Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray

• Published in: The ISME Journal Vol. 5; no. 6; pp. 1014 - 1024
• Main Authors: Lee, Patrick K H, Cheng, Dan, Hu, Ping, West, Kimberlee A, Dick, Gregory J, Brodie, Eoin L, Andersen, Gary L, Zinder, Stephen H, He, Jianzhong, Alvarez-Cohen, Lisa
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.06.2011; Oxford University Press; Nature Publishing Group
• Subjects: 631/326/252/58; 631/326/2565/855; 631/326/41/2095; 631/61/212/748; Anas; Base Sequence; Biomedical and Life Sciences; Chloroflexi - classification; Chloroflexi - genetics; Chloroflexi - isolation & purification; Chloroflexi - metabolism; Dechlorination; Dehalococcoides; Deoxyribonucleic acid; DNA; DNA probes; Ecology; Enrichment; ethene; Ethylenes - metabolism; Evolutionary Biology; Genome, Bacterial; Genomic analysis; Genomics; Genomics - methods; Life Sciences; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis; Original; original-article; Phylogeny; Physiology; Plasticity; Tetrachloroethylene; Tetrachloroethylene - metabolism; Trichloroethylene; Trichloroethylene - metabolism; Vinyl chloride; Vinyl Chloride - metabolism; systems biology; microarray; bioremediation; chlorinated solvents; comparative genomics
• ISSN: 1751-7362; 1751-7370; 1751-7370
• DOI: 10.1038/ismej.2010.202

Comparative genomics of Dehalococcoides strains and an enrichment were performed using a microarray targeting genes from all available sequenced genomes of the Dehalococcoides genus. The microarray was designed with 4305 probe sets to target 98.6% of the open-reading frames from strains 195, CBDB1, BAV1 and VS. The microarrays were validated and applied to query the genomes of two recently isolated Dehalococcoides strains, ANAS1 and ANAS2, and their enrichment source (ANAS) to understand the genome–physiology relationships. Strains ANAS1 and ANAS2 can both couple the reduction of trichloroethene, cis- dichloroethene (DCE) and 1,1-DCE, but not tetrachloroethene and trans- DCE with growth, whereas only strain ANAS2 couples vinyl chloride reduction to growth. Comparative genomic analysis 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 or high-plasticity regions. Combined results of the two isolates closely matched the results obtained using genomic DNA of the ANAS enrichment. 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 seems to be related to the presence of distinct reductive dehalogenase-encoding genes with assigned chlorinated ethene functions ( pceA , tceA in strain 195; tceA in strain ANAS1; vcrA in strain ANAS2). Overall, the microarrays are a valuable high-throughput tool for comparative genomics of unsequenced Dehalococcoides -containing samples to provide insights into their gene content and dechlorination functions.