Horizontal Heterogeneity of Denitrifying Bacterial Communities in Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis

Abstract

Although it is widely believed that horizontal patchiness exists in microbial sediment communities, determining the extent of variability or the particular members of the bacterial community which account for the observed differences among sites at various scales has not been routinely demonstrated. In this study, horizontal heterogeneity was examined in time and space for denitrifying bacteria in continental shelf sediments off Tuckerton, N.J., at the Rutgers University Long-Term Ecosystem Observatory (LEO-15). Characterization of the denitrifying community was done using PCR amplification of the nitrous oxide reductase (nosZ) gene combined with terminal restriction fragment length polymorphism analysis. Spatial scales from centimeters to kilometers were examined, while temporal variation was assayed over the course of 1995 to 1996.

Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils

“…Experiments using other denitrification gene markers confirm that denitrifier gene communities tend to be unique to the environment from which they are sampled, with few genotypes shared between locations (Braker et al, 2000(Braker et al, , 2001. Large variations in nosZ TRF distribution at distances of centimeters, meters and especially kilometers has also been found in marine studies, which is consistent with observations that terrestrial denitrifier genotypes are strongly structured by site (Scala and Kerkhof, 2000). It is also important to note that large seasonal shifts have been detected in both terrestrial (Wolsing and Priemé, 2004) and marine (Scala and Kerkhof, 2000) denitrifying communities and that this study examined samples taken only once during the summer growing season.…”

“…Large variations in nosZ TRF distribution at distances of centimeters, meters and especially kilometers has also been found in marine studies, which is consistent with observations that terrestrial denitrifier genotypes are strongly structured by site (Scala and Kerkhof, 2000). It is also important to note that large seasonal shifts have been detected in both terrestrial (Wolsing and Priemé, 2004) and marine (Scala and Kerkhof, 2000) denitrifying communities and that this study examined samples taken only once during the summer growing season. Detection of seasonal variation in denitrifying gene community structure (due directly or indirectly to temperature manipulations) depends to some extent on the timing and frequency of sampling, plus the molecular technique and gene marker employed.…”

Community Structure of Denitrifiers, Bacteria , and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase ( nirS ) and 16S rRNA Genes

“…It has been shown to be semiquantitative (20) and generates fingerprints of precise sizes that are reproducible in their T-RF patterns and peak heights from replicate samples (28, 30) with a level of resolution similar to that of denaturing gradient gel electrophoresis (24). When we analyzed the nirS T-RFLP reproducibility of two samples, patterns derived from different DNA extracts, PCR amplifications, and restriction hydrolysis were virtually identical, in agreement with published results (28,30). Peak height as a meaningful measure of gene abundance is supported by a positive correlation of relative T-RF abundance and quantitative dot blot hybridization of Ro- seobacter sp.-specific 16S rDNAs in a marine algal bloom (17).…”

“…To more systematically explore bacterial communities on a functional level, PCR-amplified functional genes such as nirS genes can be used with subsequent T-RFLP analysis. This has been demonstrated for mercury resistance (mer) genes (6), ammonia monooxygenase (amoA) genes (19), and nosZ, which encodes nitrous oxide reductase (30).…”

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

“…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. There is a growing body of empirical studies examining the spatial distribution of genetic diversity in the soil at a range of spatial scales from micrometers to kilometers [3,8,20,25,48,56,69).…”