Phyllosphere Microbiome in Plant Health and Disease

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.

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.

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.

Cold atmospheric plasma treatment induces oxidative stress and alters microbial community profile in the leaves of sweet basil (Ocimum basilicum var. Kiera) plant

The oxidative species generated by cold atmospheric plasma (CAP) treatment can impact the plant stress response system. We hypothesized that this response is not limited to the site of CAP application and it is transmitted through the plant. The resulting stress response can influence the plant microbiome on the intact plant. These hypotheses were tested by the application of CAP to live sweet basil (Ocimum basilicum var. Kiera). A single upper leaf of the plant underwent a 60 s CAP treatment at three different wattage intensity levels. Reactive oxygen species (ROS) generation in directly treated leaves and leaves in the vicinity of the treatment site (i.e., one, two, or three nodes away) was measured using the fluorescein degradation assay (ex/em: 485/525). Leaves directly exposed to CAP showed a marked increase in ROS production. Interestingly, basil leaves not directly treated by CAP also showed a significant (p < 0.05) increase in ROS generation compared to untreated control, extending to the two nearest nodes from the treatment site in all plants tested. The leaf microbiomes were evaluated using 16S rRNA gene sequencing. CAP appeared to drive restructuring of the leaf microbiota profiles, despite maintaining a similar α-diversity. CAP treatment intensity led to significant differences (p < 0.05) in the relative abundances of a variety of dominant bacterial families (e.g., Psuedomonadaceae and Streptomycetaceae) and phyla, and the effects on certain taxa were dependent on leaf distance from the treatment site. CAP's ability to restructure plant microbiota may have applications to improve produce microbial safety and shelf-life. PRACTICAL APPLICATION: Cold atmospheric plasma induces a stress response in a living plant beyond the site of application. This response includes an increase in the production of reactive oxygen species that can trigger pathways to enhance the production of phytochemicals. CAP treatment also alters the microbial community profile, possibly through plant stress response. Results from this study can be useful in developing CAP treatment of intact plant for improved growth, production of health-benefiting phytochemicals, and managing its microbiota.

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.

Groundbreaking Technologies and the Biocontrol of Fungal Vascular Plant Pathogens

This review delves into innovative technologies to improve the control of vascular fungal plant pathogens. It also briefly summarizes traditional biocontrol approaches to manage them, addressing their limitations and emphasizing the need to develop more sustainable and precise solutions. Powerful tools such as next-generation sequencing, meta-omics, and microbiome engineering allow for the targeted manipulation of microbial communities to enhance pathogen suppression. Microbiome-based approaches include the design of synthetic microbial consortia and the transplant of entire or customized soil/plant microbiomes, potentially offering more resilient and adaptable biocontrol strategies. Nanotechnology has also advanced significantly, providing methods for the targeted delivery of biological control agents (BCAs) or compounds derived from them through different nanoparticles (NPs), including bacteriogenic, mycogenic, phytogenic, phycogenic, and debris-derived ones acting as carriers. The use of biodegradable polymeric and non-polymeric eco-friendly NPs, which enable the controlled release of antifungal agents while minimizing environmental impact, is also explored. Furthermore, artificial intelligence and machine learning can revolutionize crop protection through early disease detection, the prediction of disease outbreaks, and precision in BCA treatments. Other technologies such as genome editing, RNA interference (RNAi), and functional peptides can enhance BCA efficacy against pathogenic fungi. Altogether, these technologies provide a comprehensive framework for sustainable and precise management of fungal vascular diseases, redefining pathogen biocontrol in modern agriculture.

Plant Colonization by Biocontrol Bacteria and Improved Plant Health: A Review

The use of biological control agents is one of the best strategies available to combat the plant diseases in an ecofriendly manner. Biocontrol bacteria capable of providing beneficial effect in crop plant growth and health, have been developed for several decades. It highlights the need for a deeper understanding of the colonization mechanisms employed by biocontrol bacteria to enhance their efficacy in plant pathogen control. The present review deals with the in-depth understanding of steps involved in host colonization by biocontrol bacteria. The colonization process starts from the root zone, where biocontrol bacteria establish initial interactions with the plant's root system. Moving beyond the roots, biocontrol bacteria migrate and colonize other plant organs, including stems, leaves, and even flowers. Also, the present review attempts to explore the mechanisms facilitating bacterial movement within the plant such as migrating through interconnected spaces such as vessels or in the apoplast, and applying quorum sensing or extracellular enzymes during colonization and what is needed to establish a long-term association within a plant. The impacts on microbial community dynamics, nutrient cycling, and overall plant health are discussed, emphasizing the intricate relationships between biocontrol bacteria and the plant's microbiome and the benefits to the plant's above-ground parts, the biocontrol 40 bacteria confer. By unraveling these mechanisms, researchers can develop targeted strategies for enhancing the colonization efficiency and overall effectiveness of biocontrol bacteria, leading to more sustainability and resilience.

Local Scale Biogeographic Variation in the Magnolia (Magnolia grandiflora) Phyllosphere

The phyllosphere (aerial plant surfaces colonized by microorganisms) remains an understudied ecosystem in terms of bacterial biogeography, particularly at intermediate or local spatial scales. This study characterized the phyllosphere bacterial community on the leaves of 87 Magnolia grandiflora trees sampled throughout a small town, encompassing an area of approximately 60 km2. Sequencing of the 16S ribosomal RNA gene revealed the dominant bacterial phyla to be Alphaproteobacteria, Bacteroidetes, and Acidobacteria, consistent with other studies of the phyllosphere. There was a small but significant relationship between the phyllosphere community similarity and the distance between the trees (i.e., trees further apart were more likely to have dissimilar bacterial communities). There was also a relationship between the assigned categories of tree height (low, medium, high) and the phyllosphere bacterial community composition, with the trees in the high category having more diverse bacterial communities on their leaves than the shorter trees. This study provides insight into the relationship between phyllosphere community composition and host tree characteristics and shows that the distance between M. grandiflora trees has a significant, albeit low, influence on bacterial composition. These findings contribute to a deeper understanding of phyllosphere microbiome biogeography, highlighting how individual tree characteristics and spatial proximity shape phyllosphere bacterial communities.

Roles of Phyllosphere Microbes in Rice Health and Productivity

The phyllosphere, comprising the aerial portions of plants, is a vibrant ecosystem teeming with diverse microorganisms crucial for plant health and productivity. This review examines the functional roles of phyllosphere microorganisms in rice (Oryza sativa), focusing on their importance in nutrient uptake, disease resistance, and growth promotion. The molecular mechanisms underlying these interactions are explored along with their potential applications in enhancing sustainable rice production. The symbiotic relationships between rice plants and their associated microorganisms are highlighted, offering insights into improved agricultural practices. Furthermore, this review addresses the challenges and future developments in translating laboratory findings into practical applications. By synthesizing current research, this comprehensive analysis serves as a valuable resource for leveraging phyllosphere microbes in rice farming and related fields.

Zinc oxide nanoparticles cooperate with the phyllosphere to promote grain yield and nutritional quality of rice under heatwave stress

To address rising global food demand, the development of sustainable technologies to increase productivity is urgently needed. This study revealed that foliar application of zinc oxide nanoparticles (ZnO NPs; 30 to 80 nm, 0.67 mg/d per plant, 6 d) to rice leaves under heatwave (HW) stress increased the grain yield and nutritional quality. Compared with the HW control, the HWs+ZnO group presented increases in the grain yield, grain protein content, and amino acid content of 22.1%, 11.8%, and 77.5%, respectively. Nanoscale ZnO aggregated on the leaf surface and interacted with leaf surface molecules. Compared with that at ambient temperature, HW treatment increased the dissolution of ZnO NPs on the leaf surface by 25.9% and facilitated their translocation to mesophyll cells. The Zn in the leaves existed as both ionic Zn and particulate ZnO. Compared with the HW control, foliar application of ZnO NPs under HW conditions increased leaf nutrient levels (Zn, Mn, Cu, Fe, and Mg) by 15.8 to 416.9%, the chlorophyll content by 22.2 to 24.8%, Rubisco enzyme activity by 21.2%, and antioxidant activity by 26.7 to 31.2%. Transcriptomic analyses revealed that ZnO NPs reversed HW-induced transcriptomic dysregulation, thereby enhancing leaf photosynthesis by 74.4%. Additionally, ZnO NPs increased the diversity, stability, and enrichment of beneficial microbial taxa and protected the phyllosphere microbial community from HW damage. This work elucidates how NPs interact with the phyllosphere, highlighting the potential of NPs to promote sustainable agriculture, especially under extreme climate events (e.g., HWs).

Phyllospheric microbial community structure and carbon source metabolism function in tobacco wildfire disease

The phyllospheric microbial composition of tobacco plants is influenced by multiple factors. Disease severity level is one of the main influencing factors. This study was designed to understand the microbial community in tobacco wildfire disease with different disease severity levels. Tobacco leaves at disease severity level of 1, 5, 7, and 9 (L1, L5, L7, and L9) were collected; both healthy and diseased leaf tissues for each level were collected. The community structure and diversity in tobacco leaves with different disease severity levels were compared using high-throughput technique and Biolog Eco. The results showed that in all healthy and diseased tobacco leaves, the most dominant bacterial phylum was Proteobacteria with a high prevalence of genus Pseudomonas; the relative abundance of Pseudomonas was most found at B9 diseased samples. Ascomycota represents the most prominent fungal phylum, with Blastobotrys as the predominant genus. In bacterial communities, the Alpha diversity of healthy samples was higher than that of diseased samples. In fungal community, the difference in Alpha diversity between healthy and diseased was not significant. LEfSe analysis showed that the most enriched bacterial biomarker was unclassified_Gammaproteobacteria in diseased samples; unclassified_Alcaligenaceae were the most enrich bacterial biomarker in healthy samples. FUNGuild analysis showed that saprotroph was the dominated mode in health and lower diseased samples, The abundance of pathotroph-saprotroph and pathotroph-saprotroph-symbiotroph increases at high disease levels. PICRUSt analysis showed that the predominant pathway was metabolism function, and most bacterial gene sequences seem to be independent of the disease severity level. The Biolog Eco results showed that the utilization rates of carbon sources decrease with increasing disease severity level. The current study revealed the microbial community's characteristic of tobacco wildfire disease with different disease severity levels, providing scientific references for the control of tobacco wildfire disease.

The impact of pine wilt disease on the endophytic microbial communities structure of Pinus koraiensis

Pine Wilt Disease (PWD) is a devastating pine tree disease characterized by rapid onset, high mortality rate, quick spread, and difficulty in control. Plant microbiome plays a significant role in the development of PWD. However, the endophytic microbial communities of Pinus koraiensis infected by pine wood nematode (PWN) Bursaphelenchus xylophilus remain largely unexplored. In this study, we analyzed the structural changes of endophytic communities of P. koraiensis after infection by the PWN using high-throughput sequencing technology. The results showed that the community structure underwent significant changes as the degree of PWN infection intensified. The diversity and abundance of endophytic fungi in P. koraiensis increased, while those of endophytic bacteria in P. koraiensis decreased during the infection process. Meanwhile, the abundance of some dominant microorganisms has also changed, including species such as Graphilbum and Pseudoalteromonas. Functional prediction analysis showed that the functional composition of endophytic fungi in P. koraiensis was significantly different across the development of PWD, while the composition of endophytic bacteria remained essentially similar. The results indicated that PWN infection had a significant impact on the structure, diversity, abundance, and functional gene composition of endophytic microbial communities in P. koraiensis, and most of the main endophytic microbial groups tended to coordinate with each other. This work provides a better understanding of the changes in endophytic community structure and function caused by PWD infection of P. koraiensis, which may benefit the exploration of potential endophytes for PWN biocontrol.

Concepts and criteria defining emerging microbiome applications

In recent years, microbiomes and their potential applications for human, animal or plant health, food production and environmental management came into the spotlight of major national and international policies and strategies. This has been accompanied by substantial R&D investments in both public and private sectors, with an increasing number of products entering the market. Despite widespread agreement on the potential of microbiomes and their uses across disciplines, stakeholders and countries, there is no consensus on what defines a microbiome application. This often results in non-comprehensive communication or insufficient documentation making commercialisation and acceptance of the novel products challenging. To showcase the complexity of this issue we discuss two selected, well-established applications and propose criteria defining a microbiome application and their conditions of use for clear communication, facilitating suitable regulatory frameworks and building trust among stakeholders.

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

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

The relationship between atmospheric particulate matter, leaf surface microstructure, and the phyllosphere microbial diversity of Ulmus L

BACKGROUND

Plants can retain atmospheric particulate matter (PM) through their unique foliar microstructures, which has a profound impact on the phyllosphere microbial communities. Yet, the underlying mechanisms linking atmospheric particulate matter (PM) retention by foliar microstructures to variations in the phyllosphere microbial communities remain a mystery. In this study, we conducted a field experiment with ten Ulmus lines. A series of analytical techniques, including scanning electron microscopy, atomic force microscopy, and high-throughput amplicon sequencing, were applied to examine the relationship between foliar surface microstructures, PM retention, and phyllosphere microbial diversity of Ulmus L.

RESULTS

We characterized the leaf microstructures across the ten Ulmus lines. Chun exhibited a highly undulated abaxial surface and dense stomatal distribution. Langya and Xingshan possessed dense abaxial trichomes, while Lieye, Zuiweng, and Daguo had sparsely distributed, short abaxial trichomes. Duomai, Qingyun, and Lang were characterized by sparse stomata and flat abaxial surfaces, whereas Jinye had sparsely distributed but extensive stomata. The mean leaf retention values for total suspended particulate (TSP), PM2.5, PM2.5-10, PM10-100, and PM> 100 were 135.76, 6.60, 20.10, 90.98, and 13.08 µg·cm- 2, respectively. Trichomes substantially contributed to PM2.5 retention, while larger undulations enhanced PM2.5-10 retention, as evidenced by positive correlations between PM2.5 and abaxial trichome density and between PM2.5-10 and the adaxial raw microroughness values. Phyllosphere microbial diversity patterns varied among lines, with bacteria dominated by Sediminibacterium and fungi by Mycosphaerella, Alternaria, and Cladosporium. Redundancy analysis confirmed that dense leaf trichomes facilitated the capture of PM2.5-associated fungi, while bacteria were less impacted by PM and struggled to adhere to leaf microstructures. Long and dense trichomes provided ideal microhabitats for retaining PM-borne microbes, as evidenced by positive feedback loops between PM2.5, trichome characteristics, and the relative abundances of microorganisms like Trichoderma and Aspergillus.

CONCLUSIONS

Based on our findings, a three-factor network profile was constructed, which provides a foundation for further exploration into how different plants retain PM through foliar microstructures, thereby impacting phyllosphere microbial communities.

Investigating the spatiotemporal dynamics of apple tree phyllosphere bacterial and fungal communities across cultivars in orchards

The phyllosphere, a reservoir of diverse microbial life associated with plant health, harbors microbial communities that are subject to various complex ecological processes acting at multiple scales. In this study, we investigated the determinants of the spatiotemporal variation in bacterial and fungal communities within the apple tree phyllosphere, employing 16S and ITS amplicon sequencing. Our research assessed the impact of key factors-plant compartment, site, time, and cultivar-on the composition and diversity of leaf and flower microbial communities. Our analyses, based on samples collected from three cultivars in three orchards in 2022, revealed that site and time are the strongest drivers of apple tree phyllosphere microbial communities. Conversely, plant compartment and cultivar exhibited minor roles in explaining community composition and diversity. Predominantly, bacterial communities comprised Hymenobacter (25%) and Sphingomonas (10%), while the most relatively abundant fungal genera included Aureobasidium (27%) and Sporobolomyces (10%). Additionally, our results show a gradual decrease in alpha-diversity throughout the growth season. These findings emphasize the necessity to consider local microbial ecology dynamics in orchards, especially as many groups worldwide aim for the development of biocontrol strategies (e.g., by manipulating plant-microbe interactions). More research is needed to improve our understanding of the determinants of time and site-specific disparities within apple tree phyllosphere microbial communities across multiple years, locations, and cultivars.