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Applied and Environmental Microbiology, February 2001, p. 1020-1022, Vol. 67, No. 2
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.2.1020-1022.2001
LETTERS TO THE EDITOR
Trichlorobacter thiogenes Should Be Renamed as a
Geobacter Species
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LETTER |
In a recent paper by De Wever et al. (2), it is
proposed that the recently isolated microorganism strain K1 be assigned to a new genus within the delta Proteobacteria. Those
authors state that the 16S ribosomal DNA (rDNA) sequence of strain K1 places it within a "cluster of mixed taxonomic affiliation" within the delta Proteobacteria. From this statement it is apparent
that De Wever et al. (2) are unaware of several previous
phylogenetic analyses of this group within the delta
Proteobacteria, most notably, a study by Lonergan et al.
(5). As De Wever et al. (2) note, the 16S
rDNA sequence of strain K1 is nearly identical (99% sequence identity)
to a 16S rDNA sequence recovered from a bioreactor that they
misidentify as "environmental sp. 2" but that is actually an
environmental sequence first described as a population type 1 sequence
(Desulfuromonas-like sp.) (1) and listed by
both GenBank and the Ribosomal Database Project (RDP) II
(9) release 7.1 as Desulfuromonas sp.
(GenBank accession number M80618). If De Wever et al. (2)
had known about the study by Lonergan et al. (5), they
would have realized that detailed analysis of this sequence has
demonstrated that it rests squarely within the Geobacter
cluster of the family Geobacteraceae (5). Our own analysis of the strain K1 sequence confirms not only that the
overall sequence of strain K1 is closely related to organisms in the
Geobacter cluster (Fig. 1) but also that the sequence
contains the signature secondary structures characteristic of the
Geobacter cluster (5).
At this time, the Geobacter cluster contains only one
organism, Pelobacter propionicus, that does not have the
genus designation Geobacter (Fig.
1). There are four more species of
Pelobacter within the Geobacteraceae family, but
these other Pelobacter species are interspersed throughout
two other genera outside the Geobacter cluster. Thus, it is
clear that the genus Pelobacter is not phylogenetically coherent and that organisms in the Geobacter cluster cannot
be renamed Pelobacter as this would result in organisms of
different phylogenetic clusters being placed within the same genus. It
has been suggested that the simplest way to avoid confusion with the phylogeny is to place P. propionicus in the genus
Geobacter (5).
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FIG. 1.
Phylogenetic tree inferred from 16S rRNA sequences
showing the phylogenetic placement of "Trichlorobacter
thiogenes" strain K1. Phylogenetic relationships shown here were
inferred by using neighbor joining and Kimura two-parameter genetic
distances in TREECON (10). Bootstrap values above 60 are
shown adjacent to branch nodes and were calculated from 100 resampled
data sets using neighbor joining. The scale bar shows the number of
expected nucleotide substitutions per site per unit of branch length.
Operational taxonomic units shown on the tree were obtained from
GenBank and the RDP databases. A similar tree topology was generated
for trees constructed using maximum-likelihood and maximum-parsimony
methods (data not shown).
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Therefore, designation of strain K1 as a new genus within the
Geobacter cluster, as suggested by De Wever et al.
(2), creates havoc within an otherwise logical grouping of
organisms, comprised of predominantly a single genus within a
phylogenetically coherent cluster. Designation of a new genus might be
warranted if strain K1 had some unique physiological characteristics
that distinguished it from previously described Geobacter
species, but this does not appear to be the case. Strain K1 uses
acetate as an electron donor for the reduction of S0 and
fumarate, and it has been suggested that it might also use Fe(III) as
an electron acceptor (2). The oxidation of acetate coupled
to the reduction of S0 and Fe(III) is one of the defining
physiological characteristics of Geobacter species, and many
Geobacter species can also use fumarate as an electron
acceptor for acetate oxidation (6, 7, 8). Strain K1 does
reductively dechlorinate trichloroacetic acid, a physiological capacity
not previously reported for Geobacter species. However, to
our knowledge, no other organisms in the Geobacter cluster
have been evaluated for the ability to carry out this reaction.
Therefore, it is not clear that strain K1 is unique among organisms in
the Geobacter cluster in this ability. Furthermore, De Wever
et al. (2) suggest that at least part of the reductive
dechlorination observed with strain K1 is the result of strain K1
reducing S0 to sulfide, with the subsequent reduction of
the trichloroacetic acid by sulfide. Since all organisms in the
Geobacter cluster have the ability to reduce S0
to sulfide, it is likely that all Geobacter species have the ability to dechlorinate trichloroacetic acid via this electron shuttling mechanism.
Furthermore, even if all the organisms in the Geobacter
cluster other than strain K1 were found to not be able to reductively dechlorinate trichloroacetic acid, precedence suggests that the designation of a new genus would not be warranted. When the first organism in the Desulfuromonas cluster of the
Geobacteraceae found to have the ability to carry out
reductive dechlorination was described (4), it was not
assigned to a new genus; rather, it was designated a new species in the
genus Desulfuromonas (3). This is consistent
with the concept of not cluttering phylogenetically coherent groups
with multiple genus designations.
In summary, designating strain K1 as a new genus in the
Geobacter cluster at this time advances neither clarity in
phylogeny or understanding of physiology. It is suggested that, once
the characterization of the physiology of strain K1 is completed, it be
designated a new species in the genus Geobacter.
| |
REFERENCES |
| 1.
|
Amann, R. I.,
J. Stromley,
R. Devereux,
R. Key, and D. A. Stahl.
1992.
Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms.
Appl. Environ. Microbiol.
58:614-623[Abstract/Free Full Text].
|
| 2.
|
De Wever, H.,
J. R. Cole,
M. R. Fettig,
D. A. Hogan, and J. M. Tiedje.
2000.
Reductive dehalogenation of trichloroacetic acid by Trichlorobacter thiogenes gen. nov., sp. nov.
Appl. Environ. Microbiol.
66:2297-2301[Abstract/Free Full Text].
|
| 3.
|
Krumholz, L. R.
1997.
Desulfuromonas chloroethenica sp. nov. uses tetrachloroethylene and trichloroethylene as electron acceptors.
Int. J. Syst. Bacteriol.
47:1262-1263[Abstract/Free Full Text].
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| 4.
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Krumholz, L. R.,
R. Sharp, and S. S. Fishbain.
1996.
A freshwater anaerobe coupling acetate oxidation to tetrachloroethylene dehalogenation.
Appl. Environ. Microbiol.
62:4108-4113[Abstract].
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| 5.
|
Lonergan, D. J.,
H. Jenter,
J. D. Coates,
E. J. P. Phillips,
T. Schmidt, and D. R. Lovley.
1996.
Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria.
J. Bacteriol.
178:2402-2408[Abstract/Free Full Text].
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| 6.
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Lovley, D. R.
2000.
Fe(III) and Mn(IV) reducing prokaryotes, p. 1-47.
In
M. Dworkin, S. Falkow, M. Rosenberg, and E. Stackebrandt (ed.), The prokaryotes. Springer-Verlag, New York, N.Y.
|
| 7.
|
Lovley, D. R.
2000.
Fe(III) and Mn(IV) reduction, p. 3-30.
In
D. R. Lovley (ed.), Environmental microbe-metal interactions. ASM Press, Washington, D.C.
|
| 8.
|
Lovley, D. R.,
J. D. Coates,
D. A. Saffarini, and D. J. Lonergan.
1997.
Dissimilatory iron reduction, p. 187-215.
In
G. Winkelman, and C. J. Carrano (ed.), Iron and related transition metals in microbial metabolism. Harwood Academic Publishers, Geneva, Switzerland.
|
| 9.
|
Maidak, B. L.,
J. R. Cole,
J. Charles,
T. Parker,
G. M. Garrity,
N. Larsen,
B. Li,
T. G. Lilburn,
M. J. McCaughey,
G. J. Olsen,
R. Overbeek,
S. Pramanik,
T. M. Schmidt,
J. M. Tiedje, and C. R. Woese.
1999.
A new version of the RDP (Ribosomal Database Project).
Nucleic Acids Res.
27:171-173[Abstract/Free Full Text].
|
| 10.
|
Van de Peer, Y., and Y. De Wachter.
1994.
TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment.
Comput. Appl. Biosci.
10:569-570[Free Full Text].
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| | | | |
Oona Snoeyenbos-West
Catherine Gaw Van Praagh
Derek R. Lovley
Department of Microbiology
University of Massachusetts
203 Morrill Science Center IVN
Box 35720
Amherst, Massachusetts 01003-5720
Phone: (413) 545-2051
Fax: (413) 545-1578
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| |
AUTHORS' REPLY |
The genus Geobacter has only two species with standing in
bacterial nomenclature: G. metallireducens and G. sulfurreducens. According to the rules of the International Code
of Nomenclature of Bacteria, neither the two additional
Geobacter species from Lonergan et al. (2),
nor the other four Geobacter species in Fig. 1, nor the
proposed family name "Geobacteraceae" from Lonergan et
al. has been validly published. Therefore, according to the Code, they
have no standing. In fact, we are unable to find even a GenBank
sequence record for "G. hummireducens" or "G.
bemidjiensis", and the GenBank rRNA records for "G.
arculus" and "G. akanganitreducens" indicate that
they are unpublished! A quick search of Medline drew a blank for all
four species. In any event, the Code is clear; validation of a name or
new combination is the responsibility of the name's author.
The "Geobacter cluster" contains only three valid
species: Pelobacter propionicus and the two
Geobacter species. From phylogenetic analysis, strain K1 is
most closely related to P. propionicus (94% rRNA sequence
similarity), while the two species of Geobacter form a
separate cluster (92 and 93% similarity to K1). Although 16S rRNA
similarity should not be used as the sole criterion for division of
taxa, these values are well within the range of differences seen for
related genera.
We are not sure about the relevance of the name we used for the
Desulfuromonas-like bioreactor sequence (GenBank accession number M80618), but the original publication states that "the GenBank
accession numbers for population type 1 and population type 2 partial
16S rRNA sequences are, respectively, M80617 and M80618"
(1). In addition, the RDP annotates their corresponding record as "population type 2."
We were aware of the work of Lonergan et al. (2). In fact,
we included the 16S sequences for their two proposed
Geobacter species in our analysis. If we offended by not
citing that work, we apologize but note in partial defense that the
practice of referencing sequences by GenBank accession number as
opposed to original work is quite common.
Snoeyenbos-West et al. apparently take offense at our calling this
group of organisms a "cluster of mixed taxonomic affiliation;" however, this seems to be in accordance with the conclusions of Lonergan et al., who suggest a reassessment of the affiliation of five
species in the proposed "Geobacteraceae" family. We note that none of these reassessments have taken place.
Since the number of strains belonging to this "family" is currently
growing, we suggest a full taxonomic reassessment of the entire group,
including full phenotype comparisons and species-level molecular
discrimination, e.g., by gyrB phylogeny analysis and DNA-DNA
hybridization, published in valid manner according to the international
rules of nomenclature so that the taxa are properly recognized. It is
rather common for such reassessments to occur once the number of
strains and their diversity have grown for a more informed analysis. It
may well be that it is more appropriate for strain K1 to be reassigned
as a dechlorinating species to a single generic group, but this
conclusion is premature given the current status of reporting.
| |
REFERENCES |
| 1.
|
Amann, R. I.,
J. Stromley,
R. Devereux,
R. Key, and D. A. Stahl.
1992.
Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms.
Appl. Environ. Microbiol.
58:614-623.
|
| 2.
|
Lonergan, D. J.,
H. Jenter,
J. D. Coates,
E. J. P. Phillips,
T. Schmidt, and D. R. Lovley.
1996.
Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria.
J. Bacteriol.
178:2402-2408.
|
| | | | |
Helene De Wever
Laboratory of Soil Biology and Soil Fertility
Fakulteit Landbouwkundige en Toegepaste Biologische
Wetenschappen
Kardinaal Mercierlaan 92
B-3001 Heverlee, Belgium
Phone: 32(16)329676
Fax: 32(16)321997
E-mail: heleen.dewever{at}agr.kuleuven.ac.be
|
| | | | |
James R. Cole
Michael R. Fettig
Deborah A. Hogan
James M. Tiedje
Center for Microbial Ecology
Michigan State University
East Lansing, Michigan 48824-1325
|
Applied and Environmental Microbiology, February 2001, p. 1020-1022, Vol. 67, No. 2
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.2.1020-1022.2001
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