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Phyllosphere microbes are essential in the mediation of plant–soil biogeochemical recycling during the decomposition of plant litter in wetland ecosystems. However, there are few studies into microbial community succession in phyllosphere microbial communities in wetlands, and their functional attributes across a full period of wetland plant litter decomposition remain unclear. Here, we collected leaf samples of Typha latifolia var. orientalis (C. Presl.) Rohrb., an emergent wetland plant, during various stages of decomposition (growing, standing, lodging, and submerging stages) to investigate fungal and bacterial assemblage succession in the phyllosphere. We then parsed these assemblages into specific fungal trophic modes and bacterial phenotypes. Over the litter decomposition period, both fungal and bacterial assemblages underwent distinct succession, with generally increasing alpha diversity, and the proportion of litter microbes originating from sediments increased with decomposition. Saprotrophic and pathotrophic fungi dominated the fungal assemblage in the early stages of decomposition, but their dominance was replaced by undefined fungi as decomposition progressed. Relative abundances of both pathotrophic fungi and potentially pathogenic bacteria increased from the growing to the standing stage, implying that there was a turning point in assemblage composition shortly after plant leaf death. Gram-positive and gram-negative bacteria had opposite trends in their relative abundances over successive decomposition stages. When plant litter entered the water, bacteria tolerant of oxidative stress gradually decreased in abundance, but anaerobic bacteria abundance increased. We also aimed to determine the relationships between predicted microbial functional traits and leaf litter physicochemical attributes. Lignin and N content were the predominant predictors of decomposer fungal trophic modes and bacterial phenotypes. These findings provide evidence that the complex litter decomposition seen in wetlands is accompanied by a dynamic cross-kingdom succession of phyllospheric microbial communities, coupled with distinct changes in the phenotypes of the microbes present. Insights into phyllospheric microbial functional traits have implications for better elucidating the plant litter cycle for wetland plants. [ABSTRACT FROM AUTHOR]

Epiphytic fungi are vital in enhancing their host plant performance and can also cause plant diseases. Generally, phyllosphere fungal community are majorly driven by climate, while rhizosphere fungal community are determined by soil properties and spatial distance. However, the differences in the relative effects of environmental factors on fungal community compositions and network structures remain far from clear between phyllosphere and rhizosphere.In this study, we conducted a large‐scale field survey along a 1400 km transect in the Tibetan Plateau and explored the composition and structure of phyllosphere and rhizosphere fungal communities from two dominant grass species (Leontopodium nanum and Stipa purpurea). L. nanum is widely distributed in relatively wet areas of alpine grasslands but S. purpurea prefers relatively dry areas. The geographical distributions of these two species overlap in the middle of the transectFirst, we found that precipitation was more important than temperature to affect fungal alpha diversity. High precipitation significantly promoted fungal alpha diversity in both phyllosphere and rhizosphere. Second, climate and spatial variables explained more variations in fungal community in the phyllosphere than rhizosphere. Specifically, greater precipitation promoted the relative abundances of pathotrophic fungi in the phyllosphere and rhizosphere, whereas lower precipitation only stimulated the relative abundances of symbiotrophic fungi in the rhizosphere. Third, precipitation had different impacts on phyllosphere and rhizosphere fungal networks between host species. Drought caused lower node number of fungal networks in the phyllosphere and rhizosphere of L. nanum. However, for S. purpurea, drought led to more complex and positive fungal networks in the phyllosphere and rhizosphere. Overall, these results indicated that precipitation caused different fungal community compositions along the transect between phyllosphere and rhizosphere, but consistently shaped their fungal networks.This study is among the first to provide compelling evidence on the large‐scale spatial variations and controlling factors for epiphytic fungal community in alpine grasslands. These new findings help to understand the role of epiphytic fungal community in affecting the functions of alpine grasses to cope with extreme environments. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Plants are constantly interacting with the diverse microbial community as well as insect pests throughout their life cycle. Due to their sessile nature, plants rely solely on the intracellular signaling and reprogramming of cellular events to resist against pathogens. Insect pests are usually dependent on the nutrient-rich fluid obtained from plants or directly consume plant parts to sustain their life cycle. Plants possess a plethora of microbial communities; these microbiomes constantly influence the physiology, growth, development, and immunity in plants. Hence, the phyllosphere and rhizosphere are believed to play a major role in plant-insect interaction. The phyllosphere, rhizosphere, and endosymbiotic microbiome are currently under extensive scientific investigation. Recently, the advancement of metagenomic next-generation sequencing (mNGS) platforms revolutionized plant-associated microbiome analysis and has unveiled many beneficial microbial communities protecting against diverse pathogenic microorganisms and insect pests. Mycorrhiza is also an important component of the rhizosphere, as it may play a role in soil microbiota, thus indirectly influencing the interaction of insects with plants. In this regard, the present review tries to focus on some major insect pests of plants, the molecular mechanism of plant–insect interaction, and the probable role of phyllosphere and rhizosphere microbiome in this plant–insect encounter. This review is believed to open up a new dimension in developing resistance in plants against insect pests. [ABSTRACT FROM AUTHOR]

Ground-level ozone (O3) can adversely impact tree productivity and the service functions of forest ecosystems. The deposition of atmospheric nitrogen (N) can enhance nutrient availability and mitigate the O3-mediated impairment of plant–soil–microbe systems. Interactions between plants and associated microbial communities are integral to the ability of these plants to resist environmental stressors, yet studies examining the impact of increased O3 and N levels, alone or in combination, on these phyllosphere bacterial communities have been lacking to date. Accordingly, this study was conducted to examine the impact of O3 (charcoal-filtered air vs. non-filtered ambient air + 40 ppb of O3), N addition (0, 50, and 100 kg N ha−1 year−1), and a combination of these treatments on the phyllosphere bacterial communities associated with Cathay poplars. Higher O3 levels were found to significantly reduce the relative abundance of Gammaproteobacteria phyla while increasing the relative abundance of the dominant Alphaproteobacteria and Betaproteobacteria, with these effects being independent of N levels. Consistently, while marked differences in the composition of phyllosphere bacterial communities were observed as a function of O3 treatment conditions, they were largely similar across N treatments. Higher O3 levels contributed to significant reductions in α diversity, including both observed OTUs and phylogenetic diversity, when no N or low levels of N were added. α diversity was not affected by the N addition irrespective of O3 levels. A significant correlation was observed between photosynthesis rates and both α diversity and phyllosphere bacterial community composition, indicating a close relationship between photosynthetic activity and this microbial community. Together, these data offer new ecological insights regarding O3-induced changes in the makeup of bacterial communities present on plant surfaces, providing a foundation for efforts to formulate novel management strategies aimed at adapting environmental stressors under conditions of O3 pollution and in N-enriched environments. [ABSTRACT FROM AUTHOR]

ABSTRACT 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.

Understanding the influence of the heavy metal cadmium (Cd) on the phyllosphere microbiome of hyperaccumulator plants is crucial for enhancing phytoremediation. The characteristics of the phyllosphere of Sedum alfredii Hance, a hyperaccumulator plant, were investigated using 16S rRNA and internal transcribed spacer amplicon sequencing of powdery mildew-infected leaves treated or untreated with Cd. The results showed that the colonization of powdery mildew caused severe chlorosis and necrosis in S. alfredii leaves, and the relative abundance of Leotiomycetes in infected leaves increased dramatically and significantly decreased phyllosphere microbiome diversity. However, S. alfredii preferentially accumulated higher concentrations of Cd in the leaves of infected plants than in uninfected plants by powdery mildew, which in turn significantly inhibited powdery mildew colonization in leaves; the relative abundance of the fungal class Leotiomycetes in infected leaves decreased, and alpha and beta diversities of the phyllosphere microbiome significantly increased with Cd treatment in the infected plants. In addition, the inter-kingdom networks in the microbiota of the infected leaves treated with Cd presented many nodes and edges, and the highest inter-kingdom modularity compared to the untreated infected leaves, indicating a highly connected microbial community. These results suggest that Cd significantly inhibits powdery mildew colonization by altering the composition of the phyllosphere microbiome in S. alfredii leaves, paving the way for efficient heavy metal phytoremediation and providing a new perspective on defense strategies against heavy metals.

In a world with constant population growth, and in the context of climate change, the need to supply the demand of safe crops has stimulated an interest in ecological products that can increase agricultural productivity. This implies the use of beneficial organisms and natural products to improve crop performance and control pests and diseases, replacing chemical compounds that can affect the environment and human health. Microbial biological control agents (MBCAs) interact with pathogens directly or by inducing a physiological state of resistance in the plant. This involves several mechanisms, like interference with phytohormone pathways and priming defensive compounds. In Argentina, one of the world’s main maize exporters, yield is restricted by several limitations, including foliar diseases such as common rust and northern corn leaf blight (NCLB). Here, we discuss the impact of pathogen infection on important food crops and MBCA interactions with the plant’s immune system, and its biochemical indicators such as phytohormones, reactive oxygen species, phenolic compounds and lytic enzymes, focused mainly on the maize–NCLB pathosystem. MBCA could be integrated into disease management as a mechanism to improve the plant’s inducible defences against foliar diseases. However, there is still much to elucidate regarding plant responses when exposed to hemibiotrophic pathogens.

Invasive species could benefit from being introduced to locations with more favorable species interactions, including the loss of enemies, the gain of mutualists, or the simplification of complex interaction networks. Microbiomes are an important source of species interactions with strong fitness effects on multicellular organisms, and these interactions are known to vary across regions. The highly invasive plant yellow starthistle (Centaurea solstitialis) has been shown to experience more favorable microbial interactions in its invasions of the Americas, but the microbiome that must contribute to this variation in interactions is unknown. We sequenced amplicons of 16S rRNA genes to characterize bacterial community compositions in the phyllosphere, ectorhizosphere, and endorhizosphere of yellow starthistle plants from seven invading populations in California, USA, and eight native populations in Europe. We tested for the differentiation of microbiomes by geography, plant compartment, and plant genotype. Bacterial communities differed significantly between native and invading plants within plant compartments, with consistently lower diversity in the microbiome of invading plants. The diversity of bacteria in roots was positively correlated with plant genotype diversity within both ranges, but this relationship did not explain microbiome differences between ranges. Our results reveal that these invading plants are experiencing either a simplified microbial environment or simplified microbial interactions as a result of the dominance of a few taxa within their microbiome. Our findings highlight several alternative hypotheses for the sources of variation that we observe in invader microbiomes and the potential for altered bacterial interactions to facilitate invasion success.IMPORTANCE Previous studies have found that introduced plants commonly experience more favorable microbial interactions in their non-native range, suggesting that changes to the microbiome could be an important contributor to invasion success. Little is known about microbiome variation across native and invading populations, however, and the potential sources of more favorable interactions are undescribed. Here, we report one of the first microbiome comparisons of plants from multiple native and invading populations, in the noxious weed yellow starthistle. We identify clear differences in composition and diversity of microbiome bacteria. Our findings raise new questions about the sources of these differences, and we outline the next generation of research that will be required to connect microbiome variation to its potential role in plant invasions.

Microbial symbionts account for survival, development, fitness and evolution of eukaryotic hosts. These microorganisms together with their host form a biological unit known as holobiont. Recent studies have revealed that the holobiont of agaves and cacti comprises a diverse and structured microbiome, which might be important for its adaptation to drylands. Here, we investigated the functional signatures of the prokaryotic communities of the soil and the episphere, that includes the rhizosphere and phyllosphere, associated with the cultivated Agave tequilana and the native and sympatric Agave salmiana, Opuntia robusta and Myrtillocactus geometrizans by mining shotgun metagenomic data. Consistent with previous phylogenetic profiling, we found that Proteobacteria, Actinobacteria and Firmicutes were the main represented phyla in the episphere of agaves and cacti, and that clustering of metagenomes correlated with the plant compartment. In native plants, genes related to aerobic anoxygenic phototrophy and photosynthesis were enriched in the phyllosphere and soil, while genes coding for biofilm formation and quorum sensing were enriched in both epiphytic communities. In the episphere of cultivated A. tequilana fewer genes were identified, but they belonged to similar pathways than those found in native plants. A. tequilana showed a depletion in several genes belonging to carbon metabolism, secondary metabolite biosynthesis and xenobiotic degradation suggesting that its lower microbial diversity might be linked to functional losses. However, this species also showed an enrichment in biofilm and quorum sensing in the epiphytic compartments, and evidence for nitrogen fixation in the rhizosphere. Aerobic anoxygenic phototrophic markers were represented by Rhizobiales (Methylobacterium) and Rhodospirillales (Belnapia) in the phyllosphere, while photosystem genes were widespread in Bacillales and Cyanobacteria. Nitrogen fixation and biofilm formation genes were mostly related to Proteobacteria. These analyses support the idea of niche differentiation in the rhizosphere and phyllosphere of agaves and cacti and shed light on the potential mechanisms by which epiphytic microbial communities survive and colonize plants of arid and semiarid ecosystems. This study establishes a guideline for testing the relevance of the identified functional traits on the microbial community and the plant fitness.

Abstract Background Plant microbiome and its manipulation inaugurate a new era for plant biotechnology with the potential to benefit sustainable crop production. Here, we used the large-scale 16S rDNA sequencing analysis to unravel the dynamic, structure, and composition of exophytic and endophytic microbial communities in two hybrid commercial cultivars of sugarcane (R570 and SP80–3280), two cultivated genotypes (Saccharum officinarum and Saccharum barberi) and one wild species (Saccharum spontaneum). Results Our analysis identified 1372 amplicon sequence variants (ASVs). The microbial communities’ profiles are grouped by two, root and bulk soils and stem and leave when these four components are compared. However, PCoA-based data supports that endophytes and epiphytes communities form distinct groups, revealing an active host-derived mechanism to select the resident microbiota. A strong genotype-influence on the assembly of microbial communities in Saccharum ssp. is documented. A total of 220 ASVs persisted across plant cultivars and species. The ubiquitous bacteria are two potential beneficial bacteria, Acinetobacter ssp., and Serratia symbiotica. Conclusions The results presented support the existence of common and cultivar-specific ASVs in two commercial hybrids, two cultivated canes and one species of Saccharum across tissues (leaves, stems, and roots). Also, evidence is provided that under the experimental conditions described here, each genotype bears its microbial community with little impact from the soil conditions, except in the root system. It remains to be demonstrated which aspect, genotype, environment or both, has the most significant impact on the microbial selection in sugarcane fields.

Efflux transporters such as MexAB-OprM contribute to bacterial resistance to diverse antimicrobial compounds. Here, we show that MexB contributes to epiphytic and late-stage apoplastic growth of Pseudomonas syringae strain B728a, as well as lesion formation in common bean (Phaseolus vulgaris). Although a ∆mexB mutant formed fewer lesions after topical application to common bean, these lesions contain the same number of cells (105 to 107 cells) as those caused by the wild-type strain. The internalized population size of both the wild-type and the ∆mexB mutant within small samples of surface-sterilized asymptomatic portions of leaves varied from undetectably low to as high as 105 cells/cm2. Localized bacterial populations within individual lesions consistently exceeded 105 cells/cm2. Strain B728a was capable of moderate to extensive apoplastic growth in diverse host plants, including lima bean (P. lunatus), fava bean (Vicia faba), pepper (Capsicum annuum), Nicotiana benthamiana, sunflower (Helianthus annuus), and tomato (Solanum lycopersicum), but MexB was not required for growth in a subset of these plant species. A model is proposed that MexB provides resistance to as-yet-unidentified antimicrobials that differ between plant species. [Graphic: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Abstract Background Phyllosphere microbes play important roles in host plant performance and fitness. Recent studies have suggested that tropical and temperate forests harbor diverse phyllosphere bacterial and fungal communities and their assembly is driven by host species identity and plant traits. However, no study has yet examined how seasonality (e.g. dry vs. wet seasons) influences phyllosphere microbial community assembly in natural forests. In addition, in subtropical forests characterized as the transitional zonal vegetation type from tropical to temperate forests, how tree phyllosphere microbial communities are assembled remains unknown. In this study, we quantified bacterial and fungal community structure and diversity on the leaves of 45 tree species with varying phylogenetic identities and importance values within a 20-ha lower subtropical evergreen broad-leaved forest plot in dry and wet seasons. We explored if and how the microbial community assembly varies with host species identity, plant traits and seasonality. Results Phyllosphere microbial communities in the subtropical forest are more abundant and diverse than those in tropical and temperate forests, and the tree species share a “core microbiome” in either bacteria or fungi. Variations in phyllosphere bacterial and fungal community assembly are explained more by host species identity than by seasonality. There is a strong clustering of the phyllosphere microbial assemblage amongst trees by seasonality, and the seasonality effects are more pronounced on bacterial than fungal community assembly. Host traits have different effects on community compositions and diversities of both bacteria and fungi, and among them calcium concentration and importance value are the most powerful explaining variables for bacteria and fungi, respectively. There are significant evolutionary associations between host species and phyllosphere microbiome. Conclusions Our results suggest that subtropical tree phyllosphere microbial communities vary with host species identity, plant traits and seasonality. Host species identity, compared to seasonality, has greater effects on phyllosphere microbial community assembly, and such effects differ between bacterial and fungal communities. These findings advance our understanding of the patterns and drivers of phyllosphere microbial community assembly in zonal forests at a global scale.

Phyllosphere microbiota represents a substantial but hardly explored reservoir for disease resistance mechanisms. The goal of our study was to understand the link between grapevine cultivars susceptibility to Plasmopara viticola, one of the most devastating leaf pathogens in viticulture, and the phyllosphere microbiota. Therefore, we analyzed a 16S rRNA gene library for the dominant phyllosphere bacterial phyla Alphaproteobacteria of seven Vitis genotypes at different developmental stages, i.e., flowering and harvesting, via amplicon sequencing. Young leaves had significantly higher Alphaproteobacterial richness and diversity without significant host-specificity. In contrast, the microbial communities of mature leaves were structurally distinct in accordance with P. viticola resistance levels. This statistically significant link between mature bacterial phyllosphere communities and resistant phenotypes was corroborated by beta diversity metrics and network analysis. Beyond direct host-driven effects via the provision of microhabitats, we found evidence that plants recruit for specific bacterial taxa that were likely playing a fundamental role in mediating microbe-microbe interactions and structuring clusters within mature communities. Our results on grape-microbiota interaction provide insights for targeted biocontrol and breeding strategies.

The plant phyllosphere is colonized by microbial communities that can influence the fitness and growth of their host, including the host’s resilience to plant pathogens.There are multiple factors involved in shaping the assemblages of bacterial and fungal endophytes within the phyllosphere, including host genetics and environment. In this work, the role of host genetics in plant-microbiome assembly was studied in a full-sibling family of apple (Malus x domestica) trees infected with the fungal pathogen Neonectria ditissima. A Quantitative Trait Loci (QTL) analysis showed that there are multiple loci which influence the abundance of individual endophytic taxa, with the majority of QTL having a moderate to large effect (20-40%) on endophyte abundance. QTL regions on LG 1, 3, 4, 5, 10, 12, 13, 14 and 15 were shown to affect multiple taxa. Only a small proportion of the variation in overall taxonomic composition was affected by host genotype, with significant QTL hits for principal components explaining

Summary: Many strains of Pseudomonas colonise plant surfaces, including the cherry canker pathogens, Pseudomonas syringae pathovars syringae and morsprunorum. We have examined the genomic diversity of P. syringae in the cherry phyllosphere and focused on the role of prophages in transfer of genes encoding Type 3 secreted effector (T3SE) proteins contributing to the evolution of virulence.Phylogenomic analysis was carried out on epiphytic pseudomonads in the UK orchards. Significant differences in epiphytic populations occurred between regions. Nonpathogenic strains were found to contain reservoirs of T3SE genes. Members of P. syringae phylogroups 4 and 10 were identified for the first time from Prunus.Using bioinformatics, we explored the presence of the gene encoding T3SE HopAR1 within related prophage sequences in diverse P. syringae strains including cherry epiphytes and pathogens. Results indicated that horizontal gene transfer (HGT) of this effector between phylogroups may have involved phage. Prophages containing hopAR1 were demonstrated to excise, circularise and transfer the gene on the leaf surface.The phyllosphere provides a dynamic environment for prophage‐mediated gene exchange and the potential for the emergence of new more virulent pathotypes. Our results suggest that genome‐based epidemiological surveillance of environmental populations will allow the timely application of control measures to prevent damaging diseases. [ABSTRACT FROM AUTHOR]

[Display omitted] • The critical mechanisms underlying the microbiome assembly in the tea plants are revealed. • There is a trade-off between stochastic and deterministic processes in microbiome assembly in the tea plants. • Assembly processes were dominated by deterministic processes in bulk and rhizosphere soils. • The stochastic processes in roots and leaves was critically driven by amino acids for environmental selection. • The core taxa assembled in phyllosphere could attenuate the virulence of a prevalent foliar pathogen. Assembly and co-occurrence of the host co-evolved microbiota are essential ecological and evolutionary processes, which is not only crucial for managing individual plant fitness but also ecological function. However, understanding of the microbiome assembly and co-occurrence in higher plants is not well understood. The tea plant was shown to contribute the forest fitness due to the microbiome assembled in the phyllosphere; the landscape of microbiome assembly in the tea plants and its potential implication on phyllosphere homestasis still remains untangled. This study aimed to deciphering of the microbiome networks of the tea plants at a continental scale. It would provide fundamental insights into the factors driving the microbiome assembly, with an extended focus on the resilience towards the potential pathogen in the phyllosphere. We collected 225 samples from 45 locations spanning approximately 2000-km tea growing regions across China. By integration of high-throughput sequencing data, physicochemical properties profiling and bioinformatics analyses, we investigated continental scale microbiome assembly and co-occurrence in the tea plants. Synthetic assemblages, interaction assay and RT-qPCR were further implemented to analyze the microbial interaction indexed in phyllosphere. A trade-off between stochastic and deterministic processes in microbiomes community assembly was highlighted. Assembly processes were dominated by deterministic processes in bulk and rhizosphere soils, and followed by stochastic processes in roots and leaves with amino acids as critical drivers for environmental selection. Sphingobacteria and Proteobacteria ascended from soils to leaves to sustain a core leaf taxa. The core taxa formed a close association with a prevalent foliar pathogen in the co-occurrence network and significantly attenuated the expression of a set of essential virulence genes in pathogen. Our study unveils the mechanism underpinning microbiome assembly in the tea plants, and a potential implication of the microbiome-mediated resilience framework on the phyllosphere homeostasis. [ABSTRACT FROM AUTHOR]

Tobacco target spot is a serious fungal disease and it is important to study the similarities and differences between fungal and bacterial community under different disease severities to provide guidance for the biological control of tobacco target spot. In this study, tobacco leaves at disease severity level of 1, 5, 7 and 9 (S1, S5, S7, and S9) were collected, both healthy and diseased leaf tissues for each level were sampled. The community structure and diversity of fungi and bacteria in tobacco leaves with different disease severities were compared using high-throughput sequencing technology. The results indicated that there was a significant differences in the community structure of fungi and bacteria for both healthy and diseased samples depending on the disease severity. In both healthy and diseased tobacco leaves for all four different disease severities, the most dominant fungal phylum was Basidiomycota with a high prevalence of genus Thanatephorus. The relative abundance of Thanatephorus was most found at S9 diseased samples. Proteobacteria represent the most prominent bacterial phylum, with Pseudomonas as predominant genus, followed by Pantoea. The relative abundance of Pseudomonas was most found at S7 healthy samples. In fungal community, the Alpha-diversity of healthy samples was higher than that of diseased samples. In contrast, in bacterial community, the Alpha-diversity of healthy samples was lower than that of diseased samples. LEfSe analysis showed that the most enrich fungal biomarker was Thanatephorus cucumeris in diseased samples. Clostridium disporicum and Ralstonia pickettii were the most enrich bacterial biomarker in healthy samples. FUNGuild analysis showed that the pathotroph mode was the most abundant trophic modes. The relative abundance of pathotroph mode in diseased samples changes insignificantly, but a peak at S5 was observed for healthy samples. PICRUSt analysis showed that most bacterial gene sequences seem to be independent of the disease severity. The results of this study provide scientific references for future studies on tobacco phyllosphere microecology aiming at prevention and control of tobacco target spot. [ABSTRACT FROM AUTHOR]

C1-microorganisms that can utilize C1-compounds, such as methane and methanol, are ubiquitous in nature, and contribute to drive the global carbon cycle between two major greenhouse gases, CO2 and methane. Plants emit C1-compounds from their leaves and provide habitats for C1-microorganisms. Among C1-microorganisms, Methylobacterium spp., representative of methanol-utilizing methylotrophic bacteria, predominantly colonize the phyllosphere and are known to promote plant growth. This review summarizes the interactions between C1-mircroorganisms and plants that affect not only the fixation of C1-compounds produced by plants but also CO2 fixation by plants. We also describe our recent understanding of the survival strategy of C1-microorganisms in the phyllosphere and the application of Methylobacterium spp. to improve rice crop yield. [ABSTRACT FROM AUTHOR]

Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves. Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes. [ABSTRACT FROM AUTHOR]

Methylobacterium species are abundant colonizers of the phyllosphere due to the availability of methanol, a waste product of pectin metabolism during plant cell division. The phyllosphere is an extreme environment, with a landscape that is heterogeneous and continuously changing as the plant grows and is exposed to high levels of ultraviolet irradiation. Geographically, New Zealand (NZ) has been isolated for over a million years, has a biologically diverse flora, and is considered a biodiversity hotspot, with most native plants being endemic. We therefore hypothesize that the phyllosphere of NZ native plants harbor diverse groups of Methylobacterium species. Leaf imprinting using methanol-supplemented agar medium was used to isolate bacteria, and diversity was determined using ARDRA and 16S rRNA gene sequencing. Methylobacterium species were successfully isolated from the phyllosphere of 18 of the 20 native NZ plant species in this study, and six different species were identified: M. marchantiae, M. mesophilicum, M. adhaesivum, M. komagatae, M. extorquens , and M. phyllosphaerae. Other α, β, and γ-Proteobacteria, Actinomycetes, Bacteroidetes, and Firmicutes were also isolated, highlighting the presence of other potentially novel methanol utilizers within this ecosystem. This study identified that Methylobacterium are abundant members of the NZ phyllosphere, with species diversity and composition dependent on plant species. [ABSTRACT FROM AUTHOR]

Traditional antibiotics target essential cellular components or metabolic pathways conserved in both pathogenic and nonpathogenic bacteria. Unfortunately, long-term antibiotic use often leads to antibiotic resistance and disruption of the overall microbiota. In this work, we identified a phenylamino acetamide compound, named 187R, that strongly inhibited the expression of the type III secretion system (T3SS) encoding genes and the secretion of the T3SS effector proteins in Pseudomonas aeruginosa. T3SS is an important virulence factor, as T3SS-deficient strains of P. aeruginosa are greatly attenuated in virulence. We further showed that 187R had no effect on bacterial growth, implying a reduced selective pressure for the development of resistance. 187R-mediated repression of T3SS was dependent on ExsA, the master regulator of T3SS in P. aeruginosa. The impact of 187R on the host-associated microbial community was also tested using the Arabidopsis thaliana phyllosphere as a model. Both culture-independent (Illumina sequencing) and culture-dependent (Biolog) methods showed that the application of 187R had little impact on the composition and function of microbial community compared to the antibiotic streptomycin. Together, these results suggested that compounds that target virulence factors could serve as an alternative strategy for disease management caused by bacterial pathogens. [ABSTRACT FROM AUTHOR]

Sphingomonas is one of the most abundant bacterial genera in the phyllosphere of wild Arabidopsis thaliana, but relative to Pseudomonas, the ecology of Sphingomonas and its interaction with plants is poorly described. We analyzed the genomic features of over 400 Sphingomonas isolates collected from local A. thaliana populations, which revealed much higher intergenomic diversity than for the considerably more uniform Pseudomonas isolates found in the same host populations. Variation in Sphingomonas plasmid complements and additional genomic features suggest high adaptability of this genus, and the widespread presence of protein secretion systems hints at frequent biotic interactions. While some of the isolates showed plant-protective phenotypes in lab tests, this was a rare trait. To begin to understand the extent of strain sharing across alternate hosts, we employed amplicon sequencing and a bulk-culturing metagenomics approach on both A. thaliana and neighboring plants. Our data reveal that both Sphingomonas and Pseudomonas thrive on other diverse plant hosts, but that Sphingomonas is a poor competitor in dying or dead leaves. [ABSTRACT FROM AUTHOR]

Background: Plants are found in a large percentage of indoor environments, yet the potential for bacteria associated with indoor plant leaves and soil to colonize human skin remains unclear. We report results of experiments in a controlled climate chamber to characterize bacterial communities inhabiting the substrates and leaves of five indoor plant species, and quantify microbial transfer dynamics and residence times on human skin following simulated touch contact events. Controlled bacterial propagule transfer events with soil and leaf donors were applied to the arms of human occupants and repeatedly measured over a 24-h period using 16S rRNA gene amplicon sequencing. Results: Substrate samples had greater biomass and alpha diversity compared to leaves and baseline skin bacterial communities, as well as dissimilar taxonomic compositions. Despite these differences in donor community diversity and biomass, we observed repeatable patterns in the dynamics of transfer events. Recipient human skin bacterial communities increased in alpha diversity and became more similar to donor communities, an effect which, for soil contact only, persisted for at least 24 h. Washing with soap and water effectively returned communities to their pre-perturbed state, although some abundant soil taxa resisted removal through washing. Conclusions: This study represents an initial characterization of bacterial relationships between humans and indoor plants, which represent a potentially valuable element of biodiversity in the built environment. Although environmental microbiota are unlikely to permanently colonize skin following a single contact event, repeated or continuous exposures to indoor biodiversity may be increasingly relevant for the functioning and diversity of the human microbiome as urbanization continues. [ABSTRACT FROM AUTHOR]

Nanotechnology is one of the promising techniques and shares wide ranges of applications almost in every field of life. Nanomaterials are getting continuous attractions due to specific physical and chemical properties and being applied as multifunctional material. The use of nanomaterials/nanoparticles in agriculture sector for crop improvement and protection against various environmental threats have attained greater significance. Size and nature of nanoparticles, mode of application, environmental conditions, rhizospheric and phyllospheric environment, and plant species are major factors that influence the action of nanoparticles. The mode or method of nanoparticle applications to plants is attaining greater attentions. Recently, different methods for nanoparticle applications (seed priming, foliar, and root application) are being used to improve crop growth. It is of quite worth that which method is suitable for nanoparticle application, and how nanoparticles can possibly translocate to various plant tissues from root to shoot or vice versa. These information's are poorly understood and need more investigations to explore the comprehensive mechanism by which nanoparticles make their possible entry through different plant organs and how they transport to regulate various physiological and molecular functions in plant cells. Therefore, this study comprehensively provides the knowledge of nanoparticles uptake via seed priming, foliar exposure, and root application, and their possible translocation mechanism within plants influenced by various factors that has not clearly presented. This study will provide new insights to find out an actual uptake and translocation mechanism of nanoparticles that may help researchers to develop nanoparticle-based new strategies for plants to cope with various environmental challenges. This study also focuses on different soil factors or above ground factors that are involved in nanoparticles uptake and translocation and ultimately their functioning in plants. [ABSTRACT FROM AUTHOR]

Both biotic and abiotic factors continually affect the phyllospheric ecology of plants. A better understanding of the drivers of phyllospheric community structure and multitrophic interactions is vital for developing plant protection strategies. In this study, 16S rRNA high-throughput sequencing was applied to study how summer climatic factors and bacterial wildfire disease have affected the composition and assembly of the bacterial community of tobacco (Nicotiana tabacum L.) phyllosphere. Our results indicated that three time series groups (T1, T2 and T3) formed significantly distinct clusters. The neutral community model (NCM) and beta nearest taxon index (betaNTI) demonstrated that the overall bacterial community assembly was predominantly driven by stochastic processes. Variance partitioning analysis (VPA) further showed that the complete set of the morbidity and climatic variables together could explain 35.7% of the variation of bacterial communities. The node numbers of the molecular ecological networks (MENs) showed an overall uptrend from T1 to T3. Besides, Pseudomonas is the keystone taxa in the MENs from T1 to T3. PICRUSt2 predictions revealed significantly more abundant genes of osmoprotectant biosynthesis/transport in T2, and more genes for pathogenicity and metabolizing organic substrate in T3. Together, this study provides insights into spatiotemporal patterns, processes and response mechanisms underlying the phyllospheric bacterial community. [ABSTRACT FROM AUTHOR]

The intra- and interdomain phyllosphere microbiome features of Quercus ilex L. in a Mediterranean context is reported. We hypothesized that the main driver of the phyllosphere microbiome might be the season and that atmospheric pollutants might have a co-effect. Hence, we investigated the composition of epiphytic bacteria and fungi of leaves sampled in urban and natural areas (in Southern Italy) in summer and winter, using microscopy and metagenomic analysis. To assess possible co-effects on the composition of the phyllosphere microbiome, concentrations of particulate matter and polycyclic aromatic hydrocarbons (PAHs) were determined from sampled leaves. We found that environmental factors had a significative influence on the phyllosphere biodiversity, altering the taxa relative abundances. Ascomycota and Firmicutes were higher in summer and in urban areas, whereas a significant increase in Proteobacteria was observed in the winter season, with higher abundance in natural areas. Network analysis suggested that OTUs belonging to Acidobacteria, Cytophagia, unkn. Firmicutes(p), Actinobacteria are keystone of the Q. ilex phyllosphere microbiome. In addition, 83 genes coding for 5 enzymes involved in PAH degradation pathways were identified. Given that the phyllosphere microbiome can be considered an extension of the ecosystem services offered by trees, our results can be exploited in the framework of Next-Generation Biomonitoring. [ABSTRACT FROM AUTHOR]

Plant-associated microbial communities may be important sources of functional diversity and genetic variation that influence host evolution. Bacteria provide benefits for their hosts, yet in most plant systems we know little about their taxonomic composition or variation across tissues and host range. Red Mangrove (Rhizophora mangle L.) is a vital coastal plant species that is currently expanding poleward and with it, perhaps, its microbiome. We explored variability in bacterial communities across tissues, individuals, and populations. We collected samples from six sample types from 5 to 10 individuals at each of three populations and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. Core community members and dominant bacterial classes were determined for each sample type. Pairwise PERMANOVA of Bray–Curtis dissimilarity and Indicator Species Analysis revealed significant differences in bacterial communities between sample types and populations. We described the previously unexplored microbiome of the reproductive tissues of R. mangle. Populations and most sample types were associated with distinct communities. Bacterial communities associated with R. mangle are influenced by host geography and sample type. Our study provides a foundation for future work exploring the functional roles of these microbes and their relevance to biogeochemical cycling. [ABSTRACT FROM AUTHOR]

Endophytes are endosymbiotic microorganisms that coexist within different plant species which assist the host in multifarious ways without causing any detrimental effects on the plant well-being. The current study is focused on the bacterial isolates found in the Piper nigrum in vitro culture in the basal MS medium. The growth of these bacterial isolates even after repeated surface sterilization of the explant concludes the nature of these isolates as endophytes and these isolates were identified as Pantoea sp., Luteibacter sp., Herbaspirillum sp., and Agrobacterium sp. through 16srRNA. The endophytes were tested for their potential to aid plant development by assessing the production of Indoleacetic Acid, Ammonia, Hydrogen Cyanide, 1-aminocyclopropane-1-carboxylic acid deaminase, Siderophore, fixation of Nitrogen, solubilization of Phosphate, heavy metal and salt tolerance. Pantoea sp. and Herbaspirillum sp. were found tolerant against salt and heavy metal stress respectively. Based on plant growth promotion assays, Pantoea sp. and Agrobacterium sp. were further selected for metabolomic profiling. The results indicated the effects of isolates on primary and secondary metabolite biogenesis, aminoacyl-tRNA synthesis and amino acid metabolic pathways. The profiling of important metabolites linked to crop development, revealing its metabolic mechanism of plant growth promoting activities facilitated through selected Plant Growth Promoting Bacteria. [ABSTRACT FROM AUTHOR]

[Display omitted] • NGS was used to precisely describe the microbiome of three strawberry cultivars. • Plant organs and genotype shape the composition of the microbiomes. • Strawberry microbiome delivers several beneficial functions to the plant. • Functional microbiome diversity correlates with cultivars' phenotypical differences. • Microbiome manipulation may enhance agricultural performances. Specific microbial communities are associated to host plants, influencing their phenotype and fitness. Despite the rising interest in plant microbiome, the role of microbial communities associated with perennial fruit plants remains overlooked. This work provides the first comprehensive description of the taxonomical and functional bacterial and fungal microbiota of below- and above-ground organs of three commercially important strawberry genotypes under cultural conditions. Strawberry-associated fungal and bacterial microbiomes were characterised by Next-Generation Sequencing and the potential functions expressed by the bacterial microbiome were analysed by both in silico and in vitro characterisation of plant growth-promoting abilities of native bacteria. Additionally, the association between the strawberry microbiome, plant disease tolerance, plant mineral nutrient content, and fruit quality was investigated. Results showed that the strawberry core microbiome included 24 bacteria and 15 fungal operational taxonomic units (OTUs). However, plant organ and genotype had a significant role in determining the taxonomical and functional composition of microbial communities. Interestingly, the cultivar with the highest tolerance against powdery mildew and leaf spot and the highest fruit productivity was the only one able to ubiquitously recruit the beneficial bacterium, Pseudomonas fluorescens , and to establish a mutualistic symbiosis with the arbuscular mycorrhiza Rhizophagus irregularis. This work sheds light on the interaction of cultivated strawberry genotypes with a variety of microbes and highlights the importance of their applications to increase the sustainability of fruit crop production. [ABSTRACT FROM AUTHOR]

For the first time, mycological analysis of dust, including assessment of opportunistic fungal species, was carried out for the urban ecosystems of air, vegetation, and paved surfaces in different climate areas (the cities of Murmansk and Moscow). The combined effect of environmental factors (climate, functional zone, and substrate type) on qualitative and quantitative parameters of micromycete communities was assessed using MANOVA and cluster analysis. It was found that the abundance of culturable mycobiota in the air, on tree leaves, and on paved surfaces was lower in Murmansk than in Moscow. In both cities, approximately a half of fungal species were opportunistic pathogens. The relative abundance of opportunistic fungi of the BSL-2 group was higher in the air of the traffic zone in both cities and of the residential zone in Moscow. In the residential and traffic zones of Moscow, the most abundant species in the air in on the road dust were Aspergillus fumigatus and A. niger, while in Murmansk communities were dominated by members of the genera Cephalosporium, Scopulariopsis, and Trichoderma, which are less pathogenic for humans. The most significant factors affecting the abundance and species diversity of micromycetes, including opportunistic fungi, were the substrate type (air, leaves, or paved surfaces) and the climate, while the effect of the functional zone was not significant. The recreation zones of cities located in different climate regions are the most favorable for humans due to lower abundance of opportunistic fungi in the air and to lack of micromycetes of the BSL-2 and BSL-3 groups. However, the abundance of potentially pathogenic species on the surfaces of leaves and roads in this zone was higher than in the air. Therefore, it can be recommended that city residents minimize their contact with the leaves surface and road pavements, which is especially relevant for toddlers, so as to diminish the probability of encountering opportunistic mycobiota that potentially represents a health hazard. [ABSTRACT FROM AUTHOR]

Abies concolor was introduced to Europe in the 19th century and commonly planted as an ornamental tree. In 2018, after several very warm and dry vegetation seasons, which has likely caused abiotic stress in the trees, a sudden dieback of A. concolor was observed in the city of Aranđelovac in Serbia. The external symptoms were the rapid discoloration of needles in a larger part of the crown and eventually the dieback of the trees. The aim of this study was to identify the possible agents of damage by analysing the fungal communities associated with symptomatic needles using high-throughput sequencing as no symptoms of damage were seen on the branches or stems. Symptomatic needles were collected from the lower branches of five standing trees. Half of the needles were surface sterilised and the remaining were left unsterilised. DNA was extracted, amplified using ITS2 rDNA as a marker and sequenced. Quality filtering showed the presence of 6 191 high quality reads, which, following a clustering analysis, was found to represent 79 non-singletons fungal taxa. The most common fungi in both surface sterilised and unsterilised needles were the pathogens Cytospora friesii (59.7%) and Sydowia polyspora (20.6%). The results demonstrated that C. friesii and S. polyspora can cause a rapid decline of A. concolor trees subjected to abiotic stress.

[Display omitted] • S. feltiae and S. carpocapsae successfully control Lepidopteran larvae on foliage. • Upon optimal conditions, both EPN species survive several days on leaves. • Upon optimal conditions, both EPNs need only a few hours to enter a host. • S. feltiae tend to be attracted to volatiles from infested tomato leaves. • EPNs have the potential to become major protagonists in sustainable crop protection. Entomopathogenic nematodes (EPNs) are ubiquitous soil-thriving organisms that use chemical cues to seek and infect soil-dwelling arthropods, yielding various levels of biological control. Going beyond soil application, scientists and practitioners started exploring the option of applying EPNs onto the foliage of crops in attempts to manage leaf-dwelling insect pests as well. Despite some success, particularly with protective formulations, it remains uncertain whether EPNs could indeed survive the phyllospheric environment, and successfully control foliar insect pests. In this context, we tested the potential of commercially produced Steinernema feltiae and S. carpocapsae , two of the most commonly used EPNs in the field of biological control, in controlling Lepidopteran foliar pests of economic importance, i.e. Tuta absoluta and Spodoptera spp. caterpillars as models. We first tested the survival and efficacy of both EPN species against the Lepidopteran caterpillars when applied onto tomato, sweet pepper and lettuce leaves, under controlled conditions and in commercial greenhouse conditions, respectively. Subsequently, we explored the behavioural responses of the EPNs to environmental cues typically encountered in the phyllosphere , and analysed plant volatile organic compounds (VOCs). Our results show that both S. feltiae and S. carpocapsae successfully survived and infected the foliar caterpillars, reaching similar level of control to a standard chemical pesticide in commercial practices. Remarkably, both EPN species survived and remained effective up to four days in the phyllosphere, and needed only a few hours to successfully penetrate the caterpillars. Interestingly, S. feltiae was attracted to VOCs from tomato plants, and tended to prefer those from caterpillar-induced plants, suggesting that the nematodes may actively forage toward its host, although it has never been exposed to leaf-borne volatiles during its evolution. The present study shows the high potential of steinernematids in managing major foliar pests in greenhouses and in becoming a key player in foliar biological control. In particular, the discovery that EPNs use foliar VOCs to locate caterpillar hosts opens up new opportunities in terms of application techniques and affordable effective doses. [ABSTRACT FROM AUTHOR]

Increasing evidence suggests that microbes colonizing both above- and below-ground parts of plants are critical for plant growth and agricultural productivity. However, the extent to which the interactions between above- and below-ground microbial communities affect microbial colonization and plant performance is not fully understood. To address this question, we performed a phyllosphere and rhizosphere microbiome transplantation experiment (MT-Exp) using sugarcane, followed by microbiome profiling with 16S rRNA amplicon sequencing. Plant phenotypic observation exhibited that transplanting field-grown sugarcane phyllosphere and/or rhizosphere onto sugarcane plantlets in a controlled growth condition significantly increased total biomass compared to un-transplanted plants. Notably, co-transplantation of phyllosphere (P) and rhizosphere (R) microbiomes (PR treatment) resulted in the most pronounced plant growth promotion. A comparison of alpha diversity revealed that microbiome transplantation enhanced the species richness of both phyllosphere and rhizosphere communities. Additionally, PERMANOVA results showed that microbiome transplantation strongly impacted the rhizosphere microbial community, while no significant differences were observed in the phyllosphere microbes. The PR treatment was found to be more effective in introducing a greater diversity of microbial taxa than single transplantation (P and R treatments), of which many of these transplanted taxa were recognized as plant growth-promoting bacteria (PGPB). Furthermore, the PR network displayed denser connectivity between above- and below-ground components compared to all other treatments. In conclusion, our findings highlight the interdependence of above-ground and below-ground microorganisms, demonstrating their indispensable role in colonizing and promoting sugarcane growth. • Microbiome transplantation increased species richness in both phyllosphere and rhizosphere. • Microbiome transplantation significantly influenced rhizosphere microbial communities. • Co-transplantation effectively promoted sugarcane growth and inoculant survivability. • The importance of both above- and below-ground microbes in biofertilizer applications is highlighted. [ABSTRACT FROM AUTHOR]

Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant–pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.

As an ecological index for plants, the diversity and structure of phyllosphere microbial communities play a crucial role in maintaining ecosystem stability and balance; they can affect plant biogeography and ecosystem function by influencing host fitness and function. The phyllosphere microbial communities reflect the immigration, survival, and growth of microbial colonists, which are influenced by various environmental factors and leaves’ physical and chemical properties. This study investigated the structure and diversity of phyllosphere fungal communities in three different Populus spp., namely—P. × euramaricana (BF3), P. nigra (N46), and P. alba × P. glandulosa (84K). Leaves’ chemical properties were also analyzed to identify the dominant factors affecting the phyllosphere fungal communities. N46 exhibited the highest contents of total nitrogen (Nt), total phosphorus (Pt), soluble sugar, and starch. Additionally, there were significant variations in the abundance, diversity, and composition of phyllosphere fungal communities among the three species: N46 had the highest Chao1 index and observed_species, while 84K had the highest Pielou_e index and Simpson index. Ascomycota and Basidiomycota are the dominant fungal communities at the phylum level. Results from typical correlation analyses indicate that the chemical properties of leaves, especially total phosphorus (Pt), total nitrogen (Nt), and starch content, significantly impact the structure and diversity of the phyllosphere microbial community. However, it is worth noting that even under the same stand conditions, plants from different species have distinct leaf characteristics, proving that the identity of the host species is the critical factor affecting the structure of the phyllosphere fungal community.

Abstract Background Biocontrol agents are sustainable eco-friendly alternatives for chemical pesticides that cause adverse effects in the environment and toxicity in animals including humans. An improved understanding of the phyllosphere microbiology is of vital importance for biocontrol development. Most studies have been directed towards beneficial plant-microbe interactions and ignore the pathogens that might affect humans when consuming vegetables. In this study we extended this perspective and investigated potential biocontrol strains isolated from tomato and lettuce phyllosphere that can promote plant growth and potentially antagonize human pathogens as well as plant pathogens. Subsequently, we mined into their genomes for discovery of antimicrobial biosynthetic gene clusters (BGCs), that will be further characterized. Results The antimicrobial activity of 69 newly isolated strains from a healthy tomato and lettuce phyllosphere against several plant and human pathogens was screened. Three strains with the highest antimicrobial activity were selected and characterized (Bacillus subtilis STRP31, Bacillus velezensis SPL51, and Paenibacillus sp. PL91). All three strains showed a plant growth promotion effect on tomato and lettuce. In addition, genome mining of the selected isolates showed the presence of a large variety of biosynthetic gene clusters. A total of 35 BGCs were identified, of which several are already known, but also some putative novel ones were identified. Further analysis revealed that among the novel BGCs, one previously unidentified NRPS and two bacteriocins are encoded, the gene clusters of which were analyzed in more depth. Conclusions Three recently isolated strains of the Bacillus genus were identified that have high antagonistic activity against lettuce and tomato plant pathogens. Known and unknown antimicrobial BGCs were identified in these antagonistic bacterial isolates, indicating their potential to be used as biocontrol agents. Our study serves as a strong incentive for subsequent purification and characterization of novel antimicrobial compounds that are important for biocontrol.

Biochar soil amendment alleviates plant disease through microbial-mediated processes but drivers facilitating this “biochar effect” are not fully understood. In this study, cucumber plants were inoculated with and without the fungus Fusarium oxysporum f. sp. radicis-cucumerinum in either biochar-amended or nonamended soils, and disease severity was assessed. Amplicon sequencing and shotgun metagenomics were then applied to identify bacteria and associated mechanisms potentially involved in pathogen inhibition, and candidate bacteria were tested for in vitro F. oxysporum f. sp. radicis-cucumerinum-antagonizing capacity. Biochar-amended plants showed lower F. oxysporum f. sp. radicis-cucumerinum-associated growth stagnation compared with nonamended plants, supporting the biochar effect. Their rhizosphere had a more diverse microbiome with higher levels of secondary metabolite-encoding biosynthetic gene clusters (BGCs). Families Pseudonocardiaceae (Lentzea spp.) and Myxococcaceae were significantly more abundant in biochar-amended rhizospheres of F. oxysporum f. sp. radicis-cucumerinum-inoculated plants, and metagenomically assembled genomes (MAGs) from these taxa contained genes encoding enzymes involved in binding and degradation of chitin, and novel BGCs encoding secondary metabolites. Lentzea spp. isolates related to the above MAGs showed in vitro antagonistic activity against F. oxysporum f. sp. radicis-cucumerinum. Collectively, we postulate that biochar amendment generates a “buffering effect” that reduces F. oxysporum f. sp. radicis-cucumerinum-facilitated destabilization of the root-associated microbiome, maintaining beneficial taxa that produce antagonizing enzymes and secondary metabolites that sustain plant health.

ABSTRACT Wild rice has been demonstrated to possess enriched genetic diversity and multiple valuable traits involved in disease/pest resistance and abiotic stress tolerance, which provides a potential resource for sustainable agriculture. However, unlike the plant compartments such as rhizosphere, the structure and assembly of phyllosphere microbial communities of wild rice remain largely unexplored. Through amplicon sequencing, this study compared the phyllosphere bacterial and fungal communities of wild rice and its neighboring cultivated rice. The core phyllosphere microbial taxa of both wild and cultivated rice are dominated with Pantoea, Methylobacterium, Nigrospora, and Papiliotrema, which are potentially beneficial to rice growth and health. Compared to the cultivated rice, Methylobacterium, Sphingomonas, Phaeosphaeria, and Khuskia were significantly enriched in the wild rice phyllosphere. The potentially nitrogen-fixing Methylobacterium is the dominated wild-enriched microbe; Sphingomonas is the hub taxon of wild rice networks. In addition, the microbiota of wild rice was more governed by deterministic assembly with a more complicated and stable community network than the cultivated rice. Our study provides a list of the beneficial microbes in the wild rice phyllosphere and reveals the microbial divergence between wild rice and cultivated rice in the original habitats, which highlights the potential selective role of wild rice in recruiting specific microbiomes for enhancing crop performance and promoting sustainable food production. IMPORTANCE Plant microbiota are being considered a lever to increase the sustainability of food production under a changing climate. In particular, the microbiomes associated with ancestors of modern cultivars have the potential to support their domesticated cultivars. However, few efforts have been devoted to studying the biodiversity and functions of microbial communities in the native habitats of ancestors of modern crop species. This study provides a list of the beneficial microbes in the wild rice phyllosphere and explores the microbial interaction patterns and the functional profiles of wild rice. This information could be useful for the future utilization of the plant microbiome to enhance crop performance and sustainability, especially in the framework of sustainable agroecosystems.

All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of "optimal microbiota" as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining "optimal microbiota," which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.

[This corrects the article DOI: 10.3389/fnut.2018.00090.].

We aimed to assess how biofilm formation by three Bacillus isolates was affected by changes in temperature, water potential, growth media, time, and the combinations between these factors. The strains had been selected as potential biological control agents (BCAs) in earlier studies, and they were identified as B. subtilis and B. velezensis spp. through 16 rRNA sequencing and MALDI-TOF MS. Maize leaves (ML) were used as one of the growth media, since they made it possible to simulate the nutrient content in the maize phyllosphere, from which the bacteria were originally isolated. The strains were able to form biofilm both in ML and biofilm-inducing MSgg after 24, 48, and 72 h. Biofilm development in the form of pellicles and architecturally complex colonies varied morphologically from one strain to another and depended on the conditions mentioned above. In all cases, colonies and pellicles were less complex when both temperature and water potential were lower. Scanning electron microscopy (SEM) revealed that changing levels of complexity in pellicles were correlated with those in colonies. Statistical analyses found that the quantification of biofilm produced by the isolates was influenced by all the conditions tested. In terms of motility (which may contribute to biofilm formation), swimming and swarming were possible for all strains in 0.3 and 0.7% agar, respectively. A more in-depth understanding of how abiotic factors influence biofilm formation can contribute to a more effective use of these biocontrol strains against pathogens in the maize phyllosphere.

Summary: Diverse host factors drive microbial variation in plant‐associated environments, whereas their genetic mechanisms remain largely unexplored. To address this, we coupled the analyses of plant genetics and microbiomes in this study. Using 100 tea plant (Camellia sinensis) cultivars, the microbiomes of rhizosphere, root endosphere and phyllosphere showed clear compartment‐specific assembly, whereas the subpopulation differentiation of tea cultivars exhibited small effects on microbial variation in each compartment. Through microbiome genome‐wide association studies, we examined the interactions between tea genetic loci and microbial variation. Notably, genes related to the cell wall and carbon catabolism were heavily linked to root endosphere microbial composition, whereas genes related to the metabolism of metal ions and small organic molecules were overrepresented in association with rhizosphere microbial composition. Moreover, a set of tea genetic variants, including the cytoskeleton‐related formin homology interacting protein 1 gene, were strongly associated with the β‐diversity of phyllosphere microbiomes, implying their interactions with the overall structure of microbial communities. Our results create a catalogue of tea genetic determinants interacting with microbiomes and reveal the compartment‐specific microbiome assembly driven by host genetics. [ABSTRACT FROM AUTHOR]

Aims: Litter decomposition is a complex process closely linked to terrestrial ecosystem dynamics. We examined how forest succession from Scots pine (Pinus sylvestris L.) to Pyrenean oak (Quercus pyrenaica Willd.) driven by global-change may influence litter decomposition in a Mediterranean ecotone forest. Methods: We performed a reciprocal experiment using litterbags in pure Scots pine and Pyrenean oak forests to assess the litter decomposition process of pine (needles), oak (leaves) and a 1:1 mixture of needles and leaves over a two-year period. Results: Home-field advantage was only found in the oak leaves, while needle decomposition rates were similar in both forests. There were synergistic effects of mixing litter that mainly increased the decomposition of needle litter. The litter mixing and the forest environment gained influence as drivers of litter decomposition over time by shaping the functional assembly of microbial communities and determining decomposition conditions. We found a staggered functional adjustment of the microbial community assembly driven by the litter type at early stages, followed by the convergence of colonizing microbial communities towards soil microbes and soil organic matter characteristics. Conclusions: There were specific interlinks between the litter identity and stoichiometry, the aboveground phyllosphere communities and the forest environment (through soil microclimate and soil microbial communities) affecting the cycling of C and N. These ecological feedbacks are of special interest under the current changes in climate and forestry management that may foster the secondary succession of the forest. [ABSTRACT FROM AUTHOR]

Through the process of domestication, selection is targeted on a limited number of plant traits that are typically associated with yield. As an unintended consequence, domesticated plants often perform poorly compared to their wild progenitors for a multitude of traits that were not under selection during domestication, including abiotic and biotic stress tolerance. Over the past decade, advances in sequencing technology have allowed for the rigorous characterization of host-associated microbial communities, termed the microbiome. It is now clear that nearly every conceivable plant interaction with the environment is mediated by interactions with the microbiome. For this reason, plant–microbiome interactions are an area of great promise for plant breeding and crop improvement. Here, we review the literature to assess the potential impact that domestication has had on plant–microbiome interactions and the current understanding of the genetic basis of microbiome variation to inform plant breeding efforts. Overall, we find limited evidence that domestication impacts the diversity of microbiomes, but domestication is often associated with shifts in the abundance and composition of microbial communities, including taxa of known functional significance. Moreover, genome-wide association studies and mutant analysis have not revealed a consistent set of core candidate genes or genetic pathways that confer variation in microbiomes across systems. However, such studies do implicate a consistent role for plant immunity, root traits, root and leaf exudates and cell wall integrity as key traits that control microbiome colonization and assembly. Therefore, selection on these key traits may pose the most immediate promise for enhancing plant–microbiome interactions through breeding. [ABSTRACT FROM AUTHOR]

Background: Azolla is a small floating fern living in symbiosis with nitrogen-fixing cyanobacteria and provides a variety of important ecosystem benefits. Previous studies have presented that Azolla harbors diverse bacteria that may play a key role in host fitness and productivity. However, the characteristics of endophytic bacteria inhabiting the phyllosphere of different species of Azolla have not yet been fully understood. Results: In this study, the 16S ribosomal DNA (rDNA) V5-V7 region of bacteria was determined by Illumina high-throughput sequencing platform to study the diversity and richness of endophytic bacterial communities in the phyllosphere of five Azolla species collected from different countries. A total of 1150 operational taxonomic units (OTUs) were detected for the endophytic bacteria community. According to the α diversity indices, the diversity of bacteria was ordered as Azolla imbricata > A. pinnata > A. filiculoides > A. mexicana > A. caroliniana. The PCoA results displayed that the bacterial communities of A. mexicana and A. caroliniana shared the highest similarity, followed by the similarity between A. pinnata and A. imbricata, and they were significantly distinct from the community of A. filiculoides. The dominant bacteria of Azolla mainly belonged to the phylum of Proteobacteria, followed by Actinobacteria, Chlorobillobacteria, and Firmicutes. In detail, the relative abundance of Proteobacteria in A. imbricata was 52.23%, whereas it was more than 80.00% in the other four species of Azolla. Notably, Herbaspirillum (45.91%, 44.08%) and Methylophilus (29.97%, 37.96%) were the main genera inhabiting A. mexicana and A. caroliniana respectively. Ferrovibrio (18.54%) and Rhizobium (16.68%) were the dominant genera inhabiting A. filiculoides. The group of unidentified genera (41.63%, 44.92%) consisted most of the bacteria in A. imbricata and A. pinnata respectively. Further analysis suggested that the significant different bacteria identified in LDA Effect Size analysis existed Azolla species-specific patterns. Conclusions: In summary, all results suggested that the diversity and composition of the endophytic bacterial communities were different in Azolla species. [ABSTRACT FROM AUTHOR]

The number and intensity of flood events will likely increase in the future, raising the risk of flooding stress in terrestrial plants. Understanding flood effects on plant physiology and plant‐associated microbes is key to alleviate flooding stress in sensitive species and ecosystems. Reduced oxygen supply is the main constrain to the plant and its associated microbiome. Hypoxic conditions hamper root aerobic respiration and, consequently, hydraulic conductance, nutrient uptake, and plant growth and development. Hypoxia favours the presence of anaerobic microbes in the rhizosphere and roots with potential negative effects to the plant due to their pathogenic behaviour or their soil denitrification ability. Moreover, plant physiological and metabolic changes induced by flooding stress may also cause dysbiotic changes in endosphere and rhizosphere microbial composition. The negative effects of flooding stress on the holobiont (i.e., the host plant and its associated microbiome) can be mitigated once the plant displays adaptive responses to increase oxygen uptake. Stress relief could also arise from the positive effect of certain beneficial microbes, such as mycorrhiza or dark septate endophytes. More research is needed to explore the spiralling, feedback flood responses of plant and microbes if we want to promote plant flood tolerance from a holobiont perspective. [ABSTRACT FROM AUTHOR]

Maize (Zea mays L.), a major crop in Argentina and a staple food around the world, is affected by the emergence and re‐emergence of foliar diseases. Agrochemicals are the main control strategy nowadays; however, they can cause resistance in insects and microbial pathogens and have negative effects on the environment and human health. An emerging alternative is the use of living organisms, i.e. microbial biocontrol agents, to suppress plant pathogen populations. This is a risk‐free approach when the organisms acting as biocontrol agents come from the same ecosystem as the foliar pathogens they are meant to antagonize. Some epiphytic microorganisms may form biofilm by becoming aggregated and attached to a surface, as is the case of spore‐forming bacteria from the genus Bacillus. Their ability to sporulate and their tolerance to long storage periods make them a frequently used biocontrol agent. Moreover, the biofilm that they create protects them against different abiotic and biotic factors and helps them to acquire nutrients, which ensures their survival on the plants they protect. This review analyzes the interactions that the phyllosphere‐inhabiting Bacillus genus establishes with its environment through biofilm, and how this lifestyle could serve to design effective biological control strategies. [ABSTRACT FROM AUTHOR]

Tall fescue (Schedonorus arundinaceus) is a cool-season grass which is commonly infected with the fungal endophyte Epichloë coenophiala. Although the relationship between tall fescue and E. coenophiala is well-studied, less is known about its broader fungal communities. We used next-generation sequencing of the ITS2 region to describe the complete foliar fungal microbiomes in a set of field-grown tall fescue plants over two years, and whether these fungal communities were affected by the presence of Epichloë. We used the Georgia 5 cultivar of tall fescue, grown in the field for six years prior to sampling. Plants were either uninfected with E. coenophiala, or they were infected with one of two E. coenophiala strains: The common toxic strain or the AR542 strain (sold commerically as MaxQ). We observed 3487 amplicon sequence variants (ASVs) across all plants and identified 43 ASVs which may make up a potential core microbiome. Fungal communities did not differ strongly between Epichloë treatments, but did show a great deal of variation between the two years. Plant fitness also changed over time but was not influenced by E. coenophiala infection. [ABSTRACT FROM AUTHOR]