Title: The design and validation of a Dehalococcoides genus microarray and its application to two newly isolated Dehalococcoides strains for comparative genomics

Accession Number: GSE23707

Link to Dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23707

Repository: Gene Expression Omnibus (GEO)

Data Type(s): Gene Expression

Experiment Type(s): Genome variation profiling by array

Organism(s): Dehalococcoides

Summary: The chlorinated ethene-respiring bacteria of the genus Dehalococcoides are important for bioremediation. A microarray targeting genes from all available sequenced genomes of the Dehalococcoides genus was designed with 4305 probe sets to target 98.6 of all genes from strains 195, CBDB1, BAV1, and VS. The microarrays were validated with genomic DNA (gDNA) of strains 195 and BAV1 and satisfactory analytical reproducibility, quantitative response and gene detection accuracy were obtained. These microarrays were applied to query the genomes of two recently isolated Dehalococcoides strains, ANAS1 and ANAS2. Strains ANAS1 and ANAS2 can both couple the reduction of TCE, cDCE and 1,1-DCE but not PCE and tDCE with growth while only strain ANAS2 couples VC reduction to growth. Analysis of the respective gDNA using the microarrays showed that the genomes of both strains are similar to each other and to strain 195, except for genes that are within the previously defined integrated elements (IEs) or high plasticity regions (HPRs). Similar results to the combined isolates were obtained when gDNA of ANAS, the enrichment culture from which the two Dehalococcoides isolates originated, was applied to the microarrays. The genome similarities, together with the distinct chlorinated ethene usage of strains ANAS1, ANAS2 and 195 demonstrate that closely phylogenetically related strains can be physiologically different. This incongruence between physiology and core genome phylogeny appears to be driven by the presence of distinct reductive dehalogenase (RDase)-encoding genes with characterized chlorinated ethene functions (pceA, tceA in strain 195; tceA in strain ANAS1; vcrA in strain ANAS2). Genes encoding central metabolic functions of strain 195 were all detected in strains ANAS1 and ANAS2, while interestingly, the tryptophan operon of these strains is similar to that of strain VS. Overall, the microarrays are a valuable high-throughput tool for comparative genomics of un-sequenced Dehalococcoides-containing samples.

Publication(s) associated with this dataset:

• Lee PH, Cheng D, Hu P, West KA, Dick GJ, Brodie EL, Andersen GL, Zinder SH, He J, Alvarez-Cohen L. 2011. Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. ISME J 5(6):1014-1024. doi:10.1038/ismej.2010.202 PMID:21228894 PMCID:PMC3131851