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ABSTRACT Temperature significantly impacts microbial communities’ composition and function, which plays a vital role in the global carbon cycle that determines climate change. Nutrient influxes often accompany rising temperatures due to human activity. While ecological interactions between different microorganisms could shape their response to environmental change, we do not understand how predation may influence these responses in a warmer and increasingly nutrient-rich world. Here, we assess whether predation by a ciliate community of bacterial consumers influences changes in the diversity, biomass, and function of a freshwater prokaryotic community under different temperature and nutrient conditions. We found that predator presence mediates the effects of temperature and nutrients on the total prokaryotic community biomass and composition through various mechanisms, including direct and indirect effects. However, the total community function was resilient. Our study supports previous findings that temperature and nutrients are essential drivers of microbial community composition and function but also demonstrates how predation can mediate these effects, indicating that the biotic context is as important as the abiotic context to understanding microbial responses to novel climates.IMPORTANCEWhile the importance of the abiotic environment in microbial communities has long been acknowledged, how prevalent ecological interactions like predation may influence these microbial community responses to shifting abiotic conditions is largely unknown. Our study addresses the complex interplay between temperature, nutrients, predation, and their joint effects on microbial community diversity and function. Our findings suggest that while temperature and nutrients are fundamental drivers of microbial community dynamics, the presence of predators significantly alters these responses. Our study underscores the impact of abiotic factors on microbial communities and the importance of accounting for the biotic context in which these occur to understand, let alone predict, these responses properly. 

Abstract Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry. 

Abstract Peatlands are crucial sinks for atmospheric carbon but are critically threatened due to warming climates.Sphagnum(peat moss) species are keystone members of peatland communities where they actively engineer hyperacidic conditions, which improves their competitive advantage and accelerates ecosystem-level carbon sequestration. To dissect the molecular and physiological sources of this unique biology, we generated chromosome-scale genomes of twoSphagnumspecies:S. divinumandS. angustifolium.Sphagnumgenomes show no gene colinearity with any other reference genome to date, demonstrating thatSphagnumrepresents an unsampled lineage of land plant evolution. The genomes also revealed an average recombination rate an order of magnitude higher than vascular land plants and short putative U/V sex chromosomes. These newly described sex chromosomes interact with autosomal loci that significantly impact growth across diverse pH conditions. This discovery demonstrates that the ability ofSphagnumto sequester carbon in acidic peat bogs is mediated by interactions between sex, autosomes and environment. 

ABSTRACT We present 49 metagenome assemblies of the microbiome associated with Sphagnum (peat moss) collected from ambient, artificially warmed, and geothermally warmed conditions across Europe. These data will enable further research regarding the impact of climate change on plant-microbe symbiosis, ecology, and ecosystem functioning of northern peatland ecosystems. 

Abstract Interactions between Sphagnum (peat moss) and cyanobacteria play critical roles in terrestrial carbon and nitrogen cycling processes. Knowledge of the metabolites exchanged, the physiological processes involved, and the environmental conditions allowing the formation of symbiosis is important for a better understanding of the mechanisms underlying these interactions. In this study, we used a cross-feeding approach with spatially resolved metabolite profiling and metatranscriptomics to characterize the symbiosis between Sphagnum and Nostoc cyanobacteria. A pH gradient study revealed that the Sphagnum–Nostoc symbiosis was driven by pH, with mutualism occurring only at low pH. Metabolic cross-feeding studies along with spatially resolved matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) identified trehalose as the main carbohydrate source released by Sphagnum, which were depleted by Nostoc along with sulfur-containing choline-O-sulfate, taurine and sulfoacetate. In exchange, Nostoc increased exudation of purines and amino acids. Metatranscriptome analysis indicated that Sphagnum host defense was downregulated when in direct contact with the Nostoc symbiont, but not as a result of chemical contact alone. The observations in this study elucidated environmental, metabolic, and physiological underpinnings of the widespread plant–cyanobacterial symbioses with important implications for predicting carbon and nitrogen cycling in peatland ecosystems as well as the basis of general host-microbe interactions. 

Abstract Peat mosses (Sphagnumspp.) are keystone species in boreal peatlands, where they dominate net primary productivity and facilitate the accumulation of carbon in thick peat deposits.Sphagnummosses harbor a diverse assemblage of microbial partners, including N₂‐fixing (diazotrophic) and CH₄‐oxidizing (methanotrophic) taxa that support ecosystem function by regulating transformations of carbon and nitrogen. Here, we investigate the response of theSphagnumphytobiome (plant + constituent microbiome + environment) to a gradient of experimental warming (+0°C to +9°C) and elevated CO₂(+500 ppm) in an ombrotrophic peatland in northern Minnesota (USA). By tracking changes in carbon (CH₄, CO₂) and nitrogen (NH₄‐N) cycling from the belowground environment up toSphagnumand its associated microbiome, we identified a series of cascading impacts to theSphagnumphytobiome triggered by warming and elevated CO₂. Under ambient CO₂, warming increased plant‐available NH₄‐N in surface peat, excess N accumulated inSphagnumtissue, and N₂fixation activity decreased. Elevated CO₂offset the effects of warming, disrupting the accumulation of N in peat andSphagnumtissue. Methane concentrations in porewater increased with warming irrespective of CO₂treatment, resulting in a ~10× rise in methanotrophic activity withinSphagnumfrom the +9°C enclosures. Warming's divergent impacts on diazotrophy and methanotrophy caused these processes to become decoupled at warmer temperatures, as evidenced by declining rates of methane‐induced N₂fixation and significant losses of keystone microbial taxa. In addition to changes in theSphagnummicrobiome, we observed ~94% mortality ofSphagnumbetween the +0°C and +9°C treatments, possibly due to the interactive effects of warming on N‐availability and competition from vascular plant species. Collectively, these results highlight the vulnerability of theSphagnumphytobiome to rising temperatures and atmospheric CO₂concentrations, with significant implications for carbon and nitrogen cycling in boreal peatlands. 

Summary Sphagnumpeatmosses are fundamental members of peatland ecosystems, where they contribute to the uptake and long‐term storage of atmospheric carbon. Warming threatensSphagnummosses and is known to alter the composition of their associated microbiome. Here, we use a microbiome transfer approach to test if microbiome thermal origin influences host plant thermotolerance.We leveraged an experimental whole‐ecosystem warming study to collect field‐grownSphagnum, mechanically separate the associated microbiome and then transfer onto germ‐free laboratorySphagnumfor temperature experiments. Host and microbiome dynamics were assessed with growth analysis, Chlafluorescence imaging, metagenomics, metatranscriptomics and 16S rDNA profiling.Microbiomes originating from warming field conditions imparted enhanced thermotolerance and growth recovery at elevated temperatures. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure in a manner that induced the plant heat shock response, especially the HSP70 family and jasmonic acid production. The heat shock response was induced even without warming treatment in the laboratory, suggesting that the warm‐microbiome isolated from the field provided the host plant with thermal preconditioning.Our results demonstrate that microbes, which respond rapidly to temperature alterations, can play key roles in host plant growth response to rapidly changing environments.