Hi-C metagenome sequencing reveals soil phage–host interactions

Ruonan Wu, Michelle R. Davison, William C. Nelson, Montana L. Smith, Mary S. Lipton, Janet K. Jansson, Ryan S. McClure, Jason E. McDermott and Kirsten S. Hofmockel ()
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Ruonan Wu: Pacific Northwest National Laboratory
Michelle R. Davison: Pacific Northwest National Laboratory
William C. Nelson: Pacific Northwest National Laboratory
Montana L. Smith: Pacific Northwest National Laboratory
Mary S. Lipton: Pacific Northwest National Laboratory
Janet K. Jansson: Pacific Northwest National Laboratory
Ryan S. McClure: Pacific Northwest National Laboratory
Jason E. McDermott: Pacific Northwest National Laboratory
Kirsten S. Hofmockel: Pacific Northwest National Laboratory

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: Abstract 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.

Date: 2023
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DOI: 10.1038/s41467-023-42967-z

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