Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

Abstract

Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides novel insights on the distribution, diversity and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.

Optimization and Ev a Luation of Viral Metagenomic Amplification and Sequencing Methods Toward a Genome -le Vel Resolution of the Human Fecal DNA Virome

“…Few eukaryotic viruses may be related to the ltering operation in the virus enrichment process. Interestingly, we found that a large proportion of viral AMGs was involved in sulfur metabolism, in agreement with recent reports that the viruses are widely participants in both organic and inorganic sulfur metabolism in human gut [34,35]. The sul de provides a tness advantage to viruses and viruses also are drivers of organosulfur metabolism with important implications for human health [34].…”

Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation

“…For instance, viruses carrying dsrC genes, which are involved in dissimilatory sulfate reduction, were found in Saanich Inlet that putatively infect SUP05 bacteria (Roux et al, 2014). AMGs putatively involved in sulfite oxidation, soxY, have also been observed in the ETSP (Kieft et al, 2021). Additionally, viruses carrying putative AMGs from nitrogen cycle pathways have been observed in OMZs such as amoC, which encodes for ammonia monooxygenase subunit C involved in nitrification, nirK, which encodes for a Cu-containing nitrite reductase involved in denitrification, and norB, which encodes for a nitric oxide reductase involved in denitrification (Ahlgren et al, 2019;Gazitúa et al, 2021).…”

Virus-associated organosulfur metabolism in human and environmental systems

“…One such mechanism involves viruses ''stealing'' metabolic genes from their host in order to gain fitness advantages during infection (Sullivan et al, 2006). Such host-derived viral genes are termed auxiliary metabolic genes (AMGs) and are expressed during infection to modulate microbial respiration, biosynthesis processes, and/or direct intracellular nutrients toward virus replication and virion production (Anantharaman et al, 2014;Breitbart et al, 2007;Hurwitz et al, 2013Hurwitz et al, , 2015Kieft et al, 2021;Mann et al, 2003;Roux et al, 2014;Suttle, 2005;Thompson et al, 2011;Trubl et al, 2018). For example, some viruses of Cyanobacteria encode core photosystem proteins that augment host metabolism in order to increase the biosynthesis of dNTPs that are utilized for viral genome replication (Thompson et al, 2011).…”