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The diversity of culturable and nonculturable bacterial endophytes of grapevine (Vitis vinifera L.) was examined using a combination of cultivation and molecular methods. Entire grapevines were sampled to characterize bacterial diversity from different locations throughout the vine. Gas chromatography of fatty acid methyl esters (FAMEs) was used to...
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... Our data indicate that C. pusillum is the dominant species in rice leaves (Supplementary Data), which is consistent with the fact that Curtobacterium spp. have been isolated from the leaves of many different plants [75][76][77][78] and are known to be abundant in a leaf litter communities 79 . Similarly, the Methylobacteriaceae family is a dominant presence (Fig. 1), as seen in the aerial parts of many plants 80 . ...
The plant microbiome is crucial for plant growth, yet many important questions remain, such as the identification of specific bacterial species in plants, their genetic content, and location of these genes on chromosomes or plasmids. To gain insights into the genetic makeup of the rice-phyllosphere, we perform a metagenomic analysis using long-read sequences. Here, 1.8 Gb reads are assembled into 26,067 contigs including 142 circular sequences. Within these contigs, 669 complete 16S rRNA genes are clustered into 166 bacterial species, 121 of which show low identity (<97%) to defined sequences, suggesting novel species. The circular contigs contain novel chromosomes and a megaplasmid, and most of the smaller circular contigs are defined as novel plasmids or bacteriophages. One circular contig represents the complete chromosome of a difficult-to-culture bacterium Candidatus Saccharibacteria. Our findings demonstrate the efficacy of long-read-based metagenomics for profiling microbial communities and discovering novel sequences in plant-microbiome studies.
... Endophytes have already been reported successfully as biocontrol agents (BCAs) against several phytopathogens (Fadiji et al., 2020). West et al. (2010) stated that grapevines potentially contain a diverse array of bacterial endophytes, including species common to According to the morphological and physiological analyses, the majority of bacterial isolates were Gram positive. Previous reports showed that Gram-positive bacteria (61.73%) were isolated more frequently than Gram-negative bacteria from grapevine plant tissues (Altalhi, 2009) while they were reported to be of equal proportionate in grapes (Zinniel et al., 2002). ...
The present study was conducted at ICAR-National Research Centre for Grapes in Pune, Maharashtra, India during 2021–2022 to study endophytic bacteria as biocontrol agents vis-a-via their compatibility to fungicides in grapes. Eighteen endophytic bacteria were isolated from nine varieties of grapevine (Vitis vinifera L.) viz. Manjari Naveen (MN), Nanasaheb Purple (NP), Thompson Seedless (TS), Crimson Seedless (CS), Manik Chaman (MC), Maruti Seedless (MS), Fantasy Seedless (FS) and 2A Clone (2A). The distinct colonies were selected, sub-cultured, purified and subjected to analysis of macroscopic and microscopic features followed by screening of bacterial isolates for plant growth-promoting (PGP) traits, extracellular hydrolytic enzyme production, and abiotic stress tolerance assay. Eighteen diverse endophytic bacteria were found to be Gram positive to Gram negative and with white, whitish yellow and whitish red colonies. Different biochemical tests which were needful for the identification of the bacteria were performed. Antibiotic sensitivity and antifungal assays were conducted with five antibiotics and pathogenic fungi Colletotrichum gloeosporioides respectively. Results of dual culture plate assay for antimicrobial activity revealed that 10 isolates showed significant growth inhibition of the test pathogen and were selected for the compatibility studies. The results highlighted that most of the isolates were highly compatible with all the fungicides used for powdery mildew, downy mildew, anthracnose and bacterial leaf spot. The work indicated the importance of the endophytic bacteria which can be used as promising biocontrol agents for grapevine disease management.
... (West et al., 2010) . (Khan et al., 2018) . ...
Grapevine is one of the most important agricultural products in Iran. West Azerbaijan province is considered as one of the biggest production centers of grape in Iran, due to its suitable climatic conditions. The aim of this study was to identify grape endophytic bacteria in West Azarbaijan. In this study, 67 endophytic bacteria were isolated from the stems and roots of grapevines. Then, biochemical properties such as hypersensitive reaction, fluorescent and potato soft rot test and the ability to produce proteases, amylase and gelatinase enzymes were tested. Eleven bacterial isolates were selected for molecular identification and it was found that the Bacillus and Pseudomonas are the most abundant genera. According our knowledge, three species of Stenotrophomonas sp., Bosea lathyri and Frigoribacterium faeni are reported for the first time in Iran as grapevine endophytic bacteria. Also, the antifungal effect of endophytic bacteria on three fungal species: Chaetomium globosum, Cytospora chrysosperma and Fusarium sp. was done by dual culture method and three isolates of GI6 (Priestia sp.), GI43 (Pseudomonas kilonensis) and GI45 (Bacillus sp.) showed the most growth inhibitory properties against fungi. Due to the importance of endophytic bacteria, their isolation and identification from different parts of the country seems necessary, as the result, these bacteria can be used in biological control of plant diseases and can be replaced by chemical control.
Keywords: Endophyte, bacteria, grape, biochemical properties, antifungal effect, biological control
... Endophytic microorganisms may be promising alternatives to pesticides for plant protection from fungal diseases [5]. Most studies that have investigated the endophytic communities in grapevines have focused on Vitis vinifera cultivars [13][14][15][16][17][18][19][20][21]. ...
Many grape endophytic microorganisms exhibit high potential for suppressing the development of grape diseases and stimulating grapevine growth and fitness, as well as beneficial properties of the crop. The microbiome of wild grapevines is a promising source of biocontrol agents, which can be beneficial for domesticated grapevines. Using next-generation sequencing (NGS) and classical microbiology techniques, we performed an analysis of bacterial and fungal endophytic communities of wild grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat growing in the Russian Far East. According to the NGS analysis, 24 and 18 bacterial taxa from the class level were present in V. amurensis and V. coignetiae grapevines, respectively. Gammaproteobacteria (35%) was the predominant class of endophytic bacteria in V. amurensis and Alphaproteobacteria (46%) in V. coignetiae. Three taxa, namely Sphingomonas, Methylobacterium, and Hymenobacter, were the most common bacterial genera for V. amurensis and V. coignetiae. Metagenomic analysis showed the presence of 23 and 22 fungi and fungus-like taxa of class level in V. amurensis and V. coignetiae, respectively. The predominant fungal classes were Dothideomycetes (61–65%) and Tremellomycetes (10–11%), while Cladosporium and Aureobasidium were the most common fungal genera in V. amurensis and V. coignetiae, respectively. A comparative analysis of the endophytic communities of V. amurensis and V. coignetiae with the previously reported endophytic communities of V. vinifera revealed that the bacterial biodiversity of V. amurensis and V. coignetiae was similar in alpha diversity to V. vinifera’s bacterial biodiversity. The fungal alpha diversity of V. amurensis and V. coignetiae was statistically different from that of V. vinifera. The beta diversity analysis of bacterial and fungal endophytes showed that samples of V. vinifera formed separate clusters, while V. amurensis samples formed a separate cluster including V. coignetiae samples. The data revealed that the endophytic community of bacteria and fungi from wild V. amurensis was richer than that from V. coignetiae grapes and cultivated V. vinifera grapes. Therefore, the data obtained in this work could be of high value in the search for potentially useful microorganisms for viticulture.
... poae). The RifMut strain was developed following the methods of Adorada et al. [72] and West et al. [27]. A single colony of BCA17 was streaked onto NA amended with 1 ppm of rifampicin (Sigma Chemical Co., St. Louis, MO, USA) and resulting colonies subsequently exposed to increasing concentrations of rifampicin (5, 10, 50, and 100 pm). ...
... Upward and downward movement of the RifMut strain was noted at 1 month post-inoculation and complete colonization 6 months post-inoculation, with the RifMut strain being recovered from the tip of the living tissue down to the basal end of the trunk, below the soil line, and in the lateral shoots. In 1-yr-old and 3-yr-old potted vines, West et al. [27] demonstrated movement of the bacteria Bacillus cereus from inoculated leaves down to the vine shoots. However, after 4 weeks B. cereus was found only at a 6.5 cm distance from the inoculation point. ...
Grapevine trunk diseases (GTDs) impact the sustainability of vineyards worldwide and management options are currently limited. Biological control agents (BCAs) may offer a viable alternative for disease control. With an aim to develop an effective biocontrol strategy against the GTD pathogen Neofusicoccum luteum, this study investigated the following: (1) the efficacy of the strains in suppressing the BD pathogen N. luteum in detached canes and potted vines; (2) the ability of a strain of Pseudomonas poae (BCA17) to colonize and persist within grapevine tissues; and (3) the mode of action of BCA17 to antagonize N. luteum. Co-inoculations of the antagonistic bacterial strains with N. luteum revealed that one strain of P. poae (BCA17) suppressed infection by 100% and 80% in detached canes and potted vines, respectively. Stem inoculations of a laboratory-generated rifampicin-resistant strain of BCA17 in potted vines (cv. Shiraz) indicated the bacterial strain could colonize and persist in the grapevine tissues, potentially providing some protection against GTDs for up to 6 months. The bioactive diffusible compounds secreted by BCA17 significantly reduced the spore germination and fungal biomass of N. luteum and the other representative GTD pathogens. Complementary analysis via MALDI-TOF revealed the presence of an unknown cyclic lipopeptide in the bioactive diffusible compounds, which was absent in a non-antagonistic strain of P. poae (JMN13), suggesting this novel lipopeptide may be responsible for the biocontrol activity of the BCA17. Our study provided evidence that P. poae BCA17 is a potential BCA to combat N. luteum, with a potential novel mode of action.
... The genus Bacillus was the most abundant in both vineyards (conventional vineyard: 39%, biodynamic one: 50%), and most of these bacteria were isolated in spring and summer. This genus also predominated in other studies on grapevine endophytes, e.g. in West et al. (2010), it was 26%, and in Baldan et al. (2014), it covered 30% of all examined endophytes. After the genus Bacillus, a large part of the isolates was the genus Pantoea (conventional: 23%, biodynamic: 10%), which was most common in the grapevine in summer and autumn. ...
Plants are permanently exposed to biotic and abiotic stress and have therefore developed intricate resistance mechanisms, consequently. These include the presence of microbial endophytes, which can promote plant growth and ensure better resilience against unfavourable conditions. These microorganisms colonising plant tissues can directly affect plant growth by producing phytohormones, antioxidants, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, or indirectly by the production of siderophores and antifungal agents. To the best of our knowledge, this is the first study devoted to assessing bacterial endophyte diversity and their plant growth-promoting properties in two utterly distinct vineyards in view of agricultural management (conventional, biodynamic) in the Czech Republic. With these different agricultural approaches, we hypothesised different numerical representations of bacterial endophytes acquired from vine shoots and leaves, which was not proved (P = 0.743, F = 0.129). A total of 470 distinct bacterial endophytes were isolated from the Vitis vinifera plants from the conventional and biodynamic vineyard and from which over 80% were identified by the matrix-assisted laser desorption-time-of-flight mass spectrometry (MALDI-TOF MS). In both vineyards, the dominant bacterial genus was Bacillus, followed by Pantoea, Pseudomonas and Staphylococcus. Plant-promoting endophyte properties varied with respect to the season and type of vineyard. The ability to produce indole-3-acetic acid (IAA) and ACC deaminase was higher in the biodynamic vineyard, in comparison with antioxidant activity, which was found in a higher proportion in isolates from the conventional vineyard.
... ﻣﻮﻟﮑﻮﻟﯽ ﺷﻨﺎﺳﺎﯾﯽ 5 / 96 % ﮔﻮﻧﻪ ﻣﺸﺎﺑﻪ Frigoribacterium faeni ﺑﻮد (Wang et al., 2015) . (West et al., 2010) . ...
... The cultivation-dependent method demonstrated that 10 bacterial genera prevailed in the V. amurensis endophytic community (Pantoea, Erwinia, Pseudomonas, Bacillus, Curtobacterium, Rhizobium (sphaerophysae group), Frigoribacterium, Sphingomonas, Xantomonas, and Buttiauxella) (Figure 2). The data obtained on the main genera of endophytic bacteria present in V. amurensis were similar to the previously published data on bacterial community composition in V. vinifera from Australia and Italy [6][7][8][9]27]. ...
In this paper, the composition profiles of bacterial endophytes in wild-growing Amur grape Vitis amurensis Rupr. grown in the south of the Russian Far East were analyzed using both a cultivation-dependent (sowing bacteria) and a cultivation-independent (next generation sequencing, NGS) approach. Both methods revealed the prevalent endophytes in V. amurensis were represented by Gammaproteobacteria—40.3–75.8%, Alphaproteobacteria—8.6–18.7%, Actinobacteria—9.2–15.4%, and Bacilli—6.1–6.6%. NGS also showed a large proportion of Bacteroidia (12.2%) and a small proportion of other classes (less than 5.7%). In general, NGS revealed a greater variety of classes and genera in the endophytic bacterial community due to a high number of reads (574,207) in comparison with the number of colonies (933) obtained after the cultivation-dependent method. A comparative analysis performed in this study showed that both wild grape V. amurensis from Russia and domesticated cultivars of V. vinifera from Germany and California (USA) exhibit the same basic composition of endophytic bacteria, while the percentages of major taxa and minor taxa showed some differences depending on the plant organ, grape individuals, environmental conditions, and sampling time. Furthermore, the obtained data revealed that lower temperatures and increased precipitation favored the number and diversity of endophytic bacteria in the wild Amur grape. Thus, this study firstly described and analyzed the biodiversity of endophytic bacteria in wild grapevine V. amurensis.
... Novel high-throughput sequencing (HTS) approaches have been recently used to outline the microbiome in grapevine organs such as roots, berries and leaves in mature vines due of its importance in grape production, fruit and foliar diseases management, and the effect of endemic microorganisms on the local characteristic of a wine [5][6][7]. Culture-dependent microbial approaches have historically been used to reveal microbiota present in the grapevine endospheres [8][9][10][11]. However, culture-independent high-throughput amplicon sequencing (HTAS) techniques have recently been deployed to increase the microbiome portrait of grapevine woody organs such as the trunk and cane [12][13][14][15][16][17][18]. ...
Rootstocks are the link between the soil and scion in grapevines, can provide tolerance to
abiotic and biotic stresses, and regulate yield and grape quality. The vascular system of grapevine rootstocks in nurseries is still an underexplored niche for research, despite its potential for hosting beneficial and pathogenic microorganisms. The purpose of this study was to investigate the changes in the composition of fungal communities in 110 Richter and 41 Berlandieri rootstocks at four stages of the grapevine propagation process. Taxonomic analysis revealed that the fungal community predominantly consisted of phylum Ascomycota in all stages of the propagation process. The alphadiversity of fungal communities differed among sampling times for both rootstocks, with richness
and fungal diversity in the vascular system decreasing through the propagation process. The core microbiome was composed of the genera Cadophora, Cladosporium, Penicillium and Alternaria in both rootstocks, while the pathogenic genus Neofusicoccum was identified as a persistent taxon throughout the propagation process. FUNguild analysis showed that the relative abundance of plant pathogens associated with trunk diseases increased towards the last stage in nurseries. Fungal communities in the vascular system of grapevine rootstocks differed between the different stages of the propagation process in nurseries. Numerous genera associated with potential biocontrol activity and grapevine
trunk diseases were identified. Understanding the large diversity of fungi in the rootstock vascular tissue and the interactions between fungal microbiota and grapevine will help to develop sustainable strategies for grapevine protection.
... are not known to cause any disease of plants from which they were primarily isolated [4]. Many strains have been isolated as endophytes in sugarcane [5], grapevines [6], maize [7], sorghum [8], tomatoes [9], coffee [10], black peppers [11], strawberries [12], citrus fruits [13], poplars [14] and eucalyptus [15] and have been found in oil brines [5] and marine sediments [7]. ...
The genus of Curtobacterium, belonging to the Microbacteriaceae family of the Actinomycetales order, includes economically significant pathogenic bacteria of soybeans and other agricultural crops. Thorough phylogenetic and full-genome analysis using the latest genomic data has demonstrated a complex and contradictory taxonomic picture within the group of organisms classified as the Curtobacterium species. Based on these data, it is possible to delineate about 50 new species and to reclassify a substantial part of the Curtobacterium strains. It is suggested that 53 strains, including most of the Curtobacterium flaccumfaciens pathovars, can compose a monophyletic group classified as C. flaccumfaciens. A genomic analysis using the most recent inventory of bacterial chromosomal and plasmid genomes deposited to GenBank confirmed the possible role of Microbacteriaceae plasmids in pathogenicity and demonstrated the existence of a group of related plasmids carrying virulence factors and possessing a gene distantly related to DNA polymerase found in bacteriophages and archaeal and eukaryotic viruses. A PCR diagnostic assay specific to the genus Curtobacterium was developed and tested. The presented results assist in the understanding of the evolutionary relations within the genus and can lay the foundation for further taxonomic updates.
