Spatial and Resource Factors Influencing High Microbial Diversity in Soil

Abstract

To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant. Two diversity indices, the reciprocal of Simpson's index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns. For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities. In a site richer in organic carbon, microbial communities consistently exhibited the uniform distribution pattern regardless of soil water content and depth. The uniform distribution implies that competition does not shape the structure of these microbial communities. Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone. Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity. Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility.

Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

“…Over a wide range of depths from tens of centimeters to meters, other researchers have shown that genetic diversity tends to decrease with increasing soil depth [18,24,34,35,61,75]. This decrease in diversity has been attributed to a variety of factors, including soil moisture and carbon and nitrogen availability.…”

“…It is hypothesized that the spatially structured habitat, patchiness in nutrient availability, differences among associated plant species, or interactions among members of the soil community may all contribute to this diversity [10,14,22,31,51,60,65,70,75]. To identify local factors that may influence the spatial distribution of diversity, including competitive interactions and resource availability, information on how phenotypes and genotypes are arrayed in space is crucial.…”

Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere

“…Library coverage was calculated with the nonparametric estimator C (Good, 1953). The reciprocal of Simpson's index (1/D) was used as a measure of diversity to evaluate the level of dominance in a community (Zhou et al, 2002). The number of shared OTUs between libraries was calculated using SONS (www.mothur.…”

Review: Microbial biocenoses in pristine aquifers and an assessment of investigative methods

“…chromium and many heavy metals, and recalcitrant organic contaminants. Zhou et al (2002) studied the microbial communities in different types of contaminated and pristine soils and aquifers, and found that even extremely high levels of Cr-III did not significantly influence microbial diversity. Similarly, at another site with aerobic groundwater contaminated by trichlorethylene (TCE) at low concentrations (0-3 ppm), no effect on the microbial community structure was observed.…”