Disease Suppressive Soils: New Insights from the Soil Microbiome

Suppressiveness of spent mushroom substrate amendment against eggplant Verticillium wilt

BACKGROUND

Verticillium wilt, caused by Verticillium dahliae, is a devastating soil-borne disease. Spent mushroom substrate (SMS) has shown potential as a soil amendment for controlling soil-borne diseases. However, the mechanisms underlying its disease-suppressive effects remain poorly understood. Here, the efficacy of SMS in suppressing eggplant Verticillium wilt and mechanisms related to rhizosphere microbiome regulation were investigated.

RESULTS

We tested different SMS sources (Pleurotus ostreatus, Hypsizygus marmoreus, Lentinus edodes), particle sizes (45, 75, 150, 300 μm), and addition ratios (0.5-8%, w/w). The fungus control efficacy ranged from 26 to 66%, with best results from 2% SMS of L. edodes at 150 μm. This treatment resulted in 5.7-fold reduction in the Verticillium dahliae population in eggplant rhizosphere. Eggplant fresh and dry weights of shoots and roots, and plant height, significantly increased with 2% SMS amendment. 16S rDNA sequencing revealed alterations in rhizosphere bacterial communities, with an increase in indigenous beneficial bacteria, particularly Bacillus spp., following SMS amendment. Spent mushroom substrate co-inoculated with exogenous biocontrol strain Bacillus subtilis NCD-2 achieved a synergistic effect against Verticillium wilt than both SMS or NCD-2 alone.

CONCLUSIONS

Results revealed that SMS protects eggplants against Verticillium wilt, largely by recruiting Bacillus spp. to the rhizosphere. The enrichment effect of indigenous Bacillus spp. in the rhizosphere mediated by SMS similarly applies to Bacillus inoculum, enhancing its efficacy in controlling eggplant Verticillium wilt. These findings enhance our understanding of the protective effects of SMS and its role in the biocontrol of Verticillium wilt. © 2025 Society of Chemical Industry.

Plant pathogens, microbiomes, and soil health

Healthy soil is vital for ecosystem sustainability and global food security. However, anthropogenic activities that promote intensive agriculture, landscape and biodiversity homogenization, and climate change disrupt soil health. The soil microbiome is a critical component of healthy soils, and increasing evidence suggests that soils with low diversity or homogenized microbial systems are more susceptible to soil pathogen invasion, but the extent and mechanisms that increase the threat of pathogen invasion (i.e., increase in prevalence of existing species and introduction of new species) remain unclear. This article aims to fill this knowledge gap by synthesizing the literature and providing novel insights for the scientific community and policy advisors. We also present the current and future global distribution of some dominant soil-borne pathogens. We argue that an improved understanding of the interplay between the soil microbiome, soil health, host, and pathogen distribution, and their responses to environmental changes is urgently needed to ensure the future of productive farms, safe food, sustainable environments, and holistic global well-being.

The relict plant Tetraena mongolica plantations increase the nutrition and microbial diversity in desert soil

Introduction

Tetraena mongolica was established in the West Ordos Region of northwest China approximately 140 million years ago. It plays an irreplaceable role in maintaining local ecosystem stability.

Methods

This study aimed to evaluate the effects of planting T. mongolica on soil nutrition and microbial communities by comparing the root zone soil (Rz_soil) and bare soil (B_soil) across three different plant communitie.

Results

The results showed that T. mongolica decreased soil pH and Na+ while increasing available potassium, soil organic matter, organic carbon, total nitrogen, and potassium. T. mongolica significantly improved the diversity indices (Sobs and Ace), as well as the richness index (Chao), of bacterial and fungal communities across three plant communities. Meanwhile, the relative abundances of Rubrobacter and norank_c_Actinobacteria in the bacterial communities declined significantly in the Rz_soil compared with the B_soil across all three plant communities. In contrast, the relative abundances of Fusarium and Penicillium were higher, whereas those of Monosporascus and Darksidea were lower in Rz_soil than in B_soil in the two plant communities. T. mongolica decreased the soil bacterial co-occurrence networks while increasing the soil fungal co-occurrence networks.

Discussion

These results provide a new perspective to understand the role of T. Mongolica in the desert ecosystems.

Fungicide use intensity influences the soil microbiome and links to fungal disease suppressiveness in amenity turfgrass

Disease-suppressive soils have been documented in many economically important crops, but not in turfgrass, one of the most intensively managed plant systems in the United States. Dollar spot, caused by the fungus Clarireedia jacksonii, is the most economically important disease of managed turfgrass and has historically been controlled through the intensive use of fungicides. However, previous anecdotal observations of lower dollar spot severity on golf courses with less intensive fungicide histories suggest that intensive fungicide usage may suppress microbial antagonism of pathogen activity. This study explored the suppressive activity of transplanted microbiomes against dollar spot from seven locations in the Midwestern U.S. and seven locations in the Northeastern U.S. with varying fungicide use histories. Creeping bentgrass was established in pots containing homogenized sterile potting mix and field soil and inoculated with C. jacksonii upon maturity. Bacterial and fungal communities of root-associated soil and phyllosphere were profiled with short-amplicon sequencing to investigate the microbial community associated with disease suppression. The results showed that plants grown in the transplanted soil microbiome collected from sites with lower fungicide intensities exhibited reduced disease severity. Plant growth-promoting and pathogen-antagonistic microbes may be responsible for disease suppression, but further validation is required. Additional least squares regression analysis of the fungicides used at each location suggested that contact fungicides such as chlorothalonil and fluazinam had a greater influence on the microbiome disease suppressiveness than penetrant fungicides. Potential organisms antagonistic to Clarireedia were identified in the subsequent amplicon sequencing analysis, but further characterization and validation are required.

IMPORTANCE

Given the current reliance on fungicides for plant disease control, this research provides new insights into the potential non-target effects of repeated fungicide usage on disease-suppressive soils. It also indicates that intensive fungicide usage can decrease the activity of beneficial soil microbes and lead to a more disease conducive microbial environment in turfgrass. The results from this study can be used to identify more sustainable disease management strategies for a variety of economically important and intensively managed pathosystems. Understanding the factors that facilitate disease-suppressive soils will contribute to more sustainable plant protection practices.

Continuous Cropping of Tussilago farfara L. Has a Significant Impact on the Yield and Quality of Its Flower Buds, and Physicochemical Properties and the Microbial Communities of Rhizosphere Soil

Continuous cropping obstacles pose significant constraints and urgent challenges in the production of Tussilago farfara L. This experiment investigated the effects of consecutive cropping on T. farfara over periods of 1, 2, and 3 years. It assessed the yield and quality of T. farfara flower buds, in addition to the physicochemical properties of the rhizosphere soil. The microbial community in the rhizosphere was analyzed through 16S rDNA and ITS sequencing using Illumina Novaseq high-throughput sequencing technology, while also examining the correlations among these factors. The results reveal that as the duration of continuous cropping increases, the yield of T. farfara flower buds, along with the contents of extract, tussilagone, and total flavonoids, steadily decreased; soil pH, organic matter, available phosphorus, available potassium, alkaline nitrogen, and the activities of sucrose, catalase, and alkaline phosphatase markedly decreased. As the duration of consecutive cropping increases, the quantity and diversity of bacteria in the rhizosphere soil initially increase and then decrease, while the number of fungal species increases by 22.5%. Meanwhile, continuous cropping of T. farfara contributes to a gradual reduction in the relative abundance of beneficial genera such as Ralstonia, Nitrospira, and Trichoderma in the rhizosphere soil, while harmful genera such as Mortierella, Fusarium, and Tricharina accumulate significantly. Correlation analysis shows that changes in microbial communities notably influence the growth of T. farfara and soil quality. This study elucidates the impacts of continuous cropping on the yield and quality of T. farfara flower buds, soil physicochemical properties, and the microbial communities in the rhizosphere, providing a scientific basis for further research on continuous cropping barriers and the selection of beneficial microbial genera for the growth of T. farfara.

Seasonal dynamics of kiwifruit microbiome: A case study in a KVDS-affected orchard

Over the past decade, Italian kiwifruit orchards and overall production have faced a significant threat from Kiwifruit Vine Decline Syndrome (KVDS). Despite the insights gained from metagenomics studies into the microbial communities associated with the disease, unanswered questions still remain. In this study, the evolution of bacterial, fungal, and oomycetes communities in soil and root endosphere at three different time points during the vegetative season was investigated for the first time in a KVDS-affected orchard in the Lazio Region. The fungal and oomycetes genera previously associated with the syndrome, including Fusarium, Ilyonectria, Thelonectria, Phytophthora, Pythium and Globisporangium, were identified in both groups. In contrast, the characterization of bacterial communities revealed the first instance of the presence of the genus Ralstonia in soil and root samples. The microbiome composition shifts between KVDS-affected and asymptomatic plants were significant as evidenced by the results, particularly after a temperature increase. This temperature change coincided with the onset of severe disease symptoms and may indicate a key role in the progression of KVDS.

Agronomic impacts of chemically and microbiologically characterized compost tea in Mediterranean volcanic soils

Compost tea is widely recognized for its beneficial effects on crop growth and soil health. However, its efficacy varies depending on the composition of the feedstock and brewing conditions. This study investigates the chemical composition and agronomic impact of compost tea prepared from a commercial mixture of plant residues and animal manure. Standard chemical analyses, combined with solid-state 13C CPMAS NMR spectroscopy, were employed to characterize the organic chemistry of the feedstock. High-throughput sequencing of bacterial and eukaryotic rRNA gene markers was used to profile the microbiota. Compost tea was applied to three crops, Allium cepa, Beta vulgaris, and Lactuca sativa, grown in protected Mediterranean environments on volcanic soils. The 13C CPMAS NMR analysis revealed that the feedstock is predominantly composed of plant-derived tissues, including grass straw, nitrogen-fixing hay, and animal manure, with a significant presence of O-alkyl-C and di-O-alkyl-C regions typical of sugars and polysaccharides. Additionally, the chemical profile indicated the presence of an aliphatic fraction (alkyl-C), characteristic of lipids such as waxes and cutins. The compost tea microbiome was dominated by Pseudomonadota, with Pseudomonas, Massilia, and Sphingomonas being the most prevalent genera. Compost tea application resulted in significant yield increases, ranging from +21% for lettuce to +58% for onion and +110% for chard. Furthermore, compost tea application reduced slug damage and enhanced the shelf life of lettuce. These findings highlight the bio-stimulant potential of this standardized compost tea mixture across different vegetable crops.

Understanding the microbiome-crop rotation nexus in karst agricultural systems: insights from Southwestern China

Understanding how soil properties and microbial communities respond to crop rotation is essential for the sustainability of agroecosystems. However, there has been limited research on how crop rotation alters below-ground microbial communities in soils with serious bacterial wilt within the karst agricultural system. This study investigated the effects of continuous planting of corn, tobacco, and tobacco-corn rotation on soil microbial communities in the karst regions of Southwestern China. High-throughput sequencing was used to evaluate the responses of the soil microbial community structure to crop monoculture and rotation patterns. As expected, the tobacco-corn rotation mitigated the negative effects of continuous cropping and reduced soil acidification. The tobacco-corn rotation also significantly altered the composition of microbial communities and promoted plant growth by fostering a higher abundance of beneficial microorganisms. The predominant bacteria genera Sphingomonas and Gaiella and the predominant fungal genera Mortierella and Saitozyma were identified as discriminant biomarkers that are critical to soil ecosystem health. pH, available potassium (AK), and available phosphorus (AP) were the primary soil factors related to the soil microbiome assembly. This study aimed to demonstrate the association between crop rotation and microbiomes, suggesting that altering cultivation patterns could enhance karst agricultural systems.

Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches

Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.

Cover Cropping Attenuates Population Growth of Macrophomina phaseolina by Limiting Weed Biomass, Despite Asymptomatic Colonization of Cover Crops

Macrophomina phaseolina is a fungus that causes charcoal rot in strawberry and a wide variety of crop species. Little is known about its potential to asymptomatically colonize crop plants or grow saprophytically on their tissues, both of which would create a potential for alternate, asymptomatic hosts to lead to increases in inoculum. To test the impact of cover cropping on M. phaseolina abundance, we conducted randomized-block field experiments in soils infested by M. phaseolina. None of the 15 cover crop varieties showed symptoms of charcoal rot. All Fabaceae and Brassicaceae varieties were asymptomatically colonized at varying rates, but among Poaceae M. phaseolina was recovered from only one individual oat plant. Soil samples collected at the time of planting, tillage, and 8 weeks after tillage showed that cover cropping attenuated the growth of M. phaseolina relative to fallow plots harboring the weedy legume Medicago polymorpha. This weed species was abundantly colonized by this pathogen in both living root samples and plant residue collected 8 weeks after tillage. Cover cropping also influenced the diversity and composition of bulk soil bacterial and fungal communities, but these effects were not associated with M. phaseolina population density. Although M. phaseolina was not detected in living wheat tissues, it was recovered from wheat residue, suggesting that it may be facultatively saprophytic. These results suggest that cover cropping does not pose a risk for increasing disease caused by M. phaseolina and could be beneficial as conducive weed species, such as M. polymorpha, are suppressed.[Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

How do various strategies for returning residues change microbiota modulation: potential implications for soil health

Introduction

Residue incorporation is a crucial aspect of anthropogenic land management practices in agricultural fields. However, the effects of various returning strategies on the soil microbiota, which play an essential vital role in maintaining soil health, remains largely unexplored.

Methods

In a study conducted, different residue management strategies were implemented, involving the application of chemical fertilizers and residues that had undergone chopping (SD), composting (SC), and pyrolysis (BC) processes, with conventional fertilization serving as the control (CK).

Results and discussion

Using metagenomic sequencing, the analysis revealed that while all residue returning strategies had minimal effects on the diversity (both α and β) of microbiota, they did significantly alter microbial functional genes related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling, as well as the presence of antibiotic resistance genes (ARGs) and pathogens. Specifically, chopped residues were found to enhance microbial genes associated with C, N, P, and S cycling, while composted residues primarily stimulated C and S cycling. Furthermore, all residue treatments resulted in a disruption of relationships among nutrient cycles, with varying degrees of impact observed across the different management strategies, with the sequence of impact being SD < SC < BC. Moreover, the residue additions resulted in the accumulation of ARGs, while only SC caused an increase in certain pathogens. Finally, through analyzing the correlation network among indices that exhibited active responses to residue additions, potential indicators for functional changes in response to residue additions were identified. This study further offered recommendations for future cropland management practices aimed at enhancing soil health through microbiomes.

Advancing biomonitoring of eDNA studies with the Anaconda R package: Integrating soil and One Health perspectives in the face of evolving traditional agriculture practices

Soil health and One Health are global concerns, necessitating the development of refined indicators for effective monitoring. In response, we present the Anaconda R Package, a novel tool designed to enhance the analysis of eDNA data for biomonitoring purposes. Employing a combination of different approaches, this package allows for a comprehensive investigation of species abundance and community composition under diverse conditions. This study applied the Anaconda package to examine the impact of two types of duration fire-fallow cropping systems, using natural forests as a reference, on soil fungal and bacterial communities in Maré Island (New Caledonia). Condition-specific taxa were identified, particularly pathogenic fungi and bacteria, demonstrating the importance of long-term fallowing efforts. Notably, this package also revealed the potential contributions of beneficial soil microbes, including saprophytes and plant-endophyte fungi, in suppressing soil-borne pathogens. Over-represented microbial ASVs associated with both plant and animal pathogens, including those of potential concern for human health, were identified. This underscores the importance of maintaining intrinsic balance for effective disease suppression. Importantly, the advanced analytical and statistical methods offered by this package should be harnessed to comprehensively investigate the effects of agricultural practice changes on soil health within the One Health framework. Looking ahead, the application of this method extends beyond the realm of One Health, offering valuable insights into various ecological scenarios. Its versatility holds promise for elucidating complex interactions and dynamics within ecosystems. By leveraging this tool, researchers can explore the broader implications of agricultural practice modifications, facilitating informed decisions and sustainable environmental management.

Could flooding undermine progress in building climate-resilient crops?

Flooding threatens crop productivity, agricultural sustainability, and global food security. In this article I review the effects of flooding on plants and highlight three important gaps in our understanding: (i) effects of flooding on ecological interactions mediated by plants both below (changing root metabolites and exudates) and aboveground (changing plant quality and metabolites, and weakening the plant immune system), (ii) flooding impacts on soil health and microorganisms that underpin plant and ecosystems health, and (iii) the legacy impacts of flooding. Failure to address these overlooked aspects could derail and undermine the monumental progress made in building climate-resilient crops and soil-microbe-assisted plant resilience. Addressing the outlined knowledge gaps will enhance solutions developed to mitigate flooding and preserve gains made to date.

Seed tuber microbiome can predict growth potential of potato varieties

Potato vigour, the growth potential of seed potatoes, is a key agronomic trait that varies significantly across production fields due to factors such as genetic background and environmental conditions. Seed tuber microbiomes are thought to influence plant health and crop performance, yet the precise relationships between microbiome composition and potato vigour remain unclear. Here we conducted microbiome sequencing on seed tuber eyes and heel ends from 6 potato varieties grown in 240 fields. By using time-resolved drone imaging of three trial fields in the next season to track crop development, we were able to link microbiome composition with potato vigour. We used microbiome data at varying taxonomic resolutions to build random forest predictive models and found that amplicon sequence variants provided the highest predictive accuracy for potato vigour. The model revealed variety-specific relationships between the seed tuber microbiome and next season's crop vigour in independent trial fields. With a coefficient of determination value of 0.69 for the best-performing variety, the model accurately predicted vigour in seed tubers from fields not previously included in the analysis. Moreover, the model identified key microbial indicators of vigour from which a Streptomyces, an Acinetobacter and a Cellvibrio amplicon sequence variant stood out as the most important contributors to the model's accuracy. This study shows that seed potato vigour can be reliably predicted based on the microbiota associated with seed tuber eyes, potentially guiding future microbiome-informed breeding strategies.

Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms

Organic farming utilizes farmyard manure, compost, and organic wastes as sources of nutrients and organic matter. Soil under organic farming exhibits increased microbial diversity, and thus, becomes naturally suppressive to the development of soil-borne pathogens due to the latter's competition with resident microbial communities. Such soils that exhibit resistance to soil-borne phytopathogens are called disease-suppressive soils. Based on the phytopathogen suppression range, soil disease suppressiveness is categorised as specific- or general- disease suppression. Disease suppressiveness can either occur naturally or can be induced by manipulating soil properties, including the microbiome responsible for conferring protection against soil-borne pathogens. While the induction of general disease suppression in agricultural soils is important for limiting pathogenic attacks on crops, the factors responsible for the phenomenon are yet to be identified. Limited efforts have been made to understand the systemic mechanisms involved in developing disease suppression in organically farmed soils. Identifying the critical factors could be useful for inducing disease suppressiveness in conducive soils as a cost-effective alternative to the application of pesticides and fungicides. Therefore, this review examines the soil properties, including microbiota, and assesses indicators related to disease suppression, for the process to be employed as a tactical option to reduce pesticide use in agriculture.

Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities

Associations with soil microorganisms are crucial for plants' overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here, we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 genotypes of cultivated sunflower (Helianthus annuus) at 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial, and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial, and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogen Sclerotinia were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions.IMPORTANCEDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial, and fungal communities are driven primarily by site soil and climatic differences, but genotype can interact with site to influence the composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogen Sclerotinia sclerotiorum were widespread but significantly affected by site, while a subset was also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial, and fungal community assembly and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.

Environmental associations of Ophidiomyces ophidiicola, the causative agent of ophidiomycosis in snakes

Emerging pathogenic fungi have become a topic of conservation concern due to declines observed in several host taxa. One emerging fungal pathogen, Ophidiomyces ophidiicola, is well documented as the causative agent of ophidiomycosis, otherwise known as snake fungal disease (SFD). O. ophidiicola has been found to cause disease in a variety of snake species across the United States, including the eastern massasauga (Sistrurus catenatus), a federally threatened rattlesnake species. Most work to date has involved detecting O. ophidiicola for diagnosis of infection through direct sampling of snakes, and attempts to detect O. ophidiicola in the abiotic environment to better understand its distribution, seasonality, and habitat associations are lacking. We collected topsoil and groundwater samples from four macrohabitat types across multiple seasons in northern Michigan at a site where Ophidiomyces infection has been confirmed in eastern massasauga. Using a quantitative PCR (qPCR) assay developed for O. ophidiicola, we detected Ophidiomyces DNA in topsoil but observed minimal to no detection in groundwater samples. Detection frequency did not differ between habitats, but samples grouped seasonally showed higher detection during mid-summer. We found no relationships of detection with hypothesized environmental correlates such as soil pH, temperature, or moisture content. Furthermore, the distribution of Ophidiomyces positive samples across the site was not linked to estimated space use of massasaugas. Our data suggests that season has some effect on the presence of Ophidiomyces. Differences in presence between habitats may exist but are likely more dependent on the time of sampling and currently uninvestigated soil or biotic parameters. These findings build on our understanding of Ophidiomyces ecology and epidemiology to help inform where and when snakes may be exposed to the fungus in the environment.

Balancing the scales: assessing the impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities

BACKGROUND

Understanding the interaction between environmental conditions, crop yields, and soil health is crucial for sustainable agriculture in a changing climate. Management practices to limit disease are a balancing act. For example, in potato production, dry conditions favour common scab (Streptomyces spp.) and wet conditions favour blackleg disease (Pectobacterium spp.). The exact mechanisms involved and how these link to changes in the soil microbiome are unclear. Our objectives were to test how irrigation management and bacterial pathogen load in potato seed stocks impact: (i) crop yields; (ii) disease development (blackleg or common scab); and (iii) soil microbial community dynamics.

METHODS

We used stocks of seed potatoes with varying natural levels of Pectobacterium (Jelly [high load], Jelly [low load] and Estima [Zero - no Pectobacterium]). Stocks were grown under four irrigation regimes that differed in the timing and level of watering. The soil microbial communities were profiled using amplicon sequencing at 50% plant emergence and at harvest. Generalised linear latent variable models and an annotation-free mathematical framework approach (ensemble quotient analysis) were then used to show the interacting microbes with irrigation regime and Pectobacterium pathogen levels.

RESULTS

Irrigation increased blackleg symptoms in the plots planted with stocks with low and high levels of Pectobacterium (22-34%) but not in the zero stock (2-6%). However, withholding irrigation increased common scab symptoms (2-5%) and reduced crop yields. Irrigation did not impact the composition of the soil microbiome, but planting stock with a high Pectobacterium burden resulted in an increased abundance of Planctomycetota, Anaerolinea and Acidobacteria species within the microbiome. Ensemble quotient analysis highlighted the Anaerolinea taxa were highly associated with high levels of Pectobacterium in the seed stock and blackleg symptoms in the field.

CONCLUSIONS

We conclude that planting seed stocks with a high Pectobacterium burden alters the abundance of specific microbial species within the soil microbiome and suggest that managing pathogen load in seed stocks could substantially affect soil communities, affecting crop health and productivity. Video Abstract.

Ecological shifts in soil microbiota and root rot disease progress during ginseng monoculture

Introduction

The phenomenon in which the damage of plant diseases is suppressed by continuous cropping is defined as "suppressiveness" and the development of suppressive soils and key beneficial microorganisms have been identified through various previous studies. However, no studies have been conducted on microbial communities related to disease occurrence before the initial occurrence of diseases in crop monoculture.

Methods

We aimed to investigate the ecological modifications of pathogen population density in soil, disease occurrence rate, and microbiota community shifting during ginseng monoculture to better understand the tripartite social relationships in the monoculture system. To achieve the study's objectives, a long-term monoculture of ginseng was established. The microbial diversity and community structure were analyzed using high-throughput sequencing, and the pathogen population density and disease occurrence rate were determined using qPCR and observation.

Results and discussion

The results showed that the initial rhizosphere bacterial community of ginseng had already collapsed before the development of the root rot disease. The study also identified the crucial role of soil-borne pathogens in causing disease and the loss of initial keystone taxa populations in the early stages of monoculture. Our study revealed a novel aspect of soil microbiota dynamics during ginseng monoculture, with seven distinct microbes (Beijerinckiaceae, Comamonadaceae, Devosiaceae, Rhizobiaceae, Sphingobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae) participating in soil nitrogen metabolism as an 'initial community' that regulates root rot disease through nutritional competition. The findings contribute to ecological research on disease-suppressiveness soil, disease management, and sustainable agriculture.

Plant community richness and foliar fungicides impact soil Streptomyces 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. 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.

Microbial community interactions on a chip

Multispecies microbial communities drive most ecosystems on Earth. Chemical and biological interactions within these communities can affect the survival of individual members and the entire community. However, the prohibitively high number of possible interactions within a microbial community has made the characterization of factors that influence community development challenging. Here, we report a Microbial Community Interaction (µCI) device to advance the systematic study of chemical and biological interactions within a microbial community. The µCI creates a combinatorial landscape made up of an array of triangular wells interconnected with circular wells, which each contains either a different chemical or microbial strain, generating chemical gradients and revealing biological interactions. Bacillus cereus UW85 containing green fluorescent protein provided the "target" readout in the triangular wells, and antibiotics or microorganisms in adjacent circular wells are designated the "variables." The µCI device revealed that gentamicin and vancomycin are antagonistic to each other in inhibiting the target B. cereus UW85, displaying weaker inhibitory activity when used in combination than alone. We identified three-member communities constructed with isolates from the plant rhizosphere that increased or decreased the growth of B. cereus. The µCI device enables both strain-level and community-level insight. The scalable geometric design of the µCI device enables experiments with high combinatorial efficiency, thereby providing a simple, scalable platform for systematic interrogation of three-factor interactions that influence microorganisms in solitary or community life.

Health by design; optimising our urban environmental microbiomes for human health

Humans have evolved in direct and intimate contact with their environment and the microbes that it contains, over a period of 2 million years. As a result, human physiology has become intrinsically linked to environmental microbiota. Urbanisation has reduced our exposure to harmful pathogens, however there is now increasing evidence that these same health-protective improvements in our environment may also be contributing to a hidden disease burden: immune dysregulation. Thoughtful and purposeful design has the potential to ameliorate these health concerns by providing sources of microbial diversity for human exposure. In this narrative review, we highlight the role of environmental microbiota in human health and provide insights into how we can optimise human health through well-designed cities, urban landscapes and buildings. The World Health Organization recommends there should be at least one public green space of least 0.5 ha in size within 300m of a place of residence. We argue that these larger green spaces are more likely to permit functioning ecosystems that deliver ecosystem services, including the provision of diverse aerobiomes. Urban planning must consider the conservation and addition of large public green spaces, while landscape design needs to consider how to maximise environmental, social and public health outcomes, which may include rewilding. Landscape designers need to consider how people use these spaces, and how to optimise utilisation, including for those who may experience challenges in access (e.g. those living with disabilities, people in residential care). There are also opportunities to improve health via building design that improves access to diverse environmental microbiota. Considerations include having windows that open, indoor plants, and the relationship between function, form and organization. We emphasise possibilities for re-introducing potentially health-giving microbial exposures into urban environments, particularly where the benefits of exposure to biodiverse environments may have been lost.

The impacts of ecological disturbances on the diversity of biosynthetic gene clusters in kauri (Agathis australis) soil

BACKGROUND

The ancient kauri (Agathis australis) dominated forests of Aotearoa New Zealand are under threat from a multitude of ecological disturbances such as forest fragmentation, biodiversity loss, climate change, and the spread of the virulent soil pathogen Phytophthora agathidicida. Taking a wider ecosystem-level approach, our research aimed to explore the impacts of forest disturbance and disease outbreaks on the biosynthetic potential and taxonomic diversity of the kauri soil microbiome. We explored the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in soils from a range of kauri forests that varied according to historical disturbance and dieback expression. To characterise the diversity of microbial BGCs, we targeted the non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene regions for sequencing using long-read PacBio® HiFi sequencing. Furthermore, the soil bacterial and fungal communities of each forest were characterized using 16 S rRNA and ITS gene region sequencing.

RESULTS

We identified a diverse array of naturally occurring microbial BGCs in the kauri forest soils, which may offer promising targets for the exploration of secondary metabolites with anti-microbial activity against P. agathidicida. We detected differences in the number and diversity of microbial BGCs according to forest disturbance history. Notably, soils associated with the most undisturbed kauri forest had a higher number and diversity of microbial NRPS-type BGCs, which may serve as a potential indicator of natural levels of microbiome resistance to pathogen invasion.

CONCLUSIONS

By linking patterns in microbial biosynthetic diversity to forest disturbance history, this research highlights the need for us to consider the influence of ecological disturbances in potentially predisposing forests to disease by impacting the wider health of forest soil ecosystems. Furthermore, by identifying the range of microbial BGCs present at a naturally high abundance in kauri soils, this research contributes to the future discovery of natural microbial compounds that may potentially enhance the disease resilience of kauri forests. The methodological approaches used in this study highlight the value of moving beyond a taxonomic lens when examining the response of microbial communities to ecosystem disturbance and the need to develop more functional measures of microbial community resilience to invasive plant pathogens.

Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot

BACKGROUND

Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health.

RESULTS

Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease.

CONCLUSIONS

Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe's occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops. Video Abstract.

Re-Envisioning the Plant Disease Triangle: Full Integration of the Host Microbiota and a Focal Pivot to Health Outcomes

The disease triangle is a structurally simple but conceptually rich model that is used in plant pathology and other fields of study to explain infectious disease as an outcome of the three-way relationship between a host, a pathogen, and their environment. It also serves as a guide for finding solutions to treat, predict, and prevent such diseases. With the omics-driven, evidence-based realization that the abundance and activity of a pathogen are impacted by proximity to and interaction with a diverse multitude of other microorganisms colonizing the same host, the disease triangle evolved into a tetrahedron shape, which features an added fourth dimension representing the host-associated microbiota. Another variant of the disease triangle emerged from the recently formulated pathobiome paradigm, which deviates from the classical "one pathogen" etiology of infectious disease in favor of a scenario in which disease represents a conditional outcome of complex interactions between and among a host, its microbiota (including microbes with pathogenic potential), and the environment. The result is a version of the original disease triangle where "pathogen" is substituted with "microbiota." Here, as part of a careful and concise review of the origin, history, and usage of the disease triangle, I propose a next step in its evolution, which is to replace the word "disease" in the center of the host-microbiota-environment triad with the word "health." This triangle highlights health as a desirable outcome (rather than disease as an unwanted state) and as an emergent property of host-microbiota-environment interactions. Applied to the discipline of plant pathology, the health triangle offers an expanded range of targets and approaches for the diagnosis, prediction, restoration, and maintenance of plant health outcomes. Its applications are not restricted to infectious diseases only, and its underlying framework is more inclusive of all microbial contributions to plant well-being, including those by mycorrhizal fungi and nitrogen-fixing bacteria, for which there never was a proper place in the plant disease triangle. The plant health triangle also may have an edge as an education and communication tool to convey and stress the importance of healthy plants and their associated microbiota to a broader public and stakeholdership.

Rhizospheric microbiota of suppressive soil protect plants against Fusarium solani infection

BACKGROUND

Fusarium infection has caused huge economic losses in many crops. The study aimed to compare the microbial community of suppressive and conducive soils and relate to the reduction of Fusarium wilt.

RESULTS

High-throughput sequencing and microbial network analysis were used to investigate the differences in the rhizosphere microbiota of the suppressive and conducive soils and to identify the beneficial keystone taxa. Plant pathogens were enriched in the conducive soil. Potential plant-beneficial microorganisms and antagonistic microorganisms were enriched in the suppressive soil. More positive interactions and keystone taxa existed in the suppressive soil network. Thirty-nine and 16 keystone taxa were identified in the suppressive and conducive soil networks, respectively. Sixteen fungal strains and 168 bacterial strains were isolated from suppressive soil, some of which exhibited plant growth-promotion traits. Thirty-nine bacterial strains and 10 fungal strains showed antagonistic activity against F. solani. Keystone taxa Bacillus and Trichoderma exhibited high antifungal activity. Lipopeptides produced by Bacillus sp. RB150 and chitinase from Trichoderma spp. inhibited the growth of F. solani. Microbial consortium I (Bacillus sp. RB150, Pseudomonas sp. RB70 and Trichoderma asperellum RF10) and II (Bacillus sp. RB196, Bacillus sp. RB150 and T. asperellum RF10) effectively controlled root rot disease, the spore number of F. solani was reduced by 94.2% and 83.3%.

CONCLUSION

Rhizospheric microbiota of suppressive soil protects plants against F. solani infection. Antagonistic microorganisms in suppressive soil inhibit pathogen growth and infection. Microbial consortia consisted of keystone taxa well control root rot disease. These findings help control Fusarium wilt. © 2024 Society of Chemical Industry.

Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes

Plants have coevolved together with the microbes that surround them and this assemblage of host and microbes functions as a discrete ecological unit called a holobiont. This review outlines plant-driven assembly of disease-suppressive microbiomes. Plants are colonized by microbes from seed, soil, and air but selectively shape the microbiome with root exudates, creating microenvironment hot spots where microbes thrive. Using plant immunity for gatekeeping and surveillance, host-plant genetic properties govern microbiome assembly and can confer adaptive advantages to the holobiont. These advantages manifest in disease-suppressive soils, where buildup of specific microbes inhibits the causal agent of disease, that typically develop after an initial disease outbreak. Based on disease-suppressive soils such as take-all decline, we developed a conceptual model of how plants in response to pathogen attack cry for help and recruit plant-protective microbes that confer increased resistance. Thereby, plants create a soilborne legacy that protects subsequent generations and forms disease-suppressive soils.

Elucidating the endophytic bacterial and fungal community composition and diversity in the tree fern Alsophila spinulosa through meta-amplicon sequencing

Plant tissues harbor abundant endophytes, which are crucial for plant growth. Endophytes present in Alsophila spinulosa, which is enriched with medicinal components, have not been isolated and characterized yet. Here we employed meta-amplicon sequencing to identify endophytic species and examined their diversity in the leaves, petioles, roots and stems of A. spinulosa. Our findings revealed 1,247 operational taxonomic units (OTUs) for endophytic bacteria across 210 species and 476 OTUs for endophytic fungi across 222 species. Alpha diversity analysis showed the highest endophytic bacterial diversity in A. spinulosa roots, whereas fungal diversity was similar across the leaf, petiole and root tissues. Fungal diversity in the leaves and petioles was markedly higher than that in the stems. Furthermore, beta diversity analysis revealed similarities in the endophytic bacterial and fungal compositions between the leaves and petioles, whereas the compositions in roots and stems considerably differed from those in the leaves and petioles. At the genus level, the predominant endophytic bacteria were Methylobacterium-Methylorubrum and Pseudomonas, whereas the predominant endophytic fungi were Cutaneotrichosporon and Pseudofabraea. Linear discriminant analysis effect size revealed characteristic endophytic bacterial genera specific to each tissue type and characteristic endophytic fungal genera specifically in the leaves, petioles and roots. The co-occurrence network analysis indicated that the complexity of endophyte networks was the highest in the leaves and the lowest in the stems of A. spinulosa. Overall, this study elucidates the distribution patterns of endophytes in A. spinulosa across various tissues, offering valuable microbial resources for the development of natural products for medicinal application.

Protective role of native root-associated bacterial consortium against root-knot nematode infection in susceptible plants

Root-knot nematodes (RKNs) are a global menace to agricultural crop production. The role of root-associated microbes (RAMs) in plant protection against RKN infection remains unclear. Here we observe that cucumber (highly susceptible to Meloidogyne incognita) exhibits a consistently lower susceptibility to M. incognita in the presence of native RAMs in three distinct soils. Nematode infection alters the assembly of bacterial RAMs along the life cycle of M. incognita. Particularly, the loss of bacterial diversity of RAMs exacerbates plant susceptibility to M. incognita. A diverse range of native bacterial strains isolated from M. incognita-infected roots has nematode-antagonistic activity. Increasing the number of native bacterial strains causes decreasing nematode infection, which is lowest when six or more bacterial strains are present. Multiple simplified synthetic communities consisting of six bacterial strains show pronounced inhibitory effects on M. incognita infection in plants. These inhibitory effects are underpinned via multiple mechanisms including direct inhibition of infection, secretion of anti-nematode substances, and regulation of plant defense responses. This study highlights the role of native bacterial RAMs in plant resistance against RKNs and provides a useful insight into the development of a sustainable way to protect susceptible plants.

From Microbes to Microbiomes: Applications for Plant Health and Sustainable Agriculture

Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.

Grazing exclusion-induced changes in soil fungal communities in a highly desertified Brazilian dryland

Soil desertification poses a critical ecological challenge in arid and semiarid climates worldwide, leading to decreased soil productivity due to the disruption of essential microbial community processes. Fungi, as one of the most important soil microbial communities, play a crucial role in enhancing nutrient and water uptake by plants through mycorrhizal associations. However, the impact of overgrazing-induced desertification on fungal community structure, particularly in the Caatinga biome of semiarid regions, remains unclear. In this study, we assessed the changes in both the total fungal community and the arbuscular mycorrhizal fungal community (AMF) across 1. Natural vegetation (native), 2. Grazing exclusion (20 years) (restored), and 3. affected by overgrazing-induced degradation (degraded) scenarios. Our assessment, conducted during both the dry and rainy seasons in Irauçuba, Ceará, utilized Internal Transcribed Spacer (ITS) gene sequencing via Illumina® platform. Our findings highlighted the significant roles of the AMF families Glomeraceae (∼71% of the total sequences) and Acaulosporaceae (∼14% of the total sequences) as potential key taxa in mitigating climate change within dryland areas. Moreover, we identified the orders Pleosporales (∼35% of the total sequences) and Capnodiales (∼21% of the total sequences) as the most abundant soil fungal communities in the Caatinga biome. The structure of the total fungal community differed when comparing native and restored areas to degraded areas. Total fungal communities from native and restored areas clustered together, suggesting that grazing exclusion has the potential to improve soil properties and recover fungal community structure amid global climate change challenges.

Natural plant disease suppressiveness in soils extends to insect pest control

BACKGROUND

Since the 1980s, soils in a 22-km2 area near Lake Neuchâtel in Switzerland have been recognized for their innate ability to suppress the black root rot plant disease caused by the fungal pathogen Thielaviopsis basicola. However, the efficacy of natural disease suppressive soils against insect pests has not been studied.

RESULTS

We demonstrate that natural soil suppressiveness also protects plants from the leaf-feeding pest insect Oulema melanopus. Plants grown in the most suppressive soil have a reduced stress response to Oulema feeding, reflected by dampened levels of herbivore defense-related phytohormones and benzoxazinoids. Enhanced salicylate levels in insect-free plants indicate defense-priming operating in this soil. The rhizosphere microbiome of suppressive soils contained a higher proportion of plant-beneficial bacteria, coinciding with their microbiome networks being highly tolerant to the destabilizing impact of insect exposure observed in the rhizosphere of plants grown in the conducive soils. We suggest that presence of plant-beneficial bacteria in the suppressive soils along with priming, conferred plant resistance to the insect pest, manifesting also in the onset of insect microbiome dysbiosis by the displacement of the insect endosymbionts.

CONCLUSIONS

Our results show that an intricate soil-plant-insect feedback, relying on a stress tolerant microbiome network with the presence of plant-beneficial bacteria and plant priming, extends natural soil suppressiveness from soilborne diseases to insect pests. Video Abstract.

Redundancy in microbiota-mediated suppression of the soybean cyst nematode

BACKGROUND

Soybean cyst nematodes (SCN) as animal parasites of plants are not usually interested in killing the host but are rather focused on completing their life cycle to increase population, resulting in substantial yield losses. Remarkably, some agricultural soils after long-term crop monoculture show a significant decline in SCN densities and suppress disease in a sustainable and viable manner. However, relatively little is known about the microbes and mechanisms operating against SCN in such disease-suppressive soils.

RESULTS

Greenhouse experiments showed that suppressive soils (S) collected from two provinces of China and transplantation soils (CS, created by mixing 10% S with 90% conducive soils) suppressed SCN. However, SCN suppressiveness was partially lost or completely abolished when S soils were treated with heat (80 °C) and formalin. Bacterial community analysis revealed that the specific suppression in S and CS was mainly associated with the bacterial phylum Bacteroidetes, specifically due to the enrichment of Chitinophaga spp. and Dyadobacter sp., in the cysts. SCN cysts colonized by Chitinophaga spp. showed dramatically reduced egg hatching, with unrecognizable internal body organization of juveniles inside the eggshell due to chitinase activity. Whereas, Dyadobacter sp. cells attached to the surface coat of J2s increased soybean resistance against SCN by triggering the expression of defence-associated genes. The disease-suppressive potential of these bacteria was validated by inoculating them into conducive soil. The Dyadobacter strain alone or in combination with Chitinophaga strains significantly decreased egg densities after one growing cycle of soybeans. In contrast, Chitinophaga strains alone required more than one growing cycle to significantly reduce SCN egg hatching and population density.

CONCLUSION

This study revealed how soybean monoculture for decades induced microbiota homeostasis, leading to the formation of SCN-suppressive soil. The high relative abundance of antagonistic bacteria in the cyst suppressed the SCN population both directly and indirectly. Because uncontrolled proliferation will likely lead to quick demise due to host population collapse, obligate parasites like SCN may have evolved to modulate virulence/proliferation to balance these conflicting needs. Video Abstract.

Role of microbial communities and nitrogen sources in suppressing root rot disease during ginseng cultivation

Ginsengs, widely acknowledged for their health-promoting properties, are predominantly grown for their roots, necessitating an extended cultivation period of a minimum of 4 to 6 years for maturation. The prolonged growth duration in a specific location makes ginseng plants susceptible to soil-borne ailments, such as root rot, leading to significant detrimental effects. Focusing on the crucial role of the plant microbial community in maintaining ginseng health, the study reveals that repeated and continuous cultivation leads to the collapse of the initial disease-suppressive rhizosphere community, resulting in severe root rot. The dominance of Pseudomonadaceae in the rhizosphere subsequently reinstates disease suppression, aligning with suppressive soil generation phenomena. The research investigates the applicability of identified patterns to field conditions and demonstrates that rhizosphere samples from the field closely resemble conditions observed in pot-based NH4Cl treatment experiments. These findings emphasize the critical role of the rhizosphere microbial community in ginseng health maintenance during extended cultivation, offering insights into disease prevention strategies. The study also suggests the potential of pot-based experiments in simulating field conditions and informs future approaches for sustainable ginseng cultivation.

The underground world of plant disease: Rhizosphere dysbiosis reduces above-ground plant resistance to bacterial leaf spot and alters plant transcriptome

Just as the human gut microbiome is colonized by a variety of microbes, so too is the rhizosphere of plants. An imbalance in this microbial community, known as dysbiosis, can have a negative impact on plant health. This study sought to explore the effect of rhizosphere dysbiosis on the health of tomato plants (Solanum lycopersicum L.), using them and the foliar bacterial spot pathogen Xanthomonas perforans as model organisms. The rhizospheres of 3-week-old tomato plants were treated with either streptomycin or water as a control, and then spray-inoculated with X. perforans after 24 h. Half of the plants that were treated with both streptomycin and X. perforans received soil microbiome transplants from uninfected plant donors 48 h after the streptomycin was applied. The plants treated with streptomycin showed a 26% increase in disease severity compared to those that did not receive the antibiotic. However, the plants that received the soil microbiome transplant exhibited an intermediate level of disease severity. The antibiotic-treated plants demonstrated a reduced abundance of rhizobacterial taxa such as Cyanobacteria from the genus Cylindrospermum. They also showed a down-regulation of genes related to plant primary and secondary metabolism, and an up-regulation of plant defence genes associated with induced systemic resistance. This study highlights the vital role that beneficial rhizosphere microbes play in disease resistance, even against foliar pathogens.

Screening, identification and evaluation of an acidophilic strain of Bacillus velezensis B4-7 for the biocontrol of tobacco bacterial wilt

Tobacco (Nicotiana tabacum L.) bacterial wilt, caused by Ralstonia solanacearum, is indeed a highly destructive plant disease, leading to substantial damage in tobacco production. While biological control is considered an effective measure for managing bacterial wilt, related research in this area has been relatively limited compared to other control methods. In order to discover new potential antagonistic bacteria with high biocontrol efficacy against tobacco bacterial wilt, we conducted an analysis of the microbial composition differences between disease-suppressive and disease-conducive soils using Illumina sequencing. As a result, we successfully isolated six strains from the disease-suppressive soil that exhibited antibacterial activity against Ralstonia solanacearum. Among these strains, B4-7 showed the strongest antibacterial activity, even at acidic conditions with a pH of 4.0. Based on genome analysis using Average Nucleotide Identity (ANI), B4-7 was identified as Bacillus velezensis. In greenhouse and field trials, strain B4-7 significantly reduced the disease index of tobacco bacterial wilt, with control efficiencies reaching 74.03% and 46.88% respectively. Additionally, B4-7 exhibited plant-promoting abilities that led to a 35.27% increase in tobacco production in field conditions. Quantitative real-time (qPCR) analysis demonstrated that strain B4-7 effectively reduced the abundance of R. solanacearum in the rhizosphere. Genome sequencing and Liquid Chromatography-Mass Spectrometry (LC-MS) analysis revealed that strain B4-7 potentially produces various lipopeptide metabolites, such as microlactin, bacillaene, difficidin, bacilysin, and surfactin. Furthermore, B4-7 influenced the structure of the rhizosphere soil microbial community, increasing bacterial abundance and fungal diversity, while also promoting the growth of different beneficial microorganisms. In addition, B4-7 enhanced tobacco's resistance to R. solanacearum by increasing the activities of defense enzymes, including superoxide dismutase (SOD), phenylalanine ammonia-lyase (PAL), peroxidase (POD), catalase (CAT), and polyphenol oxidase (PPO). Collectively, these findings suggest that B. velezensis B4-7 holds significant biocontrol potential and can be considered a promising candidate strain for eco-friendly management of tobacco bacterial wilt.

Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago

Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1-42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird's-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.IMPORTANCEUnderstanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.

Rhizoctonia solani disease suppression: addition of keratin-rich soil amendment leads to functional shifts in soil microbial communities

Promoting soil suppressiveness against soil borne pathogens could be a promising strategy to manage crop diseases. One way to increase the suppression potential in agricultural soils is via the addition of organic amendments. This microbe-mediated phenomenon, although not fully understood, prompted our study to explore the microbial taxa and functional properties associated with Rhizoctonia solani disease suppression in sugar beet seedlings after amending soil with a keratin-rich waste stream. Soil samples were analyzed using shotgun metagenomics sequencing. Results showed that both amended soils were enriched in bacterial families found in disease suppressive soils before, indicating that the amendment of keratin-rich material can support the transformation into a suppressive soil. On a functional level, genes encoding keratinolytic enzymes were found to be abundant in the keratin-amended samples. Proteins enriched in amended soils were those potentially involved in the production of secondary metabolites/antibiotics, motility, keratin-degradation, and contractile secretion system proteins. We hypothesize these taxa contribute to the amendment-induced suppression effect due to their genomic potential to produce antibiotics, secrete effectors via the contractile secretion system, and degrade oxalate-a potential virulence factor of R. solani-while simultaneously possessing the ability to metabolize keratin.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

Transplantation of soil from organic field confers disease suppressive ability to conducive soil

Organic agriculture is a sustainable method of farming, and confers disease-suppressing abilities to disease-conducive soils via specialized soil microbiomes. This study aimed at transforming a disease-conducive soil from a conventional field into disease-suppressive soil by inoculating soil from an organic field previously established as "disease-suppressive". The effectiveness of the transformed soil was established with the model plant wheat (Triticum aestivum) grown under natural conditions, with regard to its potential in inhibiting fungal phytopathogens, Rhizoctonia solani and Fusarium oxysporum. The conducive soil inoculated with the disease-suppressive soil performed better than the control conducive soil in terms of reduced disease severity in plants, improved soil nutrient content, increased activity of hydrolytic enzymes, and increased abundance of structural and functional microbial markers. The study demonstrates the efficacy of the soil microbiome under long-term organic agriculture in transforming disease-conducive soil into disease-suppressive soils. Such practises are simple and easy to implement, and could greatly improve the sustainability and crop yield in developing countries.

Strategies for tailoring functional microbial synthetic communities

Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.

Building soil to reduce climate change impacts on global crop yield

Improving soil health and resilience is fundamental for sustainable food production, however the role of soil in maintaining or improving global crop productivity under climate warming is not well identified and quantified. Here, we examined the impact of soil on yield response to climate warming for four major crops (i.e., maize, wheat, rice and soybean), using global-scale datasets and random forest method. We found that each °C of warming reduced global yields of maize by 3.4%, wheat by 2.4%, rice by 0.3% and soybean by 5.0%, which were spatially heterogeneous with possible positive impacts. The random forest modeling analyses further showed that soil organic carbon (SOC), as an indicator of soil quality, dominantly explained the spatial heterogeneity of yield responses to warming and would regulate the negative warming responses. Improving SOC under the medium SOC sequestration scenario would reduce the warming-induced yield loss of maize, wheat, rice and soybean to 0.1% °C-1, 2.7% °C-1, 3.4% °C-1 and - 0.6% °C-1, respectively, avoiding an average of 3%-5% °C-1 of global yield loss. These yield benefits would occur on 53.2%, 67.8%, 51.8% and 71.6% of maize, wheat, rice and soybean planting areas, respectively, with particularly pronounced benefits in the regions with negative warming responses. With improved soil carbon, food systems are predicted to provide additional 20 to over 130 million tonnes of food that would otherwise lose due to future warming. Our findings highlight the critical role of soil in alleviating negative warming impacts on food security, especially for developing regions, given that sustainable actions on soil improvement could be taken broadly.

Microbial diversity in soils suppressive to Fusarium diseases

Fusarium species are cosmopolitan soil phytopathogens from the division Ascomycota, which produce mycotoxins and cause significant economic losses of crop plants. However, soils suppressive to Fusarium diseases are known to occur, and recent knowledge on microbial diversity in these soils has shed new lights on phytoprotection effects. In this review, we synthesize current knowledge on soils suppressive to Fusarium diseases and the role of their rhizosphere microbiota in phytoprotection. This is an important issue, as disease does not develop significantly in suppressive soils even though pathogenic Fusarium and susceptible host plant are present, and weather conditions are suitable for disease. Soils suppressive to Fusarium diseases are documented in different regions of the world. They contain biocontrol microorganisms, which act by inducing plants' resistance to the pathogen, competing with or inhibiting the pathogen, or parasitizing the pathogen. In particular, some of the Bacillus, Pseudomonas, Paenibacillus and Streptomyces species are involved in plant protection from Fusarium diseases. Besides specific bacterial populations involved in disease suppression, next-generation sequencing and ecological networks have largely contributed to the understanding of microbial communities in soils suppressive or not to Fusarium diseases, revealing different microbial community patterns and differences for a notable number of taxa, according to the Fusarium pathosystem, the host plant and the origin of the soil. Agricultural practices can significantly influence soil suppressiveness to Fusarium diseases by influencing soil microbiota ecology. Research on microbial modes of action and diversity in suppressive soils should help guide the development of effective farming practices for Fusarium disease management in sustainable agriculture.

Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana

Hyaloperonospora arabidopsidis (Hpa) is an obligately biotrophic downy mildew that is routinely cultured on Arabidopsis thaliana hosts that harbour complex microbiomes. We hypothesized that the culturing procedure proliferates Hpa-associated microbiota (HAM) in addition to the pathogen and exploited this model system to investigate which microorganisms consistently associate with Hpa. Using amplicon sequencing, we found nine bacterial sequence variants that are shared between at least three out of four Hpa cultures in the Netherlands and Germany and comprise 34% of the phyllosphere community of the infected plants. Whole-genome sequencing showed that representative HAM bacterial isolates from these distinct Hpa cultures are isogenic and that an additional seven published Hpa metagenomes contain numerous sequences of the HAM. Although we showed that HAM benefit from Hpa infection, HAM negatively affect Hpa spore formation. Moreover, we show that pathogen-infected plants can selectively recruit HAM to both their roots and shoots and form a soil-borne infection-associated microbiome that helps resist the pathogen. Understanding the mechanisms by which infection-associated microbiomes are formed might enable breeding of crop varieties that select for protective microbiomes.

Studying the microbiome of suppressive soils against vascular wilt, caused by Fusarium oxysporum in cape gooseberry (Physalis peruviana)

Cape gooseberry (Physalis peruviana) is Colombia's second most exported fruit, with a market worth 37.8 million USD in 2021. Fusarium oxysporum f sp. physalis (Foph) is arguably the most devastating pathogen causing losses of up to 80%. Managing this disease is challenging due to pathogen resistance or the reduced efficacy of commercial fungicides and the production of resistant structures allowing pathogen survival in the soil for up to 30 years. Thus, new methods of control are necessary. Two cape gooseberry farms (organic vs. conventional) were detected free from Foph in Nariño. We hypothesize that the soil microbiome might have a suppressive effect against vascular wilt, caused by Foph. To test this, farm soils were propagated by adding 10% farm soil and 90% peat soil. Then, peat soil (control) and propagated soils were inoculated with Foph. A decrease of 65%-68% in disease incidence and a 70% in disease severity reduction was observed in seedlings grown in propagated soils compared to peat soil. We then used next-generation sequencing to study the soil microbiome to understand the possible mechanisms for disease suppression of propagated soils. We conclude that despite the high diversity of soil microbiomes, the relative abundance of some taxa might be a more important indicator of disease suppression than the presence of specific taxa.

The Cultured Microbiome of Pollinated Maize Silks Shifts after Infection with Fusarium graminearum and Varies by Distance from the Site of Pathogen Inoculation

Styles transmit pollen-derived sperm nuclei from pollen to ovules, but also transmit environmental pathogens. The microbiomes of styles are likely important for reproduction/disease, yet few studies exist. Whether style microbiome compositions are spatially responsive to pathogens is unknown. The maize pathogen Fusarium graminearum enters developing grain through the style (silk). We hypothesized that F. graminearum treatment shifts the cultured transmitting silk microbiome (TSM) compared to healthy silks in a distance-dependent manner. Another objective of the study was to culture microbes for future application. Bacteria were cultured from husk-covered silks of 14 F. graminearum-treated diverse maize genotypes, proximal (tip) and distal (base) to the F. graminearum inoculation site. Long-read 16S sequences from 398 isolates spanned 35 genera, 71 species, and 238 OTUs. More bacteria were cultured from F. graminearum-inoculated tips (271 isolates) versus base (127 isolates); healthy silks were balanced. F. graminearum caused a collapse in diversity of ~20-25% across multiple taxonomic levels. Some species were cultured exclusively or, more often, from F. graminearum-treated silks (e.g., Delftia acidovorans, Klebsiella aerogenes, K. grimontii, Pantoea ananatis, Stenotrophomonas pavanii). Overall, the results suggest that F. graminearum alters the TSM in a distance-dependent manner. Many isolates matched taxa that were previously identified using V4-MiSeq (core and F. graminearum-induced), but long-read sequencing clarified the taxonomy and uncovered greater diversity than was initially predicted (e.g., within Pantoea). These isolates represent the first comprehensive cultured collection from pathogen-treated maize silks to facilitate biocontrol efforts and microbial marker-assisted breeding.

Antifungal mechanism of volatile compounds emitted by Actinomycetota Paenarthrobacter ureafaciens from a disease-suppressive soil on Saccharomyces cerevisiae

Increasing evidence suggests that in disease-suppressive soils, microbial volatile compounds (mVCs) released from bacteria may inhibit the growth of plant-pathogenic fungi. However, the antifungal activities and molecular responses of fungi to different mVCs remain largely undescribed. In this study, we first evaluated the responses of pathogenic fungi to treatment with mVCs from Paenarthrobacter ureafaciens. Then, we utilized the well-characterized fungal model organism Saccharomyces cerevisiae to study the potential mechanistic effects of the mVCs. Our data showed that exposure to P. ureafaciens mVCs leads to reduced growth of several pathogenic fungi, and in yeast cells, mVC exposure prompts the accumulation of reactive oxygen species. Further experiments with S. cerevisiae deletion mutants indicated that Slt2/Mpk1 and Hog1 MAPKs play major roles in the yeast response to P. ureafaciens mVCs. Transcriptomic analysis revealed that exposure to mVCs was associated with 1,030 differentially expressed genes (DEGs) in yeast. According to gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses, many of these DEGs are involved in mitochondrial dysfunction, cell integrity, mitophagy, cellular metabolism, and iron uptake. Genes encoding antimicrobial proteins were also significantly altered in the yeast after exposure to mVCs. These findings suggest that oxidative damage and mitochondrial dysfunction are major contributors to the fungal toxicity of mVCs. Furthermore, our data showed that cell wall, antioxidant, and antimicrobial defenses are induced in yeast exposed to mVCs. Thus, our findings expand upon previous research by delineating the transcriptional responses of the fungal model. IMPORTANCE Since the use of bacteria-emitted volatile compounds in phytopathogen control is of considerable interest, it is important to understand the molecular mechanisms by which fungi may adapt to microbial volatile compounds (mVCs). Paenarthrobacter ureafaciens is an isolated bacterium from disease-suppressive soil that belongs to the Actinomycetota phylum. P. ureafaciens mVCs showed a potent antifungal effect on phytopathogens, which may contribute to disease suppression in soil. However, our knowledge about the antifungal mechanism of mVCs is limited. This study has proven that mVCs are toxic to fungi due to oxidative stress and mitochondrial dysfunction. To deal with mVC toxicity, antioxidants and physical defenses are required. Furthermore, iron uptake and CAP proteins are required for antimicrobial defense, which is necessary for fungi to deal with the thread from mVCs. This study provides essential foundational knowledge regarding the molecular responses of fungi to inhibitory mVCs.

Role of Fungi in Imparting General Disease Suppressiveness in Soil from Organic Field

Soil microbial communities are key players responsible for imparting suppressive potential to the soil against soil-borne phytopathogens. Fungi have an immense potential to inhibit soil-borne phytopathogens, but the fungal counterpart has been less explored in this context. We assessed the composition of fungal communities in soil under long-term organic and conventional farming practice, and control soil. The disease-suppressive potential of organic field was already established. A comparative analysis of the disease suppressiveness contributed by the fungal component of soil from conventional and organic farms was assessed using dual culture assays. The quantification of biocontrol markers and total fungi was done; the characterization of fungal community was carried out using ITS-based amplicon sequencing. Soil from organic field exhibited higher disease-suppressive potential than that from conventional farming, against the pathogens selected for the study. Higher levels of hydrolytic enzymes such as chitinase and cellulase, and siderophore production were observed in soil from the organic field compared to the conventional field. Differences in community composition were observed under conventional and organic farming, with soil from organic field exhibiting specific enrichment of key biocontrol fungal genera. The fungal alpha diversity was lower in soil from the organic field compared to the conventional field. Our results highlight the role of fungi in contributing to general disease-suppressive ability of the soil against phytopathogens. The identification of fungal taxa specifically associated with organic farming can aid in understanding the mechanism of disease suppression under such a practice, and can be exploited to induce general disease suppressiveness in otherwise conducive soil.

Soil Suppressiveness Against Pythium ultimum and Rhizoctonia solani in Two Land Management Systems and Eleven Soil Health Treatments

The soil microbiome is known to be crucial for the control of soil-borne plant diseases. However, there is still little knowledge on how to modify the soil microbiome to induce or increase disease suppressiveness. In the present study, we applied eleven soil health treatments combined with conventional and organic agricultural management in a long-term field experiment. Suppressiveness against Pythium ultimum and Rhizoctonia solani was assessed in bioassays for 2 years. In addition, the microbiome community composition and microbial abundance were determined. We found that while several treatments changed the microbial community composition compared to the control, only a combination treatment of anaerobic soil disinfestation, hair meal, and compost addition resulted in suppressiveness against P. ultimum. Pythium suppressiveness is likely to have been caused by an increased microbial abundance and activity. Moreover, the increased abundance of several bacterial taxa, such as Pseudomonas sp., Chryseobacterium sp., members of the family Chitinophagaceae, and the fungal genus Mortierella sp. and family Trichosporonaceae, was measured. There was no overall difference in suppressiveness between conventional and organic land management. Also, no suppressiveness against R. solani could be detected. Our results indicate that a treatment combining the reduction of microorganisms followed by a recovery phase with high amounts of organic amendments may be more effective in inducing suppressiveness than treatments consisting of only one of these measures.

Investigating the Impact of Tillage and Crop Rotation on the Prevalence of phlD-Carrying Pseudomonas Potentially Involved in Disease Suppression

Winter oilseed rape (OSR) is becoming an increasingly popular crop in rotations as it provides a cash crop and reduces the incidence of take-all fungal disease (caused by Gaeumannomyces graminis) in subsequent wheat production. The exact mechanism of this inhibition of fungal pathogens is not fully understood; however, the selective recruitment of bacterial groups with the ability to suppress pathogen growth and reproduction is thought to play a role. Here we examine the effect of tillage practice on the proliferation of microbes that possess the phlD gene involved in the production of the antifungal compound 2,4-diacetylphloroglucinol (2,4-DAPG), in the rhizospheres of both winter oilseed rape and winter wheat grown in rotation over a two-year period. The results showed that conservation strip tillage led to a significantly greater phlD gene copy number, both in the soil and in the roots, of oilseed rape and wheat crops, whereas crop rotation of oilseed rape and wheat did not increase the phlD gene copy number in winter wheat.