Plant community richness and foliar fungicides impact soil inhibition, resistance, and resource use phenotypes.

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.

Interactive transcriptome analyses of Northern Wild Rice ( L.) and show convoluted communications during the early stages of fungal brown spot development.

Fungal diseases, caused mainly by spp., are past and current threats to Northern Wild Rice (NWR) grain production and germplasm preservation in both natural and cultivated settings. Genetic resistance against the pathogen is scarce.

Abiotic and Biotic Drivers of Soil Fungal Communities in Response to Dairy Manure Amendment.

Modern agriculture often relies on large inputs of synthetic fertilizers to maximize crop yield potential, yet their intensive use has led to nutrient losses and impaired soil health. Alternatively, manure amendments provide plant available nutrients, build organic carbon, and enhance soil health. However, we lack a clear understanding of how consistently manure impacts fungal communities, the mechanisms via which manure impacts soil fungi, and the fate of manure-borne fungi in soils.

Responses of Soil Fungal Communities to Lime Application in Wheat Fields in the Pacific Northwest.

Liming is an effective agricultural practice and is broadly used to ameliorate soil acidification in agricultural ecosystems. Our understanding of the impacts of lime application on the soil fungal community is scarce. In this study, we explored the responses of fungal communities to liming at two locations with decreasing soil pH in Oregon in the Pacific Northwest using high-throughput sequencing (Illumina MiSeq).

Native yeast and non-yeast fungal communities of Cabernet Sauvignon berries from two Washington State vineyards, and persistence in spontaneous fermentation.

To address a knowledge gap about the grape berry mycobiome from Washington State vineyards, next-generation sequencing of the internal transcribed spacer region (ITS1) was used to identify native yeast and fungal species on berries of cultivar 'Cabernet Sauvignon' from two vineyards at veraison and harvest in 2015 and 2016. Four hundred fifty-six different yeast amplicon sequence variants (ASV), representing 184 distinct taxa, and 2467 non-yeast fungal ASV (791 distinct taxa) were identified in this study. A set of 50 recurrent yeast taxa, including Phaeococcomyces, Vishniacozyma and Metschnikowia, were found at both locations and sampling years.

Rhizosphere community selection reveals bacteria associated with reduced root disease.

Background: Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities.

Results: In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth.

Core Rhizosphere Microbiomes of Dryland Wheat Are Influenced by Location and Land Use History.

The Inland Pacific Northwest is one of the most productive dryland wheat production areas in the United States. We explored the bacterial and fungal communities associated with wheat in a controlled greenhouse experiment using soils from multiple locations to identify core taxa consistently associated with wheat roots and how land use history influences wheat-associated communities. Further, we examined microbial co-occurrence networks from wheat rhizospheres to identify candidate hub taxa.

Inhibitory interaction networks among coevolved Streptomyces populations from prairie soils.

Soil microbes live within highly complex communities, where community composition, function, and evolution are the product of diverse interactions among community members. Analysis of the complex networks of interactions within communities has the potential to shed light on community stability, functioning, and evolution. However, we have little understanding of the variation in interaction networks among coevolved soil populations.

Inhibitory and nutrient use phenotypes among coexisting Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil.

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.

Mining the Drilosphere: Bacterial Communities and Denitrifier Abundance in a No-Till Wheat Cropping System.

Earthworms play important roles in no-till cropping systems by redistributing crop residue to lower soil horizons, providing macropores for root growth, increasing water infiltration, enhancing soil quality and organic matter, and stimulating nitrogen cycling. The soil impacted by earthworm activity, including burrows, casts, and middens, is termed the drilosphere. The objective of this study was to determine the effect of earthworms on soil microbial community composition in the drilosphere at different landscape slope positions.

Biosolids and Tillage Practices Influence Soil Bacterial Communities in Dryland Wheat.

Class B biosolids are used in dryland wheat (Triticum aestivum L.) production in eastern Washington as a source of nutrients and to increase soil organic matter, but little is known about their effects on bacterial communities and potential for harboring human pathogens. Moreover, conservation tillage is promoted to reduce erosion and soil degradation.

Fungal community composition and diversity vary with soil depth and landscape position in a no-till wheat-based cropping system.

Soil edaphic characteristics are major drivers of fungal communities, but there is a lack of information on how communities vary with soil depth and landscape position in no-till cropping systems. Eastern Washington is dominated by dryland wheat grown on a highly variable landscape with steep, rolling hills. High-throughput sequencing of fungal ITS1 amplicons was used to characterize fungal communities across soil depth profiles (0 to 100 cm from the soil surface) among distinct landscape positions and aspects across a no-till wheat field.

Succession of Fungal and Oomycete Communities in Glyphosate-Killed Wheat Roots.

The successional dynamics of root-colonizing microbes are hypothesized to be critical to displacing fungal pathogens that can proliferate after the use of some herbicides. Applications of glyphosate in particular, which compromises the plant defense system by interfering with the production of aromatic amino acids, are thought to promote a buildup of root pathogens and can result in a "greenbridge" between weeds or volunteers and crop hosts. By planting 2 to 3 weeks after spraying, growers can avoid most negative impacts of the greenbridge by allowing pathogen populations to decline, but with the added cost of delayed planting dates.

Location, Root Proximity, and Glyphosate-Use History Modulate the Effects of Glyphosate on Fungal Community Networks of Wheat.

Glyphosate is the most-used herbicide worldwide and an essential tool for weed control in no-till cropping systems. However, concerns have been raised regarding the long-term effects of glyphosate on soil microbial communities. We examined the impact of repeated glyphosate application on bulk and rhizosphere soil fungal communities of wheat grown in four soils representative of the dryland wheat production region of Eastern Washington, USA.

Impacts of Repeated Glyphosate Use on Wheat-Associated Bacteria Are Small and Depend on Glyphosate Use History.

Glyphosate is the most widely used herbicide worldwide and a critical tool for weed control in no-till cropping systems. However, there are concerns about the nontarget impacts of long-term glyphosate use on soil microbial communities. We investigated the impacts of repeated glyphosate treatments on bacterial communities in the soil and rhizosphere of wheat in soils with and without long-term history of glyphosate use.

Leveraging ecological theory to guide natural product discovery.

Technological improvements have accelerated natural product (NP) discovery and engineering to the point that systematic genome mining for new molecules is on the horizon. NP biosynthetic potential is not equally distributed across organisms, environments, or microbial life histories, but instead is enriched in a number of prolific clades. Also, NPs are not equally abundant in nature; some are quite common and others markedly rare.

Do tradeoffs structure antibiotic inhibition, resistance, and resource use among soil-borne Streptomyces?

Background: Tradeoffs among competing traits are believed to be crucial to the maintenance of diversity in complex communities. The production of antibiotics to inhibit competitors and resistance to antibiotic inhibition are two traits hypothesized to be critical to microbial fitness in natural habitats, yet data on costs or tradeoffs associated with these traits are limited. In this work we characterized tradeoffs between antibiotic inhibition or resistance capacities and growth efficiencies or niche widths for a broad collection of Streptomyces from soil.

Plant community richness and microbial interactions structure bacterial communities in soil.

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.

Global biogeography of Streptomyces antibiotic inhibition, resistance, and resource use.

Although recent molecular techniques have greatly expanded our knowledge of microbial biogeography, the functional biogeography of soil microorganisms remains poorly understood. In this work, we explore geographic variation in Streptomyces phenotypes that are critical to species interactions. Specifically, we characterize Streptomyces from different locations from multiple continents for antibiotic inhibition, resistance, and resource use phenotypes.

Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes.

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.

Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome.

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).

Resource use of soilborne Streptomyces varies with location, phylogeny, and nitrogen amendment.

In this study, we explore variation in resource use among Streptomyces in prairie soils. Resource use patterns were highly variable among Streptomyces isolates and were significantly related to location, phylogeny, and nitrogen (N) amendment history. Streptomyces populations from soils less than 1 m apart differed significantly in their ability to use resources, indicating that drivers of resource use phenotypes in soil are highly localized.

Streptomyces competition and co-evolution in relation to plant disease suppression.

High densities of antagonistic Streptomyces are associated with plant disease suppression in many soils. Here we review use of inoculation and organic matter amendments for enriching antagonistic Streptomyces populations to reduce plant disease and note that effective and consistent disease suppression in response to management has been elusive. We argue that shifting the focus of research from short-term disease suppression to the population ecology and evolutionary biology of antagonistic Streptomyces in soil will enhance prospects for effective management.

A coevolutionary framework for managing disease-suppressive soils.

This review explores a coevolutionary framework for the study and management of disease-suppressive soil microbial communities. Because antagonistic microbial interactions are especially important to disease suppression, conceptual, theoretical, and empirical work on antagonistic coevolution and its relevance to disease suppression is reviewed. In addition, principles of coevolution are used to develop specific predictions regarding the drivers of disease-suppressive potential in soil microbial communities and to highlight important areas for future research.

Rapid and specific method for evaluating Streptomyces competitive dynamics in complex soil communities.

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 lavendulae strains in complex soil communities. This assay will be useful for evaluating the competitive dynamics of streptomycetes in soil.