Hi-C metagenome sequencing reveals soil phage–host interactions

Wu, Ruonan; Davison, Michelle R.; Nelson, William C.; Smith, Montana L.; Lipton, Mary S.; Jansson, Janet K.; McClure, Ryan S.; McDermott, Jason E.; Hofmockel, Kirsten S.

doi:10.1038/s41467-023-42967-z

Title: Hi-C metagenome sequencing reveals soil phage–host interactions

Journal Article · 22 November 2023 · Nature Communications

DOI: https://doi.org/10.1038/s41467-023-42967-z · OSTI ID:2204511

^[1]; Davison, Michelle R. ^[1];

^[1];

^[1]; Lipton, Mary S. ^[1];

^[1]; McClure, Ryan S. ^[1];

^[2];

^[3]

Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Oregon Health & Science Univ., Portland, OR (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Iowa State Univ., Ames, IA (United States)

Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi–C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates more lytic infections result in more host death and inversely influence host abundance. This study provides empirical evidence of phage-mediated bacterial population dynamics in soil by directly capturing specific phage-host interactions.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-76RL01830; AC02-05CH11231

OSTI ID:: 2204511

Alternate ID(s):: OSTI ID: 2217639

Report Number(s):: PNNL-SA-181374

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 14; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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