Methane-derived carbon flow through host-virus trophic networks in soil

Abstract

The concentration of atmospheric methane continues to increase with microbial communities controlling soil-atmosphere fluxes. While there is substantial knowledge of the diversity and function of organisms regulating methane production and consumption, the frequency and impact of interactions with viruses on their activity in soil is unknown. Metagenomic sequencing of soil microbial communities has enabled identification of linkages between viruses and hosts. However, determining host-virus linkages through sequencing does not determine whether a virus or a host are active. In this study, we identified active individual interactions in situ by following the transfer of assimilated carbon from active hosts to virus. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized methane-fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilizers of carbon, together with the recent transfer of methane-derived carbon to viruses. Sixty-three percent of viral contigs from replicated soil incubations contained genes associated with known methanotrophic and methylotrophic bacteria. Genomic sequences from 13C-enriched viruses were present in clustered regularly interspaced short palindromic repeats (CRISPR) arrays of multiple, closely-related Methylocystis populations, revealing differences in their history of viral interaction. Viruses infecting non-methanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with methane-fueled microbial food networks.

Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification

“…Capsid, terminase, portal and integrase protein sequences from these proviruses were subsequently used as search queries. While previous analysis of 12 total soil metagenome or virome libraries from the same soil samples did not enable identification of any AOA-associated virus contigs (average of 152 million quality filtered reads and 1,947 contigs ³10 kb per library) [14], this targeted approach using LBD DNA from nitrifying microcosms yielded 64 contigs predicted as derived from AOA-infecting viruses and each representing a unique vOTU. In addition, viruses infecting other nitrifier populations were identified with five and three vOTUs derived from viruses infecting ammonia-oxidising bacteria (AOB) and NOB, respectively.…”

“…A homologue-based approach was also used where an AOA host was predicted when 'best hit' shared homologues with those in genomes of Thaumarchaeota (NCBI taxonomy) were ≥3x more abundant compared to the second most dominant phylum [26]. Unlike our previous DNA-SIP analysis of methanotroph populations and associated viruses in these soils [27], spacer sequences in AOA MAG CRISPR arrays only matched predicted AOA viruses from other studies with 2 mismatches between spacer and protospacer sequences and none from this study (data not shown).…”

“…Nevertheless, identifying active interactions with specific populations or functional groups in soil remains challenging due to structural complexity and the vast diversity of hosts and viruses. Recent use of stable-isotope approaches has investigated whole community host-virus dynamics [12,13] or interactions between individual host-virus populations specific to a functional process and substrate [14]. The aim of this study was to utilise the latter approach with 13 CO2-based DNA-SIP to focus on nitrificationassociated interactions and to test the hypothesis that viruses are a dynamic component of soil AOA activity.…”

“…Microcosms were incubated at 25 o C for 30 days (Supplementary Figure 1) with a 5% 12 C-or 13 C-CO2 headspace to target viruses of autotrophs via transfer of assimilated carbon. Extracted DNA was subjected to isopycnic centrifugation in CsCl gradients, in which DNA migrates as a function of GC mol% and isotopic enrichment, before fractionation and analysis of genomic DNA of different buoyant densities [14]. Quantification of AOA genomic DNA distribution across CsCl gradients demonstrated growth of AOA populations (Figure 1A; Supplementary Figure 2) and genomic DNA in high buoyant density (HBD) fractions (>1.719 g ml -1 ) was then pooled for each replicate microcosm and metagenomes sequenced (Supplementary Table 1).…”

Borgs are giant extrachromosomal elements with the potential to augment methane oxidation

“…Some phenomena have been suggested to modulate methane oxidation rates. For example, some phages can decrease methane oxidation rates by infection and lysis of methane-oxidizing bacteria 8 and others with the critical subunit of MMO 9 likely increase the ability of their host bacteria to generate energy during phage replication. Here, we report the discovery of novel extrachromosomal elements that clearly replicate within Methanoperedens.…”