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1 Department of Plant Biotechnology, Biotechnology Research Center, University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo, Japan
2 School of Pharmaceutical Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
Correspondence
Kyung-Bum Lee
arirang{at}mail.ecc.u-tokyo.ac.jp
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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Published online ahead of print on 6 May 2005 as DOI 10.1099/ijs.0.63663-0.
A full version of Fig. 1
is available as supplementary material in IJSEM Online.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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, 1978; Zablen & Woese, 1975; Fox et al., 1980). In the 1980s, the sequences of SSU rRNA genes were determined for various kinds of organism, mainly by Woese (1987) and coworkers, and they proposed the generally accepted hierarchical structure of life, including eukaryotes, archaea and eubacteria. The system proposed by Woese was supported by various phylogenetic analyses that used other molecular techniques (Ludwig & Klenk, 2001). In Bergey's Manual of Systematic Bacteriology (BMSB), 2nd edn (Garrity & Holt, 2001), a first attempt was made to establish a hierarchical system for the domains Bacteria and Archaea. Twenty-three phyla were proposed for these domains. In the first description of the Proteobacteria by Stackebrandt et al. (1988), the Proteobacteria were defined as a class. However, in BSMB (2nd edn), the Proteobacteria were categorized as one of 23 phyla of bacteria and the five classes ‘Alphaproteobacteria’, ‘Betaproteobacteria’, ‘Gammaproteobacteria’, ‘Deltaproteobacteria’ and ‘Epsilonproteobacteria’ were proposed in the phylum. The phylum Proteobacteria is one of the largest phyla in the domain Bacteria, including more than 200 genera.
The alpha, beta, gamma and delta subclasses of the class Proteobacteria were defined by Stackebrandt et al. (1988) and the epsilon subclass was defined by Olsen et al. (1994). The monophyletism of the classes ‘Alphaproteobacteria’, ‘Betaproteobacteria’ and ‘Gammaproteobacteria’ was strongly supported by many phylogenetic analyses (Ludwig & Klenk, 2001). The classes ‘Deltaproteobacteria’ and ‘Epsilonproteobacteria’ are considered to have separated very early from the other proteobacterial classes (Olsen et al., 1994; Trust et al., 1994; Ludwig & Klenk, 2001). Species of the classes ‘Alphaproteobacteria’, ‘Betaproteobacteria’ and ‘Gammaproteobacteria’ are very heterogeneous in their physiological characteristics. Each of the three classes includes aerobes and anaerobes, photosynthetic and non-photosynthetic organisms, and is distributed ubiquitously in terrestrial and aquatic environments in very high abundance.
For construction of a phylogenetic tree, the first priority should be selection of an appropriate molecule. The most important factor in this selection is to choose molecules that are found ubiquitously in the living world, and SSU rRNA, large-subunit (LSU) rRNA (De Rijk et al., 1995; Ludwig et al., 1998), elongation factor EF-Tu/
(Ludwig et al., 1998), RNA polymerases (Klenk & Zillig, 1994), F1F0 ATPase 
-subunit (Ludwig et al., 1993, 1998; Ludwig & Schleifer, 1994), RecA protein (Wetmur et al., 1994; Eisen, 1995; Karlin et al., 1995) and Hsp60 heat-shock protein (Viale et al., 1994; Gupta, 1998) have, for this reason, proved to be good molecules for the phylogenetic inference of prokaryote taxonomy. SSU rRNA gene sequences have advantages over the other molecules. LSU rRNA is considered to be as good as SSU rRNA, but not enough sequences are available in the databases. The above-mentioned proteins also have the prerequisites for phylogenetic inference, but there are critical drawbacks (Ludwig & Klenk, 2001), as most of the genes for these proteins were produced by gene duplications. There is also a critical problem in the alignment of SSU rRNA, which has many helices and loops. The helices, together with ribosomal proteins, maintain the three-dimensional structure of SSU rRNA and the loops are related to the function of the ribosome. Significant differences in mutational rate are found among these structures. The rapidly evolving parts of SSU rRNA are called variable regions; however, because of the variable secondary structure of these variable regions, it is impossible to align the SSU rRNA gene sequences of phylogenetically diverse lineages and any kinds of alignment for such sequences include artificial inferences. These artificial alignments easily lead to the distortion of phylogenetic trees.
The aim of this study was to use SSU (16S) rRNA gene sequences available in databases to clarify the phylogenetic relationships for the class ‘Alphaproteobacteria’ of the phylum Proteobacteria.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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). The ML distance matrix was calculated by using NUCML, and NJDIST in the MOLPHY package reconstructed the initial neighbour-joining tree. The ML tree was finally produced by using NUCML with the R (local rearrangement search) option based on the HKY model (Hasegawa et al., 1985). Local bootstrap probabilities were estimated by the resampling of the estimated log-likelihood (RELL) method (Kishino et al., 1990; Hasegawa & Kishino, 1994). Variable regions in the 16S rRNA gene sequences were eliminated from the comparison of sequences. Six regions (positions 70–100, 181–219, 447–487, 1004–1036, 1133–1141 and 1446–1456 in the Escherichia coli numbering system) were eliminated from the comparison because the secondary structures of these regions differed between strains.
The ARB tree.
We obtained the ARB program package and database (developed by Wolfgang Ludwig, Oliver Strunk and colleagues in Munich, Germany) at http://www.arb.de.vu/ and installed it on a LINUX system. The phylogenetic tree of the ARB database from the ssujun02.arb version was used for comparison with the tree constructed in this study.
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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). Within this study, the nomenclature of the orders and families follows the taxonomic outline of BMSB (Garrity & Holt, 2001; Garrity et al., 2004).
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The cluster of the order Caulobacterales
In our classification, the cluster of the order Caulobacterales Henrici and Johnson 1935 has been subdivided into three clades: the families Caulobacteraceae, Hyphomonadaceae fam. nov. and ‘Rhodobacteriaceae’.
The cluster of the family Caulobacteraceae.
The genera Brevundimonas, Caulobacter, Asticcacaulis, Mycoplana and Phenylobacterium comprised this cluster with high bootstrap values. The cluster contained two subclusters. The first consisted of members of the genus Brevundimonas, including Brevundimonas diminuta (the type species of the genus), Brevundimonas vesicularis, [Caulobacter] intermedius, Brevundimonas aurantiaca, Brevundimonas intermedia, Brevundimonas variabilis, Brevundimonas alba and Brevundimonas subvibrioides. The second subcluster contained members of the genus Caulobacter, including Caulobacter fusiformis, Caulobacter bacteroides, Caulobacter crescentus (the type species) and Caulobacter henricii.
In this study, Asticcacaulis excentricus ATCC 15261T (GenBank accession no. AB016610), the type species of the genus Asticcacaulis, belonged to this cluster and was related closely to the genera Brevundimonas and Caulobacter, in agreement with Abraham et al. (2001). However, Asticcacaulis biprosthecium ATCC 27554T (GenBank accession no. AJ007799), used in this study, is related closely to the genus Sphingomonas, which concurs with Sly et al. (1999). Abraham et al. (2001) stated, however, the possibility that the Asticcacaulis strains studied by Sly et al. (1999) were misidentified on the basis of analysis of 16S rRNA gene sequences and fatty acid data. Therefore, the 16S rRNA gene sequences of Asticcacaulis species in the databases should be re-evaluated to avoid taxonomic confusion.
The cluster of the family Hyphomonadaceae fam. nov.
This cluster consisted of the genera Hyphomonas, Maricaulis, Hirschia and Oceanicaulis, and was supported by high bootstrap values. The members of this cluster, mainly isolated from marine habitats, formed a robust clade and have similar morphological, physiological and biological features (Moore et al., 1984; Schlesner et al., 1990; Abraham et al., 1999; Strömpl et al., 2003).
In our classification, the phylogenetic position of the family Hyphomonadaceae differed from that in the hierarchical system of BMSB, but was similar to that of the ARB tree. Phylogenetically, this cluster was related closely to the family Caulobacteraceae, which was consistent with the ARB tree. Garrity & Holt (2001) stated, however, that this cluster was included in the family ‘Rhodobacteraceae’. We also noticed that the phylogenetic topology of this cluster was affected by intervening taxa, which were removed in our study. Hence, it might be difficult to classify this cluster as part of the family ‘Rhodobacteraceae’.
Consequently, we propose a novel family, Hyphomonadaceae fam. nov., to accommodate the bacterial genera Hyphomonas, Hirschia, Maricaulis and Oceanicaulis.
The cluster of the family ‘Rhodobacteraceae’.
In our classification, this cluster consisted of five main subclusters. The first subcluster consisted of the genus Paracoccus, the second included the genera Rhodobacter and Pseudorhodobacter, the third contained the genus Rhodovulum, the fourth included the genus Amaricoccus and the fifth comprised the genera Antarctobacter, Ketogulonicigenium, Leisingera, Octadecabacter, Roseivivax, Roseobacter, Roseovarius, Ruegeria, Sagittula, Silicibacter, Staleya and Sulfitobacter.
The cluster of the order ‘Sphingomonadales’
The order ‘Sphingomonadales’ in our classification consisted of two subclusters: the families Sphingomonadaceae and Erythrobacteraceae fam. nov. (newly proposed).
BMSB's hierarchical system proposed the order ‘Sphingomonadales’ to include only the family Sphingomonadaceae. The ARB tree also showed that five Sphingomonas subgroups and the Porphyrobacter/Erythrobacter/Erythromicrobium groups were included in the Sphingomonas cluster. However, we found that the order ‘Sphingomonadales’ was separated into two clades: the families Sphingomonadaceae and Erythrobacteraceae fam. nov. Our tree showed that the phylogenetic relationships between the two clusters had enough distance and high enough bootstrap values to separate them into two families.
The cluster of the family Sphingomonadaceae.
Within our classification, the family Sphingomonadaceae contained the genera Sphingomonas, Zymomonas and Sandaracinobacter and the species Caulobacter leidyi and Asticcacaulis biprosthecium, as well as the misnamed ‘[Pseudomonas] abikonensis’ and [Rhizomonas] suberifaciens.
The family Sphingomonadaceae was established by Kosako et al. (2000), based on the results of 16S rRNA gene sequence and cellular lipid analyses. Takeuchi et al. (2001) divided the genus Sphingomonas into four genera, Sphingomonas, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic analysis of 16S rRNA gene sequences and chemotaxonomic and phenotypic differences.
In this study, the genus Sphingomonas contained three main subclusters: the first included Sphingomonas paucimobilis (the type species of the genus), Sphingomonas adhaesiva, Sphingomonas trueperi, Sphingomonas chlorophenolica, Sphingomonas yanoikuyae, Sphingomonas asaccharolytica, Sphingomonas pruni, Sphingomonas mali and Sphingomonas echinoides; the second consisted of Sphingomonas suberifaciens, Sphingomonas subterranea, Sphingomonas aromaticivorans, Sphingomonas capsulata and Sphingomonas subarctica; and the third contained Sphingomonas macrogoltabidus and Sphingomonas terrae. This differed slightly from the tree proposed by Takeuchi et al. (2001) and the ARB tree, which divided the genus Sphingomonas into four and five groups, respectively.
Caulobacter leidyi ATCC 15260T (GenBank accession no. AJ227812) was included in this cluster and was related to Sphingomonas trueperi, in agreement with Abraham et al. (1999). Therefore, Caulobacter leidyi should be transferred to the genus Sphingomonas following further taxonomic studies. ‘[Pseudomonas] abikonensis’ was also included in the Sphingomonas rRNA lineage and was related closely to Sphingomonas chlorophenolica, in accordance with Kersters et al. (1996) and Anzai et al. (2000). Therefore, ‘[Pseudomonas] abikonensis’ should be transferred to the genus Sphingomonas following further taxonomic studies.
The cluster of the family Erythrobacteraceae fam. nov.
In our study, the cluster that accommodated the genera Erythrobacter, Porphyrobacter and Erythromicrobium was clearly separated with high bootstrap support.
This cluster has previously been shown to belong to the lineage of the genus Sphingomonas. We have observed, however, that this cluster is separated from the main lineage of the family Sphingomonadaceae, which was strongly supported by the bootstrap value. The topology of this cluster differed from that in the ARB and BMSB trees, both of which showed this cluster to be included in the lineage of the genus Sphingomonas. The members of this cluster produce pigment (yellow, orange or pink) and mainly contain bacteriochlorophyll a, whereas members of the genus Sphingomonas do not (Shiba & Simidu, 1982; Fuerst et al., 1993; Takeuchi et al., 1994; Yurkov et al., 1994; Denner et al., 2002). Takeuchi et al. (2001) also showed that the genus Sphingomonas was related only distantly to the genera Erythrobacter, Erythromicrobium and Porphyrobacter based on 16S rRNA gene sequence similarity, which was 92·9–94·8 %, and the genus Sphingomonas had the presence of one or more oligosaccharide-type glycosphingolipid(s) (GSL) as one of its most characteristic features, whereas the genera Erythrobacter, Porphyrobacter and Erythromicrobium contained monosaccharide-type GSLs only. On the basis of this work and previous polyphasic taxonomic studies, we propose this cluster as a novel family, Erythrobacteraceae fam. nov., to accommodate the bacterial genera Erythrobacter, Porphyrobacter and Erythromicrobium.
The cluster of the order ‘Rhizobiales’
The members of this cluster are the most heterogeneous in the class ‘Alphaproteobacteria’. The order ‘Rhizobiales’ includes members with a variety of morphological, physiological and biological features, which may impede their taxonomic definition.
Garrity et al. (2004) proposed that the order ‘Rhizobiales’ comprises 11 families: Rhizobiaceae, ‘Aurantimonadaceae’, Bartonellaceae, Brucellaceae, ‘Phyllobacteriaceae’, ‘Methlocystaceae’, ‘Beijerinckiaceae’, ‘Bradyrhizobiaceae’, Hyphomicrobiaceae, ‘Methylobacteriaceae’ and ‘Rhodobiaceae’, based on 16S rRNA gene sequence analysis. In our phylogenetic tree, the order ‘Rhizobiales’ is clearly separated into two main clusters, which is consistent with the ARB tree. The first main cluster constituted the families Rhizobiaceae, Brucellaceae, Bartonellaceae and ‘Phyllobacteriaceae’ and the second contained the families ‘Methylobacteriaceae’, ‘Bradyrhizobiaceae’, ‘Methlocystaceae’, ‘Beijerinckiaceae’, Hyphomicrobiaceae, ‘Rhodobiaceae’ and the newly proposed Xanthobacteraceae fam. nov.
The cluster of the family Brucellaceae.
In this study, the cluster of the family Brucellaceae, proposed by Breed et al. (1957), consisted of the genera Brucella and Ochrobactrum, isolated from human clinical specimens (Holmes et al., 1988), and was supported by very high bootstrap values.
The cluster of the family Bartonellaceae.
Within our classification, the cluster of the family Bartonellaceae consisted of the genus Bartonella only. Bartonella bacilliformis (GenBank accession no. M65249), the type species of the genus Bartonella, was related to Bartonella koehlerae ATCC 700693T (AF076237).
The cluster of the family Rhizobiaceae.
The cluster of the family Rhizobiaceae consisted of the genera Agrobacterium, Allorhizobium, Rhizobium and Sinorhizobium and the species Blastobacter capsulatus.
Blastobacter capsulatus IFAM 1004T (GenBank accession no. X73042), isolated from freshwater habitats (Hirsch & Müller, 1985), was included in the cluster of the family Rhizobiaceae and was related closely to the genus Rhizobium, which was consistent with the ARB tree. Garrity & Holt (2001), however, showed the genus Blastobacter to be included in the family ‘Bradyrhizobiaceae’. We also found that Blastobacter denitrificans LMG 8443T (GenBank accession no. S46917) was included in the cluster of the family ‘Bradyrhizobiaceae’. However, Blastobacter henricii, the type species of the genus, was not available from any culture collection. Thus, we speculate that the genus Blastobacter is heterogeneous; further taxonomic studies are required for clarification.
Within our tree, the following members of the genus Sinorhizobium [transferred from the genus Rhizobium by Chen et al. (1988)] were related closely to the genus Rhizobium: Sinorhizobium fredii (the type species of the genus) and Sinorhizobium saheli.
Aurantimonas coralicida, a coral pathogen (Denner et al., 2003), and Fulvimarina pelagi, a marine bacterium (Cho & Giovannoni, 2003b), formed a distinct and deep evolutionary lineage in the cluster of the family Rhizobiaceae with high bootstrap support, and were proposed as the members of the family ‘Aurantimonadaceae’ by Garrity et al. (2004). The neighbours of this lineage were the genera Agrobacterium, Allorhizobium and Rhizobium, which was in accordance with the 16S rRNA gene sequence comparison of Cho & Giovannoni (2003b). However, evolutionary relationships between the neighbours were distant, with a deep branch. In our phylogenetic analysis, we observed an important point: this cluster, with a distinct and deep lineage, was placed in the family Rhizobiaceae with very high bootstrap values, although Garrity et al. (2004) proposed this cluster as a family. Therefore, it may be ambiguous to define the boundary of a family based on 16S rRNA gene sequence analysis. Further taxonomic studies should be carried out for this cluster to allow definite taxonomic conclusions to be made.
The cluster of the family ‘Phyllobacteriaceae’.
In our classification, the family ‘Phyllobacteriaceae’ was composed of three main subclusters with high bootstrap support, which concurred with Garrity et al. (2004). The first subcluster contained the genera Aminobacter, Mesorhizobium, Phyllobacterium and Pseudaminobacter, the second included the genera Ahrensia and Nitratireductor and the third contained the genera Aquamicrobium and Defluvibacter.
The cluster of the family ‘Bradyrhizobiaceae’.
This family, proposed by Garrity et al. (2004), consisted of the genera Afipia, Bosea, Bradyrhizobium, Nitrobacter, Oligotropha and Rhodopseudomonas and the species Blastobacter denitrificans, as well as the phylogenetically misnamed [Pseudomonas] carboxydohydrogena.
[Pseudomonas] carboxydohydrogena DSM 1083T (GenBank accession no. AB021393), established by Meyer et al. (1980), was a close neighbour of Afipia felis, isolated from human wound and respiratory sources (Brenner et al., 1991), which was in accordance with Anzai et al. (2000). Therefore, for appropriate positioning, [Pseudomonas] carboxydohydrogena should be transferred to the genus Afipia following further taxonomic studies.
The cluster of the family ‘Methylobacteriaceae’.
The cluster consisting of the genus Methylobacterium, established by Patt et al. (1976), was separated from the other clusters of the order ‘Rhizobiales’ with high bootstrap values. Garrity & Holt (2001) proposed this cluster as the novel family ‘Methylobacteriaceae’ to accommodate the genus Methylobacterium only, which concurs with our data.
The cluster of the family Hyphomicrobiaceae.
Within our classification, the cluster consisting of the genera Hyphomicrobium, Pedomicrobium, Filomicrobium and Rhodomicrobium was separated from the other clusters with high bootstrap values. The genus Hyphomicrobium comprised two subclusters: the first contained Hyphomicrobium hollandicum, Hyphomicrobium zavarzinii and Filomicrobium fusiforme from brackish water (Schlesner, 1987) and the second comprised Hyphomicrobium denitrificans and Hyphomicrobium facile. Pedomicrobium australicum from aquatic habitats (Gebers & Beese, 1988) was related closely to the second subcluster of the genus Hyphomicrobium, in agreement with Rainey et al. (1998). Rainey et al. (1998) also reported that the genus Hyphomicrobium should be separated into two genera on the basis of phylogenetic analysis, but the possibility that two separate genera exist was excluded because of the lack of distinguishing phenotypic properties. Our results also indicated that the two clusters are phylogenetically distant enough to be separated into two genera. Therefore, further taxonomic studies of the genus Hyphomicrobium are required to allow definite taxonomic conclusions to be made.
The cluster of the family Xanthobacteraceae fam. nov.
Within our study, the cluster that consisted of the genera Xanthobacter, Azorhizobium, Ancylobacter, Labrys and Starkeya was separated from the other clusters of the order ‘Rhizobiales’ with very high bootstrap values. This cluster contained two subclusters: the first included species of the genus Xanthobacter, Azorhizobium caulinodans and Labrys monachus, and the second contained Ancylobacter aquaticus [transferred from the bacterial genus Microcyclus Ørskov 1928 (Raj, 1983)] and Starkeya novella, reclassified from Thiobacillus novellus (Kelly et al., 2000).
The phylogenetic topology of the family Xanthobacteraceae was similar to that in the ARB tree, but differed from that of BMSB, which showed that this cluster was a subdivision of the family Hyphomicrobiaceae Babudieri 1950, including 20 species. We have found, in agreement with the ARB tree, that this cluster was placed separately from the cluster of the family Hyphomicrobiaceae Babudieri 1950.
It was difficult to find common features among the members of the family Hyphomicrobiaceae Babudieri 1950, which show a variety of characteristics. In DNA G+C content, members of the newly established family Xanthobacteraceae are highly similar (66–69·1 mol%), whereas the species of the family Hyphomicrobiaceae Babudieri 1950 have high heterogeneity (59–71·4 mol%) (Raj, 1983; Dreyfus et al., 1988; Schlesner et al., 1990; Rainey et al., 1998; Kelly et al., 2000; Fritz et al., 2004). Based on the deep branching observed in 16S rRNA gene sequence-based phylogenetic analysis, we propose a novel family, Xanthobacteraceae fam. nov., to include the genera Xanthobacter, Azorhizobium, Ancylobacter, Labrys and Starkeya.
The cluster of the family ‘Rhodobiaceae’.
The family ‘Rhodobiaceae’, accommodating the genera Rhodobium and Roseospirillum (not used in this study because of short sequence data), was proposed by Garrity et al. (2004) and was located out of the main cluster of the order ‘Rhizobiales’ in this study.
Intervening strains and a potential cluster as a taxon in the order ‘Rhizobiales’
Within our phylogenetic tree, we observed several bacteria located in an intermediate position within the order ‘Rhizobiales’. The genera Blastochloris, transferred from the genus Rhodopseudomonas (Hiraishi, 1997), Bosea, capable of oxidizing reduced inorganic sulfur compounds (Das et al., 1996), Chelatococcus, capable of utilizing nitrilotriacetate (Auling et al., 1993), Devosia, created to accommodate ‘Pseudomonas riboflavina’ (Nakagawa et al., 1996), and Prosthecomicrobium, a prosthecate freshwater bacterium (Staley, 1968), and the species Rhodoblastus acidophilus, transferred from Rhodopseudomonas acidophila (Imhoff, 2001), were located in the outline of various clusters, at the family level. Thus, it was difficult to define their taxonomic hierarchy in our phylogenetic tree. Therefore, further taxonomic studies should be carried out to allow definite taxonomic conclusions about these six taxa to be made.
In this study, Roseibium hamelinense, an aerobic, bacteriochlorophyll-containing bacterium (Suzuki et al., 2000), Pannonibacter phragmitetus, an alkalitolerant bacterium (Borsodi et al., 2003), Stappia stellulata, a marine species reclassified from the genus Agrobacterium (Uchino et al., 1998), and Ancalomicrobium adetum, a prosthecate freshwater bacterium (Staley, 1968), formed a distinct branch with high bootstrap values. Phenotypic and chemotaxonomic characteristics shared commonly among the strains did not clearly define the taxonomy of this cluster. Garrity et al. (2004) proposed that the genera Pannonibacter, Roseibium and Stappia and the genus Ancalomicrobium were classified into the families ‘Rhodobacteriaceae’ and Hyphomicrobiaceae, respectively. However, in our data, we observed that this cluster, accommodating the four genera, is robustly formed with a distinct branch. Suzuki et al. (2000) and Borsodi et al. (2003) also stated that Roseibium hamelinense and Pannonibacter phragmitetus were related closely to the members of this branch on the basis of 16S rRNA gene sequence analysis. The 16S rRNA gene sequence similarity for Pannonibacter phragmitetus supported the observation that its closest neighbours were members of the genera Roseibium and Stappia. The physiological and molecular features of the genus Ancalomicrobium were not discriminatory enough to support this cluster. Further taxonomic study of this cluster, including the four genera, may establish a novel family-level taxon.
The cluster of the order Rhodospirillales
Garrity & Holt (2001) showed that the order Rhodospirillales [established by Pfennig & Trüper (1971)] includes two families, Rhodospirillaceae and Acetobacteraceae, and the ARB tree also indicated that the order Rhodospirillales comprised a cluster with the two families. Within our tree, the order Rhodospirillales contained three distinct subclusters, which did not branch from an origin cluster. Thus, it was difficult to classify the order Rhodospirillales including the two families within our tree. To enable precise taxonomic conclusions to be made about the order Rhodospirillales, further taxonomic studies must be carried out.
The cluster of the family Rhodospirillaceae.
In this study, the topology of the family Rhodospirillaceae differs from that proposed in BMSB and the ARB tree. In the BMSB system, the family Rhodospirillaceae includes the genera Azospirillum, ‘Dechlorospirillum’, ‘Defluvicoccus’, Inquilinus, Magnetospirillum, Phaeospirillum, Rhodocista, Rhodospira, Rhodospirillum, Rhodovibrio, Roseospira, Skermanella, Thalassospira and Tistrella. The classification of Rhodospirillaceae as a family is ambiguous, because the members of the family Rhodospirillaceae proposed by BMSB were separated into two distinct phylogenetic lineages. Rhodospirillum rubrum, Rhodospira trueperi, Roseospira mediosalina, Oceanospirillum pusillum and Thalassospira lucentensis formed a cluster with relatively low bootstrap values. The genera Azospirillum, Inquilinus, Phaeospirillum, Magnetospirillum, Rhodocista, Roseomonas, Skermanella and Stella also formed a distinct lineage. Each strain had a deep branch and it was therefore problematic to define a family-level taxon based on 16S rRNA gene sequence analysis. On the basis of our results, the family Rhodospirillaceae should be re-evaluated to allow definite taxonomic conclusions to be reached.
The cluster of the family Acetobacteraceae.
Within our classification, the family Acetobacteraceae, proposed by Gillis & De Ley (1980), was subdivided into two subclusters with very high bootstrap values: the first cluster included the genera Gluconobacter, Acidomonas, Asaia, Kozakia, Acetobacter and Gluconacetobacter, and the second contained the genera Acidiphilium, Acidisphaera, Rhodopila, Rubritepida, Roseococcus, Paracraurococcus, Craurococcus, Teichococcus and Muricoccus. In our tree, we observe that the genera Rubritepida, Roseococcus, Paracraurococcus, Craurococcus, Teichococcus and Muricoccus form a distinct subcluster with very high bootstrap values. According to several studies (Saitoh et al., 1998; Alarico et al., 2002; Kämpfer et al., 2003), phylogenetic relationships between each strain were close on the basis of 16S rRNA gene sequence analysis. However, their physiological and biochemical features have impeded their phylogenetic consolidation: some strains contain bacteriochlorophyll a and some do not, and either Q-9 or Q-10 may be present. Based on the phylogenetic results, this subcluster may be classified as a novel taxon at the family level; therefore, further taxonomic studies should be carried out to determine whether a novel family is supported.
The cluster of the order Rickettsiales
Dumler et al. (2001) described the order Rickettsiales, including the families Anaplasmataceae and Rickettsiaceae, on the basis of genetic analyses of 16S rRNA, groESL and surface-protein genes.
Within our classification, the order Rickettsiales contained two main subclusters: the families Anaplasmataceae and Rickettsiaceae, which was consistent with Dumler et al. (2001). The family Anaplasmataceae comprised the genera Ehrlichia, Anaplasma, Neorickettsia, Wolbachia and ‘Candidatus Xenohaliotis’, and the family Rickettsiaceae comprised the genera Rickettsia and Orientia.
The protozoan endosymbionts Holospora obtusa and ‘Candidatus Odyssella thessalonicensis' (Birtles et al., 2000) formed a cluster with low bootstrap values in our study. The two strains also formed distinct lineages with a deep branch. The endosymbionts in the class ‘Alphaproteobacteria’ were classified into a novel family, ‘Holosporaceae’, by Garrity et al. (2004). However, we found that it was ambiguous to classify these endosymbionts as a taxon based on 16S rRNA gene sequence analysis, because of the lack of consistency in defining the boundaries of a taxon with low bootstrap values (69 %). Therefore, an extensive study for endosymbionts should be carried out to allow definite taxonomic conclusions to be made. In this study, ‘Candidatus Xenohaliotis californiensis’, an obligately intracellular, pleomorphic bacterium (Friedman et al., 2000), formed a distinct lineage outside the clusters of the families Anaplasmataceae and Rickettsiaceae, which did not concur with Garrity et al. (2004), who proposed that this strain should be included in the family Anaplasmataceae. We also found that ‘Candidatus Xenohaliotis californiensis' formed a deep enough branch to be classified as another taxon with very high bootstrap values. Therefore, further taxonomic studies should be carried out to define the phylogenetic hierarchy of ‘Candidatus Xenohaliotis californiensis’.
Intervening clusters and strains within this phylogenetic tree
Rhodobium orientis MB312T (GenBank accession no. D30792) and Rhodobium marinum DSM 2698T (D30790), purple, non-sulfur, phototrophic bacteria, were isolated and transferred to this genus by Hiraishi et al. (1995). The genus Rhodobium formed a cluster with relatively low bootstrap values and was related to the order ‘Rhizobiales’ in our phylogenetic tree, in which the genus Roseospirillum was not included because of short 16S rRNA gene sequences. Garrity et al. (2004) proposed the novel family ‘Rhodobiaceae’, including the genera Rhodobium and Roseospirillum, in the order ‘Rhizobiales’. However, we have found a general lack of consistency in defining the boundaries of such a family based on our phylogenetic analysis. Therefore, further taxonomic studies should be carried out to determine the phylogenetic relationships of the genera Rhodobium and Roseospirillum.
Rhodothalassium salexigens DSM 2132T (GenBank accession no. M59070), transferred from the genus Rhodospirillum by Imhoff et al. (1998), clustered with the family ‘Rhodobacteraceae’ in this study. We have observed a lack of consistency in defining the phylogenetic hierarchy of Rhodothalassium salexigens, even though Garrity et al. (2004) classified it as a member of the family ‘Rhodobacteraceae’, because its topology was changed by adding further strains. Therefore, further taxonomic studies should be carried out to define the phylogenetic hierarchy of Rhodothalassium salexigens.
Parvularcula bermudensis HTCC2503T (GenBank accession no. AF544015), isolated from a marine environment by Cho & Giovannoni (2003a), formed a deep branch in the ‘Alphaproteobacteria’ according to our phylogenetic data, which concur with the results of Cho & Giovannoni (2003a). Parvularcula bermudensis clustered with the order ‘Sphingomonadales’ with relatively high bootstrap values. However, phylogenetic relationships between Parvularcula bermudensis and the order ‘Sphingomonadales’ were not close. Garrity et al. (2004) proposed this branch as the order ‘Parvularculales’, including Parvularcula bermudensis only.
Approach to establish a more reliable phylogenetic hierarchical system
The tree (version ssujun02.arb) in the ARB database, maintained by W. Ludwig and O. Strunk at the Technical University of Munich, was used for comparison with our tree, which included 2154 SSU 16S rRNA sequences. In this study, we have found some discordant points between our phylogenetic tree and the ARB tree. The phylogenetic topology of some clusters in the two trees was slightly different. In our tree, the branch length of each cluster was long enough to classify it as a taxon.
We speculate that the main reason for the differences between phylogenetic hierarchical systems based on 16S rRNA gene sequences is their alignment, which has some variable regions. Ludwig & Klenk (2001) also pointed out the critical drawbacks of 16S rRNA gene sequences for phylogenetic inference. The secondary structures of the variable regions show variability, making it impossible to align the SSU rRNA sequences of phylogenetically diverse lineages. Thus, any kinds of alignment for such sequences include artificial inferences. These artificial alignments easily lead to the production of distorted phylogenetic trees. In this study, we excluded the variable regions from the alignment. Hence, our alignment includes fewer inferences and is of higher reliability for the topology. As a result, the bootstrap values of the branches were very high and the interconnecting branches between the major clusters were long.
In BMSB, Garrity & Holt (2001) proposed the establishment of a new hierarchical system for the domains Bacteria and Archaea based on 16S rRNA gene sequences. They elevated the Proteobacteria from the rank of class, making them one of 23 newly established phyla. Recently, Garrity et al. (2004) have updated the BMSB hierarchical system with newly isolated strains. In this system, the hierarchical system that we propose is for the class ‘Alphaproteobacteria’. The hierarchical system for the ‘Alphaproteobacteria’ was slightly different between our results and those of BMSB. They proposed the class ‘Alphaproteobacteria’ to be subdivided into seven orders and 20 families (Table 1). The order ‘Rhodobacterales’ (of BMSB) is eliminated and the family ‘Rhodobacteraceae’, of the order ‘Rhodobacterales’ in BMSB, is included in the order Caulobacterales in our proposed system, because the name of the order Caulobacterales has been validly published, but that of the order ‘Rhodobacterales’ has not. The family ‘Aurantimonadaceae’ in BMSB is not included in our proposed system because of the lack of consistency in defining the boundaries of this taxon based on 16S rRNA gene sequence analysis. The families Hyphomonadaceae, Xanthobacteraceae and Erythrobacteraceae are newly proposed here, because these groups were separated very clearly from other taxa in our phylogenetic tree (Fig. 1).
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Description of Hyphomonadaceae fam. nov.
Hyphomonadaceae (Hy.pho.mo.na.da'ceae. N.L. fem. n. Hyphomonas type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Hyphomonadaceae the Hyphomonas family).
Gram-negative, rod-shaped bacteria. Motile. Do not form spores. Chemo-organotrophic. Some species require peptone or B vitamins and amino acids. Aerobic or facultatively anaerobic. Some species denitrify. In most species, the major isoprenoid quinone is Q-10. Members of the family have been isolated from sea water. The family is a member of the ‘Alphaproteobacteria’. The family comprises the type genus Hyphomonas Pongratz 1957 emend. Moore et al. 1984 and the genera Hirschia Schlesner et al. 1990, Maricaulis Abraham et al. 1999 and Oceanicaulis Strömpl et al. 2003.
Description of Xanthobacteraceae fam. nov.
Xanthobacteraceae (Xan.tho.bac.te.ra'ceae. N.L. masc. n. Xanthobacter type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Xanthobacteraceae the Xanthobacter family).
Gram-negative, rod-shaped bacteria. Motile or (some species) non-motile. Do not form spores. Chemo-organotrophic. Aerobic. Some species fix N2. In most species, the major isoprenoid quinone is Q-10. Members of the family have been isolated from plant roots and stems, freshwater and lake silt. The family is a member of the ‘Alphaproteobacteria’. The family comprises the type genus Xanthobacter Wiegel et al. 1978 and the genera Ancylobacter Raj 1983, Angulomicrobium Vasil'eva et al. 1986, Azorhizobium Dreyfus et al. 1988, Labrys Vasilyeva and Semenov 1985 and Starkeya Kelly et al. 2000.
Description of Erythrobacteraceae fam. nov.
Erythrobacteraceae (E.ry.thro.bac.te.ra'ceae. N.L. masc. n. Erythrobacter type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Erythrobacteraceae the Erythrobacter family).
Gram-negative, rod-shaped bacteria. Motile or (some species) non-motile. Do not form spores. Chemo-organotrophic. Some species require biotin. Aerobic. Cells contain bacteriochlorophyll a and carotenoids. Members of the family have been isolated from freshwater. The family is a member of the ‘Alphaproteobacteria’. The family comprises the type genus Erythrobacter Shiba and Simidu 1982 and the genera Erythromicrobium Yurkov et al. 1994 and Porphyrobacter Fuerst et al. 1993.
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REFERENCES |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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H. Kumari, S. K. Gupta, S. Jindal, P. Katoch, and R. Lal Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2291 - 2296. [Abstract] [Full Text] [PDF]
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H.-Y. Xu, L.-P. Chen, S.-Z. Fu, H.-X. Fan, Y.-G. Zhou, S.-J. Liu, and Z.-P. Liu Zhangella mobilis gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae isolated from coastal seawater Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2297 - 2301. [Abstract] [Full Text] [PDF]
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 S. Tsukada, T. Aono, N. Akiba, K.-B. Lee, C.-T. Liu, H. Toyazaki, and H. Oyaizu Comparative Genome-Wide Transcriptional Profiling of Azorhizobium caulinodans ORS571 Grown under Free-Living and Symbiotic Conditions Appl. Envir. Microbiol., August 1, 2009; 75(15): 5037 - 5046. [Abstract] [Full Text] [PDF]
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K. Alain, B. J. Tindall, L. Intertaglia, P. Catala, and P. Lebaron Hellea balneolensis gen. nov., sp. nov., a prosthecate alphaproteobacterium from the Mediterranean Sea Int J Syst Evol Microbiol, November 1, 2008; 58(11): 2511 - 2519. [Abstract] [Full Text] [PDF]
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E. Lang, J. Swiderski, E. Stackebrandt, P. Schumann, C. Sproer, and N. Sahin Description of Ancylobacter oerskovii sp. nov. and two additional strains of Ancylobacter polymorphus Int J Syst Evol Microbiol, September 1, 2008; 58(9): 1997 - 2002. [Abstract] [Full Text] [PDF]
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J.-H. Yoon, S.-J. Kang, W.-T. Im, S.-T. Lee, and T.-K. Oh Chelatococcus daeguensis sp. nov., isolated from wastewater of a textile dye works, and emended description of the genus Chelatococcus Int J Syst Evol Microbiol, September 1, 2008; 58(9): 2224 - 2228. [Abstract] [Full Text] [PDF]
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C. Y. Hwang and B. C. Cho Cucumibacter marinus gen. nov., sp. nov., a marine bacterium in the family Hyphomicrobiaceae Int J Syst Evol Microbiol, July 1, 2008; 58(7): 1591 - 1597. [Abstract] [Full Text] [PDF]
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N. R. Kumar, S. Nair, S. Langer, H.-J. Busse, and P. Kampfer Altererythrobacter indicus sp. nov., isolated from wild rice (Porteresia coarctata Tateoka) Int J Syst Evol Microbiol, April 1, 2008; 58(4): 839 - 844. [Abstract] [Full Text] [PDF]
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M. F. Carvalho, P. De Marco, A. F. Duque, C. C. Pacheco, D. B. Janssen, and P. M. L. Castro Labrys portucalensis sp. nov., a fluorobenzene-degrading bacterium isolated from an industrially contaminated sediment in northern Portugal Int J Syst Evol Microbiol, March 1, 2008; 58(3): 692 - 698. [Abstract] [Full Text] [PDF]
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C. Y. Hwang and B. C. Cho Cohaesibacter gelatinilyticus gen. nov., sp. nov., a marine bacterium that forms a distinct branch in the order Rhizobiales, and proposal of Cohaesibacteraceae fam. nov. Int J Syst Evol Microbiol, January 1, 2008; 58(1): 267 - 277. [Abstract] [Full Text] [PDF]
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K. Lee, H. K. Lee, T.-H. Choi, and J.-C. Cho Robiginitomaculum antarcticum gen. nov., sp. nov., a member of the family Hyphomonadaceae, from Antarctic seawater Int J Syst Evol Microbiol, November 1, 2007; 57(11): 2595 - 2599. [Abstract] [Full Text] [PDF]
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K. K. Kwon, J.-H. Woo, S.-H. Yang, J.-H. Kang, S. G. Kang, S.-J. Kim, T. Sato, and C. Kato Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov. Int J Syst Evol Microbiol, October 1, 2007; 57(10): 2207 - 2211. [Abstract] [Full Text] [PDF]
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I. Brettar, R. Christen, J. Botel, H. Lunsdorf, and M. G. Hofle Anderseniella baltica gen. nov., sp. nov., a novel marine bacterium of the Alphaproteobacteria isolated from sediment in the central Baltic Sea Int J Syst Evol Microbiol, October 1, 2007; 57(10): 2399 - 2405. [Abstract] [Full Text] [PDF]
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 K. P. Williams, B. W. Sobral, and A. W. Dickerman A Robust Species Tree for the Alphaproteobacteria J. Bacteriol., July 1, 2007; 189(13): 4578 - 4586. [Abstract] [Full Text] [PDF]
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J.-H. Yoon, S.-J. Kang, S. Park, and T.-K. Oh Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia Int J Syst Evol Microbiol, June 1, 2007; 57(6): 1310 - 1314. [Abstract] [Full Text] [PDF]
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J.-H. Yoon, S.-J. Kang, S.-Y. Lee, and T.-K. Oh Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea Int J Syst Evol Microbiol, April 1, 2007; 57(4): 856 - 861. [Abstract] [Full Text] [PDF]
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J.-H. Yoon, S.-Y. Lee, S.-J. Kang, C.-H. Lee, and T.-K. Oh Pseudoruegeria aquimaris gen. nov., sp. nov., isolated from seawater of the East Sea in Korea Int J Syst Evol Microbiol, March 1, 2007; 57(3): 542 - 547. [Abstract] [Full Text] [PDF]
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Y.-J. Chou, G. N. Elliott, E. K. James, K.-Y. Lin, J.-H. Chou, S.-Y. Sheu, D.-S. Sheu, J. I. Sprent, and W.-M. Chen Labrys neptuniae sp. nov., isolated from root nodules of the aquatic legume Neptunia oleracea Int J Syst Evol Microbiol, March 1, 2007; 57(3): 577 - 581. [Abstract] [Full Text] [PDF]
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E. M. Jordan, F. L. Thompson, X.-H. Zhang, Y. Li, M. Vancanneyt, R. M. Kroppenstedt, F. G. Priest, and B. Austin Sneathiella chinensis gen. nov., sp. nov., a novel marine alphaproteobacterium isolated from coastal sediment in Qingdao, China Int J Syst Evol Microbiol, January 1, 2007; 57(1): 114 - 121. [Abstract] [Full Text] [PDF]
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D. Sassera, T. Beninati, C. Bandi, E. A. P. Bouman, L. Sacchi, M. Fabbi, and N. Lo 'Candidatus Midichloria mitochondrii', an endosymbiont of the tick Ixodes ricinus with a unique intramitochondrial lifestyle. Int J Syst Evol Microbiol, November 1, 2006; 56(Pt 11): 2535 - 2540. [Abstract] [Full Text] [PDF]
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J. H. Badger, T. R. Hoover, Y. V. Brun, R. M. Weiner, M. T. Laub, G. Alexandre, J. Mrazek, Q. Ren, I. T. Paulsen, K. E. Nelson, et al. Comparative Genomic Evidence for a Close Relationship between the Dimorphic Prosthecate Bacteria Hyphomonas neptunium and Caulobacter crescentus. J. Bacteriol., October 1, 2006; 188(19): 6841 - 6850. [Abstract] [Full Text] [PDF]
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T. Martens, T. Heidorn, R. Pukall, M. Simon, B. J. Tindall, and T. Brinkhoff Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera Int J Syst Evol Microbiol, June 1, 2006; 56(6): 1293 - 1304. [Abstract] [Full Text] [PDF]
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