INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY, 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 K i d , 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
ribosomal ribonucleic acid (rRNA) sequences and oligonu-
cleotide catalogs provide an important factual base for
arrangements of higher taxa of bacteria (25, 26). A recent
workshop organized by the International Committee on
Systematic Bacteriology recognized that a particularly di-
verse but related group of gram-negative bacteria, including
phototrophic and heterotrophic bacteria, needed a formal
collective name (22). These organisms are often referred to
as “purple bacteria and their relatives,” and this is not
appropriate because most of them are not purple or photo-
synthetic. We believe that they should be named at the level
of class.
This group has evolved relatively rapidly to generate a
number of branches, including organisms of great biological
significance but startlingly different physiological attributes .
These relationships invalidate the proposal for an interim set
of higher taxa proposed in Bergey’s Munual of Systematic
Bacteriology (14) separating the classes Scotobacteria (for
nonphotosynthetic true bacteria, which now prove to be
relatives of purple bacteria) and Anoxyphotobacteria (en-
compassing the photosynthetic bacteria having photosystem
I alone, including the purple bacteria). The remaining class,
Oxyphotobacteria, can be retained as a phylogenetically
valid circumscription of the bacteria having both photosys-
tems I and 11. These and the other gram-negative bacteria
forming the major phylogenetic group derived from the main
stem of bacterial evolution can still be conveniently classi-
fied as members of the division Gracilicutes until further
phylogenetic studies clarify some of the orders of branching
or the need for status at the level of division. The gram-
positive bacteria form a more clearly structured phyloge-
netic group and can remain, as recommended (22), assem-
bled in the division Firmicutes.
The outstanding attribute of the major phylogenetic
branches (a,p, y, and 6) within the purple bacteria and their
relatives is the diversity of shape and physiology. Therefore,
we propose that these organisms be designated Proteobac-
teria classis nov. (Prot.e.0.bac.ter’i.a. Gr. n. Proteus, a
Greek god of the sea, capable of assuming many different
shapes; Gr. dim. n. bakterion, a small rod; Proteobacteria
protean group of bacteria of diverse properties despite a
common ancestry). It seems appropriate to use the suffix
-bacteria at this hierarchical level because it is consistent
with an extant proposal of higher taxa (14) that is useful in
* Corresponding author.
the interim while the phylogenetic data are being integrated
into formal bacterial taxonomy. It does not appear to be
inappropriate or confusing to use the protean prefix because
of the genus Proteus among the Proteobacteria; the reasons
for use are clear enough.
This new class is so far only definable in phylogenetic
terms. Above all, it is shown by the evolutionary distance
matrix generated from homologies of complete 16s rRNAs,
from which a phylogenetic tree is derived. According to
Woese (25) a corresponding tree given by maximum parsi-
mony of sequence selection recognizing unique nucleotides
at specific sites results in a very similar topography. Few
class-specific signature nucleotides of the 16s rRNA are
determinable compared with those found in other major lines
of descent of the Gracilicutes (25). There is a preference for
adenine at position 906 and for cytosine at position 1520 (a
guanine residue is the eubacterial consensus composition at
these positions). In terms of ribonuclease T,-resistant oligo-
nucleotides, catalogs of Proteobncteria can be characterized
by the following signatures (positions and distribution in
parentheses): CUAAUACCG (170; alpha-delta), YCAC
AYYG (315; alpha-delta; Y = pyrimidine), AAUUUUG or
AAUUUUC (365; alpha-delta), CUAACUYYG (510; alpha,
gamma, delta), and UCACACCAUG (1410; alpha-delta).
The alpha, beta, and gamma groups correspond to rRNA
superfamilies IV, 111, and I+II, respectively, as defined by
De Ley and co-workers (3-6, 9, 11, 15, 16) on the basis of
rRNA similarities (members of the delta subclass have not
yet been included in such studies). The groups within the
Proteobacteria are termed “subdivisions” by Woese et al.,
(26) or “subphyla” by Woese (25). Only a comparison of full
16s rRNA sequences can be expected to convincingly
determine the common origin of the four subclasses; other
methods, such as deoxyribonucleic acid-rRNA pairing, com-
parison of 5s rRNA sequences, and 16s rRNA cataloging,
are not capable of discrimination at that level.
Table 1 lists those taxa which have been found to be
members of each of the individual groups, and the methods
that determine their phylogenetic positions are indicated in
the references cited; the names used are included without
prejudice. At this time we do not have a formal nomencla-
tural proposal for any new ranks between class and genus
because thorough study will be required to establish stable
taxonomic arrangements and phenotypic markers for those
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
emphasize that these group names have no formal status in

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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 izobium 8 9
Caulobacter NP
Erythrobacter 25
Filornicrobium 17a
Gemmobacter 17
Gluconohacter 9
Hyp homic robiurn 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
S p irillurn 25
Tuylorella 15
Thiobucillusd 25 19
Vitreoscilla 25 19
Xy lophilus 24
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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
Thiospirillurn 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 hia 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
Thiornicrospira 19
Thiothrix 19
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324 NOTES INT. J . SYST.BACTERIOL.

TABLE 1-Con tinlied

References
Subclass Taxon” 16s rRNA 16.5 rRNA-23s rRNA 5s rRNA
sequences hybridization sequences

Vibrionacea 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 defined families are included.
References are not necessarily to the original presentation of data but are selected sources giving more comprehensive overviews. The subclasses “alpha” to
“gamma” contain many misclassified strains which are not listed but which can be recognized in the original literature.
’ The numbers in parentheses are reference numbers.
I ’ NP, Unpublished data of Stackebrandt and co-workers.

Heterogeneous genus.
Genera assigned t o the Enterobacieririceae by deoxyribonucleic acid hybridization data and not by rRNA sequencing (2).

nomenclature, they are put in quotation marks and not set in
italic type. A few genera have been effectively aligned within
a group (e.g., as a family), and this is indicated by direct
reference without assignment of method. It would be appro-
priate to refer to a named organism as belonging to, for
example, the Proteobucteriu alpha group.
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