Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland

Abstract

Soil bacteria are important contributors to primary productivity and nutrient cycling in arid land ecosystems, and their populations may be greatly affected by changes in environmental conditions. In parallel studies, the composition of the total bacterial community and of members of the Acidobacterium division were assessed in arid grassland soils using terminal restriction fragment length polymorphism (TRF, also known as T-RFLP) analysis of 16S rRNA genes amplified from soil DNA. Bacterial communities associated with the rhizospheres of the native bunchgrasses Stipa hymenoides and Hilaria jamesii, the invading annual grass Bromus tectorum, and the interspaces colonized by cyanobacterial soil crusts were compared at three depths. When used in a replicated field-scale study, TRF analysis was useful for identifying broad-scale, consistent differences in the bacterial communities in different soil locations, over the natural microscale heterogeneity of the soil. The compositions of the total bacterial community and Acidobacterium division in the soil crust interspaces were significantly different from those of the plant rhizospheres. Major differences were also observed in the rhizospheres of the three plant species and were most apparent with analysis of the Acidobacterium division. The total bacterial community and the Acidobacterium division bacteria were affected by soil depth in both the interspaces and plant rhizospheres. This study provides a baseline for monitoring bacterial community structure and dynamics with changes in plant cover and environmental conditions in the arid grasslands.

FIG. 1.

Relationships between soil bacterial communities associated with interspaces (I) and the rhizospheres of Hilaria (H), Stipa (S), and Bromus (B) plants in an arid grassland, illustrated by UPGMA dendrograms generated from Jaccard distance matrices of TRF profiles. The y axis is the Jaccard distance measure. Panels A to C illustrate comparisons of the total bacterial community by PCR amplification of the 16S rRNA gene from soil DNA using primers conserved for all bacteria, followed by generation of TRF profiles. Panels D to F illustrate a similar analysis that focused on the Acidobacterium division. Each branch on a tree represents a field sample comprised of three pooled soil cores and a combination of three technical replicate TRF profiles that were averaged as described in the text. Because of significant differences between communities associated with different soil depths, comparisons between the plants are confined to a single depth. For the total bacterial community comparison, one of the Stipa samples at a depth of 10 to 20 cm was lost during processing and is missing from the figure.

FIG. 2.

Relationships between the Acidobacterium division bacterial communities by PCA. Acidobacterium division bacterial communities from the interspaces (I) and from the rhizospheres of Hilaria (H), Stipa (S), and Bromus (B) plants at a soil depth of 20 to 30 cm are shown. The proportion of variance for the first, second, and third components was 0.2441, 0.1913, and 0.1523, respectively. The first and second components explained 43.5% of the variability, and the first and third components explained 39.6% of the variability.

FIG. 3.

Relationships between soil bacterial communities at three depths in four different environments in an arid grassland, illustrated by UPGMA dendrograms generated from Jaccard distance matrices of TRF profiles. The y axis is the Jaccard distance measure. Panels A to D illustrate comparisons of the total bacterial community by PCR amplification of 16S rRNA genes from soil DNA using primers conserved for all bacteria, followed by generation of TRF profiles. Panels E to H illustrate a similar analysis that focused on the Acidobacterium division. Each branch on a tree represents a field sample comprised of three pooled soil cores and a combination of three technical replicate TRF profiles that were averaged as described in the text. Because of significant differences between communities associated with the different grass species, comparisons between soil depths are confined to a single plant species or the interspace. In the figure, 0, 10, and 20 represent soil from a depth of 0 to 10, 10 to 20, and 20 to 30 cm, respectively. For the total bacterial community comparison, one of the Stipa samples at a depth of 10 to 20 cm was lost during processing and is missing from the figure.

FIG. 4.

Seasonal changes in volumetric water content in study site soils at three soil depths from February to May in 1998.