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Comamonadaceae, a New Family Encompassing the Acidovorans Rrna Complex, Including Variovorax Paradoxus Gen

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Comamonadaceae, a New Family Encompassing the Acidovorans Rrna Complex, Including Variovorax Paradoxus Gen INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1991, p. 445450 Vol. 41, No. 3 0020-7713/91/030445-06$02.OO/O Copyright 0 1991, International Union of Microbiological Societies NOTES Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov. , comb. nov. for Alcaligenes paradoxus (Davis 1969) A. WILLEMS, J. DE LEY, M. GILLIS," AND K. KERSTERS Laboratorium voor Microbiologie en microbiele Genetica, Rijksuniversiteit Gent, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium A new family, the Comamonadaceae, is proposed for the organisms belonging to the acidovorans rRNA complex in the beta subclass of the Proteobacteria. This family includes the genera Comamonas, Acidovorax, Hydrogenophaga, Xylophilus, and Variovorax (formerly Alcaligenes paradoxus), as well as a number of phylogenetically misnamed Aquaspirillum and phytopathogenic Pseudomonas species. DNA-rRNA hybridization and 16s rRNA cataloging have duplex (i.e., when DNA and rRNA from the same reference shown that several of the large taxa described in the past as strain are used) and the Tm(,) value of a heterologous phenotypic entities (e.g., the genus Pseudomonas, spirilla, hybrid]. Comparable or slightly greater AT,(,) ranges have the genus Alcaligenes, photosynthetic bacteria) are phylo- been observed in several bacterial families, including the genetically very heterogeneous (12, 21, 27, 37-40). As a Neisseriaceae [AT,(,) range, 7.6"C (29)], the Alcaligenaceae consequence, these taxa are gradually being split up into [AT,,,, range, 6°C (9)], the Acetobacteriaceae [AT,(,) range, several genera, and only the group that includes the original 5°C (19)], the Enterobacteriaceae [AT,(,) range, 8°C (lo)], type species can retain the original genus name. the Vibrionaceae [AT,,,, range, 8°C (lo)], and the Pasteurel- The acidovorans rRNA complex is a large collection of laceae [AT,(,) range, 8°C (S)]. generically misnamed taxa that are closely related to Coma- Likewise, an analysis of 16s rRNA catalogs showed that monas acidovorans (32,33,35). This group belongs to rRNA strains of [Aquaspirillum aquaticum] (now Comamonas ter- superfamily I11 or the beta subclass of the Proteobacteria rigena [36]), C. terrigena, [Pseudomonas]acidovorans (now (30). It gradually emerged from the Pseudomonas aci- C. acidovorans [31]), [Pseudomonas] testosteroni (now Co- dovorans group, one of at least five genotypic groups that marnonas testosteroni [3 11) , and [Aquaspirillum] gracile were delineated within the genus Pseudomonas by using form a relatively tight phylogenetic cluster with the lowest DNA-rRNA hybridization (12, 26) and were later confirmed branching at an SABvalue of 0.75 (40). by using several other techniques (2, 4, 16, 24, 37). During We propose that the acidovorans rRNA complex should the last decade this group was extended considerably. A list be recognized as a new bacterial family, the Comamona- of the taxa belonging to this group is given in Table 1. The daceae, in rRNA superfamily I11 (the beta subclass of the classification of several of these species has already been Proteobacteria). The organisms belonging to this family are revised (Table 1). For the sake of clarity, taxa that are genotypically highly related and phenotypically rather di- misnamed according to present phylogenetic data are listed verse (36). They include common soil and water inhabitants, below in brackets. H, or CO oxidizers, phytopathogens, nonpathogenic isolates The criterion which we used to assign strains to the of clinical origin, a psychrophilic isolate, and rods and acidovorans rRNA complex is that their DNAs should have helical cells which are polarly, lofotrichously, or peritri- T,(,, values [T,(,) is the temperature, in degrees Celsius, at chously flagellated. Compared with the original P. aci- which one-half of a DNA-rRNA duplex is thermally dena- dovorans group (Pseudomonas section I11 [25]),the family tured] of at least 75°C when they are hybridized with labeled Comamonadaceae encompasses a much larger number of rRNA from C. acidovorans Stanier 14T (= LMG 1126T = taxa and a much larger variety of phenotypes. Many of the ATCC 15668T) (T = type strain) or any other strain belong- characteristics of the original P. acidovorans group (26) ing to the acidovorans rRNA complex. On the basis of the (e.g., meta cleavage of protocatechuate, absence of growth results of extensive DNA-rRNA hybridization, in which 15 at 41"C, absence of denitrification [25], and typical regulation labeled rRNA probes were used, the following rRNA of aromatic amino acid biosynthesis [4]) have not been branches were delineated (Fig. 1): one Xylophilus rRNA studied in all taxa belonging to the Comamonadaceae and branch, one Hydrogenophaga rRNA branch, one Variovo- therefore cannot be used to define this family phenotypi- rax rRNA branch, one Acidovorax rRNA branch, four cally. Phenotypic comparisons at the family level in this case Comamonas rRNA branches, five [Aquaspirillum] rRNA are complex because the family Comamonadaceae unites a branches, and the [Pseudomonas] avenue rRNA branch. variety of taxa that were in the past assigned to various These taxa grouped at mean AT,,,, values of 4 to 5°C [AT,(,) genera and regarded as unrelated on phenotypic grounds. is the difference between the Tm(,)value of the homologous Table 2 shows several important characteristics of the Co- mamonadaceae and other phylogenetic groups which phe- notypically resemble members of this family. As one climbs * Corresponding author. the taxonomic hierarchy, phenotypic differentiation be- 445 446 NOTES INT. J. SYST.BACTERIOL. TABLE 1. Taxa belonging to the Comamonadaceaen Present nameb Previous name(s) Reference(s) Acidovorax delajieldii Pseudomonas delajieldii, E. Falsen group 13‘ 33 Acidovorax facilis Pseudomonas facilis 33 Acidovorax temperans E. Falsen group 16“ 33 Comamonas acidovorans Pseudomonas acidovorans 31 Comamonas terrigena Comamonas terrigena, Aquaspirillum aquaticum, E. Falsen group 10“ 14, 36 Comamonas testosteroni Pseudomonas testosteroni 31 Hydrogenophaga Java Pseudomonas Java 32 Hydrogenophaga palleronii Pseudomonas palleronii 32 Hydrogenophaga pseudoflava Pseudomonas pseudoflava, “Pseudomonas carboxydoflava” 32 Hydrogenophaga taeniospiralis Pseudomonas taeniospiralis 32 [Aquaspirillum]anulus Aquaspirillum anulus 28 [Aquaspirillum]delicatum Aquaspirillum delicatum 28 [Aquaspirillum]giesbergeri Aquaspirillum giesbergeri 28 [Aquaspirillum]gracile Aquaspirillum gracile 28 [Aquaspirillum] metamorphum Aquaspirillum metamorphum 28 [Aquaspirillum]psychrophilum Aquaspirillum psychrophilum 28 [Aquaspirillum] sinuosum Aquaspirillurn sinuosum 28 [Pseudomonas] avenae Pseudomonas avenae 12, 17 [Pseudomonas] cattleyae Pseudornonas cattleyae 13, 17 [Pseudomonas pseudoalcaligenes] subsp. citrulli Pseudomonas pseudoalcaligenes subsp. citrulli 13, 17 [Pseudomonas pseudoalcaligenes] subsp. konjaci Pseudomonas pseudoalcaligenes subsp. konjaci 17 [Pseudornonas] rubrilineans Pseudomonas rubrilineans 13, 17 “[Pseudomonas]setariae” “Pseudomonas setariae” 13, 17 Variovorax paradoxus Alcaligenes paradoxus This paper Xylophilus ampelinus Xanthomonas ampelina 35 a Only species whose type strains belong to the Comumonudaceae or unidentified separate groups of bacteria are listed. In addition, individual strains erroneously assigned to Pseudomonas ulcaligenes, Pseudomonas pseudoalcaligenes subsp. pseudoalcaligenes, Bordetella bronchiseptica, and Alcaligenes denitrifcans also belong to various taxa in the Comamonadaceae. Brackets indicate taxa that are misnamed according to phylogenetic data. ‘ Group originally named by E. Falsen (Culture Collection, University of Goteborg, Goteborg, Sweden) and delineated by using immunotyping and phenotypic analyses (18). comes increasingly difficult because of the variety of pheno- below. The two biotypes that were described previously in types included in, for example, families and higher groups. this group (6) differed in their ability to grow autotrophically At such levels of classification, genotypic features are indis- in the presence of H,, but were highly related according to pensable for defining and distinguishing taxa. the results of an auxanographic analysis (21) when API The internal taxonomy of the Comamonadaceae was 50CH, API 50A0, and API 50AA galleries (API System studied in detail by using several techniques, including S.A., Montalieu-Vercieu, France) were used. DNA-rRNA and DNA-DNA hybridizations, gel electropho- The second group containing taxa that should be renamed resis of total cell proteins, numerical analysis of morpholog- is the [Pseudomonas] avenae rRNA branch (17), which ical, auxanographic, and biochemical characteristics, immu- includes several phytopathogenic [Pseudomonas] species notyping, and fatty acid analysis. On the basis of the data (see Table 1). We have studied these species in detail by obtained an improved classification has been proposed for using several techniques and will propose an improved several genera, including Comamonas (14, 31, 36), Xyfo- classification in a forthcoming paper (17). phifus (33, Hydrogenophaga (32), and Acidovorax (33). Seven [Aquaspiriffum] species (see Table 1) also belong to At present several rRNA branches belonging to the aci- the Comamonadaceae. They are only distantly related to dovorans rRNA complex contain taxa that are still to be Aquaspiriffum serpens and should in fact be removed from renamed on phylogenetic grounds. One is the [Afcafigenes] this genus (28). They have not yet been given
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