Microbiome of vineyard soils is shaped by geography and management

Abstract

BackgroundDespite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities and the extent by which these are impacted by cultivation are still poorly understood. Using 16S rRNA gene and ITS sequencing, we characterized the soil microbiota of vineyards and of neighboring permanent grassland soils in the Italian province of Trentino, and correlated their structure and composition to location, chemical properties of the soil, and land management.ResultsBacterial communities had a core of conserved taxa accounting for more than 60% of the reads of each sample, that was influenced both by geography and cultivation. The core fungal microbiota was much smaller and dominated by geography alone. Cultivation altered the structure and composition of the soil microbiota both for bacteria and fungi, with site-specific effects on their diversity. The diversity of bacterial and fungal communities was generally inversely correlated across locations. We identified several taxa that were impacted by the chemical properties and texture of the soil.ConclusionsOur results highlight the different responses of bacterial and fungal communities to environmental factors and highlight the need to characterize both components of the soil microbiota to fully understand the factors that drive their variability.

Geological Characteristics of Close Geographical Related Vineyards Influence Microbiomes of Two Soil Depth Profiles With Potential Impacts on Wine Quality

“…As a rst general consideration, we can observe that, as previously reported by other papers [16,17], the super cial layer display quite similar bacterial features with some minor differences between the two geographical related sites. Interestingly this pattern seems to be completely unattended for the deep samples: the bacterial analysis showed that there are 123 genera which signi cantly accumulate with differences in the two soil types.…”

“…It was demonstrated that, the majority of organ-associated microbes re ected the ones found in the surrounding soil, and their distribution were in turn in uenced by the highly localized biogeographic factors and vineyard management [16]. The strict relationship among geographical location and microbiome structure was also recently reported among the Italian famous wine region of Trentino [17]. In such work the authors suggested a general inverse correlation between the geographical location and the microbiome structure.…”

“…Furthermore, we also considered that the vineyard is an anthropic environment and for this reason we analyzed both the super cial (anthropic disturbed) and deep soils (almost undisturbed) to understand how the microbial composition shifts along the pro le. It is well known that one of the most important factors in uencing the microbial composition associated to grapevine plants is the geographical region in which they are growing [17,43,44]. On the other hand, it is also well known that soil microbes strongly in uence the microbial composition of their hosts, playing and important role in shaping the vine-associated microorganisms and the microbial community structures [30,45].…”

Grape cultivar features differentiate the grape rhizosphere of microbiota

“…These microorganisms identified on the varieties come from the same vineyard, and most of the grapes were planted also in 1979, cleft grafting on the same rootstock, long-term equal environment make less difference in diversity among the varieties. These bacteria and fungi may migrate from the surrounding soil and airborne environment [10,23,24] .…”

Amplicons and isolates:Rhizobiumdiversity in fields under conventional and organic management

“…A number of studies have addressed the influence of land management on the soil microbiome by comparison with undisturbed soils such as native tropical forests and permanent grasslands (Palmer & Young, 2000;Mendes et al, 2015;Coller et al, 2019). Land management was found to have an impact on the alpha-diversity of fungal and bacterial microbial communities.…”