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1 Industrial Research Institute Swinburne, Swinburne University of Technology, PO Box 218, Hawthorn, Vic 3122, Australia
2 Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Pr. 100 Let Vladivostoku 159, Russian Federation
3 UMR 6543 CNRS – Université de Nice Sophia Antipolis, Centre de Biochimie, Parc Valrose, 06108 Nice cedex 2, France
Correspondence
Elena P. Ivanova
eivanova{at}swin.edu.au
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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A 16S rRNA gene sequence similarity matrix and an analysis of the distribution of similarities, a global tree resulting from large-scale neighbour-joining analysis and detailed trees of species of Pseudoalteromonas, Alteromonas and Colwellia are available as supplementary material in IJSEM Online.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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; Garrity et al., 2002; Cavalier-Smith, 2002) that was derived from the elevated class Proteobacteria Stackebrandt et al. 1988. Many of these bacteria have similar morphological, physiological and biochemical features, which impedes their identification. The taxonomic history of Alteromonas-related bacteria is a reflection of dynamic changes in bacterial systematics due to the rapid development of phylogenetic analysis and molecular techniques. The first volume of Bergey's Manual of Systematic Bacteriology (Baumann et al., 1984b) described only one genus of Gram-negative, aerobic, heterotrophic, marine bacteria with one polar flagellum, Alteromonas Baumann et al. 1972, whose members were phenotypically similar to pseudomonads, but differed from them in the lower G+C content of their DNA. This genus originally included few species: Alteromonas macleodii, A. haloplanktis, ‘A. marinopraesens’ (reclassified as A. haloplanktis; Reichelt & Baumann, 1973), [A.] communis and [A.] vaga (Gauthier & Breittmayer, 1992). Later, a number of other species were described, namely Alteromonas rubra, A. citrea, A. luteoviolacea, A. aurantia (Gauthier & Breittmayer, 1992), A. espejiana, A. undina (Chan et al., 1978), [A.] putrefaciens (Lee et al., 1981), ‘A. thalassomethanolica’ (Yamamoto et al., 1980) and A. nigrifaciens (White, 1940; Baumann et al., 1984a; Ivanova et al., 1996a). Intensive rRNA–DNA hybridization study (Van Landschoot & De Ley, 1983) showed a high level of genetic heterogeneity among the members of the genus and allowed the following rRNA relatedness clusters to be revealed: (i) the A. macleodii cluster; (ii) the A. haloplanktis cluster, which included the majority of Alteromonas species and one species from the genus Pseudomonas, [Pseudomonas] piscicida (Bein, 1954; Buck et al., 1963); (iii) the [A.] putrefaciens and [Alteromonas] hanedai cluster (Jenson et al., 1983); and (iv) the [A.] vaga and [A.] communis cluster, which was classified as a new genus, Marinomonas (Gauthier & Breittmayer, 1992). Based on 5S rRNA sequences, the species [A.] putrefaciens, [A.] hanedai and [Alteromonas] colwelliana (Weiner et al., 1988) were combined into a new genus, Shewanella (MacDonell & Colwell, 1985). By the early 1990s, the genus Alteromonas had been supplemented with several novel species, Alteromonas denitrificans (Enger et al., 1987), A. atlantica, A. carrageenovora (Akagawa-Matsushita et al., 1992), A. tetraodonis (Simidu et al., 1990), ‘A. rava’ (Kodama et al., 1993), [A.] fuliginea, A. distincta and A. elyakovii (Romanenko et al., 1994, 1995; Ivanova et al., 1996b).
In 1995, based on the analysis of 16S rRNA gene sequences, the genus Alteromonas was revised. The revised genus Alteromonas contained only one species, A. macleodii, while a new genus Pseudoalteromonas, which included the rRNA relatedness group II species, was formed (Gauthier et al., 1995). According to DNA–DNA hybridization data and phylogenetic studies, the name A. fuliginea should be regarded as a later synonym of the name Pseudoalteromonas citrea (Ivanova et al., 1998), while the species A. distincta and A. elyakovii were transferred to the genus Pseudoalteromonas (Ivanova et al., 2000a; Sawabe et al., 2000). The species A. tetraodonis has been reclassified as A. haloplanktis subsp. tetraodonis (Akagawa-Matsushita et al., 1993). However, further studies showed that this species had to be retrieved, as Pseudoalteromonas tetraodonis (Ivanova et al., 2001a). In recent years, a number of novel species of marine pseudoalteromonads have been described, such as Pseudoalteromonas antarctica (Bozal et al., 1997) and Pseudoalteromonas prydzensis (Bowman, 1998), which was isolated from Antarctic coastal waters, Pseudoalteromonas bacteriolytica (Sawabe et al., 1998), which was isolated from wounded fronds of Laminaria japonica collected from the Sea of Japan, and Pseudoalteromonas peptidolytica (Venkateswaran & Dohmoto, 2000), which was isolated from sea water. The highly bioactive species Pseudoalteromonas tunicata (Holmström et al., 1998) was isolated from the ascidian Ciona intestinalis residing in coastal waters of western Sweden. More recently, several more species were proposed, including Pseudoalteromonas ulvae (Egan et al., 2001), Pseudoalteromonas issachenkonii (Ivanova et al., 2002a), Pseudoalteromonas ruthenica (Ivanova et al., 2002b), Pseudoalteromonas maricaloris, Pseudoalteromonas flavipulchra (former A. aurantica NCIMB 2033) (Ivanova et al., 2002c), Pseudoalteromonas translucida, Pseudoalteromonas paragorgicola (Ivanova et al., 2002d), Pseudoalteromonas agarivorans (Romanenko et al., 2003a) and Pseudoalteromonas phenolytica (Isnansetyo & Kamei, 2003).
Bowman et al. (1998b) described a group of pigmented, psychrophilic, strictly aerobic, heterotrophic organisms isolated from sea-ice cores from eastern Antarctica that formed a distinct branch adjacent to Alteromonas. These bacteria received genus status and consisted of two species, Glaciecola punicea and Glaciecola pallidula. One more species, Glaciecola mesophila, recently enlarged the genus (Romanenko et al., 2003b).
A few years later, the aerobic marine genus Idiomarina was described, which included two species, Idiomarina abyssalis and I. zobellii (Ivanova et al., 2000a). These bacteria were isolated from sea-water samples taken from depths of 4000 and 5000 m, respectively. The species were phenotypically close to bacteria of the genera Alteromonas, Pseudoalteromonas and Marinomonas, but differed from them in their cellular fatty acid profiles and their inability to use carbohydrates as sole sources of carbon and energy. The two species were distinguished by their characteristic morphology: I. zobellii cells were fimbriated, while I. abyssalis cells were enclosed in sheaths. Recently two more species were described, Idiomarina baltica (Brettar et al., 2003) and I. loihiensis (Donachie et al., 2003).
The genus Colwellia (Deming et al., 1988) originally included two facultatively anaerobic bacteria, Colwellia psychrerythraea and C. hadaliensis. The first strains of this genus were isolated from water samples taken in the Mariana Trench and near the coast of the United States. The type strain of the species C. psychrerythraea was found to be an obligate barophile. Bowman et al. (1998a) described four novel psychrophilic species of this genus, Colwellia demingiae, C. hornerae, C. rossensis and C. psychrotropica, and novel strains of C. psychrerythraea. None of these Antarctic isolates were barophilic and all of them synthesized docosahexaenoic acid (22 : 6
3) in amounts of up to 8 % of the total cellular content of fatty acids. The type strain of the species Colwellia maris was originally assigned to the genus Vibrio and was subsequently reclassified (Yumoto et al., 1998).
Another genus, closely related to genus Colwellia, Thalassomonas, represented by a single species Thalassomonas viridans, was described to accommodate halophilic chemo-organotrophic bacteria isolated from oysters cultivated off the Mediterranean coast at Valencia (Spain) (Macián et al., 2001).
Currently, the genus Shewanella MacDonell and Colwell 1985 comprises more than 20 species (Shewanella algae, S. amazonensis, S. baltica, S. benthica, S. colwelliana, S. denitrificans, S. fidelis, S. frigidimarina, S. gelidimarina, S. hanedai, S. japonica, S. livingstonensis, S. marinintestina, ‘S. massilia’, S. olleyana, S. oneidensis, S. pealeana, S. putrefaciens, S. sairae, S. schlegeliana, S. violacea, S. waksmanii and S. woodyi). These species are Gram-negative, facultatively anaerobic and aerobic, readily cultivated gammaproteobacteria mainly associated with aquatic habitats (Jensen et al., 1980; Lee et al., 1981; Weiner et al., 1988; Coyne et al., 1989; Gauthier et al., 1995; Bowman et al., 1997; Leonardo et al., 1999; Venkateswaran et al., 1999; Ivanova et al., 2001b, 2003; Bozal et al., 2002; Satomi et al., 2003). During the last decade, bacteria of this genus have been studied extensively because of their important role in co-metabolic bioremediation of halogenated organic pollutants, destructive souring of crude petroleum and the dissimilatory reduction of magnesium and iron oxides and their ability to produce high proportions of polyunsaturated fatty acids (PUFA) (Myers & Nealson, 1988; Petrovskis et al., 1994; Russell & Nichols, 1999).
The closest relatives of Shewanella species are bacteria of the genus Moritella Urakawa et al. 1998 that are represented by four species, Moritella marina (Urakawa et al., 1998), M. japonica (Nogi et al., 1998), M. yayanosii (Nogi & Kato, 1999) and M. viscosa (Benediktsdóttir et al., 2000).
Because of the initial phenotypic misclassification of [Pseudomonas] doudoroffii as a close relative of Aeromonas hydrophila and Tolumonas auensis, its taxonomic status and phylogenetic relationships within the ‘Gammaproteobacteria’ remained unclear until recently. Brown et al. (2001) proposed to create the genus Oceanimonas to accommodate the novel phenol-degrading bacterium Oceanimonas baumannii as well as [Pseudomonas] doudoroffii (Brown et al., 2001).
The final two genera comprise marine facultatively anaerobic and aerotolerant anaerobic gammaproteobacteria: Ferrimonas, represented so far by the species Ferrimonas balearica (Rosselló-Mora et al., 1995), and Psychromonas, which possesses five species Psychromonas antarctica (Mountfort et al., 1998), Psychromonas kaikoae (Nogi et al., 2002), Psychromonas marina (Kawasaki et al., 2002), Psychromonas arctica (Groudieva et al., 2003) and Psychromonas profunda (Xu et al., 2003).
This study is a further extension of our investigation of Alteromonas-like gammaproteobacteria (Ivanova & Mikhailov, 2001) and aimed to provide a basis of a delineation system based on a comprehensive overview of their phylogenetic relationships (16S rRNA gene sequences), the presence of specific compensatory mutations visible in the secondary structure of the molecule and polyphasic classification strategy. This paper mainly reviews published data with reference to the relevant publications that contain original or cited data on phenotypic and chemotaxonomic characteristics used in the identification of Alteromonas-like bacteria.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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Phylogenetic analyses.
Phylogenetic dendrograms were reconstructed according to three different methods: NJ (BIONJ), maximum-likelihood (ML) (using the Global option) and maximum-parsimony (MP). For the NJ analysis, a matrix distance was calculated according to Kimura's two-parameter correction. Bootstraps were done using 1000 replications, BIONJ and Kimura's two-parameter correction. BIONJ was according to Gascuel (1997), ML and MP were from PHYLIP (Phylogeny Inference Package, version 3.573c; distributed by J. Felsenstein, Department of Genetics, University of Washington, Seattle, USA). Preliminary phylogenetic analyses were done using the most conserved parts of the sequences. Phylogenetic dendrograms were drawn using NJPLOT (Perrière & Gouy, 1996).
Domains used to construct final phylogenetic trees excluded positions likely to show homoplasy or that were difficult to align. When bacterial sequences from different genera are used to determine phylogenetic relationships, domains used to construct a phylogenetic tree should be examined extremely carefully, since positions that can be properly aligned decrease and homoplasy increases with the depth of the phylogenetic tree. For that reason, a detailed phylogenetic tree that analyses the position of a species within a genus is usually different from that used to position this genus within its class or phylum. As a result, the tree presented in this paper (and the trees available as supplementary material) should be taken with caution near their leaves: the analysis has been done to position the genera in the ‘Gammaproteobacteria’, not to position the different species within a genus. These trees define which species belong to a genus, but not, with consistency, which are sister species. For Fig. 1, the domains used corresponded to positions 95–175, 193–442, 454–819 and 845–1393 of the sequence of Aeromonas allosaccharophila CECT 4199T (S39232). The topology shown is that of the bootstrap analysis, as it as been demonstrated that this topology is often better than that of a simple tree (Berry & Gascuel, 1996).
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shows the numbers of OGUs obtained when the cut-off was increased, and OGUs obtained at 93 % (at which a clear plateau was obtained corresponding largely to genus delimitation) of similarity are indicated in Supplementary Fig. E. In order to perform this comparison, it is necessary to compare only sequences that overlap completely (no missing 5' or 3' end); for this reason, similarity values were calculated using positions 137–1335 corresponding to Aeromonas allosaccharophila CECT 4199T (S39232).
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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are labelled to indicate which branches were found by all analyses. Labelled branches are thus particularly ‘secure’, which does not mean that unlabelled branches are wrong, simply that we cannot be sure that they represent the evolutionary history of the gene.
Phylogenetic analyses based on 16S rRNA gene sequences
As discussed below, it would have been best to be able to compare the results of analyses using different genes. However, this was not possible as only 16S rRNA gene sequences are available for representatives of the group of bacteria analysed (see below). Phylogenetic analyses of 16S rRNA gene sequences of the Alteromonas-like bacteria revealed that, despite their close phenetic similarity, bacteria of the genera Alteromonas, Pseudoalteromonas, Glaciecola, Thalassomonas, Colwellia and Idiomarina did not form a clade but several phylogenetically distinct lineages that were consistently recovered from several phylogenetic analyses. The topology shown in Fig. 1 is that of the bootstrap tree from the NJ method. Only branches with percentages indicated should be interpreted as consistent. Some other branches were retrieved by two methods only when all sequences were used (for example Pseudoalteromonas; see Supplementary Fig. B). This is sometimes a problem with character-based methods (ML or MP) when the number of sequences analysed approaches the number of significant characters; reducing the number of sequences analysed allowed us to find a monophyletic taxon with all three methods (Supplementary Figures B–D in IJSEM Online). Finally, phylogenetic analyses based on a single gene reveal the history of the gene, not always that of the species. 16S rRNA gene sequences are, however, peculiar as they pertain to a true multigene family; their presence usually in multiple copies and the phenomenon of gene conversion (Cilia et al., 1996) render them less sensitive to lateral transfer (no positive selective pressure and unlikely genetic drift) and they are thus particularly appropriate for phylogenetic analyses above the species level (Cilia et al., 1996). It is clear, however, that the precise position of each genus within the phylum Proteobacteria will become clearer as more and more housekeeping gene sequences become available, a goal that has not yet been reached for Alteromonas-like bacteria.
Housekeeping genes
Other housekeeping genes such as gyrB, rpoB and recA would have been useful, but the sequences of too many genera are still missing (gyrB, four entries for proteobacteria; rpoB, 352 entries for ‘Gammaproteobacteria’ and, for the Alteromonadales, only five sequences of Shewanella, two complete, three partial 100 nt; recA, 546 sequences for ‘Gammaproteobacteria’, for the Alteromonadales, no sequence, for vibrios, 216 entries). Finally, the 16S–23S intergenic spacer region is much too divergent for use in phylogenetic analyses at the family level.
Signature nucleotide positions
The use of signature nucleotide positions.
Signature nucleotides are nucleotide residues that are found explicitly in all currently described species of a proposed taxon and not in other taxa. Signatures sites may be particularly strong when they consist of compensatory mutations involved in maintaining the secondary structure of the molecule (see Methods). Taking into account signature sites is only an improvement in phylogenetic analyses, as no phylogenetic method can yet take into account that different positions should be weighted differently according to the selective pressure that applies at every position. It is possible to use weights, but we do not yet know how to define what weight to apply according to the position in the structure.
Taxon identification with signature positions.
Confirmation of the branching order of the Alteromonas-like bacteria was sought by searching for signature nucleotide positions (Table 1). The signature patterns must be considered tentative since, with a significant increase in the number of sequences in any phylogenetic lineage, the number of signature nucleotides may decrease because of possible new mutations (and/or sequencing errors overlooked).
Careful examination of Table 1 suggested that some mutations were compensatory (for example, a G–C pair instead of an A–T pair). We then added the E. coli sequence in our alignment and mapped all of the signatures on the secondary structure of the 16S rRNA molecule. Since all Alteromonas-like bacteria belong to the ‘Gammaproteobacteria’ and hence are related to E. coli, there is little variation in the secondary structure, except for the variable parts of helices indicated with blue dashed lines on Fig. 2. This analysis showed that signature positions can be divided into three classes: (i) single compensatory mutations, for example a G–C pair mutating to G–U, (ii) double compensatory mutations (transition), for example A–T to G–C, and finally (iii) mutations affecting nucleotides not paired in the secondary structure (indicated in Table 1). Observations of single or double compensatory mutations are rather strong arguments that the signatures observed are not the result of errors in sequences. The last type of mutations is quite interesting: since these mutations are conserved for a large cluster of species, it means that there is rather strong selective pressure on these nucleotides, suggesting that they might be part of interactions involving the structures of the rRNA at the tertiary or quaternary level (within 16S rRNA or between 16S and 23S rRNA).
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Discrimination of genera.
The results revealed that there was a good correlation at the similarity level between genera, signature sites and OGUs, though there were a few exceptions. One exception was the genus Pseudoalteromonas in its current state, but this problem was solved as proposed below, by creating a separate genus, Algicola, for [Pseudoalteromonas] bacteriolytica. A second exception was the genus Glaciecola. Bacteria of this genus shared many signature nucleotides with Alteromonas species. This finding might be a strong argument for the unification of these two genera. Indeed, these bacteria are close genetically (similar G+C content of the DNA) and share many phenotypic and chemotaxonomic characteristics. They were, however, distributed in different OGUs, which is an argument to keep distinct genera. Vibrio and Photobacterium were grouped in a single OGU (with the exception of ‘Vibrio aspartigenicus’). The taxonomic status of these genera seems far from clear, since detailed phylogenetic analyses (not shown) suggest that the two genera are in fact intermingled; a possible solution would be to reduce them to a single genus. For these taxa, data on housekeeping genes are clearly required. Oceanimonas and Oceanisphaera were in a single OGU, but we were not able to find signature nucleotides for this cluster. A close examination of the only sequences available for two of the three species suggested the presence of obvious sequencing errors (a different nucleotide at a position otherwise conserved in all other sequences). The availability of more and better sequences should solve this problem. Finally, Thalassomonas and Colwellia were also placed in a single OGU. Analysis of sequence signatures suggested splitting the genus Colwellia into two genera. A more detailed analysis of this clade is required.
Formal rules for genus identification
So far, there is no formal rule for delimitation of a taxon above the species level. The general position is to define a genus when there is a robust branch that clearly delineates a clade in phylogeny and when these organisms present distinct shared phenotypes. This is often problematic when members of a group have adapted to very different ecological niches, resulting in divergent phenotypes. Our analyses in terms of aggregative OGUs sharing a minimal level of 16S rRNA gene similarity, comparison with the phylogeny and sequence signatures suggest that it might be possible to use useful criteria for taxon delineation above the species level; this would extend the present criteria used at the species level: percentage of DNA–DNA association and 97 % 16S rRNA gene sequence similarity (Stackebrandt & Goebel, 1994). Aggregative clustering at the 93 % similarity level and the presence of site signatures may be used as a general criterion to help to decide at which level in a tree a genus can be defined. If such an approach was shown to be possible for the genera analysed in this study, studies of different groups (e.g. Actinobacteria, Cyanobacteria, Archaea) are required before we can make a definitive proposal. Presently, we were not able to use lower percentages of aggregation to try to define families, since the OGUs obtained were largely inconsistent with the phylogeny. A possible reason might be that domains that are too divergent for that level of taxonomy exist in the complete rRNA sequences. Restriction of the analysis to conserved domains might be a solution. We are presently investigating the use of more sophisticated clustering algorithms, restricting to more conserved domains as well as studying different groups of bacteria in order to propose a generalization of the procedure.
In conclusion, the following monophyletic groups can be distinguished.
Group I, including Pseudoalteromonas species and [Pseudoalteromonas] bacteriolytica
The Pseudoalteromonas cluster, encompassing more than 30 species, was relatively heterogeneous, with interstrain 16S rRNA gene sequence similarity values ranging from 90 to 99·9 % (see Supplementary Table A). The results obtained are consistent with previous detailed phylogenetic analysis (Gauthier et al., 1995) and confirmed that species of the genus consisted of several monophyletic taxa. One of them comprises a closely related group of so-called non-pigmented species (currently includes 15 species, including the type strain of the genus, Pseudoalteromonas haloplanktis; Pseudoalteromonas nigrifaciens and Pseudoalteromonas distincta can produce melanin-like pigments depending on culture medium) with high interstrain similarity values of 98–99·9 %. Other species in the genus are pigmented, synthesizing a variety of pigments (prodigiosin-like, carotenoids and some other pigments), and could be split into six clusters: (i) Pseudoalteromonas citrea and Pseudoalteromonas aurantica, (ii) Pseudoalteromonas ruthenica, (iii) Pseudoalteromonas rubra, Pseudoalteromonas luteoviolacea, Pseudoalteromonas peptidolytica, Pseudoalteromonas piscicida, Pseudoalteromonas flavipulchra and Pseudoalteromonas mariscaloris, (iv) Pseudoalteromonas tunicata and Pseudoalteromonas ulvae, (v) Pseudoalteromonas denitrificans and (vi) [Pseudoalteromonas] bacteriolytica (see detailed tree; Supplementary Fig. B). This last species branched deeply and was a sister species to all other species. The deep branching (low similarity levels for nucleotides of 16S rRNA down to 90·3 %), the lack of sequence signature, the lack of association with other species of the genus, low DNA–DNA hybridization values (3–5 %) and some characteristic phenotypic traits (bacteriolytic activity, requirement for organic growth factors, different pattern of carbohydrate utilization) indicated that this bacterium should be placed in a separate genus. Therefore, we propose to create a new family, Pseudoalteromonadaceae fam. nov., which comprises two genera, Pseudoalteromonas and Algicola gen. nov., which contains Algicola bacteriolytica comb. nov. as its type species.
Group II, including Idiomarina species, Colwellia species and Thalassomonas viridans
Group II appeared as a clade that comprised two subclades strongly supported by bootstrap (Fig. 1 and Supplementary Fig. D): one cluster including all Colwellia species and Thalassomonas viridans and a second cluster including Idiomarina species. Species of the genus Colwellia failed to share common signature nucleotides, except when the deeply branched sequence of Colwellia hornerae was removed from the analysis. It is possible that some errors in sequences might be responsible for the failure to find characteristic signatures; on the other hand, the deep branching of C. hornerae and peculiar characteristic phenotypic traits (sensitivity to vibriostatic agent O/129, the lack of sequence signature, the lack of the ability to produce chitinase, different pattern of carbohydrate utilization) and distinct cellular fatty acid composition, e.g. significantly high proportions of 15 : 1(n-8), 15 : 0 and i16 : 0 fatty acids (Bowman et al., 1998a), are indications that this species may need to be recognized as representing a separate genus. A detailed study of this cluster is necessary.
Because of the weak bootstrap percentage uniting Idiomarina with the other genera, it should be retained as a separate taxon. In this context, we propose to create the new families Colwelliaceae fam. nov., restricted to bacteria of the genera Colwellia and Thalassomonas, and Idiomarinaceae fam. nov. Further sequences for novel species or different genes may help to improve certainty in this part of the tree.
Group III, including Alteromonas and Glaciecola species
This clade included the genus Alteromonas and two species of Glaciecola. We therefore propose to restrict the recently proposed family Alteromonadaceae (Ivanova & Mikhailov, 2001) to only these two genera, since the taxonomic placement of bacteria of the genera Pseudoalteromonas, Idiomarina and Colwellia within the family appears not to be appropriate (Fig. 1 and Supplementary Fig. C).
Group IV, including Aeromonas, Oceanisphaera and Oceanimonas species
Oceanimonas and Oceanisphaera species formed a loosely supported clade (only two methods) and, with Aeromonas species, a loosely supported clade was also revealed (two methods also, although different ones). For the reasons mentioned above, taxonomic affiliation on the family level remains unclear and the recognition of a family should await more sequences.
Group V, including Vibrio, Salinivibrio and Photobacterium species
These genera formed a robust cluster that constitutes the family Vibrionaceae. Importantly, it included the sequences of Allomonas enterica and Hyphomicrobium indicum; the grouping of the genus Allomonas (and also the genus Listonella) within the genus Vibrio still awaits nomenclatural clarification. Since these sequences could result from sequencing of contaminants, one should await the appearance of at least a second sequence before adjusting their taxonomy (as also suggested by Thompson et al., 2003).
Isolated genera
Bacteria of the four genera Shewanella, Moritella, Psychromonas and Ferrimonas (Fig. 1) did not form a monophyletic clade with other genera included in this study, at least when using 16S rRNA gene sequences as support of phylogenetic information. The Shewanella cluster, encompassing 22 species, was rather heterogeneous, with 16S rRNA gene sequence similarity values ranging from 93 to 99·9 %. Notably, a single signature nucleotide, 858 (C), was identified; this small number may result from errors in some sequences. Our results confirmed previous observations (Venkateswaran et al., 1999; Nogi & Kato, 2002) that a few monophyletic clusters are constantly recovered for Shewanella species.
Bacteria of the genera Moritella, Psychromonas and Ferrimonas clustered separately at the family level (supported by specific signature nucleotides; Table 1) and could not be grouped with any other taxa.
Thus, phylogenetic classification performed in this study was consistent with phenotypic and polyphasic classifications and has led to the grouping of these bacteria into several taxa on the family level as follows: Alteromonadaceae emend., including genera Alteromonas and Glaciecola, Pseudoalteromonadaceae fam. nov., including genera Pseudoalteromonas and Algicola gen. nov., Colwelliaceae fam. nov., comprising Colwellia and Thalassomonas, and the monogeneric families Idiomarinaceae fam. nov., Ferrimonadaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov. and Psychromonadaceae fam. nov.
The sources, habitats and differential characteristics of the proposed taxa are summarized in Table 2. Bacteria of the family Alteromonadaceae are aerobic, slightly halophilic organisms, distinct in the inability to hydrolyse chitin and agar, but able to utilize a range of carbohydrates. Bacteria of these genera can be distinguished by pigmented colonies, G+C content of their DNA and psychrophily. The numerous species of the family Pseudoalteromonadaceae are diverse in their phenotypic traits and difficult even in tentative classification. However, bacteria of the newly proposed genus Algicola can be easily differentiated from other pseudoalteromonads by the lack (or weak activity) of catalase, limited temperatures for growth (from 15 to 35 °C) and presence of bacteriolytic activity (Sawabe et al., 1998). Though the bacteria of the two families Alteromonadaceae and Pseudoalteromonadaceae have similar cellular fatty acid compositions, the different ratio of major cellular fatty acids allows separation at the genus level (Svetashev et al., 1995; Ivanova et al., 2000b). Bacteria of the family Colwelliaceae are both aerobic and facultatively anaerobic, obligatorily marine organisms that require sodium ions for growth and include pigmented and non-pigmented species; many of those hydrolyse chitin, gelatin, starch and Tween 80. Bacteria of the genus Colwellia are different from those of Thalassomonas in their ability to reduce nitrate to nitrite and psychrophily. Bacteria of the family Idiomarinaceae differ from colwellias and thalassomonads by the ability to tolerate high concentrations of NaCl and limited ability to utilize carbohydrates. The bacteria of the genera Colwellia, Thalassomonas and Idiomarina have characteristic patterns of cellular fatty acids (Bowman et al., 1997; Russell & Nichols, 1999; Macián et al., 2001). Bacteria of the families Shewanellaceae and Moritellaceae consist of both aerobic and facultatively anaerobic organisms that require sea water or sodium ions for growth and can be distinguished by halophilicity and by the ability to synthesize either eicosapentaenoic (20 : 53) or docosahexaenoic (22 : 63) acid, respectively.
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Gram-negative, rod-shaped bacteria. Motile. Do not form endospores or microcysts. Chemo-organotrophs. Oxygen is used as the electron acceptor. Aerobic or facultatively anaerobic. Usually do not denitrify. Arginine dihydrolase is absent. Require Na+ ions for growth. In most species, the major isoprenoid quinone is Q8. The major fatty acids are 16 : 0, 16 : 117 and 16 : 17. Members of the family have been isolated from coastal, open and deep-sea waters and invertebrates from marine environments. The family is a member of the ‘Gammaproteobacteria’ with the following nucleotide sequence characteristics: 304 (A), 734 (A), 736 (T), 770 (T), 809 (A). The family comprises the type genus Alteromonas Baumann et al. 1972 emend. Gauthier et al. 1995 and the genus Glaciecola Bowman et al. 1998.
Description of Pseudoalteromonadaceae fam. nov.
Pseudoalteromonadaceae (Pseu.do.al.te.ro.mo.na.da'ce.ae. N.L. fem. n. Pseudoalteromonas type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Pseudoalteromonadaceae the Pseudoalteromonas family).
Gram-negative, rod-shaped bacteria. Motile by means one or several flagella (sometimes coated); some species have lateral or bipolar flagella. Some species produce capsules. Chemo-organotrophs. Require Na+ ions for growth; some strains are capable of growing in media containing 15 % NaCl. Aerobic or facultatively anaerobic. Usually do not denitrify. Arginine dihydrolase is absent. In most species, the major isoprenoid quinone is Q8. The major fatty acids are 16 : 0, 16 : 17 and 18 : 17. Members of the family have been isolated from coastal, open and deep-sea waters, sediments, marine invertebrates, fish and algae from marine environments. The family is a member of the ‘Gammaproteobacteria’ with the following nucleotide sequence characteristics: 733 (A), 744 (T), 833 (C), 852 (T), 853 (T). The family comprises the type genus Pseudoalteromonas Gauthier et al. 1995 and the genus Algicola gen. nov.
Description of Algicola gen. nov.
Algicola (Al.gi.co'la. L. n. alga -ae a seaweed; L. suff. -cola from L. n. incola an inhabitant, dweller; N.L. fem. n. Algicola inhabitant of algae).
Gram-negative, strictly aerobic, chemo-organotrophic organisms. Motile by means of a single flagellum. Oxidase-positive. Requires sea water or addition of marine salts and organic factors for growth. Mesophilic. Have bacteriolytic activity. The genus is affiliated to the ‘Gammaproteobacteria’ and contains one species, Algicola bacteriolytica, which is the type species.
Description of Algicola bacteriolytica (Sawabe et al. 1998) comb. nov.
Basonym: Pseudoalteromonas bacteriolytica Sawabe et al. 1998.
Description is identical to that given by Sawabe et al. (1998). The DNA G+C content of the type strain is 46·0 mol%. The type strain is IAM 14595T (=ATCC 700679T=CIP 105725T).
Description of Shewanellaceae fam. nov.
Shewanellaceae (She.wa.nel.la'ce.ae. N.L. fem. n. Shewanella type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Shewanellaceae the Shewanella family).
Gram-negative, rod-shaped bacteria. Motile. Do not form endospores or microcysts. Chemo-organotrophs. Aerobic or facultatively anaerobic. Able to reduce nitrate to nitrite and grow anaerobically by reducing trimethylamine N-oxide and ferric compounds. Some species do not require Na+ ions for growth. In most species, the major isoprenoid quinones are Q7, Q8 and MK7. The major fatty acids are 14 : 0, 16 : 17, 16 : 0 and 17 : 16. Most species produce PUFA. Members of the family have been isolated from coastal, open and deep-sea waters and invertebrates from marine environments. The family is a member of the ‘Gammaproteobacteria’. The type genus is Shewanella MacDonell and Colwell 1985.
Description of Moritellaceae fam. nov.
Moritellaceae (Mo.ri.tel.la'ce.ae. N.L. fem. n. Moritella type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Moritellaceae the Moritella family).
Gram-negative, curved or straight rod-shaped bacteria. Motile. Do not form endospores or microcysts. Chemo-organotrophs. Aerobic or facultatively anaerobic. Require Na+ ions for growth. Usually do not denitrify. Arginine dihydrolase is absent. Require Na+ ions for growth. In most species, the major isoprenoid quinones are Q7 and Q8. The major fatty acids are i13 : 0, 14 : 0, 14 : 1, 16 : 0 and 16 : 1. Most species produce PUFA. Members of the family have been isolated from deep-sea waters from marine environments. The family is a member of the ‘Gammaproteobacteria’ with the following nucleotide sequence characteristics: 399(A), 858(T), 1311 (G), 1326 (C). The type and only genus is Moritella Urakawa et al. 1998.
Description of Idiomarinaceae fam. nov.
Idiomarinaceae (Idio.ma.ri.na'ce.ae. N.L. fem. n. Idiomarina type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Idiomarinaceae the Idiomarina family).
Gram-negative, rod-shaped bacteria. Motile. Do not form endospores or microcysts. Chemo-organotrophs. Oxygen is used as the electron acceptor. Aerobic or facultatively anaerobic. Usually do not denitrify. Arginine dihydrolase is absent. Require Na+ ions for growth. The major fatty acids are i15 : 0 and i17 : 0. Members of the family have been isolated from open and deep-sea waters. The family is a member of the ‘Gammaproteobacteria’ with the following nucleotide sequence characteristics: 143 (C), 662 (A), 682 (A), 830 (T), 856 (A). The type and only genus is Idiomarina Ivanova et al. 2000.
Description of Colwelliaceae fam. nov.
Colwelliaceae (Col.wel.li.a'ce.ae. N.L. fem. n. Colwellia type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Colwelliaceae the Colwellia family).
Gram-negative, curved rod-shaped bacteria. Motile. Some species are non-motile. Do not form endospores or microcysts. Require Na+ ions for growth. Chemo-organotrophs. Facultatively anaerobic. The major fatty acids are 15 : 18, 15 : 0, i16 : 0, 16 : 17 and 16 : 0. Produce PUFA. The family is a member of the ‘Gammaproteobacteria’ with the following nucleotide sequence characteristics: 579 (T), 762 (A). Genera belonging to the family are the type genus Colwellia Deming et al. 1988 and the genus Thalassomonas Macián et al. 2001.
Description of Ferrimonadaceae fam. nov.
Ferrimonadaceae (Fer.ri.mo.na.da'ce.ae. N.L. fem. n. Ferrimonas type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Ferrimonadaceae the Ferrimonas family).
Gram-negative, rod-shaped bacteria. Motile. Do not form endospores or microcysts. Chemo-organotrophs. Facultatively anaerobic. Nitrate is reduced to nitrite. Require Na+ ions for growth. The major fatty acids are i15 : 0, 16 : 19 and 17 : 19. The family is a member of the ‘Gammaproteobacteria’. The type genus is Ferrimonas Rosselló-Mora et al. 1995.
Description of Psychromonadaceae fam. nov.
Psychromonadaceae (Psy.chro.mo.na.da'ce.ae. N.L. fem. n. Psychromonas type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Psychromonadaceae the Psychromonas family).
Gram-negative, rod- to oval-shaped bacteria. Motile. Do not form endospores or microcysts. Chemo-organotrophs. Aerotolerant anaerobes. Some species do not require Na+ ions for growth. Arginine dihydrolase is absent. In most species, the major isoprenoid quinone is Q8. The major fatty acids are 16 : 0 and 16 : 17. Members of the family have been isolated from coastal, open and deep-sea waters and invertebrates from marine environments. The family is a member of the ‘Gammaproteobacteria’ with the following nucleotide sequence characteristics: 385 (T), 811 (A), 842 (A), 845 (T), 1336 (T). The type and only genus is Psychromonas Mountfort et al. 1998.
Description of Photobacterium indicum (Johnson and Weisrock 1969) comb. nov.
Basonym: Hyphomicrobium indicum Johnson and Weisrock 1969.
The description is identical to that given by Johnson & Weisrock (1969). The type strain is MBIC 3157T [=ATCC 19614T=DSM 5151T=IFO (now NBRC) 14233T].
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