Pyrosequencing detects human and animal pathogenic taxa in the grapevine endosphere

Yousaf, Sohail; Bulgari, Daniela; Bergna, Alessandro; Pancher, Michael; Quaglino, F.; Casati, P.; Campisano, A.

doi:10.3389/fmicb.2014.00327

Cited by 25 publications

(23 citation statements)

References 56 publications

(72 reference statements)

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“…The latter seems rather unlikely given the number of strains recovered and their phylogenetic diversity. Moreover, earlier studies using cultivation-independent techniques also identified OTUs (operational taxonomic units) affiliated with the genera Bacillus and Staphylococcus in the endosphere of grapevine, although not to such a great extent as that observed in our study Yousaf et al, 2014). Interestingly, the vineyard from which we sampled our leaf material is an organically managed one and OTUs affiliated with Staphylococcus have been reported to be more abundant in organically managed fields than in conventional ones (Campisano et al, 2014).…”

Section: Resultssupporting

confidence: 52%

Microbial life in the grapevine: what can we expect from the leaf microbiome?

Vionnet¹,

Vrieze

Dutartre³

et al. 2018

OENO One

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Aim: Recent studies have shown that plants harbor complex bacterial communities, the so-called “microbiome”. We are only beginning to unravel the origin of these bacterial plant inhabitants, their community structure and their roles, which, in analogy to the gut microbiome, are likely to be of essential nature. The aim of this work was to analyze the abundance and diversity of the cultivable members of the bacterial microbiome living in and on the leaves of grapevine, and to identify microbiome members with putative plant-protective activities against phytopathogenic organisms.Methods and results: Grapevine leaves were sampled three times during the growing season at one location and used to quantify the abundance and isolate representative members of the epiphytic and endophytic bacterial communities. Results were compared for three grapevine cultivars: Pinot noir, Chasselas and Solaris. Greater bacterial abundance and diversity was observed among epiphytes than among endophytes. Leaf imprints revealed a higher colonization density for the upper than for the lower surface of leaves. A high relative frequency of strains belonging to the genera Staphylococcus and Bacillus was observed, especially in the endophytic communities.Conclusions: The first results of this ongoing study led to the conclusion that epiphytic bacteria of the cultivable grapevine microbiome were more abundant and diverse than endophytic bacteria. A tendency towards more abundant bacteria in the resistant variety Solaris than in the susceptible varieties Chasselas and Pinot noir contrasted with a higher diversity of epiphytic bacteria in the Pinot noir variety. A trend for higher frequency of strains showing antagonistic activity towards the grapevine pathogen Botrytis cinerea among isolates from the resistant variety Solaris could indicate a putative contribution of microbiome bacteria to this resistant phenotype, even though this remains to be confirmed.Significance and impact of the study: This study constitutes a first step in characterizing the endo- and epiphytic cultivable bacterial communities of three grapevine varieties grown at the same location. Further, presently ongoing studies shall reveal i) the true complexity of these leaf-associated communities through cultivation-independent, next generation sequencing techniques, and ii) their potential as a source of biofungicidal agents. In this last point, the contribution of the emission of volatile organic compounds (VOCs) as a newly discovered type of bacterial weapon against fungal and oomycetal pathogens shall be quantified.

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Section: Resultssupporting

confidence: 52%

Microbial life in the grapevine: what can we expect from the leaf microbiome?

Vionnet¹,

Vrieze

Dutartre³

et al. 2018

OENO One

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“…In this study we identified 96 genera and discriminated over 30 species that were present during wine fermentation. Importantly, most of the species we detected have not been reported previously during wine fermentation (Table S4 ), with the exception of a few species (i.e., Propionibacterium acnes, Bacillus thermoamylovorans, Pseudomonas stutzeri ) that were isolated from grapevine, palm wine, and wine corks (Combet-Blanc et al, 1995 ; Bañeras et al, 2013 ; Yousaf et al, 2014 ). The genus Gluconobacter increased significantly during organic fermentation (from 3.28 to 49.42%), while it exhibited less notable changes during the conventional fermentation (from 5.63 to 7.57%) process (Table 3 ).…”

Section: Discussionmentioning

confidence: 71%

Insights into the bacterial community and its temporal succession during the fermentation of wine grapes

Piao

Hawley²,

Kopf³

et al. 2015

Front. Microbiol.

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Grapes harbor complex microbial communities. It is well known that yeasts, typically Saccharomyces cerevisiae, and bacteria, commonly the lactic acid fermenting Oenococcus oeni, work sequentially during primary and secondary wine fermentation. In addition to these main players, several microbes, often with undesirable effects on wine quality, have been found in grapes and during wine fermentation. However, still little is known about the dynamics of the microbial community during the fermentation process. In previous studies culture dependent methods were applied to detect and identify microbial organisms associated with grapes and grape products, which resulted in a picture that neglected the non-culturable fraction of the microbes. To obtain a more complete picture of how microbial communities change during grape fermentation and how different fermentation techniques might affect the microbial community composition, we employed next-generation sequencing (NGS)—a culture-independent method. A better understanding of the microbial dynamics and their effect on the final product is of great importance to help winemakers produce wine styles of consistent and high quality. In this study, we focused on the bacterial community dynamics during wine vinification by amplifying and sequencing the hypervariable V1–V3 region of the 16S rRNA gene—a phylogenetic marker gene that is ubiquitous within prokaryotes. Bacterial communities and their temporal succession was observed for communities associated with organically and conventionally produced wines. In addition, we analyzed the chemical characteristics of the grape musts during the organic and conventional fermentation process. These analyses revealed distinct bacterial population with specific temporal changes as well as different chemical profiles for the organically and conventionally produced wines. In summary these results suggest a possible correlation between the temporal succession of the bacterial population and the chemical wine profiles.

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“…Yousaf and collaborators 75 , by pyrosequencing approach, found opportunistic human pathogens in the grapevine endosphere; in this work, four bacterial genera (Burkholderia, Propionibacterium, Staphylococcus and Clostridium), which include opportunistic human pathogens, were detected. In the same year, Campisano and colleagues reported the presence of opportunistic human pathogens in grapevine 76 .…”

Section: Discussionmentioning

confidence: 59%

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

Gamalero

Bona

Novello

et al. 2020

Sci Rep

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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. open Scientific RepoRtS | (2020) 10:6453 | https://doi.org/10.1038/s41598-020-63154-w www.nature.com/scientificreports www.nature.com/scientificreports/ On the other hand, the microbiota associated to grapevine is affected by the chemical treatments applied in conventional viticulture; negative effects on soil microbial communities are induced by the use of fungicides 20,21 , by acidification of the soil following the fertilizer application 22,23 , and by pesticide application 24 . Altogether, these practices can result in modification of the dynamic interactions between grapevines and microorganisms.More recently, the grapevine microbiota has been placed at the center of the investigation aiming at understanding the possible beneficial effects of microorganisms on grape production. Thanks to culture-independent methods, and especially to the recent advances in next-generation sequencing methods, the complexity of the grapevine/rhizosphere microbial community has been deeply explored. In a previous work 25 , we characterized, by a metabarcoding approach, the bacteriome of the roots of V. vinifera cv. Pinot Noir, in a vineyard subjected to integrated pest management (IPM), looking at the shifts induced by the plant phenological stage and/or by the presence of the plant itself. The main result of that work was that the bacterial community, dominated by Actinobacteria, Proteobacteria, Gemmatimonadetes and Bacteroidetes, responds more intensely to the rhizosphere effect than to the phenological stage of the plant.In a further study, we used a metaproteome approach in order to characterize the microbial community associated to this IPM vineyard soil and to the ro...

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Pyrosequencing detects human and animal pathogenic taxa in the grapevine endosphere

Cited by 25 publications

References 56 publications

Microbial life in the grapevine: what can we expect from the leaf microbiome?

Microbial life in the grapevine: what can we expect from the leaf microbiome?

Insights into the bacterial community and its temporal succession during the fermentation of wine grapes

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

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