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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

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Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including 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 , is proposed for the organisms belonging to the acidovorans rRNA complex in the beta subclass of the . This family includes the genera , , , Xylophilus, and Variovorax (formerly Alcaligenes paradoxus), as well as a number of phylogenetically misnamed Aquaspirillum and phytopathogenic 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 ) 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 Pseudomonas facilis 33 E. Falsen group 16“ 33 Pseudomonas acidovorans 31 Comamonas terrigena Comamonas terrigena, Aquaspirillum aquaticum, E. Falsen group 10“ 14, 36 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 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 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 a more paradoxus rRNA branch, which is not related to the type appropriate name because of a lack of phenotypic data (28). species of the genus Alcafigenes, Afcafigenes faecafis (Fig. Description of Vuriovorax gen. nov. Variovorax (Va.ri.0’ 1). This rRNA branch contains [Alcaligenes] paradoxus vo.rax. L. adj. varius, various; L. adj. vorax, voracious; strains having Tm(e)values of at least 79.0”C versus labeled M.L. masc. n. Variovorax, [bacteria] devouring a variety [of rRNA from [Afcafigenes] paradoxus ATCC 17713tlT. No substrates]). Cells are straight to slightly curved rods that are other strains belonging to the acidovorans rRNA complex 0.5 to 0.6 by 1.2 to 3.0 pm and occur singly or in pairs. belong to this rRNA branch. DNA-DNA hybridizations Motile by means of degenerate peritrichous flagella. Colo- between [Alcafigenes] paradoxus strains and representative nies are yellow because of the presence of carotenoid strains belonging to the other rRNA branches of the aci- pigments. Oxidase and catalase positive. Aerobic. Chemoor- dovorans rRNA complex (e.g., members of the genera ganotrophic. Some strains are capable of lithoautotrophic Hydrogenophaga and Xyfophilus) resulted in no significant growth in which hydrogen is used as an energy source; these degrees of DNA binding (1, 35). Phenotypically, [Afcafi- strains have been described as biotype I. The strains that are genes] paradoxus forms a separate entity within the aci- unable to use hydrogen have been described as biotype I1 dovorans rRNA complex (36). We propose that [Afcafi- (6). Oxidative carbohydrate metabolism with oxygen as the genes] paradoxus should be transferred to a new genus, terminal electron acceptor. Good growth is obtained on Variovorax, as Variovorax paradoxus. A description is given media containing carbohydrates, organic acids (including VOL. 41, 1991 NOTES 447

notypic characteristics have been given by Davis et al. (6) 60 70 80 TNm) (Q I I I I I and Kersters and De Ley (21). V. paradoxus strains have been isolated from soil. The type strain is strain ATCC 17713 [P.] SOLANACEARUM (= LMG 1797t1 = LMG 1797t2); it was isolated from soil -- under an atmosphere containing 91% H,, 4% O,, and 5% CO,. The G+C content of strain ATCC 17713TDNA is 67.0 mol%. COMAMONAS Description of Comamonaduceae fam. nov. Comamona- daceae (Co.ma.mo.na.da'ce.ae. M. L. fem. n. Comamonas, type genus of the family; -aceae, suffix to denote family; M. XYLOPHILUS L. fem. pl. n. Comamonadaceae, Comamonas family). Cells HYDROGENOPHAGA are straight or slightly curved rods or spirilla. Gram nega- tive. Mostly motile by means of either one polar flagellum, VARIOVORAX bipolar tufts of one to five flagella, or degenerate peritrichous ACIDOVORAX flagella. No endospores or microcysts are formed. Coccoid bodies are rarely formed in some [Aquaspirillurn] species. Chemoorganotrophic or chemolithotrophic at the expense of H, or CO oxidation. Oxidative metabolism, using oxygen as [AQUASPIRILLUM] a terminal electron acceptor; some species can also use t nitrates. Oxidase positive, except for members of the genus <- Xylophilus. The optimal growth temperature ranges from 28 [P.] AVENAE to 30°C, except for Xylophilus spp. and [Aquaspirillum] psychrophilum, which grow best at 24 and 18"C, respec- t R. GELATINOSUS tively. Yellow insoluble pigments are produced by Xylo- L. DISCOPHORA philus, Hydrogenophaga, and Variovorax strains. Nitrogen fixation has been described for some Hydrogenophaga strains (20). Generally, these organisms use only very few ALCALIGENACEAE carbohydrates, but they use a wide variety of organic acids, including amino acids. The major fatty acids are palmitoleic acid (16:1), palmitic acid (16:0), and cis-vaccenic acid (All- AUTHENTIC PSEUDOMONAS 18:l). The mean G+C contents of the DNAs range from 57 1 XANTHOMONAS to 70 mol%. Strains have been isolated from soil, water in - natural and industrial environments, clinical samples, and I I I I I infected plant material. No pathogenic effects have been 60 70 80 reported for the strains isolated from clinical samples (gen- TN.1 ("C) era Comamonas and Acidovorax). Members of the genus FIG. 1. Simplified rRNA cistron similarity dendrogram of rRNA Xylophilus are pathogenic for grapevines, and the strains superfamily 111. The T,(,, values are from references 12-14,28, and belonging to the [P.]avenae rRNA branch are pathogenic for 36. The rRNA branch of the authentic genus Pseudomonas is the various grasses, orchids, or members of the family Cucurb- Pseudomonas fluorescens rRNA branch, which contains the type itaceae. The family Comamonadaceae belongs to rRNA species. The roman numerals indicate the roots of the rRNA superfamily I11 or the beta subclass of the Proteobacteria. superfamilies sensu De Ley (7). L., ; P., Pseudomonas; Strains belonging to this family have Tm(elvalues of at least R., Rubrivivax. 75°C versus rRNA from C. acidovorans Stanier 14T. All strains group within a AT,,,, range of 5°C. The type genus is Comamonas (De Vos et al. 1985) Tamaoka et al. 1987. The following other taxa belong to the Comamonadaceae: the amino acids), or peptone. The mean G+C contents of the genera Acidovorax, Variovorax, Hydrogenophaga, and Xy- DNAs range from 66.8 to 69.4 mol%. In DNA-rRNA hybrid- lophilus, [Aquaspirillum]anulus, [Aquaspirillum]delicatum, izations, Variovorax strains have T,,,) values of 79.0 to [Aquaspirillum] giesbergeri, [Aquaspirillum] gracile, 81.O"C versus rRNA from Variovorax paradoxus ATCC [Aquaspirillum] metamorphum, [Aquaspirillum] sinuosum, 17713tlT. The genus Variovorax belongs to the Comamon- [Aquaspirillum]psychrophilum, and the [P.] avenae rRNA adaceae and is equidistantly related to the other taxa in this branch, which contains [Pseudomonas] cattleyae, "[Pseu- family (e.g., the genera Acidovorax, Comamonas, Hydro- domonas] setariae," [Pseudomonas]rubrilineans, [Pseudo- genophaga, and Xylophilus). The only species is Variovorax monas pseudoalcaligenes] subsp. citrulli, and [Pseudomo- paradoxus (Davis 1969) comb. nov. nus pseudoalcaligenes] subsp. konjaci. Differentiating Description of Variovorax paradoxus (Davis 1969) comb. features have been described previously (36). A key for the nov. The description of Variovorax paradoxus (pa.ra. differentiation of the different groups in the Comamona dox'us. Gr. prep. para, contrary to; Gr. n. doxa, opinion; daceae is presented below: M.L. n. paradoxus, contrary to expectation, referring to the organotrophic and facultatively chemolithotrophic metabo- I. Not maintainable on nutrient agar (36) lism of this organism) is the same as that of the genus. From A. Yellow pigmented, very slow growth in general many strains two stable colony types have been isolated. and oxidase absent: Xylophilus One type is round and convex with smooth margins and B. Unpigmented, oxidase present: [Aquaspirillum surfaces; the other type is round and umbonate with scal- species (see above) loped to smooth margins. Detailed descriptions of the phe- 11. Good growth on nutrient agar 00P

z TABLE 2. Comparison of the Comamonadaceae with phenotypically similar taxa" v,8 Aquaspinllum Authentic genus [Pseudomonas] Xanthomonasd Alcaligenaceae Characteristic Comamonadaceae Pseudomonasb solanacearum group' sensu stricto"

Cell morphology Rods or spirilla Rods Rods Rods Rods or coccobacilli Spirilla Flagella Polar or peritrichous Polar Polar Polar Peritrichous Polar Pigments None or yellow None or fluorescent Several nonfluorescent Yellow xanth- None None or green insoluble pigments soluble pyoveridines pigments omonadines fluorescent pigments Occurrence Soil, water, clinical Soil, water, clinical Soil, water, infected Infected plants, Soil, water, clinical Pond water samples, infected samples, infected plants and animals, clinical samples samples, infected plants plants clinical samples warm-blooded animals Poly-P-hydroxybutyrate + + + + accumulation Oxidase if + + -/weak + + H, oxidation +/- - - - +/- - Ubiquinong Q8 Q9 Q8 Q8 Q8 Major polyaminesh PUT, HPUT PUT, SPM PUT, HPUT SPD' PUT, HPUT G+C content (mol%) 5 7-70 59-68 64-70 63-70 56-70 49-52 Occurrence of 3-hydromalm- - - + - - itic acid (3-OH 16:Oy' Tmce,("C) vs rRNA from the type strain OF: C. acidovorans 75-81 62 4 2 70 f 1 62 % 2 70 + 1 68 2 1 Pseudomonas fluorescens 62 2 2 76-8 1 62 f 2 67 f 1 62 2 2 62 + 2 [Pseudomonas]solanacearum 70 2 1 62 f 2 74-81.5 62 +2 70 f 1 68 k 1 Xanthomonas campestris 62 f 2 67 f 1 62 & 2 76.5-81.5 62 % 2 62 f 1 Alcaligenes faecalis 70 + 1 62 -+ 1 70 f 1 62 % 2 75-82 68 % 1 Aquaspirillum serpens 68 f 1 62 -+ 1 68 f 1 62 2 2 68 k 1 79.5-80.5 rRNA superfamily I11 I1 I11 I1 111 I11 Group according to 16s rRNA P-1 r-3 P-3 Y-3 P-2 P-2 signature analysis' Subclass in the Proteobacteria Beta Gamma Beta Gamma Beta Beta

a Data from Bergey 's Manual of Systematic Bacteriology, unless indicated otherwise. Comprising the species of Pseudomonas section I (24) and additional species belonging to the Pseudomonas fluorescens rRNA branch in rRNA superfamily I1(12, 13, 15). Comprising the species of Pseudomonas section I1 (25)and additional species belonging to the [Pseudomonas] solanacearum rRNA branch in rRNA superfamily I11(12, 13, 15). Including Xanthomonas maltophilia. Comprising Aquaspirillum sevens (28). f Negative for the genus Xylophilus. g Data from references 5, 23, and 24. Data from reference 3. HPUT, 2-hydroxyputrescine;PUT, putrescine; SPD, spermidine; SPM, spermine. Data from references 11 and 22. J Data from reference 24. Data from references 9, 12, 13, and 28. Data from references 39 and 40. VOL.41, 1991 NOTES 449

A. Yellow pigmented and usually capable of chemo- ceedings of the 4th International Conference of Plant Pathogenic lithotrophic growth with hydrogen Bacteria, Angers, vol. 1. Gibert-Clarey, Tours, France. 1. Grows with L-arabitol, mesaconate, and citrate 8. De Ley, J., W. Mannheim, R. Mutters, K. Piechulla, R. Tytgat, as sole carbon sources: Variovorax P. Segers, M. Bisgaard, W. Frederiksen, K.-H. Hinz, and M. Vanhoucke. 1990. Inter- and intrafamilial similarities of the 2. Does not use L-arabitol, mesaconate, and citrate Pasteurellaceae. Int. J. Syst. Bacteriol. 40:126-137. as sole carbon sources: Hydrogenophaga 9. De Ley, J., P. Segers, K. Kersters, W. Mannheim, and A. B. Unpigmented, no chemolithotrophic growth with Lievens. 1986. Intra- and intergeneric similarities of the Borde- hydrogen tella ribosomal ribonucleic acid cistrons: proposal for a new 1. Bipolar tufts of flagella, does not grow with family, Alcaligenaceae. Int. J. Syst. Bacteriol, 36:405-414. D-glucose as a sole carbon source: Coma- 10. De Ley, J., and R. Tytgat. Unpublished data. monas 11. De Vos, P. Unpublished data. 2. One polar flagellum, grows with D-glucose as a 12. De Vos, P., and J. De Ley. 1983. Intra- and intergeneric sole carbon source similarities of Pseudomonas and Xanthomonas ribosomal ribo- nucleic acid cistrons. Int. J. Syst. Bacteriol. 33:487-509. a. Isolated from infected plant material: [P.] 13. De Vos, P., M. Goor, M. Gillis, and J. De Ley. 1985. Ribosomal avenue rRNA branch (see above) ribonucleic acid cistron similarities of phytopathogenic Pseudo- b. Not isolated from infected plant material: monas species. Int. J. Syst. Bacteriol. 35:169-184. Acidovorax 14. De Vos, P., K. Kersters, E. Falsen, B. Pot, M. Gillis, P. Segers, and J. De Ley. 1985. Comamonas Davis and Park 1962 gen. nov, Nearest neighbors of the Comanonaduceae. The faculta- nom. rev. emend., and Comamonas terrigena Hugh 1962 sp. tively photolithotrophic organism Rubrivivax gelatinosus, nov., nom. rev. Int. J. Syst. Bacteriol. 35:443453. [Pseudomonas]saccharophila [Alcali- 15. De Vos, P., A. Van Landschoot, P. Segers, R. Tytgat, M. Gillis, the H, oxidizers and M. Bauwens, R. Rossau, M. Goor, B. Pot, K. Kersters, genes] latus, and the sheathed bacteria belonging to the P. Lizzaraga, and J. De Ley. 1989. Genotypic relationships and genera Leptothrix and Sphaerotilus have been reported to be taxonomic localization of unclassified Pseudomonas and Pseu- closely related or to belong to the acidovorans rRNA com- domonas-like strains by deoxyribonucleic acid:ribosomal ribo- plex (12, 21, 34). We prefer not to include these taxa in the nucleic acid hybridizations. Int. J. Syst. Bacteriol. 39:3549. Comamonadaceae for the reasons given below. These taxa 16. Dubow, M. S., and T. Ryan. 1977. Host factor for coliphage QP have Tm,e)values of 73.4 2 1.4"C [corresponding to AT,,,, RNA replication as an aid in elucidating phylogenetic relation- values of 7.1 5 1.4"CI versus labeled rRNAs from members ships: the genus Pseudomonas. J. Gen. Microbiol. 102:263-268. of the Comamonadaceae (34) and represent a separate 17. Goor, M., A. Willems, and M. Gillis. Unpublished data. cluster in rRNA superfamily I11 (Fig. 1). A 16s rRNA 18. Falsen, E. 1986. Catalogue of strains. Culture Collection, Uni- (40) R. gelatinosus versity of Goteborg, Goteborg, Sweden. catalog analysis showed that and 19. Gillis, M., and J. De Ley. 1980. Intra- and intergeneric similar- group at S,, values of 0.61 to 0.67 with ities of the ribosomal ribonucleic acid cistrons of Acetobacter taxa belonging to the Comamonadaceae. This AT,,,, range and Gluconobacter. Int. J. Syst. Bacteriol. 30:7-27. and the difference in S,, values with members of the 20. Jenni, B., C. Isch, and M. Aragno. 1989. 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