Soil microbial communities are influenced by many factors, including root presence, soil disturbance, variation in soil type and texture, and gradients in resource availability. We investigated the relationship between these factors and the associated soil microbial communities under Pinot Noir grapevines in the Carneros region of Napa County, Ca. We hypothesized that soil microbial communities would 1) change with depth due to shifts in soil resources, or soil C content and moisture, and 2) differ between rhizosphere and bulk soils. Also, we anticipated that soil microbial communities would differ with slope position due to the high level of soil heterogeneity across the vineyard.

Soil pits were excavated adjacent to grapevines at three slope positions: shoulder, mid-slope and toe-slope. Three transects containing all slope positions were sampled, for a total of nine soil pits. From the upper four horizons in each pit (ca. 0 to 1-1.5 m depth), samples for soil microbial community composition were collected from rhizosphere and bulk soil. The soil microbial community was described by phospholipid fatty acids (PLFA). In order to compare several methods for describing soil diversity, soil samples from one transect were cultured on S1 media to select for Pseudomonas spp. and TBSA media to select for a wider array of isolates. These isolates were identified by fatty acid methyl esters (FAME) and 16SrDNA analyses. Soil characteristics were measured in the bulk samples, including bulk density, total C and N, exchangeable cations and cation exchange capacity, texture (i.e., sand, silt and clay), and gravimetric water content.

According to Canonical Correspondence Analysis (CCA) of PLFA from all pits, soil microbial communities surprisingly did not differ between rhizosphere and bulk soil. Depth was the significant factor in determining the segregation of soil microbial communities. In the surface layer, or Ap horizon, soil microbial communities were most similar to each other and were distinctly different from the lower depths. This suggests that conditions in the surface Ap horizon strongly influenced the soil microbial community composition despite differences in slope position and soil heterogeneity associated with each soil pit.

Using a second CCA with PLFA and soil characteristics from bulk soils only, we showed that decreases in soil C and N and increases in soil bulk density were highly correlated with increasing depth and tended to explain the differentiation of soil microbial communities with increasing depth. Soil C and N content in the surface ranged from 10.0 - 13.7 g/kg and 1.0 - 1.5 g/kg, respectively. In the lowest depth, soil C ranged from 0.30 - 4.2 g/kg while soil N was less than 0.4 g/kg.

Relative concentrations of PLFA biomarkers for fungi decreased with increasing depth but markers for Gram^- and Gram⁺ did not follow patterns observed in previous studies. FAME and 16SrDNA analyses showed a less clear pattern with increasing with depth. Diversity of Pseudomonas spp. tended to be relatively less than previously reported findings in annual cropping systems while Gram⁺ bacteria was relatively greater.