Untangling Genomes from Metagenomes

Abstract

Abundant and evolutionarily diverse populations of microbes dramatically shape the ecology of every marine environment on Earth. While it is straightforward to detect and classify members of these natural communities using molecular methods, the vast majority remain inaccessible to laboratory investigation of their physiology and genetic potential, due to the difficulty of predicting and replicating the conditions they may require for growth. This is doubly true for viruses, where to isolate and study a given virus, a susceptible host organism must first be brought into laboratory culture. Metagenomics has developed as an alternative approach, revealing genetic information about entire microbial communities at once. With rapid technological improvements placing metagenome-scale DNA sequencing within reach of individual researchers, the challenge has shifted to the analysis and interpretation of the enormous resulting datasets. This work describes the development and use of new computational tools to investigate and assemble two metagenomes sampled from Puget Sound during autumn and spring. Community taxonomic classification and quantification revealed a diverse and changing assemblage of Bacteria and Archaea, including enigmatic members of the uncultured marine Euryarchaeota. Targeted metagenomic assembly produced the first genome representing the marine group II Euryarchaeota, describing a motile, photoheterotrophic lifestyle, and clarifying the evolutionary origin of the proteorhodopsin gene found in numerous marine Bacteria. This genome further enabled identification and metagenomic assembly of five genomes describing the first reported non-extremophilic archaeal viruses. These genomes reveal a dramatic evolutionary arms race between the viruses and their hosts over control of essential archaeal protein folding machinery in the euryarchaeal host cell. Whether marine Euryarchaeota will ever be isolated into culture remains unknown, but through the use of metagenomic genome assembly, key details about how they survive--and perish--in the world's oceans have been revealed.