more accurately reflect the role played by Archaea in the global carbon cycle.

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Castelle, C. J., K. C. Wrighton, B. C. Thomas, L. A. Hug, C. T. Brown, M. J. Wilkins, K. R. Frischkorn, S. G. Tringe, A. Singh, L. M. Markillie, R. C. Taylor, K. H. Williams, and J. F. Banfield. “Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling,” Current Biology 25(6), 690-701. DOI: 10.1016/j.cub.2015.01.014.