Transcriptomics

Dataset Information

3

PhyloChip-based characterization of wastewater reactors


ABSTRACT: We developed a laboratory-scale model to improve our understanding and capacity to assess the biological risks of genetically engineered bacteria and their genetic elements in the natural environment. Our hypothetical scenario concerns an industrial bioreactor failure resulting in the introduction of genetically engineered bacteria to a downstream municipal wastewater treatment plant (MWWTP). As the first step towards developing a model for this scenario, we sampled microbial communities from the aeration basin of a MWWTP at three seasonal time points. Having established a baseline for community composition, we investigated how the community changed when propagated in the laboratory, including cell culture media conditions that could provide selective pressure in future studies. Specifically, using PhyloChip 16S rRNA gene-targeting microarrays, we compared the compositions of sampled communities to those of inoculates propagated in the laboratory in simulated wastewater conditionally amended with various carbon sources (glucose, chloroacetate, D-threonine) or the ionic liquid 1-ethyl-3-methylimidazolium chloride ([C2mim]Cl). Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in aeration basin and laboratory-cultured populations. Laboratory-cultured populations were enriched in Gammaproteobacteria. Enterobacteriaceae and Aeromonadaceae were enriched by glucose, Pseudomonadaceae by chloroacetate and D-threonine, and Burkholderiaceae by high (50 mM) concentrations of chloroacetate. Microbial populations cultured with chloroacetate and D-threonine were more similar to sampled populations than thoes cultured with glucose or [C2mim]Cl. Although observed relative richness in operational taxonomic units was lower for laboratory cultures than for sampled populations, both flask and reactor systems cultured phylogenetically diverse communities. These results importantly provide a foundation for laboratory models of industrial bioreactor failure scenarios. 46 samples, flask and reactor experiments were conducted in triplicate with two exceptions: [C2mim]Cl_flask and No-Carbon_flask treatments had only one sample (no replicates).

ORGANISM(S): mixed sample  

SUBMITTER: Cindy H Wu   Yvette M Piceno  Francine C Reid  Adam P Arkin  Terry C Hazen  Tamas Torok  Daniel R Tarjan  Mary Singer  Sangwon Lee  Nathan J Hillson  Jil T Geller 

PROVIDER: E-GEOD-58251 | ArrayExpress | 2014-06-06

SECONDARY ACCESSION(S): GSE58251PRJNA251735

REPOSITORIES: GEO, ArrayExpress

Similar Datasets

| GSE58251 | GEO
2014-12-03 | E-GEOD-63781 | ArrayExpress
| GSE52079 | GEO
| GSE81263 | GEO
2013-10-18 | E-GEOD-44411 | ArrayExpress
2014-01-15 | E-GEOD-54055 | ArrayExpress
2013-08-24 | E-GEOD-50164 | ArrayExpress
2015-01-23 | E-MTAB-3041 | ArrayExpress
2013-12-10 | E-MEXP-3851 | ArrayExpress
2008-03-22 | GSE9221 | GEO