Bacterial diversity in cucumber (Cucumis sativus) rhizosphere in response to salinity, soil pH, and boron

Soil salinity is a major factor relating microbial communities to environmental stress in the microbial selection process as stress can reduce bacterial diversity. In the San Joaquin Valley (SJV) of California, the problem of increasing salinity and consequently, decreasing crop productivity, due to reuse of saline drainage water are major concerns. An experiment was conducted in a closed, recirculating volumetric lysimeter system (VLS) consisting of 24 experimental plant growth units to determine the interactive effects of salinity, boron and pH on rhizosphere and non-rhizosphere microbial composition of cucumber (Cucumis sativus L. cv. Seminis Turbo hybrid). Plants in the VLS were irrigated from individual reservoirs containing a modified half-strength Hoagland's nutrient solution combined with salinity, boron (B), and pH treatments. The results indicated that salinity and pH were the most influential factors affecting the growth of plants and the effect of boron on the plant was more severe under slightly acidic conditions. Total bacterial DNA was extracted from rhizosphere and non-rhizosphere samples, and a 236-bp DNA fragment in the V3 region of the small subunit ribosomal RNA genes of eubacteria was amplified. The 16S rRNA and the products were subjected to denaturing gradient gel electrophoresis (DGGE) and sequencing. Analyses of bacterial diversity showed that the effects of salinity, boron, and pH were more severe on the rhizosphere bacterial population during the first week of growing cucumber, with decreasing impacts with plant growth. However, there was no salinity–B–pH interaction effects on plant biomass, but the effects were seen in the number of heterotrophic bacteria in the rhizosphere and on species richness and diversity during week seven of the study. These suggest that the effects of salinity–B–pH interactions may influence microorganisms first before plants and may pose long term effects on soil quality.