Characterization of Microbial Communities in Vineyard Soils

Microbial communities are responsible for numerous processes in soil important to agriculture. The development of new methods now makes it possible to rapidly characterize the complex microbial communities inhabiting soils. Such information ultimately will be useful in solving agronomic problems and improving management systems. The objective of this project was to measure microbial biomass, diversity and community composition by analyzing membrane lipids extracted from whole communities in vineyard soils. We sampled ten Pinot Noir vineyards in Carneros, Anderson, and Russian River Valleys in June 1998, 2000, and 2001. Vineyards sampled included Buena Vista, Cuvaison, Gloria Ferrer, Handley, Roederer, Scharffenberger, Sterling, Steve Kistler, Swan, and Vino Farms, primarily under 3309 rootstock. Microbial properties of vineyard and immediately adjacent soils under different land uses, as well as communities under different grapevine rootstocks on the same soil type, were also compared.
There were no distinctive regional patterns (e.g. by wine growing region) in microbial biomass or diversity. Across all vineyards, samples from 1998 had higher biomass and lipid diversity than 2000 or 2001 samples, most likely due to heavier than normal rainfall in 1997-1998. Microbial biomass over the 3 years varied four-fold over all vineyards, with the Scharffenberger soils consistently highest. Biomass in adjacent pasture/woodland soil was approximately two times higher than mean values in vineyard soils. Differences in “diversity” (measured by number of lipids detected) were small across vineyards as well as between vineyards and adjacent pasture soils. There were no consistent patterns in microbial biomass associated with particular rootstocks.

There were no distinct differences in microbial community composition among wine-growing regions. Despite biomass differences, annual variations in community composition were small and usually less than differences between vineyards. Microbial communities in rootstock 3309 in Roederer, Scharffenberger, Gloria Ferrer, Vino Farms, Sterling, Cuvaison, and Swan vineyards were suprisingly similar, with Kistler vineyards somewhat distinct but still not very different from the other vineyards. Several but not all samples collected in 2001 from Buena Vista and Handley were substantially different from other vineyard samples. At Cuvaison, communities associated with rootstock 110R and UCDS SO4 were distinctly different from the 3309 rootstock, yet such strong differences were not evident at Gloria Ferrer. Microbial community composition in pasture/woodland soils were very similar to the compositions of adjacent 3309 vineyard soils at Gloria Ferrer, Cuvaison, and Buena Vista, but not at Sterling Vineyards where differences were greater. Fungi were a minor component of all communities sampled, most abundant in the Kistler vineyard, and more abundant in pasture/woodland than vineyard soils. High relative proportions of bacteria, particularly gram positive bacteria (e.g., actinomycetes), were present in all soils. Future work should explore the agronomic significance of differences observed among microbial communities on different rootstocks and whether the relatively small differences between community composition of vineyards and adjacent pasture/woodlands will increase with time under cultivation. It is worth exploring whether more sensitive methods (e.g., DNA fingerprinting) will reveal larger differences among Pinot Noir soil communities than were detected using lipid analysis.

PDF: Characterization of Microbial Communities in Vineyard Soils