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Soil bacteria spend significant periods in dormant or semi‐dormant states that are interrupted by resource pulses which can lead to periods of rapid growth and intense nutrient competition. Microbial populations have evolved diverse strategies to circumvent competitive interactions and facilitate coexistence. Here, we show that nutrient use of soilborne Streptomyces is temporally partitioned during experimental resource pulses, leading to reduced niche overlap, and potential coexistence. Streptomyces grew rapidly on the majority of distinct 95 carbon sources but varied in which individual resources were utilized in the first 24 h. Only a handful of carbon sources (19 out of 95) were consistently utilized (>95% of isolates) most rapidly in the first 24 h. These consistently utilized carbon sources also generated the majority of biomass accumulated by isolates. Our results shed new light on a novel mechanism microbes may employ to alleviate competitive interactions by temporally partitioning the consumption of carbon resources. As competitive interactions have been proposed to drive the suppression of disease‐causing microbes in agronomic soils, our findings may hold widespread implications for soil management for plant health. [ABSTRACT FROM AUTHOR]

Plant biodiversity and consumers are important mediators of energy and carbon fluxes in grasslands, but their effects on within‐season variation of plant biomass production are poorly understood. Here we measure variation in control of plant biomass by consumers and plant diversity throughout the growing season and their impact on plant biomass phenology. To do this, we analysed 5 years of biweekly biomass measures (NDVI) in an experiment manipulating plant species richness and three consumer groups (foliar fungi, soil fungi and arthropods). Positive plant diversity effects on biomass were greatest early in the growing season, whereas the foliar fungicide and insecticide treatments increased biomass most late in the season. Additionally, diverse plots and plots containing foliar fungi reached maximum biomass almost a month earlier than monocultures and plots treated with foliar fungicide, demonstrating the dynamic and interactive roles that biodiversity and consumers play in regulating biomass production through the growing season. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Summary: Bacteria and fungi are key components of virtually all natural habitats, yet the significance of fungal‐bacterial inhibitory interactions for the ecological and evolutionary dynamics of specific bacterial and fungal populations in natural habitats have been overlooked. More specifically, despite the broad consensus that antibiotics play a key role in providing a fitness advantage to competing microbes, the significance of antibiotic production in mediating cross‐kingdom coevolutionary interactions has received relatively little attention. Here, we characterize reciprocal inhibition among Streptomyces and Fusarium populations from prairie soil, and explore antibiotic inhibition in relation to niche overlap among sympatric and allopatric populations. We found evidence for local adaptation between Fusarium and Streptomyces populations as indicated by significantly greater inhibition among sympatric than allopatric populations. Additionally, for both taxa, there was a significant positive correlation between the strength of inhibition against the other taxon and the intensity of resource competition from that taxon among sympatric but not allopatric populations. These data suggest that coevolutionary antagonistic interactions between Fusarium and Streptomyces are driven by resource competition, and support the hypothesis that antibiotics act as weapons in mediating bacterial–fungal interactions in soil. [ABSTRACT FROM AUTHOR]

Abstract: Plants face a range of trade‐offs as they attempt to maximize their fitness within a complex web composed of competitors, mutualists, and herbivores. In addition to growth–defense and competition–defense trade‐offs, plants must balance their response to a wide range of potential enemies including pathogens and vertebrate and invertebrate herbivores. We tested for trade‐offs in plant species’ responses to different types of consumers using a foodweb manipulation experiment in which we selectively excluded large vertebrate herbivores and removed foliar fungi, soil fungi, and insects from natural and experimentally planted grassland communities. We found no evidence for trade‐offs in the ability of plants to defend themselves against different sets of consumers, although plants varied widely in their responses to removal of different consumer groups. In addition, the species‐level responses to consumer removal in monoculture were uncorrelated with each species’ response in more diverse communities, highlighting the important role of local context (e.g., competition and apparent competition) in determining the effects of consumers. Plants must balance their allocation of energy among a wide variety of tasks including growing, competing for limited resources, and defending themselves against an array of potential enemies. We found that while plant species differed greatly in their response to the removal of consumers, species that were susceptible to the effects of one consumer group (e.g., insect herbivores) also were susceptible to other consumer groups (e.g., fungal pathogens). This suggests that plants differ in their overall allocation to defense, but defense investment can proffer protection against a wide array of natural enemies. We also found that plant responses to consumers depended on the diversity of the surrounding plant community, suggesting that among‐plant interactions can alter their susceptibility to the impacts of consumers. [ABSTRACT FROM AUTHOR]

Semi-natural perennial grasslands are of increasing importance as components of multifunctional agroecosystems, combining biomass production with provision of other ecosystem services. Soil legacies from previous land use or exotic species can hinder their establishment, but might be overcome through a multi-stage successional strategy, whereby certain species are used to facilitate native grassland species establishment. We tested this strategy via a feedback experiment examining soil-conditioning effects on interference interactions between native and exotic species., Soils in a former maize-soybean production field in Minnesota, USA, were conditioned for 3 years with native or invasive exotic perennials or a maize-soybean crop rotation. Nitrogen (N) fertilization was an additional treatment in field plots. In a greenhouse, native and invasive exotic perennial grassland seedlings were grown on these soils, in monoculture and in native-exotic species pairs, with and without N fertilization. The impact of soil conditioning and field and greenhouse N fertilization on interactions between native and exotic seedlings in mixture was determined., Neighbouring plants suppressed biomass production in all native and exotic species. The maize-soybean rotation left a soil legacy that enhanced suppression of native species when grown with exotic species, while exotic species suffered no such disadvantage., The strong and specific disadvantage to native species of maize-soybean soils decreased with greenhouse N fertilization, but remained significant, while field N addition did not alter this effect., Synthesis and applications. We found that the negative soil legacy of the maize-soybean rotation for native plant performance in interaction with exotics was greatly diminished in soils conditioned by native or exotic perennial species, irrespective of nitrogen addition. This highlights the potential value of perennial species in conversion from row-crop agriculture to grasslands, because all perennial species alleviated the enhanced suppression of natives observed on maize-soybean soils. We did not find strong evidence that these perennial species were capable of specifically facilitating native species over exotics, but a broader range of species should be evaluated. [ABSTRACT FROM AUTHOR]

Methods to ensure the health of crops owe their efficacy to the extent to which we understand the ecology and biology of environmental microorganisms and the conditions under which their interactions with plants lead to losses in crop quality or yield. However, in the pursuit of this knowledge, notions of the ecology of plant-pathogenic microorganisms have been reduced to a plant-centric and agro-centric focus. With increasing global change, i.e. changes that encompass not only climate, but also biodiversity, the geographical distribution of biomes, human demographic and socio-economic adaptations and land use, new plant health problems will emerge via a range of processes influenced by these changes. Hence, knowledge of the ecology of plant pathogens will play an increasingly important role in the anticipation and response to disease emergence. Here, we present our opinion on the major challenges facing the study of the ecology of plant-pathogenic bacteria. We argue that the discovery of markedly novel insights into the ecology of plant-pathogenic bacteria is most likely to happen within a framework of more extensive scales of space, time and biotic interactions than those that currently guide much of the research on these bacteria. This will set a context that is more propitious for the discovery of unsuspected drivers of the survival and diversification of plant-pathogenic bacteria and of the factors most critical for disease emergence, and will set the foundation for new approaches to the sustainable management of plant health. We describe the contextual background of, justification for and specific research questions with regard to the following challenges: Development of terminology to describe plant-bacterial relationships in terms of bacterial fitness., Definition of the full scope of the environments in which plant-pathogenic bacteria reside or survive., Delineation of pertinent phylogenetic contours of plant-pathogenic bacteria and naming of strains independent of their presumed life style., Assessment of how traits of plant-pathogenic bacteria evolve within the overall framework of their life history., Exploration of possible beneficial ecosystem services contributed to by plant-pathogenic bacteria. [ABSTRACT FROM AUTHOR]

The content and ratio of nutrients in plants can be constrained by a wide array of factors, including nutrient supply, light intensity, herbivory, infection or intrinsic growth rate and can, in turn, affect many ecosystem processes including photosynthesis, decomposition, resource limitation and nutrient cycling. Studies of plant stoichiometry and stoichiometric homeostasis have focused primarily on the role of nutrient supply as a constraint on plant tissue chemistry, yet recent work suggests that local plant diversity, plant species composition and consumers may change the nutrient composition of whole plant communities., By experimentally removing insects, foliar fungi and soil fungi from a long-term experiment manipulating plant diversity, we found that the foliar stoichiometry of individual plant species depends on biotic context., Local plant diversity and the composition of the consumer community each altered foliar tissue carbon and nutrient chemistry of four different grassland species. The greatest impacts of consumers on foliar chemistry occurred at low plant diversity, and these changes induced by altering the food web were of a similar magnitude to the effects of fertilization or drought found in previous work. Consumers and plant diversity acted primarily on foliar carbon and nitrogen, whereas changes in foliar phosphorus were associated with the productivity of the local plant community. Thus, changes in whole-community stoichiometry that have been documented in response to alterations of the consumer food web or plant community are underlain by stoichiometric changes in individual species as well as plant species compositional changes., Synthesis. These results suggest a new pathway by which loss of consumer or plant diversity may significantly impact the wide variety of ecosystem processes that depend on foliar nutrient content. [ABSTRACT FROM AUTHOR]

Plant species, plant community diversity and microbial interactions can significantly impact soil microbial communities, yet there are few data on the interactive effects of plant species and plant community diversity on soil bacterial communities. We hypothesized that plant species and plant community diversity affect soil bacterial communities by setting the context in which bacterial interactions occur. Specifically, we examined soil bacterial community composition and diversity in relation to plant "host" species, plant community richness, bacterial antagonists, and soil edaphic characteristics. Soil bacterial communities associated with four different prairie plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, and Lupinus perennis) grown in plant communities of increasing species richness (1, 4, 8, and 16 species) were sequenced. Additionally, soils were evaluated for populations of antagonistic bacteria and edaphic characteristics. Plant species effects on soil bacterial community composition were small and depended on plant community richness. In contrast, increasing plant community richness significantly altered soil bacterial community composition and was negatively correlated with bacterial diversity. Concentrations of soil carbon, organic matter, nitrogen, phosphorus, and potassium were similarly negatively correlated with bacterial diversity, whereas the proportion of antagonistic bacteria was positively correlated with soil bacterial diversity. Results suggest that plant species influences on soil bacterial communities depend on plant community diversity and are mediated through the effects of plant-derived resources on antagonistic soil microbes. [ABSTRACT FROM AUTHOR]

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A conceptual model emphasizing direct host-microbe interactions has dominated work on host-associated microbiomes. To understand plant-microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant-plant and microbe-microbe interactions. We sampled soil microbiomes associated with target plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in communities varying in plant richness (1-, 4-, 8- or 16-species). We assessed Streptomyces antagonistic activity and analysed bacterial and Streptomyces populations via 454 pyrosequencing. Host plant species and plant richness treatments altered networks of coassociation among bacterial taxa, suggesting the potential for host plant effects on the soil microbiome to include changes in microbial interaction dynamics and, consequently, co-evolution. Taxa that were coassociated in the rhizosphere of a given host plant species often showed consistent correlations between operational taxonomic unit (OTU) relative abundance and Streptomyces antagonistic activity, in the rhizosphere of that host. However, in the rhizosphere of a different host plant species, the same OTUs showed no consistency, or a different pattern of responsiveness to such biotic habitat characteristics. The diversity and richness of bacterial and Streptomyces communities exhibited distinct relationships with biotic and abiotic soil characteristics. The rhizosphere soil microbiome is influenced by a complex and nested array of factors at varying spatial scales, including plant community, plant host, soil edaphics and microbial taxon and community characteristics. [ABSTRACT FROM AUTHOR]

Ecosystem productivity commonly increases asymptotically with plant species diversity, and determining the mechanisms responsible for this well-known pattern is essential to predict potential changes in ecosystem productivity with ongoing species loss. Previous studies attributed the asymptotic diversity-productivity pattern to plant competition and differential resource use (e.g., niche complementarity). Using an analytical model and a series of experiments, we demonstrate theoretically and empirically that host-specific soil microbes can be major determinants of the diversity productivity relationship in grasslands. In the presence of soil microbes, plant diseasedecreased with increasing diversity, and productivity increased nearly 500%, primarily because of the strong effect of density-dependent disease on productivity at low diversity. Correspondingly, disease was higher in plants grown in conspecific-trained soils than heterospecific-trained soils (demonstrating host-specificity), and productivity increased and host-specific disease decreased with increasing community diversity, suggesting that disease was the primary cause of reduced productivity in species- poor treatments. In sterilized, microbe-free soils, the increase in productivity with increasing plant species number was markedly lower than the increase measured in the presence of soil microbes, suggesting that niche complementarity was a weaker determinant of the diversity- productivity relationship. Our results demonstrate that soil microbes play an integral role as determinants of the diversity-productivity relationship. [ABSTRACT FROM AUTHOR]