Abstract
The soil microbiome is linked to the microbial ecosystem of aboveground plant tissues and it is able to modulate and stimulate plant responses. The community composition, i.e. diversity and abundance, is influenced by several factors such as agronomical practices, agrochemical practices and geographical location. For the first time, we present here the investigation of the microbial community related to the soil of a long-established cultivated vineyard using the meta-barcoding approach. Specifically, we analyzed the bacterial and fungal communities of the bulk soils associated with esca-symptomatic and asymptomatic vines. Results showed no significant differences in richness between the two types of samples. Conversely, we observed that esca-related pathogens and grapevine trunk disease (GTD) pathogens were more abundant in the bulk soils of symptomatic plants, suggesting that the soil could represent an important source of inoculum. We also identified two fungal genera, Curvularia and Coprinopsis, which are exclusive to the soil associated with asymptomatic plants. Moreover, Actinobacteria, a well-known group of bacteria symbionts, are over-represented in asymptomatic soils. Further studies are needed to expand the knowledge about these microorganisms, since they could have a role in controlling the development and/or spread of esca pathogens.
Highlights
The decline of vineyards associated with esca syndrome and grapevine trunk diseases (GTDs) is becoming an issue of increasing concern for viticulture, leading to economic losses and threatening the final product quality (Scheck et al, 1998; Mugnai et al, 1999; Bertsch et al, 2009)
A number of fungal species are associated with esca syndrome, but two tracheomycotic fungi, both belonging to the Ascomycota phylum, are considered to be essential for syndrome development: Phaeomoniella chlamydospora (Phaeomoniellales: Phaeomoniellaceae) and Phaeoacremonium minimum (Diaporthales: Togniniaceae) (Crous et al, 1996; Crous and Gams, 2000; Fischer, 2006; Kuntzmann et al, 2010)
Raw reads obtained from the MiSeq apparatus were cleaned from adaptor and quality filtered using a Macrogen Inc. in-house script based on the Illumina conversion software package bcl2fastq v1.8.4
Summary
The decline of vineyards associated with esca syndrome and grapevine trunk diseases (GTDs) is becoming an issue of increasing concern for viticulture, leading to economic losses and threatening the final product quality (Scheck et al, 1998; Mugnai et al, 1999; Bertsch et al, 2009). Esca is a chronic and complex wood disease in which multiple pathogens simultaneously or sequentially colonize plant tissues (Bertsch et al, 2013), causing mild to severe symptoms. One of the best-known symptoms is tiger-striped leaves (Viala, 1926), in which interveinal discoloration and scorching of leaves is observed. This symptom was initially described as the lighter form of esca and as the chronic form (Surico, 2009), which is thought to be due to both the activity of phytotoxic metabolite secreted by the invading fungi and by the degrading activity of fungal enzymes (Mugnai et al, 1999; Andolfi et al, 2011). The white rot fungus Fomitiporia mediterranea (belonging to the Basidiomycota phylum) and Botryosphaeriaceae species, e.g. Neofusicoccum parvum, seem to play an important role in chronic wood disease development (Cloete et al, 2014; Abou-Mansour et al, 2015)
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