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 and Resource Factors Influencing High Microbial Diversity in Soil

http://www.vliz.be/imisdocs/publications/72119.pdf

Stable isotopes and biomarkers in microbial ecology

Measuring stable isotope fractionation of carbon, hydrogen, and other elements by Compound Specific Isotope Analysis (CSIA) is a new, innovative approach to assess organic pollutant degradation in the environment. Central to this concept is the Rayleigh equation which relates degradation-induced decreases in concentrations directly to concomitant changes in bulk (= average over the whole compound) isotope ratios. The extent of in situ transformation may therefore be inferred from measured isotope ratios in field samples, provided that an appropriate enrichment factor (ebulk) is known. This ebulk value, however, is usually only valid for a specific compound and for specific degradation conditions. Therefore, a direct comparison of ebulk values for different compounds and for different types of reactions has in general not been feasible. In addition, it is often uncertain how robust and reproducible ebulk values are and how confidently they can be used to quantify contaminant degradation in the field. To im...

/pdf/a-new-concept-linking-observable-stable-isotope-2dkfmbda8m.pdf

A new concept linking observable stable isotope fractionation to transformation pathways of organic pollutants.

▪ Abstract The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been the likely driving force for the evolution of an unexpectedly high microbial capacity to dehalogenate different classes of xenobiotic haloorganics. This contribution provides an update on the current knowledge on metabolic and phylogenetic diversity of anaerobic microorganisms that are capable of dehalogenating—or completely mineralizing—halogenated hydrocarbons by fermentative, oxidative, or reductive pathways. In particular, research of the past decade has focused on halorespiring anaerobes, which couple the dehalogenation by dedicated enzyme systems to the generation of energy by electron transport–driven phosphorylation. Significant advances in the biochemistry and molecular genetics of degradation pathways have revealed mechanistic and structural similarities between dehalogenating enzymes from phylogenetically distinct anaerobes. The availability of two almost complete genome sequenc...

Anaerobic microbial dehalogenation.

Stable isotope fractionation analysis as a tool to monitor biodegradation in contaminated acquifers.

Area 6 at Dover Air Force Base (Dover, DE) has been the location of an in-depth study by the RTDF (Remediation Technologies Development Forum Bioremediation of Chlorinated Solvents Action Team) to evaluate the effectiveness of natural attenuation of chlorinated ethene contamination in groundwater. Compound-specific stable carbon isotope measurements for dissolved PCE and TCE in wells distributed throughout the anaerobic portion of the plume confirm that stable carbon isotope values are isotopically enriched in 13C consistent with the effects of intrinsic biodegradation. During anaerobic microbial reductive dechlorination of chlorinated hydrocarbons, the light (12C) versus heavy isotope (13C) bonds are preferentially degraded, resulting in isotopic enrichment of the residual contaminant in 13C. To our knowledge, this study is the first to provide definitive evidence for reductive dechlorination of chlorinated hydrocarbons at a field site based on the δ13C values of the primary contaminants spilled at the s...

J. Spivack

Papers

Stable carbon isotope evidence for intrinsic bioremediation of tetrachloroethene and trichloroethene at area 6, Dover Air Force Base

Contrasting carbon isotope fractionation during biodegradation of trichloroethylene and toluene: Implications for intrinsic bioremediation