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

Abstract

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.

Metagenomic analysis of a stable trichloroethene-degrading microbial community

“…The complement of RDase genes varies greatly between strains and corresponds to variation in dechlorination abilities (Kube et al, 2005;Seshadri et al, 2005;McMurdie et al, 2009;Lee et al, 2011). Further, the suite of Dhc RDase genes that have been tied to functional activity are far fewer, currently numbering six in all (pceA, tceA, vcrA, bvcA, cbrA and mbrA) (Magnuson et al, 1998(Magnuson et al, , 2000KrajmalnikBrown et al, 2004;Mü ller et al, 2004;Adrian et al, 2007;Chow et al, 2010).…”

“…Previously sequenced Dhc strains have genes encoding for enzymes in the second part of the cobalamin biosynthesis pathway, lower ligand attachment and rearrangement (Maymó -Gatell et al, 1997;Kube et al, 2005;McMurdie et al, 2009), but not for the first part of the pathway, corrin ring synthesis. Even when Dhc isolates are provided sufficient hydrogen, acetate and cobalamin, they do not grow or dechlorinate as robustly as when grown in mixed communities or defined consortia (He et al, 2007;Lee et al, 2011;Men et al, 2012).…”

“…This culture was derived from sediment collected at the Alameda Naval Air Station and is referred to as ANAS (Richardson et al, 2002). The phylogenetic composition of ANAS has been studied using clone libraries (Richardson et al, 2002;Lee et al, 2006), and the Dhc strains in ANAS have been analyzed using quantitative PCR and whole-genome microarrays West et al, 2008;Lee et al, 2011). ANAS contains two Dhc strains, which have recently been isolated Lee et al, 2011).…”

“…The phylogenetic composition of ANAS has been studied using clone libraries (Richardson et al, 2002;Lee et al, 2006), and the Dhc strains in ANAS have been analyzed using quantitative PCR and whole-genome microarrays West et al, 2008;Lee et al, 2011). ANAS contains two Dhc strains, which have recently been isolated Lee et al, 2011). A comparative genomics analysis showed these strains to have very similar core genomes, but different RDase genes, with correspondingly different dechlorination abilities (Lee et al, 2011).…”

“…ANAS contains two Dhc strains, which have recently been isolated Lee et al, 2011). A comparative genomics analysis showed these strains to have very similar core genomes, but different RDase genes, with correspondingly different dechlorination abilities (Lee et al, 2011).…”