Biomedical Engineering Reference
In-Depth Information
2.6 PHYLOGENY OF
DEHALOCOCCOIDES
AND RELATED BACTERIA
The analysis of the 16S rRNA gene sequence of
Dhc
strain 195 showed that it was affiliated
with the domain
Bacteria
, but this phylogenetic marker was distantly related to other sequences
deposited in the GenBank database in 1997. Soon after, 16S rRNA gene sequences from
uncultured organisms (i.e., environmental clone sequences) appeared in the database and
these led to the affiliation of strain 195 with the phylum
Chloroflexi
(green non-sulfur bacteria).
This bacterial phylum is poorly characterized and encompasses a phylogenetically diverse
collection of 16S rRNA gene sequences, yet it is represented by remarkably few isolates
(Hugenholtz et al.,
1998b
) Figure
2.3
illustrates the two main
Chloroflexi
lineages, one of
which includes both the
Thermomicrobia
and the classical
Chloroflexus aurantiacus
isolate, the
namesake of the group (Hugenholtz and Stackebrandt,
2004
).
“Traditional”
Chloroflexi
in the
Thermomicrobium
/
Chloroflexus
branch are not known to
catalyze reductive dechlorination. The other branch leads to three lineages, including the
Anaerolinea
(which includes sludge isolates and environmental clone sequences from subsur-
face, marine, and aquatic habitats), the SAR202 cluster of marine
Chloroflexi
, and the
Dhc
(and related obligate dechlorinators) (Hugenholtz et al.,
1998a
; Hugenholtz and Stackebrandt,
2004
; Morris et al.,
2004
). The phylogenetic branch leading to the
Dhc
is deeply rooted,
suggesting an ancient origin of this unusual bacterial group and possibly the reductive
dechlorination process.
In studies using PCR primers targeting
Dhc
16S rRNA genes, it soon became evident that
Dhc
were present in microcosms that dechlorinated PCE or TCE to ethene and were associated
with sites where reductive dehalogenation of PCE and TCE to VC and ethene was occurring
(Fennell et al.,
2001
;L¨ffler et al.,
2000
). An extensive survey of sites contaminated with
chlorinated ethenes in North America and Europe corroborated the correlation between the
presence of
Dhc
16S rRNA genes and dehalogenation products past DCE (i.e., VC and ethene)
(Hendrickson et al.,
2002
). These findings have since been observed worldwide and
Dhc
have
always been detected when DCE and VC dechlorination to ethene occurred. Apparently, the
ability to reductively dechlorinate DCEs and VC is not widespread among the bacterial domain
and may in fact be limited to select members of the
Dhc
group.
Members of the
Dhc
group possess highly similar 16S rRNA gene sequences, sharing
greater than 98% sequence identity (Cupples,
2008
; Ritalahti et al.,
2006
). Within this tight
cluster, Hendrickson et al. (
2002
) distinguished three phylogenetic subgroups of
Dhc
: the
“Cornell” subgroup that includes strain 195, the “Victoria” subgroup that includes strain VS,
and the “Pinellas” subgroup, which comprises most of the cultured
Dhc
strains and isolates as
well as the majority of the environmental clone sequences. The “Pinellas” cluster includes the
chloroethene-dechlorinating
Dhc
strains BAV1, FL2 and GT and KB-1VC (Duhamel and
Edwards,
2006
; He et al.,
2003b
,
2005
; Sung et al.,
2006b
), the 1,2-dichloropropane- dechlor-
inating
Dhc
strains KS1 and RC1 (Ritalahti and L¨ffler,
2004a
) as well as the chlorobenzene-
dechlorinating
Dhc
strain CBDB1 (Adrian et al.,
2000b
), and
Dhc
strains that dechlorinate PCBs
(Adrian et al.,
2009
; Bedard et al.,
2006
,
2007
; Bedard,
2008
). Members of the “Pinellas” group
share identical or highly similar (1-3 nucleotide differences) 16S rRNA gene sequences, and 14-
16 and 23-24 bases distinguish the 16S rRNA genes of members of the Pinellas subgroup from
members of the Victoria and Cornell subgroups, respectively (He et al.,
2003a
; Hendrickson
et al.,
2002
). The phylogenetic grouping into three subgroups has endured as additional
Dhc
16S
rRNA gene sequences have accumulated.
A survey of 117 nearly full-length (
1,400 bases)
Dhc
16S rRNA sequences deposited in the
GenBank database (April 2009) showed that 77 sequences were affiliated with the Pinellas
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