Microbial phyllosphere populations are more complex than previously realized

Construction of high-quality genomes and gene catalogue for culturable microbes of sugarcane (Saccharum spp.)

Microbes living inside or around sugarcane (Saccharum spp.) are crucial for their resistance to abiotic and biotic stress, growth, and development. Sequences of microbial genomes and genes are helpful to understand the function of these microbes. However, there is currently a lack of such knowledge in sugarcane. Here, we combined Nanopore and Illumina sequencing technologies to successfully construct the first high-quality metagenome-assembled genomes (MAGs) and gene catalogues of sugarcane culturable microbes (GCSCMs), which contained 175 species-level genome bins (SGBs), and 7,771,501 non-redundant genes. The SGBs included 79 novel culturable bacteria genomes, and 3 bacterial genomes with nitrogen-fixing gene clusters. Four single scaffold near-complete circular MAGs (cMAGs) with 0% contamination were obtained from Nanopore sequencing data. In conclusion, we have filled a research gap in the genomes and gene catalogues of culturable microbes of sugarcane, providing a vital data resource for further understanding the genetic basis and functions of these microbes. In addition, our methodology and results can provide guidance and reference for other plant microbial genome and gene catalogue studies.

Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome

The important role of microbial associations in mediating plant protection and responses to abiotic stresses has been widely recognized. However, there have been limited studies on the functional profile of the phyllosphere microbiota from tobacco (Nicotiana tabacum), hindering our understanding of the mechanisms underlying stress resilience in this representative and easy-to-cultivate model species from the solanaceous family. To address this knowledge gap, our study employed shotgun metagenomic sequencing for the first time to analyze the genetic catalog and identify putative plant growth promoting bacteria (PGPB) candidates that confer abiotic stress resilience throughout the growth period of cigar tobacco in the phyllosphere. We identified abundant genes from specific bacterial lineages, particularly Pseudomonas, within the cigar tobacco phyllospheric microbiome. These genes were found to confer resilience against a wide range of stressors, including osmotic and drought stress, heavy metal toxicity, temperature perturbation, organic pollutants, oxidative stress, and UV light damage. In addition, we conducted a virome mining analysis on the metagenome to explore the potential roles of viruses in driving microbial adaptation to environmental stresses. Our results identified a total of 3,320 scaffolds predicted to be viral from the cigar tobacco phyllosphere metagenome, with various phages infecting Pseudomonas, Burkholderia, Enterobacteria, Ralstonia, and related viruses. Within the virome, we also annotated genes associated with abiotic stress resilience, such as alkaline phosphatase D (phoD) for nutrient solubilization and glutamate-5-semialdehyde dehydrogenase (proA) for osmolyte synthesis. These findings shed light on the unexplored roles of viruses in facilitating and transferring abiotic stress resilience in the phyllospheric microbiome through beneficial interactions with their hosts. The findings from this study have important implications for agricultural practices, as they offer potential strategies for harnessing the capabilities of the phyllosphere microbiome to enhance stress tolerance in crop plants.

Rhizocompartmental microbiomes of arrow bamboo (Fargesia nitida) and their relation to soil properties in Subalpine Coniferous Forests

Arrow bamboo (Fargesia nitida) is a pioneer plant in secondary forest succession in the Sichuan Province mountains. To comprehensively investigate the microbial communities and their functional variations in different rhizocompartments (root endosphere, rhizosphere, and root zone) of arrow bamboo (Fargesia nitida), a high-throughput metagenomic study was conducted in the present study. The results showed that the abundances of the dominant bacterial phyla Proteobacteria and Actinobacteria in the bamboo root endosphere were significantly lower than those in the rhizosphere and root zones. In contrast, the dominant fungal phyla, Ascomycota and Basidiomycota, showed the opposite tendency. Lower microbial diversity, different taxonomic composition and functional profiles, and a greater abundance of genes involved in nitrogen fixation (nifB), cellulose degradation (beta-glucosidase), and cellobiose transport (cellulose 1, 4-beta-cellobiosidase) were found in the bamboo root endosphere than in the other rhizocompartments. Greater soil total carbon, total nitrogen, NH4+-N, microbial biomass carbon, and greater activities of invertase and urease were found in the bamboo root zone than in the adjacent soil (spruce root zone). In contrast, the soil microbial community and functional profiles were similar. At the phylum level, invertase was significantly related to 31 microbial taxa, and the effect of NH4+-N on the microbial community composition was greater than that of NO3--N. The soil physicochemical properties and enzyme activities were significantly correlated with microbial function. These results indicate that the root endosphere microbiomes of arrow bamboo were strongly selected by the host plant, which caused changes in the soil nutrient properties in the subalpine coniferous forest.

Diversity of Methylobacterium species associated with New Zealand native plants

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.

Interaction between C1-microorganisms and plants: contribution to the global carbon cycle and microbial survival strategies in the phyllosphere

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.

Effects of Variety, Plant Location, and Season on the Phyllosphere Bacterial Community Structure of Alfalfa (Medicago sativa L.)

Plant phyllosphere bacteria are vital for plant health and productivity and are affected by both abiotic and biotic factors. In this study, we surveyed the structure of the phyllosphere bacterial community associated with alfalfa. For two varieties of alfalfa, forty-eight samples of phyllosphere communities were collected at two locations over four seasons in 2020. Proteobacteria and actinobacteria were associated with the dominating phylum in the bacterial communities of the alfalfa phyllosphere. Sphingomonas was the most abundant genus-level bacteria, followed by Methylobacterium, Burkholderia-Caballeronia-Paraburkholderia, and Pseudomonas. Sampling time had a greater affect than site and variety on alfalfa surface microorganisms. The variation in phyllosphere bacterial community assembly was mostly explained by the season–site interaction (43%), season–variety interaction (35%), and season (28%). Variety, site–variety interaction, and season–site–variety interactions did not have a meaningful effect on phyllosphere bacterial diversity and community structure. The bacterial community in the phyllosphere of alfalfa showed seasonal changes over time. The environmental factors that contributed most to the phyllosphere bacterial community of alfalfa were temperature and sunshine duration, which were significantly positively correlated with most of the dominant bacterial genera in the alfalfa phyllosphere.

Kribbellichelins A and B, Two New Antibiotics from Kribbella sp. CA-293567 with Activity against Several Human Pathogens

Current needs in finding new antibiotics against emerging multidrug-resistant superbugs are pushing the scientific community into coming back to Nature for the discovery of novel active structures. Recently, a survey of halophilic actinomyectes from saline substrates of El Saladar del Margen, in the Cúllar-Baza depression (Granada, Spain), led us to the isolation and identification of 108 strains from the rhizosphere of the endemic plant Limonium majus. Evaluation of the potential of these strains to produce new anti-infective agents against superbug pathogens was performed through fermentation in 10 different culture media using an OSMAC approach and assessment of the antibacterial and antifungal properties of their acetone extracts. The study allowed the isolation of two novel antibiotic compounds, kribbellichelin A (1) and B (2), along with the known metabolites sandramycin (3), coproporphyrin III (4), and kribelloside C (5) from a bioassay-guided fractionation of scaled-up active extracts of the Kribbella sp. CA-293567 strain. The structures of the new molecules were elucidated by ESI-qTOF-MS/MS, 1D and 2D NMR, and Marfey’s analysis for the determination of the absolute configuration of their amino acid residues. Compounds 1–3 and 5 were assayed against a panel of relevant antibiotic-resistant pathogenic strains and evaluated for cytotoxicity versus the human hepatoma cell line HepG2 (ATCC HB-8065). Kribbellichelins A (1) and B (2) showed antimicrobial activity versus Candida albicans ATCC-64124, weak potency against Acinetobacter baumannii MB-5973 and Pseudomonas aeruginosa MB-5919, and an atypical dose-dependent concentration profile against Aspergillus fumigatus ATCC-46645. Sandramycin (3) confirmed previously reported excellent growth inhibition activity against MRSA MB-5393 but also presented clear antifungal activity against C. albicans ATCC-64124 and A. fumigatus ATCC-46645 associated with lower cytotoxicity observed in HepG2, whereas Kribelloside C (5) displayed high antifungal activity only against A. fumigatus ATCC-46645. Herein, we describe the processes followed for the isolation, structure elucidation, and potency evaluation of these two new active compounds against a panel of human pathogens as well as, for the first time, the characterization of the antifungal activities of sandramycin (3).

Microbial Community, Metabolic Potential and Seasonality of Endosphere Microbiota Associated with Leaves of the Bioenergy Tree Paulownia elongata × fortunei

The microbial structure and metabolic function of plant-associated endophytes play a key role in the ecology of various environments, including trees. Here, the structure and functional profiles of the endophytic bacterial community, associated with Paulownia elongata × fortunei, in correlation with seasonality, were evaluated using Biolog EcoPlates. Biolog EcoPlates was used to analyse the functional diversity of the microbiome. The total communities of leaf endophyte communities were investigated using 16S rRNA V5–V7 region amplicon deep sequencing via Illumina MiSeq. Community level physiological profiling (CLPP) analysis by the Biolog EcoPlate™ assay revealed that the carboxylic acids (19.67–36.18%) and amino acids (23.95–35.66%) were preferred by all by all communities, whereas amines and amides (0.38–9.46%) were least used. Seasonal differences in substrate use were also found. Based on the sequencing data, mainly phyla Proteobacteria (18.4–97.1%) and Actinobacteria (2.29–78.7%) were identified. A core microbiome could be found in leaf-associated endophytic communities in trees growing in different locations. This work demonstrates the application of Biolog EcoPlates in studies of the functional diversity of microbial communities in a niche other than soil and shows how it can be applied to the functional analyses of endomicrobiomes. This research can contribute to the popularisation of Biolog EcoPlates for the functional analysis of the endomicrobiome. This study confirms that the analysis of the structure and function of the plant endophytic microbiome plays a key role in the health control and the development of management strategies on bioenergy tree plantations.

Microbiomes Associated With the Surfaces of Northern Argentinian Fruits Show a Wide Species Diversity

The fiber, vitamin, and antioxidant contents of fruits contribute to a balanced human diet. In countries such as Argentina, several tropical fruits are witnessing a high yield in the harvest season, with a resulting surplus. Fruit fermentation using autochthonous starter cultures can provide a solution for food waste. However, limited knowledge exists about the microbiota present on the surfaces of fruits and the preceding flowers. In the present exploratory study, the microbiomes associated with the surfaces of tropical fruits from Northern Argentina, such as white guava, passion fruit and papaya were investigated using a shotgun metagenomic sequencing approach. Hereto, one sample composed of 14 white guava fruits, two samples of passion fruits with each two to three fruits representing the almost ripe and ripe stage of maturity, four samples of papaya with each two to three fruits representing the unripe, almost ripe, and ripe stage of maturity were processed, as well as a sample of closed and a sample of open Japanese medlar flowers. A considerable heterogeneity was found in the composition of the fruits’ surface microbiota at the genus and species level. While bacteria dominated the microbiota of the fruits and flowers, a small number of the metagenomic sequence reads corresponded with yeasts and filamentous fungi. A minimal abundance of bacterial species critical in lactic acid and acetic acid fermentations was found. A considerable fraction of the metagenomic sequence reads from the fruits’ surface microbiomes remained unidentified, which suggested that intrinsic species are to be sequenced or discovered.

Cytokinin-microbiome interactions regulate developmental functions

BACKGROUND

The interaction of plants with the complex microbial networks that inhabit them is important for plant health. While the reliance of plants on their microbial inhabitants for defense against invading pathogens is well documented, the acquisition of data concerning the relationships between plant developmental stage or aging, and microbiome assembly, is still underway. The plant hormone cytokinin (CK) regulates various plant growth and developmental processes. Here, examining the relationships between plant development and microbiome assembly, we observed developmental-age dependent changes in the phyllopshere microbiome. We show that age-related shifts in microbiome content vary based on content of, or sensitivity to, CK.

RESULTS

We found a developmental age associated decline in microbial richness and diversity, accompanied by a decline in the presence of growth promoting and resistance inducing Bacilli in the phyllosphere. This decline was absent from CK-rich or CK-hypersensitive genotypes. Bacillus isolates we obtained from CK rich genotypes were found to alter the expression of developmental genes to support morphogenesis and alter the leaf developmental program when applied to seedlings, and enhance yield and agricultural productivity when applied to mature plants.

CONCLUSIONS

Our results support the notion that CK supports developmental functions in part via the bacterial community.

Cytokinin drives assembly of the phyllosphere microbiome and promotes disease resistance through structural and chemical cues

The plant hormone cytokinin (CK) is an important developmental regulator, promoting morphogenesis and delaying differentiation and senescence. From developmental processes, to growth, to stress tolerance, CKs are central in plant life. CKs are also known to mediate plant immunity and disease resistance, and several classes of microbes can also produce CKs, affecting the interaction with their plant hosts. While host species and genotype can be a driving force in shaping the plant microbiome, how plant developmental hormones such as CK can shape the microbiome is largely uninvestigated. Here, we examined the relationship between CK and the phyllosphere microbiome, finding that CK acts as a selective force in microbiome assembly, increasing richness, and promoting the presence of Firmicutes. CK-mediated immunity was found to partially depend on the microbial community, and bacilli isolated from previously described CK-rich plant genotypes, which overexpress a CK biosynthesis gene or have increased CK sensitivity, induced plant immunity, and promoted disease resistance. Using a biomimetic system, we investigated the relationship between the leaf microstructure, which is differentially patterned upon changes in CK content or signaling, and the growth of different phyllosphere microbes. We found that leaf structures derived from CK-rich plant genotypes support bacilli in the biomimetic system. CK was able to promote the growth, swarming, and biofilm formation of immunity inducing bacillus isolates in vitro. Overall, our results indicate that host genotype and hormonal profiles can act as a strong selective force in microbiome assembly, underlying differential immunity profiles, and pathogen resistance as a result.

Urban greenness and plant species are key factors in shaping air microbiomes and reducing airborne pathogens

Urban green space has been implicated in shaping airborne microbes, but there is an only rudimentary understanding of the key factors of urban green space affecting the composition and structures of airborne microbes. Here, we selected 40 urban sites based on stratified random sampling design and investigated the effects of multiple factors including landscapes, plant, soil, and anthropogenic factors on airborne microbial communities, especially bacterial and fungal pathogens. Bacterial and fungal communities in the control area with lower greenness were significantly (P < 0.05) different from those in other areas with a gradient of green space. The relative abundance of bacterial and fungal pathogens significantly (P < 0.05) decreased with increasing greenness. Other than soil thickness, soil type, slope position, and population density, plant species considerably contributed to the shift in the composition and abundance of potential bacterial and fungal pathogens. A significantly (P < 0.05) reduced abundance of bacterial and fungal pathogens was observed in areas with >30% masson pine. Together, these results provide insights into the importance of green space for providing health benefits for city dwellers by reducing pathogens in air, as well as providing support for the inclusion of plant species in the management of urban green space to reduce exposure risk of airborne pathogens.

Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage

The phyllosphere is the aerial part of plants that is exposed to different environmental conditions and is also known to harbor a wide variety of bacteria including both plant and human pathogens. However, studies on phyllosphere bacterial communities have focused on bacterial composition at different stages of plant growth without correlating their functional capabilities to bacterial communities. In this study, we examined the seasonal effects and temporal variabilities driving bacterial community composition and function in spinach phyllosphere due to increasing salinity and season and estimated the functional capacity of bacterial community16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on metagenomics inference tool Piphillin. The experimental design involved three sets of spinach (Spinacia oleracea L., cv. Racoon) grown with saline water during different seasons. Total bacteria DNA from leaf surfaces were sequenced using MiSeq® Illumina platform. About 66.35% of bacteria detected in the phyllosphere were dominated by four phyla- Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Permutational analysis of variance (PERMANOVA) showed that phyllosphere microbiomes were significantly (P < 0.003) affected by season, but not salinity (P = 0.501). The most abundant inferred functional pathways in leaf samples were the amino acids biosynthesis, ABC transporters, ribosome, aminoacyl-tRNA biosynthesis, two-component system, carbon metabolism, purine metabolism, and pyrimidine metabolism. The photosynthesis antenna proteins pathway was significantly enriched in June leaf samples, when compared to March and May. Several genes related to toxin co-regulated pilus biosynthesis proteins were also significantly enriched in June leaf samples, when compared to March and May leaf samples. Therefore, planting and harvesting times must be considered during leafy green production due to the influence of seasons in growth and proliferation of phyllosphere microbial communities.

Physiology of Methylotrophs Living in the Phyllosphere

Methanol is abundant in the phyllosphere, the surface of the above-ground parts of plants, and its concentration oscillates diurnally. The phyllosphere is one of the major habitats for a group of microorganisms, the so-called methylotrophs, that utilize one-carbon (C1) compounds, such as methanol and methane, as their sole source of carbon and energy. Among phyllospheric microorganisms, methanol-utilizing methylotrophic bacteria, known as pink-pigmented facultative methylotrophs (PPFMs), are the dominant colonizers of the phyllosphere, and some of them have recently been shown to have the ability to promote plant growth and increase crop yield. In addition to PPFMs, methanol-utilizing yeasts can proliferate and survive in the phyllosphere by using unique molecular and cellular mechanisms to adapt to the stressful phyllosphere environment. This review describes our current understanding of the physiology of methylotrophic bacteria and yeasts living in the phyllosphere where they are exposed to diurnal cycles of environmental conditions.

Divergence of Phyllosphere Microbial Communities Between Females and Males of the Dioecious Populus cathayana

Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microbiota in dioecious plants remains largely unexplored. Here, the diversity and composition of female and male Populus cathayana phyllosphere bacterial and fungal communities were investigated using 16S rRNA/ITS1 gene-based MiSeq sequencing. The divergences of bacterial and fungal community compositions occurred between females and males. Both females and males had their unique phyllosphere bacterial and fungal microbiota, such as bacterial Gemmata spp. (5.41%) and fungal Pringsheimia spp. (0.03%) in females and bacterial Chitinophaga spp. (0.009%) and fungal Phaeococcomyces spp. (0.02%) in males. Significant differences in the relative abundance of phyla Proteobacteria and Planctomycetes bacteria and phyla Ascomycota and Basidiomycota fungi (P < 0.05) were also found between females and males. Some bacterial species of genera Spirosoma and Amnibacterium and fungal genera Venturia, Suillus, and Elmerina spp. were significantly enriched in males (P < 0.05). In contrast, levels of fungal genera Phoma and Aureobasidium spp. were significantly higher in females than in males (P < 0.05). The mineral, inorganic, and organic nutrients content contributed differently to the divergence of female and male phyllosphere microbial communities, with 87.08 and 45.17% of the variations being explained for bacterial and fungal communities, respectively. These results highlight the sexual discrimination of phyllosphere microbes on the dioecious plants and provide hints on the potential host-associated species in phyllosphere environments.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Organic nitrogen modulates not only cadmium toxicity but also microbial activity in plants

It is known that organic nitrogen may modify uptake and toxicity of metals but direct metabolic and microbial comparison of various organic N sources is not available. We therefore studied comparative impact of additional N sources (nitrate, urea or allantoin as 1 mM of N for each compound in addition to 15 mM of inorganic N in the Hoagland solution) on Cd toxicity and microbial activity in common crop cucumber. Organic N significantly elevated the growth, chlorophyll content and photosynthetic activity under Cd excess in comparison with inorganic N though the impact on Cd uptake was negligible. Both organic N compounds also affected accumulation of mineral nutrients, total N, amino acids, and protein content in Cd-stressed plants. Among organic acids, mainly allantoin and partially urea affected accumulation of citrate and tartrate. The most notably, we detected that allantoin was decomposed even within 24 h by microbes into the urea, but it significantly elevated rhizosphere microbial activity. All these data indicate that allantoin is metabolized by plants/microbes into the urea and that it affects microbes mainly in the rhizosphere, which could contribute to amelioration of Cd toxicity.

Microbial Flow Within an Air-Phyllosphere-Soil Continuum

The phyllosphere is populated by numerous microorganisms. Microbes from the wider environment, i.e., air and soil, are considered key contributors to phyllosphere microbial communities, but their contribution is unclear. This study seeks to address this knowledge gap by controlling the movement of microbes along the air-phyllosphere-soil continuum. Customized equipment with dual chambers was constructed that permitted airflow to enter the first chamber while the second chamber recruited filtered microbe-free air from the initial chamber. Allium schoenoprasum (chive) and Sonchus oleraceus (sow thistle) were cultivated in both chambers, and the microbial communities from air, phyllosphere, and soil samples were characterized. Shares of microbial OTUs in the equipment suggested a potential interconnection between the air, phyllosphere, and soil system. Fast expectation-maximization microbial source tracking (FEAST) suggested that soil was the major source of airborne microbial communities. In contrast, the contribution of airborne and soil microbes to phyllosphere microbial communities of either A. schoenoprasum or S. oleraceus was limited. Notably, the soilborne microbes were the only environmental sources to phyllosphere in the second chamber and could affect the composition of phyllosphere microbiota indirectly by air flow. The current study demonstrated the possible sources of phyllosphere microbes by controlling external airborne microbes in a designed microcosm system and provided a potential strategy for recruitment for phyllosphere recruitment.

Isolation and Characterization of Cold-Tolerant Hyper-ACC-Degrading Bacteria from the Rhizosphere, Endosphere, and Phyllosphere of Antarctic Vascular Plants

1-Aminociclopropane-1-carboxylate (ACC)-degrading bacteria having been widely studied for their use in alleviating abiotic stresses in plants. In the present study, we isolated and characterized ACC-degrading bacteria from the rhizosphere, phyllosphere, and endosphere of the Antarctic vascular plants Deschampsia antarctica and Colobanthus quitensis. One hundred and eighty of the 578 isolates (31%) were able to grow on minimal medium containing ACC, with 101 isolates (23, 37, and 41 endosphere-, phyllosphere- and rhizosphere-associated isolates, respectively) identified as being genetically unique by enterobacterial repetitive intergenic consensus (ERIC)-PCR. Subsequently, freeze/thaw treatments and ice-recrystallization-inhibition (IRI) activity assays were performed, the results of which revealed that 77 (13%) of cold-tolerant isolates exhibited putative ACC deaminase activity. Significant (p ≤ 0.05) differences in IRI activity were also observed between the studied plant niches. Surprisingly, all the cold-tolerant isolates showed ACC deaminase activity, independent of the plant niches, with 12 isolates showing the highest ACC deaminase activities of 13.21-39.56 mmol α KB mg protein^-1 h^-1. These isolates were categorized as 'cold-tolerant hyper-ACC-degrading bacteria', and identified as members of Pseudomonas, Serratia, and Staphylococcus genera. The results revealed the occurrence of cold-tolerant hyper-ACC-degrading bacteria in diverse plant niches of Antarctic vascular plants, that could be investigated as novel microbial inoculants to alleviate abiotic stresses in plants.

Sampling of Plant Material to Study Endophytes in Small, Large, and Woody Plants

The study of fungal, bacterial, and other endophytic microorganisms using high throughput DNA sequencing requires sampling and processing of plant material that eliminates phylloplane microorganisms and retains those inside the plant compartment. Leaves, stems, roots, and other plant tissues are removed from the plant, washed, surface sterilized, and stored for downstream applications. Especially in ecological studies, field work for sample collection may take place in remote locations where laboratory equipment and resources are rudimentary, and accessing samples from target plants can be challenging. This chapter serves as a guide to basic protocols in the design and sample collection for studies focused on the endophytes of leaf, stem, and root tissues.

The unexplored bacterial lifestyle on leaf surface

Social interactions impact microbial communities and these relationships are mediated by small molecules. The chemical ecology of bacteria on the phylloplane environment is still little explored. The harsh environmental conditions found on leaf surface require high metabolic performances of the bacteria in order to survive. That is interesting both for scientific fields of prospecting natural molecules and for the ecological studies. Important queries about the bacterial lifestyle on leaf surface remain not fully comprehended. Does the hostility of the environment increase the populations' cellular altruism by the production of molecules, which can benefit the whole community? Or does the reverse occur and the production of molecules related to competition between species is increased? Does the phylogenetic distance between the bacterial populations influence the chemical profile during social interactions? Do phylogenetically related bacteria tend to cooperate more than the distant ones? The phylloplane contains high levels of yet uncultivated microorganisms, and understanding the molecular basis of the social networks on this habitat is crucial to gain new insights on the ecology of the mysterious community members due to interspecies molecular dependence. Here, we review and discuss what is known about bacterial social interactions and their chemical lifestyle on leaf surface.

Bacillus subtilis and Bacillus velezensis population dynamics and quantification of spores after inoculation on ornamental plants

Bacillus subtilis and Bacillus velezensis are used in organic agriculture as an alternative to chemical pesticides to fight against phytopathogen organisms. These Gram-positive soil-dwelling bacteria are able to resist harsh conditions and survive by differentiating into endospores. Few studies have examined how bacterial populations change on plants over time, and whether they remain active or enter a dormant state. Nonetheless, these characteristics are strikingly important to determine the usage of B. subtilis and B. velezensis and their efficacy in environmental conditions. Here, we investigated the population dynamics of B. subtilis NCIB3610 and B. velezensis QST713 when applied as spores on different ornamental plants. We report that on all the plants studied (Echinacea purpurea 'Salsa red', Echinacea purpurea 'Fatal attraction', and Lavandula angustifolia 'Hidecote blue'), spores rapidly germinated and colonized the rhizoplane, maintaining a relatively low proportion of spores in the population over time, whereas the bacterial population on the leaves rapidly declined. Bacteria in the surrounding soil did not germinate and persisted as spores. Taken together, these results suggest that only cells found at the rhizosphere remain metabolically active to allow the formation of a lasting relationship with the plant, making possible beneficial effects from the inoculated bacteria.

Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants

Climate change directly affecting the Antarctic Peninsula has been reported to induce the successful colonization of ice-free lands by two Antarctic vascular plants (Deschampsia antarctica and Colobanthus quitensis). While studies have revealed the importance of microbiota for plant growth and stress tolerance in temperate climates, the role that plant-associated microbes play in the colonization of ice-free lands remains unknown. Consequently, we used high-throughput DNA sequence analyses to explore the composition, predicted functions, and interactive networks of plant-associated microbial communities among the rhizosphere, endosphere, and phyllosphere niches of D. antarctica and C. quitensis. Here we report a greater number of operational taxonomic units (OTUs), diversity, and richness in the microbial communities from the rhizosphere, relative to endosphere and phyllosphere. While taxonomic assignments showed greater relative abundances of Proteobacteria, Bacteroidetes, and Actinobacteria in plant niches, principal coordinate analysis revealed differences among the bacterial communities from the other compartments examined. More importantly, however, our results showed that most of OTUs were exclusively found in each plant niche. Major predicted functional groups of these microbiota were attributed to heterotrophy, aerobic heterotrophy, fermentation, and nitrate reduction, independent of plant niches or plant species. Co-occurrences network analyses identified 5 (e.g., Microbacteriaceae, Pseudomonaceae, Lactobacillaceae, and Corynebacteriaceae), 23 (e.g., Chitinophagaceae and Sphingomonadaceae) and 7 (e.g., Rhodospirillaceae) putative keystone taxa present in endosphere, phyllosphere, and rhizosphere, respectively. Our results revealed niche differentiation in Antarctic vascular plants, highlighting some putative microbial indicators and keystone taxa in each niche. However, more studies are required to determine the pivotal role that these microbes play in the successful colonization of ice-free lands by Antarctic plants.

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.

Core endophyte communities of different citrus varieties from citrus growing regions in China

The native microbiomes of citrus trees play important roles in plant health, with good communication between the native microbiome and the host plant. Here, we report on the native endophytes in 24 citrus varieties in nine citrus growing regions in China; some of the trees were healthy and others had asymptomatic or symptomatic huanglongbing, which is caused by the pathogen Candidatus Liberibacter asiaticus (CLas). We used culture-dependent analysis and characterized the isolates by partial 16S rRNA gene sequencing. The endophytes were compared between different citrus varieties, regions, and disease states (healthy, asymptomatic, and symptomatic). The total number of endophytes isolated from most of the citrus varieties was 104-106 CFU/g of leaves, but it differed significantly by disease state, with the highest numbers in the healthy leaves and the lowest in the symptomatic leaves (p < 0.05). Among the citrus varieties, the Valencia variety had the maximum number of endophyte species (22). The most dominant endophytes were Bacillus subtilis, B. velezensis, Curtobacterium luteum, and Microbacterium testaceum. The higher frequency of B. subtilis in the healthy/asymptomatic plants compared to the symptomatic plants suggests that it has a role in huanglongbing resistance. Native endophyte communities in various citrus varieties could be used to improve citrus growth and combat CLas.

Agricultural activities affect the pattern of the resistome within the phyllosphere microbiome in peri-urban environments

The plant microbiome represents a crucial pathway for human exposure to environmental antibiotic resistance. However, little information is available regarding the plant associated resistome in human-related environments at a larger scale. Here, by high-throughput quantitative-PCR chip-based array and amplicon sequencing, we characterized antibiotic resistance genes (ARGs) and bacterial communities in plant and soil microbiomes from human highly disturbed peri-urban farmland and less disturbed forest at a watershed scale. A total of 71 ARGs were detected in the phyllosphere, which covered almost all the major recognized classes of antibiotics that are administered commonly to humans and animals. The overall pattern of the plant associated resistome in intensive anthropogenic influenced farmland was significantly different from that of forest environments (PERMANOVA, P < 0.01), indicating that agricultural activities might be important drivers in shaping the plant resistome. A bipartite network analysis suggested that all ARGs detected in the plant microbiome were also present in the soil microbiome. Together, our findings provide a better understanding of the plant resistome and suggest that land use is a key contributor to the composition of ARG profiles in the plant phyllosphere, and that the soil resistome may represent a critical reservoir of plant associated ARGs.

Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew

The reduction of antimicrobial treatments and mainly the application of environmentally friendly compounds, such as resistance elicitors, is an impelling challenge to undertake more sustainable agriculture. We performed this research to study the effectiveness of non-conventional compounds in reducing leaf fungal attack and to investigate whether they influence the grape phyllosphere. Pathogenicity tests were conducted on potted Vitis vinifera "Nebbiolo" and "Moscato" cultivars infected with the powdery mildew agent (Erysiphe necator) and treated with three elicitors. Differences in the foliar microbial community were then evaluated by community-level physiological profiling by using Biolog^TM EcoPlates, high throughput sequencing of the Internal Transcribed Spacer (ITS) region, and RNA sequencing for the viral community. In both cultivars, all products were effective as they significantly reduced pathogen development. EcoPlate analysis and ITS sequencing showed that the microbial communities were not influenced by the alternative compound application, confirming their specific activity as plant defense elicitors. Nevertheless, "Moscato" plants were less susceptible to the disease and presented different phyllosphere composition, resulting in a richer viral community, when compared with the "Nebbiolo" plants. The observed effect on microbial communities pointed to the existence of distinct genotype-specific defense mechanisms independently of the elicitor application.

Metagenomic Characterization Reveals Pronounced Seasonality in the Diversity and Structure of the Phyllosphere Bacterial Community in a Mediterranean Ecosystem

We explore how the phyllosphere microbial community responds to a very seasonal environment such as the Mediterranean. For this, we studied the epiphytic bacterial community of a Mediterranean ecosystem in summer and winter, expecting to detect seasonal differences at their maximum. With high-throughput sequencing (HTS), we detected the operational taxonomic units (OTUs) present in the phyllosphere and also in the surrounding air. The epiphytic community is approximately five orders of magnitude denser than the airborne one and is made almost exclusively by habitat specialists. The two communities differ considerably but Proteobacteria and Actinobacteria are dominant in both. Of the five most abundant phyllosphere OTUs, two were closely related to Sphingomonas strains, one to Methylobacterium and the other two to Rhizobiales and Burkholderiales. We found the epiphytic community to become much richer, more distinct, even and diverse, denser and more connected in summer. In contrast, there was no difference in the level of bacterial colonization of the phyllosphere between the two seasons, although there were seasonal differences for individual taxonomic groups: Firmicutes, Gemmatimonadetes and Chlroroflexi had a higher participation in summer, whereas the major Proteobacteria classes presented reverse patterns, with Betaproteobacteria increasing in summer at the expense of the prominent Alphaproteobacteria.

Effects of imazethapyr spraying on plant growth and leaf surface microbial communities in Arabidopsis thaliana

Imazethapyr (IM) is an acetolactate synthase (ALS)-inhibiting herbicide that has been widely used in recent years. However, IM spraying can lead to the accumulation of herbicide residues in leaves. Here, we determined the effects of IM spraying on the plant growth and leaf surface microbial communities of Arabidopsis thaliana after 7 and 14 days of exposure. The results suggested that IM spraying inhibited plant growth. Fresh weight decreased to 48% and 26% of the control value after 7 and 14 days, respectively, of 0.035 kg/ha IM exposure. In addition, anthocyanin content increased 9.2-fold and 37.2-fold relative to the control content after 7 and 14 days of treatment, respectively. Furthermore, IM spraying destroyed the cell structures of the leaves, as evidenced by increases in the number of starch granules and the stomatal closure rate. Reductions in photosynthetic efficiency and antioxidant enzyme activity were observed after IM spraying, especially after 14 days of exposure. The diversity and evenness of the leaf microbiota were not affected by IM treatment, but the composition of community structure at the genus level was altered by IM spraying. Imazethapyr application increased the abundance of Pseudomonas, a genus that includes species pathogenic to plants and humans, indicating that IM potentially increased the abundance of pathogenic bacteria on leaves. Our findings increase our understanding of the relationships between herbicide application and the microbial community structures on plant leaves, and they provide a new perspective for studying the ecological safety of herbicide usage.

Leaf mineral content govern microbial community structure in the phyllosphere of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia)

The plant microbiome is an important factor for plant health and productivity. While the impact of nitrogen (N) availability for plant growth and development is well established, its influence on the microbial phyllosphere community structure is unknown. We hypothesize that nitrogen impacts the growth and abundance of several microorganisms on the leaf surface. The bacterial and fungal communities of baby leaf spinach (Spinacia oleracea), and rocket (Diplotaxis tenuifolia) were investigated in a field trial for two years in a commercial setting. Nitrogen fertilizer was tested in four doses (basic nitrogen, basic + suboptimal, basic + commercial, basic + excess) with six replicates in each. Culture-independent (Illumina sequencing) and culture-dependent (viable count and identification of bacterial isolates) community studies were combined with monitoring of plant physiology and site weather conditions. This study found that alpha diversity of bacterial communities decreased in response to increasing nitrogen fertilizer dose, whereas viable counts showed no differences. Correspondingly, fungal communities of the spinach phyllosphere showed a decreasing pattern, whereas the decreasing diversity of fungal communities of rocket was not significant. Plant species and effects of annual variations on microbiome structure were observed for bacterial and fungal communities on both spinach and rocket. This study provides novel insights on the impact of nitrogen fertilizer regime on a nutrient scarce habitat, the phyllosphere.

Shared and unique features of bacterial communities in native forest and vineyard phyllosphere

Phyllosphere bacteria have received little attention despite their important roles in shaping plant performance traits. In this study, we characterize the bacterial communities on leaves of native trees inhabiting sclerophyllous forests in central Chile, one of the world's biodiversity hotspots. Additionally, we provide profiles of bacterial communities on grape leaves and berries of organic and conventional vineyards. Results of 16S rRNA gene amplicon sequence analysis showed that 45% of OTUs were shared across forest leaves, grape leaves, and grape berries. Conventional management had higher number of OTUs shared with forest leaves than organic management. In addition, grape leaves subjected to conventional management had higher alpha diversity than those with organic management, while no significant effect of agricultural management was observed in grape berries. Indicator analysis showed that Bdellovibrio, Beijerinckia, and Spirosoma were typical for forest leaves, whereas Enhydrobacter, Delftia, Proteiniclasticum, Arsenicicoccus, and Alkaliphilus were typical for the vineyard phyllosphere. Regarding agricultural managements, Beijerinckia, Sedimentibacter, Nesterenkonia, Gluconobacter, Conexibacter, and Anaeromyxobacter were typical for conventional grape leaves, whereas no genus-level indicator was found for organic vineyard leaves. These results provide new insights of the diversity patterns of the phyllosphere microbiome in native and cultivated lands and suggest that both of these microbiomes are connected and integrated systems.

Plant Phenotypic Traits Eventually Shape Its Microbiota: A Common Garden Test

Plant genotype drives the development of plant phenotypes and the assembly of plant microbiota. The potential influence of the plant phenotypic characters on its microbiota is not well characterized and the co-occurrence interrelations for specific microbial taxa and plant phenotypic characters are poorly understood. We established a common garden experiment, which quantifies prokaryotic and fungal communities in the phyllosphere and rhizosphere of six spruce (Picea spp.) tree species, through Illumina amplicon sequencing. We tested for relationships between bacterial/archaeal and fungal communities and for the phenotypic characters of their plant hosts. Host phenotypic characters including leaf length, leaf water content, leaf water storage capacity, leaf dry mass per area, leaf nitrogen content, leaf phosphorous content, leaf potassium content, leaf δ¹³C values, stomatal conductance, net photosynthetic rate, intercellular carbon dioxide concentration, and transpiration rate were significantly correlated with the diversity and composition of the bacterial/archaeal and fungal communities. These correlations between plant microbiota and suites of host plant phenotypic characters suggest that plant genotype shape its microbiota by driving the development of plant phenotypes. This will advance our understanding of plant-microbe associations and the drivers of variation in plant and ecosystem function.

Various Phyllosphere and Soil Bacterial Communities of Natural Grasses and the Impact Factors in a Copper Tailings Dam

Copper mining caused severe damage to the ecological environment of mining areas. The combination of microbe and plant remediation has an application potential in improving the absorption and transformation efficiency of heavy metals. The phyllosphere is the largest biointerface on the planet, and bacteria are the dominant microbial inhabitants of the phyllosphere, believed to be critical to plant growth and health. This study investigated the phyllospheric and soil bacteria communities using high-throughput sequencing, and endophyte infection statuses of four natural grasses by toluidine blue heparin assay. Results showed variation in phyllospheric bacterial community structure. Gammaproteobacteria were the most abundant bacterial population. Bacilli were found in the phyllosphere of Bothriochloa ischaemum and Imperata cylindrica, while Clostridia were only found in Calamagrostis epigejos. Alphaproteobacteria were the dominant bacteria in soil. In addition, bacterial communities were influenced by endophytic infection statuses. Oxalobacteraceae was associated with soil carbon and sulfur. Enterobacteriaceae had negative correlation with the ratio of soil carbon and nitrogen, and had positive correlation with Cd content. These results offer useful insights into phyllospheric bacterial community variance in four different natural grasses in a copper tailings dam.

Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine's Phyllosphere and Carposphere: An NGS Approach

Plant surface or phyllosphere is the habitat of hyperdiverse microbial communities and it is always exposed to the fluctuating environmental factors, which is thought to be one of the potential drivers of microbial community structuring. Impact of grapevine genotypes in variable environmental factors (i.e., at different geographic locations) on the phyllosphere has never been studied and is the main objective of this report. Using high throughput short amplicon sequencing of 16S rRNA genes and internal transcribed spacer (ITS), we analyzed the impacts of genotypes of Vitis Vinifera (coming from three genetic pool), on the microbial (bacterial and fungal) assemblage in the phyllosphere. First, we performed the analysis of the phyllosphere microbiome while using fifteen genotypes that were chosen to maximize intra-specific diversity and grown in two Mediterranean vineyards. Then, the same analysis was performed on five commercially important varieties of Vitis vinifera that were sampled from three different French agro-climatic zones (or terroir: a combination of climate, soils, and human practices). Our study revealed that, at a particular geographic location, genotypes have an impact on microbial assemblage in the phyllosphere and carposphere of leaf and fruit (or berries), respectively, which is more prominent on the carposphere but the effect of terroir was much stronger than the genotype when the leaf phyllosphere of five grapevine varieties grown in different agro-climatic zones was compared. Impacts of the season and exterior plant organs (leaf and berries) on microbial taxa structuring in the phyllosphere was also assessed and presented in this report.

Bacteria colonising Penstemon digitalis show volatile and tissue-specific responses to a natural concentration range of the floral volatile linalool

Bacteria on floral tissue can have negative effects by consuming resources and affecting nectar quality, which subsequently could reduce pollinator visitation and plant fitness. Plants however can employ chemical defences to reduce bacteria density. In North American, bee-pollinated Penstemon digitalis, the nectar volatile S-(+)-linalool can influence plant fitness, and terpenes such as linalool are known for their antimicrobial properties suggesting that it may also play a role in plant–microbe interactions. Therefore, we hypothesized linalool could affect bacterial growth on P. digitalis plants/flowers. Because P. digitalis emits linalool from nectar and nectary tissue but not petals, we hypothesised that the effects of linalool could depend on tissue of origin due to varying exposure. We isolated bacteria from nectary tissue, petals and leaves, and compared their growth relative to control using two volatile concentrations representing the natural emission range of linalool. To assess whether effects were specific to linalool, we compared results with the co-occurring nectar volatile, methyl nicotinate. We show that response to floral volatiles can be substance and tissue-origin specific. Because linalool could slow growth rate of bacteria across the P. digitalis phyllosphere, floral emission of linalool could play a role in mediating plant–bacteria interactions in this system.

Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere

Genome analyses are being used to characterize plant growth-promoting (PGP) bacteria living in different plant compartiments. In this context, we have recently isolated bacteria from the phyllosphere of an Antarctic plant (Deschampsia antarctica) showing ice recrystallization inhibition (IRI), an activity related to the presence of antifreeze proteins (AFPs). In this study, the draft genomes of six phyllospheric bacteria showing IRI activity were sequenced and annotated according to their functional gene categories. Genome sizes ranged from 5.6 to 6.3 Mbp, and based on sequence analysis of the 16S rRNA genes, five strains were identified as Pseudomonas and one as Janthinobacterium. Interestingly, most strains showed genes associated with PGP traits, such as nutrient uptake (ammonia assimilation, nitrogen fixing, phosphatases, and organic acid production), bioactive metabolites (indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase), and antimicrobial compounds (hydrogen cyanide and pyoverdine). In relation with IRI activity, a search of putative AFPs using current bioinformatic tools was also carried out. Despite that genes associated with reported AFPs were not found in these genomes, genes connected to ice-nucleation proteins (InaA) were found in all Pseudomonas strains, but not in the Janthinobacterium strain.

Template Preparation Affects 16S rRNA High-Throughput Sequencing Analysis of Phyllosphere Microbial Communities

Phyllosphere microbial communities are highly diverse and have important ecological implications; in that context, bacterial identification based on 16S rRNA genes is an important research issue. In studies of phyllosphere microbial communities, microporous filtration and centrifugation are used to collect microorganism samples, but it is unclear which one has a better collection efficiency. In this study, we compared these two microorganism collection methods and investigated the effects of the DNA extraction process on the estimation of microbial community composition and organization. The following four treatments were examined: (A) filtration, resuspension, and direct PCR; (B) filtration, DNA isolation, and PCR; (C) centrifugation, resuspension, and direct PCR; (D) centrifugation, DNA isolation, and PCR. Our results showed that the percentage of chloroplast sequence contaminants was affected by the DNA extraction process. The bacterial compositions clearly differed between treatments A and C, suggesting that the collection method has an influence on the determination of community structure. Compared with treatments B and D, treatments A and C resulted in higher Shannon index values, indicating that the DNA extraction process might reduce the observed phyllosphere microbial alpha diversity. However, with respect to community structure, treatments B and D yielded very similar results, suggesting that the DNA extraction process erases the effect of the collection method. Our findings provide key information to ensure accurate estimates of diversity and community composition in studies of phyllosphere microorganisms.

Nutrients and host attributes modulate the abundance and functional traits of phyllosphere microbiome in rice

The abundance of phyllosphere bacterial communities of seven genotypes of rice ADT- 38, ADT-43, CR-1009, PB-1, PS-5, P-44, and PB-1509 was investigated, in relation to nutrient dynamics of rhizosphere and leaves. P-44 genotype recorded highest pigment accumulation, while genotypes CR-1009 and P-44 exhibited most number of different bacterial morphotypes, Colony forming units in two media (Nutrient agar and R2A) varied significantly and ranged from 10⁶-10⁷ per g plant tissues. Among the selected 60 distinct morphotypes, IAA and siderophore producers were the dominant functional types. Biocontrol activity against Drechslera oryzae was shown by 38 isolates, while 17 and 9 isolates were potent against Rhizoctonia solani and Magnaporthe oryzae respectively. Principal Component Analysis (PCA) illustrated the significant effects of selected soil and leaf nutrients of seven rice varieties on the culturable phyllospheric population (log CFU), particularly in the R2A medium. Eigen values revealed that 83% of the variance observed could be assigned to Leaf-Fe, Leaf-Mn, chlorophyll b and soil organic carbon (OC). Quantitative PCR analyses of abundance of bacteria, cyanobacteria and archaebacteria revealed a host-specific response, with CR-1009 showing highest number of 16S rRNA copies of bacterial members, while both P-44 and PS-5 had higher cyanobacterial abundance, but lowest number of those belonging to archaebacteria. Nutritional aspects of leaf and soil influenced the abundance of bacteria and their functional attributes; this is of interest for enhancing the efficacy of foliar inoculants, thereby, improving plant growth and disease tolerance.

The dynamics of the bacterial communities developed in maize silage

Ensilage provides an effective means of conserving summer‐grown green forage to supply as winter feed to ruminants. The fermentation process involved in the ensilage process relies on lactic acid bacteria (LAB). Here, 16S ribosomal DNA amplicon pyrosequencing was used to follow the dynamic behaviour of the LAB community during the ensilage of maize biomass, with a view to identify the key species involved in the process. The biomass used for ensilage was a single‐cross maize hybrid, harvested at the milk‐line stage. The crop was grown at three contrasting locations. Aspects of the physico‐chemical composition of the material and the LAB species present were sampled at 0, 3, 6, 14, 21 and 32 days after ensilage was initiated. In all three cases, members of the Leuconostocaceae family dominated the epiphytic bacterial community, notably Leuconostoc and Weissella, but some variation was noted in the abundance of certain Leuconostocaceae and Lactobacillaceae species, as well as that of some Acetobacteraceae, Enterobacteriaceae and Moraxellaceae species. The constellation of the microbiome which developed during the ensilage process differed markedly from that of the epiphytic one, with Lactobacillaceae, particularly Lactobacillus and Pediococcus spp. dominating. The abundance of heterofermentative Leuconostocaceae spp. in the epiphytic community and the extent of the transition from hetero‐ to homo‐fermentation during the initial ensilage period are important factors in determining silage quality.

Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases

The phyllosphere supports a large and complex bacterial community that varies both across plant species and geographical locations. Phyllosphere bacteria can have important effects on plant health. The sweet chestnut (Castanea sativa Mill.) is an economically important tree species affected worldwide by the fungal pathogens Cryphonectria parasitica and Phytophthora cinnamomi. We examined the culturable phyllosphere bacterial community of the sweet chestnut at two nearby locations in Central Spain in order to know its geographical variability and to explore its potential as source of biological control agents against these two pathogenic fungi. The bacterial diversity at strain level was high but it varied significantly between locations; however, phylotype richness and diversity were more comparable. The isolates were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Most of them were members of recognized bacterial species, with a notable proportion of representative of the genera Dietzia and Lonsdalea, but a small fraction of the strains revealed the existence of several potential novel species or even genera. Antagonism tests showed the occurrence in the chestnut phyllosphere of bacterial strains potentially useful as biological control agents against the two pathogenic fungi, some of which belong to species never before described as fungal antagonists. Chestnut phyllosphere, therefore, contains a great diversity of culturable bacteria and may represent an untapped source of potential biocontrol agents against the fungi causing blight and ink diseases of this tree species.

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area

Plants and their associated bacteria have been suggested to play a role in air pollution mitigation, especially in urban areas. Particularly, epiphytic bacteria might be able to degrade atmospheric hydrocarbons. However, phyllospheric bacterial communities are highly variable depending on several factors, e.g. tree species, leaf age and physiology, environmental conditions. In this work, bacterial communities hosted by urban Platanus x acerifolia leaves were taxonomically characterized using high throughput sequencing of 16S rRNA gene, and their temporal and spatial variability was assessed by comparing samples collected from different locations in the city of Milan (Italy) and in different months. The diversity of alkane hydroxylase (alkB) phylotypes harboured by phyllospheric bacteria associated to urban Platanus trees was also evaluated. Results revealed that temporal changes, which are related to seasonality, acted as a stronger driver both on Platanus phyllospheric community structure and on alkB phylotype diversity than sampling location. Biodiversity of bacterial communities decreased along the growing season, leading to a strong dominance by the genus Stenotrophomonas. On the contrary, diversity of hydrocarbon-degrading populations increased over the months, although it resulted lower than that reported for other habitats. It was therefore hypothesized that atmospheric hydrocarbons might play a key role in the selection of phyllospheric populations in urban areas.

Using a Control to Better Understand Phyllosphere Microbiota

An important data gap in our understanding of the phyllosphere surrounds the origin of the many microbes described as phyllosphere communities. Most sampling in phyllosphere research has focused on the collection of microbiota without the use of a control, so the opportunity to determine which taxa are actually driven by the biology and physiology of plants as opposed to introduced by environmental forces has yet to be fully realized. To address this data gap, we used plastic plants as inanimate controls adjacent to live tomato plants (phyllosphere) in the field with the hope of distinguishing between bacterial microbiota that may be endemic to plants as opposed to introduced by environmental forces. Using 16S rRNA gene amplicons to study bacterial membership at four time points, we found that the vast majority of all species-level operational taxonomic units were shared at all time-points. Very few taxa were unique to phyllosphere samples. A higher taxonomic diversity was consistently observed in the control samples. The high level of shared taxonomy suggests that environmental forces likely play a very important role in the introduction of microbes to plant surfaces. The observation that very few taxa were unique to the plants compared to the number that were unique to controls was surprising and further suggests that a subset of environmentally introduced taxa thrive on plants. This finding has important implications for improving our approach to the description of core phytobiomes as well as potentially helping us better understand how foodborne pathogens may become associated with plant surfaces.

Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites

Pseudomonas citronellolis is a Gram negative, motile gammaproteobacterium belonging to the order Pseudomonadales and the family Pseudomonadaceae. We isolated strain P3B5 from the phyllosphere of basil plants (Ocimum basilicum L.). Here we describe the physiology of this microorganism, its full genome sequence, and detailed annotation. The 6.95 Mbp genome contains 6071 predicted protein coding sequences and 96 RNA coding sequences. P. citronellolis has been the subject of many studies including the investigation of long-chain aliphatic compounds and terpene degradation. Plant leaves are covered by long-chain aliphates making up a waxy layer that is associated with the leaf cuticle. In addition, basil leaves are known to contain high amounts of terpenoid substances, hinting to a potential nutrient niche that might be exploited by P. citronellolis. Furthermore, the isolated strain exhibited resistance to several antibiotics. To evaluate the potential of this strain as source of transferable antibiotic resistance genes on raw consumed herbs we therefore investigated if those resistances are encoded on mobile genetic elements. The availability of the genome will be helpful for comparative genomics of the phylogenetically broad pseudomonads, in particular with the sequence of the P. citronellolis type strain PRJDB205 not yet publicly available. The genome is discussed with respect to a phyllosphere related lifestyle, aliphate and terpenoid degradation, and antibiotic resistance.