Temporal Changes in the Bacterial Communities of Soil, Rhizosphere, and Endorhiza Associated with Field-Grown Cucumber (Cucumis sativus L.)

Abstract

In order to understand how bacterial communities develop in natural ecosystems, the culturable aerobic-heterotroph bacterial communities of three habitats (rhizosphere, endorhiza, and soil) associated with field-grown cucumber roots were examined for quantitative and qualitative changes in structure, over time. Soil and root samples were taken 0, 7, 14, 21, 35, and 70 days after planting (DAP) in 1994, and 0, 7, 14, 28, 42, and 70 DAP in 1995. Individual bacterial colonies of aerobic- heterotroph bacteria were sampled randomly and characterized using the Sherlock System (Microbial ID, Inc., Newark, Del), for fatty acid methyl ester analysis. More than 6,000 bacterial isolates were identified to the genus level and used in calculating richness, diversity, and similarity indices for the three habitats. Diversity was assessed using Hill's modifications of Shannon's index and Simpson's index (N1 and N2, respectively), while similarity was determined using the coefficient of biotic similarity. The same general trends were observed for the community structures of each habitat in both years. The soil was the least diverse and the rhizosphere was most diverse throughout both growing seasons. Bacillus and Arthrobacter spp. were dominant in soil, while Gram-negative bacteria tended to be more abundant in the rhizosphere and endorhiza. The initial membership of the endorhiza (7–14 DAP) appeared to be a function of the rhizosphere community, since both habitats were composed of similar genera. However, the endorhiza was less diverse than the rhizosphere because one or two genera tended to be dominant in each sample, particularly Agrobacterium and Enterobacter spp. Analysis of community similarity indicated that the soil was a distinct habitat and remained relatively unchanged throughout the study. The rhizosphere and endorhiza were dissimilar from the soil and from each other at particular sampling times. These results indicate that the soil, rhizosphere, and endorhiza communities are structurally distinct (the relative abundance of a particular bacterial genera differs among habitats) but share a common membership. Thus, when examining bacterial communities, both the qualitative (i.e., membership) and quantitative (i.e., abundance) aspects must be examined in order to study shifts in community structure.