The phyllosphere microbiome shifts toward combating melanose pathogen

Phyllosphere microbiome assists the hyperaccumulating plant in resisting heavy metal stress

Phyllosphere microbiome plays an irreplaceable role in maintaining plant health under stress, but its structure and functions in heavy metal-hyperaccumulating plants remain elusive. Here, the phyllosphere microbiome, inhabiting hyperaccumulating (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii grown in soils with varying heavy metal concentration, was characterized. Compared with NHE, the microbial community α-diversity was greater in HE. Core phyllosphere taxa with high relative abundance (>10 %), including Streptomyces and Nocardia (bacteria), Cladosporium and Acremonium (fungi), were significantly related to cadmium (Cd) and zinc (Zn) concentration and biomass of host plants. Moreover, microbial co-occurrence networks in HE exhibited greater complexity than those in NHE. Additionally, proportions of positive associations in HE bacterial networks increased with the rising heavy metal concentration, indicating a higher resistance of HE phyllosphere microbiome to heavy metal stress. Furthermore, in contrast to NHE, microbial community functions, primarily involved in heavy metal stress resistance, were more abundant in HE, in which microbiome assisted hosts to resist heavy metal stress better. Collectively, this study indicated that phyllosphere microbiome of the hyperaccumulator played an indispensable role in assisting hosts to resist heavy metal stress, and provided new insights into phyllosphere microbial application potential in phytoremediation.

Role of the beneficial phyllosphere microbiome in the defense against red clover anthracnose caused by Colletotrichum americae-borealis

Red clover (Trifolium pratense), a high-quality forage plant, faces significant threats from anthracnose in northeastern China, but the pathogen responsible remains unidentified. The phyllosphere microbiota is crucial in plantpathogen interactions, yet its role in the resistance of red clover to anthracnose is poorly understood. Using morphological, molecular, and multigene phylogenetic analyses, we identified Colletotrichum americae-borealis (Cab) as the pathogen that causes anthracnose in red clover in China. We also investigated changes in the phyllosphere microbiomes of highly resistant (XJ) and susceptible (SC) red clover materials after Cab infection, via 16S rRNA gene sequencing. The results revealed significant differences in bacterial α- and β-diversity, with novel microbial taxa and a complex microbial network emerging postinfection. Notably, after Cab inoculation, the Shannon diversity index in XJ exhibited more pronounced changes, manifested as an increase in the abundance of beneficial microorganisms such as Bacillus, Pantoea, and Pseudomonas. Network analysis revealed that the XJ microbiome was more complex and stable than the SC microbiome was, regardless of infection status. Bacillus J2, the dominant bacterium, significantly inhibited Cab growth in vitro and reduced the disease index by 33.4-47.7 % when it was reapplied to the leaf surface, suggesting its role in enhancing disease resistance. This study is the first to report that C. americae-borealis causes anthracnose in red clover in China, and demonstrates the potential of the beneficial bacterium J2 in enhancing disease resistance, providing insights into disease resistance mechanisms and the role of the phyllosphere microbiome in pathogen challenge.

Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress

Pcc is one of the key pathogenic factors responsible for destructive soft rot in konjac. To date, the assembly and functional adaptation of the plant endophytic microbiome under Pcc stress remain poorly understood. Here, we found that Pcc stress leads to rapid reorganization of the endogenous microbiome in multiple organs of both susceptible and resistant konjac plants. Under Pcc stress, the negative interactions within the bacterial-fungal interdomain network intensified, suggesting an increase in ecological competition between bacterial and fungal taxa. We further discovered that the relative abundance dynamics of the classes Dothideomycetes and Sordariomycetes, as core fungal taxa, changed in response to Pcc stress. By isolating culturable microorganisms, we demonstrated that 46 fungal strains strongly inhibited the growth of Pcc. This implies that endophytic fungal taxa in konjac may protect the host plant through ecological competition or by inhibiting the growth of pathogenic bacteria. Metagenomic analysis demonstrated that microbial communities associated with resistant Amorphophallus muelleri exhibited unique advantages over susceptible Amorphophallus konjac in enhancing environmental adaptability, regulating plant immune signaling, strengthening cell walls, and inducing defense responses. Our work provides important evidence that endophytic fungal taxa play a key role in the host plant's defense against necrotizing bacterial pathogens.

Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota

BACKGROUND

Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.

RESULTS

This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.

CONCLUSIONS

Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.

A comparative study: impact of chemical and biological fungicides on soil bacterial communities

Soil microbial communities play key roles in agroecosystems, particularly in processes like organic matter decomposition and nutrient cycling. However, human activities can negatively impact their community structure and, consequently, soil function. SoilGard and Ridomil are effective methods for controlling carrot cavity spots caused by Pythium spp., but their effects on bacterial taxonomic and metabolic function shifts are not well understood. This study aims to investigate the comparative impact of the chemical fungicide Ridomil and the biological fungicide SoilGard on the bacterial communities in soils cultivated with carrots. Our results showed that both SoilGard and Ridomil significantly impacted soil bacterial diversity, but their effects were distinct and time-dependent. Ridomil had an immediate negative effect on soil bacterial diversity two weeks after treatment, whereas SoilGard was initially less disruptive but showed delayed negative consequences 12 weeks after treatment, particularly when combined with Pythium inoculation. Ridomil treatment led to an increase in Proteobacteria, especially the Pseudomonas population, as confirmed by both MiSeq and qPCR data. In contrast, SoilGard depleted the Mycobacterium population at 12 weeks after treatment. Furthermore, the results of community-level physiological profiling using Biolog Ecoplates showed significant differences in substrate-level diversity between Ridomil and SoilGard-treated samples, indicating a shift in the metabolic activity of bacterial communities. Ridomil-treated samples showed the lowest metabolic activity of bacterial communities, based on the diversity and richness of carbon source utilization, compared to control. Overall, this research highlights the distinct and time-dependent effects of biological and chemical fungicides on soil bacterial communities when applied at recommended doses.

Host selection and nutrient status jointly drive algal and bacterial interactions in epiphytic biofilms of submerged macrophytes: Structural and functional insights

Epiphytic biofilms play a crucial role in aquatic biogeochemical cycles but are simultaneously influenced by host selection and eutrophication. However, the compositional structure and interaction mechanisms of these factors on algal and bacterial communities remain poorly understood. In this study, we employed Confocal Laser Scanning Microscopy (CLSM), Scanning Electron Microscopy (SEM), and high-throughput sequencing to investigate the physicochemical properties, algal and bacterial diversity, and community structure of epiphytic biofilms on two submerged macrophytes - Vallisneria natans (VN) and Hydrilla verticillata (HV) - across three urban shallow lakes with varying trophic levels in the Yangtze River Basin. Our results revealed distinct algal and bacterial communities influenced by both host plants and lake nutrient conditions, with unique core species identified in VN, HV, and the surrounding water. Host-environment effects index (HEEI = 1.79) indicated that bacterial communities were predominantly shaped by host selection, exhibiting lower diversity in HV (1.66 ± 0.92) and VN (2.31 ± 1.12) biofilms compared to surrounding waters (3.80 ± 0.47). In contrast, algal communities were primarily regulated by environmental factors (HEEI = 0.43), with higher diversity in less eutrophic lakes. Algal-bacterial co-occurrence network analysis revealed greater network complexity in VN biofilms than that in HV, with predominantly synergistic interactions facilitating carbon and nitrogen cycling. Eutrophication increased biofilm thickness, nutrient content, and extracellular polymeric substance (EPS) production but reduced microbial diversity and altered community interaction patterns. This study advances our understanding of epiphytic biofilms and offers insights into optimizing host-microbe interactions for improving lake restoration strategies.

DNA metabarcode analyses reveal similarities and differences in plant microbiomes of industrial hemp and medicinal Cannabis in China

Endophytic bacteria within plant tissues play crucial roles in plant health, stress tolerance, and contribute to the metabolite diversity of host plants. Cannabis sativa L. is an economically significant plant, with industrial hemp (IH) and medicinal Cannabis (MC) being the two main cultivars. However, the composition and functional traits of their endophytic bacterial communities in roots and leaves are not well understood. In this study, DNA metabarcode sequencing were employed to compare the bacterial communities between IH and MC. Significant differences were observed in the root and leaf niches. IH roots were enriched with stress-tolerant bacteria, while MC roots showed higher levels of biofilm-forming bacteria. In leaves, differences were even more pronounced, particularly in the abundance of Gram-negative bacteria, potential pathogens, stress-tolerant bacteria, and biofilm-forming bacteria. PICRUSt2 functional predictions revealed differences in nitrogen metabolism and secondary metabolite biosynthesis pathways in different cultivars and niches, while FAPROTAX analysis highlighted variations in carbon, nitrogen, and sulfur cycling functions. These findings underscore the distinct roles of bacterial communities in regulating plant health, stress responses, and metabolic processes in different niches and cultivars, providing insights for improving cultivation practices and plant resilience.

Unraveling the Intricacies of Powdery Mildew: Insights into Colonization, Plant Defense Mechanisms, and Future Strategies

Powdery mildew, a debilitating phytopathogen caused by biotrophic fungi within the order Erysiphales, endangers crop yields and global food security. Although traditional approaches have largely emphasized resistant cultivar development and chemical control, novel strategies are necessary to counter the advent of challenges, such as pathogen adaptation and climate change. This review fully discusses three principal areas of pathogen effector functions, e.g., the reactive oxygen species (ROS)-suppressive activity of CSEP087, and host susceptibility factors, like vesicle trafficking regulated by Mildew Locus O (MLO). It also briefly mentions the transcriptional regulation of resistance genes mediated by factors, like WRKY75 and NAC transcription factors, and post-transcriptional regulation via alternative splicing (As). In addition, this discussion discusses the intricate interactions among powdery mildew, host plants, and symbiotic microbiomes thereof, highlighting the mechanism through which powdery mildew infections disrupt the foliar microbiota balance. Lastly, we present a new biocontrol approach that entails synergistic microbial consortia, such as combinations of Bacillus and Trichoderma, to induce plant immunity while minimizing fungicide dependency. Through the study of combining knowledge of molecular pathogenesis with ecological resilience, this research offers useful insights towards climate-smart crop development and sustainable disease-management strategies in the context of microbiome engineering.

Bacillus vallismortis acts against ginseng root rot by modifying the composition and microecological functions of ginseng root endophytes

Introduction

The endophytic microbiome serves a crucial function as a secondary line of defense against pathogen invasion in plants. This study aimed to clarify the mechanism of action of the ginseng plant growth-promoting rhizobacteria (PGPR) Bacillus vallismortis SZ-4 synergizing with endophytic microorganisms in the prevention and control of root rot.

Methods

Ginseng root samples from a susceptible group (CK) with a disease level of 0-2 and a biocontrol group (BIO) treated with strain SZ-4 were collected. We employed high-throughput sequencing to examine the microbial community structure of ginseng roots at different disease levels, explore beneficial endophytic bacteria, and evaluate the efficacy of strain SZ-4 in mitigating root rot through synergistic interactions with ginseng endophytic flora.

Results

The application of the PGPR B. vallismortis SZ-4 biocontrol fungicide has been found to help ginseng resist Fusarium solani by modulating the richness and structure of endophytic microbial populations. The endophytic bacteria HY-43 and HY-46 isolated from ginseng roots treated with B. vallismortis SZ-4 were identified as Bacillus velezensis based on morphological, physiological, and biochemical characteristics, as well as 16S rDNA and gyrB sequencing analyses. The endophytic bacteria HY-43 and HY-46 were combined with strain SZ-4 to generate the bacterial consortia CS4-43 and CS4-46, respectively. Both CS4-43 and CS4-46 significantly enhanced the inhibitory effects of the single strain SZ-4, as well as HY-43 and HY-46, against ginseng root rot, while also promoting plant growth.

Discussion

These findings offers a theoretical foundation for studying the microecological prevention and control of ginseng diseases as well as new insights for conducting research on the efficient and precise management of plant diseases.

Weather parameters and biotic factors synergistically shape the phyllosphere microbiome of pomelo (Citrus maxima (Burm.) Merr.) across annual cycle

Phyllosphere microbiome plays important roles in crop adaptation to the changing environments. Perennial woody crops undergo annual cycles with the changing weather parameters and the biological factors, which might shape the phyllosphere microbial community. In this study, we aimed to investigate the dynamics of phyllosphere microbiome of pomelo (Citrus maxima (Burm.) Merr.), an economically important horticultural crops worldwide, and to compare the respective contribution of the weather parameters and the biotic factors to the microbial community assembly, with special focus on the amino acids in leaves. Hi-Seq analysis revealed that both bacterial and fungal communities showed annual cycle dynamics, and the bacterial community in summer was much different from those in other seasons probably due to high temperature and precipitation. However, contribution of the biotic factors (e.g., leaf traits) (12%-29%) to microbial community assembly was higher than that of the weather parameters (4%-15%). Redundancy analysis indicated that the leaf amino acids significantly affected bacterial community while sugars significantly affected fungal community, highlighting the differential patterns of bacterial and fungal community as affected by the biotic factors. Finally, structure equation model showed that the weather parameters influenced microbial community colonizing pomelo leaves both in a direct way and in an indirect way via leaf traits (mainly amino acids). These results demonstrate the primary role of weather parameters and the key role of leaf amino acids in shaping phyllosphere microbiome.

Microbial diversity and interactions: Synergistic effects and potential applications of Pseudomonas and Bacillus consortia

Microbial diversity and interactions in the rhizosphere play a crucial role in plant health and ecosystem functioning. Among the myriads of rhizosphere microbes, Pseudomonas and Bacillus are prominent players known for their multifaceted functionalities and beneficial effects on plant growth. The molecular mechanism of interspecies interactions between natural isolates of Bacillus and Pseudomonas in medium conditions is well understood, but the interaction between the two in vivo remains unclear. This paper focuses on the possible synergies between Pseudomonas and Bacillus associated in practical applications (such as recruiting beneficial microbes, cross-feeding and niche complementarity), and looks forward to the application prospects of the consortium in agriculture, human health and bioremediation. Through in-depth understanding of the interactions between Pseudomonas and Bacillus as well as their application prospects in various fields, this study is expected to provide a new theoretical basis and practical guidance for promoting the research and application of rhizosphere microbes.

Temporal dynamics of walnut phyllosphere microbiota under synergistic pathogen exposure and environmental perturbation

Introduction

Phyllosphere-associated microbes directly influence plant-pathogen interactions, and the external environment and the plant shape the phyllosphere microbiome.

Methods

In this study, we integrated 16S rRNA and ITS high-throughput sequencing to systematically investigate changes in the phyllosphere microbiome between symptomatic and asymptomatic walnut leaves affected by spot disease, with consideration of phenological stage progression. Additionally, we explored how abiotic (AT, DT, SCTCC & LPDD) and biotic factors (Pn & Gs) impact microbial communities.

Results

Our findings revealed significant differences in the diversity of the phyllosphere microbiome between symptomatic and asymptomatic leaves at the same phenological stage. Furthermore, the structure and function of phyllosphere-associated microbiome changed as the phenological stage progressed. Fungal taxa that related to the function Plant_Pathogen and bacterial taxa that related to the KEGG pathway functions Fatty acid biosynthesis and Biotin metabolism were increased in the symptomatic group. The keystone species driving the walnut phyllosphere microbiome was Pseudomonas spp., which substantially influenced the microbiome of symptomatic vs. asymptomatic leaves. Notably, Pseudomonas spp. interacted with Xanthomonas spp. and Pantoea spp. Correlation analysis revealed that the dew point temperature constituted the primary abiotic factor of phyllosphere bacterial community composition, whereas liquid precipitation depth dimension was identified as the dominant factor shaping fungal taxa. Additionally, leaf net photosynthetic rate and stomatal conductance were closely linked to the phyllosphere microbiome.

Discussion

These results advance our understanding of community-level microbial responses to pathogen invasion and highlight the multifactorial drivers of phyllosphere microbiome assembly. Ultimately, they contribute to predicting and managing walnut leaf-related diseases.

Unveiling Microbial Dynamics: How Forest Aging Shapes the Microbial Communities of Pinus massoniana

Plants host diverse microbial communities essential for nutrient acquisition, growth, and responses to biotic and abiotic stresses. Despite their importance, the variation and stability of these communities during forest succession remain poorly understood. This study investigated the microbial communities in Pinus massoniana forests at different stand ages (12, 22, 30, and 40 years). Results showed that the phyllosphere and roots of P. massoniana harbor diverse microbial communities, which shift dynamically with forest aging. Bacterial species diversity consistently surpassed fungal diversity across all habitats. Forest aging significantly influenced the alpha diversity of phyllosphere and soil microbes, whereas root-associated microbial diversity remained stable. Co-occurrence network analysis revealed that bacterial communities formed more complex networks than fungal communities and exhibited greater stability. Functional annotation confirmed that bacterial communities were functionally more stable, predominantly involving metabolic processes. In contrast, endophytes dominated the phyllosphere fungi, while ectomycorrhizal fungi were prevalent in root and soil fungal communities. Environmental factors, including total nitrogen, total phosphorus, available potassium, and pH, emerged as key drivers of microbial dynamics. These findings provide novel insights into the differing responses of bacterial and fungal communities to forest aging, highlighting the critical role of ecological niches in shaping microbial dynamics.

Plant-microbiome interactions and their impacts on plant adaptation to climate change

Plants have co-evolved with a wide range of microbial communities over hundreds of millions of years, this has drastically influenced their adaptation to biotic and abiotic stress. The rapid development of multi-omics approaches has greatly improved our understanding of the diversity, composition, and functions of plant microbiomes, but how global climate change affects the assembly of plant microbiomes and their roles in regulating host plant adaptation to changing environmental conditions is not fully known. In this review, we summarize recent advancements in the community assembly of plant microbiomes, and their responses to climate change factors such as elevated CO2 levels, warming, and drought. We further delineate the research trends and hotspots in plant-microbiome interactions in the context of climate change, and summarize the key mechanisms by which plant microbiomes influence plant adaptation to the changing climate. We propose that future research is urgently needed to unravel the impact of key plant genes and signal molecules modulated by climate change on microbial communities, to elucidate the evolutionary response of plant-microbe interactions at the community level, and to engineer synthetic microbial communities to mitigate the effects of climate change on plant fitness.

From glycans to green biotechnology: exploring cell wall dynamics and phytobiota impact in plant glycopathology

Filamentous plant pathogens, including fungi and oomycetes, pose significant threats to cultivated crops, impacting agricultural productivity, quality and sustainability. Traditionally, disease control heavily relied on fungicides, but concerns about their negative impacts motivated stakeholders and government agencies to seek alternative solutions. Biocontrol agents (BCAs) have been developed as promising alternatives to minimize fungicide use. However, BCAs often exhibit inconsistent performances, undermining their efficacy as plant protection alternatives. The eukaryotic cell wall of plants and filamentous pathogens contributes significantly to their interaction with the environment and competitors. This highly adaptable and modular carbohydrate armor serves as the primary interface for communication, and the intricate interplay within this compartment is often mediated by carbohydrate-active enzymes (CAZymes) responsible for cell wall degradation and remodeling. These processes play a crucial role in the pathogenesis of plant diseases and contribute significantly to establishing both beneficial and detrimental microbiota. This review explores the interplay between cell wall dynamics and glycan interactions in the phytobiome scenario, providing holistic insights for efficiently exploiting microbial traits potentially involved in plant disease mitigation. Within this framework, the incorporation of glycobiology-related functional traits into the resident phytobiome can significantly enhance the plant's resilience to biotic stresses. Therefore, in the rational engineering of future beneficial consortia, it is imperative to recognize and leverage the understanding of cell wall interactions and the role of the glycome as an essential tool for the effective management of plant diseases.

Microbiome Analysis of Area in Proximity to White Spot Lesions Reveals More Harmful Plant Pathogens in Maize

Plant microbiomes play a major role in plant health, growth, and development, enhancing resistance to pathogen invasion. However, despite the extensive research on the phyllosphere microbiome, it remains unclear how the microbiome of leaves in proximity to diseased leaves responds to pathogen invasion. We investigate the response of the maize phyllosphere microbiome to maize white spot by assessing the microbiome dynamics associated with the white spot portion and the area in proximity using 16S and ITS high-throughput sequencing analysis. Our results showed that the bacterial diversities were higher in the diseased portion and area in proximity to the spot than those in healthy plants. At the same time, lower fungal diversity was recorded in the diseased portion compared to portions in proximity to it and healthy leaves. The spot portion had a significant influence on the microbial composition. The diseased portion, the area in proximity to it, and the healthy leaves were dominated by the bacterial genera Sphingomonas, Delftia, Chryseobacterium, Stenotrophomonas, Methylobacterium-methylorubrum, and Bacteroides. Still, the abundance of Sphingomonas decreased in the healthy leaves with a corresponding increase in Stenotrophomonas. Conversely, the fungal genus Setophoma dominated the diseased portion, while the fungal pathogens Cladosporium, Alternaria, and Exserohilum were highly abundant in the samples from the area in proximity to it. In addition, a co-occurrence network analysis revealed a complex fungal network in healthy leaves and those in proximity to leaves infected with white spot compared to the diseased portion. This study suggests that the area in proximity to the maize leaf infected with white spot disease is colonized by more harmful plant pathogenic fungi for disease progression.

Desiccation as a suitable alternative to cold-storage of phyllosphere samples for DNA-based microbial community analyses

The study of microbial communities of the plant phyllosphere in remote locations using DNA-based approaches is limited by the challenges associated with their preservation in the field and during transportation. Freezing is a common DNA preservation strategy, but it may be unsuitable for leaf samples, or inaccessible in some locations. Other methods such as desiccation, ethanol or commercial preservatives are potential alternative DNA preservation methods for ambient temperature storage. In this study, we assessed the efficacy of desiccation (with silica gel packs), and of three preservation solutions (95% ethanol, RNAlater, LifeGuard) for the preservation of epiphytic phyllosphere communities of Populus tremuloides and Picea glauca at ambient indoor temperature (21 °C) for up to three weeks. We assessed effects on DNA concentration and quality and used metabarcoding to detect changes in bacterial and fungal communities between treatments over time. A secondary study was conducted on leaves of Populus grandidentata to further test the ability of the desiccation treatment to resolve differences between sampling sites. Silica gel packs were identified as effective ambient temperature preservative of phyllosphere bacterial and fungal communities. There were some changes in the communities compared to immediate extraction due to this treatment, but these changes did not affect the ability to distinguish tree species and sampling locations. Overall, our study supports the use of silica gel pack short term preservation at ambient temperature for phyllosphere samples intended for DNA-based microbial community analyses.

Established Pseudomonas syringae pv. tomato infection disrupts immigration of leaf surface bacteria to the apoplast

Bacterial disease alters the infection court creating new niches. The apoplast is an oasis from the hardships of the leaf surface and is generally inaccessible to nonpathogenic members of the phyllosphere bacterial community. Previously, we demonstrated that Salmonella enterica serovar Typhimurium (S. Typhimurium) immigrants to the leaf surface can both enter the apoplast and replicate due to conditions created by an established Xanthomonas hortorum pv. gardneri (Xhg) infection in tomato. Here, we have expanded our investigation of how infection changes the host by examining the effects of another water-soaking pathogen, Pseudomonas syringae pv. tomato (Pst), on immigrating bacteria. We discovered that, despite causing macroscopically similar symptoms as Xhg, Pst infection disrupts S. Typhimurium colonization of the apoplast. To determine if these effects were broadly applicable to phyllosphere bacteria, we examined the fates of immigrant Xhg and Pst arriving on an infected leaf. We found that this effect is not specific to S. Typhimurium, but that immigrating Xhg or Pst also struggled to fully join the infecting Pst population established in the apoplast. To identify the mechanisms underlying these results, we quantified macroscopic infection symptoms, examined stomata as a pinch point of bacterial entry, and characterized aspects of interbacterial competition. While it may be considered common knowledge that hosts are fundamentally altered following infection, the mechanisms that drive these changes remain poorly understood. Here, we investigated these pathogens to reach a deeper understanding of how infection alters a host from a rarely accessible, inhabitable environment to an obtainable, habitable niche.

Microbial Inoculants Drive Changes in Soil and Plant Microbiomes and Improve Plant Functions in Abandoned Mine Restoration

The application of microbial inoculants holds promise for the sustainable restoration of abandoned mine sites by affecting soil nutrients and microbial communities. However, the responses of plant microbial communities to microbial inoculants in mine restoration remain largely unknown. To bridge this knowledge gap, we conducted a 4-year field experiment at an abandoned carbonate mine site to assess the impacts of microbial inoculants on the soil-plant microbiome. Our findings revealed that microbial inoculants significantly changed roots, fine root bacterial and fungal communities. Further, no significant correlations were observed between the soil-plant nutrient content (Z-score) and microbial alpha diversity. However, a significantly positive correlation was found between the relative abundance of the keystone ecological cluster (Module #1) and soil-plant nutrient content. The application of microbial inoculants also increased complexity, albeit decreased stability of plant microbiome networks, alongside a reduction in stochastic assembly. Conversely, they decreased the complexity but increased the stability of soil microbiome networks, accompanied by an increase in stochastic assembly. Notably, the number of specifically enriched microbiome functional traits of roots and root nodules under the microbial inoculant treatments surpassed that of the control. In summary, our findings underscored the potential of microbial inoculants to enhance soil-plant functionality at abandoned mine restoration sites.

Diffusive Phyllosphere Microbiome Potentially Regulates Harm and Defence Interactions Between Stephanitis nashi and Its Crabapple Host

Pear lace bug (Stephanitis nashi) is a significant herbivorous pest, harbouring a diverse microbiome crucial for crabapple (Malus sp.) host adaptation. However, the mutual influence of S. nashi- and plant-associated microbiomes on plant responses to pest damage remains unclear. This study found that S. nashi damage significantly altered bacterial community structure and reduced bacterial evenness in the crabapple phyllosphere. Notably, bacterial diversity within S. nashi was significantly lower than that in the environment, potentially influenced by insect developmental stage, bacterial diffusion stage and endosymbiont species number and abundance. Extensive bacterial correlation and diffusion effect between S. nashi and adjacent plant environments were observed, evident in a gradual decrease in bacterial diversity and an increase in bacterial acquisition ratio from soil to phyllosphere to S. nashi. Correspondingly, S. nashi significantly impacted the metabolic response of crabapple leaves, altering pathways involved in vitamin, amino acid and lipid metabolism and so forth. Furthermore, association analysis linked these metabolic changes to phyllosphere bacterial alterations, emphasizing the important role of diffusive phyllosphere microbiome in regulating S. nashi-crabapple interactions. This study highlights bacterial diffusion effect between insect and plants and their potential role in regulating insect adaptability and plant defence responses, providing new insights into plant-insect-microbiome interactions.

Host selection is not a universal driver of phyllosphere community assembly among ecologically similar native New Zealand plant species

BACKGROUND

A growing body of evidence demonstrates that host-associated microbial communities of plant leaf surfaces (i.e. the phyllosphere) can influence host functional traits. However, it remains unclear whether host selection is a universal driver of phyllosphere community assembly. We targeted mānuka (Leptospermum scoparium) and three neighbouring non-mānuka plant species along an 1800-m transect in a New Zealand native bush to conduct a hypothesis-driven investigation of the relative influence of host species identity and stochastic dispersal on the composition of natural phyllosphere bacterial communities.

RESULTS

We detected significant correlations between host species identity and mānuka phyllosphere communities that are consistent with a dominant role of host selection in the assembly of the mānuka phyllosphere microbiome. In contrast, the phyllosphere community compositions of neighbouring, ecologically similar native plants were highly variable, suggesting that stochastic processes, such as dispersal, had a stronger influence on the phyllosphere microbiomes of those non-mānuka plants compared to the phyllosphere microbiome of mānuka. Furthermore, the distribution of phyllosphere taxa among plant species was congruent with a scenario in which microorganisms had dispersed from mānuka to non-mānuka phyllosphere microbiomes.

CONCLUSIONS

We conclude that host selection of phyllosphere communities is not and should not be presumed to be a universal trait across plant species. The specificity of the mānuka phyllosphere microbiome suggests the presence of functionally significant bacteria that are under direct, possibly chemically mediated, selection by the host. Furthermore, we propose that phyllosphere microbiomes under strong host selection, such as that of mānuka, may act as a source of microorganisms for the phyllosphere microbiomes of neighbouring plants. Video Abstract.

Differential responses of root and leaf-associated microbiota to continuous monocultures

Continuous monocultures alter the composition and function of root-associated microbiota, and thus compromise crop health and productivity. In comparison, little is known about how leaf-associated microbiota respond to continuous monocultures. Here, we profiled root and leaf-associated microbiota of peanut plants under monocropping and rotation conditions. Additionally, their protective effects against root pathogen Fusarium oxysporum and leaf pathogen Alternaria alstroemeriae were evaluated. We found that monocropping increased root and leaf disease severity. Meanwhile, the peanut growth and productivity were inhibited by monocropping. Microbiota analysis revealed that monocropping reduced rhizosphere microbial population and diversity, while increased leaf epiphytic microbial population and did not influence leaf epiphytic microbial diversity. Cropping conditions had a greater impact on the microbiota composition of leaf epiphytes than that of the rhizosphere. Moreover, in vitro and in vivo experiments, combined with correlation analyses showed that monocropping weakened the antagonistic activity of rhizosphere microbiota against F. oxysporum and root rot disease. This effect may be associated with the depletion of Bacillus sp. and Sphingomonas sp.. By contrast, leaf epiphytic microbiota under monocropping exhibited greater inhibition of A. alstroemeriae growth and leaf spot control. Together, our results demonstrated a differential response pattern of root and leaf-associated microbiota to continuous monocultures.

Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation

BACKGROUND

Seed-associated microorganisms play crucial roles in maintaining plant health by providing nutrients and resistance to biotic and abiotic stresses. However, their functions in seed germination and disease resistance remain poorly understood. In this study, we investigated the microbial community assembly features and functional profiles of the spermosphere and endosphere microbiomes related to germinated and ungerminated seeds of Astragalus mongholicus by using amplicon and shotgun metagenome sequencing techniques. Additionally, we aimed to elucidate the relationship between beneficial microorganisms and seed germination through both in vitro and in vivo pot experiments.

RESULTS

Our findings revealed that germination significantly enhances the diversity of microbial communities associated with seeds. This increase in diversity is driven through environmental ecological niche differentiation, leading to the enrichment of potentially beneficial probiotic bacteria such as Pseudomonas and Pantoea. Conversely, Fusarium was consistently enriched in ungerminated seeds. The co-occurrence network patterns revealed that the microbial communities within germinated and ungerminated seeds presented distinct structures. Notably, germinated seeds exhibit more complex and interconnected networks, particularly for bacterial communities and their interactions with fungi. Metagenome analysis showed that germinated seed spermosphere soil had more functions related to pathogen inhibition and cellulose degradation. Through a combination of culture-dependent and germination experiments, we identified Fusarium solani as the pathogen. Consistent with the metagenome analysis, germination experiments further demonstrated that bacteria associated with pathogen inhibition and cellulose degradation could promote seed germination and vigor. Specifically, Paenibacillus sp. significantly enhanced A. mongholicus seed germination and plant growth.

CONCLUSIONS

Our study revealed the dynamics of seed-associated microorganisms during seed germination and confirmed their ecological role in promoting A. mongholicus seed germination by suppressing pathogens and degrading cellulose. This study offers a mechanistic understanding of how seed microorganisms facilitate successful seed germination, highlighting the potential for leveraging these microbial communities to increase plant health. Video Abstract.

Pepper root exudate alleviates cucumber root-knot nematode infection by recruiting a rhizobacterium

Root-knot nematodes (Meloidogyne spp.) have garnered significant attention from researchers owing to the substantial damage they cause to crops and their worldwide distribution. However, controlling these nematodes is challenging because a limited number of chemical pesticides and biocontrol agents are effective against them. Here, we demonstrate that pepper rotation markedly reduces Meloidogyne incognita infection in cucumber and diminishes the presence of p-hydroxybenzoic acid in the soil, a compound known to exacerbate M. incognita infection. Pepper rotation also restructures the rhizobacterial community, leading to the colonization of the cucumber rhizosphere by two Pseudarthrobacter oxydans strains (RH60 and RH97), facilitated by enrichment of palmitic acid in pepper root exudates. Both strains exhibit high nematocidal activity against M. incognita and have the ability to biosynthesize indoleacetic acid and biodegrade p-hydroxybenzoic acid. RH60 and RH97 also induce systemic resistance in cucumber plants and promote their growth. These data suggest that the pepper root exudate palmitic acid alleviates M. incognita infection by recruiting beneficial P. oxydans to the cucumber rhizosphere. Our analyses identify a novel chemical component in root exudates and reveal its pivotal role in crop rotation for disease control, providing intriguing insights into the keystone function of root exudates in plant protection against root-knot nematode infection.

Host Metabolic Alterations Mediate Phyllosphere Microbes Defense upon Xanthomonas oryzae pv oryzae Infection

Rice bacterial leaf blight, caused by Xanthomonas oryzae pv oryzae (Xoo), is a significant threat to global food security. Although the microbiome plays an important role in protecting plant health, how the phyllosphere microbiome is recruited and the underlying disease resistance mechanism remain unclear. This study investigates how rice phyllosphere microbiomes respond to pathogen invasion through a comprehensive multiomics approach, exploring the mechanisms of microbial defense and host resistance. We discovered that Xoo infection significantly reshapes the physicosphere microbial community. The bacterial network became more complex, with increased connectivity and interactions following infection. Metabolite profiling revealed that l-ornithine was a key compound to recruiting three keystone microbes, Brevundimonas (YB12), Pantoea (YN26), and Stenotrophomonas (YN10). These microbes reduced the disease index by up to 67.6%, and these microbes demonstrated distinct defense mechanisms. Brevundimonas directly antagonized Xoo by disrupting cell membrane structures, while Pantoea and Stenotrophomonas enhanced plant immune responses by significantly increasing salicylic acid and jasmonic acid levels and activating defense-related enzymes. Our findings provide novel insights into plant-microbe interactions, demonstrating how host metabolic changes recruit and activate beneficial phyllosphere microbes to combat pathogenic invasion. This research offers promising strategies for sustainable agricultural practices and disease management.

Beyond correlation: Understanding the causal link between microbiome and plant health

Understanding the causal link between the microbiome and plant health is crucial for the future of crop production. Established studies have shown a symbiotic relationship between microbes and plants, reshaping our knowledge of plant microbiomes' role in health and disease. Addressing confounding factors in microbiome study is essential, as standardization enables precise identification of microbiome features that influence outcomes. The microbiome significantly impacts plant development, necessitating holistic investigation for maintaining plant health. Mechanistic studies have deepened our understanding of microbiome structure and function related to plant health, though much research still needs to be carried out. This review, therefore, discusses current challenges and proposes advancing studies from correlation to causation and translation. We explore current knowledge on the microbiome and plant health, emphasizing multi-omics approaches and hypothesis-driven research. Future studies should focus on developing translational research for producing probiotics and prebiotics from biomarkers that regulate the microbiome-plant health connection, promoting sustainable crop production through microbiome applications.

Captivity increased the abundance of high-risk antibiotic resistance genes in the giant panda gut microbiome

Captivity is a key strategy for protecting endangered species, but research has primarily focused on artificial breeding and reintroduction to bolster wild populations, often overlooking the environmental and health risks associated with antibiotic resistance genes (ARGs). Here, we conducted a comprehensive analysis of the microbiome and ARG profiles in the gut of wild giant pandas across five representative populations, as well as one captive population, utilizing 16S rRNA gene sequencing and High-Throughput Quantitative PCR. Our findings revealed that both geographic location and captivity significantly influenced the gut microbial community and ARG composition in the gut of giant pandas. Additionally, we identified core microbiomes with essential ecological functions, particularly those related to food utilization, were identified in the giant panda gut across different regions. The gut ARGs in giant pandas exhibited a broad range of subtypes, with multidrug resistance genes being the most prevalent. Notably, the captive population harbored the highest abundance of high-risk ARGs, especially those conferring tetracycline resistance. High-risk multidrug ARGs (e.g., tolC, mepA, and mdtA) were found to be strongly correlated with the potential pathogens, such as Escherichia_Shigellina and Pseudomonas. Furthermore, bamboo-associated ARGs and mobile genetic elements (MGEs) contributed significantly to the ARG abundance in the giant panda gut, indicating that diet plays a crucial role in shaping gut resistome. Collectively, our study provides a detailed mapping of giant panda gut microbiomes and ARG distribution, offering valuable insights for conservation efforts and advancing our understanding of ARG dynamics in giant panda populations.

Pyoluteorin-deficient Pseudomonas protegens improves cooperation with Bacillus velezensis, biofilm formation, co-colonizing, and reshapes rhizosphere microbiome

Plant-beneficial Pseudomonas and Bacillus have been extensively studied and applied in biocontrol of plant diseases. However, there is less known about their interaction within two-strain synthetic communities (SynCom). Our study revealed that Pseudomonas protegens Pf-5 inhibits the growth of several Bacillus species, including Bacillus velezensis. We established a two-strain combination of Pf-5 and DMW1 to elucidate the interaction. In this combination, pyoluteorin conferred the competitive advantage of Pf-5. Noteworthy, pyoluteorin-deficient Pf-5 cooperated with DMW1 in biofilm formation, production of metabolites, root colonization, tomato bacterial wilt disease control, as well as in cooperation with beneficial bacteria in tomato rhizosphere, such as Bacillus spp. RNA-seq analysis and RT-qPCR also proved the pyoluteorin-deficient Pf-5 mutant improved cell motility and metabolite production. This study suggests that the cooperative effect of Bacillus-Pseudomonas consortia depends on the balance of pyoluteorin. Our finding needs to be considered in developing efficient SynCom in sustainable agriculture.

Meddling with the microbiota: Fungal tricks to infect plant hosts

Plants associate with a wealth of microbes, collectively referred to as the plant microbiota, whose composition is determined by host plant genetics, immune responses, environmental factors and intermicrobial relations. Unsurprisingly, microbiota compositions change during disease development. Recent evidence revealed that some of these changes can be attributed to effector proteins with antimicrobial activities that are secreted by plant pathogens to manipulate host microbiota to their advantage. Intriguingly, many of these effectors have ancient origins, predating land plant emergence, and evolved over long evolutionary trajectories to acquire selective antimicrobial activities to target microbial antagonists in host plant microbiota. Thus, we argue that host-pathogen co-evolution likely involved arms races within the host-associated microbiota.

The Phyllosphere Microbial Community Structure of Three Camellia Species upon Anthracnose

Anthracnose of Camellia plants is caused by the Colletotrichum species. The fungal pathogens mainly infect the leaves of plants and lead to serious economic losses. However, knowledge of Camellia phyllosphere microbial community after Colletotrichum infection has not been explored which limited our understanding of the relationship between the Camellia anthracnose outbreak and interacting microorganisms. In this study, three economically and ecologically important Camellia species with anthracnose symptoms were collected and subjected to bacterial and fungal composition analysis, diversity, co-occurrence characteristics, isolation of key strains, and tie-back pathogenicity test. The results indicated that Sphingomonas and Methylobacterium were the dominant bacterial genera over the three Camellia species and Pallidocercospora, Colletotrichum, and Pichia were the dominant fungal genera. The co-occurrence analysis showed that Methylobacterium, Sphingomonas, Massilia, and Allorhizobium were the key bacterial taxa and Colletotrichum, Pallidocercospora, Pichia, Septophoma, and Septoria were the key fungal taxa over the three infected plants. The hub taxa, including the species significantly associated with the Colletotrichum abundance, were mostly beneficial bacteria over the three Camellia species. Further co-culture and tie-back pathogenicity tests verified that the hub taxa associated with pathogenic Colletotrichum in the microbial networks may play promoting/inhibiting roles on Colletotrichum infection. The results highlight the importance of phytopathological conditions for the interactions between microbial members of foliar fungal and bacterial communities.

Effects of Coffea canephora genotypes on the microbial community of soil and fruit

In recent years, the role of microbial communities in agricultural systems has received increasing attention, particularly concerning their impact on plant health and productivity. However, the influence of host plant genetic factors on the microbial composition of coffee plants remains largely unexplored. This study provides the first comprehensive investigation into how genotype affects the microbial communities present in the rhizosphere and fruits of Coffea canephora. Conducted on a commercial coffee farm in Brazil, we analyzed six genotypes of C. canephora var. Conilon. Soil and fruit samples were collected from which microbial DNA was extracted and sequenced, targeting the V3-V4 region of the 16 S rDNA and the ITS1 region for fungi. A total of 12,239,769 reads were generated from the 16 S rDNA and ITS1 regions. The PCoA revealed distinct patterns of beta diversity, with genotype 153 exhibiting significant isolation in soil bacterial communities. The dominant bacterial orders included Rhizobiales and Rhodobacterales, while the fungal community comprised diverse taxa from Saccharomycetales and Hypocreales. LEfSe analysis identified key metagenomic biomarkers, highlighting genotype Baiano 4 for its richness in fruit-associated taxa, whereas genotype 153 exhibited lower diversity in both soil and fruit samples. This work enhances our understanding of the microbiomes associated with different coffee genotypes, providing evidence of how host genetic variation influences microbial community composition. Our findings indicate that specific microbial taxa are enriched in the fruits and soil of various genotypes. Future research should focus on identifying these microorganisms and elucidating their specific functions within the rhizosphere and coffee fruits.

Cross-niche protection of kiwi plant against above-ground canker disease by beneficial rhizosphere Flavobacterium

Beneficial rhizosphere microorganisms are widely employed to shield crops from underground pathogen infections. In this study, we challenge this conventional idea by employing rhizosphere soil bacteria to safeguard kiwi plants against the above-ground canker, caused by Pseudomonas syringae pv. actinidiae (Psa). Microbiome comparisons were conducted in different resistant cultivars Actinidia chinensis var. deliciosa 'Hayward' and A. chinensis var. chinensis 'Hongyang'. Our findings reveal the most notable disparity in the rhizosphere soil microbiome, with the Flavobacterium significantly enriched in the rhizosphere soil of more resistant cultivar, 'Hayward'. We isolated Flavobacterium isolates and observed their efficacy in preventing Psa infection, which is further confirmed in field trial by using a representative strain Flavobacterium soyae F55. Furthermore, undescribed gene clusters responsible for antimicrobial metabolite biosynthesis were identified in F. soyae F55, and F. soyae F55 growth was evidently promoted by the root exudates of 'Hayward'. The results underscore the potential of beneficial rhizosphere soil bacteria in protection against above-ground disease.

Deciphering Phyllomicrobiome of Cauliflower Leaf: Revelation by Metagenomic and Microbiological Analysis of Tolerant and Susceptible Genotypes Against Black Rot Disease

Understanding the phyllomicrobiome dynamics in cauliflower plants holds significant promise for enhancing crop resilience against black rot disease, caused by Xanthomonas campestris pv. campestris. In this study, the culturable microbiome and metagenomic profile of tolerant (BR-161) and susceptible (Pusa Sharad) cauliflower genotypes were investigated to elucidate microbial interactions associated with disease tolerance. Isolation of phyllospheric bacteria from asymptomatic and black rot disease symptomatic leaves of tolerant and susceptible cultivars yielded 46 diverse bacterial isolates. Molecular identification via 16S rRNA sequencing revealed differences in the diversity of microbial taxa between genotypes and health conditions. Metagenomic profiling using next-generation sequencing elucidated distinct microbial communities, with higher diversity observed in black rot disease symptomatic leaf of BR-161. Alpha and beta diversity indices highlighted differences in microbial community structure and composition between genotypes and health conditions. Taxonomic analysis revealed a core microbiome consisting of genera such as Xanthomonas, Psychrobacillus, Lactobacillus, and Pseudomonas across all the samples. Validation through microbiological methods confirmed the presence of these key genera. The findings provide novel insights into the phyllomicrobiome of black rot-tolerant and susceptible genotypes of cauliflower. Harnessing beneficial microbial communities identified in this study offers promising avenues for developing sustainable strategies to manage black rot disease and enhance cauliflower crop health and productivity.

Planting density effect on poplar growth traits and soil nutrient availability, and response of microbial community, assembly and function

BACKGROUND

The interaction between soil characteristics and microbial communities is crucial for poplar growth under different planting densities. Yet, little is understood about their relationships and how they respond to primary environmental drivers across varying planting densities.

RESULTS

In this study, we investigated poplar growth metrics, soil characteristics, and community assembly of soil bacterial and fungal communities in four poplar genotypes (M1316, BT17, S86, and B331) planted at low, medium, and high densities. Our findings reveal that planting density significantly influenced poplar growth, soil nutrients, and microbial communities (P < 0.05). Lower and medium planting densities supported superior poplar growth, higher soil nutrient levels, increased microbial diversity, and more stable microbial co-occurrence networks. The assembly of bacterial communities in plantation soils was predominantly deterministic (βNTI < -2), while fungal communities showed more stochastic assembly patterns (-2 < βNTI < 2). Soil available phosphorus (AP) and potassium (AK) emerged as pivotal factors shaping microbial communities and influencing bacterial and fungal community assembly. Elevated AP levels promoted the recruitment of beneficial bacteria such as Bacillus and Streptomyces, known for their phosphate-solubilizing abilities. This facilitated positive feedback regulation of soil AP, forming beneficial loops in soils with lower and medium planting densities.

CONCLUSIONS

Our study underscores the critical role of planting density in shaping soil microbial communities and their interaction with poplar growth. This research carries significant implications for enhancing forest management practices by integrating microbiological factors to bolster forest resilience and productivity.

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.

Genotype-associated core bacteria enhance host resistance against kiwifruit bacterial canker

Both the phyllosphere and rhizosphere are inhabited by different kinds of microorganisms that are closely related to plant growth and health. However, it is not clear whether disease-resistant cultivars shape the microbiome to facilitate disease resistance. In this study, significant differences were found in the aboveground and belowground bacterial communities of disease-resistant and disease-susceptible cultivars grown in the same kiwifruit orchard. The phyllosphere of the resistant cultivar 'Wanjin' showed greater enrichment of Pseudomonas spp. and Sphingomonas spp. than the susceptible cultivar 'Donghong'. The rhizosphere microbes of 'Wanjin' were less affected by field location, with significantly greater bacterial abundance than those of 'Donghong' and more bacteria with potential biocontrol properties. Pseudomonas syringae pv. actinidiae (Psa) infection significantly affected the microbiome of the phyllosphere of kiwifruit plants, especially that of 'Donghong'. Resistant and susceptible kiwifruit cultivars exhibit distinct beneficial microbial recruitment strategies under Psa challenge. The phyllosphere of 'Donghong' in Jinzhai was enriched with Sphingomonas spp. and Pantoea spp. under Psa infection, while the rhizosphere of 'Wanjin' was enriched with Sphingomonas spp. and Novosphingobium spp. We further identified five key biomarkers within the microbial community associated with Psa infection. Inoculation experiments showed that Lysobacter sp. R34, Stenotrophomonas sp. R31, Pseudomonas sp. R10 and RS54, which were isolated from belowground compartments of 'Wanjin', could positively affect plant performance under Psa challenge. The combination use of Pseudomonas sp. R10 and Stenotrophomonas sp. R31 significantly improve the management of kiwifruit canker. Our findings provided novel insights into soil-microbe-plant interactions and the role of microbes in plant disease resistance and susceptibility.

A Novel Strain Burkholderia theae GS2Y Exhibits Strong Biocontrol Potential Against Fungal Diseases in Tea Plants (Camellia sinensis)

BACKGROUND

Tea plants (Camellia sinensis) are widely cultivated cash crops. However, fungal diseases lead to significant reductions in both the yield and quality of tea. Therefore, searching for economical, eco-friendly, and efficient biological control measures is crucial for protecting tea plants from pathogenic fungi.

METHODS

The confrontation assays were performed to identify the antagonistic bacteria against tea pathogenic fungi and evaluate the antifungal activity of these bacteria.

RESULTS

Here, three tea pathogenic fungi were identified: Colletotrichum siamense HT-1, Diaporthe phaseolorum HT-3, and Fusarium fujikuroi HT-4. Notably, D. phaseolorum was the first to be reported in tea plants in China. Some tea pathogenic fungi showed a high relative abundance, suggesting a potential disease risk in tea plantations. Strain GS2Y, isolated from tea rhizosphere soil, exhibited strong antifungal activity against tea pathogenic fungi and represented a novel species within the genus Burkholderia, designated as Burkholderia theae. GS2Y could directly inhibit tea pathogenic fungi by disrupting the cellular structures and protect tea plants from fungal diseases caused by C. siamense HT-1 and D. phaseolorum HT-3.

CONCLUSIONS

B. theae GS2Y might function as a potentially valuable resource for biocontrol agents, laying the foundation for the development of strategies to manage fungal diseases in tea plants.

Integrated Analysis of Metabolites and Microorganisms Reveals the Anthracnose Resistance Benefits from Cyanidin Mediated by Proteobacteria in Tea Plants

Anthocyanins, key quality components of tea, act as an important bridge between plants and the environment due to their function on protecting plants from biotic and abiotic irritants. This study aimed to assess the interactions between anthocyanins metabolism and the environment. Purple (P) and green (G) leaves with different anthocyanin contents were inoculated with tea plant anthracnose. High-throughput metabolomics and 16S microbial diversity sequencing methods were used to screen the anthocyanin fractions of tea plant leaves responsive to anthracnose. The interconnections between metabolites and the resistance of phyllosphere microorganisms to fungal pathogens were then analyzed. The results showed that leaves with high anthocyanin content (0.14% of diseased area ratio) were less impacted by anthracnose infestation than leaves with low anthocyanin (3.12%). The cyanidin content decreased after infection in purple leaves (PR) and increased in green leaves (GR). The relative abundance of Cyanobacteria was suppressed by the significant enrichment of Proteobacteria after anthracnose infection in green leaves. However, there were no significant differences between these two groups of microorganisms in purple leaves. Collinear network analysis revealed a strong correlation between Cyanobacteria and Dihydrosorbinol and between Proteobacteria and cyanidin metabolites. Among them, OTU456 (Bosea) was identified as the key taxonomic group of bacterial communities in the green-infected leaf network. In summary, the anthracnose resistance benefits from cyanidin mediated by proteobacteria in tea plants. These results deepen our understanding of the regulation of secondary metabolism in tea plants and the formation of plant resistance.

The epidemic occurrence of decline disease in bayberry trees altered plant and soil related microbiome and metabolome

BACKGROUND

In China, decline disease with unknown etiology appeared as an epidemic among bayberry trees in the southern area of the Yangtze River. Furthermore, the use of beneficial microbes has been reported to be able to reduce the incidence of this disease, emphasizing the association of this disease with microorganisms. Therefore, it has become critical to uncover the microbiome's function and related metabolites in remodeling the immunity of bayberry trees under biotic or abiotic stresses.

RESULTS

The amplicon sequencing data revealed that decline disease significantly altered bacterial and fungal communities, and their metabolites in the four distinct niches, especially in the rhizosphere soils and roots. Furthermore, the microbial communities in the four niches correlated with the metabolites of the corresponding niches of bayberry plants, and the fungal and bacterial networks of healthy trees were shown to be more complex than those of diseased trees. In addition, the role of microbiome in the resistance of bayberry trees to the occurrence of decline disease was justified by the isolation, identification, and characterization of important microorganisms such as significantly enriched Bacillus ASV804, Pseudomonas ASV815 in healthy plants, and significantly enriched Stenotrophomonas ASV719 in diseased plants.

CONCLUSION

Overall, our study revealed that the occurrence of decline disease altered the microbiome and its metabolites in four ecological niches in particular rhizosphere soils and roots of bayberry, which provides new insight into the control of bayberry decline disease.

DNA metabarcoding analyses reveal fine-scale microbiome structures on Western Canadian bat wings

Healthy wings are vital for the survival and reproduction of bats, and wing microbiome is a key component of bat wing health. However, relatively little is known about the wing microbiome of bats in western Canada where the white nose syndrome has become an increasing threat. Here, we used DNA metabarcoding to investigate the bacterial and fungal communities on the wings of three bat species: the big brown bat (Eptesicus fuscus), the Yuma myotis (Myotis yumanensis), and the little brown myotis (M. lucifugus) from four field sites in Lillooet, British Columbia, Canada. The bacterial 16S rRNA metabarcoding revealed a total of 4,167 amplicon sequence variants (ASVs) belonging to 27 phyla, 639 genera, and 533 known and 2,423 unknown species. The wing bacteria were dominated by phyla Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria, and the most common genera were Delftia, Bordetella, Sphingomonas, Phyllobacterium, Bradyrhizobium, Pseudomonas, and Corynebacterium. The fungal internal transcribed spacer (ITS) metabarcoding revealed a total of 11,722 ASVs belonging to 16 phyla, 806 genera, and 1,420 known and 10,302 unknown species. The wing fungi were dominated by phyla Ascomycota, Basidiomycota, and Motierellomycota, and the most common genera were Cladosporium, Aspergillus, and Mycosphaerella. Principal coordinates analysis showed that both bat species and field sites contributed variably to the diversity and distribution of bacterial and fungal communities on bat wings. Interestingly, both positive and negative correlations were found in their relative abundances among several groups of microbial taxa. We discuss the implications of our results for bat health, including the management of P. destructans infection and white-nose syndrome spread.

IMPORTANCE

Microbiomes play important roles in host health. White-nose syndrome (WNS), a fungal infection of bat wings and muzzles, has threatened bat populations across North America since 2006. Recent research suggest that the skin microbiome of bats may play a significant role in bat's susceptibility to WNS. However, relatively little is known about the skin microbiome composition and function in bats in Western Canada, a region with a high diversity of bats, but WNS has yet to be a major issue. Here, we revealed high bacterial and fungal diversities on the skin of three common bat species in Lillooet, British Columbia, including several highly prevalent microbial species that have been rarely reported in other regions. Our analyses showed fine-scale structures of bat wing microbiome based on local sites and bat species. The knowledge obtained from WNS-naïve bat populations in this study may help develop mitigation and management strategies against WNS.

The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota

The microbiota of medicinal plants is known to be highly specific and can contribute to medicinal activity. However, the majority of plant species have not yet been studied. Here, we investigated the phyllosphere composition of two common Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii, by a polyphasic approach combining analyses of metagenomic DNA and isolates. Microbial abundance estimated via qPCR using specific marker gene primers showed that all leaf samples were densely colonized, with up to 108 per gram of leaf, with higher bacterial and fungal abundance than Archaea. While no statistically significant differences between both plant species were found for abundance, amplicon sequencing of 16S rRNA and ITS genes revealed distinct microbiota compositions. Only seven of the 27 genera isolated were represented on both plants, e.g. dominant Sphingomonas spp., and numerous members of Xanthomonadaceae and Enterobacteriaceae. The most dominant fungal families on both plants were Cladosporiaceae, Mycosphaerellaceae and Trichosphaeriaceae. In addition, 225 plant-specific isolates were identified, with Pseudomonadota and Enterobacteriaceae being dominant. Interestingly, 29 isolates are likely species previously unknown, and 14 of these belong to Burkholderiales. However, a high proportion, 56% and 40% of the isolates from E. lateriflora and F. thonningii, respectively, were characterized as various Escherichia coli. The growth of most of the bacterial isolates was not influenced by extractable secondary metabolites of plants. Our results suggest that a specific and diverse microbial community inhabits the leaves of both E. lateriflora and F. thonningii, including potentially new species and producers of antimicrobials.

Selenium in soil enhances resistance of oilseed rape to Sclerotinia sclerotiorum by optimizing the plant microbiome

Plants can recruit beneficial microbes to enhance their ability to resist disease. It is well established that selenium is beneficial in plant growth, but its role in mediating microbial disease resistance remains poorly understood. Here, we investigated the correlation between selenium, oilseed rape rhizosphere microbes, and Sclerotinia sclerotiorum. Soil application of 0.5 and 1.0 mg kg-1 selenium [selenate Na2SeO4, Se(VI) or selenite Na2SeO3, Se(IV)] significantly increased the resistance of oilseed rape to Sclerotinia sclerotiorum compared with no selenium application, with a disease inhibition rate higher than 20% in Se(VI)0.5, Se(IV)0.5 and Se(IV)1.0 mg kg-1 treatments. The disease resistance of oilseed rape was related to the presence of rhizosphere microorganisms and beneficial bacteria isolated from the rhizosphere inhibited Sclerotinia stem rot. Burkholderia cepacia and the synthetic community consisting of Bacillus altitudinis, Bacillus megaterium, Bacillus cereus, Bacillus subtilis, Bacillus velezensis, Burkholderia cepacia, and Flavobacterium anhui enhanced plant disease resistance through transcriptional regulation and activation of plant-induced systemic resistance. In addition, inoculation of isolated bacteria optimized the bacterial community structure of leaves and enriched beneficial microorganisms such as Bacillus, Pseudomonas, and Sphingomonas. Bacillus isolated from the leaves were sprayed on detached leaves, and it also performed a significant inhibition effect on Sclerotinia sclerotiorum. Overall, our results indicate that selenium improves plant rhizosphere microorganisms and increase resistance to Sclerotinia sclerotiorum in oilseed rape.

The response of microbiome assembly within different niches across four stages to the cultivation of glyphosate-tolerant and conventional soybean varieties

Introduction

Plants are inherently connected with the microbiome, which plays a crucial role in regulating various host plant biological processes, including immunity, nutrient acquisition, and resistance against abiotic and biotic stresses. Many factors affect the interaction between plants and microbiome.

Methods and results

In this study, microbiome samples were collected from five niches (bulk soil, rhizoplane, root endosphere, phylloplane, and leaf endosphere) across four developmental stages (seedling, flowering, podding, and maturity) of various soybean varieties. Composition and structure of bacterial and fungal communities were analyzed using 16S rRNA gene and ITS (Internally Transcribed Spacer) region amplicon sequencing. It was observed that both niches and developmental stages significantly impact on the assembly and composition of soybean microbiome. However, variety, presence of a transgene, and glyphosate application had minimal effects on microbial communities. The dominant microbiome varied across the five niches, with most containing beneficial microbial communities capable of promoting plant growth or increasing disease resistance. Types and abundance of the dominant microbes affected network stability, potentially resulting in functional changes in different ecological niches.

Conclusion

This study provides theoretical evidence for microbial protection of plants against diseases and demonstrates that systematic analysis of the composition and diversity of soybean microbiomes can contribute to the development of biological control technologies.

Biological Decline of Alfalfa Is Accompanied by Negative Succession of Rhizosphere Soil Microbial Communities

The growth and biological decline of alfalfa may be linked to the rhizosphere microbiome. However, plant-microbe interactions in the rhizosphere of alfalfa and associated microbial community variations with stand age remain elusive. This study explored the successional pattern of rhizosphere microbial communities across different aged alfalfa stands and its relationship with alfalfa decline. Rhizosphere soils were collected from 2- and 6-year-old alfalfa stands. Control soils were collected from interspaces between alfalfa plants in the same stands. Soil bacterial and fungal communities were characterized by 16S and ITS rRNA gene sequencing, respectively. Specific microbial taxa colonized the rhizosphere soils, but not the control soils. The rhizosphere-specific taxa mainly included potentially beneficial genera (e.g., Dechloromonas, Verrucomicrobium) in the young stand and harmful genera (e.g., Peziza, Campylocarpon) in the old stand. Alfalfa roots regulated soil microbial communities by selective promotion or inhibition of distinct taxa. The majority of time-enriched taxa were reported as harmful fungi, whose relative abundances were negatively correlated with plant traits. Time-depleted taxa were mostly known as beneficial bacteria, which had relative abundances positively correlated with plant traits. The relative abundances of functional bacterial genes associated with vancomycin biosynthesis, zeatin biosynthesis, and amino acid metabolism trended lower in rhizosphere soils from the old stand. An upward trend was observed for fungal pathogens and wood saprotrophs with increasing stand age. The results suggest that root activity drives the negative succession of rhizosphere microbial communities during alfalfa decline in old stands.

Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere

Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.

Effects of Grazing and Leaf Spot Disease on the Structure and Diversity of Phyllosphere Microbiome Communities in Leymus chinensis

Leymus chinensis is a high-quality forage with wide distribution. Disease is an important factor affecting the yield and quality of L. chinensis. To investigate the effect of grazing on the phyllosphere microbiome community and leaf spot disease in L. chinensis, high-throughput sequencing technology was used to study the differences in the composition and structure of the phyllosphere fungal and bacterial communities of healthy and diseased leaves under different grazing intensities. The results showed that grazing significantly reduced leaf spot disease incidence and severity. There were significant differences in the phyllosphere microbiome composition between healthy and diseased leaves, and interestingly, diseased leaves showed more complex microbial activity. Grazing altered the relative abundance of micro-organisms and affected microbial dispersal and colonization either directly through behavior or indirectly by altering plant community structure. In this study, we found that the phyllosphere microbiome responded strongly to pathogen infection, and that plants recruited beneficial microbes to protect themselves after disease development. Grazing could regulate microbial community composition and structure, either directly or indirectly, and plays a crucial role in maintaining the health of L. chinensis.

Environmentally responsive changes in mucus indicators and microbiota of Chinese sturgeon Acipensersinensis

The impact of environmental factors on the health of the endangered Chinese sturgeon (Acipenser sinensis) and the potential hazards associated with sample collection for health monitoring pose urgent need to its conservation. In this study, Chinese sturgeons were selected from indoor and outdoor environments to evaluate metabolic and tissue damage indicators, along with a non-specific immune enzyme in fish mucus. Additionally, the microbiota of both water bodies and fish mucus were determined using 16S rRNA high-throughput sequencing. The correlation between the indicators and the microbiota was investigated, along with the measurement of multiple environmental factors. The results revealed significantly higher levels of two metabolic indicators, total protein (TP) and cortisol (COR) in indoor fish mucus compared to outdoor fish mucus (p < 0.05). The activities of acid phosphatase (ACP), alkaline phosphatase (ALP), creatine kinase (CK), alanine aminotransferase (ALT), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH) were significantly higher in indoor fish, serving as indicators of tissue damage (p < 0.05). The activity of lysozyme (LZM) was significantly lower in indoor fish (p < 0.01). Biomarker analysis at the phylum and genus levels in outdoor samples revealed that microorganisms were primarily related to the catabolism of organic nutrients. In indoor environments, microorganisms displayed a broader spectrum of functions, including ecological niche establishment, host colonization, potential pathogenicity, and antagonism of pathogens. KEGG functional enrichment corroborated these findings. Dissolved oxygen (DO), electrical conductivity (EC), ammonia nitrogen (NH3-N), turbidity (TU), and chemical oxygen demand (COD) exerted effects on outdoor microbiota. Temperature (TEMP), nitrate (NO3-), total phosphorus (TP), and total nitrogen (TN) influenced indoor microbiota. Changes in mucus indicators, microbial structure, and function in both environments were highly correlated with these factors. Our study provides novel insights into the health impacts of different environments on Chinese sturgeon using a non-invasive method.

Stress mitigation mechanism of rice leaf microbiota amid atmospheric deposition of heavy metals

Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.

Rhizosphere Bacteria Help to Compensate for Pesticide-Induced Stress in Plants

Although exogenous chemicals frequently exhibit a biphasic response in regulating plant growth, characterized by low-dose stimulation and high-dose inhibition, the underlying mechanisms remain elusive. This study demonstrates, for the first time, the compensatory function of rhizosphere microbiota in assisting plants to withstand pesticide stress. It was observed that pak choi plants, in response to foliar-spraying imidacloprid at both low and high doses, could increase the total number of rhizosphere bacteria and enrich numerous beneficial bacteria. These bacteria have capabilities for promoting plant growth and degrading the pesticide, such as Nocardioides, Brevundimonas, and Sphingomonas. The beneficial bacterial communities were recruited by stressed plants through increasing the release of primary metabolites in root exudates, such as amino acids, fatty acids, and lysophosphatidylcholines. At low doses of pesticide application, the microbial compensatory effect overcame pesticide stress, leading to plant growth promotion. However, with high doses of pesticide application, the microbial compensatory effect was insufficient to counteract pesticide stress, resulting in plant growth inhibition. These findings pave the way for designing improved pesticide application strategies and contribute to a better understanding of how rhizosphere microbiota can be used as an eco-friendly approach to mitigate chemical-induced stress in crops.

Comprehensive analysis of spatial heterogeneity reveals the important role of the upper-layer fermented grains in the fermentation and flavor formation of Qingxiangxing baijiu

Different spatial positions lead to inconsistent fermentation effects and flavors, however, the spatial heterogeneity of Qingxiangxing (QXX) Baijiu remains unknown. We investigated the microbes, flavors, and physicochemical properties of different layers in fermented grains of QXX Baijiu using Illumina HiSeq sequencing, two-dimensional gas chromatography-mass spectrometry (GC × GC-MS) and ultra-high performance liquid chromatography-mass (UHPLC-MS). A total of 79 volatiles, 1596 metabolites, 50 bacterial genera, and 52 fungal genera were identified. The contents distribution followed the order: upper layer > bottom layer > middle layer. Organic acids and derivatives were the main differential metabolites across the three layers. Starch, pH, and reducing sugar levels increased from the upper to bottom layer. Saccharomyces and Lactobacillus were dominant microbes. Pediococcus, the biomarker of upper layer, showed positive correlations with formic acid, ethyl lactate, acetic acid, ethyl linoleate, and ethyl oleate. These findings deepen our understanding of the fermentation and flavor formation mechanisms of QXX Baijiu.