Fig. 1. Schematic of the experimental design and data analysis workflow.

a Description of sample treatment and the collected sequencing data. Soil samples were collected pre- (75% water holding capacity, represented by the first soil jar icon) and post-desiccation (soil dried to consistent weight, represented by the second soil jar icon). Shotgun metagenomes (sequenced on the total DNA, demonstrated in the first box), (bulk) metatranscriptomes (sequenced on the total RNA, demonstrated in the first box), and Hi-C metagenomes (sequenced on the cross-linked DNA, demonstrated in the second box) were generated from each replicate sample. b Data analysis and integration. Shotgun metagenome-assembled contigs were used to screen for viral contigs. The normalized read coverages of the identified viral contigs in shotgun metagenomes and metatranscriptomes were used to detect the viral (phage) community compositions and transcriptional activities in the soil samples before and after desiccation. Hi-C metagenomes containing the sequenced cross-linked DNA of the extracted host microbial cells were used to identify contig-contig linkages. The quality-filtered linkages were used to cluster linked contigs into metagenome assembled genomes (MAGs) and to identify phage-host pairs. Co-analysis of the paired shotgun and Hi-C metagenomes was performed for the detection of phage-host interactions under wet and dry soil conditions and to determine phage-host interactions.