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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]

Soil bacteria produce a diverse array of antibiotics, yet our understanding of the specific roles of antibiotics in the ecological and evolutionary dynamics of microbial interactions in natural habitats remains limited. Here, we show a significant role for antibiotics in mediating antagonistic interactions and nutrient competition among locally coexisting Streptomycete populations from soil. We found that antibiotic inhibition is significantly more intense among sympatric than allopatric Streptomycete populations, indicating local selection for inhibitory phenotypes. For sympatric but not allopatric populations, antibiotic inhibition is significantly positively correlated with niche overlap, indicating that inhibition is targeted toward bacteria that pose the greatest competitive threat. Our results support the hypothesis that antibiotics serve as weapons in mediating local microbial interactions in soil and suggest that coevolutionary niche displacement may reduce the likelihood of an antibiotic arms race. Further insight into the diverse roles of antibiotics in microbial ecology and evolution has significant implications for understanding the persistence of antibiotic inhibitory and resistance phenotypes in environmental microbes, optimizing antibiotic drug discovery and developing strategies for managing microbial coevolutionary dynamics to enhance inhibitory phenotypes. [ABSTRACT FROM AUTHOR]

Though traditionally perceived as weapons, antibiotics are also hypothesized to act as microbial signals in natural habitats. However, while subinhibitory concentrations of antibiotics (SICA) are known to shift bacterial gene expression, specific hypotheses as to how SICA influence the ecology of natural populations are scarce. We explored whether antibiotic ‘signals’, or SICA, have the potential to alter nutrient utilization, niche overlap, and competitive species interactions among Streptomyces populations in soil. For nine diverse Streptomyces isolates, we evaluated nutrient utilization patterns on 95 different nutrient sources in the presence and absence of subinhibitory concentrations of five antibiotics. There were significant changes in nutrient use among Streptomyces isolates, including both increases and decreases in the capacity to use individual nutrients in the presence vs. in the absence of SICA. Isolates varied in their responses to SICA and antibiotics varied in their effects on isolates. Furthermore, for some isolate-isolate-antibiotic combinations, competition-free growth (growth for an isolate on all nutrients that were not utilized by a competing isolate), was increased in the presence of SICA, reducing the potential fitness cost of nutrient competition among those competitors. This suggests that antibiotics may provide a mechanism for bacteria to actively minimize niche overlap among competitors in soil. Thus, in contrast to antagonistic coevolutionary dynamics, antibiotics as signals may mediate coevolutionary displacement among coexisting Streptomyces, thereby hindering the emergence of antibiotic resistant phenotypes. These results contribute to our broad understanding of the ecology and evolutionary biology of antibiotics and microbial signals in nature. [ABSTRACT FROM AUTHOR]

We investigated soil streptomycete communities associated with four host plant species (two warm season C4 grasses: Andropogon gerardii, Schizachyrium scoparium and two legumes: Lespedeza capitata, Lupinus perennis), grown in plant communities varying in species richness. We used actinobacteria-selective PCR coupled with pyrosequencing to characterize streptomycete community composition and structure. The greatest pairwise distances between communities were observed in contrasts between monocultures of different plant species, indicating that plant species exert distinct selective effects on soil streptomycete populations. Increasing plant richness altered the composition and structure of streptomycete communities associated with each host plant species. Significant relationships between plant community characteristics, soil edaphic characteristics, and streptomycete community structure suggest that host plant effects on soil microbial communities may be mediated through changes to the soil environment. Co-occurring streptomycete taxa also shared consistent relationships with soil edaphic properties, providing further indication of the importance of habitat preference for taxon occurrence. Physical distance between sampling points had a significant influence on streptomycete community similarity. This work provides a detailed characterization of soil streptomycete populations across a field scale and in relation to plant host identity and plant community richness. [ABSTRACT FROM AUTHOR]

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]

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]

Aims: Soil microbiomes and their interactions with crop plants are important drivers of agricultural health and productivity. Our objective was to examine short-term responses of soil microbiota to agricultural management (i.e. cover cropping and nitrogen fertilization). Methods: Following three years of cropping, soil samples were collected from replicated field plots at two southern Minnesota field sites (Lamberton and Waseca). We used amplicon-based gene sequencing (ITS2 and 16S rRNA V4) to investigate short-term soil fungal and bacterial community responses to cover crops and urea-nitrogen (N) fertilization (0, 80, 100, and 120% of recommended rates) in a corn (Zea mays)-soybean (Glycine max) cropping system planted with and without cover crops. Results: We found that rates of N-fertilizer applied, more than cover crops, significantly impacted soil chemical properties at both sites. Different cropping or N fertilization treatments did not lead to strong differences in fungal or bacterial alpha (local) diversity. At both sites, cover crop was a significant predictor of fungal community compositions and specific fungal and bacterial taxa were significantly impacted by cover crops. While, N fertilization was not a strong predictor of community compositions, urea-N additions, at any rate, resulted in changes in the relative abundances of the fungal phyla Glomeromycota in addition to a number of bacterial phyla. Conclusions: Our findings suggest that after three years of cropping, fungal communities respond to cover crops, while bacterial community responses may depend on soil chemical conditions. [ABSTRACT FROM AUTHOR]

Soil microbiota play important and diverse roles in agricultural crop nutrition and productivity. Yet, despite increasing efforts to characterize soil bacterial and fungal assemblages, it is challenging to disentangle the influences of sampling design on assessments of communities. Here, we sought to determine whether composite samples—often analyzed as a low cost and effort alternative to replicated individual samples—provide representative summary estimates of microbial communities. At three Minnesota agricultural research sites planted with an oat cover crop, we conducted amplicon sequencing for soil bacterial and fungal communities (16SV4 and ITS2) of replicated individual or homogenized composite soil samples. We compared soil microbiota from within and among plots and then among agricultural sites using both sampling strategies. Results indicated that single or multiple replicated individual samples, or a composite sample from each plot, were sufficient for distinguishing broad site-level macroecological differences among bacterial and fungal communities. Analysis of a single sample per plot captured only a small fraction of the distinct OTUs, diversity, and compositional variability detected in the analysis of multiple individual samples or a single composite sample. Likewise, composite samples captured only a fraction of the diversity represented by the six individual samples from which they were formed, and, on average, analysis of two or three individual samples offered greater compositional coverage (i.e., greater number of OTUs) than a single composite sample. We conclude that sampling design significantly impacts estimates of bacterial and fungal communities even in homogeneously managed agricultural soils, and our findings indicate that while either strategy may be sufficient for broad macroecological investigations, composites may be a poor substitute for replicated samples at finer spatial scales. [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]

Though traditionally perceived as weapons, antibiotics are also hypothesized to act as microbial signals in natural habitats. However, while subinhibitory concentrations of antibiotics (SICA) are known to shift bacterial gene expression, specific hypotheses as to how SICA influence the ecology of natural populations are scarce. We explored whether antibiotic ‘signals’, or SICA, have the potential to alter nutrient utilization, niche overlap, and competitive species interactions among Streptomyces populations in soil. For nine diverse Streptomyces isolates, we evaluated nutrient utilization patterns on 95 different nutrient sources in the presence and absence of subinhibitory concentrations of five antibiotics. There were significant changes in nutrient use among Streptomyces isolates, including both increases and decreases in the capacity to use individual nutrients in the presence vs. in the absence of SICA. Isolates varied in their responses to SICA and antibiotics varied in their effects on isolates. Furthermore, for some isolate-isolate-antibiotic combinations, competition-free growth (growth for an isolate on all nutrients that were not utilized by a competing isolate), was increased in the presence of SICA, reducing the potential fitness cost of nutrient competition among those competitors. This suggests that antibiotics may provide a mechanism for bacteria to actively minimize niche overlap among competitors in soil. Thus, in contrast to antagonistic coevolutionary dynamics, antibiotics as signals may mediate coevolutionary displacement among coexisting Streptomyces, thereby hindering the emergence of antibiotic resistant phenotypes. These results contribute to our broad understanding of the ecology and evolutionary biology of antibiotics and microbial signals in nature. [ABSTRACT FROM AUTHOR]

Quantifying target microbial populations in complex communities remains a barrier to studying species interactions in soil environments. Quantitative PCR (qPCR) assays were developed for quantifying pathogenic Streptomyces scabiei and antibiotic-producing Streptomyces Iavendulae strains in complex soil communities. This assay will be useful for evaluating the competitive dynamics of streptomycetes in soil. [ABSTRACT FROM AUTHOR]

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-associated Streptomyces phenotypes. 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 that Streptomyces phenotypes varied more between richness plots-with the Streptomyces from 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., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Michalska-Smith, Schlatter, Pombubpa, Castle, Grandy, Borer, Seabloom and Kinkel.)

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., (© 2021. The Author(s).)

Plant community characteristics impact rhizosphere Streptomyces nutrient competition and antagonistic capacities. However, the effects of Streptomyces on, and their responses to, coexisting microorganisms as a function of plant host or plant species richness have received little attention. In this work, we characterized antagonistic activities and nutrient use among Streptomyces and Fusarium from the rhizosphere of Andropogon gerardii (Ag) and Lespedeza capitata (Lc) plants growing in communities of 1 (monoculture) or 16 (polyculture) plant species. Streptomyces from monoculture were more antagonistic against Fusarium than those from polyculture. In contrast, Fusarium isolates from polyculture had greater inhibitory capacities against Streptomyces than isolates from monoculture. Although Fusarium isolates had on average greater niche widths, the collection of Streptomyces isolates in total used a greater diversity of nutrients for growth. Plant richness, but not plant host, influenced the potential for resource competition between the two taxa. Fusarium isolates had greater niche overlap with Streptomyces in monoculture than polyculture, suggesting greater potential for Fusarium to competitively challenge Streptomyces in monoculture plant communities. In contrast, Streptomyces had greater niche overlap with Fusarium in polyculture than monoculture, suggesting that Fusarium experiences greater resource competition with Streptomyces in polyculture than monoculture. These patterns of competitive and inhibitory phenotypes among Streptomyces and Fusarium populations are consistent with selection for Fusarium-antagonistic Streptomyces populations in the presence of strong Fusarium resource competition in plant monocultures. Similarly, these results suggest selection for Streptomyces-inhibitory Fusarium populations in the presence of strong Streptomyces resource competition in more diverse plant communities. Thus, landscape-scale variation in plant species richness may be critical to mediating the coevolutionary dynamics and selective trajectories for inhibitory and nutrient use phenotypes among Streptomyces and Fusarium populations in soil, with significant implications for microbial community functional characteristics.

Pathogens traverse disciplinary and taxonomic boundaries, yet infectious disease research occurs in many separate disciplines including plant pathology, veterinary and human medicine, and ecological and evolutionary sciences. These disciplines have different traditions, goals, and terminology, creating gaps in communication. Bridging these disciplinary and taxonomic gaps promises novel insights and important synergistic advances in control of infectious disease. An approach integrated across the plant-animal divide would advance our understanding of disease by quantifying critical processes including transmission, community interactions, pathogen evolution, and complexity at multiple spatial and temporal scales. These advances require more substantial investment in basic disease research.

Two actinomycete strains, 32U-2T and 32U-4, were isolated from a prairie soil in Minnesota and subjected to characterization by means of polyphasic taxonomy. The 16S rRNA gene sequences were determined following PCR amplification and cloning. A phylogenetic analysis, based on comparative analysis of 16S rRNA gene sequences, indicated that the organisms consistently formed a well-separated, distinct sub-branch within the radiation of the genus Amycolatopsis of the family Pseudonocardiaceae. The levels of 16S rRNA sequence similarity between the isolates and the type strains of recognized Amycolatopsis species ranged from 94.1 to 97.9 %. The highest levels of sequence similarity were found between the isolates and Amycolatopsis coloradensis (97.6-97.9 %), Amycolatopsis alba and Amycolatopsis orientalis (97.3-97.6 %) and Amycolatopsis lurida (97.2-97.5 %). Chemotaxonomic characteristics supported the phylogenetic relationships between the organisms and members of the genus Amycolatopsis. However, a broad range of phenotypic and genetic data revealed that the isolates should be classified as novel species of the genus Amycolatopsis, for which the name Amycolatopsis minnesotensis sp. nov. is proposed. The type strain is 32U-2T (=KCCM 42246T = NRRL B-24435T).