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Ribosomal Database Project: data and tools for high throughput rRNA analysis
TLDR
RDP now includes a collection of fungal large subunit rRNA genes, and most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines. Expand
Microbial biogeography: putting microorganisms on the map
TLDR
Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity, but recent studies also dispute the idea that 'everything is everywhere'. Expand
Phylogenetic Specificity and Reproducibility and New Method for Analysis of Terminal Restriction Fragment Profiles of 16S rRNA Genes from Bacterial Communities
TLDR
An analytical procedure is developed that reduces variation and extracts a reproducible subset of data from replicate TRF profiles and can be used with other DNA fingerprinting techniques for microbial communities or microbial genomes. Expand
Assessment of Microbial Diversity in Four Southwestern United States Soils by 16S rRNA Gene Terminal Restriction Fragment Analysis
TLDR
The combined results demonstrate that TRF analysis is an excellent method for rapidly comparing the relationships between bacterial communities in environmental samples, however, for highly complex communities, the method appears unable to provide classical measures of relative community diversity. Expand
Wide Distribution and Diversity of Members of the Bacterial Kingdom Acidobacterium in the Environment
TLDR
Members of the Acidobacterium kingdom are as genetically and metabolically diverse, environmentally widespread and perhaps as ecologically important as the well-known Proteobacteria and gram-positive bacterial kingdoms. Expand
Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils
TLDR
Combining the genomic evidence with available culture traits, it is postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration. Expand
COMMUNITY AND ECOSYSTEM GENETICS: A CONSEQUENCE OF THE EXTENDED PHENOTYPE
TLDR
It is demonstrated that the extended phenotype can be traced from the individuals possessing the trait, to the community, and to ecosystem processes such as leaf litter decomposition and N mineralization, which provides a genetic framework for community structure and ecosystem processes. Expand
Small-Scale DNA Sample Preparation Method for Field PCR Detection of Microbial Cells and Spores in Soil
TLDR
A small-scale procedure to rapidly extract and purify DNA from soils was developed for in-the-field use and found that combining a hot-detergent treatment with bead mill homogenization gave the highest DNA yields from all three microbial cell types and provided DNA from the broadest range of microbial groups in a natural soil community. Expand
Acidobacteria Phylum Sequences in Uranium-Contaminated Subsurface Sediments Greatly Expand the Known Diversity within the Phylum
TLDR
Analysis of sequences from this study and public databases produced a revised and greatly expanded phylogeny of the Acidobacteria phylum consisting of 26 subgroups. Expand
Empirical and Theoretical Bacterial Diversity in Four Arizona Soils
TLDR
A simple approach to constructing theoretical null models of bacterial species abundance provides detailed descriptions of soil bacterial community structure that can be used to guide experimental design and estimate the required survey scale to document specified fractions of community diversity. Expand
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