Examples of virion structures. Pictures modified from ViperDB (http://viperdb.scripps.edu/) and RCSB (http://www.rcsb.org).
Microbes drive biogeochemical cycling on a global scale, but do so under strong constraints by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Using recent advances in experimental approaches and sequencing technologies, environmental viral diversity that has proved challenging to isolate and study in the lab can now be explored at an unprecedented scale and level of detail.
Through large-scale mining of shotgun metagenomic data, the DOE JGI has substantially expanded known viral sequence space. The Earth Virome project identified over 125,000 partial and complete viral genomes, increasing the number of known viral genes by a factor of 16. The effort also utilized information from the CRISPR-Cas system and transfer RNAs (tRNAs) to link viruses to putative microbial hosts, and provided a view of global viral biogeography. To further viral research, this rich dataset has been made widely available to the community through the IMG/VR system and currently hosts more than 260,000 partial viral genomes. Work is currently underway to improve detection of viral sequence data from shotgun metagenomes and metatranscriptomes.
References:
Roux S, et al. (2014) Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell and metagenomics. Elife. 3:e03125.
Roux S, et al. (2015) Viral dark matter and virus-host interactions resolved from publically available microbial genomes. Elife. 4:e08490.
Roux S, et al. (2016) Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature. 537:689-93.
Paez-Espino D, et al. (2016) Uncovering Earth’s virome. Nature. 536:425-30.
Paez-Espino D, et al. (2017) IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 45(D1):D457-D465.