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The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.

Bacteria on and inside leaves can influence forest tree health and resilience. The distribution and limits of a tree species' range can be influenced by various factors, with biological interactions among the most significant. We investigated the processes shaping the bacterial needle community across the species distribution of limber pine, a widespread Western conifer inhabiting a range of extreme habitats. We tested four hypotheses: (i) Needle community structure varies across sites, with site-specific factors more important to microbial assembly than host species selection; (ii) dispersal limitation structures foliar communities across the range of limber pine; (iii) the relative significance of dispersal and selection differs across sites in the tree species range; and (iv) needle age structures bacterial communities. We characterized needle communities from the needle surface and tissue of limber pine and co-occurring conifers across 16 sites in the limber pine distribution. Our findings confirmed that site characteristics shape the assembly of bacterial communities across the host species range and showed that these patterns are not driven by dispersal limitation. Furthermore, the strength of selection by the host varied by site, possibly due to differences in available microbes. Our study, by focusing on trees in their natural setting, reveals real needle bacterial dynamics in forests, which is key to understanding the balance between stochastic and deterministic processes in shaping forest tree-microbe interactions. Such understanding will be necessary to predict or manipulate these interactions to support forest ecosystem productivity or assist plant migration and adaptation in the face of global change.

Urban trees are crucial in delivering essential ecosystem services, including air pollution mitigation. This service is influenced by plant associated microbiomes, which can degrade hydrocarbons, support tree health, and influence ecological processes. Yet, our understanding of tree microbiomes remains limited, thus affecting our ability to assess and quantify the ecosystem services provided by trees as complex systems. The main hypothesis of this work was that tree microbiomes concur to hydrocarbon biodegradation, and was tested through three case studies, which collectively investigated two tree micro-habitats (phyllosphere and tree cavity organic soil—TCOS) under various conditions representing diverse ecological scenarios, by applying different culture-based and molecular techniques and at different scales. The integration of all results provided a more comprehensive understanding of the role of microbiomes in urban trees. Firstly, bacterial strains isolated from the phyllosphere of Quercus ilex were characterized, indicating the presence of Plant-Growth Promoting bacteria and strains able to catabolize PAHs, particularly naphthalene and phenanthrene. Secondly, naphthalene biodegradation on artificially spiked Hedera helix leaves was quantified in greenhouse experiments on inoculated and untreated plants. The persistence of the inoculated strain and community structure of epiphytic bacteria were assessed by Illumina sequencing of V5–V6 hypervariable regions of 16S rRNA gene. Results showed that naphthalene degradation was initially faster on inoculated plants but later the degradation rates became similar, probably because bacterial populations with hydrocarbon-degrading abilities gradually developed also on non-inoculated plants. Finally, we explored bacterial and fungal biodiversity hosted by TCOS samples, collected from six large trees located in an urban park and belonging to different species. Microbial communities were characterized by Illumina sequencing of V5–V6 hypervariable regions of bacterial gene 16S rRNA and of fungal ITS1. Results indicated TCOS as a distinct substrate, whose microbiome is determined both by the host tree and by canopy environmental conditions and has a pronounced aerobic hydrocarbon degradation potential. Overall, a better assessment of biodiversity associated with trees and the subsequent provision of ecosystem services constitute a first step toward developing future new microbe-driven sustainable solutions, especially in terms of support for urban green planning and management policy. [ABSTRACT FROM AUTHOR]

Background: The extensive use of antibiotics in the global livestock industry in recent decades has accelerated the accumulation and dissemination of antibiotic-resistance genes (ARGs) within terrestrial ecosystems. This occurs due to the limited absorption of most antibiotics, leading to their release into the environment through feces and urine. This poses a significant threat to both the environment and human health. However, the response of antibiotic-resistant microorganisms and their ARGs in grasslands to prolonged grazing, as well as the primary microbial taxa driving the ARG distribution, remain poorly understood, especially within various microhabitats. In this study, we characterized ARGs in the phyllosphere, litter, and soil after decades of livestock grazing in a meadow steppe. We particularly focused on identifying the major members of the microbial community influencing ARGs and the distinction between microbial generalists and specialists. Results: Our findings indicate that a core set of ARGs accounted for 90% of the abundance in this plant-soil ecosystem. While the soil exhibited the highest ARG abundance, the phyllosphere, and litter displayed higher ARG diversity and diverse distribution patterns after overgrazing. Grazing increased ARG abundance by elevating the proportion of core ARGs and suppressing stochastic ARGs in the phyllosphere and litter, while it had little effect on the ARGs in the soil. Additionally, microbial generalist abundance increased, but specialist abundance decreased in the phyllosphere and litter, with no effect in the soil, under grazed conditions. Ultimately, microbial microhabitats and grazing influenced ARG community characteristics through direct (i.e., feces and other exogenous ARG input) and indirect (i.e., trampling and selective feeding) effects on nutrient availability, microbial community composition, and mobile genetic elements. The generalist community, with its broad ecological niches and phylogenetic composition, made the most significant contribution to the ARG characteristics. Conclusions: This study underscores the impact of environmental disturbances on the distributional patterns of ARGs in ecosystems, mediated by the regulation of microbial generalized species. These insights enhance our understanding of microbial control over ARGs and facilitate predictions regarding the dynamics and risk of ARGs in diverse ecological niches subjected to anthropogenic disturbances. 7ey-7_XWoViaAbs3ZbZRu7 Video Abstract [ABSTRACT FROM AUTHOR]

Plant–microbe interactions play a pivotal role in shaping host fitness, especially concerning chemical defense mechanisms. In cycads, establishing direct correlations between specific endophytic microbes and the synthesis of highly toxic defensive phytochemicals has been challenging. Our research delves into the intricate relationship between plant–microbe associations and the variation of secondary metabolite production in two closely related Zamia species that grow in distinct habitats; terrestrial and epiphytic. Employing an integrated approach, we combined microbial metabarcoding, which characterize the leaf endophytic bacterial and fungal communities, with untargeted metabolomics to test if the relative abundances of specific microbial taxa in these two Zamia species were associated with different metabolome profiles. The two species studied shared approximately 90% of the metabolites spanning diverse biosynthetic pathways: alkaloids, amino acids, carbohydrates, fatty acids, polyketides, shikimates, phenylpropanoids, and terpenoids. Co-occurrence networks revealed positive associations among metabolites from different pathways, underscoring the complexity of their interactions. Our integrated analysis demonstrated to some degree that the intraspecific variation in metabolome profiles of the two host species was associated with the abundance of bacterial orders Acidobacteriales and Frankiales, as well as the fungal endophytes belonging to the orders Chaetothyriales, Glomerellales, Heliotiales, Hypocreales, and Sordariales. We further associate individual metabolic similarity with four specific fungal endophyte members of the core microbiota, but no specific bacterial taxa associations were identified. This study represents a pioneering investigation to characterize leaf endophytes and their association with metabolomes in tropical gymnosperms, laying the groundwork for deeper inquiries into this complex domain. [ABSTRACT FROM AUTHOR]

Plants and microorganisms have been co-evolving and interacting for billions of years. Prior researchers have explored the plant's immune system responses and interaction with diverse microbes, but several ambiguities need further explanation. This review provides insight into mechanisms underlying plant–microbe interaction and knowledge dearth domains, along with possibilities to use beneficial microbes to improve plant growth, disease resistance, nutritional value, and productivity. Microorganisms in the phyllosphere and the rhizosphere could be beneficial or pathogenic. Host plants use their innate immune system and the antagonistic competence of plant-growth-promoting microbes against pathogens. The innate immune system of plants has two paramount protection forms involving different types of immune receptors, which assist in recognizing non-self-components. The first group of receptors is membrane-resident pattern recognition receptors (PRRs), which are responsible for sensing microbe-associated molecular patterns (MAMPs) and damage-associated molecular patterns (DAMPs). The second group consists of intracellular immune sensors, specifically resistance (R) proteins, astute in recognizing the structure or function of strain-specific pathogen effectors injected into host plant cells. Plants activate their pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) defense mechanisms to counter the infection. Plants benefit from certain microbes by promoting their growth, disease resistance, and resilience under various stress conditions in exchange for shelter and nutrients. [ABSTRACT FROM AUTHOR]

Background: While substantial research has explored rhizosphere and phyllosphere microbiomes, knowledge on flower microbiome, particularly in wild plants remains limited. This study explores into the diversity, abundance, and composition of bacterial and fungal communities on leaves and flowers of wild flowering plants in their natural alpine habitat, considering the influence of environmental factors. Methods: We investigated 50 wild flowering plants representing 22 families across seven locations in Austria. Sampling sites encompassed varied soil types (carbonate/silicate) and altitudes (450–2760 m). Amplicon sequencing to characterize bacterial and fungal communities and quantitative PCR to assess microbial abundance was applied, and the influence of biotic and abiotic factors assessed. Results: Our study revealed distinct bacterial and fungal communities on leaves and flowers, with higher diversity and richness on leaves (228 fungal and 91 bacterial ASVs) than on flowers (163 fungal and 55 bacterial ASVs). In addition, Gammaproteobacteria on flowers and Alphaproteobacteria on leaves suggests niche specialization for plant compartments. Location significantly shaped both community composition and fungal diversity on both plant parts. Notably, soil type influenced community composition but not diversity. Altitude was associated with increased fungal species diversity on leaves and flowers. Furthermore, significant effects of plant family identity emerged within a subset of seven families, impacting bacterial and fungal abundance, fungal Shannon diversity, and bacterial species richness, particularly on flowers. Conclusion: This study provides novel insights into the specific microbiome of wild flowering plants, highlighting adaptations to local environments and plant–microbe coevolution. The observed specificity indicates a potential role in plant health and resilience, which is crucial for predicting how microbiomes respond to changing environments, ultimately aiding in the conservation of natural ecosystems facing climate change pressures. [ABSTRACT FROM AUTHOR]

Cyanobacteria, known for their remarkable adaptability, are a diverse group of oxygenic photoautotrophic organisms found in various habitats worldwide. While their presence in aquatic ecosystems has been extensively studied, research on terrestrial and aerophytic cyanobacteria remains relatively limited, particularly concerning their taxonomic diversity and molecular characteristics. In this study, utilizing morphological and molecular data derived from the 16S rRNA gene, we unveiled and described two new species of filamentous cyanobacteria growing epiphytically on Laurus novocanariensis in the laurel forest (laurisilva) of the Canary Islands. The first species, Brasilonema novocanariensis sp. nov., belongs to a genus of aerophytic and subaerophytic nostocalean cyanobacteria. The second, Rhizonema melkonianarum sp. nov., belongs to the genus Rhizonema. The discovery of a new species of Brasilonema from the Canary Islands related to species initially found on the opposite side of the Atlantic Ocean, and recently in Asia, Europe, and Portugal, raises questions about their dispersal mechanisms, whether through natural means or human-mediated processes, prompting the need for future studies to investigate these propagation patterns. In the case of Rhizonema melkonianarum sp. nov., the transition from adapting to a basidiolichen host to inhabiting the phyllosphere of angiosperms raises ecological and evolutionary adaptation questions regarding cyanobacterial adaptability and their ecological roles in diverse habitats. This research expands our understanding of the diversity and geographic distribution of these terrestrial phyllosphere-associated cyanobacteria. [ABSTRACT FROM AUTHOR]

Currently, phylloremediation has emerged as a highly effective method for eliminating air pollutants, particularly polyaromatic hydrocarbons (PAHs). When PAHs accumulate on the phyllosphere, they significantly impact the fungal communities residing on leaf surfaces. This study aimed to investigate how pollution distribution patterns affect the diversity and PAH-degrading abilities of phyllosphere fungi, alongside identifying suitable mathematical models for PAH degradation. Leaf samples from two locations, Maradana and Sapugaskanda, were identified as having the highest PAH concentrations through principal component analysis. The fungal diversity in these highly contaminated regions was varied, with dominant species exhibiting greater PAH-degrading capabilities than those in less polluted areas. Thirty-five morphologically different epiphytic fungal strains were isolated on Potato Dextrose Agar (PDA) medium using the sample leaf wash. Two different fungal strains were selected as the best PAH degraders among those 35 different strains. These fungal strains were identified as Trichoderma harzianum P4M-16, and Fusarium solani P11M-46 based on ITS sequence data. Notably, these fungal species were more prevalent in highly polluted urban areas compared to less contaminated sites. High-Performance Liquid Chromatography (HPLC) analysis revealed that these two fungal species degrade PAHs more efficiently than others. Their kinetics assays demonstrated alignment with four degradation models when breaking down phenanthrene, naphthalene, pyrene, and anthracene. Scanning electron microscopy images showed that these fungi function as endophytes, extending their mycelium into the core leaf tissue layers beyond the epidermis. Gas Chromatography-Mass Spectrometry (GCMS) analysis indicated that F. solani P11M-46 produced non-toxic byproducts during the breakdown of phenanthrene and anthracene, confirming their eco-friendly nature. Overall, our findings suggest the promising potential of using phyllosphere fungi in bioremediation processes for environmental pollutants such as PAHs. [ABSTRACT FROM AUTHOR]

Shelter‐building insects are important ecosystem engineers, playing critical roles in structuring arthropod communities. Nonetheless, the influence of leaf shelters and arthropods on plant–associated microbiota remains largely unexplored. Arthropods that visit or inhabit plants can contribute to the leaf microbial community, resulting in significant changes in plant–microbe interactions. By artificially constructing leaf shelters, we provide evidence that shelter‐building insects influence not only the arthropod community structure but also impact the phyllosphere microbiota. Leaf shelters exhibited higher abundance and richness of arthropods, changing the associated arthropod community composition. These shelters also altered the composition and community structure of phyllosphere microbiota, promoting greater richness and diversity of bacteria at the phyllosphere. In leaf shelters, microbial diversity positively correlated with the richness and diversity of herbivores. These findings demonstrate the critical role of leaf shelters in structuring both arthropod and microbial communities through altered microhabitats and species interactions. [ABSTRACT FROM AUTHOR]

The role that aquatic aerosols might play in inter-ecosystem exchanges in freshwater riparian environments has largely been understudied. In these environments, where freshwater streams are used both as drinking water and for treated waste disposal, water features like waterfalls, downed trees, and increased streamflow can serve as bioaerosol producers. Such water features could have an important role in the bacterial colonization of surrounding surfaces, including the riparian phyllosphere. In this study, we explore the influence of a freshwater stream's bacterial community composition and micropollution on riparian maple leaves exposed to bioaerosols produced from that stream. Using culture-based and non-culture-based techniques, we compared phylloplane microbial communities in riparian zones, adjacent non-riparian forested zones, and the surface waters of the stream. In this system, riparian zone maple leaf surfaces had higher bacterial counts than non-riparian zone trees. Using metagenomic profiling of the 16S rRNA gene, we found that, while microbial communities on leaves in both the riparian zone and forested sites were diverse, riparian zone bacterial communities were significantly more diverse. In addition, we found that riparian leaf bacterial communities shared more amplicon sequence variants (ASVs) with stream bacterial communities than forest leaves, indicating that the riparian zone phyllosphere is likely influenced by bioaerosols produced from water surfaces. [ABSTRACT FROM AUTHOR]

Abstract Background The extensive use of antibiotics in the global livestock industry in recent decades has accelerated the accumulation and dissemination of antibiotic-resistance genes (ARGs) within terrestrial ecosystems. This occurs due to the limited absorption of most antibiotics, leading to their release into the environment through feces and urine. This poses a significant threat to both the environment and human health. However, the response of antibiotic-resistant microorganisms and their ARGs in grasslands to prolonged grazing, as well as the primary microbial taxa driving the ARG distribution, remain poorly understood, especially within various microhabitats. In this study, we characterized ARGs in the phyllosphere, litter, and soil after decades of livestock grazing in a meadow steppe. We particularly focused on identifying the major members of the microbial community influencing ARGs and the distinction between microbial generalists and specialists. Results Our findings indicate that a core set of ARGs accounted for 90% of the abundance in this plant-soil ecosystem. While the soil exhibited the highest ARG abundance, the phyllosphere, and litter displayed higher ARG diversity and diverse distribution patterns after overgrazing. Grazing increased ARG abundance by elevating the proportion of core ARGs and suppressing stochastic ARGs in the phyllosphere and litter, while it had little effect on the ARGs in the soil. Additionally, microbial generalist abundance increased, but specialist abundance decreased in the phyllosphere and litter, with no effect in the soil, under grazed conditions. Ultimately, microbial microhabitats and grazing influenced ARG community characteristics through direct (i.e., feces and other exogenous ARG input) and indirect (i.e., trampling and selective feeding) effects on nutrient availability, microbial community composition, and mobile genetic elements. The generalist community, with its broad ecological niches and phylogenetic composition, made the most significant contribution to the ARG characteristics. Conclusions This study underscores the impact of environmental disturbances on the distributional patterns of ARGs in ecosystems, mediated by the regulation of microbial generalized species. These insights enhance our understanding of microbial control over ARGs and facilitate predictions regarding the dynamics and risk of ARGs in diverse ecological niches subjected to anthropogenic disturbances. Video Abstract

Abstract Plants and microorganisms have been co-evolving and interacting for billions of years. Prior researchers have explored the plant’s immune system responses and interaction with diverse microbes, but several ambiguities need further explanation. This review provides insight into mechanisms underlying plant–microbe interaction and knowledge dearth domains, along with possibilities to use beneficial microbes to improve plant growth, disease resistance, nutritional value, and productivity. Microorganisms in the phyllosphere and the rhizosphere could be beneficial or pathogenic. Host plants use their innate immune system and the antagonistic competence of plant-growth-promoting microbes against pathogens. The innate immune system of plants has two paramount protection forms involving different types of immune receptors, which assist in recognizing non-self-components. The first group of receptors is membrane-resident pattern recognition receptors (PRRs), which are responsible for sensing microbe-associated molecular patterns (MAMPs) and damage-associated molecular patterns (DAMPs). The second group consists of intracellular immune sensors, specifically resistance (R) proteins, astute in recognizing the structure or function of strain-specific pathogen effectors injected into host plant cells. Plants activate their pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) defense mechanisms to counter the infection. Plants benefit from certain microbes by promoting their growth, disease resistance, and resilience under various stress conditions in exchange for shelter and nutrients. Graphical Abstract

Abstract Background While substantial research has explored rhizosphere and phyllosphere microbiomes, knowledge on flower microbiome, particularly in wild plants remains limited. This study explores into the diversity, abundance, and composition of bacterial and fungal communities on leaves and flowers of wild flowering plants in their natural alpine habitat, considering the influence of environmental factors. Methods We investigated 50 wild flowering plants representing 22 families across seven locations in Austria. Sampling sites encompassed varied soil types (carbonate/silicate) and altitudes (450–2760 m). Amplicon sequencing to characterize bacterial and fungal communities and quantitative PCR to assess microbial abundance was applied, and the influence of biotic and abiotic factors assessed. Results Our study revealed distinct bacterial and fungal communities on leaves and flowers, with higher diversity and richness on leaves (228 fungal and 91 bacterial ASVs) than on flowers (163 fungal and 55 bacterial ASVs). In addition, Gammaproteobacteria on flowers and Alphaproteobacteria on leaves suggests niche specialization for plant compartments. Location significantly shaped both community composition and fungal diversity on both plant parts. Notably, soil type influenced community composition but not diversity. Altitude was associated with increased fungal species diversity on leaves and flowers. Furthermore, significant effects of plant family identity emerged within a subset of seven families, impacting bacterial and fungal abundance, fungal Shannon diversity, and bacterial species richness, particularly on flowers. Conclusion This study provides novel insights into the specific microbiome of wild flowering plants, highlighting adaptations to local environments and plant–microbe coevolution. The observed specificity indicates a potential role in plant health and resilience, which is crucial for predicting how microbiomes respond to changing environments, ultimately aiding in the conservation of natural ecosystems facing climate change pressures.

Abstract 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.

Abstract Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems.

Abstract 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.

Abstract The foliage of the small-leaved lime (Tilia cordata) is characterised by the nerve axils being grown by non-glandular trichomes, which trait contributes to the enhanced retention of the particulate matter (PM). This fact may disturb the ecological service of T. cordata related to the structure of its leaves, which is to provide acarodomatia (micro-shelters) for the predatory mites of the Phytoseiidae family. Phytoseiids are natural enemies of a variety of plant pests, widely applied in integrated pest management (IPM). Their occurrence is largely related to acarodomatia in which these mites hide, feed, reproduce, and develop. For the first time, the influence of PM deposition within spaces typically occupied by phytoseiids is investigated. Experimental populations of Euseius finlandicus were reared on T. cordata leaves in the progressive PM-pollution. The results showed that the values of life table parameters of the predator depended significantly on the level of PM deposition on leaves. Contrary to clean leaves from the control, the medium and high contamination intensities significantly reduced the daily (by 47% and 70%, respectively) and the total fecundity (by 62% and 77%, respectively) of females which, in turn, resulted in a decreased net reproductive rate (by 67% and 81%, respectively), intrinsic rate of increase (by 40% and 55%, respectively) and finite rate of increase (by 8% and 10%, respectively) of E. finlandicus. The pre-ovipositional period was prolonged, while the oviposition duration was shortened and the mites matured longer. In high pollution level the mortality of phytoseiids was boosted by 19% and some females were observed with pollutant lumps adhered to the idiosoma. Also, significant shares of juvenile forms (13%) and adult females (25%) made attempts to escape from highly contaminated experimental arenas. The implications of PM retention on the shelter vegetation are discussed in the context of IPM and ecological services.

Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems. [ABSTRACT FROM AUTHOR]

The structure of the leaf microbiome can alter host fitness and change in response to abiotic and biotic factors, like seasonality, climate, and leaf age. However, relatively few studies consider the influence of host age on microbial communities at a time scale of a few days, a short time scale relevant to microbes. To understand how host age modulates changes in the fungal and bacterial leaf microbiome on a short time scale, we ran independent field and greenhouse-based studies and characterized phyllosphere communities using next-generation sequencing approaches. Our field study characterized changes in the fungal and bacterial phyllosphere by examining leaves of different relative ages across individuals, whereas the greenhouse study examined changes in the fungal microbiome by absolute leaf age across individuals. Together, these results indicate that fungal communities are susceptible to change as a leaf ages as evidenced by shifts in the diversity of fungal taxa both in the field and the greenhouse. Similarly, there were increases in the diversity of fungal taxa by leaf age in the greenhouse. In bacterial communities in the field, we observed changes in the diversity, composition, and relative abundance of common taxa. These findings build upon previous literature characterizing host-associated communities at longer time scales and provide a foundation for targeted work examining how specific microbial taxa might interact with each other, such as fine-scale interactions between pathogenic and non-pathogenic species. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Developing an effective method for isolating bacterial genetic material from plants is a relatively challenging task and often does not yield adequately prepared material for further analyses. Previous studies often overlook connections, primarily focusing on laboratory investigations. With advancements in high-throughput sequencing techniques, we can now revisit and delve deeper into these interactions. Our study focuses on the initial phase of these investigations: genetic material isolation. Extracting bacterial DNA from aboveground plant parts, known as the phyllosphere, poses a significant challenge due to plant-derived contaminants. Existing isolation protocols frequently yield inconsistent results, necessitating continuous refinement and optimization. In our study, we developed an effective isolation protocol employing mechanical–chemical lysis, sonication, and membrane filtration. This approach yielded high-quality DNA at a concentration of 38.08 ng/µL, suitable for advanced sequencing applications. Our results underscore the effectiveness and necessity of these methods for conducting comprehensive microbiological analyses. Furthermore, our research not only lays the groundwork for further studies on lettuce microbiota, but also highlights the potential for utilizing our developed protocol in investigating other plants and their microbiomes. [ABSTRACT FROM AUTHOR]

Plant leaves harbor a rich diversity of bacteria and fungi that, through their interactions with host plants, assume an influential role in plant physiological and metabolic processes. The unique phyllosphere environment of different plant species may shape and select distinct phyllosphere microbial communities. While most academic research has focused on the phyllosphere microorganisms within the same plant variety, there is relatively limited research on the phyllosphere microbial communities between different varieties. Populus L. is a typical tree species in temperate monsoon climates, widely distributed in northern China, and it constitutes a crucial component of China's forestry resources. For the purpose of this study, we investigated the community structure and diversity of phyllosphere fungi and bacteria in different poplar varieties under identical growth conditions to elucidate the main factors contributing to differences in phyllosphere microbial communities among these varieties. Our findings revealed variations in nitrogen, phosphorus, starch, and soluble sugar contents among the three poplar species studied. Additionally, there were considerable disparities in both abundance and α diversity index of phyllosphere fungal and bacterial communities among these species. At the phylum level, Ascomycota and Basidiomycota have been identified as the dominant fungal communities; while Proteobacteria and Actinomycetes were dominant bacterial communities. The correlation analysis pointed out that chemical traits in the leaves, in particular the total phosphorus and the quantity of soluble sugar, had a significant correlation with the structure and diversity of the microbial community residing in the phyllosphere. Overall, our results demonstrate that even under identical site conditions, each poplar species harbors its own unique phyllosphere microbial community composition as well as distinct leaf characteristics—highlighting host plant diversity as a crucial factor driving differences in phyllosphere microbial composition. [ABSTRACT FROM AUTHOR]

The foliage of the small-leaved lime (Tilia cordata) is characterised by the nerve axils being grown by non-glandular trichomes, which trait contributes to the enhanced retention of the particulate matter (PM). This fact may disturb the ecological service of T. cordata related to the structure of its leaves, which is to provide acarodomatia (micro-shelters) for the predatory mites of the Phytoseiidae family. Phytoseiids are natural enemies of a variety of plant pests, widely applied in integrated pest management (IPM). Their occurrence is largely related to acarodomatia in which these mites hide, feed, reproduce, and develop. For the first time, the influence of PM deposition within spaces typically occupied by phytoseiids is investigated. Experimental populations of Euseius finlandicus were reared on T. cordata leaves in the progressive PM-pollution. The results showed that the values of life table parameters of the predator depended significantly on the level of PM deposition on leaves. Contrary to clean leaves from the control, the medium and high contamination intensities significantly reduced the daily (by 47% and 70%, respectively) and the total fecundity (by 62% and 77%, respectively) of females which, in turn, resulted in a decreased net reproductive rate (by 67% and 81%, respectively), intrinsic rate of increase (by 40% and 55%, respectively) and finite rate of increase (by 8% and 10%, respectively) of E. finlandicus. The pre-ovipositional period was prolonged, while the oviposition duration was shortened and the mites matured longer. In high pollution level the mortality of phytoseiids was boosted by 19% and some females were observed with pollutant lumps adhered to the idiosoma. Also, significant shares of juvenile forms (13%) and adult females (25%) made attempts to escape from highly contaminated experimental arenas. The implications of PM retention on the shelter vegetation are discussed in the context of IPM and ecological services. [ABSTRACT FROM AUTHOR]

Exploring the intricate relationships between plants and their resident microorganisms is crucial not only for developing new methods to improve disease resistance and crop yields but also for understanding their co-evolutionary dynamics. Our research delves into the role of the phyllosphere-associated microbiome, especially Actinomycetota species, in enhancing pathogen resistance in Theobroma grandiflorum, or cupuassu, an agriculturally valuable Amazonian fruit tree vulnerable to witches' broom disease caused by Moniliophthora perniciosa. While breeding resistant cupuassu genotypes is a possible solution, the capacity of the Actinomycetota phylum to produce beneficial metabolites offers an alternative approach yet to be explored in this context. Utilizing advanced long-read sequencing and metagenomic analysis, we examined Actinomycetota from the phyllosphere of a disease-resistant cupuassu genotype, identifying 11 Metagenome-Assembled Genomes across eight genera. Our comparative genomic analysis uncovered 54 Biosynthetic Gene Clusters related to antitumor, antimicrobial, and plant growth-promoting activities, alongside cutinases and type VII secretion system-associated genes. These results indicate the potential of phyllosphere-associated Actinomycetota in cupuassu for inducing resistance or antagonism against pathogens. By integrating our genomic discoveries with the existing knowledge of cupuassu's defense mechanisms, we developed a model hypothesizing the synergistic or antagonistic interactions between plant and identified Actinomycetota during plant-pathogen interactions. This model offers a framework for understanding the intricate dynamics of microbial influence on plant health. In conclusion, this study underscores the significance of the phyllosphere microbiome, particularly Actinomycetota, in the broader context of harnessing microbial interactions for plant health. These findings offer valuable insights for enhancing agricultural productivity and sustainability. [ABSTRACT FROM AUTHOR]

Background: Nanotechnology holds revolutionary potential in the field of agriculture, with zinc oxide nanoparticles (ZnO NPs) demonstrating advantages in promoting crop growth. Enhanced photosynthetic efficiency is closely linked to improved vigor and superior quality in tea plants, complemented by the beneficial role of phyllosphere microorganisms in maintaining plant health. However, the effects of ZnO NPs on the photosynthesis of tea plants, the sprouting of new shoots, and the community of phyllosphere microorganisms have not been fully investigated. Results: This study investigated the photosynthetic physiological parameters of tea plants under the influence of ZnO NPs, the content of key photosynthetic enzymes such as RubisCO, chlorophyll content, chlorophyll fluorescence parameters, transcriptomic and extensive targeted metabolomic profiles of leaves and new shoots, mineral element composition in these tissues, and the epiphytic and endophytic microbial communities within the phyllosphere. The results indicated that ZnO NPs could enhance the photosynthesis of tea plants, upregulate the expression of some genes related to photosynthesis, increase the accumulation of photosynthetic products, promote the development of new shoots, and alter the content of various mineral elements in the leaves and new shoots of tea plants. Furthermore, the application of ZnO NPs was observed to favorably influence the microbial community structure within the phyllosphere of tea plants. This shift in microbial community dynamics suggests a potential for ZnO NPs to contribute to plant health and productivity by modulating the phyllosphere microbiome. Conclusion: This study demonstrates that ZnO NPs have a positive impact on the photosynthesis of tea plants, the sprouting of new shoots, and the community of phyllosphere microorganisms, which can improve the growth condition of tea plants. These findings provide new scientific evidence for the application of ZnO NPs in sustainable agricultural development and contribute to advancing research in nanobiotechnology aimed at enhancing crop yield and quality. [ABSTRACT FROM AUTHOR]

The abiotic environment exerts strong effects on plant‐associated microbes, shaping their interactions with plants and resulting ecosystem processes. However, these abiotic effects on plant–microbe interactions are often highly specific and contingent on the abiotic driver or microbial group, requiring synthesis work describing general patterns and from this generate hypotheses and guide mechanistic work. To address this, we conducted a meta‐analysis of the effects of climate change‐related abiotic factors, namely warming, drought, and eCO2, on plant‐associated microbes distinguishing by microbial taxonomic or biological group (bacteria, fungi or virus) and the plant part where microbes are found or associated with (phyllosphere or rhizosphere). We found abiotic driver‐specific patterns, whereby drought significantly reduced microbial abundance, whereas warming and eCO2 had no significant effects. In addition, these abiotic effects were contingent on the microbial taxonomic group, with fungi being negatively affected by drought but positively affected by warming (eCO2 enrichment had no effect), whereas bacteria and viruses were not significantly affected by any factor. Likewise, rhizospheric microbes were negatively affected by drought but positively affected by warming (eCO2 enrichment had no effect), whereas phyllospheric microbes were not significantly affected by any factor. Collectively, these findings point to important implications for global change research by highlighting contrasting effects of climate change‐related abiotic drivers on plant‐associated microbes and the contingency of such effects on microbe life histories and the nature of their interactions with plants. [ABSTRACT FROM AUTHOR]

Coffee leaf rust, caused by the fungus Hemileia vastatrix , has become a major concern for coffee-producing countries. Additionally, there has been an increase in the resistance of certain races of the fungus to fungicides and breeding cultivars, making producers use alternative control methods. In this work, we transplanted the leaf surface microbiota of rust-resistant coffee species (Coffea racemosa and Coffea stenophylla) to Coffea arabica and tested whether the new microbiota would be able to minimize the damage caused by H. vastatrix. It was seen that the transplant was successful in controlling rust, especially from C. stenophylla , but the protection depended on the concentration of the microbiota. Certain fungi, such as Acrocalymma, Bipolaris, Didymella, Nigrospora, Setophaeosphaeria, Simplicillium, Stagonospora and Torula , and bacteria, such as Chryseobacterium, Sphingobium and especially Enterobacter , had their populations increased and this may be related to the antagonism seen against H. vastatrix. Interestingly, the relative population of bacteria from genera Pantoea, Methylobacterium and Sphingomonas decreased after transplantation, suggesting a positive interaction between them and H. vastatrix development. Our findings may help to better understand the role of the microbiota in coffee leaf rust, as well as help to optimize the development of biocontrol agents. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Heat stress has a substantial impact on black gram (Vigna mungo L.) by reducing growth, grain yield, and quality. Black gram is highly sensitive to temperature; it requires a range of 27–35 °C for flowering and pod formation. Therefore, to mitigate heat stress during the summer season in black gram, phyllosphere-associated methylotrophic bacteria (Methylobacterium brachiatum (KD1 and SD3), M. thiocyanatum (SD2), and Methylorubrum populi (KD5) were chosen from the previously identified strains. Screening for plant growth-promoting properties revealed that all strains (KD1, KD5, SD2, and SD3) were able to grow on nitrogen-free (N2) medium, produced siderophore (12.57 to 69.10%), indole-acetic acid (IAA) like substances (91.93 to 94.14 µg/mL), and 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase) (0. 34 to 1.33 nmol α-ketobutyrate/mg protein/h). A pot study experiment during the summer season (average temperature 42 °C) revealed that black gram seeds treated with methylotrophic bacteria had a higher biomass. Moreover, the chlorophyll content was significantly enhanced, ranging from least 188.00% to maximum 264.94%, and carotenoid pigments ranging from least 104.82% to maximum 155.10% compared to the control plants group. Similarly, the inoculation with methylotrophs also enhanced antioxidant enzymes such as POD in leaves (with least 7.14 and maximum 66.66%) and stems (with least 2.94 and maximum 191.17%), SOD (with least 92.30 and maximum 607.69%) and (with least 30.76 and maximum 150.00%), and PAL (with least 1.33 and maximum 89.33%) and (with least 25.58 and maximum 60.46%) compared to the control plants. In addition, Methylobacterium strains reduced oxidative stress in plants by managing the production of hydrogen peroxide (H2O2) and superoxide radicals (O2.−). These results showed that methylotrophs have a strong ability to protect black gram plants, and enhance their biomass under heat stress. [ABSTRACT FROM AUTHOR]

Given the importance of biological nitrogen (N) fixation in agroecosystems, using inoculants with phyllosphere N fixers effective across various crops would revolutionize agriculture. In this study, the application of an inoculant prepared from Methylobacterium symbioticum was tested on young olive trees. The pot experiment was arranged in a factorial design, with inoculant (Yes and No) and mineral N applied to the soil [0 (N0), 25 (N25), 50 (N50), and 100 (N100) kg ha−1], and four replicates. The inoculant application did not increase plant dry matter yield (DMY), whereas the application of mineral N had a significant and pronounced effect. The inoculant also did not significantly increase N concentration in tissues, unlike the strong increase observed with N applied to the soil. The inoculant significantly increased plant N recovery, a cumulative effect resulting from small increases in DMY and N concentration in tissues. This increase represented 5.2% more N in plants receiving the inoculant compared to untreated ones. However, only treatments receiving mineral N recorded positive values of fixed N, with the highest value observed in the N50 treatment (12.4%), whereas a negative value (−7.7%) was observed in the N0 treatment. Overall, these low values of fixed N question the economic rationale of using this inoculant by farmers and especially render it unsuitable for organic farming systems, where plants tend to have lower N levels in tissues. [ABSTRACT FROM AUTHOR]

Leaves harbor distinct microbial communities that can have an important impact on plant health and microbial ecosystems worldwide. Nevertheless, the ecological processes that shape the composition of leaf microbial communities remain unclear, with previous studies reporting contradictory results regarding the importance of bacterial dispersal versus host selection. This discrepancy could be driven in part because leaf microbiome studies typically consider the upper and lower leaf surfaces as a single entity despite these habitats possessing considerable anatomical differences. We characterized the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces across 24 plant species. Leaf surface pH and stomatal density were found to shape phyllosphere community composition, and the underside of leaves had lower richness and higher abundances of core community members than upper leaf surfaces. We found fewer endemic bacteria on the upper leaf surfaces, suggesting that dispersal is more important in shaping these communities, with host selection being a more important force in microbiome assembly on lower leaf surfaces. Our study illustrates how changing the scale in which we observe microbial communities can impact our ability to resolve and predict microbial community assembly patterns on leaf surfaces. IMPORTANCE Leaves can harbor hundreds of different bacterial species that form unique communities for every plant species. Bacterial communities on leaves are really important because they can, for example, protect their host against plant diseases. Usually, bacteria from the whole leaf are considered when trying to understand these communities; however, this study shows that the upper and lower sides of a leaf have a very different impact on how these communities are shaped. It seems that the bacteria on the lower leaf side are more closely associated with the plant host, and communities on the upper leaf side are more impacted by immigrating bacteria. This can be really important when we want to treat, for example, crops in the field with beneficial bacteria or when trying to understand host-microbe interactions on the leaves.

ABSTRACT Phyllosphere-associated microbes can significantly alter host plant fitness, with distinct functions provided by bacteria inhabiting the epiphytic (external surface) vs endophytic niches (internal leaf tissue). Hence, it is important to understand the assembly and stability of these phyllosphere communities, especially in field conditions. Broadly, epiphytic communities should encounter more environmental fluctuations and frequent immigration, whereas endophytic microbiota should face stronger host selection. As a result, we expect greater variability in epiphytic than endophytic communities. We analyzed the structure and stability of leaf phyllosphere microbiota of four traditionally cultivated rice landraces and one commercial variety from northeast India grown in the field for 3 consecutive years, supplemented with opportunistic sampling of eight other landraces. Epiphytic and endophytic bacterial communities shared dominant core genera such as Methylobacterium and Sphingomonas. Consistent with an overall strong environmental effect, both communities varied more across sampling years than across host landraces. Seeds sampled from a focal landrace did not support vertical transmission of phyllosphere bacteria, suggesting that both types of communities are assembled anew each generation. Despite these points of convergence, epiphytic communities had distinct composition and significantly higher microbial load and were more rich, diverse, modular, and unstable than endophytic communities. Finally, focused sampling of one landrace across developmental stages showed that the divergence between the two types of communities arose primarily at the flowering stage. Thus, our results show both convergent and divergent patterns of community assembly and composition in distinct phyllosphere niches in rice, identifying key bacterial genera and host developmental stages that may aid agricultural interventions to increase rice yield.IMPORTANCEPhyllosphere (leaf-associated) microbes significantly impact plant fitness, making it crucial to understand how these communities are assembled and maintained. While many studies have analyzed epiphytic (surface) phyllosphere communities, we have a relatively poor understanding of endophytic communities which colonize the very distinct niche formed inside leaf tissues. We found that across several rice landraces, both communities are largely colonized by the same core genera, indicating divergence at the species level across the two leaf niches and highlighting the need to understand the mechanisms underlying this divergence. Surprisingly, both epiphytic and endophytic communities were only weakly shaped by the host landrace, with a much greater role for environmental factors that likely vary over time. Thus, microbiome-based agricultural interventions for increasing productivity could perhaps be generalized across rice varieties but would need to account for the temporal instability of the microbiota. Our results thus highlight the importance of data sets such as ours—with extensive sampling across landraces and years—for understanding phyllosphere microbiota and their applications in the field.

Urban trees are crucial in delivering essential ecosystem services, including air pollution mitigation. This service is influenced by plant associated microbiomes, which can degrade hydrocarbons, support tree health, and influence ecological processes. Yet, our understanding of tree microbiomes remains limited, thus affecting our ability to assess and quantify the ecosystem services provided by trees as complex systems. The main hypothesis of this work was that tree microbiomes concur to hydrocarbon biodegradation, and was tested through three case studies, which collectively investigated two tree micro-habitats (phyllosphere and tree cavity organic soil—TCOS) under various conditions representing diverse ecological scenarios, by applying different culture-based and molecular techniques and at different scales. The integration of all results provided a more comprehensive understanding of the role of microbiomes in urban trees. Firstly, bacterial strains isolated from the phyllosphere of Quercus ilex were characterized, indicating the presence of Plant-Growth Promoting bacteria and strains able to catabolize PAHs, particularly naphthalene and phenanthrene. Secondly, naphthalene biodegradation on artificially spiked Hedera helix leaves was quantified in greenhouse experiments on inoculated and untreated plants. The persistence of the inoculated strain and community structure of epiphytic bacteria were assessed by Illumina sequencing of V5–V6 hypervariable regions of 16S rRNA gene. Results showed that naphthalene degradation was initially faster on inoculated plants but later the degradation rates became similar, probably because bacterial populations with hydrocarbon-degrading abilities gradually developed also on non-inoculated plants. Finally, we explored bacterial and fungal biodiversity hosted by TCOS samples, collected from six large trees located in an urban park and belonging to different species. Microbial communities were characterized by Illumina sequencing of V5–V6 hypervariable regions of bacterial gene 16S rRNA and of fungal ITS1. Results indicated TCOS as a distinct substrate, whose microbiome is determined both by the host tree and by canopy environmental conditions and has a pronounced aerobic hydrocarbon degradation potential. Overall, a better assessment of biodiversity associated with trees and the subsequent provision of ecosystem services constitute a first step toward developing future new microbe-driven sustainable solutions, especially in terms of support for urban green planning and management policy.

Abstract The epiphytic and endophytic bacteria play an important role in the healthy growth of plants. Both plant species and growth environmental influence the bacterial population diversity, yet it is inconclusive whether it is the former or the latter that has a greater impact. To explore the communities of the epiphytic and endophytic microbes in Camellia oleifera, this study assessed three representative C. oleifera cultivars from three areas in Hunan, China by Illumina high-throughput sequencing. The results showed that the diversity and species richness of endophytic microbial community in leaves were significantly higher than those of microbial community in the epiphytic. The diversity and species richness of epiphytic and endophytic microbes are complex when the same cultivar was grown in different areas. The C. oleifera cultivars grown in Youxian had the highest diversity of epiphytic microbial community, but the lowest abundance, while the cultivars grown in Changsha had the highest diversity and species richness of endophytic microbes in leaves. It was concluded that the dominant phylum mainly included Proteobacteria, Actinobacteriota and Firmicutes through the analysis of the epiphytic and endophytic microbial communities of C. oleifera. The species and relative abundances of epiphytic and endophytic microbial community were extremely different at the genus level. The analysis of NMDS map and PERMANOVA shows that the species richness and diversity of microbial communities in epiphytes are greatly influenced by region. However, the community structure of endophytic microorganisms in leaves is influenced by region and cultivated varieties, but the influence of cultivars is more significant. Molecular ecological network analysis showed that the symbiotic interaction of epiphytic microbial community was more complex.

Elucidating the plant−microbiome network is of importance in understanding species coexistence in natural ecosystems. The phyllosphere, which is the aerial parts of terrestrial plants, is inhabited by diverse microbes. However, few studies have focused on the phyllosphere microbiome and plant-microbiome network in temperate grasslands. In this study, we explored the diversity, community structure, and network architecture of phyllosphere bacteria and fungi in 19 plant species native to the temperate grassland in Inner Mongolia, China. We obtained 3,313 and 758 phyllosphere bacterial and fungal operational taxonomic units, respectively, and found that the bacterial community was dominated by Proteobacteria, Actinobacteriota, and Firmicutes, whereas the fungal community was dominated by Ascomycota and Basidiomycota. Plant identity exerted significant impacts on α-diversities of both bacterial and fungal communities. The composition of bacterial and fungal communities differed among plant species. Plant identity had a greater effect on fungal than bacterial communities. Both bacterial and fungal network structures were characterized by specialized, modular, lowly connected, and no nested properties. The plant−fungal network had a high level of specification, modularity, antinestedness, and connectance compared with the plant−bacterial network. Our results suggest more intimate relationships between plants and phyllosphere fungi than between plants and phyllosphere bacteria and also that the phyllosphere fungal community in the temperate grassland ecosystem is more resistant to environmental disturbance than the phyllosphere bacterial community. These findings may contribute to our understanding of the mechanisms by which species coexist and communities stabilize in grassland ecosystems.

Abstract Background The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce). Results We profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families. Conclusions While our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning.

Plants encounter various biotic and abiotic stresses throughout their lifecycle, which can adversely impact their productivity and lead to yield loss. This ultimately results in a significant decline in food production with global pressure on declining agriculture. The agrochemical pesticides have been proven effective in controlling various diseases in major crops, their excessive use poses significant risks to the environment and human health and negatively impacts non-target host microbiota. Novel approaches in the form of host plant microbiome as an alternative strategy to overcome these stresses have recently gained increasing attention. Emerging evidence suggests that plants subjected to biotic and abiotic stress experience diverse microbial local (diffusible) and distant (volatile organic compounds) metabolites and respond with the expression of defense genes (transcriptomic variations) that result in changing leaf and root exudates and alter resident microbial community structure. The relative abundance of symbiotic microorganisms under stress may favor plant survival and enhance adaptation during stress. Thus, to counter the negative effects, introducing an efficient microbiome into the host crop is highly desirable due to the attractive functional potential of the phytomicrobiome. Here, we summarize more effective and reproducible strategies to use microbial activities in crop production and protection to promote a suitable agricultural environment. In addition, detailed molecular mechanisms of phytomicrobiome in stimulating plant immune system, the interaction between microbiome and plant defense system, and defense strategies of microbiome against biotic and abiotic factors have been described. Finally, we explored the plant-based strategies for microbiome engineering and bioinformatics methods to predict microbiome functions.

The American cranberry is a perennial North American fruit plant that is grown successfully on commercial plantations in Poland. The purpose of this study was to recognize filamentous fungi that colonize roots, leaves, and fruits without visible disease symptoms. Pure fungal cultures were isolated from disinfected plant fragments in agar media and identified by sequencing common taxonomic DNA markers such as the ITS region, the TEF-1α, or RPB2 genes. Of the 141 isolates studied, 59% were identified as closely related to soil saprotrophs. They were classified primarily as showing the greatest similarity to type strains of Trichoderma amoenum, Trichoderma dorothopsis, Paraphaeosphaeria sporulosa, and Penicillium murcianum. Additionally, isolates that are most similar to strains of Penicillium crustosum, Aspergillus flavus, and Aspergillus versicolor that produced mycotoxins were detected. The fungi identified as closest to Alternaria geophila, Alternaria senecionicola, Paraphoma radicina, Pestalotiopsis unicolor, Pestalotiopsis scoparia, and Neopestalotiopsis spp., whose hosts are plants other than American cranberry, represented 33.81% of the isolates tested. Only 7.2% of the isolates corresponded to the species of Physalospora vaccinia, Diaporthe vaccinii, and Diaporthe eres, known cranberry pathogens. The results of this study can be used to identify latent plant infection and potential disease risks. [ABSTRACT FROM AUTHOR]

Plant microbiomes play important roles in plant health and fitness. Bacterial horizontal gene transfer (HGT) can influence plant health outcomes, driving the spread of both plant growth-promoting and phytopathogenic traits. However, community dynamics, including the range of genetic elements and bacteria involved in this process are still poorly understood. Integrons are genetic elements recently shown to be abundant in plant microbiomes, and are associated with HGT across broad phylogenetic boundaries. They facilitate the spread of gene cassettes, small mobile elements that collectively confer a diverse suite of adaptive functions. Here, we analysed 5,565 plant-associated bacterial genomes to investigate the prevalence and functional diversity of integrons in this niche. We found that integrons are particularly abundant in the genomes of Pseudomonadales, Burkholderiales, and Xanthomonadales. In total, we detected nearly 9,000 gene cassettes, and found that many could be involved in plant growth promotion or phytopathogenicity, suggesting that integrons might play a role in bacterial mutualistic or pathogenic lifestyles. The rhizosphere was enriched in cassettes involved in the transport and metabolism of diverse substrates, suggesting that they may aid in adaptation to this environment, which is rich in root exudates. We also found that integrons facilitate cross-species HGT, which is particularly enhanced in the phyllosphere. This finding may provide an ideal opportunity to promote plant growth by fostering the spread of genes cassettes relevant to leaf health. Together, our findings suggest that integrons are important elements in plant microbiomes that drive HGT, and have the potential to facilitate plant host adaptation. [ABSTRACT FROM AUTHOR]

Many microorganisms inhabit the aboveground parts of plants (i.e. the phyllosphere), which mainly comprise leaves. Understanding the structure of phyllosphere microbial communities and their drivers is important because they influence host plant fitness and ecosystem functions. Despite the high prevalence of ant–plant associations, few studies have used quantitative community data to investigate the effects of ants on phyllosphere microbial communities. In the present study, we investigated the effects of ants on the phyllosphere fungal communities of Mallotus japonicus using high‐throughput sequencing. Mallotus japonicus is a myrmecophilous plants that bears extrafloral nectaries, attracting several ant species, but does not provide specific ant species with nest sites like myrmecophytes do. We experimentally excluded ants with sticky resins from the target plants and collected leaf discs to extract fungal DNA. The ribosomal DNA internal transcribed spacer 1 (ITS1) regions of the phyllosphere fungi were amplified and sequenced to obtain fungal community data. Our results showed that the exclusion of ants changed the phyllosphere fungal community composition; however, the effect of ants on OTU richness was not clear. These results indicate that ants can change the community of phyllosphere fungi, even if the plant is not a myrmecophyte. [ABSTRACT FROM AUTHOR]

Objetive/Background. The aim of this was to assess the diversity and antibiotic resistance of bacteria isolated from 19 crops with bacterial infection symptoms. Material and Methods: This collection was identified using 16S rRNA gene sequencing and the Biolog system. Susceptibility and minimum inhibitory concentration (MIC) for streptomycin, tetracycline, and gentamicin were determined using disk diffusion and E-test methods, respectively. Results: A total of 55 species belonging to 20 bacterial genera were identified, with Pseudomonas, Serratia, Pantoea, and Stenotrophomonas being the most abundant. Approximately 27% of the isolates were categorized as pathogenic through the hypersensitivity reaction test, including phytopathogenic species like Pseudomonas syringae, P. cichorii, Pantoea anthophila, P. stewartii, Stenotrophomonas maltophilia, Dickeya oryzae, Erwinia billingiae, Pectobacterium aroidearum, and Enterobacter cloacae subsp. dissolvens. Resistance to at least one antibiotic was detected in 60% of isolates from 17 crops, with tomatoes, heart of palm, and lettuce exhibited the highest proportion of resistant bacteria (>80%). Streptomycin resistance was most common (35%), followed by tetracycline (28%) and gentamicin (9%). Conclusions: The findings indicate the presence of antibiotic resistance in saprophytic and pathogenic bacteria associated with 17 out of 19 assessed crops, posing risks to the environment, phytosanitary conditions, and public health. [ABSTRACT FROM AUTHOR]

Background: The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce). Results: We profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families. Conclusions: While our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning. [ABSTRACT FROM AUTHOR]

Summary: DNA contamination can critically confound microbiome studies. Here, we take a systematic approach to review the current literature and investigate the prevalence of contamination controls in phyllosphere microbiome research over the past decade. By utilising systematic review principles for this review, we were able to conduct a thorough investigation, screening 450 articles from three databases for eligibility and extracting data in a controlled and methodical manner. Worryingly, we observed a surprisingly low usage of both positive and negative contamination controls in phyllosphere research. As a result, we propose a set of minimum standards to combat the effects of contamination in future phyllosphere research. [ABSTRACT FROM AUTHOR]

Despite rapid progress in plant–microbe interaction research within terrestrial environments, our knowledge of aquatic plant and macroalgae microbiome structure, function, and ecology remains scarce, even though these hosts are key players in structuring the lacustrine environments. Here, we used the co-occurring, fast-growing hosts Hydrilla verticillata (Hydrocharitaceae) and Cladophora spp. (Chlorophyta), which dominate the littoral zones of a nitrogen-limited, hard-water lake, Lake Atitlán (Guatemala). The aim of this study was: (1) to assess the structure of Hydrilla phyllosphere-associated and Cladophora filament-associated bacterial and fungal assemblages in the context of host specificity; (2) to predict microbial potential to contribute to biogeochemical cycling in the lake littoral; and (3) to compare the aquatic microbiome structure to available datasets from terrestrial ecosystems, using next-generation amplicon sequencing, co-occurrence network analysis, and N2-fixation activity measurements. We show that the microbiomes associated with the phyllosphere of aquatic macrophytes and macroalgal filaments are surprisingly similar, with taxonomic and functional complexity analogous to that of rhizospheric assemblages in terrestrial plants, and have a potential to efficiently recycle nutrients from organic matter. We suggest that especially the fungal associations with these hosts represent an untapped research area of microbial ecology that warrants further attention. [ABSTRACT FROM AUTHOR]

Leaves are colonized by a complex mix of microbes, termed the leaf microbiota. Even though the leaf microbiota is increasingly recognized as an integral part of plant life and health, our understanding of its interactions with the plant host is still limited. Here, mature, axenically grown Arabidopsis thaliana plants were spray inoculated with six diverse leaf‐colonizing bacteria. The transcriptomic changes in leaves were tracked over time and significant changes in ethylene marker (ARL2) expression were observed only 2–4 days after spray inoculation. Whole‐transcriptome sequencing revealed that 4 days after inoculation, leaf transcriptional changes to colonization by nonpathogenic and pathogenic bacteria differed in strength but not in the type of response. Inoculation of plants with different densities of the nonpathogenic bacterium Williamsia sp. Leaf354 showed that high bacterial titers resulted in disease phenotypes and led to severe transcriptional reprogramming with a strong focus on plant defense. An in silico epigenetic analysis of the data was congruent with the transcriptomic analysis. These findings suggest (1) that plant responses are not rapid after spray inoculation, (2) that plant responses only differ in strength, and (3) that plants respond to high titers of nonpathogenic bacteria with pathogen‐like responses. [ABSTRACT FROM AUTHOR]

Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/ M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity. [ABSTRACT FROM AUTHOR]