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1. Fungal communities driven by Rhododendron species correlate with pathogen protection against Phytophthora cinnamomi

   https://doi.org/10.1007/s11104-025-07847-z  

   Ahmad, Saliha; Burke, David J; Carrino-Kyker, Sarah R; Medeiros, Juliana S; Burns, Jean H (September 2025, Plant and Soil)

   Abstract Background and aimsPlant interactions with soil microbial communities are critical for understanding plant health, improving horticultural and agricultural outcomes, and maintaining diverse natural communities. In some cases, disease suppressive soils enhance plant survival in the presence of pathogens. However, species-specific differences and seasonal variation complicate our understanding of the drivers of soil fungal communities and their consequences for plants. Here, we aim to describe soil fungal communities acrossRhododendronspecies and seasons as well as the test for fungal indicators ofRhododendronspecies in the soil. Further, we test possible mechanisms governing disease suppressive soils to the oomycete pathogenPhytophthora cinnamomi. Variation in disease susceptibility to this pathogen across species and clades allows us to test for possible fungal drivers of disease suppressive soils. MethodsWe conducted high throughput sequencing of the fungal communities found in soil collected under 14Rhododendronspecies and across 2 seasons (April, October) at two sites in Ohio, USA. Phylogenetic analyses were used to ask whether fungal community composition correlated with increased plant survival with the addition of whole soil communities from a prior greenhouse experiment. ResultsEffects ofRhododendronspecies (R² = 0.13), season (R² = 0.01) and their interaction on fungal communities (R² = 0.11) were statistically significant. Fungal community composition negatively correlated with survival following exposure to whole soil microbial communities, though this result depended on the presence ofR. minus. Forty-fiveTrichodermataxa were identified across our soil samples, and someTrichodermawere significantly associated with particularRhododendronspecies (e.g.Trichoderma atroviridewas associated withR. molle) in indicator species analyses. ConclusionThe correlation between plant responses to soil biotic communities and fungal community composition, as well as the presence of potential beneficial taxa such asTrichodermaand mycorrhizal fungi, are consistent with fungal-mediated survival benefits from the pathogenPhytophthora cinnamomi. 

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2. Phosphite indirectly mediates protection against root rot disease via altering soil fungal community in Rhododendron species

   https://doi.org/10.17605/OSF.IO/HU35A  

   Liu, Yu; J, David Burke; S, Juliana Medeiros; R, Sarah Kyker; H., Jean Burns (January 2023, Open Science Framework)

   The soil-borne pathogen Phytophthora cinnamomi causes a deadly plant disease. Phosphite is widely used as an effective treatment to protect plants from Phytophthora cinnamomi. Phosphite as a common fungicide might influence the composition of soil fungal communities. However, whether the belowground mechanisms of phosphite-mediated protections are direct or indirectly mediated through soil biota are unknown. Therefore, exploring belowground mechanisms could contribute to the evaluation of the sustainability of phosphite use and tests hypotheses about direct versus indirect mechanisms in pathogen response. Our greenhouse pot experiment on Rhododendron species had either an after-pathogen or a before-pathogen use of phosphite to compare and evaluate plant and soil fungal responses to phosphite and the presence of an oomycete pathogen phytophthora cinnamomi. The factorial experiment also included with and without pathogen and soil biota treatments, for a test of interactive effects. High throughput sequencing analyzed the soil fungal communities, and we measured the diversity, evenness and richness of soil fungi. Phosphite effectively increased survival of Rhododendron species. It altered the composition of soil fungal communities, and the timing of using phosphite determined the way in which the fungal communities changed. Trichoderma taxa also responded to soil phosphite and Phytophthora cinnamomi. The benefits of antagonistic fungi such as Trichoderma are context-dependent, suggesting protection against pathogens depends on the timing of phosphite application. This study provides the first evidence that phosphite-mediated pathogen protection includes both direct benefits to plants and indirect effects mediated through the soil microbial community. 

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3. Phosphite indirectly mediates protection against root rot disease via altering soil fungal community in Rhododendron species

   https://doi.org/10.1007/s11104-023-06129-w  

   Liu, Yu; Burke, David J.; Medeiros, Juliana S.; Carrino-Kyker, Sarah R.; Burns, Jean H. (June 2023, Plant and Soil)

   Background and Aims The soil-borne pathogen Phytophthora cinnamomi causes a deadly plant disease. Phosphite is widely used as an effective treatment to protect plants from Phytophthora cinnamomi. Phosphite as a common fungicide might influence the composition of soil fungal communities. However, whether the belowground effects of phosphitemediated protections are direct or indirectly mediated through soil biota are unknown. Therefore, exploring belowground effects could contribute to the evaluation of the sustainability of phosphite use and tests hypotheses about direct versus indirect effects in pathogen response. Methods Our greenhouse pot experiment on Rhododendron species had either an after-pathogen or a before-pathogen use of phosphite to compare and evaluate plant and soil fungal responses to phosphite and the presence of an oomycete pathogen Phytophthora cinnamomi. The factorial experiment also included with and without pathogen and soil biota treatments, for a test of interactive effects. High throughput sequencing analyzed the soil fungal communities, and we measured the diversity, evenness and richness of soil fungi. Results Phosphite effectively increased survival of Rhododendron species. It altered the composition of soil fungal communities, and the timing of using phosphite determined the way in which the fungal communities changed. Trichoderma taxa also responded to soil phosphite and Phytophthora cinnamomi. Conclusions The benefits of antagonistic fungi such as Trichoderma are context-dependent, suggesting protection against pathogens depends on the timing of phosphite application. This study provides evidence that phosphite-mediated pathogen protection includes both direct benefits to plants and indirect effects mediated through the soil fungal community. 

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4. Long-Term Nutrient Enrichment of an Oligotroph-Dominated Wetland Increases Bacterial Diversity in Bulk Soils and Plant Rhizospheres

   https://doi.org/10.1128/mSphere.00035-20  

   Bledsoe, Regina B.; Goodwillie, Carol; Peralta, Ariane L. (June 2020, mSphere)

   Campbell, Barbara J. (Ed.)

   ABSTRACT In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C 3 forb, C 4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling. IMPORTANCE Over the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter diversity and metabolism of rhizosphere bacterial communities in unexpected ways. 

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5. Divergence in Diversity and Composition of Root-Associated Fungi Between Greenhouse and Field Studies in a Semiarid Grassland

   https://doi.org/10.1007/s00248-018-1277-y  

   Chung, Y. Anny; Jumpponen, A.; Rudgers, Jennifer A. (November 2018, Microbial Ecology)

   Investigations of plant-soil feedbacks (PSF) and plant-microbe interactions often rely exclusively on greenhouse experiments, yet we have little understanding of how, and when, results can be extrapolated to explain phenomena in nature. A systematic comparison of microbial communities using the same host species across study environments can inform the generalizability of such experiments. We used Illumina MiSeq sequencing to characterize the root-associated fungi of two foundation grasses from a greenhouse PSF experiment, a field PSF experiment, field monoculture stands, and naturally occurring resident plants in the field. A core community consisting < 10% of total fungal OTU richness but > 50% of total sequence abundance occurred in plants from all study types, demonstrating the ability of field and greenhouse experiments to capture the dominant component of natural communities. Fungal communities were plant species-specific across the study types, with the core community showing stronger host specificity than peripheral taxa. Roots from the greenhouse and field PSF experiments had lower among sample variability in community composition and higher diversity than those from naturally occurring, or planted monoculture plants from the field. Core and total fungal composition differed substantially across study types, and dissimilarity between fungal communities did not predict plant-soil feedbacks measured in experiments. These results suggest that rhizobiome assembly mechanisms in nature differ from the dynamics of short-term, inoculation studies. Our results validate the efficacy of common PSF experiment designs to test soil inoculum effects, and highlight the challenges of scaling the underlying microbial mechanisms of plant responses from whole-community inoculation experiments to natural ecosystems. 

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