Disease-induced changes in plant microbiome assembly and functional adaptation

Rhizobacterial Bacillus enrichment in soil enhances smoke tree resistance to Verticillium wilt

Verticillium wilt, caused by the soilborne fungus Verticillium dahliae, poses a serious threat to the health of more than 200 plant species worldwide. Although plant rhizosphere-associated microbiota can influence plant resistance to V. dahliae, empirical evidence underlying Verticillium wilt resistance of perennial trees is scarce. In this study, we systemically investigated the effect of the soil microbiota on the resistance of smoke trees (Cotinus coggygria) to Verticillium wilt using field, greenhouse and laboratory experiments. Comparative analysis of the soil microbiota in the two stands of smoke trees suggested that Bacillus represented the most abundant and key microbial genus related to potential disease suppression. Smoke tree seedlings were inoculated with isolated Bacillus strains, which exhibited disease suppressiveness and plant growth-promoting properties. Furthermore, repletion of Bacillus agents to disease conducive soil significantly resulted in reduced incidence of smoke tree wilt and increased resistance of the soil microbiota to V. dahliae. Finally, we explored a more effective combination of Bacillus agents with the fungicide propiconazole to combat Verticillium wilt. The results establish a foundation for the development of an effective control for this disease. Overall, this work provides a direct link between Bacillus enrichment and disease resistance of smoke trees, facilitating the development of green control strategies and measurements of soil-borne diseases.

Pinewood nematode induced changes in the assembly process of gallery microbiomes benefit its vector beetle's development

Microbiomes play crucial roles in insect adaptation, especially under stress such as pathogen invasion. Yet, how beneficial microbiomes assemble remains unclear. The wood-boring beetle Monochamus alternatus, a major pest and vector of the pine wilt disease (PWD) nematode, offers a unique model. We conducted controlled experiments using amplicon sequencing (16S rRNA and ITS) within galleries where beetles and microbes interact. PWD significantly altered bacterial and fungal communities, suggesting distinct assembly processes. Deterministic factors like priority effects, host selection, and microbial interactions shaped microbiome composition, distinguishing healthy from PWN-infected galleries. Actinobacteria, Firmicutes, and Ophiostomataceae emerged as potentially beneficial, aiding beetle's development and pathogen resistance. This study unveils how nematode-induced changes in gallery microbiomes influence beetle's development, shedding light on microbiome assembly amid insect-pathogen interactions. Insights gleaned enhance understanding of PWD spread and suggest novel management strategies via microbiome manipulation.IMPORTANCEThis study explores the assembly process of gallery microbiomes associated with a wood-boring beetles, Monochamus alternatus, a vector of the pine wilt disease (PWD). By conducting controlled comparison experiments and employing amplicon approaches, the study reveals significant changes in taxonomic composition and functional adaptation of bacterial and fungal communities induced by PWD. It identifies deterministic processes, including priority effects, host selection, and microbial interactions, as major drivers in microbiome assembly. Additionally, the study highlights the presence of potentially beneficial microbes such as Actinobacteria, Firmicutes, and Ophiostomataceae, which could enhance beetle development and resistance to pathogens. These findings shed light on the intricate interplay among insects, microbiomes, and pathogens, contributing to a deeper understanding of PWD prevalence and suggesting innovative management strategies through microbiome manipulation.

Dynamic alterations and ecological implications of rice rhizosphere bacterial communities induced by an insect-transmitted reovirus across space and time

BACKGROUND

Cereal diseases caused by insect-transmitted viruses are challenging to forecast and control because of their intermittent outbreak patterns, which are usually attributed to increased population densities of vector insects due to cereal crop rotations and indiscriminate use of pesticides, and lack of resistance in commercial varieties. Root microbiomes are known to significantly affect plant health, but there are significant knowledge gaps concerning epidemics of cereal virus diseases at the microbiome-wide scale under a variety of environmental and biological factors.

RESULTS

Here, we characterize the diversity and composition of rice (Oryza sativa) root-associated bacterial communities after infection by an insect-transmitted reovirus, rice black-streaked dwarf virus (RBSDV, genus Fijivirus, family Spinareoviridae), by sequencing the bacterial 16S rRNA gene amplified fragments from 1240 samples collected at a consecutive 3-year field experiment. The disease incidences gradually decreased from 2017 to 2019 in both Langfang (LF) and Kaifeng (KF). BRSDV infection significantly impacted the bacterial community in the rice rhizosphere, but this effect was highly susceptible to both the rice-intrinsic and external conditions. A greater correlation between the bacterial community in the rice rhizosphere and those in the root endosphere was found after virus infection, implying a potential relationship between the rice-intrinsic conditions and the rhizosphere bacterial community. The discrepant metabolites in rhizosphere soil were strongly and significantly correlated with the variation of rhizosphere bacterial communities. Glycerophosphates, amino acids, steroid esters, and triterpenoids were the metabolites most closely associated with the bacterial communities, and they mainly linked to the taxa of Proteobacteria, especially Rhodocyclaceae, Burkholderiaceae, and Xanthomonadales. In addition, the greenhouse pot experiments demonstrated that bulk soil microbiota significantly influenced the rhizosphere and endosphere communities and also regulated the RBSDV-mediated variation of rhizosphere bacterial communities.

CONCLUSIONS

Overall, this study reveals unprecedented spatiotemporal dynamics in rhizosphere bacterial communities triggered by RBSDV infection with potential implications for disease intermittent outbreaks. The finding has promising implications for future studies exploring virus-mediated plant-microbiome interactions. Video Abstract.

Fusarium as potential pathogenic fungus of Ginger (Zingiber officinale Roscoe) wilt disease

The wilt disease of ginger, caused by various Fusarium species, imperils the cultivation of this valuable crop. However, the pathogenic mechanisms and epidemiology of ginger wilt remain elusive. Here, we investigate the association between ginger rhizome health and the prevalence of Fusarium conidia, as well as examine fungal community composition in symptomatic and asymptomatic ginger tissues. Our findings show that diseased rhizomes have reduced tissue firmness, correlating negatively with Fusarium conidia counts. Pathogenicity assays confirmed that both Fusarium oxysporum and Fusarium solani are capable of inducing wilt symptoms in rhizomes and sterile seedlings. Furthermore, Fungal community profiling revealed Fusarium to be the dominant taxon across all samples, yet its relative abundance was significantly different between symptomatic and asymptomatic tissues. Specifically, there is a higher incidence of Fusarium amplicon sequence variants (ASVs) in symptomatic above-ground parts. Our results unequivocally implicate F. oxysporum or F. solani as the etiological agents responsible for ginger wilt and demonstrate that Fusarium is the principal fungal pathogen associated with this disease. These findings provide critical insights for efficacious disease management practices within the ginger industry.

Distinct biogeographic patterns for bacteria and fungi in association with Bursaphelenchus xylophilus nematodes and infested pinewood

Pinewood nematodes (PWN, Bursaphelenchus xylophilus) are destructive plant parasitic nematodes that cause pine wilt disease (PWD) by attacking the vascular systems of pine trees, resulting in widespread tree mortality. Research has shown that there are connections between nematode-associated microbes and PWD. Yet the variations in microbial communities across different geographic regions are not well-understood. In this study, we examined the bacterial and fungal communities associated with nematodes and infested wood collected from 34 sites across three vegetation zones in China, as well as samples from the United States, using 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing. The predominant genera Pseudomonas and Rhodococcus were found in nematodes, and Acinetobacter was present in the wood of PWD-infected pine trees across China. Network analysis revealed that core bacterial taxa belonged to the Pseudomonadota and Actinomycetota phyla for the nematodes, whereas the Pseudomonadota and Bacteroidota phyla were dominant in the infested wood. Identification of enriched key microbial taxa in nematodes and infested wood across vegetation zones indicates distinct biogeographic microbial community structures and key bacterial species. Although the nematode-associated bacterial community showed consistency across geographic distances, the similarity of the PWD pine trees' bacterial community decreased with distance, suggesting a spatial correlation with environmental variables. Our findings enhance our understanding of the microbiota associated with pinewood nematode (PWN) and offer valuable insights into PWD management.

IMPORTANCE

Our research uncovered specific bacteria and fungi linked to pinewood nematode (PWN) and infested wood in three different vegetation zones in China, as well as samples from the United States. This sheds light on the critical roles of certain microbial groups, such as Pseudomonas, Acinetobacter, and Stenotrophomonas, in influencing PWN fitness. Understanding these patterns provides valuable insights into the dynamics of PWN-associated microbiomes, offering potential strategies for managing pine wilt disease (PWD). We found significant correlations between geographic distance and similarity in bacterial communities in the infested wood, indicating a spatial influence on wood-associated microbial communities due to limited dispersal and localized environmental conditions. Further investigations of these spatial patterns and driving forces are crucial for understanding the ecological processes that shape microbial communities in complex ecosystems and, ultimately, for mitigating the transmission of PWN in forests.

Bacterial community composition of wheat aboveground compartments correlates with yield during the reproductive phase

Plant-associated microbial communities play important roles in agricultural productivity, and their composition has been shown to vary across plant compartments and developmental stages. However, the response of microbial communities within different plant compartments and at different developmental stages to diverse long-term fertilization treatments, as well as their linkages with crop yields, remains underexplored. This study analyzed wheat-associated bacterial communities within various soil and plant compartments under three fertilization treatments throughout the vegetative and reproductive phases. The variance in bacterial community was primarily attributed to compartments, followed by fertilization treatments and developmental stages. The composition of belowground bacterial communities (bulk soil, rhizosphere soil, and root) exhibited stronger responses to fertilization treatments than aboveground compartments (stem and leaf). The composition of belowground bacterial communities responded to fertilization treatments at all developmental stages, and it was significantly correlated with crop yields during the vegetative phase, whereas the aboveground community composition only showed a response to fertilization during the reproductive phase, at which point it was significantly correlated with crop yields. Moreover, during this reproductive phase, the co-occurrence network of aboveground bacterial communities exhibited enhanced complexity, and it contained an increased number of keystone species associated with crop yields, such as Sphingomonas spp., Massilia spp., and Frigoribacterium spp. Structural equation modeling indicated that augmenting total phosphorus levels in aboveground compartments could enhance crop yields by increasing the relative abundance of these keystone species during the reproductive phase. These findings highlight the pivotal role of aboveground bacterial communities in wheat production during the reproductive phase.

IMPORTANCE

The developmental stage significantly influences crop-associated bacterial communities, but the relative importance of bacterial communities in different compartments to crop yields across various stages is still not well understood. This study reveals that belowground bacterial communities during the vegetative phase are significantly correlated with crop yields. Notably, during the reproductive phase, the composition of aboveground bacterial communities was significantly correlated with crop yields. During this phase, the complexity and enriched keystone species within the aboveground co-occurrence network underscore their role in boosting crop production. These results provide a foundation for developing microbiome-based products that are phase-specific and promote sustainable agricultural practices.

Biochar promotes compost humification by regulating bacterial and fungal communities

Introduction

Humus can be formed during composting through biological pathways, nonetheless, the mechanisms through which bacterial and fungal communities govern the development of humus in compost with the addition of biochar remain uncertain.

Methods

In this study, compost with cow dung and maize stover as feedstock was employed as a control group, and compost with 10% biochar added on top of the feedstock was adopted as a treatment group to investigate the effect of bacterial and fungal communities on humus formation during biochar composting.

Results and Discussion

The results demonstrated that the humic acid content increased by 24.82 and 25.10% at the cooling and maturation stages, respectively, after adding biochar. Besides, the degree of polymerization content in the maturation stage was elevated by 90.98%, which accelerated the humification process of the compost. During the thermophilic and maturity stages, there was a respective increase of 51.34 and 31.40% in reducing sugar content, suggesting that the inclusion of biochar could furnish ample reducing sugar substrate for the Maillard reaction. The addition of biochar reduced the number of humus precursor-associated genera by 35, increased the number of genera involved in humus synthesis by two, and enhanced the stability of the cross-domain network between bacteria and fungi, which confirms that microorganisms contribute to the humification process by decreasing humus precursor consumption as well as increasing humus synthesis with the addition of biochar. Additionally, adding biochar could enhance the humification capacity of the compost pile by dominating the Maillard reaction with reducing sugars as the substrate and strengthening the function of humus synthesis-associated genera. This study enhances our comprehension of the regulatory pathways of biochar in the humification process during composting.

Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles

BACKGROUND

Plants have evolved various defense mechanisms against insect herbivores, including the formation of physical barriers, the synthesis of toxic metabolites, and the activation of phytohormone responses. Although plant-associated microbiota influence plant growth and health, whether they play a role in plant defense against insect pests in natural ecosystems is unknown.

RESULTS

Here, we show that leaves of beetle-damaged weeping willow (Salix babylonica) trees are more resistant to the leaf beetle Plagiodera versicolora (Coleoptera) than those of undamaged leaves. Bacterial community transplantation experiments demonstrated that plant-associated microbiota from the beetle-damaged willow contribute to the resistance of the beetle-damaged willow to P. versicolora. Analysis of the composition and abundance of the microbiome revealed that Pseudomonas spp. is significantly enriched in the phyllosphere, roots, and rhizosphere soil of beetle-damaged willows relative to undamaged willows. From a total of 49 Pseudomonas strains isolated from willows and rhizosphere soil, we identified seven novel Pseudomonas strains that are toxic to P. versicolora. Moreover, re-inoculation of a synthetic microbial community (SynCom) with these Pseudomonas strains enhances willow resistance to P. versicolora.

CONCLUSIONS

Collectively, our data reveal that willows can exploit specific entomopathogenic bacteria to enhance defense against P. versicolora, suggesting that there is a complex interplay among plants, insects, and plant-associated microbiota in natural ecosystems.

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.

Applicability of metabolomics to improve sustainable grapevine production

Metabolites represent the end product of gene expression, protein interaction and other regulatory mechanisms. The metabolome reflects a biological system's response to genetic and environmental changes, providing a more accurate description of plants' phenotype than the transcriptome or the proteome. Grapevine (Vitis vinifera L.), established for the production of wine grapes, table grapes, and raisins, holds immense agronomical and economic significance not only in the Mediterranean region but worldwide. As all plants, grapevines face the adverse impact of biotic and abiotic stresses that negatively affect multiple stages of grape and wine industry, including plant and berry development pre- and post-harvest, fresh grapes processing and consequently wine quality. In the present review we highlight the applicability of metabolome analysis in the understanding of the mechanisms involved in grapevine response and acclimatization upon the main biotic and abiotic constrains. The metabolome of induced morphogenic processes such as adventitious rooting and somatic embryogenesis is also explored, as it adds knowledge on the physiological and molecular phenomena occurring in the explants used, and on the successfully propagation of grapevines with desired traits. Finally, the microbiome-induced metabolites in grapevine are discussed in view of beneficial applications derived from the plant symbioses.

Role of bacterial pathogens in microbial ecological networks in hydroponic plants

Plant-associated microbial communities are crucial for plant growth and health. However, assembly mechanisms of microbial communities and microbial interaction patterns remain elusive across vary degrees of pathogen-induced diseases. By using 16S rRNA high-throughput sequencing technology, we investigated the impact of wildfire disease on the microbial composition and interaction network in plant three different compartments. The results showed that pathogen infection significantly affect the phyllosphere and rhizosphere microbial community. We found that the primary sources of microbial communities in healthy and mildly infected plants were from the phyllosphere and hydroponic solution community. Mutual exchanges between phyllosphere and rhizosphere communities were observed, but microbial species migration from the leaf to the root was rarely observed in severely infected plants. Moreover, wildfire disease reduced the diversity and network complexity of plant microbial communities. Interactions among pathogenic bacterial members suggested that Caulobacter and Bosea might be crucial "pathogen antagonists" inhibiting the spread of wildfire disease. Our study provides deep insights into plant pathoecology, which is helpful for the development of novel strategies for phyllosphere disease prediction or prevention.

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.

Differential responses of soil bacteria, fungi and protists to root exudates and temperature

The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.

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.

Pathogen-driven Pseudomonas reshaped the phyllosphere microbiome in combination with Pseudostellaria heterophylla foliar disease resistance via the release of volatile organic compounds

BACKGROUND

Continuous monocropping obstacles are common in plants, especially medicinal plants, resulting in disease outbreaks and productivity reductions. Foliar disease, mainly caused by Fusarium oxysporum, results in a severe decrease in the yield of Pseudostellaria heterophylla annually. Determining an effective biomethod to alleviate this disease is urgently needed to improve its productivity and quality.

RESULTS

This study screened thirty-two keystone bacterial genera induced by pathogens in P. heterophylla rhizosphere soil under continuous monocropping conditions. Pseudomonas, Chryseobacterium, and Flavobacterium, referred to as the beneficial microbiota, were significantly attracted by pathogen infection. The P. palleroniana strain B-BH16-1 can directly inhibit the growth and spore formation of seven primary pathogens of P. heterophylla foliar disease by disrupting fusaric acid production via the emission of volatile organic compounds (VOCs). In addition, strain B-BH16-1 enhances the disease resistance of P. heterophylla by obliterating the pathogen and assembling beneficial microbiota.

CONCLUSION

Pathogen-induced Pseudomonas reshaped phyllosphere microbial communities via direct antagonism of pathogens and indirect disruption of the pathogen virulence factor biosynthesis to enhance disease suppression and improve yields. These results show that inhibiting pathogen virulence biosynthesis to reshape the plant microbial community using disease-induing probiotics will be an innovative strategy for managing plant disease, especially under continuous monoculture conditions.

Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot

BACKGROUND

Microbes colonizing each compartment of terrestrial plants are indispensable for maintaining crop health. Although corn stalk rot (CSR) is a severe disease affecting maize (Zea mays) worldwide, the mechanisms underlying host-microbe interactions across vertical compartments in maize plants, which exhibit heterogeneous CSR-resistance, remain largely uncharacterized.

RESULTS

Here, we investigated the microbial communities associated with CSR-resistant and CSR-susceptible maize cultivars using multi-omics analysis coupled with experimental verification. Maize cultivars resistant to CSR reshaped the microbiota and recruited Bacillus species with three phenotypes against Fusarium graminearum including niche pre-emption, potential secretion of antimicrobial compounds, and no inhibition to alleviate pathogen stress. By inducing the expression of Tyrosine decarboxylase 1 (TYDC1), encoding an enzyme that catalyzes the production of tyramine and dopamine, Bacillus isolates that do not directly suppress pathogen infection induced the synthesis of berberine, an isoquinoline alkaloid that inhibits pathogen growth. These beneficial bacteria were recruited from the rhizosphere and transferred to the stems but not grains of the CSR-resistant plants.

CONCLUSIONS

The current study offers insight into how maize plants respond to and interact with their microbiome and lays the foundation for preventing and treating soil-borne pathogens. Video Abstract.

The Mechanisms of Cadmium Stress Mitigation by Fungal Endophytes from Maize Grains

Maize is a crucial staple crop that ensures global food security by supplying essential nutrients. However, heavy metal (HM) contamination inhibits maize growth, reduces output, and affects food security. Some endophytic fungi (EFs) in maize seeds have the potential to enhance growth and increase dry biomass, offering a solution to mitigate the negative effect of HM contamination. Using these functional EFs could help maintain crop production and ensure food safety in HM-contaminated areas. In the present study, the diversity of EFs in corn grains from various HM-contaminated areas in China was studied through culture-dependent and culture-independent methods. We tested the plant growth-promoting (PGP) traits of several dominant culturable isolates and evaluated the growth-promoting effects of these twenty-one isolates through pot experiments. Both studies showed that HM contamination increased the diversity and richness of corn grain EFs and affected the most dominant endophytes. Nigrospora and Fusarium were the most prevalent culturable endophytes in HM-contaminated areas. Conversely, Cladosporium spp. were the most isolated endophytes in non-contaminated areas. Different from this, Saccharomycopsis and Fusarium were the dominant EFs in HM-contaminated sites, while Neofusicoccum and Sarocladium were dominant in non-contaminated sites, according to a culture-independent analysis. PGP trait tests indicated that 70% of the tested isolates (forty-two) exhibited phosphorus solubilization, IAA production, or siderophore production activity. Specifically, 90% of the tested isolates from HM-contaminated sites showed better PGP results than 45% of the isolates from non-contaminated sites. The benefit of the twenty-one isolates on host plant growth was further studied through pot experiments, which showed that all the isolates could improve host plant growth. Among them, strains derived from HM-contaminated sites, including AK18 (Nigrospora), AK32 (Beauveria), SD93 (Gibberellia), and SD64 (Fusarium), had notable effects on enhancing the dry biomass of shoots and roots of maize under Cd stress. We speculate that the higher ratio of PGP EFs in corn grains from HM-contaminated areas may explain their competitiveness in such extreme environments. Fusarium and Cladosporium isolates show high PGP properties, but they can also be phytopathogenic. Therefore, it is essential to evaluate their pathogenic properties and safety for crops before considering their practical use in agriculture.

The impact of filamentous plant pathogens on the host microbiota

When a pathogen invades a plant, it encounters a diverse microbiota with some members contributing to the health and growth of the plant host. So far, the relevance of interactions between pathogens and the plant microbiota are poorly understood; however, new lines of evidence suggest that pathogens play an important role in shaping the microbiome of their host during invasion. This review aims to summarize recent findings that document changes in microbial community composition during the invasion of filamentous pathogens in plant tissues. We explore the known mechanisms of interaction between plant pathogens and the host microbiota that underlie these changes, particularly the pathogen-encoded traits that are produced to target specific microbes. Moreover, we discuss the limitations of current strategies and shed light on new perspectives to study the complex interaction networks between filamentous pathogens and the plant microbiome.

Streptomyces-Secreted Fluvirucin B6 as a Potential Bio-Fungicide for Managing Banana Fusarium Wilt and Mycotoxins and Modulating the Soil Microbial Community Structure

Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc TR4) is the most destructive soil-borne fungal disease. Until now, there has been a lack of effective measures to control the disease. It is urgent to explore biocontrol agents to control Foc TR4 and the secretion of mycotoxin. In this study, fluvirucin B6 was screened from Streptomyces solisilvae using an activity-guided method. Fluvirucin B6 exhibited strong antifungal activity against Foc TR4 (0.084 mM of EC50 value) and significantly inhibited mycelial growth and spore germination. Further studies demonstrated that fluvirucin B6 could cause the functional loss of mitochondria, the disorder of metabolism of Foc TR4 cells, and the decrease of enzyme activities in the tricarboxylic acid cycle and electron transport chain, ultimately inhibiting mycotoxin metabolism. In a pot experiment, the application of fluvirucin B6 significantly decreased the incidence of banana Fusarium wilt and the amount of Foc TR4 and controlled fungal toxins in the soil. Additionally, fluvirucin B6 could positively regulate the changes in the structure of the banana rhizosphere microbial community, significantly enriching beneficial microbes associated with disease resistance. In summary, this study identifies fluvirucin B6, which plays versatile roles in managing fungal diseases and mycotoxins.

Immune-enriched phyllosphere microbiome in rice panicle exhibits protective effects against rice blast and rice false smut diseases

Activation of immune responses leads to an enrichment of beneficial microbes in rice panicle. We therefore selected the enriched operational taxonomy units (OTUs) exhibiting direct suppression effects on fungal pathogens, and established a simplified synthetic community (SynCom) which consists of three beneficial microbes. Application of this SynCom exhibits protective effect against fungal pathogen infection in rice.

Harnessing co-evolutionary interactions between plants and Streptomyces to combat drought stress

Streptomyces is a drought-tolerant bacterial genus in soils, which forms close associations with plants to provide host resilience to drought stress. Here we synthesize the emerging research that illuminates the multifaceted interactions of Streptomyces spp. in both plant and soil environments. It also explores the potential co-evolutionary relationship between plants and Streptomyces spp. to forge mutualistic relationships, providing drought tolerance to plants. We propose that further advancement in fundamental knowledge of eco-evolutionary interactions between plants and Streptomyces spp. is crucial and holds substantial promise for developing effective strategies to combat drought stress, ensuring sustainable agriculture and environmental sustainability in the face of climate change.

Exploring the Influence of Date Palm Cultivars on Soil Microbiota

Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses.

Dazomet fumigation modification of the soil microorganism community and promotion of Panax notoginseng growth

Introduction

Panax notoginseng, a medicinal herb in China, is attacked by several pathogens during its cultivation. Dazomet (DZ) is a soil fumigant that is effective in controlling soil-borne pathogens, but its long-term effects on P. notoginseng growth and soil properties are unknown.

Methods

We conducted field experiments over two consecutive years to assess the impact of three concentrations of DZ fumigation (35 kg/666.7 m2, 40 kg/666.7 m2, and 45 kg/666.7 m2) on soil physicochemical properties, microbial diversity, and P. notoginseng growth. Correlation analyses were performed between microbial community changes and soil properties, and functional predictions for soil microorganisms were conducted.

Results

DZ fumigation increased total nitrogen, total phosphorus, total potassium, available phosphorus, available potassium, and ammonia nitrogen levels in the soil. DZ fumigation promoted the nutrient accumulation and improvement of agronomic traits of P. notoginseng, resulted in a 2.83-3.81X yield increase, with the highest total saponin content increasing by 24.06%. And the 40 kg/666.7 m2 treatment had the most favorable impact on P. notoginseng growth and saponin accumulation. After DZ fumigation, there was a decrease in the relative abundance of pathogenic fungi such as Fusarium, Plectosphaerella, and Ilyonectria, while beneficial bacteria such as Ramlibacter, Burkholderia, and Rhodanobacteria increased. The effects of fumigation on soil microorganisms and soil physicochemical properties persisted for 18 months post-fumigation. DZ fumigation enhanced the relative abundance of bacteria involved in the biosynthesis of secondary metabolites and arbuscular mycorrhizal fungi, reduced the relative abundance of plant-animal pathogenic fungi, reduced the occurrence of soil-borne diseases.

Conclusion

In conclusion, DZ fumigation enhanced soil physicochemical properties, increased the proportion of beneficial bacteria in the soil, and rebalanced soil microorganism populations, consequently improving the growth environment of P. notoginseng and enhancing its growth, yield, and quality. This study offers a theoretical foundation for DZ fumigation as a potential solution to the continuous cropping issue in perennial medicinal plants such as P. notoginseng.

Ecological processes of bacterial microbiome assembly in healthy and dysbiotic strawberry farms

The bacterial microbiome plays crucial role in plants' resistance to diseases, nutrient uptake and productivity. We examined the microbiome characteristics of healthy and unhealthy strawberry farms, focusing on soil (bulk soil, rhizosphere soil) and plant (roots and shoots). The relative abundance of most abundant taxa were correlated with the chemical soil properties and shoot niche revealed the least amount of significant correlations between the two. While alpha and beta diversities did not show differences between health groups, we identified a number of core taxa (16-59) and marker bacterial taxa for each healthy (Unclassified Tepidisphaerales, Ohtaekwangia, Hydrocarboniphaga) and dysbiotic (Udaeobacter, Solibacter, Unclassified Chitinophagales, Unclassified Nitrosomonadaceae, Nitrospira, Nocardioides, Tardiphaga, Skermanella, Pseudomonas, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Curtobacterium) niche. We also revealed selective pressure of strawberry rhizosphere soil and roots plants in unhealthy plantations increased stochastic ecological processes of bacterial microbiome assembly in shoots. Our findings contribute to understanding sustainable agriculture and plant-microbiome interactions.

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.

Enhancement of nitrogen on core taxa recruitment by Penicillium oxalicum stimulated microbially-driven soil formation in bauxite residue

Microbially-driven soil formation process is an emerging technology for the ecological rehabilitation of alkaline tailings. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. Herein, a 1-year field-scale experiment was applied to demonstrate the effect of nitrogen input on the structure and function of the microbiome in alkaline bauxite residue. Results showed that the contents of nutrient components were increased with Penicillium oxalicum (P. oxalicum) incorporation, as indicated by the increasing of carbon and nitrogen mineralization and enzyme metabolic efficiency. Specifically, the increasing enzyme metabolic efficiency was associated with nitrogen input, which shaped the microbial nutrient acquisition strategy. Subsequently, we evidenced that P. oxalicum played a significant role in shaping the assemblages of core bacterial taxa and influencing ecological functioning through intra- and cross-kingdom network analysis. Furthermore, a recruitment experiment indicated that nitrogen enhanced the enrichment of core microbiota (Nitrosomonas, Bacillus, Pseudomonas, and Saccharomyces) and may provide benefits to fungal community bio-diversity and microbial network stability. Collectively, these results demonstrated nitrogen-based coexistence patterns among P. oxalicum and microbiome and revealed P. oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. It will aid in promoting soil formation and ecological rehabilitation of bauxite residue. ENVIRONMENT IMPLICATION: Bauxite residue is a highly alkaline solid waste generated during the Bayer process for producing alumina. Attempting to transform bauxite residue into a stable soil-like substrate using low-cost microbial resources is a highly promising engineering. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. In this study, we evidenced the nitrogen-based coexistence patterns among Penicillium oxalicum and microbiome and revealed Penicillium oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. This study can improve the understanding of core microbes' assemblies that affect the microbiome physiological traits in soil formation processes.

Status of Cassava Witches' Broom Disease in the Philippines and Identification of Potential Pathogens by Metagenomic Analysis

Cassava witches' broom disease (CWBD) is one of the most devastating diseases of cassava (Manihot esculenta Crantz), and it threatens global production of the crop. In 2017, a phytoplasma, Candidatus Phytoplasma luffae (Ca. P. luffae), was reported in the Philippines, and it has been considered as the causal agent, despite unknown etiology and transmission of CWBD. In this study, the nationwide occurrence of CWBD was assessed, and detection of CWBD's pathogen was attempted using polymerase chain reaction (PCR) and next-generation sequencing (NGS) techniques. The results showed that CWBD has spread and become severe, exhibiting symptoms such as small leaf proliferation, shortened internodes, and vascular necrosis. PCR analysis revealed a low phytoplasma detection rate, possibly due to low titer, uneven distribution, or absence in the CWBD-symptomatic cassava. In addition, NGS techniques confirm the PCR results, revealing the absence or extremely low phytoplasma read counts, but a surprisingly high abundance of fastidious and xylem-limited fungus, Ceratobasidium sp. in CWBD-symptomatic plants. These findings cast doubt over the involvement of phytoplasma in CWBD and instead highlight the potential association of Ceratobasidium sp., strongly supporting the recent findings in mainland Southeast Asia. Further investigations are needed to verify the etiology of CWBD and identify infection mechanisms of Ceratobasidium sp. to develop effective diagnostic and control methods for disease management.

Comparative Metagenomic Analysis Reveals Rhizosphere Microbiome Assembly and Functional Adaptation Changes Caused by Clubroot Disease in Chinese Cabbage

Clubroot is a major disease and severe threat to Chinese cabbage, and it is caused by the pathogen Plasmodiophora brassicae Woron. This pathogen is an obligate biotrophic protist and can persist in soil in the form of resting spores for more than 18 years, which can easily be transmitted through a number of agents, resulting in significant economic losses to global Chinese cabbage production. Rhizosphere microbiomes play fundamental roles in the occurrence and development of plant diseases. The changes in the rhizosphere microorganisms could reveal the severity of plant diseases and provide the basis for their control. Here, we studied the rhizosphere microbiota after clubroot disease infections with different severities by employing metagenomic sequencing, with the aim of exploring the relationships between plant health, rhizosphere microbial communities, and soil environments; then, we identified potential biomarker microbes of clubroot disease. The results showed that clubroot disease severity significantly affected the microbial community composition and structure of the rhizosphere soil, and microbial functions were also dramatically influenced by it. Four different microbes that had great potential in the biocontrol of clubroot disease were identified from the obtained results; they were the genera Pseudomonas, Gemmatimonas, Sphingomonas, and Nocardioides. Soil pH, organic matter contents, total nitrogen, and cation exchange capacity were the major environmental factors modulating plant microbiome assembly. In addition, microbial environmental information processing was extremely strengthened when the plant was subjected to pathogen invasion, but weakened when the disease became serious. In particular, oxidative phosphorylation and glycerol-1-phosphatase might have critical functions in enhancing Chinese cabbage's resistance to clubroot disease. This work revealed the interactions and potential mechanisms among Chinese cabbage, soil environmental factors, clubroot disease, and microbial community structure and functions, which may provide a novel foundation for further studies using microbiological or metabolic methods to develop disease-resistant cultivation technologies.

Kiwifruit resistance to gray mold is enhanced by yeast-induced modulation of the endophytic microbiome

The influence of endophytic microbial community on plant growth and disease resistance is of considerable importance. Prior research indicates that pre-treatment of kiwifruit with the biocontrol yeast Debaryomyces hansenii suppresses gray mold disease induced by Botrytis cinerea. However, the specific underlying mechanisms remain unclear. In this study, Metagenomic sequencing was utilized to analyze the composition of the endophytic microbiome of kiwifruit under three distinct conditions: the healthy state, kiwifruit inoculated with B. cinerea, and kiwifruit treated with D. hansenii prior to inoculation with B. cinerea. Results revealed a dominance of Proteobacteria in all treatment groups, accompanied by a notable increase in the relative abundance of Actinobacteria and Firmicutes. Ascomycota emerged as the major dominant group within the fungal community. Treatment with D. hansenii induced significant alterations in microbial community diversity, specifically enhancing the relative abundance of yeast and exerting an inhibitory effect on B. cinerea. The introduction of D. hansenii also enriched genes associated with energy metabolism and signal transduction, positively influencing the overall structure and function of the microbial community. Our findings highlight the potential of D. hansenii to modulate microbial dynamics, inhibit pathogenic organisms, and positively influence functional attributes of the microbial community.

Multiple Chitin- or Avirulent Strain-Triggered Immunity Induces Microbiome Reassembly in Rice

Magnaporthe oryzae is one of the most important fungal pathogens of rice. Chitin and avirulent strains can induce two layers of immunity response, pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI), in rice with cognate R genes. However, little is known about the assembly of the rice microbiome induced by PTI and ETI in rice. In this study, we investigate the impact of continuous treatment of the avirulent M. oryzae strain with AvrPi9 and chitin on the bacterial endophytic community of rice varieties harboring resistant gene Pi9 and their antagonistic activity against rice blast fungus. Analysis of the 16S rRNA showed a significant increase in the diversity and microbial co-occurrence network complexity and the number of beneficial taxa-Bacillus, Pseudomonas, Microbacterium, and Stenotrophomonas spp.-following the chitin and avirulent strain treatments. The antifungal assay with bacterial endophytes recovered from the leaves showed few bacteria with antagonistic potential in rice treated with avirulent strains, suggesting that the sequential treatment of the avirulent strain decreased the antagonistic bacteria against M. oryzae. Moreover, we identified Bacillus safensis Ch_66 and Bacillus altitudinis Nc_68 with overall antagonistic activities in vivo and in vitro. Our findings provide a novel insight into rice microbiome assembly in response to different innate immunity reactions.

Microbial Community Shifts in Tea Plant Rhizosphere under Seawater Stress: Enrichment of Beneficial Taxa

Seawater intrusion has a significant impact on the irrigation quality of agricultural water, thereby posing a threat to plant growth and development. We hypothesized that the rhizosphere of tea plants harbors beneficial microorganisms, which may improve the tolerance of tea plants to seawater stress. This study utilized 16s and ITS techniques to analyze microbial community shifts in the tea plant rhizosphere and non-rhizosphere under seawater stress conditions. The findings suggest that seawater stress leads to a reduction in microbial diversity, although the rhizosphere microbial diversity in stressed soils showed a relatively higher level. Moreover, the rhizosphere of the tea plant under seawater stress exhibited an enrichment of plant growth-promoting rhizobacteria alongside a higher presence of pathogenic fungi. Network analysis revealed that seawater stress resulted in the construction of a more complex and stable rhizosphere microbial network compared to normal conditions. Predictions of bacterial potential functions highlighted a greater diversity of functional groups, enhancing resource utilization efficiency. In general, the rhizosphere microorganisms of tea plants are jointly selected by seawater and the host. The microorganisms closely related to the rhizosphere of tea plants are retained and, at the same time, attract beneficial microorganisms that may alleviate stress. These findings provide new insights into plant responses to saline stress and have significant implications for leveraging vegetation to enhance the resilience of coastal saline soils and contribute to economic progress.

Temporal heterogeneity of the root microbiome in Panax ginseng soils across ecological compartments under mild soil disturbance

Introduction

Knowledge on spatiotemporal heterogeneity of plant root microbiomes is lacking. The diversity of the root microbiome must be revealed for understanding plant-microbe interactions and the regulation of functionally crucial microbial taxa.

Methods

We here investigated the dynamics of microbial group characteristics within each soil ecological compartment [rhizoplane (B), rhizosphere (J), and bulk soil (T)] across different cultivation years (year 4: F4 and year 5: F5) by using high-throughput sequencing (16S and ITS).

Results

According to the species diversity, microbiome diversity and the ASV (amplified sequence variant) number in the rhizoplane ecotone increased significantly with an increase in the planting years. By contrast, the microbiome diversity of the rhizosphere soil remained relatively stable. PCoA and PERMANOVA analyses revealed that microbial taxa among different planting years and ecological compartments varied significantly. Planting years exerted the least effect on the rhizosphere microbiome, but their impact on fungi in the rhizoplane and bacteria in the bulk soil was the most significant.

Discussion

Planting years influenced the microbial community composition in various ecological compartments of ginseng root soil. Potentially harmful fungi such as Cryptococcus (2.83%), Neonectria (0.89%), llyonectria (0.56%), Gibberella (0.41%), Piloderma (4.44%), and Plectosphaerella (3.88%) were enriched in F5B with an increase in planting years, whereas the abundance of potentially beneficial Mortierella increased. Correlation analysis indicated associations between bacterial taxa and soil pH/S-CAT, and between fungal taxa and soil moisture content/total potassium. Our study highlights the significance of changes in rhizoplane fungi and the stability of the rhizosphere microbial community in comprehending plant ecological sustainability.

Highly diverse microbial community of regenerated seedlings reveals the high capacity of the bulb in lily, Lilium brownii

Lily bulbs, which have both nutrient storage and reproductive functions, are a representative group of plants for studying the maintenance and transfer of plant-associated microbiomes. In this study, a comparison of the microbial composition of bulbs and their regenerated seedlings cultured under aseptic conditions, as well as subcultured seedlings that succeeded five times, was examined by amplicon sequencing. A total of 62 bacterial taxa and 56 fungal taxa were found to be transferred to the 5th generation in seedlings, which are the core microbiome of lily. After the regeneration of seedlings from bulbs, there was a significant increase in the number of detectable microbial species, and after 1, 3, and 5 successive generations, there was a decrease in the number of detectable species. Interestingly, some "new" microorganisms appeared in each generation of samples; for instance, 167 and 168 bacterial operational taxonomic units (OTUs) in the 3rd and 5th generations of seedlings that were not detected in either bulbs or seedlings of the previous two generations. These results suggest that bulbs can maintain a high diversity of microorganisms, including some with ultra-low abundance, and have a high transfer capacity to tuck shoots through continuous subculture. The diversity and maintenance of the microbiome can provide the necessary microbial reservoir support for regenerating seedlings. This habit of maintaining low abundance and high diversity may be biologically and ecologically critical for maintaining microbiome stability and function due to the sequestration nature of the plant.

Dataset of core and differentially abundant bacteria in various compartments of farm-cultivated and home-planted chilli plants (Capsicum frutescens)

Chillies are members of the genus Capsicum L. (family Solanaceae). They are native to Central and South America and consist of approximately 35 species [1,2]. Among these, five species (C. annuum L., C. baccatum L., C. chinense Jacq., C. frutescens L., and C. pubescens Ruiz & Pav.) have been domesticated and are mainly cultivated for consumption as vegetables and spices. Of the domesticated chillies, C. annuum is commercially cultivated worldwide, while C. frutescens and C. chinense are mainly cultivated in American, Asian, and African countries [3]. We compared the diversity of microbiota in various compartments of farm-cultivated (FC) and home-planted (HP) chilli plants (Capsicum frutescens). Targeted 16S rRNA gene (V5-V6 region) was sequenced using the Illumina NovaSeq 6000 platform. Proteobacteria, Actinobacteriota, Acidobacteriota, Gemmatimonadota, Bacteroidota, and Firmicutes were present in all compartments of both the FC and HP plants. Proteobacteria (or Pseudomonadota) was the predominant phylum in all the compartments of both HP and FC plants, while Actinobacteriota (or Actinomycetota) was the second most abundant phylum. Most plant compartments (leaves, fruits and roots) exhibited a higher relative abundance of Proteobacteria compared to the soil samples. With few exceptions, the soil compartments (bulk and rhizospheric soils) displayed a higher relative abundance of the phyla Myxococcota, Acidobacteriota, Gemmatimonadota, Bacteroidota, Nitrospirota, Verrucomicrobiota, and Firmicutes than the plant compartments. Diversity indices revealed that the bacterial community in chili plants clustered based on both compartment and cultivation area.

Potential Biocontrol Microorganisms Causing Attenuated Pathogenicity in Plasmopara viticola

A phenomenon of pathogenicity attenuation of Plasmopara viticola was consistently observed during its subculture on grape. To clarify the causes of attenuated pathogenicity of P. viticola, culturable microbes were isolated from the P. viticola mass (mycelia, sporangiophores, and sporangia) in each generation and tested for their biocontrol efficacies on grape downy mildew (GDM). The results showed that the incidence of GDM decreased with the increase in the number of subculture times on both vineyard-collected leaves and grape leaves from in vitro-grown seedlings. The number of culturable microbial taxa on the surface of P. viticola decreased, whereas the population densities of four specific strains (i.e., K2, K7, P1, and P5) increased significantly with the increase in subculture times. Compared with the control, the biocontrol efficacies of the bacterial strain K2 reached 87.5%, and those of both fungal strains P1 and P5 reached 100.0%. Based on morphological characteristics and molecular sequences, strains K2, P1, and P5 were identified as Curtobacterium herbarum, Thecaphora amaranthi, and Acremonium sclerotigenum, respectively, and these three strains survived very well and multiplied on the surface of P. viticola. As the number of times P. viticola was subcultured increased, all three of these strains became the predominant strains, leading to greater P. viticola inhibition, attenuated P. viticola pathogenicity, and effective GDM biological control. To the best of our knowledge, this is the first report of C. herbarum and T. amaranthi having biological control activity against GDM.

Plants attacked above-ground by leaf-mining flies change below-ground microbiota to enhance plant defense

Root-associated microbiomes play a crucial role in plant responses to biotic and abiotic stresses. Plants can enrich beneficial microbes to increase their stress-relieving ability. Above-ground insect herbivory is among the most detrimental stresses for plants, especially to crop production. However, few studies have explored how root-associated microbiomes respond to herbivores and influence plant-defense functions under herbivory stress. We investigate the changes and functional role of root-associated microbial communities under herbivory stress using leafminer (Liriomyza trifolii) and cowpea (Vigna unguiculata) as a focal system. We did this by using a combination of 16S ribosomal RNA gene profiling and metagenomic sequencing to test for differences in co-occurrence networks and functions between cowpea plants infested and noninfested with leafminers. The results demonstrated that leafminer infestation caused a shift in the rhizosphere microbiome, which was characterized by a significant variation in microbiome community structure and composition, the selection of hub microbes involved in nitrogen (N) metabolism, and functional enrichment related to N metabolism. Notably, nitrogen-fixing bacteria Bradyrhizobium species were actively enriched and selected to be hubs in the rhizosphere. Inoculation with Bradyrhizobium enhanced cowpea performance under leafminer stress and increased protease inhibitor levels to decrease leafminer fitness. Overall, our study characterized the changes of root-associated microbiota between leafminer-infested and noninfested cowpea plants and revealed the mechanisms underlying the rhizosphere microbiome shift that enhance plant performance and defense against herbivory. Our findings provide further support for the notion that plants enrich rhizosphere microbes to counteract aboveground insect herbivores.

Interpretable machine learning decodes soil microbiome's response to drought stress

BACKGROUND

Extreme weather events induced by climate change, particularly droughts, have detrimental consequences for crop yields and food security. Concurrently, these conditions provoke substantial changes in the soil bacterial microbiota and affect plant health. Early recognition of soil affected by drought enables farmers to implement appropriate agricultural management practices. In this context, interpretable machine learning holds immense potential for drought stress classification of soil based on marker taxa.

RESULTS

This study demonstrates that the 16S rRNA-based metagenomic approach of Differential Abundance Analysis methods and machine learning-based Shapley Additive Explanation values provide similar information. They exhibit their potential as complementary approaches for identifying marker taxa and investigating their enrichment or depletion under drought stress in grass lineages. Additionally, the Random Forest Classifier trained on a diverse range of relative abundance data from the soil bacterial micobiome of various plant species achieves a high accuracy of 92.3 % at the genus rank for drought stress prediction. It demonstrates its generalization capacity for the lineages tested.

CONCLUSIONS

In the detection of drought stress in soil bacterial microbiota, this study emphasizes the potential of an optimized and generalized location-based ML classifier. By identifying marker taxa, this approach holds promising implications for microbe-assisted plant breeding programs and contributes to the development of sustainable agriculture practices. These findings are crucial for preserving global food security in the face of climate change.

Temporal patterns of endophytic microbial heterogeneity across distinct ecological compartments within the Panax ginseng root system following deforestation for cultivation

Alterations in the microbial community significantly impact the yield and quality of ginseng. Yet, the dynamics of microbial community shifts within the root endophytes of ginseng across varying cultivation periods remain inadequately understood. This study zeroes in on the microbial community variations within the xylem (M), phloem (R), and fibrous roots (X) of ginseng during the fourth (F4) and fifth (F5) years of cultivation, aiming to bridge this research gap. We assessed soil physicochemical properties, enzyme activities, and nine individual saponins, complemented by high-throughput sequencing techniques (16S rDNA and ITS) to determine their profiles. The results showed that cultivation years mainly affected the microbial diversity of endophytic bacteria in ginseng fibrous roots compartment: the ASVs number and α-diversity Chao1 index of bacteria and fungi in F5X compartment with higher cultivation years were significantly higher than those in F4X compartment with lower cultivation years. It is speculated that the changes of fibrous roots bacterial groups may be related to the regulation of amino acid metabolic pathway. Such as D-glutamine and D-glutamate metabolism D-glutamine, cysteine and methionine metabolism regulation. The dominant bacteria in ginseng root are Proteobacteria (relative abundance 52.07-80.35%), Cyanobacteria (1.97-42.52%) and Bacteroidota (1.11-5.08%). Firmicutes (1.28-3.76%). There were two dominant phyla: Ascomycota (60.10-93.71%) and Basidiomycota (2.25-30.57%). Endophytic fungi were more closely related to soil physicochemical properties and enzyme activities. AN, TK, OP, SWC and EC were the main driving factors of endophytic flora of ginseng root. Tetracladium decreased with the increase of cultivation years, and the decrease was more significant in phloem (F4R: 33.36%, F5R: 16.48%). The relative abundance of Bradyrhizobium, Agrobacterium and Bacillus in each ecological niche increased with the increase of cultivation years. The relative abundance of Bradyrhizobium and Agrobacterium in F5X increased by 8.35 and 9.29 times, respectively, and Bacillus in F5M increased by 5.57 times. We found a variety of potential beneficial bacteria and pathogen antagonists related to ginseng biomass and saponins, such as Bradyrhizobium, Agrobacterium, Bacillus and Exophiala, which have good potential for practical application and development.

Unveiling Dominant Fungal Pathogens Associated with Root Rot of Hybrid Bermudagrass Based on Culture Dependent and Independent Methods

Hybrid bermudagrass (Cynodon dactylon × C. transvaalensis) is widely used as turf in southern and transition zones of China. From June to September in 2022, an unknown disease was consistently observed on hybrid bermudagrass in different regions of Nanjing, China, that exhibited distinct symptoms of leaf necrosis, severe root rot, and circular or irregular necrotic patches with 20- to 300-cm diameters. In this study, culture-independent and -dependent methods were used to elucidate the dominant fungal pathogens associated with the disease. Basidiomycota and Marasmiellus were shown to be the dominant phyla (51.96 to 70.60%) and genera (50.09 to 69.84%) in the symptomatic samples. A total of 128 fungal strains were isolated from symptomatic root tissues, and 40 strains representing the largest proportion (31.25%) were identified as Marasmiellus mesosporus based on the morphological characteristics, phylogenetic analysis of the ITS and LSU rDNA region, and pathogenicity testing. Temperature sensitivity tests revealed that M. mesosporus grew well at high temperatures (growth rate of 13.74 mm/day at 36°C). To our knowledge, this is the first report of M. mesosporus causing root rot disease on hybrid bermudagrass during hot summer months. The study will have important implications for the management of the disease.

Disease-induced changes in bacterial and fungal communities from plant below- and aboveground compartments

The plant microbes are an integral part of the host and play fundamental roles in plant growth and health. There is evidence indicating that plants have the ability to attract beneficial microorganisms through their roots in order to defend against pathogens. However, the mechanisms of plant microbial community assembly from below- to aboveground compartments under pathogen infection remain unclear. In this study, we investigated the bacterial and fungal communities in bulk soil, rhizosphere soil, root, stem, and leaf of both healthy and infected (Potato virus Y disease, PVY) plants. The results indicated that bacterial and fungal communities showed different recruitment strategies in plant organs. The number and abundance of shared bacterial ASVs between bulk and rhizosphere soils decreased with ascending migration from below- to aboveground compartments, while the number and abundance of fungal ASVs showed no obvious changes. Field type, plant compartments, and PVY infection all affected the diversity and structures of microbial community, with stronger effects observed in the bacterial community than the fungal community. Furthermore, PVY infection, rhizosphere soil pH, and water content (WC) contributed more to the assembly of the bacterial community than the fungal community. The analysis of microbial networks revealed that the bacterial communities were more sensitive to PVY infection than the fungal communities, as evidenced by the lower network stability of the bacterial community, which was characterized by a higher proportion of positive edges. PVY infection further increased the bacterial network stability and decreased the fungal network stability. These findings advance our understanding of how microbes respond to pathogen infections and provide a rationale and theoretical basis for biocontrol technology in promoting sustainable agriculture. KEY POINTS: • Different recruitment strategies between plant bacterial and fungal communities. • Bacterial community was more sensitive to PVY infection than fungal community. • pH and WC drove the microbial community assembly under PVY infection.

The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil-Root Continuum Niche Gradient

Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil-root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil-root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root-soil continuum.

Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress

The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.

Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review

Comprehending the structure and function of rhizobacteria components and their regulation are crucial for sustainable agricultural management. However, obtaining comprehensive species information for most bacteria in the natural environment, particularly rhizobacteria, presents a challenge using traditional culture methods. To obtain diverse and pure cultures of rhizobacteria, this study primarily reviews the evolution of rhizobacteria culturomics and associated culture methods. Furthermore, it explores new strategies for enhancing the application of culturomics, providing valuable insights into efficiently enriching and isolate target bacterial strains/groups from the environment. The findings will help improve rhizobacteria's culturability and enrich the functional bacterial library.

The Dynamic Changes of Brassica napus Seed Microbiota across the Entire Seed Life in the Field

The seed microbiota is an important component given by nature to plants, protecting seeds from damage by other organisms and abiotic stress. However, little is known about the dynamic changes and potential functions of the seed microbiota during seed development. In this study, we investigated the composition and potential functions of the seed microbiota of rapeseed (Brassica napus). A total of 2496 amplicon sequence variants (ASVs) belonging to 504 genera in 25 phyla were identified, and the seed microbiota of all sampling stages were divided into three groups. The microbiota of flower buds, young pods, and seeds at 20 days after flowering (daf) formed the first group; that of seeds at 30 daf, 40 daf and 50 daf formed the second group; that of mature seeds and parental seeds were clustered into the third group. The functions of seed microbiota were identified by using PICRUSt2, and it was found that the substance metabolism of seed microbiota was correlated with those of the seeds. Finally, sixty-one core ASVs, including several potential human pathogens, were identified, and a member of the seed core microbiota, Sphingomonas endophytica, was isolated from seeds and found to promote seedling growth and enhance resistance against Sclerotinia sclerotiorum, a major pathogen in rapeseed. Our findings provide a novel perspective for understanding the composition and functions of microbiota during seed development and may enhance the efficiency of mining beneficial seed microbes.

Enriched rhizospheric functional microbiome may enhance adaptability of Artemisia lavandulaefolia and Betula luminifera in antimony mining areas

Dominant native plants are crucial for vegetation reconstruction and ecological restoration of mining areas, though their adaptation mechanisms in stressful environments are unclear. This study focuses on the interactions between dominant indigenous species in antimony (Sb) mining area, Artemisia lavandulaefolia and Betula luminifera, and the microbes in their rhizosphere. The rhizosphere microbial diversity and potential functions of both plants were analyzed through the utilization of 16S, ITS sequencing, and metabarcoding analysis. The results revealed that soil environmental factors, rather than plant species, had a more significant impact on the composition of the rhizosphere microbial community. Soil pH and moisture significantly affected microbial biomarkers and keystone species. Actinobacteria, Proteobacteria and Acidobacteriota, exhibited high resistance to Sb and As, and played a crucial role in the cycling of carbon, nitrogen (N), phosphorus (P), and sulfur (S). The genes participating in N, P, and S cycling exhibited metabolic coupling with those genes associated with Sb and As resistance, which might have enhanced the rhizosphere microbes' capacity to endure environmental stressors. The enrichment of these rhizosphere functional microbes is the combined result of dispersal limitations and deterministic assembly processes. Notably, the genes related to quorum sensing, the type III secretion system, and chemotaxis systems were significantly enriched in the rhizosphere of plants, especially in B. luminifera, in the mining area. The phylogenetic tree derived from the evolutionary relationships among rhizosphere microbial and chloroplast whole-genome resequencing results, infers both species especially B. luminifera, may have undergone co-evolution with rhizosphere microorganisms in mining areas. These findings offer valuable insights into the dominant native rhizosphere microorganisms that facilitate plant adaptation to environmental stress in mining areas, thereby shedding light on potential strategies for ecological restoration in such environments.

Root rot destabilizes the Sanqi rhizosphere core fungal microbiome by reducing the negative connectivity of beneficial microbes

The stability of microbial communities, especially among core taxa, is essential for supporting plant health. However, the impacts of disease infection on the stability of rhizosphere fungal core microbiome remain largely unexplored. In this study, we delved into the effects of root rot infestation on the community structure, function, network complexity, and stability of Sanqi fungal core microbiomes, employing amplicon sequencing combined with co-occurrence network and cohesion analyses. Our investigation revealed that root rot disease led to a decrease in the α-diversity but an increase in the β-diversity of the Sanqi fungal core microbiomes in the rhizosphere. Notably, Ilyonectria, Plectosphaerella, and Fusarium emerged as indicator species in the rhizosphere core microbiome of root rot-infected Sanqi plants, while Mortierella predominated as the dominant biomarker taxa in healthy soils. Additionally, root rot diminished the complexity and modularity of the rhizosphere networks by reducing the metrics associated with nodes, edges, degrees, and modularity. Furthermore, root rot resulted in a reduction in the proportion of negative connections in the network and the negative/positive cohesion of the entire core fungal microbiome. Particularly noteworthy was the observation that root rot infection destabilized the rhizosphere core fungal microbiome by weakening the negative connectivity associated with beneficial agents. Collectively, these results highlight the significance of the negative connectivity of beneficial agents in ensuring the stability of core microbial community.IMPORTANCERoot rot disease has been reported as the most devastating disease in the production process of artificial cultivated Sanqi ginseng, which seriously threatens the Sanqi industry. This study provides valuable insights into how root rot influences microbial relationships within the community. These findings open up opportunities for disease prevention and the promotion of plant health by regulating microbial interactions. In summary, the research sheds light on the ecological consequences of root rot on rhizosphere fungal microbiomes and offers potential strategies for managing soil-borne diseases and enhancing plant health.

Microbial community interactions determine the mineralization of soil organic phosphorus in subtropical forest ecosystems

In subtropical forest ecosystems with few phosphorus (P) inputs, P availability and forest productivity depend on soil organic P (Po) mineralization. However, the mechanisms by which the microbial community determines the status and fate of soil Po mineralization remain unclear. In the present study, soils were collected from three typical forest types: secondary natural forest (SNF), mixed planting, and monoculture forest of Chinese fir. The P fractions, Po-mineralization ability, and microbial community in the soils of different forest types were characterized. In addition, we defined Po-mineralizing taxa with the potential to interact with the soil microbial community to regulate Po mineralization. We found that a higher labile P content persisted in SNF and was positively associated with the Po-mineralization capacity of the soil microbial community. In vitro cultures of soil suspensions revealed that soil Po mineralization of three forest types was distinguished by differences in the composition of fungal communities. We further identified broad phylogenetic lineages of Po-mineralizing fungi with a high intensity of positive interactions with the soil microbial community, implying that the facilitation of Po-mineralizing taxa is crucial for soil P availability. Our dilution experiments to weaken microbial interactions revealed that in SNF soil, which had the highest interaction intensity of Po-mineralizing taxa with the community, Po-mineralization capacity was irreversibly lost after dilution, highlighting the importance of microbial diversity protection in forest soils. In summary, this study demonstrates that the interactions of Po-mineralizing microorganisms with the soil microbial community are critical for P availability in subtropical forests.IMPORTANCEIn subtropical forest ecosystems with few phosphorus inputs, phosphorus availability and forest productivity depend on soil organic phosphorus mineralization. However, the mechanisms by which the microbial community interactions determine the mineralization of soil organic phosphorus remain unclear. In the present study, soils were collected from three typical forest types: secondary natural forest, mixed planting, and monoculture forest of Chinese fir. We found that a higher soil labile phosphorus content was positively associated with the organic phosphorus mineralization capacity of the soil microbial community. Soil organic phosphorus mineralization of three forest types was distinguished by the differences in the composition of fungal communities. The positive interactions between organic phosphorus-mineralizing fungi and the rest of the soil microbial community facilitated organic phosphorus mineralization. This study highlights the importance of microbial diversity protection in forest soils and reveals the microbial mechanism of phosphorus availability maintenance in subtropical forest ecosystems.

Distinct microbiota assembly and functional patterns in disease-resistant and susceptible varieties of tobacco

The plant microbiota is believed to be an accessory genome that extends plant functions, forming holobionts together with the host plant. Plant disease resistance, therefore, is inextricably linked with plant microbiota, which play important roles in plant growth and health. To explore the relationship between plant microbiota and disease resistance, we investigated the tobacco microbiome of two varieties with contrasting disease-resistance levels to bacterial wilt and black shank diseases. Comparative microbiome analysis indicated that the resistant variety assembled a distinct microbiota with higher network complexity and diversity. While Pseudomonas and Ensifer, which contain biocontrol and beneficial members, were enriched in the rhizosphere of the resistant variety, Ralstonia, a genus including the known causative pathogen, was enriched in the susceptible variety. Metagenome sequencing revealed that biocontrol functions, such as hydrogen cyanide synthase, pyochelin biosynthesis, and arthrofactin-type cyclic lipopeptide synthetase, were more abundant in the resistant variety. Further analysis indicated that contigs encoding the corresponding genes were mostly assigned to Pseudomonas. Among all the metagenome-assembled genomes, positive selection was suggested in the genome assigned to Pseudomonas only in the rhizosphere of the resistant variety. The search of biosynthetic gene clusters in the Pseudomonas genome revealed a non-ribosomal peptide synthetase, the compound of which was brabantamide A, with known antimicrobial activity. Collectively, our study suggests that the plant microbiota might be involved in microbe-mediated disease resistance. Particularly, our results highlight Pseudomonas in the rhizosphere of the disease-resistant variety as a promising biocontrol candidate. Our study may facilitate further screening of bacterial isolates and the targeted design of microbial communities.

The endophytic fungal community plays a crucial role in the resistance of host plants to necrotic bacterial pathogens

Konjac species (Amorphophallus spp.) are the only plant species in the world that are rich in a large amount of konjac glucomannan (KGM). These plants are widely cultivated as cash crops in tropical and subtropical countries in Asia, including China. Pectobacterium carotovorum subsp. carotovorum (Pcc) is one of the most destructive bacterial pathogens of konjac. Here, we analyzed the interactions between Pcc and susceptible and resistant konjac species from multiple perspectives. At the transcriptional and metabolic levels, the susceptible species A. konjac and resistant species A. muelleri exhibit similar molecular responses, activating plant hormone signaling pathways and metabolizing defense compounds such as phenylpropanoids and flavonoids to resist infection. Interestingly, we found that Pcc stress can lead to rapid recombination of endophytic microbial communities within a very short period (96 h). Under conditions of bacterial pathogen infection, the relative abundance of most bacterial communities in konjac tissue decreased sharply compared with that in healthy plants, while the relative abundance of some beneficial fungal communities increased significantly. The relative abundance of Cladosporium increased significantly in both kinds of infected konjac compared to that in healthy plants, and the relative abundance in resistant A. muelleri plants was greater than that in susceptible A. konjac plants. Among the isolated cultivable microorganisms, all three strains of Cladosporium strongly inhibited Pcc growth. Our results further elucidate the potential mechanism underlying konjac resistance to Pcc infection, highlighting the important role of endophytic microbial communities in resisting bacterial pathogen infections, especially the more direct role of fungal communities in inhibiting pathogen growth.

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.