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High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum Lenarviricota, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts.

Soil surface consortia are easily observed and sampled, allowing examination of their interactions with soil microbiomes. Here, we present metatranscriptomic sequences from Dark Green 1 (DG1), a cyanobacterium-based soil surface consortium, in the presence and absence of an underlying soil microbiome and/or urea.

Summary: Leaf decomposition varies widely across temperate forests, shaped by factors like litter quality, climate, soil properties, and decomposers, but forest heterogeneity may mask local tree influences on decomposition and litter‐associated microbiomes. We used a 24‐yr‐old common garden forest to quantify local soil conditioning impacts on decomposition and litter microbiology.We introduced leaf litter bags from 10 tree species (5 arbuscular mycorrhizal; 5 ectomycorrhizal) to soil plots conditioned by all 10 species in a full‐factorial design. After 6 months, we assessed litter mass loss, C/N content, and bacterial and fungal composition. We hypothesized that (1) decomposition and litter‐associated microbiome composition would be primarily shaped by the mycorrhizal type of litter‐producing trees, but (2) modified significantly by underlying soil, based on mycorrhizal type of the conditioning trees.Decomposition and, to a lesser extent, litter‐associated microbiome composition, were primarily influenced by the mycorrhizal type of litter‐producing trees. Interestingly, however, underlying soils had a significant secondary influence, driven mainly by tree species, not mycorrhizal type. This secondary influence was strongest under trees from the Pinaceae.Temperate trees can locally influence underlying soil to alter decomposition and litter‐associated microbiology. Understanding the strength of this effect will help predict biogeochemical responses to forest compositional change. [ABSTRACT FROM AUTHOR]

The gut microbiome can influence host fitness and, consequently, the ecology and evolution of natural populations. Microbiome composition can be driven by environmental exposure but also by the host's genetic background and phenotype. To contrast environmental and genetic effects on the microbiome we leverage preserved specimens of eastern fence lizards from allopatric lineages east and west of the Mississippi River but reared in standardized conditions. Bacterial composition was indistinguishable between lineages but responded significantly to host age—a proxy for environmental exposure. This was accompanied by a continuous decrease in bacterial diversity in both lineages, partially driven by decreasing evenness seen only in western lizards. These findings indicate that longer exposure to a homogeneous habitat may have a depreciating effect on microbiome diversity in eastern fence lizards, a response shared by both lineages. We highlight the importance of such effects when extrapolating patterns from laboratory experiments to the natural world. [ABSTRACT FROM AUTHOR]

Soil microbial responses to climate warming in temperate regions may interact with the effects of increased atmospheric N deposition. In addition, the combined effects of these factors on microbial activity during the plant growing season may differ from the effects over winter, when reduced plant soil C inputs and soil freezing can alter microbial nutrient availability and demand. We examined seasonal changes in soil extracellular enzyme activity (EEA), microbial biomass C and N, and soil fungal and bacterial content in a warming and N addition experiment in a temperate old field. For EEA, we examined both hydrolases (organic C degrading enzymes, a chitinase and phospharase) and ligninases (phenol oxidase and peroxidase). While both hydrolase and ligninase activities exhibited significant seasonal variation, EEA was unresponsive to the experimental treatments. Microbial biomass C increased with warming year round, however, and microbial biomass N increased with N addition but only over summer. Despite increased microbial biomass m response to warming, phosphatase was the only enzyme that exhibited a significant change in specific activity (enzyme activity per unit of microbial biomass) in response to warming. Likewise, soil fungal and bacterial biomass varied seasonally, but treatment effects on these variables were minimal. Overall, while the effects of N addition on microbial N varied seasonally, microbial responses were relatively insensitive to the warming and N addition treatments in our experiment. This insensitivity was unexpected given the large treatment effects on plant productivity and soil N dynamics documented during the same time frame in the field experiment. Abbreviations: EEA, extracellular enzyme assay; NAG, N-acetyl-glucosaminidase. doi: 10.2136/sssaj2009.0036

Summary: Climate change‐related soil salinization increases plant stress and decreases productivity. Soil microorganisms are thought to reduce salt stress through multiple mechanisms, so diverse assemblages could improve plant growth under such conditions. Previous studies have shown that microbiome selection can promote desired plant phenotypes, but with high variability. We hypothesized that microbiome selection would be more consistent in saline soils by increasing potential benefits to the plants.In both salt‐amended and untreated soils, we transferred forward Brassica rapa root microbiomes (from high‐biomass or randomly selected pots) across six planting generations while assessing bacterial (16S rRNA) and fungal (ITS) composition in detail. Uniquely, we included an add‐back control (re‐adding initial frozen soil microbiome) as a within‐generation reference for microbiome and plant phenotype selection.We observed inconsistent effects of microbiome selection on plant biomass across generations, but microbial composition consistently diverged from the add‐back control. Although salt amendment strongly impacted microbial composition, it did not increase the predictability of microbiome effects on plant phenotype, but it did increase the rate at which microbiome selection plateaued.These data highlight a disconnect in the trajectories of microbiomes and plant phenotypes during microbiome selection, emphasizing the role of standard controls to explain microbiome selection outcomes. [ABSTRACT FROM AUTHOR]