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 in B. cinerea is a promising alternative. This research aims 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, Canada. 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 were significantly more frequent in B. cinerea isolates from either strawberry or raspberry and with 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. 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 produce viral particles, which is a promising feature for their use as biocontrol agents.
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. [Formula: see text] 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 August 12, 2023, in Denver, CO, 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 NSF-funded Agricultural Microbiomes Research Coordination Network (AgMicrobiomes RCN), this community-based workshop emphasized collaborative thinking, interdisciplinary dialogue, and the co-creation 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.
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.
The invasion of Erwinia amylovora (Ea) from soft plant tissues to wood forms fire blight cankers, which serve as reservoirs for pathogen overwintering and infection in spring. Understanding the poorly explored ecological niche of Ea within cankers provides valuable insight into its biology, ecology, and pathogenicity. This study analyzed bacterial communities in healthy and cankered wood samples from six apple cultivars in Augusta County, Virginia, using SMRT (single molecule, real-time) PacBio Hi-Fi metabarcoding. Significant differences in bacterial diversity and richness were found between healthy and cankered wood tissues, with Erwinia spp. dominating the cankered samples. The highest number of Ea amplicon sequence variants was detected in the apple cultivar Cripps Pink, followed by Gala, Aztec Fuji, Granniwinkle, Hewe's Crab, and an unknown cultivar used as a blind control. Machine learning algorithms identified the prevalence of Erwinia, Sphingomonas, Massilia, and Pantoea in cankered wood samples. Bacterial interactions in healthy and cankered wood networks showed a mixture of cooccurrence and coexclusion, including significant negative (e.g., Rhizobia group) and positive (e.g., Pantoea spp.) correlations with Ea and several other bacterial species in the canker microbiome. The canker networks identified Novosphingobium, Variovorax, and Nocardioides as module hubs. Bacillus spp. were prominent in the healthy wood tissue microbiome. The increasing number of amplicon sequence variants assigned to different bacterial taxa indicated a shift in community composition from microbiome to pathobiome. Functional profiling revealed ecological differences between healthy tissues and cankers (e.g., canker phytopathogenic determinants enrichment). Our results pave the way for the development of potential synthetic microbial communities that can effectively manage fire blight.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Plants harbor different microbial communities on and in their organs. The differences reflect not only the various environmental conditions to which plant parts are exposed but also organ-specific expression profiles of genes, proteins, and metabolites. Consequently, the phyllosphere microbiota can differ strongly from root-associated communities. We hypothesized that the grapevine phyllosphere is a valuable source of biocontrol bacteria, whose adaptation to the aerial plant environment may enable them to reach their full protective potential against foliar pathogens. In previous work, we isolated phyllosphere bacteria and showed that many were very effective against such pathogens in vitro, inhibiting mycelial growth and spore development. Here, we investigated the biocontrol ability of these bacteria in leaf disc assays against two foliar pathogens, Botrytis cinerea (gray mold) and Plasmopara viticola (downy mildew). Our results showed that 40 strains out of 46 affected at least one pathogen by altering spore physiology, reducing disease progression, and/or stimulating plant defenses. Among these strains, 27 affected both pathogens, and 20 also stimulated plant defenses. Because bacterial consortia might perform better than single strains, we compared individual bacteria with associations of up to three strains. When combined, bacteria from the genera Bacillus, Cupriavidus, and Herbaspirillum showed improved efficacy in vitro against B. cinerea and in whole-plant experiments against P. viticola, resulting in stronger protection than that obtained with individual strains, likely due to complementary effects on pathogen development and plant defense stimulation. These data suggest that phyllosphere bacteria could provide an effective and sustainable tool for managing foliar diseases.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
In this study, we explored the relationship between ecologically distinct soil/compost microbiomes and their role in plant growth promotion through organic matter (OM) decomposition. Using a controlled experimental system, we tested whether living microbiomes from geographically and ecologically distinct environments impact plant biomass when provided with OM in the form of dried, ground leaves sourced from pre-flowering Avena barbata to mimic cover cropping conditions with annual grasses. Results showed a consistent threefold increase in plant biomass when a living microbiome and OM were present, regardless of the microbiome's origin, which included agricultural fields, desert soil, and pine-oak forest soil; municipal compost; and the microbiome on unautoclaved OM. Bacterial community profiling based on 16S amplicon sequencing revealed genera (e.g., Massilia) that were significantly associated with decomposition and plant growth promotion. This suggests a conserved functional capacity within specific taxa for plant growth promotion via OM decomposition across diverse microbiomes, likely due to evolutionary pressures, to efficiently break down plant material for nutrient acquisition. The study provides a framework for further investigation into microbial consortia that enhance plant growth via decomposition, offering a robust experimental system to identify microbes and microbial processes that could be harnessed to improve nutrient uptake from organic inputs such as cover crops.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Both plant and soil microbiomes are key drivers of agroecosystem function, especially the retention and cycling of nutrients. Individual plant species will uniquely shape soil microbiomes based on their life-history traits and environmental conditions, but what is the impact of growing plants in combination? For instance, cover crop (CC) mixtures are often created to copromote multiple ecosystem services, including those mediated by microorganisms. In this study, we assessed soil microbial trajectories when three common CCs with distinct life-history traits were grown in monocultures or in mixtures across different nitrogen (N) amendment concentrations. We hypothesized that each CC within a mixture would have equal influence on plant biomass and nutrient concentrations but that soil microbiome composition within mixtures would reflect the disproportionate influence of specific plant species. We established a full factorial pot experiment with three CC species-canola, clover, and triticale-grown in monoculture, biculture, and triculture, analyzed across two levels of N fertilization. We quantified soil microbial biomass and composition, along with plant growth and nutrient concentrations in both plants and soil. Plant biomass, soil microbial biomass, and soil nutrients of CC mixtures generally reflected the expected values based on the relative influence of each plant species, even when standardized by aboveground biomass. However, these patterns were nutrient-dependent, as nonnodulating CC species averaged higher microbial biomass and dissolved organic carbon in moderate N than in high N, suggesting resource allocation to carbon exudation for microbial recruitment under N limitation stress. The CC treatments significantly impacted bacterial and fungal composition, but not evenly; fungal composition in canola-containing pots differed significantly from other pots in the high and moderate N treatments, indicating that canola had a disproportionate influence on soil fungal composition. Our results suggest that differences in plant life-history traits within CC mixtures may influence shifts in the belowground recruitment of soil microbes, which further varies with nutrient changes. Further research into specific plant-microbe links can create manageable regulation of soil microbiomes with potential for agronomic, economic, and environmental benefits.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Microbial technologies are increasingly adopted to improve sustainable agriculture amid escalating economic, regulatory, and ecological pressures, yet few, if any, are supported by mechanistic understanding and are translated into products with demonstrated real-world performance and adoption. Pink-pigmented facultative methylotrophs (PPFMs) are known to promote plant growth and enhance pathogen resistance, but their impact on insect defense remains largely unexplored. Here, we report on a PPFM species, Methylorubrum extorquens strain NLS0042, developed as TS201, a U.S. EPA-registered bioinsecticide that mitigates maize pest damage and improves yield. Across 7 years (2016 to 2022) of field trials at 22 Midwest U.S. locations, TS201 increased maize yield by 220 kg/ha under moderate to high pressure of corn rootworms, the most destructive insect pest complex of maize in North America. Additionally, TS201 improved root architecture and reduced plant lodging. Large-scale on-farm evaluations across 81 sites in eight U.S. states (2023 to 2024) validated its agronomic benefit under diverse production conditions. Transcriptomic and volatile metabolite analyses revealed that TS201 induces anthranilate biosynthesis and accumulation of methyl anthranilate, a volatile compound that repels western corn rootworm larvae. Insect choice assays demonstrated significant larval avoidance of TS201-treated roots and confirmed the repellent effect of methyl anthranilate on corn rootworm larvae. These findings demonstrate that TS201 primes maize defense through multiple modes of action, offering a novel and effective microbial strategy to enhance crop resilience and support sustainable pest management.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
The seed microbiome plays an important role in seed quality, germination, and crop establishment. Soybean (Glycine max [L.] Merr.) is one of the most economically important field crops. However, information about soybean seed microbiomes is lacking, especially regarding how field environmental conditions and the prevalent seed pathogen Diaporthe longicolla across different years shape soybean seed microbiomes. In this study, we used amplicon sequencing to assess the seed endophytic microbiomes of a soybean cultivar, Dudley, collected in four successive years of field trials. The alpha diversity of both fungal and bacterial communities remained relatively stable across years with D. longicolla treatments. The microbial compositions were significantly influenced by years (P = 0.001), with environmental variables (air temperature, precipitation, and relative humidity) contributing to shifts in community structure. The seed core microbiome comprised bacterial members from genera Methylorubrum, Peribacillus, and Priestia and fungal taxa from classes Dothideomycetes, Sordariomycetes, and Tremellomycetes. Pathogen inoculation altered bacterial composition, positively associated with taxa from genera Sphingomonas, Microbacterium, and Nocardioides, but did not notably affect fungal community. Soybean seed microbiome assembly appears driven primarily by interannual environmental variations. Pathogen inoculation exerts a secondary but detectable effect on the bacterial community. To the best of our knowledge, this is the first multiyear field-based study of soybean seed endophytic microbiomes and the impact of seedborne pathogen inoculation. The findings of this research advance our understanding of soybean seed microbiomes and provide insights into the potential use of seed microbes, thereby aiding in the development of novel microbiome-based alternatives to manage soybean seed diseases.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Plant-associated microbes affect the functioning of their host. However, holistic studies that consider interactions between plants and microbes both above- and belowground are lacking. We hypothesized that soil is a reservoir for both root and leaf microbes and that herbivory disrupts the composition of the leaf microbial community. We further hypothesized that the root-associated microbial communities correlate with the leaf metabolome (as a measure of function), suggesting a linkage between the root microbes and the leaf phenotype. To test these hypotheses, the microbial communities of herbivore-damaged and undamaged leaves, roots, and surrounding soil were characterized from 15 Plantago major populations sampled across Denmark. Microbial communities were then compared against the leaf metabolome. Initially, we found that herbivory had no effect on the leaf microbiome or metabolome. We did find that the fungal communities showed significant overlap between leaf, root, and soil samples, but the bacteria were mainly specialized to each sample type. Interestingly, the leaf microbiome correlated with the leaf metabolome, but the root bacteria and fungi did not. However, additional analyses of arbuscular mycorrhizal fungi found that these specialist root microbes were associated with variation in the leaf metabolome. This study demonstrates the complexity of plant metabolome-microbiome interactions and the need to fully integrate the microbiome of different tissue types to fully understand plant-microbe interactions.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Groundcovers are increasingly planted in perennial cropping systems to improve soil health. In vineyards, grass groundcovers can influence many edaphic properties, yet the effects of these groundcovers on bulk soil microbiomes remain unclear. We examined bacterial and fungal composition in a temperate vineyard where a grass groundcover (Festuca rubra) was either included (GC) or excluded (noGC) under the vine row. Soils were sampled in July of two consecutive years, from depths of 0 to 33, 33 to 66, and 66 to 100 cm, and subjected to bacterial (16S ribosomal RNA gene) and fungal (ITS region) amplicon sequencing. Across the study, alpha diversity (Shannon index) varied primarily by depth and year, and showed no consistent differences attributable to groundcover. However, comparisons of microbiome composition revealed differences between plots with and without groundcover, most notably in shallow (0 to 33 cm) soils for fungal communities. Moreover, differential abundance analyses showed that groundcover decreased the relative abundance of taxa expected to perform saprotrophic roles (e.g., Papiliotrema laurentii and Solicoccozyma terricola) but increased putatively beneficial root-associated taxa (e.g., Periconia circinata and Apiotrichum scarabaeorum) in shallow soils. Given the life history of these taxa, we infer these findings may reflect the tendency for groundcovers to shift belowground resource availability and highlight the potential for shallow-rooted plants to indirectly influence microbial communities well beyond their rooting zone. Despite not increasing alpha diversity, groundcovers modulated bacterial and fungal composition in our system, indicating that vegetation management may potentially affect agroecological health in perennial agricultural systems via changes to soil microbiome composition.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Plant genetics can exert a strong effect on soil rhizosphere microbes. Broad-sense heritability estimates quantify the degree to which plant genotype predicts microbiome composition, enabling characterization of plant genotype effects on rhizosphere microbes. We used 16S rRNA and internal transcribed spacer marker gene sequencing data from rhizosphere soil from 95 field-grown sunflower (Helianthus annuus) inbred lines to test the heritability of archaeal, bacterial, and fungal rhizosphere communities, as well as alpha- and beta-diversity metrics and differences in the relative abundance of microbial zero-radius operational taxonomic units (ZOTUs). The majority of taxa passing prevalence and relative abundance cutoffs of 25 and 0.01% were heritable across all taxonomic levels for both prokaryotes (archaea and bacteria) and fungi, with higher heritabilities at finer taxonomic resolution. Metrics of alpha and beta diversity were also heritable, particularly for prokaryotes. Prokaryotic and fungal communities were both heritable, but there was significantly higher fungal heritability at the ZOTU, genus, and family levels. Prokaryotic richness and fungal richness were only weakly positively correlated, and beta diversity was not correlated, suggesting that sunflower inbred lines affect prokaryotes and fungi in different ways. Our work provides valuable information for crop breeding and provides a general methodological framework for assessing the strength and types of genotype-microbial associations. Because of high heritability for individual microbial taxa, as well as for microbial diversity metrics more broadly, sunflowers are clearly an important species to study the ecology, evolution, and genetics of plant-microbe interactions, and this knowledge can be used to improve sustainability of the crop.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Heterosis, or hybrid vigor, refers to the phenotypic superiority of hybrids relative to their parental inbred lines. Recent work showed that manipulation of the soil microbial community consistently altered heterosis, but the direction of the effect was dependent on microbiome composition, environment, or both. Abiotic factors such as temperature, water availability, and soil nutrients are known modifiers of heterosis expression; however, whether interactions between the soil microbial community and abiotic properties affect heterosis is largely unknown. To further understand how microbes influence heterosis, we characterized variation in maize heterosis when grown in soil inocula derived from historical maize farms or prairies. Although we did not observe consistent differences in heterosis among plants grown in these inocula, our observations affirm that microbial effects on heterosis are likely specific to the local microbial community. The introduction of a nutrient amendment resulted in greater heterosis in the presence of an agricultural soil inoculum than in the presence of a prairie soil inoculum. In addition, the interaction between soil inoculum and nutrient treatment structured bacterial and fungal community composition in the root endosphere. Root bacterial diversity was also significantly higher under nutrient-limited conditions. These results suggest that the contributions of genotype-by-environment interactions to heterosis are dependent on microbial context. They also provide direct evidence for the interactive effect of the soil microbial community and abiotic environment on heterosis and suggest that consideration of the soil microbial community may be helpful for breeding hybrid maize varieties for high performance in diverse environmental contexts.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Cover crops are often incorporated between cash crop seasons to improve or maintain soil health. Although their effects on certain soil properties (e.g., erosion control) are well described, their potential to steer soil microbial composition and function remains poorly understood. Most studies use direct soil sampling to investigate this relationship, but long-dormant microorganisms and legacy DNA can mask treatment effects, leading to signals that may not reflect active contributors to key functions such as biogeochemical cycling and decomposition. In this study, we deployed microbial traps (i.e., sterile soil enclosed in permeable mesh) to contrast active recolonization with direct soil sampling across 11 cover crop treatments applied after fall cash crop harvests in the northeast United States. Bulk and recolonized soil were collected for 16S rRNA gene and internal transcribed spacer region amplicon sequencing before (i) winter and (ii) spring planting. We hypothesized that different cover crop mixtures would stimulate distinct pools of microbial colonizers, with stronger between-treatment effects in recolonized soil compared with bulk. Our results showed that crop treatments significantly influenced microbial composition of active colonizers; however, effect sizes were similar in both bulk and recolonized (explaining 12 to 18% of community variance). The presence or absence of plant cover was the strongest driver of compositional differences in both soil compartments, suggesting microbial traps and bulk soil can capture similar signals despite containing ecologically distinct microbiome subsets. Future work coupling community assembly in situ with functionally informative methods may further resolve whether active colonizers overlap with root-associated taxa and can lead to management-relevant outcomes.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Biodiversity-ecosystem function (BEF) relationships have been a major topic since the 1990s, because of sustainability and extinction crises, although BEF relationships are not easily correlated with habitat, taxa, or diversity. We proposed and tested two predictors for BEF relationship shapes: (i) individual species abundance (indicating coexistence and competitive abilities) and functional performance, and (ii) specific functions underlying a broader function. Darlingtonia californica is a carnivorous plant with modified leaves housing bacteria that contribute to insect degradation and nitrogen provision. We isolated 14 distinct bacterial strains from D. californica leaf fluid, grew the isolates in monocultures and mixed cultures, and evaluated each using insect degradation assays and protein, ammonia, nitrate, chitinase, and protease quantification assays. We asked three questions related to our two predictors of BEF shapes: First, can function of a bacterial community be predicted based on functions of individual species? Second, are there correlations between bacterial species function and abundance change? Finally, does degradative function in bacterial communities correlate with nitrogen-related processes in the context of this key limiting nutrient? We found that increased degradative function correlated with decreased species abundance changes, highly functioning mixed cultures could result from both highly or moderately functioning isolates, and degradative function did not rely on tested nitrogen-related functions. BEF relationships present a trade-off between degradative function and bacterial abundance changes, but not with the specific nitrogen assays. Although species with strong functional contributions can also be good competitors, they may also be poor competitors or play complex roles in community assembly.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Citrus huanglongbing (HLB) disease progression has been associated with 'Candidatus Liberibacter asiaticus' (CLas) and with changes in the endophytic microbiome. Metagenomic analysis was widely used to study citrus endophytic microbiomes. However, the standard 16S sequencing approaches do not differentiate bacterial compositions resulting from the amplification of DNA from dead or live cells. Propidium monoazide (PMA) treatment of tissues before DNA extraction can effectively exclude DNA from dead CLas cells. However, there are no reports of its use to decipher the "viable" microbiome in HLB-affected citrus trees. In this study, we explored PMA's utility in assessing the viable microbial communities in HLB-affected citrus trees after oxytetracycline (OTC) treatment, using 16S rRNA amplicon sequencing in conjunction with PMA treatment (PMA-seq). The results showed that PMA-seq could increase the overall operational taxonomic units and potentially boost the coverage of low-abundance species. However, it may not uniformly represent microbial viability in complex communities. Results indicated that PMA is more efficient at excluding DNA from dead gram-negative bacterial cells than from gram-positive bacteria, likely because of different cell wall compositions. Moreover, alteration of microbial composition by OTC treatment and temporal variations can influence PMA's effectiveness in detecting several bacterial species. In summary, our findings indicate that although implementing PMA-seq may aid in enriching low-abundance bacterial communities, the overall diversity profiles could be different when compared with traditional 16S seq without PMA treatment.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
The emerald ash borer (EAB), Agrilus planipennis, is a destructive invasive insect of North American ash (Fraxinus). While microorganisms associated with the beetle may contribute to tree decline and death, the microbial community succession during an EAB attack is unknown. We repeatedly sampled the bottom two meters of green ash (Fraxinus pennsylvanica) and black ash (Fraxinus nigra) in seven stands across an infestation gradient over four years. Amplicon libraries were sequenced from control phloem tissue of trees showing no symptoms of infestation, uninfested phloem of trees with EAB, infested phloem (galleries), frass, and larvae to determine if there are shifts in the fungal and bacterial communities as trees succumb to EAB attack. We found that the control phloem communities significantly differed from the beetle-infested phloem in both tree species. Furthermore, as EAB progressed in its attack from the top limbs to the tree’s base, the microbial communities in uninfested phloem outside the galleries shifted away from communities in phloem of control trees. In infested phloem, more than 80% of the detected taxa were absent from control trees (i.e., most taxa were non-latent). However, the relative abundance of latent taxa in infested phloem was higher than the relative abundance of the non-latent taxa, especially for potential canker-causing fungi, which increased 21-fold and 32-fold in black ash and green ash trees, respectively. These findings provide valuable insight into how a woodboring beetle shapes the microbial environment within trees over time, influencing the overall microbial diversity, such as canker-causing and wood decay taxa.
Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is a serious threat to soybean production worldwide. Genetic resistance and crop rotation are the primary management strategies. However, because of limited genetic resources, long-term implementation of crop rotation, and environmental effects, alternative measures are needed. Plant microbiomes play an important role in plant health, but their contribution to SCN resistance remains unclear. In this study, we profiled the rhizosphere microbiomes in 10 soybean cultivars, including 5 SCN-resistant and 5 SCN-susceptible cultivars, using amplicon sequencing. The resistant cultivars harbored distinct rhizosphere microbiomes, compared with the susceptible cultivars. Permutational multivariate analysis of variance revealed that both the host genotype and SCN resistance trait significantly influenced microbial community composition, with host genotype explaining greater variation. Resistant cultivars were found to be enriched in specific microbial taxa from Phenylobacterium, Pseudoduganella, Comamonadaceae, and Arthrobotrys. Furthermore, microbial inoculants derived from resistant cultivars reduced SCN populations in the susceptible cultivar Williams 82. These results suggest that host genotype and SCN resistance trait interacted to shape rhizosphere microbiomes and influence SCN suppression. Overall, this study highlighted the potential for engineering plant microbiomes to enhance soybean resistance to SCN, complementing traditional crop health improvement practices.The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2026.
