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Purple Bacteria and Their Relatives” INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1988, p. 321-325 Vol. 38, No. 3 0020-7713/88/03032 1-05$02.OOtO Copyright 0 1988, International Union of Microbiological Societies Proteobacteria classis nov. a Name for the Phylogenetic Taxon That Includes the “Purple Bacteria and Their Relatives” E. STACKEBRANDT,l R. G. E. MURRAY,2* AND H. G. TRUPER3 Lehrstuhl fur Allgemeine Mikrobiologie, Biologiezentrum, Christian-Albrechts Universitat, 2300 Kid, Federal Republic of Germany’; Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada N6A 5C12; and Institut fur Mikrobiulogie, Universitat Bonn, 5300 Bonn I, Federal Republic of Germany3 Proteobacteria classis nov. is suggested as the name for a new higher taxon to circumscribe the a, p, y, and 6 groups that are included among the phylogenetic relatives of the purple photosynthetic bacteria and as a suitable collective name for reference to that group. The group names (alpha, etc.) remain as vernacular terms at the level of subclass pending further studies and nomenclatural proposals. Phylogenetic interpretations derived from the study of the interim while the phylogenetic data are being integrated ribosomal ribonucleic acid (rRNA) sequences and oligonu- into formal bacterial taxonomy. It does not appear to be cleotide catalogs provide an important factual base for inappropriate or confusing to use the protean prefix because arrangements of higher taxa of bacteria (25, 26). A recent of the genus Proteus among the Proteobacteria; the reasons workshop organized by the International Committee on for use are clear enough. Systematic Bacteriology recognized that a particularly di- This new class is so far only definable in phylogenetic verse but related group of gram-negative bacteria, including terms. Above all, it is shown by the evolutionary distance phototrophic and heterotrophic bacteria, needed a formal matrix generated from homologies of complete 16s rRNAs, collective name (22). These organisms are often referred to from which a phylogenetic tree is derived. According to as “purple bacteria and their relatives,” and this is not Woese (25) a corresponding tree given by maximum parsi- appropriate because most of them are not purple or photo- mony of sequence selection recognizing unique nucleotides synthetic. We believe that they should be named at the level at specific sites results in a very similar topography. Few of class. class-specific signature nucleotides of the 16s rRNA are This group has evolved relatively rapidly to generate a determinable compared with those found in other major lines number of branches, including organisms of great biological of descent of the Gracilicutes (25). There is a preference for significance but startlingly different physiological attributes . adenine at position 906 and for cytosine at position 1520 (a These relationships invalidate the proposal for an interim set guanine residue is the eubacterial consensus composition at of higher taxa proposed in Bergey’s Munual of Systematic these positions). In terms of ribonuclease T,-resistant oligo- Bacteriology (14) separating the classes Scotobacteria (for nucleotides, catalogs of Proteobncteria can be characterized nonphotosynthetic true bacteria, which now prove to be by the following signatures (positions and distribution in relatives of purple bacteria) and Anoxyphotobacteria (en- parentheses): CUAAUACCG (170; alpha-delta), YCAC compassing the photosynthetic bacteria having photosystem AYYG (315; alpha-delta; Y = pyrimidine), AAUUUUG or I alone, including the purple bacteria). The remaining class, AAUUUUC (365; alpha-delta), CUAACUYYG (510; alpha, Oxyphotobacteria, can be retained as a phylogenetically gamma, delta), and UCACACCAUG (1410; alpha-delta). valid circumscription of the bacteria having both photosys- The alpha, beta, and gamma groups correspond to rRNA tems I and 11. These and the other gram-negative bacteria superfamilies IV, 111, and I+II, respectively, as defined by forming the major phylogenetic group derived from the main De Ley and co-workers (3-6, 9, 11, 15, 16) on the basis of stem of bacterial evolution can still be conveniently classi- rRNA similarities (members of the delta subclass have not fied as members of the division Gracilicutes until further yet been included in such studies). The groups within the phylogenetic studies clarify some of the orders of branching Proteobacteria are termed “subdivisions” by Woese et al., or the need for status at the level of division. The gram- (26) or “subphyla” by Woese (25). Only a comparison of full positive bacteria form a more clearly structured phyloge- 16s rRNA sequences can be expected to convincingly netic group and can remain, as recommended (22), assem- determine the common origin of the four subclasses; other bled in the division Firmicutes. methods, such as deoxyribonucleic acid-rRNA pairing, com- The outstanding attribute of the major phylogenetic parison of 5s rRNA sequences, and 16s rRNA cataloging, branches (a,p, y, and 6) within the purple bacteria and their are not capable of discrimination at that level. relatives is the diversity of shape and physiology. Therefore, Table 1 lists those taxa which have been found to be we propose that these organisms be designated Proteobac- members of each of the individual groups, and the methods teria classis nov. (Prot.e.0.bac.ter’i.a. Gr. n. Proteus, a that determine their phylogenetic positions are indicated in Greek god of the sea, capable of assuming many different the references cited; the names used are included without shapes; Gr. dim. n. bakterion, a small rod; Proteobacteria prejudice. At this time we do not have a formal nomencla- protean group of bacteria of diverse properties despite a tural proposal for any new ranks between class and genus common ancestry). It seems appropriate to use the suffix because thorough study will be required to establish stable -bacteria at this hierarchical level because it is consistent taxonomic arrangements and phenotypic markers for those with an extant proposal of higher taxa (14) that is useful in ranks (22). The groups corresponding to the immediate separations within the Proteobncteria should be at the subclass rank and are so shown in Table 1; however, to * Corresponding author. emphasize that these group names have no formal status in 321 322 NOTES INT. J. SYST.BACTERIOL. TABLE 1. Genera recognized as members of the class Proteobacteria“ References Subclass Taxonb 16s rRNA 16s rRNA-23s rRNA 5s rRNA sequences hybridization sequences “Alpha” Rhodohacter 25 9 Rhodomicrobium 25 Rhodopseudomonas 25 9 Rhodopila 25 Rhodospirillum 25 9 13 Acetobacter 9 Acidiphilium 13 Agrobacteriurn 25 9 Ancalornicrobium N P” Aquaspirillum 25 9 Azospirillurn 25 9 Beijerinckia NP 9 Blastobacter 17 Brady rh izo bium 8 9 Caulobacter NP Erythrobacter 25 Filornicrobium 17a Gemmobacter 17 Gluconohacter 9 Hyp homic ro biurn 17a 17a Hyphornonas 17a Me thy lobacteriurn NP My coplana Nitrobacter 25 17a Paracoccus 25 13 Pedornicrobium 17a Phy llobacterium Phenylobacterium 25 Prosthecornicrobium NP Rhizohium 25 Rochalimaea 25 Stella 17a NP Xanthobacter NP Zymornonas 9 “Beta” R hodocyclus 25 13 Achromohacter 11 Alcaligenaceae 4 Alcaligenes 25 15 Bordetella 15 Aquaspirillum 25 Chrornobacteriurn 25 5 Comamonas 25 6 Derxia NP 5 Janthinobacterium 25 5 King ella 16 Leptothrix 19 Methylomonas Clara 28 Methanolomonas 28 Methanomonas 28 Neisseria 25 16 Nitrosococcus 25 Nitrosolobus 25 Nitrosospira 25 Nitrosovibrio 25 Oligella 15 Pseudornonas acidovorans complex 25 5 Pseudornonas solanacearum complex 25 5 13 Sirnonsiella NP Sphaerotilus 25 Spirill urn 25 Tuy lorella 15 Thiobucillusd 25 19 Vitreoscilla 25 19 Xylophilus 24 Continued on following page VOL. 38, 1988 NOTES 323 TABLE 1-Continued References Subclass Taxonb 16s rRNA 16s rRNA-23s rRNA 5s rRNA sequences hybridization sequences "Gamma" Chrornatiaceae 25 Amoehohacter 7 Chrornatiurn 25 13 Larnprocystis 25 Thiocapsa 25 Thiocystis 25 Thiodictyon 25 Thiosp irill urn 25 Ectothiorhodospiraceae 25 Eciothiorhodospira 25 Acinetobacter 25 16 Aeromonadaceae 3 Aerornonas 27 3 Alterornonas 27 3 13 Alysiella NP Azornonas 5 Azotobacter 5 Beggiatoa 25 19 Branhamella 16 Deleya NP 5 Enterohacteriaceae 27 3 Budvicia (1) Buttiauxella' Cedecea" Citrobacter" Edwardsiella' Enterohacter 27 Erwinia' Es ch e ric h ia 27 3 Hafnia' Klebsiella' Kluyvera' Leclercia (21) Leminorella' Moellerella' Morganella' Obesurnbacterium' Proteus 27 Providencia' Rahnella' Salmonella'' Serratia 27 Shigella" Taturnella' Yersinia 27 Yokenella (= Koserella) (12) Xenorhabdus 6a Frateuria 5 Halornonas 27 Legionella 27 Leucothrix 27 Lysohacter 27 Marinornonas 5 Moraxella 16 Oceanospirillurn 25 Pasteurellaceue 3 Pasteurella 25 3 Plesiornonas 3 Pseudomonas juorescens complex 25 5 13 Psychrobacter (10) Ruminobacter 18, 25 Serpens 25 Thiorn icrospira 19 Thiothrix 19 Continued on following page 324 NOTES INT. J. SYST.BACTERIOL. TABLE 1-Con tin lied References Subclass Taxon” 16s rRNA 16.5 rRNA-23s rRNA 5s rRNA sequences hybridization sequences Vibrion acea e 3 3 Enhydrobacter (20) Listonella Vibrio 27 Photobacterium 27 3 Skewanella Xanthomonas 25 5 Xy lella 23 ‘‘Delta’ ’ Bdellovibrio 25 Desulfobucter 25 Desulfobulbus 25 Desulfococcus 25 Desulfonema 25 Desulfovibrio 25 Desulfuromonas 25 Myxococcuceae 2s Chondromyces NP Cystobacter 25 Myxococcits 25 Nannocystis 25 Sorangium 25 Stigmatella 25 Pelobacter NP ‘’ Genera of phototrophic bacteria head the list of taxa and are followed by other taxa in alphabetical order. Only phylogenetically
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