Left to Right: Rex Malmstrom, head of Micro-Scale Applications; Emiley Eloe-Fadrosh, head of theMetagenome Program; and, research scientist Simon Roux.
In a special issue of mSystems, out May 14, 2019, JGI researchers are among the authors who offer perspectives on what the next five years of innovation could look like.
In one article, Micro-Scale Applications head Rex Malmstrom and Metagenome Program head Emiley Eloe-Fadrosh outline more targeted approaches to reconstruct individual microbes in an environmental sample beyond the tried-and-true method of traditional shotgun metagenomics. One approach uses fluorescence-activated cell sorting (FACS) to sort cells into several small pools before sequencing to recover rare microbes. The technique was applied to a recent Nature Communications paper, uncovering giant virus sequences in soil for the first time.
A second approach known as DNA stable isotope probing (DNA SIP) relies on incubating DNA with isotopically-labeled compounds to link active microbes with specific metabolic processes. A third approach steps away from reconstructing genomes directly from the environment and focuses on sequence reads to link mobile elements such as plasmids to microbial host cells.
In a separate article, research scientist Simon Roux, a member of Eloe-Fadrosh’s Environmental Genomics group, makes a pitch for readers to get involved in the developing field of virus ecogenomics. While microbes regulate the planet’s biogeochemical cycles, viruses infecting microbes shape global ecological and environmental processes, especially by modifying host cell metabolism and altering cell fitness. As the vast majority of viruses remain uncultivated, Roux outlines what’s been achieved thus far based on computational predictions, and future directions integrating computational and experimental approaches with the aim of eventually studying virus-host dynamics in nature.
In the last few years, mapping the planet’s viral diversity has advanced drastically, aided by genome assembly from metagenomes. This is a critical step toward better understanding the impact of viruses upon microbes. A comprehensive map of viruses including host information, Roux says, would be the foundation upon which researchers can develop high-throughput and high-resolution studies of interactions between host cells and viruses in the environment.
Eloe-Fadrosh and Roux are part of the first cohort to receive Early Career Development awards as part of the Laboratory-Directed Research and Development (LDRD) Program at Lawrence Berkeley National Laboratory (Berkeley Lab). JGI is a DOE Office of Science user facility at Berkeley Lab.
References:
- Malmstrom R.R. and E. Eloe-Fadrosh. Advancing genome-resolved metagenomics beyond the shotgun. mSystems. 2019 May 14. doi: 10.1128/mSystems.00118-19.
- Roux, S. A viral ecogenomics framework to uncover the secrets of Nature’s “microbe whisperers.” mSystems. 2019 May 14. doi: 10.1128/mSystems.00111-19.
- JGI publication: Schulz F et al. Hidden diversity of soil giant viruses. Nature Communications. 2018 Nov 19. doi: 10.1038/s41467-018-07335-2
- JGI publication: Roux S et al. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nat Biotechnol. 2018 Dec 17. doi: 10.1038/nbt.4306.
- IMG/VR data portal: https://img.jgi.doe.gov/vr