High-Throughput Chromosomal Confirmation Capture (Hi-C) Metagenome Sequencing Reveals Moisture Impact on Soil Phage-Host Interactions

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The impacts of soil moisture on virus-host interactions are largely unknown. Here, we applied high-throughput chromosomal confirmation capture (Hi-C) metagenomics to directly link phages with their hosts in soils under wet and dry conditions. Metatranscriptomics showed transcriptional levels of the host-associated phages were higher in wetter soils. Richness of the host-associated phages and the average viral copies per host (VPH), however, increased following soil desiccation. A significantly negative correlation of VPH host abundance was only detected in wet soils,These results suggest that viral infections were mostly lytic under wet conditions while more prevalent and lysogenic after soil drying. An infection network analysis revealed that different soil moisture altered the host. Some hosts were central in microbial bacterial co-occurrence networks, highlighting the phage impact on microbiome structure. This study provides the first empirical evidence of phage-mediated bacterial dynamics with changing soil moisture. 

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The Phenotypic Response of the Soil Microbiome to Environmental Perturbations Project (Soil Microbiome SFA) at Pacific Northwest National Laboratory is a Genomic Sciences Program Science Focus Area (SFA) Project operating under the Environmental Microbiome Science Research Area. The Soil Microbiome...

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Staff Scientist at Pacific Northwest National Laboratory