Methane-derived carbon flow through host-virus trophic networks

Abstract:

While there is an increasing understanding of the scale of viral diversity in soil, compared to other habitats, there is relatively little known about the dynamics of host-virus interactions in situ due to the complexity of both soil structure and microbial diversity. Deep high throughput sequencing of soil microbial metagenomes enables identification of linkages between viruses and hosts through the historical record of interactions encoded in CRISPR spacers or horizontally transferred genes. In this study we aimed to identify active virus-host interactions with high resolution by focussing on a taxonomically and functionally restricted group of organisms. Specifically, by following carbon flow, we aimed to identify viruses of microbial populations actively using methane, including those of methanotrophs and also secondary utilisers of methanotroph-fixed carbon. Using a combination of DNA stable-isotope probing and metagenomic analyses, we characterised methane-fuelled microbial networks in acidic and neutral pH soils. Replicate soil microcosms were incubated with a headspace of 10% ¹²C- or ¹³C-methane and genomic DNA extracted, subjected to isopycnic ultracentrifugation in CsCl gradients, and high buoyant density DNA sequenced using the Illumina NovaSeq platform before contig assembly and analysis. Methylocystaceae and Methylococcaceae methanotrophs dominated at pH 4.5 and 7.5, respectively, and 23 medium and high-quality metagenome-assembled genomes were recovered, all associated with methanotrophic, methylotrophic or predatory bacteria. Metagenomic viral contigs were identified with 63% containing gene homologues associated with methanotrophs. Genomic sequences from multiple ¹³C-enriched viruses were present in the CRISPR arrays of closely-related Methylocystis populations, with differences in their history of viral interaction and also between ancestral vs contemporary strains. Viral genomes were also linked to methylotrophic and heterotrophic predatory bacteria, demonstrating that carbon is rapidly transferred to a diverse range of viruses associated with methane-fueled microbial networks in soil.