Evaluation of subsampling-based normalization strategies for tagged high-throughput sequencing data sets from gut microbiomes.

Several subsampling-based normalization strategies were applied to different high-throughput sequencing data sets originating from human and murine gut environments. Their effects on the data sets' characteristics and normalization efficiencies, as measured by several β-diversity metrics, were compared. For both data sets, subsampling to the median rather than the minimum number appeared to improve the analysis.

Strategy for modular tagged high-throughput amplicon sequencing.

The use and validation of a strategy that allows a universal set of bar-coded sequencing primers to be appended to an amplified PCR product is described. The strategy allows a modular approach, in that the same bar code can be used with two or more target-specific primer sets, even simultaneously.

Microbial community differences between propionate-fed microbial fuel cell systems under open and closed circuit conditions.

We report the electrochemical characterization and microbial community analysis of closed circuit microbial fuel cells (CC-MFCs) and open circuit (OC) cells continuously fed with propionate as substrate. Differences in power output between MFCs correlated with their polarization behavior, which is related to the maturation of the anodophilic communities. The microbial communities residing in the biofilm growing on the electrode, biofouled cation-exchange membrane and anodic chamber liquor of OC-and CC-MFCs were characterized by restriction fragment length polymorphism screening of 16S rRNA gene clone libraries.

The introduction of genetically modified microorganisms designed for rhizoremediation induces changes on native bacteria in the rhizosphere but not in the surrounding soil.

A 168-day microcosms experiment was used to assess the possible functional and structural shifts occurring in the bacterial community of a site with a historical record of polychlorinated biphenyl (PCB) contamination, after the introduction of plants whose roots have been inoculated with genetically modified (GM) microorganisms, designed for rhizoremediation. Salix sp. plants were inoculated with two different GM Pseudomonas fluorescens strains or with their parental wild-type strain.

Changes in bacterial populations and in biphenyl dioxygenase gene diversity in a polychlorinated biphenyl-polluted soil after introduction of willow trees for rhizoremediation.

The aim of this study was to analyze the structural and functional changes occurring in a polychlorinated-biphenyl (PCB)-contaminated soil ecosystem after the introduction of a suitable host plant for rhizoremediation (Salix viminalis). We have studied the populations and phylogenetic distribution of key bacterial groups (Alpha- and Betaproteobacteria, Acidobacteria, and Actinobacteria) and the genes encoding iron-sulfur protein alpha (ISPalpha) subunits of the toluene/biphenyl dioxygenases in soil and rhizosphere by screening gene libraries using temperature gradient gel electrophoresis. The results, based on the analysis of 415 clones grouped into 133 operational taxonomic units that were sequence analyzed (>128 kbp), show that the rhizospheric bacterial community which evolved from the native soil community during the development of the root system was distinct from the soil community for all groups studied except for the Actinobacteria.