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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 Climate change is affecting how energy and matter flow through ecosystems, thereby altering global carbon and nutrient cycles. Microorganisms play a fundamental role in carbon and nutrient cycling and are thus an integral link between ecosystems and climate. Here, we highlight a major black box hindering our ability to anticipate ecosystem climate responses: viral infections within complex microbial food webs. We show how understanding and predicting ecosystem responses to warming could be challenging—if not impossible—without accounting for the direct and indirect effects of viral infections on different microbes (bacteria, archaea, fungi, protists) that together perform diverse ecosystem functions. Importantly, understanding how rising temperatures associated with climate change influence viruses and virus-host dynamics is crucial to this task, yet is severely understudied. In this perspective, we (i) synthesize existing knowledge about virus-microbe-temperature interactions and (ii) identify important gaps to guide future investigations regarding how climate change might alter microbial food web effects on ecosystem functioning. To provide real-world context, we consider how these processes may operate in peatlands—globally significant carbon sinks that are threatened by climate change. We stress that understanding how warming affects biogeochemical cycles in any ecosystem hinges on disentangling complex interactions and temperature responses within microbial food webs. 

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. 

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.