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U.S. Department of Energy Office of Biological and Environmental Research

PI-Submitted Research Highlights for
Subsurface Biogeochemical Research Program

Berkeley Lab Researchers Identify New Microbial Players in the Global Sulfur Cycle

Susan Hubbard

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April 15, 2018

The Science
Sulfate is ubiquitous in the environment, and sulfate reduction—a key control on anaerobic carbon turnover—impacts a number of other processes such as carbon oxidation and sulfide production. Until now, sulfate reduction was believed to be restricted to organisms from select bacterial and archael phyla. But scientists at University of California, Berkeley, have now found this ability to be more widespread. They used genome-resolved metagenomics to discover roles in sulfur cycling for organisms from 16 microbial phyla not previously associated with this process.

The Impact
Sulfate-reducing bacteria are anaerobic microorganisms essential to sulfur and carbon cycling. Sulfate reduction drives other key processes and produces hydrogen sulfide, an important but potentially toxic gas present in sediments, wetlands, aquifers, the human gut, and the deep sea. The discovery of novel microbes connected to sulfur cycling is relevant in biogeochemistry, ecosystem science, and engineering, and can fundamentally reshape understanding of microbial function and capabilities associated with phylogenetic information.

Summary
Phylogenetic information shapes expectations regarding microbial capabilities. In fact, this is the basis of currently used methods that link gene surveys to metabolic predictions of community function. Sulfate reduction, an important anaerobic metabolism, impacts carbon, nitrogen, and hydrogen transformations in numerous environments across the planet and is known to be restricted to organisms from selected bacterial and archaeal phyla. The authors used genome-resolved metagenomic analyses to determine the metabolic potential of microorganisms from six complex marine and terrestrial environments. By analyzing >4,000 genomes, they identified 123 near-complete genomes that encode dissimilatory sulfite reductases involved in sulfate reduction. They discovered roles in sulfur cycling for organisms from 16 microbial phyla not previously known to be associated with this process. Additional findings include some of the earliest-evolved sulfite reductases in bacteria, identification of a novel protein unique to sulfate-reducing bacteria, and a key sulfite reductase gene in putatively symbiotic candidate phyla radiation (CPR) bacteria. This study fundamentally reshapes expectations regarding the roles of a remarkable diversity of organisms in the biogeochemical cycle of sulfur.

Contacts
BER Program Manager
David Lesmes
SC-23.1, 301-903-2977

Principal Investigator
Susan Hubbard
Lawrence Berkeley National Laboratory
sshubbard@lbl.gov

Funding
This work was supported by the Subsurface Biogeochemical Research program of the Office of Biological and Environmental Research within the U.S. Department of Energy Office of Science.

Publication
K. Anantharaman, B. Hausmann, S.P. Jungbluth, R.S. Kantor, A. Lavy, L.A. Warren, M.S. Rappé, M. Pester, A. Loy, B.C. Thomas, and J.F. Banfield. “Expanded diversity of microbial groups thatshape the dissimilatory sulfur cycle.” The ISME Journal. In press (2017). [12, 1715–28 (2018). DOI:10.1038/s41396-018-0078-0].

LBNL Watershed Function SFA (UCB subcontract)

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