bergeysoutline_5_2004

DOI:10.1007/bergeysoutline200405

TAXONOMIC OUTLINE OF THE PROKARYOTES
BERGEY’S MANUAL® OF SYSTEMATIC BACTERIOLOGY,

SECOND EDITION

Release 5.0 May 2004

George M. Garrity
Julia A. Bell

and Timothy G. Lilburn

George M. Garrity
Bergey’s Manual Trust and Department of Microbiology and Molecu-
lar Genetics
Michigan State University
East Lansing, MI 48824–1101

Julia A. Bell
Food Safety and Toxicology Center
Michigan State University
East Lansing, MI 48824–1101

Timothy G. Lilburn
Bioinformatics Group
American Type Culture Collection
Manassas, VA 20110

© 2004 Bergey’s Manual Trust

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This document was produced by the editorial ofce of Bergey’s Man-
ual Trust using Epic Document Architect and Epic Editor (Version 5.0,
ArborText, Ann Arbor, MI) and a prototype document type denition
developed expressly for taxonomic hierarchies.

DOI 10.1007/bergeysoutline200405

Springer New York Berlin Heidelberg

Taxonomic Outline of the Prokaryotes Release 5.0
Bergey’s Manual® of Systematic Bacteriology, 2nd Edition
GEORGE M. GARRITY, JULIA A. BELL AND TIMOTHY G. LILBURN

Background The classication presented below was ini- Technical notes Release 5.0 coincides with the publica-
tiated in the early 1990s in the editorial ofce of Bergey’s tion of Volume 2 of the second edition of the Systematics.
Manual Trust as a preliminary step in organizing the con- As stated earlier, we continue to search the taxonomic
tent of the second edition of Bergey’s Manual of System- literature and the public databases for new, high quality
atic Bacteriology (the Systematics). The primary objec- 16S rDNA sequences (dened as >1400 nts, < 4% am-
tive was to devise a classication that would reect the biguity, and fewer than 10 missing positions) and have
phylogeny of prokaryotes, as dened by 16S rDNA se- added these sequences to our phylogenetic models. In
quence analysis, while simultaneously placing all of the this release, we list 4540 unique sequences that are as-
validly named members of a given taxon into the clas- sociated with 4504 type strains and 894 synonyms. We
sication at a single point, based on the sequence of the have also added 197 new species/new combinations, 40
type strain, type species, or type genus. 1 new genera, 3 new families, 1 new order, and 1 new class
to our taxonomic model. New additions are summarized
Under ideal conditions, such a task would be relatively in Table 1.
straightforward. All species assigned to a genus would
be in agreement with the phylogenetic model and this The taxonomic model Within this classication, we rec-
would be reected in the nomenclature. Furthermore, ognize two prokaryotic domains: the Archaea and Bacte-
each species would bear a single name that would reect ria. The domains are divided into phyla which are in turn
both its taxonomic and phylogenetic position. However, divided into classes, orders (except for the Cyanobacte-
we nd this not to be the case as there are a number of ex- ria for which we use the rank of subdivision), families,
isting genera (e.g., Clostridium, Aquaspirillum) that are and genera. In the Actinobacteria, subclasses and sub-
paraphyletic based on the 16S rDNA model. It is our orders are recognized, and suborders occur within the
view that such instances indicate a need for taxonomic Myxococcales. The rank of kingdom is not used to avoid
revision. In addition, prior taxonomic revisions have led possible conicts with the Botanical Code, where some
to numerous instances in which the same species may overlap exists. Readers are advised that the Code of
bear more than one validly published name, indicating Prokaryotic Nomenclature does not cover taxa above the
differences in taxonomic opinion. To ensure complete- Class, even though the domain and phylum names ap-
ness, we have opted to include the majority of these syn- pearing in the Outline and in the Manual have appeared
onyms within the Outline. in Validation List 85. As of May 2004, 6661 validly
named prokaryotic species appeared either in the Ap-
Placement of species within the Outline is dictated by proved List of Bacterial Names (Skerman et al., 1980), in
the genus name rather than the position within any given original papers published in the International Journal of
phylogenetic model. We believe that periodic publica- Systematic Bacteriology or the International Journal of
tion of updated versions of this Outline will provide the Systematic and Evolutionary Microbiology, or in Valida-
community with an indication of the progress that has tion Lists 1–96. 2 In this version of the Outline, we extend
been made in resolving such problems, as well as point- our list of synonyms to 1226 by including forthcoming
ing out any remaining or new discrepancies that have oc- assertions of synonymy that will appear in Volume 2 of
curred between revisions. Therefore, any reference to the Systematics. Readers should be aware that, in some
the outline should include the release number, the publi- cases, we have opted to exclude some names that have
cation date, and the digital object identier (the DOI) of not found widespread usage, even though those names
the release being referenced. are validly published.

1 A more detailed discussion of the historical aspects of this effort are presented in the rst release of the Outline and by Garrity and Holt in
Volume 1 of the Systematics.
2 Lists 1-96 were published in the International Journal of Systematic Bacteriology and lists 72-82 in the International Journal of Systematic
and Evolutionary Microbiology, 27 (1977) 306; 29 (1979) 79, 436; 30 (1980) 601, 676; 31 (1981) 215, 382; 32 (1982) 266, 384; 33 (1983)
438, 672, 896; 34 (1984) 91, 270, 355, 503; 35 (1985) 223, 375, 535; 36 (1986) 354, 489, 573; 37 (1987) 179; 38 (1988) 136, 220, 328, 449;
39 (1989) 93, 205, 371, 495; 40 (1990) 105, 212, 320, 470; 41 (1991) 178, 331, 456, 580; 42 (1992) 191, 327, 511, 656; 43 (1993) 188, 398,
624, 864; 44 (1994) 182, 370, 595, 852; 45 (1995) 197, 418, 619, 879; 46 (1996) 362, 625, 836, 1189; 47 (1997) 242, 601, 915, 1274; 48
(1998) 327, 627, 631, 1083; 49 (1999) 1, 341, 935, 1325;50 (2000) 3, 423, 949, 1415, 1699, 1953; 51 (2001) 1, 263, 793, 1229, 1619, 1945;
52(2002) 3, 293, 685, 1075, 1437, 1915; 53 (2003) 1, 373, 627, 935, 1221, 1701;54:(2004) 3, 307.

© 2004 Bergey’s Manual Trust
All rights reserved.

1

Taxonomic Outline of the Procaryotes

Adoption of a hierarchical classication presents several gle type of data that will soon be available for all validly
difculties that must also be recognized. By denition, named species. Given the rapid advancements in se-
each species must be a member of successively higher quencing technology, we expect that sequences of other
ranks (six of which are recognized for the majority of genes will follow in the near future and help in resolving
taxa in the second edition of the Systematics). Yet there is the placement of problem taxa.
considerable reluctance among many contemporary sys-
tematic procaryotic biologists to place new species and Interpretation of the taxonomic outline At present, the
genera into higher taxa, especially at the intermediate two procaryotic domains have been subdivided into 26
levels (family, order, and class) because of uncertainty of phyla 3, two of which occur within the Archaea. The re-
phylogenetic models. In compiling and maintaining the maining 24 phyla are ascribed to the Bacteria. The fact
outline we have often had to deal with instances where that the Archaea and deeply branching Bacteria are pre-
new species were variously assigned to a class or do- sented rst is based largely on the early versions of the
main without being ascribed membership in any of the RDP tree. Since the branching order of species within
intervening taxa. This may be attributed to a lack of genera is frequently ambiguous and the data set is known
clear rules for delineating higher taxa. It may also reect to be incomplete, the use of phylogenetic trees as a guide
the inherent limitations of the 16S rRNA gene for den- for ordering taxa, both in the outline and the Systematics
ing a higher taxonomic structure, especially when con- Manual proved to be untenable. Thus, we have adopted a
temporary phylogenetic techniques, which rely on tree more workable and all-inclusive strategy. The type taxon
graphs as the principal interpretive device, are used to always appears rst. Within lower taxa, members of the
analyze small and inherently biased data sets. We have rank will usually appear in alphabetical order. The hi-
also observed a general lack of consistency in dening erarchical numbering scheme used in the outline is arbi-
the boundaries of genera based on 16S rDNA sequence trary, especially at the lower levels. It is also subject to
analysis. This is particularly problematic in bushy areas change as new taxa are described and existing taxa re-
of the ARB and RDP trees where uncertainty of branch- classied. Therefore, we advise against using the num-
ing order is high and clear demarcation of taxonomic bering scheme as an organizational or mnemonic device.
groups is impossible in the absence of other supporting
data. Decoding the entries Within this document, as well as
within the Systematics, we follow the American style
In dealing with such problems, we have lled in the for rendering Latinized names. Regardless of rank, all
missing taxa to complete the hierarchy. Names of names appear in italics. The superscript AL indicates
higher taxa are based largely on priority, except in that the name was included on the Approved Lists of
instances where such a strategy might lead to unnec- Bacterial Names published in 1980. The superscript VP
essary confusion (e.g., Helicobacteraceae rather than indicates that the name was validly published in the In-
“Wolinellaceae”). Considerable effort has been spent in ternational Journal of Systematic Bacteriology (now the
conrming the placement of genera within higher taxa. International Journal of Systematic and Evolutionary
Each of these higher taxa has also been scrutinized for Microbiology) or appeared on one of the validation lists
phylogenetic coherence so as to avoid paraphyletic or published in that journal. Names appearing in quotes
polyphyletic groupings wherever possible. However, have no standing in nomenclature, although they may
since 16S rDNA sequences are not yet available for have been effectively published elsewhere. Names fol-
all validly named species, some such instances will re- lowed with superscripted NP are indicative of proposals
main for the foreseeable future. We have annotated the for new taxa that will appear in the forthcoming second
species level outline in many areas to provide users some volume of the Systematics.
insight into our rationale for placements that might be
deemed controversial or to alert the reader to problems In the case of species names, each is followed with the
concerning the validity or legitimacy of names. Readers authority for the name and year of the original descrip-
are invited to pass along any comments or observations tion, in abbreviated form. The type strain (species), type
– along with supporting data – regarding other potential species (genus), type genus (family and order), and type
misplacements or errors. order (class and above) are indicated by an uppercase T,
enclosed in parentheses and in superscript. New taxa (re-
Despite some limitations, it is our view that the use of the cently added) are highlighted in red type and those which
well established phylogeny based on the 16S rRNA gene have been relocated within the outline as a result of com-
provides a marked improvement over the earlier articial ments from experts appear in magenta. Readers should
classications of prokaryotes. The technique (16S rDNA understand that the taxa are not, in reality moved, but are
sequencing) is universally applicable and provides a sin- the subject of alternative taxonomic views.

3 It is likely that this number understates the true number of phylum level lineages within the Bacteria. Hugenholtz recognizes at least four
other phyla within the Firmicutes.

2

Bergey’s Manual of Systematic Bacteriology, 2nd Edition

In the unabridged version of the outline that includes Citation Garrity, G.M., J.A. Bell and T.G. Lilburn.
species names and associated information, proposals for (2004) Taxonomic Outline of the Prokaryotes. Bergey’s
new combinations typically result in multiple changes Manual of Systematic Bacteriology, Second Edition.,
within the taxonomy. The new name is followed by the Release 5.0., Springer-Verlag, New York. pages. DOI:
basonym, which is identied by the symbol <- preced- 10.1007/bergeysoutline200405
ing the old name. Basonyms are also homotypic syn-
onyms (formerly referred to as objective synonyms) by Acknowledgments We also would like to acknowledge
default. To minimize redundancy, we will not identify Drs. Wolfgang Ludwig and Karl-Heinz Schleifer (Tech-
them as such. The old name is also retained within the nical University of Munich), Sean Turner (NCBI), Philip
outline, in the original location. However, older names Hugenholtz (UC. Berkeley), and James Cole and Qiong
are preceded by a dagger symbol (†) and should be con- Wang (RDP/Center for Microbial Ecology, Michigan
sidered deprecated under most circumstances. Follow- State) for their numerous and helpful discussions on
ing the old name and information about the taxonomic resolving discrepancies between the Bergey’s Outline
authority the new name appears in green type preceded and the phylogenetic reference trees and uncovering
by an arrow (->). In instances of synonymy, the syn- annotation errors; Drs. Jean Euzéby (École Nationale
onyms (either homotypic or heterotypic) are identied as Vétérinaire de Toulouse), Brian Tindall (Deutsche
such and preceded by an equals sign (=). Synonyms are Sammlung von Mikroorganismen und Zellkulturen,
further categorized as either senior or junior, indicating GmbH) and Aharon Oren for numerous helpful and
priority. More detailed information regarding the topics spirited comments on nomenclature and editorial re-
of synonymy and priority are available in the Interna- marks. We would also like to extend our thanks to Drs.
tional Code of Nomenclature of Bacteria (1990 Revision) David Boone, Paul De Vos, Michael Goodfellow, Noel
4and in Minutes of the Judicial Commission on Prokary- Kreig, Fred Rainey, Erko Stackebrandt, James Staley,
otic Nomenclature published in the International Jour- Joseph Tully, and William Whitman for their helpful
nal of Systematic and Evolutionary Microbiology. discussions and constructive comments.

Immediately following the nomenclature section of each This document was developed and is maintained as an
entry follows key information regarding the type strain, XML instance of a custom document type denition for
including the original strain designation, when reported, taxonomic hierarchies using Epic Architect and Epic
and all known deposits in major culture collections 5. Editor, Version 5.0, (ArborText, Ann Arbor, MI). The
Each such deposit is set off by a small vertical bar ( DTD was authored by George M. Garrity (Michigan
| ). If one or more high quality 16S rDNA sequences State University, East Lansing, MI) and Catherine Lyons
have been reported for that strain, information regarding (Explicatrix llc, Sterling, NJ) and is interoperable with
those sequences will follow. The rst value will be the the Bergey’s Manual DTD. This research was supported
GenBank, EMBL or DDBJ accession number(s). This in part by the Biological and Environmental Research
will be followed by the RDP short identier, which is Program (BER), U.S. Department of Energy, Grant No.
typically an alphanumeric abbreviation derived from the DE-FG02-02ER63315.
species name. Each such triplet is set off from others by
the small vertical bar (|).

4 Lapage et al., (1992) ASM Press, Washington, DC.
5 With this release of the Outline, we have implemented a change in the prex of the former Institute of Fermentation, Osaka culture collection
(IFO) to the new designation as the NITE (National Institute of Technology and Evaluation) Biological Resource Center (NBRC).

3