Blackwood, C. 2001. Spatial organization in soil bacterial communities. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.
Spatial variability of soil resources is high due to the heterogeneous arrangement of pores and mineral and organic matter particles in soil, and due to the activity of plants and soil fauna. The spatial organization of soil microbial communities was investigated using terminal restriction fragment length polymorphism (T-RFLP) of eubacterial ribosomal 16S genes, a molecular genetic technique independent of the cultivation of microbes outside their natural environment. Methods for optimal data processing and multivariate statistical analysis of complex community T-RFLP profiles were investigated using analytically-replicated datasets. Spatially-defined microbial habitats were detected by testing the significance of the differences between eubacterial community T-RFLP profiles. Light fraction and shoot residue (partially-decomposed organic matter particles) were found to contain communities different from both the rhizosphere and the soil heavy fraction (soil minerals with associated humified organic matter). Communities in the external and internal portions of soil aggregates were found to be slightly different, while those of different aggregate sizes were not different. The establishment of soil fractions as distinct microbial habitats seemed to be dependent on the differences in the organic matter contents of different fractions. However, different cropping systems also caused divergence in communities which could not be explained on the basis of organic matter contents of samples. Microscopic cell counts were shown to be primarily sensitive to organic matter contents of samples, and not to qualitative differences between cropping systems, in contrast to community composition. Number of large cells (>0.18 μm 3 ) was significantly affected by both soil fraction and cropping system. In another approach to understanding spatial organization of soil eubacterial communities, communities within soil samples of varying sizes and from differing locations within replicated 1.5 × 2 m plots were assayed by T-RFLP. The spatial structure of the communities was investigated using a generalized multivariate extension of blocked-quadrat analysis and semivariance analyses, integrating analyses based on varying sampling grain and extent. Significant hierarchical spatial structure was detected within the eubacterial communities, manifest by phase shifts in the relationship between community variability and spatial scale. These studies indicate that significant spatial organization exists in eubacterial communities in soil, which implies that soil communities are not randomly assembled and may be regulated by mechanisms analogous to those for plant and animal communities.
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