Archaea, a domain of single-celled microorganisms, represent a significant fraction of the earth’s biodiversity, yet they remain much less understood than bacteria. One reason for this lack of knowledge is relatively poor genome sampling, which has limited accuracy of the Archaeal phylogenetic tree. In a recent study, researchers approximately doubled the genomic diversity sampled from this domain and reconstructed the first complete genomes for Archaea using cultivation-independent methods resulting in an extensive revision of the Archaeal tree of life.
The study revealed Archaea in the terrestrial subsurface contribute primarily to carbon and hydrogen cycling, suggesting these organisms may be involved in processing the sizeable reservoir of buried organic carbon. This finding can be immediately implemented within genome-resolved ecosystem models to more accurately reflect the key role played by Archaea in the global carbon cycle.
Researchers from University of California, Berkeley; The Ohio State University; Columbia University; the Department of Energy’s (DOE) Joint Genome Institute; EMSL, the Environmental Molecular Sciences Laboratory, a DOE national scientific user facility; Pacific Northwest National Laboratory and Lawrence Berkeley National Laboratory used genome-resolved metagenomic analyses to investigate the diversity, genomes sizes, metabolic capacities and potential roles of Archaea in terrestrial subsurface biogeochemical cycles. They sequenced DNA in sediment and groundwater samples from a uranium-contaminated aquifer at DOE’s Integrated Field Research Challenge site near Rifle, Colo. This is a former uranium mill and the primary site for DOE’s Subsurface Systems Scientific Focus Area. RNA-Seq was conducted using the 5500XL SOLiD sequencers at EMSL.
By sampling genomes of 100 different Archaea, researchers identified two novel phyla—named Woesearchaeota and Pacearchaeota—within the recently proposed DPANN superphylum. The unprecedented reconstruction of two complete genomes for members of this major superphylum showed these organisms have small genomes and limited metabolic capacities. Detailed metabolic analyses of DPANN representatives revealed their primary contributions to the earth’s biogeochemical cycles involve carbon and hydrogen metabolism. Moreover, most core biosynthetic pathways were absent or incomplete in DPANN Archaea, suggesting they are symbionts or parasites that depend on other organisms for basic metabolic requirements.
Strikingly, the key features of DPANN Archaea closely parallel those of a putative bacterial superphylum. Their members are also predicted to have small genomes and to lack core metabolic pathways. Taken together, findings suggest these organisms depend on other members of the microbial community to survive and similar conditions have shaped two of the three major branches of the tree of life.
Publication: Castelle Cindy J, Kelly C Wrighton, Brian C Thomas, Laura A Hug, Christopher T Brown, Michael J Wilkins, Kyle R Frischkorn, Susannah G Tringe, A Singh, Lye M Markillie, Ronald C Taylor, Kenneth H Williams, and Jillian F Banfield. "Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling." Current Biology. DOI:10.1016/j.cub.2015.01.014
Programs: Sustainable Systems Scientific Focus Area and Systems Biology Knowledge Base Focus Area