INTERNATIONAL
JOURNAL
OF SYSTEMATIC
BACTERIOLOGY,
July 1988, p. 321-325
0020-7713/88/03032 1-05$02.OOtO
Copyright 0 1988, International Union of Microbiological Societies
Vol. 38, No. 3
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.
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 parsimony 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 oligonucleotides, 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, comparison 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 nomenclatural 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
Phylogenetic interpretations derived from the study of
ribosomal ribonucleic acid (rRNA) sequences and oligonucleotide 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 diverse 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 photosynthetic. 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 (encompassing 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 photosystems 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 classified 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 grampositive bacteria form a more clearly structured phylogenetic group and can remain, as recommended (22), assembled 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 Proteobacteria 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.
321
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322
INT. J. SYST.BACTERIOL.
NOTES
TABLE 1. Genera recognized as members of the class Proteobacteria“
References
Subclass
“Alpha”
“Beta”
Taxonb
16s rRNA
sequences
16s rRNA-23s rRNA
hybridization
Rhodohacter
Rhodomicrobium
Rhodopseudomonas
Rhodopila
Rhodospirillum
Acetobacter
Acidiphilium
Agrobacteriurn
Ancalornicrobium
Aquaspirillum
Azospirillurn
Beijerinckia
Blastobacter
Brady rh izobium
Caulobacter
Erythrobacter
Filornicrobium
Gemmobacter
Gluconohacter
Hyp homic robiurn
Hyphornonas
Me thy lobacteriurn
My coplana
Nitrobacter
Paracoccus
Pedornicrobium
Phy llobacterium
Phenylobacterium
Prosthecornicrobium
Rhizohium
Rochalimaea
Stella
Xanthobacter
Zymornonas
25
25
25
25
25
9
25
N P”
25
25
NP
17
8
9
R hodocyclus
Achromohacter
Alcaligenaceae
Alcaligenes
Bordetella
Aquaspirillum
Chrornobacteriurn
Comamonas
Derxia
Janthinobacterium
King ella
Leptothrix
Methylomonas Clara
Methanolomonas
Methanomonas
Neisseria
Nitrosococcus
Nitrosolobus
Nitrosospira
Nitrosovibrio
Oligella
Pseudornonas acidovorans complex
Pseudornonas solanacearum complex
Sirnonsiella
Sphaerotilus
S p irillurn
Tuylorella
Thiobucillusd
Vitreoscilla
Xy lophilus
25
5s rRNA
sequences
9
9
9
13
13
9
9
9
9
NP
25
17a
17
9
17a
17a
17a
NP
25
25
17a
17a
13
25
NP
25
25
17a
NP
NP
9
13
11
4
25
25
25
25
NP
25
15
15
5
6
5
5
16
19
28
28
28
25
25
25
25
25
25
25
NP
25
25
16
15
5
5
13
15
25
25
19
19
24
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VOL. 38, 1988
NOTES
323
TABLE 1-Continued
References
Subclass
"Gamma"
Taxonb
Chrornatiaceae
Amoehohacter
Chrornatiurn
Larnprocystis
Thiocapsa
Thiocystis
Thiodictyon
Thiospirillurn
Ectothiorhodospiraceae
Eciothiorhodospira
Acinetobacter
Aeromonadaceae
Aerornonas
Alterornonas
Alysiella
Azornonas
Azotobacter
Beggiatoa
Branhamella
Deleya
Enterohacteriaceae
Budvicia (1)
Buttiauxella'
Cedecea"
Citrobacter"
Edwardsiella'
Enterohacter
Erwinia'
Es ch e ric hia
Hafnia'
Klebsiella'
Kluyvera'
Leclercia (21)
Leminorella'
Moellerella'
Morganella'
Obesurnbacterium'
Proteus
Providencia'
Rahnella'
Salmonella''
Serratia
Shigella"
Taturnella'
Yersinia
Yokenella (= Koserella) (12)
Xenorhabdus
Frateuria
Halornonas
Legionella
Leucothrix
Lysohacter
Marinornonas
Moraxella
Oceanospirillurn
Pasteurellaceue
Pasteurella
Plesiornonas
Pseudomonas juorescens complex
Psychrobacter (10)
Ruminobacter
Serpens
Thiornicrospira
Thiothrix
16s rRNA
sequences
25
7
25
25
25
25
25
25
25
25
25
27
27
NP
16s rRNA-23s rRNA
hybridization
5s rRNA
sequences
13
16
3
3
3
13
5
5
19
25
NP
27
16
5
3
27
3
27
27
27
27
6a
5
27
27
27
27
5
16
25
3
25
25
5
3
3
13
18, 25
25
19
19
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324
INT. J . SYST.BACTERIOL.
NOTES
TABLE 1-Con tinlied
References
Subclass
‘‘Delta’’
Taxon”
16s rRNA
sequences
Vibrionacea e
Enhydrobacter (20)
Listonella
Vibrio
Photobacterium
Skewanella
Xanthomonas
Xy lella
27
27
Bdellovibrio
Desulfobucter
Desulfobulbus
Desulfococcus
Desulfonema
Desulfovibrio
Desulfuromonas
Myxococcuceae
Chondromyces
Cystobacter
Myxococcits
Nannocystis
Sorangium
Stigmatella
Pelobacter
25
25
25
25
25
25
25
2s
NP
25
25
25
25
25
NP
25
23
16.5 rRNA-23s rRNA
hybridization
5s rRNA
sequences
3
3
3
5
‘’ 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 appropriate to refer to a named organism as belonging to, for
example, the Proteobucteriu alpha group.
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VOL. 38, 1988
NOTES
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