Biomedical Engineering Reference
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identified at many geographically-diverse contaminated and uncontaminated sites, and have
been successfully enriched from soil microcosms to liquid culture in several laboratories.
Several isolates of Dehalococcoides spp. have been obtained, and complete genome
sequences are currently available for five strains (strains 195, CBDB1, BAV1, VS, and GT)
(Kube et al., 2005 ; McMurdie et al., 2009 ; Seshadri et al., 2005 ; Frank L¨ffler 2009, University
of Tennessee, personal communication). Metagenome sequences of Dehalococcoides -contain-
ing cultures are available for three cultures: DonnaII, KB-1 # , and ANAS (publicly available
through the Joint Genomes Institute) (Duhamel et al., 2004 ; Fennell et al., 1997 ; West
et al., 2008 ).
The depth of information available for the Dehalococcoides , while still incomplete, represents
an abnormally high level of characterization compared to the rest of the bacterial phylum
Chloroflexi, of which Dehalococcoides represents a relatively deep-branching group (Figure 12.1 ).
The 16S ribosomal ribonucleic acid ( rRNA) gene diversity within the Dehalococcoides ranges
from 98% to 100% nucleotide identity, indicating that all currently isolated strains are extremely
closely related evolutionarily despite their relatively diverse substrate profiles. The ubiquity of
the Dehalococcoides as dechlorinating organisms identified at contaminated sites and the
close genomic conservation seen within the group may be evidence of an extremely restricted
group filling a specific niche, or may be an artifact of shared culture and isolation techniques
uncultured bacterium SJA-170 (AJ009500)
Anaerolinea thermophila (AB046413)
uncultured eubacterium H1.43.f (AF005749)
uncultured bacterium SHA-21 (AJ249103)
uncultured bacterium a2b042 (AF419664)
Caldilinea aerophila
(AB067647)
Kouleothrix aurantiaca (AB079639)
Roseiflexus castanholzii
(AB041226)
C. aurantiacus (CFXRRDA)
H. aurantiacus
(HESRRDA)
D. radiodurans (DEIRGDA)
T. roseum
(THRRRDA)
uncultured bacterium clones (3)
uncultured bacterium clones (2)
BL-DC-8 (EU679418)
Dehalogenimonas lykanthroporepellens BL-DC-9 (EU679419)
Dehalogenimonas lykanthroporepellens
Dehalococcoides spp. (9)
Dehalobium chlorocoercia (AF005750)
PCB-dechlorinating bacterium (AY559064)
uncultured bacterium clones (7)
unidentified eubacterium clone vadinBA26 (UEU81649)
uncultured bacterium clone (AY093458)
0.1
Figure 12.1. Maximum likelihood phylogeny of the known 16S rRNA diversity within the
phylum Chloroflexi, including representative environmental clones. Cultured strains are labeled
in black while environmental clones are in grey. Species sharing high sequence similarity (
95%)
have been condensed into wedges, where the depth of the wedge represents the average length of
the condensed branches. Numbers after the wedge labels indicate the number of branches
condensed.
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