Botrytis cinerea causes significant economic losses in many crops, including vegetables, fruits, and ornamental plants, and its management is becoming increasingly difficult due to increasing fungicide resistance. Harnessing mycoviruses that reduce virulence (hypovirulence) in B. cinerea is a promising alternative. Over 100 mycoviruses have been identified in Botrytis to date, including several hypovirulence-inducing mycoviruses. This study is the first to investigate the mycovirome of B. cinerea in Canada. This research aimed to characterize mycovirus diversity using high-throughput sequencing and identify potential hypovirulence-inducing mycoviruses. B. cinerea isolates were collected from raspberries, strawberries, and grapevine in the province of Quebec. Indicators of fungal fitness and pathogenicity criteria, including colony morphotype and lesion size, were evaluated. A double-stranded RNA (dsRNA) extraction protocol optimized for the detection of mycoviruses was used to sequence dsRNA from 45 isolates, most of which had reduced fitness and pathogenicity. Mycoviruses were identified in 98% of the selected isolates. A total of 94% of mycoviruses had positive-sense single-stranded RNA or dsRNA genomes, and 6% had negative-sense single-stranded RNA, single-stranded DNA, or reverse-transcribing single-stranded RNA genomes. A co-occurrence analysis revealed that several mycoviruses occurred significantly more frequently in B. cinerea isolates from either strawberry or raspberry and in isolates exhibiting specific colony morphotypes. Potential hypovirulence-inducing mycoviruses, including Botrytis cinerea mitovirus 1, Botrytis cinerea hypovirus 1, and Botrytis porri botybirnavirus 1 were identified. We also identified 62 unique novel genomic species representing new variants of known mycovirus species. In addition, four putative novel mycovirus species were identified belonging to the families Endornaviridae, Botybirnaviridae, Peribunyaviridae, and the order Elliovirales. Two of these novel mycoviruses belonged to taxa known to include hypovirulence-inducing viruses, suggesting potential as biocontrol agents.Copyright (c) 2026 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada. This is an open access article distributed under the CC BY 4.0 International license.
Root systems comprise distinct primary and lateral roots, yet conventional microbiome studies often rely on composite root samples, potentially obscuring root type-specific profiles. We hypothesized that (i) primary and lateral roots harbor distinct microbial communities that may be masked by composite sampling, (ii) soil phosphorus (P) acts as an environmental filter with root type-dependent effects on microbial diversity and composition, and (iii) composite sampling obscures root type-enriched, functionally relevant taxa. We investigated rhizosphere soil- and root-associated bacterial and fungal communities of field-grown canola under P-fertilized (+P; 18.7 kg P ha-1 as monoammonium phosphate) and P-omitted (-P) conditions using segmented (primary and lateral roots separately) or composite root sampling. In the rhizosphere, P fertilization reduced bacterial alpha diversity and significantly shifted both bacterial and fungal community structure, with an additional contribution of root type for bacteria. In roots, alpha-diversity patterns were primarily associated with root type, whereas community structure was microbial domain-specific: bacterial communities exhibited root type-dependent responses to P, whereas fungal communities differed mainly between root types. Consistent with our hypotheses, segmented sampling revealed root type-associated taxonomic enrichments and P-responsive shifts that were diminished or lost in composite samples, underrepresenting potentially important plant-associated taxa. Collectively, this study demonstrates that composite sampling can mask ecologically and agronomically relevant microbial associations within root systems, highlighting the importance of root-type resolution in plant-microbiome research.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Forecasted increases in drought events resulting from climate change pose a serious threat to bioenergy crop yields, and improving the resilience of crops against water stress is essential to bioenergy development. Many plants exhibit a conserved drought response that is partially mediated by their associated microbiomes. Panicum hallii , a close relative of the promising bioenergy crop switchgrass, is a model organism for this grass due to its genetic tractability and short generation time. Nevertheless, little is known regarding the effects of drought on its associated microbiome. A comprehensive analysis of bacterial and archaeal microbiomes of drought-exposed P. hallii combining 16S rRNA amplicon and shotgun metagenomic data supports a drought response similar to that observed in other crops and offers new insights. Over the course of one growth cycle, exposure of P. hallii to drought led to a decrease in bacterial diversity in the rhizosphere-associated microbiome, corresponding with a decrease in Proteobacteria (Pseudomonadota) and Bacteroidota and an increase in Actinobacteriota (Actinomycetota). Genome-resolved metagenomic analysis further revealed an enrichment in Patescibacteria and specific Bacteroidota under drought. Functional analysis linked the changes in community structure with increased capacities for complex carbohydrate metabolism, molecular salvaging, chemotaxis, and antioxidant accumulation. By confirming that drought stress effects similar changes to the P. hallii rhizosphere microbiome as observed in switchgrass and other plants, we reinforce the strength of P. hallii as a model organism for crop improvement studies and emphasize the value of a dual amplicon and shotgun-based analysis for a comprehensive interpretation of community composition. Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
The Agricultural Microbiomes Thinkathon, held on 12 August 2023, in Denver, CO, U.S.A. brought together early-career and established scientists from academia, government, and industry to explore new approaches to microbiome research design, integration, and application. Organized by the U.S. National Science Foundation-funded Agricultural Microbiomes Research Coordination Network (AgMicrobiomes RCN), this community-based workshop emphasized collaborative thinking, interdisciplinary dialogue, and the cocreation of research ideas. Participants engaged in team-based activities aimed at transforming microbiome data into knowledge and actionable outcomes. Through structured breakout sessions, they developed research questions, interpreted microbiome datasets, and proposed projects focused on improving plant health and agricultural sustainability. These projects reflected systems thinking, practical applications, and shared interests in microbial function, plant–microbiome interactions, and data-informed management strategies. The Thinkathon demonstrated the value of workshop formats that move beyond passive or technical training to emphasize critical thinking, collaboration, and creativity. As microbiome data become more accessible and computational tools grow increasingly complex, the ability to pose thoughtful questions and connect research to real-world outcomes is essential. By combining active learning with interdisciplinary team science, the Thinkathon model provides a replicable framework for building capacity, empowering early-career scientists, and advancing innovation in agricultural microbiome research. [Figure: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Microbial associations can protect cultivated sunflowers (Helianthus annuus L.) from being infected by the ascomycete fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary, potentially saving millions of dollars in losses annually. Here, we isolated bacteria from sunflower rhizosphere soil, performed full-length 16S rRNA gene sequencing for identification, and then measured inhibition of S. sclerotiorum in co-cultures. Isolated bacterial strains that inhibited S. sclerotiorum (n = 13) matched six environmental operational taxonomic units (OTUs) sequenced from rhizosphere soils of resistant sunflower genotypes. Four of these six OTUs were detected in sunflower rhizosphere soils from 15 different sites across the Great Plains region of the United States, indicating a broad distribution and potential for use as biocontrol agents. However, the relative abundance of inhibitor OTUs across 95 sunflower genotypes was not negatively correlated with S. sclerotiorum incidence at the Carrington, ND, field evaluation site. All inhibitors we isolated are known to possess antifungal properties and have been tested as potential biocontrol agents in previous studies. Our work shows that soils associated with resistant sunflower plants naturally contain inhibitory bacterial strains. This opens up the potential for using augmentation of locally occurring bacteria as a strategy for biocontrol, potentially by coating seeds or spraying aboveground parts with slurries of one or more of these taxa.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
