TAXONOMIC OUTLINE OF THE PROCARYOTES BERGEY S MANUAL OF SYSTEMATIC BACTERIOLOGY, SECOND EDITION Release 2.0, January 2002

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1 TAXONOMIC OUTLINE OF THE PROCARYOTES BERGEY S MANUAL OF SYSTEMATIC BACTERIOLOGY, SECOND EDITION Release 2.0, January 2002 George M. Garrity Matthew Winters Austin W. Kuo and Denise B. Searles

2 George M. Garrity Bergey s Manual Trust Department of Microbiology and Molecular Genetics Michigan State University East Lansing, MI USA 2002 Bergey s Manual Trust All rights reserved. This work may not be transferred or copied in whole or in part without written permission of the publisher, (Springer- Verlag New York, Inc. 175 Fifth Avenue, New York, NY 10010, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software or by similar methodology now known or hereafter developed is forbidden. While the advice and information contained within this document are believed to be true and accurate at the time of publication, neither the authors, the publisher, nor Bergey s Manual Trust can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. This document was produced by the editorial office of Bergey s Manual Trust using Epic Document Architect and Epic Editor (Version 4.01, ArborText, Ann Arbor, MI) and a prototype document type definition developed expressly for taxonomic hierarchies. DOI /bergeysoutline Springer-Verlag New York Berlin Heidelberg A member of BertelsmanSpringer Science+Business Media GmbH

3 Taxonomic Outline of the Procaryotes Bergey s Manual of Systematic Bacteriology, 2nd Edition GEORGE M. GARRITY, MATTHEW WINTERS, AUSTIN W. KUO AND DENISE B. SEARLES Background The classification presented below was initiated in the early 1990s in the editorial office of Bergey s Manual Trust as a preliminary step in organizing the content of the second edition of Bergey s Manual of Systematic Bacteriology (the Systematics). The main objective was to devise a classification that would reflect the phylogeny of procaryotes (as defined by 16S rdna sequence analysis) while simultaneously placing all of the validly named taxa into the classification at a single point, based on the sequence of the type strain, type species, or type genus. 1 We recognize that some workers will raise objections to this approach, as there are a number of existing taxa (e.g., Clostridium) that are paraphyletic. It is our view that such instances indicate a need for taxonomic revision, as the species appearing in clades apart from the type strain are clearly misclassified. To that end, we believe that publication and distribution of this outline may assist interested parties in detecting and resolving such problems. It is our intention to periodically distribute updated versions of this outline that include recently described taxa and new combinations along with remarks from the community indicating possible errors in classification or regions of ambiguity. Therefore, any reference to the outline should include the release number and publication date. Technical notes We continue to search the taxonomic literature and the public databases for new sequence data and will periodically add such to our phylogenetic models and to the Outline. Only high quality 16S rdna sequences (defined as >1400 nts, < 4% ambiguity, and fewer than 10 missing positions) are used. Since publication of Release 1.0, we have added 309 new species and new combinations, which are summarized in Table 1. We have also identified 506 additional sequences for 483 validly named type strains or new combinations that were described prior to March However, there remain a number of type strains for which high quality sequences cannot yet be positively identified in the public databases. As a result, provisional placement of some strains, at times based only on phenotypic similarity to sequenced strains, remains the only option. Within the classification, we recognize two procaryotic domains: the Archaea and Bacteria. The Domains are divided into Phyla which are in turn, divided into Classes, Orders (except for the Cyanobacteria which use the rank of subdivision), Families, and Genera. In the Actinobacteria, subclasses and suborders are also recognized. The rank of Kingdom is not used to avoid possible conflicts with the Botanical Code, where some overlap exists. As of December 2001, 5694 validly named procaryotic species had appeared either in the Approved List of Bacterial Names (Skerman et al., 1980) or in Validation Lists In addition, more than 1000 synonymies have been recorded as a result of taxonomic emendments, of which 915 are reflected in the current list. In some cases, we have opted to exclude names that were not in widespread usage, even though validly published. Adoption of a hierarchical classification presents several difficulties that must also be recognized. By definition, each species must be a member of successively higher ranks (six of which are recognized for the majority of taxa in the second edition of the Systematics Manual). Yet, there is considerable reluctance among many contemporary systematic procaryotic biologists to place new species and genera into higher taxa, especially at the intermediate levels (family, order, and class). In compiling and maintaining the outline we have often had to deal with instances where new species were variously assigned to a class or domain without being ascribed membership in any of the intervening taxa. This may be attributed to a lack of clear rules for delineating higher taxa. It may also reflect the inherent limitations of the 16S rrna gene for defining a higher taxonomic structure, especially when contemporary phylogenetic techniques, which rely solely on tree graphs as the principal interpretive device, are used to analyze small and inherently biased data sets. We have also observed a general 1 A more detailed discussion of the historical aspects of this effort are presented in the first release of the outline and by Garrity and Holt in Volume1oftheSystematics. 2 Lists1-71werepublishedintheInternational Journal of Systematic Bacteriology andlists72-82intheinternational 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, Bergey s Manual Trust All rights reserved. 1

4 Taxonomic Outline of the Procaryotes lack of consistency in defining the boundaries of genera based on 16S rdna sequence analysis. This is particularly problematic in bushy areas of the ARB and RDP trees where uncertainty of branching order is high and clear demarcation of taxonomic groups is impossible in the absence of other supporting data. In dealing with such problems, we have filled-in the missing taxa to complete the hierarchy. Names of higher taxa are based largely on priority, except in instances where such a strategy might lead to unnecessary confusion (e.g., Helicobacteraceae rather than Wolinellaceae). Considerable effort has been spent in confirming the placement of genera within higher taxa. Each of these higher taxa has also been scrutinized for phylogenetic coherence so as to avoid paraphyletic or polyphyletic groupings, wherever possible. However, since 16S rdna sequences are not yet available for all validly named species, some such instances will remain for the foreseeable future. We have annotated the species level outline in many areas to provide users some insight into our rationale for placements that might be deemed controversial. Readers are invited to pass along any comments or observations (along with supporting data) regarding other potential misplacements or errors. Despite some limitations, it is our view that the use of the well established phylogeny based on the 16S rrna gene provides a marked improvement over the earlier artificial classifications of procaryotes. The technique (16S rdna sequencing) is universally applicable and provides a single type of data that will soon be available for all validly named species. Given the rapid advancements in sequencing technology, we expect that sequences of other genes will follow in the near future and help in resolving the placement of problem taxa. Interpretation of the taxonomic outline At present, the two procaryotic domains have been subdivided into 25 phyla 3, two of which occur within the Archaea. Theremaining 23 phyla are ascribed to the Bacteria. Thefact that the Archaea and deeply branching Bacteria are presented first is based largely on the early versions of the RDP tree. Since the branching order of species within genera is frequently ambiguous and the data set is known to be incomplete, the use of phylogenetic trees as a guide for ordering taxa, both in the outline and the Systematics Manual proved to be untenable. Thus, we have adopted a more workable and all-inclusive strategy. The type taxon always appears first with other members of the same rank appearing in alphabetical order. The hierarchical numbering scheme used in the outline is arbitrary, especially at the lower levels. It is also subject to change as new taxa are described and existing taxa reclassified. Therefore, we advise against using the numbering scheme as an organizational or mnemonic device. Taxonomic names of all ranks appear in italics, in accordance to the Bacteriological Code. The superscript AL indicates that the name was included on the Approved Lists of Bacterial Names published in The superscript VP indicates that the name was validly published in the International Journal of Systematic Bacteriology (now the International Journal of Systematic and Evolutionary Microbiology) or appeared on one of the validation lists published in that journal. Names appearing in quotes have no standing in nomenclature, although they may have been effectively published elsewhere. Names followed with abbreviated terms such as phy. nov., class nov, fam. nov. are indicative of proposals for new taxa that will appear in the Systematic Manual. In the case of species names, each is followed with the authority for the name and year of the original description, in abbreviated form. The type strain (species), type species (genus), type genus (family and order), and type order (class and above) are indicated by an uppercase T, enclosed in parenthesis and in superscript. New taxa (recently added) are highlighted in red type and those which have been relocated within the outline as a result of comments from experts appear in magenta, followed by the string moved. Proposals for new combinations typically result in multiple changes within the outline. The new name is followed by the basonym, which is identified by the <- preceding the old name. Basonyms are also objective synonyms by default. To minimize redundancy, we will not identify them as such. The old name is also retained within the outline, in the original location. However, older names are preceded by a dagger symbol ( ) and should be considered deprecated under most circumstances. Following the old name and information about the taxonomic authority appears the new name, in green type, preceded by an arrow (->). In instances of synonymy, the synonyms (either objective or subjective) are identified as such and preceded by an equals sign (=). Synonyms are further categorized as either senior or junior, indicating priority. Immediately following the nomenclature section follows key information regarding the type strain including the authors original strain designation, when reported, and all known deposits in major culture collections. Each such deposit is set off by a small vertical bar ( ). If one or more high quality 16S rdna sequences have been 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

5 Bergey s Manual of Systematic Bacteriology, 2nd Edition reported for that strain, information regarding those sequences will follow. The first value will be the GenBank, EMBL or DDBJ accession number(s). This will be followed by the RDP short identifier, which is typically an alphanumeric abbreviation derived from the species name. Each such triplet is set off from others by the small vertical bar ( ). Citation Garrity,G.M.,M.Winters,A.W.KuoandD.B. Searles. (2002) Taxonomic Outline of the Procaryotes. Bergey s Manual of Systematic Bacteriology, Second Edition., Release 2.0., Springer-Verlag, New York. 284 pages. DOI: /bergeysoutline Acknowledgements We extend our thanks to Drs. Timothy Lilburn of the American Type Culture Collection, and Peter Sneath of the University of Leichester, who provided invaluable assistance in building and testing evolutionary models and statistical concepts that were vital in compiling and maintaining this outline. We also would like to acknowledge Drs. Wolfgang Ludwig and Karl-Heinz Schleifer of the Technical University of Munich for their numerous and helpful discussions on resolving discrepancies between the Bergey s Outline and the phylogenetic reference trees and Dr. John Holt, a coauthor of the first version of the taxonomic outline appearing in Volume I of the second edition of the Systematics. We would also like to extend our thanks to Drs. Fred Rainey, Joseph Tully, Floyd Dewhirst, Philip Hugenholtz, Thomas Schmidt, Norman Pace, Bonnie Maidak, David Boone, Erko Stackebrandt, Ross Overbeek, Niels Larsen, Oliver Strunk, and Gary Olsen for their helpful discussions and constructive comments. This document was developed and is maintained as an XML instance of a custom document type definition for taxonomic hierarchies using Epic Architect and Epic Editor, Version 4.2.1, (ArborText, Ann Arbor, MI). The DTD was authored by George M. Garrity and Catherine Lyons (Explicatrix llc, Sterling, NJ) and is interoperable with the Bergey s Manual DTD. This research was supported in part by the Biological and Environmental Research Program (BER), U.S. Department of Energy, Grant No. DE-FG02-02ER

6 Taxonomic Outline of the Procaryotes Table 1. New additions to the Taxonomic Outline, Version 2.0, January 2002 Taxon Phylum Class Order Acidithiobacillales Proteobacteria Gammaproteobacteria Families Acidithiobacillaceae Proteobacteria Gammaproteobacteria Hahellaceae Proteobacteria Gammaproteobacteria Opitutaceae Verrucomicrobia Verrucomicrobiae Thermithiobacillaceae Proteobacteria Gammaproteobacteria Genera Acidithiobacillus Proteobacteria Gammaproteobacteria Actinopolymorpha Actinobacteria Actinobacteria Agreia Actinobacteria Actinobacteria Albibacter Proteobacteria Alphaproteobacteria Alcalilimnicola Proteobacteria Gammaproteobacteria Alkalibacterium Firmicutes Bacilli Alkaliphilus Firmicutes Clostridia Anaerococcus Firmicutes Clostridia Arenibacter Bacteroidetes Flavobacteria Carboxydobrachium Firmicutes Clostridia Cellulosimicrobium Actinobacteria Actinobacteria Crossiella Actinobacteria Actinobacteria Dechloromonas Proteobacteria Betaproteobacteria Dechlorosoma Proteobacteria Betaproteobacteria Desulfomusa Proteobacteria Deltaproteobacteria Desulforegula Proteobacteria Deltaproteobacteria Desulfotignum Proteobacteria Deltaproteobacteria Ferribacterium Proteobacteria Betaproteobacteria Filobacillus Firmicutes Bacilli Gallicola Firmicutes Clostridia Geobacillus Firmicutes Bacilli Hahella Proteobacteria Gammaproteobacteria Halonatronum Firmicutes Clostridia Halothiobacillus Proteobacteria Gammaproteobacteria Hydrogenobaculum Aquificae Aquificae Hydrogenothermus Aquificae Aquificae Jeotgalibacillus Firmicutes Bacilli 4

7 Bergey s Manual of Systematic Bacteriology, 2nd Edition Taxon Phylum Class Ketogulonicigenium Proteobacteria Alphaproteobacteria Lachnobacterium Firmicutes Clostridia Lechevalieria Actinobacteria Actinobacteria Limnobacter Proteobacteria Betaproteobacteria Marinibacillus Firmicutes Bacilli Marinitoga Thermotogae Aquificae Methylosarcina Proteobacteria Gammaproteobacteria Muricauda Bacteroidetes Flavobacteria Mycetocola Actinobacteria Actinobacteria Neochlamydia Chlamydiae Chlamydiae Novosphingobium Proteobacteria Alphaproteobacteria Oceanomonas Proteobacteria Gammaproteobacteria Olsenella Actinobacteria Actinobacteria Opitutus Verrucomicrobia Verrucomicrobiae Ornithinimicrobium Actinobacteria Actinobacteria Paucimonas Proteobacteria Betaproteobacteria Peptoniphilus Firmicutes Clostridia Pigmentiphaga Proteobacteria Betaproteobacteria Planomicrobium Firmicutes Bacilli Propionispora Firmicutes Clostridia Raoultella Proteobacteria Gammaproteobacteria Rhodobaca Proteobacteria Alphaproteobacteria Rhodoblastus Proteobacteria Alphaproteobacteria Roseibium Proteobacteria Alphaproteobacteria Roseospirillum Proteobacteria Alphaproteobacteria Salana Actinobacteria Actinobacteria Samsonia Proteobacteria Gammaproteobacteria Schineria Proteobacteria Gammaproteobacteria Selenihalanaerobacter Firmicutes Clostridia Sphingobium Proteobacteria Alphaproteobacteria Sphingopyxis Proteobacteria Alphaproteobacteria Streptomonospora Actinobacteria Actinobacteria Tenacibaculum Bacteroidetes Flavobacteria Thalassomonas Proteobacteria Gammaproteobacteria Thermithiobacillus Proteobacteria Gammaproteobacteria 5

8 Taxonomic Outline of the Procaryotes Taxon Phylum Class Thialkalimicrobium Proteobacteria Gammaproteobacteria Thialkalivibrio Proteobacteria Gammaproteobacteria Thialkalicoccus Proteobacteria Gammaproteobacteria Thioflavicoccus Proteobacteria Gammaproteobacteria Trichlorobacter Proteobacteria Deltaproteobacteria Tropheryma Actinobacteria Actinobacteria Ureibacillus Firmicutes Bacilli Virgisporangium Actinobacteria Actinobacteria Xenophilus Proteobacteria Betaproteobacteria Zobellia Bacteroidetes Flavobacteria Species Acetobacter estunensis Proteobacteria Alphaproteobacteria Acetobacter indonesiensis Proteobacteria Alphaproteobacteria Acetobacterium tundrae Firmicutes Clostridia Acetobacter lovaniensis Proteobacteria Alphaproteobacteria Acetobacter orleanensis Proteobacteria Alphaproteobacteria Acetobacter tropicalis Proteobacteria Alphaproteobacteria Acidithiobacillus albertis Proteobacteria Gammaproteobacteria Acidithiobacillus caldus Proteobacteria Gammaproteobacteria Acidithiobacillus ferrooxidans Proteobacteria Gammaproteobacteria Acidithiobacillus thiooxidans Proteobacteria Gammaproteobacteria Acinetobacter schindleri Proteobacteria Gammaproteobacteria Acinetobacter ursingii Proteobacteria Gammaproteobacteria Actinocorallia aurantiaca Actinobacteria Actinobacteria Actinocorallia glomerata Actinobacteria Actinobacteria Actinocorallia libanotica Actinobacteria Actinobacteria Actinocorallia longicatena Actinobacteria Actinobacteria Actinocorallia longicatena Actinobacteria Actinobacteria Actinomyces catuli Actinobacteria Actinobacteria Actinomyces funkei Actinobacteria Actinobacteria Actinomyces marimammalium Actinobacteria Actinobacteria Actinomyces radicidentis Actinobacteria Actinobacteria Actinomyces suimastitidis Actinobacteria Actinobacteria Actinoplanes capillaceus Actinobacteria Actinobacteria 6

9 Bergey s Manual of Systematic Bacteriology, 2nd Edition Taxon Phylum Class Actinoplanes friuliensis Actinobacteria Actinobacteria Actinopolymorpha singaporensis Actinobacteria Actinobacteria Aerococcus sanquinicola Firmicutes Bacilli Aerococcus urinaehominis Firmicutes Bacilli Agreia bicolorata Actinobacteria Actinobacteria Agreia bicolorata Proteobacteria Alphaproteobacteria Agreia bicolorata Actinobacteria Actinobacteria Agromyces luteolus Actinobacteria Actinobacteria Agromyces rhizosphaerae Actinobacteria Actinobacteria Albibacter methylovorans Proteobacteria Alphaproteobacteria Albibacter halodurans Proteobacteria Gammaproteobacteria Albibacter olivapovliticus Firmicutes Bacilli Alkaliphilus transvaalensis Firmicutes Clostridia Amycolatopsis albidoflavus Actinobacteria Actinobacteria Amycolatopsis rubida Actinobacteria Actinobacteria Amycolatopsis sacchari Actinobacteria Actinobacteria Anaerobranca gottschalkii Firmicutes Clostridia Anaerococcus hydrogenalis Firmicutes Clostridia Anaerococcus lactolyticus Firmicutes Clostridia Anaerococcus octavius Firmicutes Clostridia Anaerococcus prevotii Firmicutes Clostridia Anaerococcus tetradius Firmicutes Clostridia Anaerococcus vaginalis Firmicutes Clostridia Anaplasma bovis Proteobacteria Alphaproteobacteria Anaplasma phagocytophila Proteobacteria Alphaproteobacteria Anaplasma platys Proteobacteria Alphaproteobacteria Arcanobacterium pluranimalium Actinobacteria Actinobacteria Arenibacter latericius Bacteroidetes Flavobacteria Asaia siamensis Proteobacteria Alphaproteobacteria Azospirillum doebereinerae Proteobacteria Alphaproteobacteria Bacillus arseniciselenatis Firmicutes Bacilli Bacillus jeotgali Firmicutes Bacilli Bacillus selenitireducens Firmicutes Bacilli Bacillus sonorensis Firmicutes Bacilli Bartonella schoenbuchii Proteobacteria Alphaproteobacteria 7

10 Taxonomic Outline of the Procaryotes Taxon Phylum Class Bordetella petrii Proteobacteria Betaproteobacteria Borrelia sinica Spirochaetes Spirochaetes Brevibacterium paucivorans Actinobacteria Actinobacteria Burkholderia ambifaria Proteobacteria Betaproteobacteria Burkholderia caledonica Proteobacteria Betaproteobacteria Burkholderia fungorum Proteobacteria Betaproteobacteria Burkholderia sacchari Proteobacteria Betaproteobacteria Caloranaerobacter azorensis Firmicutes Clostridia Campylobacter hominis Proteobacteria Epsilonproteobacteria Carboxydobrachium pacificum Firmicutes Clostridia Cellulosimicrobium cellulans Actinobacteria Actinobacteria Chromohalobacter canadensis Proteobacteria Gammaproteobacteria Chromohalobacter israelensis Proteobacteria Gammaproteobacteria Chromohalobacter salexigens Proteobacteria Gammaproteobacteria Clostridium hiranonis Firmicutes Clostridia Clostridium hungatei Firmicutes Clostridia Clostridium saccharobutylicum Firmicutes Clostridia Clostridium saccharoperbutylacetonicum Firmicutes Clostridia Clostridium uliginosum Firmicutes Clostridia Comamonas denitrificans Proteobacteria Betaproteobacteria Comamonas nitrativorans Proteobacteria Betaproteobacteria Corynebacterium capitovis Actinobacteria Actinobacteria Corynebacterium casei Actinobacteria Actinobacteria Corynebacterium felinum Actinobacteria Actinobacteria Corynebacterium freneyi Actinobacteria Actinobacteria Corynebacterium mooreparkense Actinobacteria Actinobacteria Corynebacterium testudinoris Actinobacteria Actinobacteria Crossiella cryophila Actinobacteria Actinobacteria Cryptosporangium aurantiacum Actinobacteria Actinobacteria Cryptosporangium minutisporangium Actinobacteria Actinobacteria Dechloromonas agitata Proteobacteria Betaproteobacteria Dechlorosoma suillum Proteobacteria Betaproteobacteria Desulfacinum infernum Proteobacteria Deltaproteobacteria Desulfitobacterium chlororespirans Firmicutes Clostridia Desulfobacula phenolica Proteobacteria Deltaproteobacteria 8

11 Bergey s Manual of Systematic Bacteriology, 2nd Edition Taxon Phylum Class Desulfomicrobium orale Proteobacteria Deltaproteobacteria Desulfomonile limimaris Proteobacteria Deltaproteobacteria Desulfomusa hansenii Proteobacteria Deltaproteobacteria Desulforegula conservatrix Proteobacteria Deltaproteobacteria Desulfosporosinus meridiei Firmicutes Clostridia Desulfotignum balticum Proteobacteria Deltaproteobacteria Desulfovibrio dechloracetivorans Proteobacteria Deltaproteobacteria Desulfovibrio mexicanus Nitrospira Nitrospira Desulfovibrio mexicanus Nitrospira Nitrospira Desulfurococcus amylolyticus Crenarchaeota Thermoprotei Dethiosulfovibrio acidaminovorans Firmicutes Clostridia Dethiosulfovibrio marinus Firmicutes Clostridia Dethiosulfovibrio russensis Firmicutes Clostridia Ehrlichia ruminantium Proteobacteria Alphaproteobacteria Enterobacter cowanii Proteobacteria Gammaproteobacteria Enterococcus haemoperoxidus Firmicutes Bacilli Enterococcus moraviensis Firmicutes Bacilli Enterococcus porcinus Firmicutes Bacilli Enterococcus ratti Firmicutes Bacilli Enterococcus villorum Firmicutes Bacilli Facklamia miroungae Firmicutes Bacilli Ferribacterium limneticum Proteobacteria Betaproteobacteria Filobacillus milosensis Firmicutes Bacilli Flavobacterium frigidarium Bacteroidetes Flavobacteria Fusobacterium equinum Fusobacteria Fusobacteria Gallicola barnesae Firmicutes Clostridia Geobacillus caldoxylosilyticus Firmicutes Bacilli Geobacillus kaustophilus Firmicutes Bacilli Geobacillus stearothermophilus Firmicutes Bacilli Geobacillus subterraneus Firmicutes Bacilli Geobacillus thermocatenulatus Firmicutes Bacilli Geobacillus thermodenitrificans Firmicutes Bacilli Geobacillus thermoglucosidasius Firmicutes Bacilli Geobacillus thermoleovorans Firmicutes Bacilli Geobacillus uzenensis Firmicutes Bacilli 9

12 Taxonomic Outline of the Procaryotes Taxon Phylum Class Geobacter bremensis Proteobacteria Deltaproteobacteria Geobacter chapellei Proteobacteria Deltaproteobacteria Geobacter grbiciae Proteobacteria Deltaproteobacteria Geobacter hydrogenophilus Proteobacteria Deltaproteobacteria Geobacter pelophilus Proteobacteria Deltaproteobacteria Globicatella sulfidifaciens Firmicutes Bacilli Gluconacetobacter azotocaptans Proteobacteria Alphaproteobacteria Gluconacetobacter johannae Proteobacteria Alphaproteobacteria Hahella chejuensis Proteobacteria Gammaproteobacteria Halomonas campisalis Proteobacteria Gammaproteobacteria Halomonas magadiensis Proteobacteria Gammaproteobacteria Halomonas marisflavi Proteobacteria Gammaproteobacteria Halomonas maura Proteobacteria Gammaproteobacteria Halonatronum saccharophilum Firmicutes Clostridia Helicobacter ganmani Proteobacteria Epsilonproteobacteria Heliobacterium sulfidophilum Firmicutes Clostridia Heliobacterium undosum Firmicutes Clostridia Heliorestis baculata Firmicutes Clostridia Herbaspirillum frisingense Proteobacteria Betaproteobacteria Hydrogenobacter hydrogenophilus Aquificae Aquificae Hydrogenobacter subterraneus Aquificae Aquificae Hydrogenobaculum acidophilum Aquificae Aquificae Hydrogenophaga intermedia Proteobacteria Betaproteobacteria Hydrogenophilus hirschii Proteobacteria Betaproteobacteria Hydrogenothermus marinus Aquificae Aquificae Hyphomicrobium chloromethanicum Proteobacteria Alphaproteobacteria Jeotgalibacillus alimentarius Firmicutes Bacilli Ketogulonicigenium robustum Proteobacteria Alphaproteobacteria Ketogulonicigenium vulgare Proteobacteria Alphaproteobacteria Kitasatospora cineracea Actinobacteria Actinobacteria Kitasatospora niigatensis Actinobacteria Actinobacteria Lachnobacterium bovis Firmicutes Clostridia Lactobacillus coleohominis Firmicutes Bacilli Lactobacillus cypricasei Firmicutes Bacilli Lactobacillus psittaci Firmicutes Bacilli 10

13 Bergey s Manual of Systematic Bacteriology, 2nd Edition Taxon Phylum Class Lamprocystis purpurea Proteobacteria Gammaproteobacteria Lechevalieria aerocolonigenes Actinobacteria Actinobacteria Lechevalieria flava Actinobacteria Actinobacteria Legionella beliardensis Proteobacteria Gammaproteobacteria Legionella drozanskii Proteobacteria Gammaproteobacteria Legionella fallonii Proteobacteria Gammaproteobacteria Legionella gresilensis Proteobacteria Gammaproteobacteria Legionella rowbothamii Proteobacteria Gammaproteobacteria Lentzea albida Actinobacteria Actinobacteria Lentzea californiensis Actinobacteria Actinobacteria Lentzea violacea Actinobacteria Actinobacteria Lentzea waywayandensis Actinobacteria Actinobacteria Leuconostoc gasicomitatum Firmicutes Bacilli Limnobacter thiooxidans Proteobacteria Betaproteobacteria Marinibacillus marinus Firmicutes Bacilli Marinitoga camini Thermotogae Thermotogae Mesorhizobium chacoense Proteobacteria Alphaproteobacteria Methanobacterium congolense Euryarchaeota Methanobacteria Methanoculleus chikugoensis Euryarchaeota Methanobacteria Methanofollis aquaemaris Euryarchaeota Methanobacteria Methylobacterium chloromethanicum Proteobacteria Alphaproteobacteria Methylobacter psychrophilus Proteobacteria Gammaproteobacteria Methylomicrobium buryatense Proteobacteria Gammaproteobacteria Methylomonas scandinavica Proteobacteria Gammaproteobacteria Methylophilus leisingeri Proteobacteria Betaproteobacteria Methylosarcina fibrata Proteobacteria Gammaproteobacteria Methylosarcina quisquiliarum Proteobacteria Gammaproteobacteria Methylovorus mays Proteobacteria Betaproteobacteria Microbacterium foliorum Actinobacteria Actinobacteria Microbacterium gubbeenense Actinobacteria Actinobacteria Microbacterium phyllosphaerae Actinobacteria Actinobacteria Microbacterium resistens Actinobacteria Actinobacteria Moritella viscosa Proteobacteria Gammaproteobacteria Muricauda ruestringensis Bacteroidetes Flavobacteria Mycetocola lacteus Actinobacteria Actinobacteria 11

14 Taxonomic Outline of the Procaryotes Taxon Phylum Class Mycetocola saprophilus Actinobacteria Actinobacteria Mycetocola tolaasinivorans Actinobacteria Actinobacteria Mycobacterium doricum Actinobacteria Actinobacteria Mycobacterium frederiksbergense Actinobacteria Actinobacteria Mycobacterium heckeshornense Actinobacteria Actinobacteria Mycobacterium immunogenum Actinobacteria Actinobacteria Mycoplasma agassizii Firmicutes Mollicutes Mycoplasma alligatoris Firmicutes Mollicutes Mycoplasma microti Firmicutes Mollicutes Natrialba aegyptia Euryarchaeota Halobacteria Natrialba chahannaoensis Euryarchaeota Halobacteria Natrialba hulunbeirensis Euryarchaeota Halobacteria Natrialba taiwanensis Euryarchaeota Halobacteria Natronobacterium nitratireducens Euryarchaeota Halobacteria Neochlamydia hartmannellae Chlamydiae Chlamydiae Neorickettsia risticii Proteobacteria Alphaproteobacteria Neorickettsia sennetsu Proteobacteria Alphaproteobacteria Nitrobacter alkalicus Proteobacteria Alphaproteobacteria Nitrobacter hamburgensis Proteobacteria Alphaproteobacteria Nitrobacter vulgaris Proteobacteria Alphaproteobacteria Nitrosomonas aestuarii Proteobacteria Betaproteobacteria Nitrosomonas communis Proteobacteria Betaproteobacteria Nitrosomonas eutropha Proteobacteria Betaproteobacteria Nitrosomonas halophila Proteobacteria Betaproteobacteria Nitrosomonas marina Proteobacteria Betaproteobacteria Nitrosomonas nitrosa Proteobacteria Betaproteobacteria Nitrosomonas oligotropha Proteobacteria Betaproteobacteria Nitrosomonas ureae Proteobacteria Betaproteobacteria Nocardia africana Actinobacteria Actinobacteria Nocardia beijingensis Actinobacteria Actinobacteria Nocardia cummidelens Actinobacteria Actinobacteria Nocardia cyriacigeorgici Actinobacteria Actinobacteria Nocardia fluminea Actinobacteria Actinobacteria Nocardia ignorata Actinobacteria Actinobacteria Nocardia soli Actinobacteria Actinobacteria 12

15 Bergey s Manual of Systematic Bacteriology, 2nd Edition Taxon Phylum Class Nocardia veterana Actinobacteria Actinobacteria Nonomuraea dietzii Actinobacteria Actinobacteria Novosphingobium aromaticivorum Proteobacteria Alphaproteobacteria Novosphingobium capsulatum Proteobacteria Alphaproteobacteria Novosphingobium roseae Proteobacteria Alphaproteobacteria Novosphingobium stygiae Proteobacteria Alphaproteobacteria Novosphingobium subarcticum Proteobacteria Alphaproteobacteria Novosphingobium subterraneae Proteobacteria Alphaproteobacteria Oceanomonas baumannii Proteobacteria Gammaproteobacteria Oceanomonas doudoroffii Proteobacteria Gammaproteobacteria Olsenella profusa Actinobacteria Actinobacteria Olsenella uli Actinobacteria Actinobacteria Opitutus terrae Verrucomicrobia Verrucomicrobiae Ornithinimicrobium humiphilum Actinobacteria Actinobacteria Paenibacillus azoreducens Firmicutes Bacilli Paenibacillus borealis Firmicutes Bacilli Paenibacillus granivorans Firmicutes Bacilli Paenibacillus jamilae Firmicutes Bacilli Paracoccus kondratievae Proteobacteria Alphaproteobacteria Paucimonas lemoignei Proteobacteria Betaproteobacteria Peptoniphilus asaccharolyticus Firmicutes Clostridia Peptoniphilus harei Firmicutes Clostridia Peptoniphilus indolicus Firmicutes Clostridia Peptoniphilus ivorii Firmicutes Clostridia Peptoniphilus lacrimalis Firmicutes Clostridia Pigmentiphaga kullae Proteobacteria Betaproteobacteria Planococcus alkanoclasticus Firmicutes Bacilli Planomicrobium koreense Firmicutes Bacilli Planomicrobium mcmeekinii Firmicutes Bacilli Planomicrobium okeanokoites Firmicutes Bacilli Porphyromonas gulae Bacteroidetes Bacteroidetes Propionibacterium microaerophilum Actinobacteria Actinobacteria Propionispora vibrioides Firmicutes Clostridia Pseudoalteromonas peptidolytica Proteobacteria Gammaproteobacteria Pseudoalteromonas tetraodonis Proteobacteria Gammaproteobacteria 13

16 Taxonomic Outline of the Procaryotes Taxon Phylum Class Pseudoalteromonas ulvae Proteobacteria Gammaproteobacteria Pseudomonas alcaliphila Proteobacteria Gammaproteobacteria Pseudomonas frederiksbergensis Proteobacteria Gammaproteobacteria Pseudomonas kilonensis Proteobacteria Gammaproteobacteria Pseudonocardia kongjuensis Actinobacteria Actinobacteria Psychrobacter proteolyticus Proteobacteria Gammaproteobacteria Psychrobacter proteolyticus Crenarchaeota Thermoprotei Pyrobaculum oguniense Crenarchaeota Thermoprotei Ralstonia campinensis Proteobacteria Betaproteobacteria Ralstonia mannitolilytica Proteobacteria Betaproteobacteria Ralstonia metallidurans Proteobacteria Betaproteobacteria Ralstonia taiwanensis Proteobacteria Betaproteobacteria Raoultella ornithinolytica Proteobacteria Gammaproteobacteria Raoultella planticola Proteobacteria Gammaproteobacteria Raoultella terrigena Proteobacteria Gammaproteobacteria Rhizobium radiobacter Proteobacteria Alphaproteobacteria Rhizobium rhizogenes Proteobacteria Alphaproteobacteria Rhizobium rubi Proteobacteria Alphaproteobacteria Rhizobium vitis Proteobacteria Alphaproteobacteria Rhizobium yanglingense Proteobacteria Alphaproteobacteria Rhodobaca bogoriensis Proteobacteria Alphaproteobacteria Rhodoblastus acidophilus Proteobacteria Alphaproteobacteria Rhodoferax antarcticus Proteobacteria Betaproteobacteria Rickettsia felis Proteobacteria Alphaproteobacteria Roseospirillum parvum Proteobacteria Alphaproteobacteria Saccharopolyspora flava Actinobacteria Actinobacteria Saccharopolyspora thermophila Actinobacteria Actinobacteria Salana multivorans Actinobacteria Actinobacteria Samsonia erythrinae Proteobacteria Gammaproteobacteria Schineria larvae Proteobacteria Gammaproteobacteria Selenihalanaerobacter shriftii Firmicutes Clostridia Shewanella japonica Proteobacteria Gammaproteobacteria Sphingobium chlorophenolicum Proteobacteria Alphaproteobacteria Sphingobium herbicidovorans Proteobacteria Alphaproteobacteria Sphingobium yanoikuyae Proteobacteria Alphaproteobacteria 14

17 Bergey s Manual of Systematic Bacteriology, 2nd Edition Taxon Phylum Class Sphingomonas alaskensis Proteobacteria Alphaproteobacteria Sphingomonas aquatilis Proteobacteria Alphaproteobacteria Sphingomonas cloacae Proteobacteria Alphaproteobacteria Sphingomonas koreensis Proteobacteria Alphaproteobacteria Sphingomonas pituitosa Proteobacteria Alphaproteobacteria Sphingomonas pituittaejonensisosa Proteobacteria Alphaproteobacteria Sphingomonas wittichii Proteobacteria Alphaproteobacteria Sphingopyxis macrogoltabida Proteobacteria Alphaproteobacteria Sphingopyxis terrae Proteobacteria Alphaproteobacteria Sporosarcina aquimarina Firmicutes Bacilli Sporosarcina globispora Firmicutes Bacilli Sporosarcina pasteurii Firmicutes Bacilli Sporosarcina psychrophila Firmicutes Bacilli Streptococcus australis Firmicutes Bacilli Streptococcus ovis Firmicutes Bacilli Streptomonospora salina Actinobacteria Actinobacteria Streptomyces asiaticus Actinobacteria Actinobacteria Streptomyces cangkringensis Actinobacteria Actinobacteria Streptomyces indonesiensis Actinobacteria Actinobacteria Streptomyces javensis Actinobacteria Actinobacteria Streptomyces rhizosphaericus Actinobacteria Actinobacteria Streptomyces yogyakartensis Actinobacteria Actinobacteria Syntrophus aciditrophicus Proteobacteria Deltaproteobacteria Taylorella asinigenitalis Proteobacteria Betaproteobacteria Tenacibaculum amylolyticum Bacteroidetes Flavobacteria Tenacibaculum maritimum Bacteroidetes Flavobacteria Tenacibaculum mesophilum Bacteroidetes Flavobacteria Tenacibaculum ovolyticum Bacteroidetes Flavobacteria Thalassomonas viridans Proteobacteria Gammaproteobacteria Thauera chlorobenzoica Proteobacteria Betaproteobacteria Thermoanaerobacterium polysaccharolyticum Firmicutes Clostridia Thermoanaerobacterium zeae Firmicutes Clostridia Thermoanaerobacter tengcongensis Firmicutes Clostridia Thermoanaerobacter yonseiensis Firmicutes Clostridia Thermococcus acidaminovorans Euryarchaeota Thermococci 15

18 Taxonomic Outline of the Procaryotes Taxon Phylum Class Thermococcus litoralis Euryarchaeota Thermococci Thermococcus sibiricus Euryarchaeota Thermococci Thermococcus waiotapuensis Euryarchaeota Thermococci Thermoproteus uzoniensis Crenarchaeota Thermoprotei Thermosipho geolei Thermotogae Thermotogae Thermotoga naphthophila Thermotogae Thermotogae Thermotoga petrophila Thermotogae Thermotogae Thialkalimicrobium aerophilum Proteobacteria Gammaproteobacteria Thialkalimicrobium sibiricum Proteobacteria Gammaproteobacteria Thialkalivibrio denitrificans Proteobacteria Gammaproteobacteria Thialkalivibrio nitratis Proteobacteria Gammaproteobacteria Thialkalivibrio versutus Proteobacteria Gammaproteobacteria Thioflavicoccus moilis Proteobacteria Gammaproteobacteria Treponema parvum Spirochaetes Spirochaetes Tropheryma whipplei Actinobacteria Actinobacteria Ureibacillus terrenus Firmicutes Bacilli Ureibacillus thermosphaericus Firmicutes Bacilli Vibrio agarivorans Proteobacteria Gammaproteobacteria Vibrio cyclotrophicus Proteobacteria Gammaproteobacteria Vibrio lentus Proteobacteria Gammaproteobacteria Vibrio shiloi Proteobacteria Gammaproteobacteria Vibrio wodanis Proteobacteria Gammaproteobacteria Virgisporangium aurantiacum Actinobacteria Actinobacteria Virgisporangium ochraceum Actinobacteria Actinobacteria Xenophilus azovorans Proteobacteria Betaproteobacteria Zobellia galactanivorans Bacteroidetes Flavobacteria Zobellia uliginosa Bacteroidetes Flavobacteria Subspecies Alcaligenes faecalis parafaecalis Proteobacteria Betaproteobacteria Clostridium stercorarium leptospartum Firmicutes Clostridia Clostridium stercorarium thermolacticum Firmicutes Clostridia Nonomuraea roseoviolacea carminata Actinobacteria Actinobacteria Prochlorococcus marinus marinus Cyanobacteria Cyanobacteria Prochlorococcus marinus pastoris Cyanobacteria Cyanobacteria Salinivibrio costicola vallismortis Proteobacteria Gammaproteobacteria 16

19 Bergey s Manual of Systematic Bacteriology, 2nd Edition Domain Archaeadom. nov. Phylum AI. Crenarchaeota phy. nov. 4 Class I. Thermoprotei class. nov. VP (T) Order I. Thermoproteales Family I. Thermoproteaceae VP VP (T) Genus I. Thermoproteus Thermoproteus tenax VP (T) Zillig and Stetter 1982 DSM 2078 Thermoproteus neutrophilus VP Zillig 1989 DSM 2338 JCM 9278, AB009618, Thp.neutro Thermoproteus uzoniensis VP Bonch-Osmolovskaya et al Z-605 DSM 5263 Genus II. Caldivirga VP Caldivirga maquilingensis VP (T) Itoh et al IC-167, AB JCM MCC- UPLB 1200 ANMR 0178 Genus III. Pyrobaculum VP Pyrobaculum islandicum VP (T) Huber et al GEO3, L07511, Pyb.island DSM 4184 Pyrobaculum aerophilum VP Völkl et al IM2, L07510, Pyb.aeroph DSM 7523 Pyrobaculum arsenaticum VP Huber et al PZ6, AJ ATCC DSM Pyrobaculum organotrophum VP Huber et al H10 DSM 4185 Pyrobaculum oguniense VP Sako et al TE7, AB DSM JCM Genus IV. Thermocladium VP Thermocladium modestius VP (T) Itoh et al IC-125, AB005296, Tcl.modest JCM Family II. Thermofilaceae VP VP (T) Genus I. Thermofilum Thermofilum pendens VP (T) Zillig and Gierl 1983 Hvv3, X14835, Tmf.penden DSM 2475, X14835, Tmf.penden Order II. Desulfurococcales ord. nov. Family I. Desulfurococcaceae VP VP (T) Genus I. Desulfurococcus Desulfurococcus mucosus VP (T) Zillig and Stetter 1983 DSM 2162 Desulfurococcus amylolyticus VP Bonch-Osmolovskaya et al Z 533, AF DSM 3822 JCM 9188 Desulfurococcus mobilis VP Zillig and Stetter 1983 DSM 2161 Genus II. Acidolobus VP 5 Acidilobus aceticus VP (T) Prokofeva et al DSM 11585, AF Genus III. Aeropyrum VP Aeropyrum pernix VP (T) Sako et al K1, AB008745, Ap.pernix2 K1, D83259, Ap.pernix1 DSM JCM 9820 Genus IV. Ignicoccus VP Ignicoccus islandicus VP (T) Huber et al Kol8, X99536 ATCC DSM Ignicoccus pacificus VP Huber and Stetter 2000 LPC33, AJ ATCC DSM Genus V. Staphylothermus VP Staphylothermus marinus VP (T) Stetter and Fiala 1986 F1, X99560, Sth.marinu ATCC DSM 3639, X99560, Sth.marinu Staphylothermus hellenicus VP Arab et al P8, AJ DSM JCM Genus VI. Stetteria VP Stetteria hydrogenophila VP (T) Jochimsen et al ABC, Y07784, Str.hygen2 4ABC, Y07963, Str.hygeno DSM Both the ARB and RDP trees provide support for the general taxonomic structure proposed for the Crenarchaeota. Ludwig indicates that Sulfolobales and Desulfurococcales are sister groups but states that the Thermoproteales may not be monophyletic. 5 Prokofeva et al. suggest that Acidolobus represents a separate lineage within the Crenarchaeota. This has not yet been confirmed in either the ARB or RDP trees. 17

20 Taxonomic Outline of the Procaryotes Genus VII. Sulfophobococcus VP Sulfophobococcus zilligii VP (T) Hensel et al K1, X98064, Slp.zillig DSM JCM Genus VIII. Thermodiscus gen. nov. Thermodiscus maritimus sp. nov. (T) Stetter 2001 S2, X99554 Genus IX. Thermosphaera VP Thermosphaera aggregans VP (T) Huber et al M11TL, X99556, Thm.aggreg DSM Family II. Pyrodictiaceae VP VP (T) Genus I. Pyrodictium Pyrodictium occultum VP (T) Stetter et al PL-19, M21087, Pyr.occult DSM 2709 Pyrodictium abyssi VP Pley et al AV2 DSM 6158, X99559, Pyr.abyssi Pyrodictium brockii VP Stetter et al S1 DSM 2708 Genus II. Hyperthermus VP Hyperthermus butylicus VP (T) Zillig et al DSM 5456, X99553, Hth.butyli Genus III. Pyrolobus VP Pyrolobus fumari VP (T) Blöchl et al A, X99555, Pyl.fumari DSM Order III. Sulfolobales VP Family I. Sulfolobaceae VP AL (T) Genus I. Sulfolobus Sulfolobus acidocaldarius AL (T) Brock et al ATCC 33909, D14876, Sul.acalda DSM 639, D14053, Sul.acald4 DSM 639, U32320, Sul.acald5 NCIB Sulfolobus brierleyi AL Zillig et al > Acidianus brierleyi DSM 1651, X90477, Adi.brier3 IFO Sulfolobus hakonensis VP Takayanagi et al HO1-1 ATCC DSM 7519 IAM JCM 8857 Sulfolobus metallicus VP Huber and Stetter 1992 Kra 23 DSM 6482, D85519, Sul.metal2 DSM 6482, X90479, Sul.metall Sulfolobus shibatae VP Grogan et al B12 DSM 5389 DSM 5389, M32504, Sul.shibat Sulfolobus solfataricus AL Zillig et al ATCC DSM 1616, D26490, Sul.solfa4 DSM 1616, X90478, Sul.solfa6 Sulfolobus yangmingensis VP Jan et al YM1, AB Genus II. Acidianus VP Acidianus infernus VP (T) Segerer et al So4a DSM 3191, D38773, Adi.infern DSM 3191, D85505, Adi.infer3 DSM 3191, X89852, Adi.infer2 Acidianus ambivalens VP (Zillig and Böck 1987) Fuchs et al <- Desulfurolobus ambivalens (basonym) Lei 10 DSM 3772, D38774, Adi.ambivl DSM 3772, D85506, Adi.ambiv3 DSM 3772, X90484, Adi.ambiv2 Acidianus brierleyi VP (Zillig et al. 1980) Segerer et al <- Sulfolobus brierleyi (basonym) DSM 1651, D26489, Adi.brier2 DSM 1651, X90477, Adi.brier3 Genus III. Metallosphaera VP Metallosphaera sedula VP (T) Huber et al TH2 DSM 5348, D26491, Mts.sedula DSM 5348, X90481, Mts.sedul3 Metallosphaera prunae VP Fuchs et al Ron 12/II, X90482, Mts.prunae DSM 10039, X90482, Mts.prunae Genus IV. Stygiolobus VP Stygiolobus azoricus VP (T) Segerer et al FC6 DSM 6296, D85520, Sl.azoric2 DSM 6296, X90480, Sl.azoricu Genus V. Sulfurisphaera VP Sulfurisphaera ohwakuensis VP (T) Kurosawa et al TA-1, D85507, Sfr.ohwaku DSM IFO 15161, D85507, Sfr.ohwaku Genus VI. Sulfurococcus VP Sulfurococcus mirabilis VP (T) Golovacheva et al INMI AT-59 Sulfurococcus yellowstonensis VP Karavaiko et al Str6kar 18

21 Bergey s Manual of Systematic Bacteriology, 2nd Edition Phylum AII. Euryarchaeota phy. nov. 6 Class I. Methanobacteria class. nov. VP (T) Order I. Methanobacteriales Family I. Methanobacteriaceae AL AL (T) Genus I. Methanobacterium Methanobacterium formicicum AL (T) Schnellen 1947 MF ATCC DSM 1535 OCM 55 Methanobacterium alcaliphilum VP Worakit et al WeN4 DSM 3387 OCM 11 Methanobacterium arbophilicum AL Zeikus and Henning > Methanobrevibacter arboriphilicus DH1 ATCC DSM 1125 Methanobacterium bryantii VP Balch and Wolfe 1981 M.o.H. ATCC DSM 863, M59124, Mb.bryanti Methanobacterium congolense VP Cuzin et al C, AF DSM 7095 OCM 779 Methanobacterium defluvii VP Kotelnikova et al > Methanothermobacter defluvii ADZ, X99046, Mbt.dfluvi DSM 7466, X99046, Mbt.dfluvi VKM B-1962, X99046, Mbt.dfluvi 7 Methanobacterium espanolae VP Pateletal.1990 GP9, AF095260, Mb.espanol DSM 5982 NRC 5912 Methanobacterium ivanovii VP Jain et al DSM 2611 Ivanov OCM 140, AF095261, Mb.ivanovi Methanobacterium mobile AL Paynter and Hungate > Methanomicrobium mobile ATCC DSM 1539, M59142, Mm.mobile Methanobacterium oryzae VP Joulian et al Fpi, AF DSM Methanobacterium palustre VP Zellner et al F, AF095263, Mb.palustr DSM 3108 Methanobacterium ruminantium AL Smith and Hungate > Methanobrevibacter ruminantium DSM 1093 Methanobacterium subterraneum VP Kotelnikova et al A8p, X99044, Mb.subterr DSM 11074, X99044, Mb.subterr Methanobacterium thermaggregans VP Blotevogel and Fischer 1988 ATCC DSM 3266 OCM 141, AF095264, Mb.thaggre Methanobacterium thermalcaliphilum VP Blotevogel et al = Methanobacterium thermautotrophicum (senior subjective synonym) AC60 ATCC DSM 3267 Methanobacterium thermautotrophicum AL Zeikus and Wolfe 1972 = Methanobacterium thermoformicicum (junior subjective synonym) = Methanobacterium thermalcaliphilum (junior subjective synonym) -> Methanothermobacter thermautotrophicus DH, X68720 DSM 1053 ATCC Methanobacterium thermoflexum VP Kotelnikova et al > Methanothermobacter thermoflexus IDZ, X99047, Mbt.thflex DSM 7268, X99047, Mbt.thflex VKM B-1963, X99047, Mbt.thflex 8 Methanobacterium thermoformicicum VP Zhilina and Ilarionov 1986 = Methanobacterium thermautotrophicum (senior subjective synonym) DSM 3720 INMI Z-245, X68712, Mb.tauZ245 Methanobacterium thermophilum VP Laurinavichus et al > Methanothermobacter thermophilus M, X99048, Mbt.thphil DSM 6529, X99048, Mbt.thphil VKM B-1786, X99048, Mbt.thphil 9 Methanobacterium uliginosum VP König 1985 P2St DSM 2956 Methanobacterium wolfei VP Winter et al > Methanothermobacter wolfeii ATCC DSM In Ludwig and Klenk s chapter, they indicate that the Halobacteriales, Methanomicrobiales and Thermoplasmatales share a common root with Methanobacteriales, branching off of the first two. Ludwig indicates that he was not able to stably resolve a relationship among the Methanomicrobiales, Halobacteriales and Methanobacteriales with the Archaeoglobales, Methanococcales, Thermococcales and Methanopyrales. He makes no mention of the Methanosarcinales which is clearly evident in the RDP tree. 7 Methanothermobacter defluvii comb. nov. is proposed in Volume 1 of Bergey s Manual of Systematic Bacteriology, 2ndEd. 8 Methanothermobacter thermoflexus comb. nov. is proposed in Volume 1 of Bergey s Manual of Systematic Bacteriology, 2nd Ed. 9 Methanothermobacter thermophilus comb. nov. is proposed in Volume 1 of Bergey s Manual of Systematic Bacteriology, 2nd Ed. 19

22 Taxonomic Outline of the Procaryotes Genus II. Methanobrevibacter VP Methanobrevibacter ruminantium VP (T) (Smith and Hungate 1958) Balch and Wolfe 1981 <- Methanobacterium ruminantium (basonym) M1 DSM 1093 Methanobrevibacter arboriphilicus VP (Zeikus and Henning 1975) Balch and Wolfe 1981 <- Methanobacterium arbophilicum (basonym) DH1 ATCC DSM 1125 Methanobrevibacter curvatus VP Leadbetter and Breznak 1997 RFM-2, U62533, Mbb.curvat DSM Methanobrevibacter cuticularis VP Leadbetter and Breznak 1997 RFM-1, U41095, Mbb.cuticl DSM Methanobrevibacter filiformis VP Leadbetter et al RFM-3, U82322, Mbb.filfor DSM Methanobrevibacter oralis VP Ferrari et al ZR DSM 7256 Methanobrevibacter smithii VP Balch and Wolfe 1981 PS, U55233, Mbb.smithi ATCC 3506 DSM 861 Genus III. Methanosphaera VP Methanosphaera stadtmanae VP (T) Miller and Wolin 1985 MCB-3 DSM 3091, M59139, Mpr.stadtm Methanosphaera cuniculi VP Biavatietal R7 DSM 4103 Genus IV. Methanothermobacter VP Methanothermobacter defluvii (Kotelnikova et al. 1994) Boone 2001 comb. nov. <- Methanobacterium defluvii (basonym) ADZ, X99046, Mbt.dfluvi DSM 7466, X99046, Mbt.dfluvi OCM 570 VKM B-1962, X99046, Mbt.dfluvi Methanothermobacter marburgensis VP Wasserfallen et al Marburg, X15364, Mb.tautotr DSM 2133 OCM 82 Methanothermobacter thermautotrophicus VP (Zeikus and Wolfe 1972) Wasserfallen et al <- Methanobacterium thermautotrophicum (basonym) DH, X68720, Mb.tauDELH ATCC DSM 1053 Methanothermobacter thermoflexus (Kotelnikova et al. 1994) Boone 2001 comb. nov. <- Methanobacterium thermoflexum (basonym) IDZ, X99047, Mbt.thflex DSM 7268, X99047, Mbt.thflex OCM 571 VKM B-1963, X99047, Mbt.thflex Methanothermobacter thermophilus (Laurinavichus et al. 1990) Boone 2001 comb. nov. <- Methanobacterium thermophilum (basonym) M, X99048, Mbt.thphil OCM 231 DSM 6529, X99048, Mbt.thphil Methanothermobacter wolfeii VP (Winters et al. 1985) Wasserfallen et al <- Methanobacterium wolfei (basonym) ATCC DSM 2970 OCM 154 Family II. Methanothermaceae VP VP (T) Genus I. Methanothermus Methanothermus fervidus VP (T) Stetter et al DSM 2088, M59145, Mt.fervidu Methanothermus sociabilis VP Lauerer et al DSM 3496 Class II. Methanococci class. nov. VP (T) Order I. Methanococcales Family I. Methanococcaceae VP AL (T) Genus I. Methanococcus Methanococcus vannielii AL (T) Stadtman and Barker 1951 ATCC DSM 1224 Methanococcus deltae VP Corder et al = Methanococcus maripaludis (senior subjective synonym) Delta RC, U38485, Mc.deltae2 ATCC DSM 2771 Methanococcus fervens VP Jeanthon et al > Methanocaldococcus fervens AG86, AF056938, Mcd.ferven DSM 4213, AF056938, Mcd.ferven Methanococcus frisius VP Blotevogel et al > Methanosarcina frisia C16 DSM 3318 DSM 3318 Methanococcus halophilus VP Zhilina > Methanohalophilus halophilus DSM 3094 INMI Z-7982 OCM