Application of Amplicon Pyrosequencing in Soil Microbial Ecology

Analysis of Microbial Diversity by Amplicon Pyrosequencing

Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness fo...

Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment

The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past ye...

Shedding Light on the Microbial Community of the Macropod Foregut Using 454-Amplicon Pyrosequencing

Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as 'shared' OTUS (i.e. p...

Microbial Ecology of Hydrocarbon Degradation in the Soil: A Review

Soil microbial assortment is affected by hydrocarbon perturbation, thus selective enrichment of hydrocarbon degraders occurs. Hydrocarbons interact with the terrestrial ecosystem and soil microorganisms shaping the fate of the contaminants relative to their chemical nature and microbial degradative capabilities, respectively. Microbial methods for monitoring bioremediation of hydrocarbons inclu...