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Abstract Microbes adopt a diversity of strategies to successfully compete with coexisting strains for space and resources. One common strategy is the production of toxic compounds to inhibit competitors, but the strength and direction of selection for this strategy varies depending on the environment. Existing theoretical and experimental evidence suggests growth in spatially structured environments makes toxin production more beneficial because competitive interactions are localized. Because higher growth rates reduce the length-scale of interactions in structured environments, theory predicts that toxin production should be especially beneficial under these conditions. We tested this hypothesis by developing a genome-scale metabolic modeling approach and complementing it with comparative genomics to investigate the impact of growth rate on selection for costly toxin production. Our modeling approach expands the current abilities of the dynamic flux balance analysis platform COMETS to incorporate signaling and toxin production. Using this capability, we find that our modeling framework predicts that the strength of selection for toxin production increases as growth rate increases. This finding is supported by comparative genomics analyses that include diverse microbial species. Our work emphasizes that toxin production is more likely to be maintained in rapidly growing, spatially structured communities, thus improving our ability to manage microbial communities and informing natural product discovery. 

Plants serve as critical links between above- and below-ground microbial communitites, both influencing and being influenced by microbes in these two realms. Below-ground microbial communities are expected to respond to soil resource environments, which are mediated by the roots of plants that can, in turn, be influenced by the above-ground community of foliar endophytes. For instance, diverse plant communities deposit more, and more diverse, nutrients into the soil, and this deposition is often increased when foliar pathogens are removed. Differences in soil resources can alter soil microbial composition and phenotypes, including inhibitory capacity, resource use, and antibiotic resistance. In this work, we consider plots differing in plant richness and application of foliar fungicide, evaluating consequences on soil resource levels and root-associatedStreptomycesphenotypes. Soil carbon, nitrogen, phosphorus, potassium, and organic matter were greater in samples from polyculture than monoculture, yet this increase was surprisingly offset when foliar fungal communities were disrupted. We find thatStreptomycesphenotypes varied more between richness plots—with theStreptomycesfrom polyculture showing lower inhibitory capacity, altered resource-use profiles, and greater antibiotic resistance—than between subplots with/without foliar fungicide. Where foliar fungicide affected phenotypes, it did so differently in polyculture than in monoculture, for instance decreasing niche width and overlap in monoculture while increasing them in polyculture. No differences in phenotype were correlated with soil nutrient levels, suggesting the need for further research looking more closely at soil resource diversity and particular compounds that were found to differ between treatments. 

Abstract A combination of theory and experiments predicts that increasing soil nutrients will modify herbivore and microbial impacts on ecosystem carbon cycling.However, few studies of herbivores and soil nutrients have measured both ecosystem carbon fluxes and carbon pools. Even more rare are studies manipulating microbes and nutrients that look at ecosystem carbon cycling responses.We added nutrients to a long‐term, experiment manipulating foliar fungi, soil fungi, mammalian herbivores and arthropods in a low fertility grassland. We measured gross primary production (GPP), ecosystem respiration (ER), net ecosystem exchange (NEE) and plant biomass throughout the growing season to determine how nutrients modify consumer impacts on ecosystem carbon cycling.Nutrient addition increased above‐ground biomass and GPP, but not ER, resulting in an increase in ecosystem carbon uptake rate. Reducing foliar fungi and arthropods increased plant biomass. Nutrients amplified consumer effects on plant biomass, such that arthropods and foliar fungi had a threefold larger impact on above‐ground biomass in fertilized plots.Synthesis. Our work demonstrates that throughout the growing season soil resources modify carbon uptake rates as well as animal and fungal impacts on plant biomass production. Taken together, ongoing nutrient pollution may increase ecosystem carbon uptake and drive fungi and herbivores to have larger impacts on plant biomass production. 

Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grassAndropogon gerardiiand characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities ofA.gerardii. 

Abstract Plants face trade‐offs between allocating resources to growth, while also defending against herbivores or pathogens. Species differences along defense trade‐off axes may promote coexistence and maintain diversity. However, few studies of plant communities have simultaneously compared defense trade‐offs against an array of herbivores and pathogens for which defense investment may differ, and even fewer have been conducted in the complex natural communities in which these interactions unfold. We tested predictions about the role of defense trade‐offs with competition and growth in diversity maintenance by tracking plant species abundance in a field experiment that removed individual consumer groups (mammals, arthropods, fungi) and added nutrients. Consistent with a growth–defense trade‐off, plant species that increased in mass in response to nutrient addition also increased when consumers were removed. This growth–defense trade‐off occurred for all consumer groups studied. Nutrient addition reduced plant species richness, which is consistent with trade‐off theory. Removing foliar fungi increased plant diversity via increased species evenness, whereas removal of other consumer groups had little effect on diversity, counter to expectations. Thus, while growth–defense trade‐offs are general across consumer groups, this trade‐off observed in wild plant communities does not necessarily support plant diversity maintenance. 

This review covers intercellular signalling in the soil microbiome and its importance in regulating key beneficial functions. We consider the possibilities for how we can engineer soil microbiome signalling to unlock tangible benefits to crops. 

Abstract All multicellular organisms host a diverse microbiome composed of microbial pathogens, mutualists, and commensals, and changes in microbiome diversity or composition can alter host fitness and function. Nonetheless, we lack a general understanding of the drivers of microbiome diversity, in part because it is regulated by concurrent processes spanning scales from global to local. Global-scale environmental gradients can determine variation in microbiome diversity among sites, however an individual host’s microbiome also may reflect its local micro-environment. We fill this knowledge gap by experimentally manipulating two potential mediators of plant microbiome diversity (soil nutrient supply and herbivore density) at 23 grassland sites spanning global-scale gradients in soil nutrients, climate, and plant biomass. Here we show that leaf-scale microbiome diversity in unmanipulated plots depended on the total microbiome diversity at each site, which was highest at sites with high soil nutrients and plant biomass. We also found that experimentally adding soil nutrients and excluding herbivores produced concordant results across sites, increasing microbiome diversity by increasing plant biomass, which created a shaded microclimate. This demonstration of consistent responses of microbiome diversity across a wide range of host species and environmental conditions suggests the possibility of a general, predictive understanding of microbiome diversity. 

Abstract Endophytes often have dramatic effects on their host plants. Characterizing the relationships among members of these communities has focused on identifying the effects of single microbes on their host, but has generally overlooked interactions among the myriad microbes in natural communities as well as potential higher-order interactions. Network analyses offer a powerful means for characterizing patterns of interaction among microbial members of the phytobiome that may be crucial to mediating its assembly and function. We sampled twelve endophytic communities, comparing patterns of niche overlap between coexisting bacteria and fungi to evaluate the effect of nutrient supplementation on local and global competitive network structure. We found that, despite differences in the degree distribution, there were few significant differences in the global network structure of niche-overlap networks following persistent nutrient amendment. Likewise, we found idiosyncratic and weak evidence for higher-order interactions regardless of nutrient treatment. This work provides a first-time characterization of niche-overlap network structure in endophytic communities and serves as a framework for higher-resolution analyses of microbial interaction networks as a consequence and a cause of ecological variation in microbiome function. 

Summary High‐quality microbiome research relies on the integrity, management and quality of supporting data. Currently biobanks and culture collections have different formats and approaches to data management. This necessitates a standard data format to underpin research, particularly in line with the FAIR data standards of findability, accessibility, interoperability and reusability. We address the importance of a unified, coordinated approach that ensures compatibility of data between that needed by biobanks and culture collections, but also to ensure linkage between bioinformatic databases and the wider research community.