Understanding soil microbial community dynamics in vineyard soils: soil structure, climate and plant effects

This thesis aimed at characterising the structure of the bacterial and fungal community living in vineyard soils, identifying and describing the parameters that explain the distribution of the microbial communities in this environment. Vineyards represent an economical relevant agro-ecosystem, where vines, long-lived woody-perennial plants, are normally cultivated at different altitudes. The maintenance of the soil quality is at the base of a productive agriculture and thus the investigation of its biological component, its structure and all the processes that take place into the soil are of importance. Microorganisms represent one of the main biological components of the soil and they are involved in numerous bio-geochemical processes, such as nutrient cycling and degradation of the soil organic matter (SOM). The understanding of the effect of abiotic and biotic factors on the soil microbial communities is crucial for the maintenance of this agro-ecosystem. Considering that viticulture is widespread in North Italy we selected the Trentino region as study area at the basis of our investigations. A first on field study was carried out on soils collected in nine vineyards located along three altitudinal transects. The sites were selected on the basis of the same soil origin, texture and pH, and similar weather conditions. Our aim was to understand the effect of altitude considered as a climatic and physicochemical gradient on the soil bacterial and fungal community, comparing the soil microbial structure at different altitudes (200, 450, 700 m a.s.l.) and in different seasons. Along these altitudinal gradients, soil temperature is decreasing while soil moisture is increasing, thus offering an experimental design to investigate the effect of these climatic parameters. To further exploit the effect of soil temperature, we then carried out one year microcosm experiment. Temperature is one of the main factors affecting soil microbial communities and the recent worries about climate change stimulated the interest in a better understanding of its effect. Our aim was to assess the effect of temperature alone, isolating its effect from all the other parameters present in the field. In particular we investigated the effect of soil seasonal temperature fluctuations and the effect of a moderate soil warming of 2 °C above normal seasonal temperatures. Furthermore we assessed the effect of stable temperatures without fluctuations (3 and 20°C). To fully characterise the vineyard environment we conducted a third experiment to understand the effect of weeds and of soil type on the bacterial and fungal community structure, to reflect on their role in this environment. Weeds are widespread plants in the vineyards and are usually controlled because they compete for nutrients with vines. Through a greenhouse experiment where we used a combination of three different weeds (Taraxacum officinalis, Trifolium repens and Poa trivialis) and four different soils collected in vineyard, we aimed at characterising the bacterial and fungal communities of the bulk and rhizosphere soil and of the roots. The genetic structure of the soil bacterial and fungal communities in the three different experiments was assessed by automated ribosomal intergenic spacer analysis (ARISA), a fingerprinting technique based on the analysis of the length heterogeneity of the bacterial and fungal internal transcribed spacer (ITS) fragment. Multivariate analyses were carried out to visualise and determine the effect of the different parameters investigated on the soil microbial community ordination. We found that altitude, behaving as a physicochemical gradient separates the soil microbial community living at 200 and 700 m a.s.l. Different parameters correlating with altitude explained the distribution of bacteria and fungi in the altitudinal transects. Qualitatively the different vineyards were characterised by a stable core microbiome, a number of ribotypes stable in time and space. Among the climatic parameters, while soil moisture was correlating with altitude and helped explaining the distribution of the microbial communities, the soil temperature did not play any role. Seasonally the soil microbial communities were stable and the differences among the soil microbial communities living at the lower and higher sites were related to the physicochemical parameters and not to the temperature effect. Investigating the effect of temperature in microcosm experiment, isolating its effect from all the other parameters, we determined the presence of a direct effect of temperature, soil type dependent. The soil bacterial community was fluctuating under the effect of temperature fluctuations, while the fungal community was mainly stable. Soil warming did not have any effect on the microbial community as observed on field in the altitudinal gradient, where temperature was not the factor explaining the differences between the microbial community at 200 and 700 m a.s.l. Vineyards, as other temperate environments, are quite stable to subtle changes in soil temperatures in the range forecasted by the climate change events. Even if we did not find a direct effect of temperature on the soil microbial communities, temperature could indirectly affect the soil microorganisms, acting on plant cover, nutrients availability, soil moisture and plant exudation. The soil structure was the main determinant of the microbial community associated to the bulk soil also in presence of plants. Characterising the microbial community associated to the weeds, we found that the different compartments (roots, rhizosphere and bulk soil) were colonised by qualitatively and quantitative different microbial structure, in particular on the roots. Differences in the microbial community associated to the rhizosphere and to the bulk soil were plant type dependent. The structure of the microbial community associated to the roots was mainly determined by the plant species, while the soil type was the main determinant of the microbial community associated to the bulk soil. Weeds are not expected to particularly affect the bacterial community associated to the bulk soil in vineyards, while they could play a role shaping the soil fungal community