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The concentration of atmospheric methane (CH4) continues to increase with microbial communities controlling soil–atmosphere fluxes. While there is substantial knowledge of the diversity and function of prokaryotes regulating CH4 production and consumption, their active interactions with viruses in soil have not been identified. Metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts. However, this does not determine if these represent current or historical interactions nor whether a virus or host are active. In this study, we identified active interactions between individual host and virus populations in situ by following the transfer of assimilated carbon. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized CH4-fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilizers, together with the recent transfer of CH4-derived carbon to viruses. A total of 63% of viral contigs from replicated soil incubations contained homologs of genes present in known methylotrophic bacteria. Genomic sequences of 13C-enriched viruses were represented in over one-third of spacers in CRISPR arrays of multiple closely related Methylocystis populations and revealed differences in their history of viral interaction. Viruses infecting nonmethanotrophic 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 CH4-fueled microbial food networks.

Here, we investigated overlooked microbes in soil, candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes.

BackgroundRewetting of seasonally dry soils induces a burst of microbial activity and carbon mineralization that changes nutrient availability and leads to taxonomic succession. Yet the microbial functions that underpin succession are not well described. Further, how previous precipitation regimes frame microbial functional capacities after rewetting and the length of time that these effects persist remain unknown. To address these questions, we performed rewetting of seasonally dry grassland soil that experienced either mean annual or reduced precipitation during the growing season using isotopically labeled water, and sampled at five time points. We used quantitative stable isotope probing (qSIP)-informed genome-resolved metagenomics to identify actively growing bacteria and archaea, to predict their traits and analyze how these traits differ over time and between precipitation treatments.ResultsWe reconstructed 503 genomes representing bacteria and archaea from 11 phyla and 23 classes, of which 77 were from active organisms (15% of organisms). Actively growing organisms at any time point and in any treatment were primarily Actinobacteria, Alphaproteobacteria and Gammaproteobacteria. Growing organisms were significantly more abundant than non-growing organisms prior to the wet-up, suggesting that the traits that initiate succession are pre-defined at the end of the growing season or by survival over the dry season. Fast growing organisms had a relatively low number of carbohydrate active enzymes per genome compared to slower growing organisms. This suggests that although they are capable of degrading complex C sources such as plant material, they do not specialize in this process. Differential abundance of carbohydrate active enzymes in growing organisms throughout the succession implies variation in substrates over time. However, nitrogen cycling pathways differed between precipitation treatments, but in growing organisms there was no change in the abundance of genes involved over time following wetup. Comparison of gene inventories prior to wet-up revealed that many genes were significantly differentially abundant between the precipitation treatments. Surprisingly, this legacy effect waned after just one week, indicating that microbial community functions likely converge early in the growing season.ConclusionsUse of isotopic labeling of genomes of soil microorganisms during the first week after wetup revealed differences in the abundance and functional traits of actively growing organisms under two precipitation regimes. Although the legacy effect due to different rainfall inputs was short lived, it is important, given the extent of soil organic matter breakdown that occurs immediately after the first rain event in Mediterranean climates. Changes in the potential to degrade complex organic matter during the succession imply that the current paradigm that succession relies solely on labile carbon sources needs to be revisited.

The beneficial human gut bacterium Akkermansia muciniphila provides metabolites to other members of the gut microbiota by breaking down host mucin, but most of its other metabolic functions have not been investigated. A. muciniphila strain MucT is known to use cobamides, the vitamin B12 family of cofactors with structural diversity in the lower ligand. However, A. muciniphila MucT is unable to synthesize cobamides de novo, and the specific forms that can be used by A. muciniphila have not been examined. We found that the levels of growth of A. muciniphila MucT were nearly identical with each of seven cobamides tested, in contrast to nearly all bacteria that had been studied previously. Unexpectedly, this promiscuity is due to cobamide remodeling—the removal and replacement of the lower ligand—despite the absence of the canonical remodeling enzyme CbiZ in A. muciniphila. We identified a novel enzyme, CbiR, that is capable of initiating the remodeling process by hydrolyzing the phosphoribosyl bond in the nucleotide loop of cobamides. CbiR does not share similarity with other cobamide remodeling enzymes or B12-binding domains and is instead a member of the apurinic/apyrimidinic (AP) endonuclease 2 enzyme superfamily. We speculate that CbiR enables bacteria to repurpose cobamides that they cannot otherwise use in order to grow under cobamide-requiring conditions; this function was confirmed by heterologous expression of cbiR in Escherichia coli. Homologs of CbiR are found in over 200 microbial taxa across 22 phyla, suggesting that many bacteria may use CbiR to gain access to the diverse cobamides present in their environment. IMPORTANCE Cobamides, comprising the vitamin B12 family of cobalt-containing cofactors, are required for metabolism in all domains of life, including most bacteria. Cobamides have structural variability in the lower ligand, and selectivity for particular cobamides has been observed in most organisms studied to date. Here, we discovered that the beneficial human gut bacterium Akkermansia muciniphila can use a diverse range of cobamides due to its ability to change the cobamide structure via a process termed cobamide remodeling. We identify and characterize the novel enzyme CbiR that is necessary for initiating the cobamide remodeling process. The discovery of this enzyme has implications for understanding the ecological role of A. muciniphila in the gut and the functions of other bacteria that produce this enzyme.