Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota.
Ecosystems are shaped by complex communities of mostly unculturable microbes. Metagenomes provide a fragmented view of such communities, but the ecosystem functions of major groups of organisms remain mysterious. To better characterize members of these communities, we developed methods to reconstruct genomes directly from mate-paired short-read metagenomes. We closed a genome representing the as-yet uncultured marine group II Euryarchaeota, assembled de novo from 1.7% of a metagenome sequenced from surface seawater. The genome describes a motile, photo-heterotrophic cell focused on degradation of protein and lipids and clarifies the origin of proteorhodopsin. It also demonstrates that high-coverage mate-paired sequence can overcome assembly difficulties caused by interstrain variation in complex microbial communities, enabling inference of ecosystem functions for uncultured members.
School of Oceanography, University of Washington, Seattle, WA 98195, USA.
Vaughn
V
Iverson
Robert M
RM
Morris
Christian D
CD
Frazar
Chris T
CT
Berthiaume
Rhonda L
RL
Morales
E Virginia
EV
Armbrust
D019843:Archaeal Proteins / Q000235:genetics* / Q000378:metabolism; D058448:Biota; D017753:Ecosystem; D004798:Enzymes / Q000235:genetics / Q000378:metabolism; D019605:Euryarchaeota / Q000145:classification / Q000235:genetics* / Q000378:metabolism / Q000502:physiology*; D019766:Genes, Archaeal; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D052836:Heterotrophic Processes; D050356:Lipid Metabolism / Q000235:genetics; D053858:Metabolic Networks and Pathways / Q000235:genetics; D054892:Metagenome; D059013:Microbial Consortia; D008969:Molecular Sequence Data; D010140:Pacific Ocean; D010447:Peptide Hydrolases / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D011506:Proteins / Q000378:metabolism; D012243:Rhodopsin / Q000235:genetics; D025604:Rhodopsins, Microbial; D012623:Seawater / Q000382:microbiology*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D019843:Archaeal Proteins; D004798:Enzymes; D011506:Proteins; D025604:Rhodopsins, Microbial; C413548:proteorhodopsin; D012243:Rhodopsin; D010447:Peptide Hydrolases