DEHALOCOCCOIDES AND REDUCTIVE DECHLORINATION OF CHLORINATED SOLVENTS - Bioaugmentation for Groundwater Remediation - page 60

Considering that there are presently hundreds of thousands of nearly complete bacterial 16S rRNA
gene sequences collected fromdiverse habitats in publicly accessible databases, it is striking that no
“transitional” organisms between Dhc and their non-dechlorinating relatives are present in this
collection.
2.7 DEHALOCOCCOIDES GENETICS
2.7.1 Insights from Dehalococcoides Genomes
The genomes of Dhc strains 195, CBDB1, BAV1, VS and GT have been sequenced and the
genome analysis revealed many interesting features. Dhc have circular chromosomes of 1.3 to
1.5 mega (10 6 ) bases (Mb) in length. These are among the smallest genomes known for free-
living organisms (for comparison, Escherichia coli genomes are at least three times larger),
indicative of genome streamlining and specialization (Giovannoni et al., 2005 ). Comparative
genome analyses demonstrated that Dhc share essentially identical sets of core “housekeeping”
genes for cellular functions like biosynthesis of amino acids and other cellular components,
transcription and translation, nutrient transport, and energy conservation. Further, these core
genes are organized in the same order (synteny) in all of the sequenced Dhc genomes. This
conservation of gene sequence and synteny in Dhc genomes of isolates that were obtained from
geographically distinct locations is remarkable and differs from the findings with other
bacterial groups such as closely related Shewanella strains (Konstantinidis et al., 2006 ).
This highly conserved and stable Dhc genome core is interrupted by High Plasticity Regions
(HPRs) near the origin of replication (ori) (Figure 2.4 ). These HPRs differ noticeably from the
rest of the genome and show signs of extensive genomic rearrangements including insertions,
deletions and inversions. Contained in these HPRs are distinct genomic islands, in which
RDase, transposase, and phage integrase as well as hypothetical genes are noticeably overrep-
resented (Kube et al., 2005 ; McMurdie et al., 2009 ).
A total of 96 putative RDase genes are present on the genomes of strains 195 (17 genes),
CBDB1 (32 genes), BAV1 (11 genes), and VS (36 genes), and 91 of them are located in HPRs.
The reasons for this highly localized genome plasticity, and its consequences, are currently
unresolved but obviously of great interest because these HPRs contain the majority of the
genomic islands with the (putative) RDase genes. It should be noted that bvcA , a gene
implicated in VC dechlorination in strain BAV1, is embedded in a genomic island located
outside an HPR suggesting that RDase genes implicated in reductive dechlorination are not
limited to the HPRs (McMurdie et al., 2009 ).
The first characterized Dhc RDase gene was tceA (Magnuson et al., 2000 ) encoding a
TCE-to-VCRDase. The tceA gene is located within an integrated genetic element (i.e., a genomic
island) on the genome of strain 195, suggesting that this gene had been acquired via horizontal
gene transfer from another organism (Seshadri et al., 2005 ). When chromosome walking was
applied to examine the extragenic regions flanking the tceA genes in several TCE-dechlorinating
Dhc strains, similar sequences of variable length and flanked by insertion sequences were found
upstream and downstream of the tceA genes (Krajmalnik-Brown et al., 2007 ).
The presence of highly similar RDase genes (e.g., tceA )in Dhc strains from geographically
distinct origins suggests that horizontal gene transfer (HGT) events between Dhc are not
uncommon and contribute to RDase gene dissemination. The bvcA gene of strain BAV1 and
the vcrA genes of strains VS and GT also reside in regions flanked by mobile genetic elements.
Compared to other genes on Dhc genomes, these VC RDase genes display an unusual bias
towards the nucleotide T in the third position of the codons (triplets of nucleotides that code for
specific amino acids) suggestive that these genes were horizontally acquired from a foreign