Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process

Regional diversity and leaf microbiome interactions of the fungal maize pathogen Exserohilum turcicum in Switzerland: A metagenomic analysis

The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allowed us to monitor eco-evolutionary dynamics and interactions between host, pathogen and plant microbiome. Exserohilum turcicum, the causal agent of northern corn leaf blight (NCLB) in maize, is distributed in multiple clonal lineages throughout Europe. To characterize regional pathogen diversity, we conducted metagenomic DNA sequencing on 241 infected leaf samples from the highly susceptible Swiss maize landrace Rheintaler Ribelmais, collected over 3 years (2016-2018) from an average of 14 agricultural farms within the Swiss Rhine Valley. All major European clonal lineages of E. turcicum were identified. Lineages differ by their mating types which indicates potential for sexual recombination and rapid evolution of new pathogen strains, although we found no evidence of recent recombination. The associated eukaryotic and prokaryotic leaf microbiome exhibited variation in taxonomic diversity between years and locations and is likely influenced by local weather conditions. A network analysis revealed distinct clusters of eukaryotic and prokaryotic taxa that correlates with the frequency of E. turcicum sequencing reads, suggesting causal interactions. Notably, the yeast genus Metschnikowia exhibited a strongly negative association with E. turcicum, supporting its known potential as biological control agent against fungal pathogens. Our findings show that metagenomic sequencing is a useful tool for analysing the role of environmental factors and potential pathogen-microbiome interactions in shaping pathogen dynamics and evolution, suggesting their potential for effective pathogen management strategies.

Leaf Health Status Regulates Endophytic Microbial Community Structure, Network Complexity, and Assembly Processes in the Leaves of the Rare and Endangered Plant Species Abies fanjingshanensis

The rare and endangered plant species Abies fanjingshanensis, which has a limited habitat, a limited distribution area, and a small population, is under severe threat, particularly due to poor leaf health. The plant endophytic microbiome is an integral part of the host, and increasing evidence indicates that the interplay between plants and endophytic microbes is a key determinant for sustaining plant fitness. However, little attention has been given to the differences in the endophytic microbial community structure, network complexity, and assembly processes in leaves with different leaf health statuses. Here, we investigated the endophytic bacterial and fungal communities in healthy leaves (HLs) and non-healthy leaves (NLs) of A. fanjingshanensis using 16S rRNA gene and internal transcribed spacer sequencing and evaluated how leaf health status affects the co-occurrence patterns and assembly processes of leaf endophytic microbial communities based on the co-occurrence networks, the niche breadth index, a neutral community model, and C-score metrics. HLs had significantly greater endophytic bacterial and fungal abundance and diversity than NLs, and there were significant differences in the endophytic microbial communities between HLs and NLs. Leaf-health-sensitive endophytic microbes were taxonomically diverse and were mainly grouped into four ecological clusters according to leaf health status. Poor leaf health reduced the complexity of the endophytic bacterial and fungal community networks, as reflected by a decrease in network nodes and edges and an increase in degrees of betweenness and assortativity. The stochastic processes of endophytic bacterial and fungal community assembly were weakened, and the deterministic processes became more important with declining leaf health. These results have important implications for understanding the ecological patterns and interactions of endophytic microbial communities in response to changing leaf health status and provide opportunities for further studies on exploiting plant endophytic microbes to conserve this endangered Abies species.

Microbiome Analysis Revealed Acholeplasma as a Possible Factor Influencing the Susceptibility to Bacterial Leaf Blight Disease of Two Domestic Rice Cultivars in Vietnam

The microbiomes of two important rice cultivars in Vietnam which differ by their susceptibility to the bacterial leaf blight (BLB) disease were analyzed through 16S rRNA amplicon technology. A higher number of operational taxonomic units and alpha-diversity indices were shown in the BLB-resistant LA cultivar than in the BLB-susceptible TB cultivar. The BLB pathogen Xanthomonas was scantly found (0.003%) in the LA cultivar, whereas was in a significantly higher ratio in the TB cultivar (1.82%), reflecting the susceptibility to BLB of these cultivars. Of special interest was the genus Acholeplasma presented in the BLB-resistant LA cultivar at a high relative abundance (22.32%), however, was minor in the BLB-sensitive TB cultivar (0.09%), raising a question about its roles in controlling the Xanthomonas low in the LA cultivar. It is proposed that Acholeplasma once entered the host plant would hamper other phytopathogens, i.e. Xanthomonas, by yet unknown mechanisms, of which the triggering of the host plants to produce secondary metabolites against pathogens could be a testable hypothesis.

Current Status and Future Perspectives on Distribution of Fungal Endophytes and Their Utilization for Plant Growth Promotion and Management of Grapevine Diseases

Grapevine is one of the economically most important fruit crops cultivated worldwide. Grape production is significantly affected by biotic constraints leading to heavy crop losses. Changing climatic conditions leading to widespread occurrence of different foliar diseases in grapevine. Chemical products are used for managing these diseases through preventive and curative application in the vineyard. High disease pressure and indiscriminate use of chemicals leading to residue in the final harvest and resistance development in phytopathogens. To mitigate these challenges, the adoption of potential biocontrol control agents is necessary. Moreover, multifaceted benefits of endophytes made them eco-friendly, and environmentally safe approach. The genetic composition, physiological conditions, and ecology of their host plant have an impact on their dispersion patterns and population diversity. Worldwide, a total of more than 164 fungal endophytes (FEs) have been characterized originating from different tissues, varieties, crop growth stages, and geographical regions of grapevine. These diverse FEs have been used extensively for management of different phytopathogens globally. The FEs produce secondary metabolites, lytic enzymes, and organic compounds which are known to possess antimicrobial and antifungal properties. The aim of this review was to understand diversity, distribution, host-pathogen-endophyte interaction, role of endophytes in disease management and for enhanced, and quality production.

Taxonomic analysis reveals host preference of rare fungi in endophytes of Vitis vinifera from the Czech Republic

This paper represents the results of screening a diversity of fungal endophytes associated with Vitis vinifera leaves and canes in the Czech Republic. The characterization of strains is based on morphological and phylogenetic analyses of ITS, EF1α and TUB2 sequence data. Our strain selection covers 16 species and seven orders belonging to Ascomycota and Basidiomycota. Together with ubiquitous fungi, we report on several poorly known plant-associated fungi, Angustimassarina quercicola (= A. coryli, a synonym proposed in this study) and Pleurophoma pleurospora. Other species, such as Didymella negriana, D. variabilis, Neosetophoma sp. (species identical or sister to N. rosae), Phragmocamarosporium qujingensis and Sporocadus rosigena, have so far been little known and rarely found, but are frequent on V. vinifera in different parts of the world and obviously belong to a microbiota with a strong preference for this plant. Detailed taxonomical identification allowed us to identify species with apparent stable associations with V. vinifera, for which further interactions with V. vinifera can be expected. Our study is the first to focus on V. vinifera endophytes in Central Europe and expands the knowledge about their taxonomy, ecology and geography.

Diversity of Fungal Communities on Diseased and Healthy Cinnamomum burmannii Fruits and Antibacterial Activity of Secondary Metabolites

The composition and structure of fungal communities on healthy and diseased fruits of Cinnamomum burmannii (Nees and Nees) Blume were characterized, with evaluation of the antibacterial activity of secondary metabolites from culturable fungi following the first identification of secondary metabolites in the fungus Medicopsis romeroi (Esf-14; GenBank accession number OK242756). These results are significant for understanding the functional variation in bioactivity in fungal communities and developing a broader range of bioactive resources. High-throughput sequencing results indicated that the fungal community in diseased fruit differed from that in healthy fruit at the phylum, class, order, or genus level, with significant differences in the species and relative abundance of the dominant flora. A total of 49 (healthy fruit) and 122 (diseased fruit) artificially cultivable endophytic fungi were isolated, and 41 different strains (11 from healthy fruit and 30 from diseased fruit) were successfully identified by morphological and molecular biological analyses, which were classified into 8 groups and 23 genera by phylogenetic tree analysis, with Pleosporales, Glomerellales, and Hypocreales being the dominant groups at the order level and Colletotrichum being the dominant group at the genus level. The results of the antibacterial assay demonstrated that the secondary metabolites of all strains had different degrees of antibacterial activity, while the secondary metabolites of endophytic fungi from diseased fruit were generally stronger than those of fungi from healthy fruit, with the active secondary metabolites dominated by small and moderately polar compounds. Combined analysis of fungal communities, phylogenetic tree analysis, and bioactivity analysis of culturable strains revealed strong antibacterial activity of both upregulated and downregulated flora in diseased fruit. Five compounds, including two new (5,6-dimethoxy-[1',1:4,1″-terphenyl]-2-ol [compound 1] and 5-(methoxycarbonyl)-2-methylbenzo[d][1,3]dioxole-2-carboxylic acid [compound 2]) and three known compounds (3,7-dihydroxy-1,9-dimethyldibenzofuran [compound 3], methyl 3-hydroxybenzoate [compound 4], and uracil [compound 5]), were isolated and identified for the first time from the endophytic fungus Medicopsis romeroi. In general, the diversity of fungal communities on diseased fruit was lower than that on healthy fruits, while the antibacterial activity of artificially cultured endophytic fungi on diseased fruits was generally stronger than that on healthy fruits, suggesting excellent promise for the development of secondary metabolites from active strains on diseased fruit as antibacterial agents. IMPORTANCE Powdery fruit disease is a notorious disease of Cinnamomum burmannii that causes severe loss in fruit production. Studies on the function of endophytic fungal communities in healthy plant tissues are not new, while little is known about the functional changes of fungal communities in disease-causing plant tissues. Our results demonstrate that fungal communities in diseased fruits differ from those in healthy fruits at the level of phylum, class, order, or genus, with significant differences in the species and relative abundance of dominant groups. Endophytic fungi in diseased fruits appeared to produce secondary metabolites with stronger antibacterial properties, although the community diversity was not as varied as that in healthy fruits. In addition, secondary metabolites of the Medicopsis romeroi strain from diseased fruits were identified for the first time. These results have important implications for understanding the functional variation of bioactivity in fungal communities and for developing a broader resource of bioactivity.

Effects of Colletotrichum gloeosporioides and Poplar Secondary Metabolites on the Composition of Poplar Phyllosphere Microbial Communities

Poplar anthracnose caused by Colletotrichum gloeosporioides is a common disease affecting poplars globally that causes the destruction and alteration of poplar phyllosphere microbial communities; however, few studies have investigated these communities. Therefore, in this study, three species of poplar with different resistances were investigated to explore the effects of Colletotrichum gloeosporioides and poplar secondary metabolites on the composition of poplar phyllosphere microbial communities. Evaluation of the phyllosphere microbial communities before and after inoculation of the poplars with C. gloeosporioides revealed that both bacterial and fungal OTUs decreased after inoculation. Among bacteria, the most abundant genera were Bacillus, Plesiomonas, Pseudomonas, Rhizobium, Cetobacterium, Streptococcus, Massilia, and Shigella for all poplar species. Among fungi, the most abundant genera before inoculation were Cladosporium, Aspergillus, Fusarium, Mortierella, and Colletotrichum, while Colletotrichum was the main genus after inoculation. The inoculation of pathogens may regulate the phyllosphere microorganisms by affecting the secondary metabolites of plants. We investigated metabolite contents in the phyllosphere before and after the inoculation of the three poplar species, as well as the effects of flavonoids, organic acids, coumarins, and indoles on poplar phyllosphere microbial communities. We speculated that coumarin had the greatest recruitment effect on phyllosphere microorganisms, followed by organic acids through regression analysis. Overall, our results provide a foundation for subsequent screening of antagonistic bacteria and fungi against poplar anthracnose and investigations of the mechanism by which poplar phyllosphere microorganisms are recruited. IMPORTANCE Our findings revealed that the inoculation of Colletotrichum gloeosporioides has a greater effect on the fungal community than the bacterial community. In addition, coumarins, organic acids, and flavonoids may have recruitment effects on phyllosphere microorganisms, while indoles may have inhibitory effects on these organisms. These findings may provide the theoretical basis for the prevention and control of poplar anthracnose.

Metabolite-Mediated Responses of Phyllosphere Microbiota to Rust Infection in Two Malus Species

Plants recruit beneficial microbes to enhance their ability to fight pathogens. However, the current understanding of microbial recruitment is largely limited to belowground systems (root exudates and the rhizosphere). It remains unclear whether the changes in leaf metabolites induced by infectious pathogens can actively recruit beneficial microbes to mitigate the growth of foliar pathogens. In this study, we integrated microbiome and metabolomic analyses to systematically explore the dynamics of phyllosphere fungal and bacterial communities and key leaf metabolites in two crabapple species (Malus sp. "Flame" and Malus sp. "Kelsey") at six stages following infection with Gymnosporangium yamadae. Our results showed that the phyllosphere microbiome changed during lesion expansion, as highlighted by a reduction in bacterial alpha-diversity and an increase in fungal alpha-diversity; a decreasing and then an increasing complexity of the microbial co-occurrence network was observed in Kelsey and a decreasing complexity occurred in Flame. In addition, nucleotide sugars, diarylheptanoids, and carboxylic acids with aromatic rings were more abundant in early stages of collection, which positively regulated the abundance of bacterial orders Pseudomonadales (in Kelsey), Acidimicrobiales, Bacillales, and Flavobacteriales (in Flame). In addition, metabolites such as flavonoids, lignin precursors, terpenoids, coumarins, and quaternary ammonium salts enriched with the expansion of lesions had a positive regulatory effect on fungal families Rhynchogastremataceae and Golubeviaceae (in Flame) and the bacterial order Actinomycetales (in Kelsey). Our findings highlight that plants may also influence phyllosphere microorganisms by adjusting leaf metabolites in response to biotic stress. IMPORTANCE Our findings demonstrate the response patterns of bacterial and fungal communities in the Malus phyllosphere to rust fungus G. yamadae infection, and they also reveal how the phyllosphere microbiome changes with the expansion of lesions. We identified several metabolites whose relative abundance varied significantly with lesion expansion. Using a framework for assessing the role of leaf metabolites in shaping the phyllosphere microbiome of the two Malus species, we identified several specific metabolites that have profoundly selective effects on the microbial community. In conclusion, our study provides new evidence of the ecological niche of the phyllosphere in supporting the "cry for help" strategy for plants.

Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees

BACKGROUND

The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Studies about spatio-temporal variation of the root-associated microbiome focused so far primarily on community-compositional changes of annual plants, while little is known about their perennial counterparts. The aim of this work was to get deep insight into the spatial patterns and temporal dynamics of the root associated microbiota of apple trees.

RESULTS

The bacterial community structure in rhizospheric soil and endospheric root material from orchard-grown apple trees was characterized based on 16S rRNA gene amplicon sequencing. At the small scale, the rhizosphere and endosphere bacterial communities shifted gradually with increasing root size diameter (PERMANOVA R²-values up to 0.359). At the larger scale, bulk soil heterogeneity introduced variation between tree individuals, especially in the rhizosphere microbiota, while the presence of a root pathogen was contributing to tree-to-tree variation in the endosphere microbiota. Moreover, the communities of both compartments underwent seasonal changes and displayed year-to-year variation (PERMANOVA R²-values of 0.454 and 0.371, respectively).

CONCLUSIONS

The apple tree root-associated microbiota can be spatially heterogeneous at field scale due to soil heterogeneities, which particularly influence the microbiota in the rhizosphere soil, resulting in tree-to-tree variation. The presence of pathogens can contribute to this variation, though primarily in the endosphere microbiota. Smaller-scale spatial heterogeneity is observed in the rhizosphere and endosphere microbiota related to root diameter, likely influenced by root traits and processes such as rhizodeposition. The microbiota is also subject to temporal variation, including seasonal effects and annual variation. As a consequence, responses of the tree root microbiota to further environmental cues should be considered in the context of this spatio-temporal variation.

Changes of Endophytic Bacterial Community in Mature Leaves of Prunus laurocerasus L. during the Seasonal Transition from Winter Dormancy to Vegetative Growth

Diverse communities of bacterial endophytes inhabit plant tissues, and these bacteria play important roles for plant growth and health. Cherry laurel (Prunus laurocerasus L.) is a broadleaf evergreen shrub that is widely grown in temperate zones for its ornamental and medicinal properties, however virtually nothing is known about its associated bacterial community. In this study, we analysed the matured one-year-old leaves of this plant using Illumina-based 16S rRNA gene metabarcoding to reveal the community structure of endophytic bacteria and understand its shifts during the seasonal transition from winter dormancy to a spring vegetative state. The overall community was composed of four dominant phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes). Corynebacterium, Acinetobacter, and Chryseobacterium genera were the most prevalent bacteria, comprising 13.3%, 6.9%, and 6.8% of the amplicon sequence variants (ASVs), respectively. The ASV richness and diversity increased significantly in May as compared to other sampling months (February, March, and April). We observed high variation in the overall community structure of endophytic bacteria among collection dates. The variation was only reflected by a few core community members, suggesting that the changes of the endophytic community during winter/spring seasonal transition are mostly associated with the less abundant community members. We identified biomarker taxa for late winter, mid spring, and late spring collection dates. This study is the first one to report on the diversity and composition of bacterial endophytes in the leaves of cherry laurel and its shifts across the dormancy-to-vegetative seasonal transition.

Unlocking the Changes of Phyllosphere Fungal Communities of Fishscale Bamboo (Phyllachora heterocladae) under Rhombic-Spot Disease Stressed Conditions

As an important nonwood bioresource, fishscale bamboo (Phyllachora heterocladae Oliver) is widely distributed in the subtropical region of China. Rhombic-spot disease, caused by Neostagonosporella sichuanensis, is one of the most serious diseases that threatens fishscale bamboo health. However, there is limited knowledge about how rhombic-spot disease influences the diversity and structures of phyllosphere fungal communities. In this study, we investigated the phyllosphere fungal communities from stems, branches, and leaves of fishscale bamboo during a rhombic-spot disease outbreak using 18S rRNA sequencing. We found that only the phyllosphere fungal community from stems was significantly affected by pathogen invasion in terms of community richness, diversity, and structure. FUNGuild analysis revealed that the major classifications of phyllosphere fungi based on trophic modes in stems, branches, and leaves changed from symbiotroph-pathotroph, no obvious dominant trophic mode, and symbiotroph to saprotroph, saprotroph–pathotroph–symbiotroph, and saprotroph–symbiotroph, respectively, after pathogen invasion. The fungal community composition of the three tissues displayed significant differences at the genus level between healthy and diseased plants. The associations among fungal species in diseased samples showed more complex co-occurrence network structures than those of healthy samples. Taken together, our results highlight the importance of plant pathological conditions for the assembly of phyllosphere fungal communities in different tissues.

The microbiota of the grapevine holobiont: A key component of plant health

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Grapevine interacts different microbiota living around and within its tissues

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Addition of microbial genes to plant genome gives supplementary functions to the holobiont

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The composition of grapevine microbiota varies according to endogenous and exogenous factors

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Microbiota variations can lead to perturbations of grapevine metabolism

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The link between symptom emergence of dieback and microbial imbalance is currently studied

Background

Grapevine is a woody, perennial plant of high economic importance worldwide. Like other plants, it lives in close association with large numbers of microorganisms. Bacteria, fungi and viruses are structured in communities, and each individual can be beneficial, neutral or harmful to the plant. In this sense, microorganisms can interact with each other and regulate plant functions (including immunity) and even provide new ones. Thus, the grapevine associated with its microbial communities constitutes a supra-organism, also called a holobiont, whose functioning is linked to established plant-microorganism interactions.

Aim of review

The overall health of the plant may be conditioned by the diversity and structure of microbial communities. Consequently, an optimal microbial composition will consist of a microbial balance allowing the plant to be healthy. Conversely, an imbalance of microbial populations could lead to (or be generated by) a decline of the plant. The microbiome is an active component of the host also responsive to biotic and abiotic changes; in that respect, a better understanding of the most important drivers of the composition of plant microbiomes is needed.

Key scientific concepts of review

This article presents the current state of the art about the grapevine microbiota and its composition according to the plant compartments and the influencing factors. We also focus on situations of imbalance, in particular during plant disease or decline. Finally, we discuss the possible interest of microbial engineering in an agrosystem such as viticulture.

Diazotroph Paenibacillus triticisoli BJ-18 Drives the Variation in Bacterial, Diazotrophic and Fungal Communities in the Rhizosphere and Root/Shoot Endosphere of Maize

Application of diazotrophs (N2-fixing microorganisms) can decrease the overuse of nitrogen (N) fertilizer. Until now, there are few studies on the effects of diazotroph application on microbial communities of major crops. In this study, the diazotrophic and endospore-forming Paenibacillus triticisoli BJ-18 was inoculated into maize soils containing different N levels. The effects of inoculation on the composition and abundance of the bacterial, diazotrophic and fungal communities in the rhizosphere and root/shoot endosphere of maize were evaluated by sequencing the 16S rRNA, nifH gene and ITS (Inter Transcribed Spacer) region. P. triticisoli BJ-18 survived and propagated in all the compartments of the maize rhizosphere, root and shoot. The abundances and diversities of the bacterial and diazotrophic communities in the rhizosphere were significantly higher than in both root and shoot endospheres. Each compartment of the rhizosphere, root and shoot had its specific bacterial and diazotrophic communities. Our results showed that inoculation reshaped the structures of the bacterial, diazotrophic and fungal communities in the maize rhizosphere and endosphere. Inoculation reduced the interactions of the bacteria and diazotrophs in the rhizosphere and endosphere, while it increased the fungal interactions. After inoculation, the abundances of Pseudomonas, Bacillus and Paenibacillus in all three compartments, Klebsiella in the rhizosphere and Paenibacillus in the root and shoot were significantly increased, while the abundances of Fusarium and Giberella were greatly reduced. Paenibacillus was significantly correlated with plant dry weight, nitrogenase, N2-fixing rate, P solubilization and other properties of the soil and plant.

Phyllosphere microbiota: Community dynamics and its interaction with plant hosts

Plants are colonized by various microorganisms in natural environments. While many studies have demonstrated key roles of the rhizosphere microbiota in regulating biological processes such as nutrient acquisition and resistance against abiotic and biotic challenges, less is known about the role of the phyllosphere microbiota and how it is established and maintained. This review provides an update on current understanding of phyllosphere community assembly and the mechanisms by which plants and microbes establish the phyllosphere microbiota for plant health.

Plant Health and Sound Vibration: Analyzing Implications of the Microbiome in Grape Wine Leaves

Understanding the plant microbiome is a key for plant health and controlling pathogens. Recent studies have shown that plants are responsive towards natural and synthetic sound vibration (SV) by perception and signal transduction, which resulted in resistance towards plant pathogens. However, whether or not native plant microbiomes respond to SV and the underlying mechanism thereof remains unknown. Within the present study we compared grapevine-associated microbiota that was perpetually exposed to classical music with a non-exposed control group from the same vineyard in Stellenbosch, South Africa. By analyzing the 16S rRNA gene and ITS fragment amplicon libraries we found differences between the core microbiome of SV-exposed leaves and the control group. For several of these different genera, e.g., Bacillus, Kocuria and Sphingomonas, a host-beneficial or pathogen-antagonistic effect has been well studied. Moreover, abundances of taxa identified as potential producers of volatile organic compounds that contribute to sensory characteristics of wines, e.g., Methylobacterium, Sphingomonas, Bacillus and Sporobolomyces roseus, were either increased or even unique within the core music-exposed phyllosphere population. Results show an as yet unexplored avenue for improved plant health and the terroir of wine, which are important for environmentally friendly horticulture and consumer appreciation. Although our findings explain one detail of the long-term positive experience to improve grapevine’s resilience by this unusual but innovative technique, more mechanistic studies are necessary to understand the whole interplay.

Biodiversity of endophytic bacteria and fungi of wild grapes Vitis amurensis Rupr

The diversity of endophytic bacteria and fungi of V. amurensis grape plants growing in the suburbs of Vladivostok in the summer and autumn periods of 2018-2020 was analyzed. About 600 strains of bacteria and 160 strains of fungi were inoculated from peripherally sterilized leaves and stems of V. amurensis. Isolated bacteria were representatives of 36 genera: Actinobacterium, Acinetobacter, Agrobacterium, Arthrobacter, Bacillus, Buttiauxella, Curtobacterium, Duganella, Erwinia, Enterobacter, Frigoribacterium, Frondihabitans, Klebsiella, Leclercia, Lelliottia, Methylobacterium, Microbacterium, Mucilaginibacter, Luteibacter, Lysinimonas, Pantoea, Paenibacillus, Parageobacillus, Pedobacter, Phyllobacterium, Plantibacter, Pseudomonas, Pullulanibacillus, Raoultella, Rhizobium, Sphingomonas, Staphylococcus, Stenotrophomonas, Streptomyces, Serratia, Xanthomonas. The largest number of strains were representatives of the genera Erwinia, Pantoae and Pseudomonas. Endophytic grape fungi were represented by 25 genera: Alternaria, Annulohypoxylon, Aureobasidium, Biscogniauxia, Cladosporium, Colletotrichum, Coniochaeta, Coprinellus, Davidiellaceae, Didymella, Discosia, Epicoccum, Fusarium, Hypoxylon, Neosetophoma, Nemania, Neurospora, Nigrospora, Paraphoma, Penicillium, Pestalotiopsis, Pestalosphaeria, Phoma, Trichoderma, Xylaria. The largest number of representatives were of the genus Didymella, Cladosporium and Colletotrichum.

Crop management system and carrot genotype affect endophyte composition and Alternaria dauci suppression

Managing pests in carrot production is challenging. Endophytic microbes have been demonstrated to improve the health and productivity of many crops, but factors affecting endophyte dynamics in carrot is still not well understood. The goal of this study was to determine how crop management system and carrot genotype interact to affect the composition and potential of endophytes to mitigate disease caused by Alternaria dauci, an important carrot pathogen. Twenty-eight unique isolates were collected from the taproots of nine diverse genotypes of carrot grown in a long-term trial comparing organic and conventional management. Antagonistic activity was quantified using an in vitro assay, and potential for individual isolates to mitigate disease was evaluated in greenhouse trials using two carrot cultivars. Results confirm that carrot taproots are colonized by an abundant and diverse assortment of bacteria and fungi representing at least distinct 13 genera. Soils in the organic system had greater total organic matter, microbial biomass and activity than the conventional system and endophyte composition in taproots grown in this system were more abundant and diverse, and had greater antagonistic activity. Carrot genotype also affected endophyte abundance as well as potential for individual isolates to affect seed germination, seedling growth and tolerance to A. dauci. The benefits of endophytes on carrot growth were greatest when plants were subject to A. dauci stress, highlighting the importance of environmental conditions in the functional role of endophytes. Results of this study provide evidence that endophytes can play an important role in improving carrot performance and mediating resistance to A. dauci, and it may someday be possible to select for these beneficial plant-microbial relationships in carrot breeding programs. Implementing soil-building practices commonly used in organic farming systems has potential to promote these beneficial relationships and improve the health and productivity of carrot crops.

Discovering the bacteriome of Vitis vinifera cv. Pinot Noir in a conventionally managed vineyard

The structure of the bacteriome associated with grapevine roots can affect plant development, health and grape quality. We previously investigated the bacterial biodiversity of the Vitis vinifera cv. Pinot Noir rhizosphere in a vineyard subjected to integrated pest management. The aim of this work is to characterize the bacteriome of V. vinifera cv. Pinot Noir in a conventionally managed vineyard using a metabarcoding approach. Comparisons between the microbial community structure in bulk soil and rhizosphere (variable space) were performed and shifts of bacteriome according to two sampling times (variable time) were characterized. Bacterial biodiversity was higher at the second than at the first sampling and did not differ according to the variable space. Actinobacteria was the dominant class, with Gaiella as the most represented genus in all the samples. Among Proteobacteria, the most represented classes were Alpha, Beta and Gamma-Proteobacteria, with higher abundance at the second than at the first sampling time. Bradyrhizobium was the most frequent genus among Alpha-Proteobacteria, while Burkholderia was the predominant Beta-Proteobacteria. Among Firmicutes, the frequency of Staphylococcus was higher than 60% in bulk soil and rhizosphere. Finally, the sampling time can be considered as one of the drivers responsible for the bacteriome variations assessed.

Proposal of A New Bois Noir Epidemiological Pattern Related to 'Candidatus Phytoplasma Solani' Strains Characterized by A Possible Moderate Virulence in Tuscany

Bois noir (BN), associated with 'Candidatus Phytoplasma solani' (CaPsol), is the most widespread disease of the grapevine yellows complex worldwide. In this work, BN epidemiology was investigated in a case study vineyard where an unusual CaPsol strain, previously detected only in other host plants, was found to be prevalent in grapevine. Experimental activities included: symptom observation; sampling of symptomatic vines, Auchenorrhyncha specimens, and weeds; molecular detection and typing of CaPsol strains; statistical analyses for determining possible relationships between CaPsol relative concentration, strain type, and symptom severity. Among insects, Reptalus quinquecostatus was the most abundant and was found to be highly infected by CaPsol, while Hyalesthes obsoletus, the main CaPsol vector, was not caught. Moreover, R. quinquecostatus harbored CaPsol strains carrying uniquely the stamp sequence variant St10, also identified as prevalent in vines and in the majority of weeds, and all the secY variants identified in the vineyard. Statistical analyses revealed that CaPsol strains carrying the St10 variant are not associated with severe symptoms, suggesting their possible moderate virulence. Based on such evidence, a new BN epidemiological pattern related to these CaPsol strains and involving grapevine, R. quinquecostatus, and/or weeds is proposed. Furthermore, the possible presence of other players (vectors and weeds) involved in CaPsol transmission to grapevines was highlighted.

Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi

High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant-associated microbiomes using molecular fingerprinting methodologies, including single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH-PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.

Distinguishing nutrient-dependent plant driven bacterial colonization patterns in alfalfa

To understand factors that influence the assembly of microbial communities, we inoculated Medicago sativa with a series of nested bacterial synthetic communities and grew plants in distinct nitrogen concentrations. Two isolates in our eight-member synthetic community, Williamsia sp. R60 and Pantoea sp. R4, consistently dominate community structure across nitrogen regimes. While Pantoea sp. R4 consistently colonizes plants to a higher degree compared to the other six organisms across each community and each nutrient level, Williamsia sp. R60 exhibits nutrient specific colonization differences. Williamsia sp. R60 is more abundant in plants grown at higher nitrogen concentrations, but exhibits the opposite trend when no plant is present, indicating plant-driven influence over colonization. Our research discovered unique, repeatable colonization phenotypes for individual microbes during plant microbiome assembly, and identified alterations caused by the host plant, microbes, and available nutrients.

The Role of the Endophytic Microbiome in the Grapevine Response to Environmental Triggers

Endophytism within Vitis represents a topic of critical relevance due to the multiple standpoints from which it can be approached and considered. From the biological and botanical perspectives, the interaction between microorganisms and perennial woody plants falls within the category of stable relationships from which the plants can benefit in multiple ways. The life cycle of the host ensures persistence in all seasons, repeated chances of contact, and consequent microbiota accumulation over time, leading to potentially high diversity compared with that of herbaceous short-lived plants. Furthermore, grapevines are agriculturally exploited, highly selected germplasms where a profound man-driven footprint has indirectly and unconsciously shaped the inner microbiota through centuries of cultivation and breeding. Moreover, since endophyte metabolism can contribute to that of the plant host and its fruits' biochemical composition, the nature of grapevine endophytic taxa identities, ecological attitudes, potential toxicity, and clinical relevance are aspects worthy of a thorough investigation. Can endophytic taxa efficiently defend grapevines by acting against pests or confer enough fitness to the plants to endure attacks? What are the underlying mechanisms that translate into this or other advantages in the hosting plant? Can endophytes partially redirect plant metabolism, and to what extent do they act by releasing active products? Is the inner microbial colonization necessary priming for a cascade of actions? Are there defined environmental conditions that can trigger the unleashing of key microbial phenotypes? What is the environmental role in providing the ground biodiversity by which the plant can recruit microsymbionts? How much and by what practices and strategies can these symbioses be managed, applied, and directed to achieve the goal of a better sustainable viticulture? By thoroughly reviewing the available literature in the field and critically examining the data and perspectives, the above issues are discussed.

High-Throughput Sequencing Analysis of the Bacterial Community in Stone Fruit Phloem Tissues Infected by "Candidatus Phytoplasma prunorum"

"Candidatus Phytoplasma prunorum" (CPp) is a highly destructive phytopathogenic agent in many stone fruit-growing regions in Europe and the surrounding countries. In this work, we focused on documenting entire bacterial community in the phloem tissues of 60 stone fruit trees. Nested PCR and two real-time PCR assays were used to select CPp-positive (group A) and CPp-negative samples (group B). Afterwards, high-throughput amplicon sequencing was performed to assess bacterial community compositions in phloem tissues. The bacterial composition in phloem tissue consisted of 118 distinct genera, represented mainly by Pseudomonas, Acinetobacter, Methylobacterium, Sphingomonas, and Rhizobium. Statistics showed that CPp influenced the bacterial composition of infected plants (group A) and that the bacterial community depended on the geographical origin of the sample. This is the first work focusing on an analysis of the influence of CPp on the bacteria coexisting in the phloem tissues of stone fruit trees.

Green Technology: Bacteria-Based Approach Could Lead to Unsuspected Microbe⁻Plant⁻Animal Interactions

The recent and massive revival of green strategies to control plant diseases, mainly as a consequence of the Integrated Pest Management (IPM) rules issued in 2009 by the European Community and the increased consumer awareness of organic products, poses new challenges for human health and food security that need to be addressed in the near future. One of the most important green technologies is biocontrol. This approach is based on living organisms and how these biocontrol agents (BCAs) directly or indirectly interact as a community to control plant pathogens and pest. Although most BCAs have been isolated from plant microbiomes, they share some genomic features, virulence factors, and trans-kingdom infection abilities with human pathogenic microorganisms, thus, their potential impact on human health should be addressed. This evidence, in combination with the outbreaks of human infections associated with consumption of raw fruits and vegetables, opens new questions regarding the role of plants in the human pathogen infection cycle. Moreover, whether BCAs could alter the endophytic bacterial community, thereby leading to the development of new potential human pathogens, is still unclear. In this review, all these issues are debated, highlighting that the research on BCAs and their formulation should include these possible long-lasting consequences of their massive spread in the environment.

Temporal shifts in endophyte bacterial community composition of sessile oak (Quercus petraea) are linked to foliar nitrogen, stomatal length, and herbivory

We studied the relationship between plant functional foliar traits and the endophytic bacterial communities associated in trees, taking the example of sessile oak (Quercus petraea (Matt.) Liebl). Forty-five samples with replicates of eight leaves per sample were collected in spring, summer and autumn. Bacterial community diversity was analyzed via Automated Ribosomal Intergenic Spacer Analysis (ARISA). The leaf traits specific leaf area, level of herbivory, stomatal number, stomatal length, carbon and nitrogen concentration were measured for the leaves of each sample. For statistical analysis, linear mixed effect models, the Canonical Correlation Analysis (CCA) and Non-Parametric Multivariate Analysis of Variance (NPMANOVA) were applied. Herbivory, nitrogen and carbon concentration were significantly different in autumn compared to spring and summer (p value < 0.05), while stomatal length was differentiated between spring and the other two seasons (p value < 0.01). The seasonal differentiation of the bacterial community structure was explained by the first and second axes (29.7% and 25.3%, respectively) in the CCA. The bacterial community structure significantly correlated with herbivory, nitrogen concentration and stomatal length. We conclude that herbivory, nitrogen content, and size of stomatal aperture at the leaf level are important for endophyte colonization in oaks growth in alpine forest environments.

The Endophytic Bacterial Microbiota Associated with Sweet Sorghum (Sorghum bicolor) Is Modulated by the Application of Chemical N Fertilizer to the Field

Sweet sorghum (Sorghum bicolor) is a multipurpose crop used as a feedstock to produce bioethanol, sugar, energy, and animal feed. However, it requires high levels of N fertilizer application to achieve the optimal growth, which causes environmental degradation. Bacterial endophytes, which live inside plant tissues, play a key role in the health and productivity of their host. This particular community may be influenced by different agronomical practices. The aim of the work was to evaluate the effects of N fertilization on the structure, diversity, abundance, and composition of endophytic and diazotrophic bacterial community associated with field-grown sweet sorghum. PCR-DGGE, quantitative PCR, and high-throughput sequencing were performed based on the amplification of rrs and nifH genes. The level of N fertilization affected the structure and abundance but not the diversity of the endophytic bacterial communities associated with sweet sorghum plants. This effect was pronounced in the roots of both bacterial communities analyzed and may depend on the physiological state of the plants. Specific bacterial classes and genera increased or decreased when the fertilizer was applied. The data obtained here contribute to a better understanding on the effects of agronomical practices on the microbiota associated with this important crop, with the aim to improve its sustainability.

Isolation, Diversity, and Growth-Promoting Activities of Endophytic Bacteria From Tea Cultivars of Zijuan and Yunkang-10

Endophytes are rich in plant tissues and play important roles in plant-microbial interactions and plant-growth regulation. Here, endophytic bacteria from two closely related tea cultivars of Zijuan and Yunkang-10 were isolated, and the diversities were compared. Plant-growth promoting (PGP) activities were determined on the dominant groups or nitrogen-fixing genera from the two cultivars. Endophytic bacteria were isolated by using of different selective media and methods, and the PGP activities were investigated by analytical and molecular technologies. A total of 110 isolates of 18 genera belonging to three phylums (Proteobacteria, Firmicutes, and Bacteroidetes) were obtained from Zijuan, while 164 isolates of 22 genera belonging to two phylums (Proteobacteria and Firmicutes) were obtained from Yunkang-10. PGP screening indicated that Herbaspirillum spp., Methylobacterium spp., and Brevundimonas spp. showed different PGP abilities. The PGP ability decreased in order of Herbaspirillum spp., Brevundimonas spp. and Methylobacterium spp., and the majority of Methylobacterium spp. did not showed PGP activity of nitrogen-fixation, P-solubilization, siderophore, indole-3-acetic acid (IAA) production or 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The study of bacterial community and PGP activities confirmed that endophytes in tea plants are constantly changing in different seasons and tea cultivars, and the PGP bacteria in Zijuan are much abundant than those of Yunkang-10.

Isolation, Diversity, and Antimicrobial and Immunomodulatory Activities of Endophytic Actinobacteria From Tea Cultivars Zijuan and Yunkang-10 (Camellia sinensis var. assamica)

Endophytic actinobacteria exist widely in plant tissues and are considered as a potential bioresource library of natural products. Tea plants play important roles in human health and in the lifestyles of Asians, especially the Chinese. However, little is known about the endophytic actinobacteria of tea plants. In this study, 16 actinobacteria of 7 different genera and 28 actinobacteria of 8 genera were isolated and analyzed by 16S rRNA gene sequencing from tea cultivars of Zijuan and Yunkang-10 (Camellia sinensis var. assamica), respectively. The diversity of actinobacteria species from Zijuan were higher in July than December (6 vs. 3 genera), but the diversity of species from Yunkang-10 were higher in December than July (7 vs. 3 genera). No actinobacteria isolates were obtained from any tea cultivar in September. Ten isolates from Yunkang-10 exhibited antimicrobial activity against at least one human pathogenic microorganism (Staphylococcus epidermidis, Shigella flexneri, and Escherichia coli), but none of the isolates from Zijuan exhibited antimicrobial activities. Fourteen strains were further exammined the genes of polyketide synthetase (PKS)-I and PKS-II and non-ribosomal peptide synthetase (NRPS). Brevibacterium sp. YXT131 from Yunkang-10 showed strong inhibitory activity against S. epidermidis, Sh. flexneri, and E. coli, and PKS-I and PKS-II and NRPS genes were obtained from the strain. In in vitro assays, extracts from 14 actinobacteria that were tested for antibiotic biosynthetic genes showed no inhibition of concanavalin A (ConA)-induced murine splenocyte proliferation. In in vivo assays, the crude extract of YXT131 modulated the immune response by decreasing the proinflammatory cytokines interleukin (IL)-12/IL-23 p40 and tumor necrosis factor (TNF)-α in the serum of mice. These results confirm that endophytic actinobacteria from tea plants might be an undeveloped bioresource library for active compounds.

Advancement in LH-PCR methodology for multiple microbial species detections in fermented foods

The length-heterogeneity PCR is a low throughput molecular biology methods explored to monitor bacteria populations in different environments. It could be more used in food microbiology analysis, not only for fingerprinting analysis, but it has been hampered until now by a limiting factor which relates to the high percentage of secondary peaks. With the aim to overcome this problem, different experiments were performed focusing on changing PCR parameters in order to obtain more specific amplicon patterns and also to reduce the complexity of community patterns. With this purpose, different annealing temperatures were tested on complex fermented food matrices taken from both animal and vegetable origin and also on the bacteria isolated from the same food source. In particular, the optimal annealing temperature identified for the fermented food samples is 59 °C and the optimal for bacterial strains varied between 63 °C and 65 °C. The approach allowed the modification of the LH-PCR protocol increasing the amplification efficiency and therefore the bacteria species discrimination. These temperatures also allowed the implementation of the previous LH-PCR published database. The modification in the level of accuracy of the LH-PCR technique could also allow an improvement in the relative species quantification by the peak area evaluation.

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality

BACKGROUND

The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The majority of phyllosphere endophytes originate from the soil and migrate up to the aerial compartments through the root endosphere. Thus, the soil and root endosphere partially define the aerial endosphere in the leaves and berries, contributing to the terroir of the fruit. However, V. vinifera cultivars are invariably grafted onto the rootstocks of other Vitis species and hybrids. It has been hypothesized that the plant species determines the microbiome of the root endosphere and, as a consequence, the aerial endosphere. In this work, we test the first part of this hypothesis. We investigate whether different rootstocks influence the bacteria selected from the surrounding soil, affecting the bacterial diversity and potential functionality of the rhizosphere and root endosphere.

METHODS

Bacterial microbiomes from both the root tissues and the rhizosphere of Barbera cultivars, both ungrafted and grafted on four different rootstocks, cultivated in the same soil from the same vineyard, were characterized by 16S rRNA high-throughput sequencing. To assess the influence of the root genotype on the bacterial communities' recruitment in the root system, (i) the phylogenetic diversity coupled with the predicted functional profiles and (ii) the co-occurrence bacterial networks were determined. Cultivation-dependent approaches were used to reveal the plant-growth promoting (PGP) potential associated with the grafted and ungrafted root systems.

RESULTS

Richness, diversity and bacterial community networking in the root compartments were significantly influenced by the rootstocks. Complementary to a shared bacterial microbiome, different subsets of soil bacteria, including those endowed with PGP traits, were selected by the root system compartments of different rootstocks. The interaction between the root compartments and the rootstock exerted a unique selective pressure that enhanced niche differentiation, but rootstock-specific bacterial communities were still recruited with conserved PGP traits.

CONCLUSION

While the rootstock significantly influences the taxonomy, structure and network properties of the bacterial community in grapevine roots, a homeostatic effect on the distribution of the predicted and potential functional PGP traits was found.

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.

The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard

Microorganisms associated with Vitis vinifera (grapevine) can affect its growth, health and grape quality. The aim of this study was to unravel the biodiversity of the bacterial rhizosphere microbiota of grapevine in an integrated pest management vineyard located in Piedmont, Italy. Comparison between the microbial community structure in the bulk and rhizosphere soil (variable: space) were performed. Moreover, the possible shifts of the bulk and rhizosphere soil microbiota according to two phenological stages such as flowering and early fruit development (variable: time) were characterized. The grapevine microbiota was identified using metagenomics and next-generation sequencing. Biodiversity was higher in the rhizosphere than in the bulk soil, independent of the phenological stage. Actinobacteria were the dominant class with frequencies ≥ 50% in all the soil samples, followed by Proteobacteria, Gemmatimonadetes, and Bacteroidetes. While Actinobacteria and Proteobacteria are well-known as being dominant in soil, this is the first time the presence of Gemmatimonadetes has been observed in vineyard soils. Gaiella was the dominant genus of Actinobacteria in all the samples. Finally, the microbiota associated with grapevine differed from the bulk soil microbiota and these variations were independent of the phenological stage of the plant.

Illumina-based analysis of endophytic bacterial diversity of tree peony (Paeonia Sect. Moutan) roots and leaves

Diverse communities of bacteria inhabit plant tissues and those bacteria play a crucial role for plant health and growth. Tree peony (Paeonia Sect. Moutan) is known for its excellent ornamental and medicinal values as Chinese traditional plant, but little is known about its associated bacterial community under natural conditions. To examine how endophytic bacteria in tree peony vary across tissues and cultivars, PCR-based Illumina was applied to reveal the diversity of endophytic bacteria in tree peony. A total of 149,842 sequences and 21,463 operational taxonomic units (OTUs) were obtained. The OTU abundance of roots was higher than leaves across other three cultivars except for ‘Kinkaku’ and ‘Luoyanghong’. The community was composed of five dominant groups (Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria and Actinobacteria) in all samples. Endophytic bacteria community structures had changed in leaves and roots. Sequences of Pseudomonas and Enterobacteriaceae were prevalent in root samples, whereas Succinivibrio and Acinetobacter were the dominant genus in leaf samples. Otherwise, the distribution of each dominant genus among the 5 cultivars was either varied. These findings suggested that both plant genotype and tissues contribute to the shaping of the bacterial communities associated with tree peony.

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.

Harnessing Host-Vector Microbiome for Sustainable Plant Disease Management of Phloem-Limited Bacteria

Plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. Of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as Candidatus (Ca.) Phytoplasma species and several species of Ca. Liberibacter. Recent studies on plant-microbe and plant-insect interactions of these pathogens have demonstrated that plant-microbe-insect interactions have far reaching consequences for the functioning and evolution of the organisms involved. These interactions take place within complex pathosystems and are shaped by a myriad of biotic and abiotic factors. However, our current understanding of these processes and their implications for the establishment and spread of insect-borne diseases remains limited. This article highlights the molecular, ecological, and evolutionary aspects of interactions among insects, plants, and their associated microbial communities with a focus on insect vectored and phloem-limited pathogens belonging to Ca. Phytoplasma and Ca. Liberibacter species. We propose that innovative and interdisciplinary research aimed at linking scales from the cellular to the community level will be vital for increasing our understanding of the mechanisms underpinning plant-insect-microbe interactions. Examination of such interactions could lead us to applied solutions for sustainable disease and pest management.

Grapevine (Vitis vinifera) Crown Galls Host Distinct Microbiota

Crown gall disease of grapevine is caused by virulent Agrobacterium strains and establishes a suitable habitat for agrobacteria and, potentially, other bacteria. The microbial community associated with grapevine plants has not been investigated with respect to this disease, which frequently results in monetary losses. This study compares the endophytic microbiota of organs from grapevine plants with or without crown gall disease and the surrounding vineyard soil over the growing seasons of 1 year. Amplicon-based community profiling revealed that the dominating factor causing differences between the grapevine microbiota is the sample site, not the crown gall disease. The soil showed the highest microbial diversity, which decreased with the distance from the soil over the root and the graft union of the trunk to the cane. Only the graft union microbiota was significantly affected by crown gall disease. The bacterial community of graft unions without a crown gall hosted transient microbiota, with the three most abundant bacterial species changing from season to season. In contrast, graft unions with a crown gall had a higher species richness, which in every season was dominated by the same three bacteria (Pseudomonas sp., Enterobacteriaceae sp., and Agrobacterium vitis). For in vitro-cultivated grapevine plantlets, A. vitis infection alone was sufficient to cause crown gall disease. Our data show that microbiota in crown galls is more stable over time than microbiota in healthy graft unions and that the microbial community is not essential for crown gall disease outbreak.

IMPORTANCE

The characterization of bacterial populations in animal and human diseases using high-throughput deep-sequencing technologies, such as 16S amplicon sequencing, will ideally result in the identification of disease-specific microbiota. We analyzed the microbiota of the crown gall disease of grapevine, which is caused by infection with the bacterial pathogen Agrobacterium vitis. All other Agrobacterium species were found to be avirulent, even though they lived together with A. vitis in the same crown gall tumor. As has been reported for human cancer, the crown gall tumor also hosted opportunistic bacteria that are adapted to the tumor microenvironment. Characterization of the microbiota in various diseases using amplicon sequencing may help in early diagnosis, to serve as a preventative measure of disease in the future.

Members of the genus Burkholderia: good and bad guys

In the 1990s several biocontrol agents on that contained Burkholderia strains were registered by the United States Environmental Protection Agency (EPA). After risk assessment these products were withdrawn from the market and a moratorium was placed on the registration of Burkholderia-containing products, as these strains may pose a risk to human health. However, over the past few years the number of novel Burkholderia species that exhibit plant-beneficial properties and are normally not isolated from infected patients has increased tremendously. In this commentary we wish to summarize recent efforts that aim at discerning pathogenic from beneficial Burkholderia strains.

Response of leaf endophytic bacterial community to elevated CO2 at different growth stages of rice plant

Plant endophytic bacteria play an important role in plant growth and health. In the context of climate change, the response of plant endophytic bacterial communities to elevated CO2 at different rice growing stages is poorly understood. Using 454 pyrosequencing, we investigated the response of leaf endophytic bacterial communities to elevated CO2 (eCO2) at the tillering, filling, and maturity stages of the rice plant under different nitrogen fertilization conditions [low nitrogen fertilization (LN) and high nitrogen fertilization (HN)]. The results revealed that the leaf endophytic bacterial community was dominated by Gammaproteobacteria-affiliated families, such as Enterobacteriaceae and Xanthomonadaceae, which represent 28.7-86.8% and 2.14-42.6% of the total sequence reads, respectively, at all tested growth stages. The difference in the bacterial community structure between the different growth stages was greater than the difference resulting from the CO2 and nitrogen fertilization treatments. The eCO2 effect on the bacterial communities differed greatly under different nitrogen application conditions and at different growth stages. Specifically, eCO2 revealed a significant effect on the community structure under both LN and HN levels at the tillering stage; however, the significant effect of eCO2 was only observed under HN, rather than under the LN condition at the filling stage; no significant effect of eCO2 on the community structure at both the LN and HN fertilization levels was found at the maturity stage. These results provide useful insights into the response of leaf endophytic bacterial communities to elevated CO2 across rice growth stages.

Seasonal variation of bacterial endophytes in urban trees

Bacterial endophytes, non-pathogenic bacteria residing within plants, contribute to the growth and development of plants and their ability to adapt to adverse conditions. In order to fully exploit the capabilities of these bacteria, it is necessary to understand the extent to which endophytic communities vary between species and over time. The endophytes of Acer negundo, Ulmus pumila, and Ulmus parvifolia were sampled over three seasons and analyzed using culture dependent and independent methods (culture on two media, terminal restriction fragment length polymorphism, and tagged pyrosequencing of 16S ribosomal amplicons). The majority of culturable endophytes isolated were Actinobacteria, and all the samples harbored Bacillus, Curtobacterium, Frigoribacterium, Methylobacterium, Paenibacilllus, and Sphingomonas species. Regardless of culture medium used, only the culturable communities obtained in the winter for A. negundo could be distinguished from those of Ulmus spp. In contrast, the nonculturable communities were dominated by Proteobacteria and Actinobacteria, particularly Erwinia, Ralstonia, and Sanguibacter spp. The presence and abundance of various bacterial classes and phyla changed with the changing seasons. Multivariate analysis on the culture independent data revealed significant community differences between the endophytic communities of A. negundo and Ulmus spp., but overall season was the main determinant of endophytic community structure. This study suggests studies on endophytic populations of urban trees should expect to find significant seasonal and species-specific community differences and sampling should proceed accordingly.