DOI:10.1007/bergeysoutline200405 TAXONOMIC OUTLINE OF THE PROKARYOTES BERGEY’S MANUAL ® OF SYSTEMATIC BACTERIOLOGY, S ECOND 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 All rights reserved. This work may not be transferred or copied in whole or in part without written permission of the publisher, (Springer New York, Inc. 223 Spring Street, 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, elec- tronic 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 le- gal 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 Man- ual Trust using Epic Document Architect and Epic Editor (Version 5.0, ArborText, Ann Arbor, MI) and a prototype document type definition 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 classification presented below was ini- tiated in the early 1990s in the editorial office of Bergey’s Manual Trust as a preliminary step in organizing the con- tent of the second edition of Bergey’s Manual of System- atic Bacteriology (the Systematics). The primary objec- tive was to devise a classification that would reflect the phylogeny of prokaryotes, as defined by 16S rDNA se- quence analysis, while simultaneously placing all of the validly named members of a given taxon into the clas- sification at a single point, based on the sequence of the type strain, type species, or type genus. 1 Under ideal conditions, such a task would be relatively straightforward. All species assigned to a genus would be in agreement with the phylogenetic model and this would be reflected in the nomenclature. Furthermore, each species would bear a single name that would reflect both its taxonomic and phylogenetic position. However, we find this not to be the case as there are a number of ex- isting genera (e.g., Clostridium, Aquaspirillum)thatare paraphyletic based on the 16S rDNA model. It is our view that such instances indicate a need for taxonomic revision. In addition, prior taxonomic revisions have led to numerous instances in which the same species may bear more than one validly published name, indicating differences in taxonomic opinion. To ensure complete- ness, we have opted to include the majority of these syn- onyms within the Outline. Placement of species within the Outline is dictated by the genus name rather than the position within any given phylogenetic model. We believe that periodic publica- tion of updated versions of this Outline will provide the community with an indication of the progress that has been made in resolving such problems, as well as point- ing out any remaining or new discrepancies that have oc- curred between revisions. Therefore, any reference to the outline should include the release number, the publi- cation date, and the digital object identifier (the DOI) of the release being referenced. Technical notes Release 5.0 coincides with the publica- tion of Volume 2 of the second edition of the Systematics. As stated earlier, we continue to search the taxonomic literature and the public databases for new, high quality 16S rDNA sequences (defined as >1400 nts, < 4% am- biguity, and fewer than 10 missing positions) and have added these sequences to our phylogenetic models. In this release, we list 4540 unique sequences that are as- sociated with 4504 type strains and 894 synonyms. We have also added 197 new species/new combinations, 40 new genera, 3 new families, 1 new order, and 1 new class to our taxonomic model. New additions are summarized in Table 1. The taxonomic model Within this classification, we rec- ognize two prokaryotic domains: the Archaea and Bacte- ria. The domains are divided into phyla which are in turn divided into classes, orders (except for the Cyanobacte- ria for which we use the rank of subdivision), families, and genera. In the Actinobacteria, subclasses and sub- orders are recognized, and suborders occur within the Myxococcales. The rank of kingdom is not used to avoid possible conflicts with the Botanical Code, where some overlap exists. Readers are advised that the Code of Prokaryotic Nomenclature does not cover taxa above the Class, even though the domain and phylum names ap- pearing in the Outline and in the Manual have appeared in Validation List 85. As of May 2004, 6661 validly named prokaryotic species appeared either in the Ap- proved List of Bacterial Names (Skerman et al., 1980), in original papers published in the International Journal of Systematic Bacteriology or the International Journal of Systematic and Evolutionary Microbiology, or in Valida- tion Lists 1–96. 2 In this version of the Outline, we extend our list of synonyms to 1226 by including forthcoming assertions of synonymy that will appear in Volume 2 of the Systematics. Readers should be aware that, in some cases, we have opted to exclude some names that have not found widespread usage, even though those names are validly published. 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 Lists 1-96 were published in the International 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, 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 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). Yet there is considerable reluctance among many contemporary sys- tematic procaryotic biologists to place new species and genera into higher taxa, especially at the intermediate levels (family, order, and class) because of uncertainty of phylogenetic models. In compiling and maintaining the outline we have often had to deal with instances where new species were variously assigned to a class or do- main 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 defin- ing a higher taxonomic structure, especially when con- temporary phylogenetic techniques, which rely on tree graphs as the principal interpretive device, are used to analyze small and inherently biased data sets. We have also observed a general 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 branch- ing 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 filledinthe 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 unnec- essary 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 re- main 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 or to alert the reader to problems concerning the validity or legitimacy of names. 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 prokaryotes. The technique (16S rDNA sequencing) is universally applicable and provides a sin- gle type of data that will soon be available for all validly named species. Given the rapid advancements in se- quencing 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 26 phyla 3 , two of which occur within the Archaea.There- maining 24 phyla are ascribed to the Bacteria.Thefact that the Archaea and deeply branching Bacteria are pre- sented 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. Within lower taxa, members of the rank will usually appear in alphabetical order. The hi- erarchical numbering scheme used in the outline is arbi- trary, especially at the lower levels. It is also subject to change as new taxa are described and existing taxa re- classified. Therefore, we advise against using the num- bering scheme as an organizational or mnemonic device. Decoding the entries Within this document, as well as within the Systematics, we follow the American style for rendering Latinized names. Regardless of rank, all names appear in italics. The superscript AL indicates that the name was included on the Approved Lists of Bacterial Names published in 1980. The superscript VP indicates that the name was validly published in the In- ternational 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 fol- lowed with superscripted NP are indicative of proposals for new taxa that will appear in the forthcoming second volume of the Systematics. In the case of species names, each is followed with the authority for the name and year of the original descrip- tion, 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 parentheses and in superscript. New taxa (re- cently added) are highlighted in red type and those which have been relocated within the outline as a result of com- ments from experts appear in magenta. Readers should understand that the taxa are not, in reality moved, but are 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 species names and associated information, proposals for new combinations typically result in multiple changes within the taxonomy. The new name is followed by the basonym, which is identified by the symbol <- preced- ing the old name. Basonyms are also homotypic syn- onyms (formerly referred to as 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 con- sidered deprecated under most circumstances. Follow- ing the old name and information about the taxonomic authority the new name appears in green type preceded by an arrow (->). In instances of synonymy, the syn- onyms (either homotypic or heterotypic) are identified as such and preceded by an equals sign (=). Synonyms are further categorized as either senior or junior, indicating priority. More detailed information regarding the topics of synonymy and priority are available in the Interna- tional Code of Nomenclature of Bacteria (1990 Revision) 4 and in Minutes of the Judicial Commission on Prokary- otic Nomenclature published in the International Jour- nal of Systematic and Evolutionary Microbiology. Immediately following the nomenclature section of each entry follows key information regarding the type strain, including the original strain designation, when reported, and all known deposits in major culture collections 5 . Each such deposit is set off by a small vertical bar ( | ). If one or more high quality 16S rDNA sequences have been 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., J.A. Bell and T.G. Lilburn. (2004) Taxonomic Outline of the Prokaryotes. Bergey’s Manual of Systematic Bacteriology, Second Edition., Release 5.0., Springer-Verlag, New York. pages. DOI: 10.1007/bergeysoutline200405 Acknowledgments We also would like to acknowledge Drs. Wolfgang Ludwig and Karl-Heinz Schleifer (Tech- nical University of Munich), Sean Turner (NCBI), Philip Hugenholtz (UC. Berkeley), and James Cole and Qiong Wang (RDP/Center for Microbial Ecology, Michigan State) for their numerous and helpful discussions on resolving discrepancies between the Bergey’s Outline and the phylogenetic reference trees and uncovering annotation errors; Drs. Jean Euzéby (École Nationale Vétérinaire de Toulouse), Brian Tindall (Deutsche Sammlung von Mikroorganismen und Zellkulturen, GmbH) and Aharon Oren for numerous helpful and spirited comments on nomenclature and editorial re- marks. We would also like to extend our thanks to Drs. David Boone, Paul De Vos, Michael Goodfellow, Noel Kreig, Fred Rainey, Erko Stackebrandt, James Staley, Joseph Tully, and William Whitman 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 5.0, (ArborText, Ann Arbor, MI). The DTD was authored by George M. Garrity (Michigan State University, East Lansing, MI) 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-FG02-02ER63315. 4 Lapage et al., (1992) ASM Press, Washington, DC. 5 With this release of the Outline, we have implemented a change in the prefix 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 Taxonomic Outline of the Procaryotes Rank Taxon Phylum Class Class Anaerolineae Chloroflexi Order Anaerolinaeles Chloroflexi Anaerolineae Family Anaerolinaeceea Chloroflexi Anaerolineae Hydrogenimonaceae Proteobacteria Epsilonproteobacteria Thermodesulfobiaceae Firmicutes Clostridia Genus Aeriscardovia Actinobacteria Actinobacteria Aestuariibacter Proteobacteria Gammaproteobacteria Alistipes Bacteroidetes Bacteroidetes Anaerolinea Chloroflexi Anaerolineae Anaerotruncus Firmicutes Clostridia Aquicella Proteobacteria Gammaproteobacteria Arsenicicoccus Actinobacteria Actinobacteria Balnearium Aquificae Aquificae Belliella Bacteroidetes Sphingobacteria Bryantella Firmicutes Clostridia Caldanaerobacter Firmicutes Clostridia Caldilinea Chloroflexi Anaerolineae Caldithrix Deferribacteres Deferribacteres Desulfatibacillum Proteobacteria Deltaproteobacteria Fulvimarina Proteobacteria Alphaproteobacteria Gillisia Bacteroidetes Flavobacteria Hespellia Firmicutes Clostridia Hongiella Bacteroidetes Sphingobacteria Hydrogenimonas Proteobacteria Epsilonproteobacteria Hylemonella Proteobacteria Betaproteobacteria Kerstersia Proteobacteria Betaproteobacteria Mesonia Bacteroidetes Flavobacteria Methanomethylovorans Euryarchaeota Methanomicrobia Nitratireductor Proteobacteria Alphaproteobacteria Oceanicaulis Proteobacteria Alphaproteobacteria Oceanisphaera Proteobacteria Gammaproteobacteria Ottowia Proteobacteria Betaproteobacteria Parasporobacterium Firmicutes Clostridia Phytoplasma Firmicutes Mollicutes Propionicimonas Actinobacteria Actinobacteria Rhabdochlamydia Chlamydiae Chlamydiae Salinibacterium Actinobacteria Actinobacteria 4 Bergey’s Manual of Systematic Bacteriology, 2nd Edition Rank Taxon Phylum Class Silicibacter Proteobacteria Alphaproteobacteria Soehngenia Firmicutes Clostridia Sulfurimonas Proteobacteria Epsilonproteobacteria Thalassolituus Proteobacteria Gammaproteobacteria Thermodesulfatator Thermodesulfobacteria Thermodesulfobacteria Thermodesulfobium Firmicutes Clostridia Wautersia Proteobacteria Betaproteobacteria Xylanibacterium Actinobacteria Actinobacteria Yania Actinobacteria Actinobacteria Species Achromobacter denitrificans Proteobacteria Betaproteobacteria Achromobacter insolitus Proteobacteria Betaproteobacteria Achromobacter spanius Proteobacteria Betaproteobacteria Actinomadura mexicana Actinobacteria Actinobacteria Actinomadura meyerii Actinobacteria Actinobacteria Actinomyces hongkongensis Actinobacteria Actinobacteria Aeriscardovia aeriphila Actinobacteria Actinobacteria Aeromicrobium marinum Actinobacteria Actinobacteria Aeromonas simiae Proteobacteria Gammaproteobacteria Aeropyrum camini Crenarchaeota Thermoprotei Aestuariibacter halophilus Proteobacteria Gammaproteobacteria Aestuariibacter salexigens Proteobacteria Gammaproteobacteria Agreia pratensis Actinobacteria Actinobacteria Alistipes finegoldii Bacteroidetes Bacteroidetes Alistipes putredinis Bacteroidetes Bacteroidetes Amycolatopsis decaplanina Actinobacteria Actinobacteria Amycolatopsis lurida Actinobacteria Actinobacteria Amycolatopsis palatopharyngis Actinobacteria Actinobacteria Anaerolinea thermophila Chloroflexi Anaerolineae Anaerotruncus colihominis Firmicutes Clostridia Ancylobacter rudongensis Proteobacteria Alphaproteobacteria Aneurinibacillus danicus Firmicutes Bacilli Aquicella lusitana Proteobacteria Gammaproteobacteria Aquicella siphonis Proteobacteria Gammaproteobacteria Arsenicicoccus bolidensis Actinobacteria Actinobacteria Arthrobacter gandavensis Actinobacteria Actinobacteria Asaia krungthepensis Proteobacteria Alphaproteobacteria Bacillus aeolius Firmicutes Bacilli 5 Taxonomic Outline of the Procaryotes Rank Taxon Phylum Class Bacillus bataviensis Firmicutes Bacilli Bacillus drentensis Firmicutes Bacilli Bacillus galactosidilyticus Firmicutes Bacilli Bacillus novalis Firmicutes Bacilli Bacillus odysseyi Firmicutes Bacilli Bacillus shackletonii Firmicutes Bacilli Bacillus soli Firmicutes Bacilli Bacillus vireti Firmicutes Bacilli Balnearium lithotrophicum Aquificae Aquificae Bartonella chomelii Proteobacteria Alphaproteobacteria Belliella baltica Bacteroidetes Sphingobacteria Bifidobacterium psychraerophilum Actinobacteria Actinobacteria Brachybacterium muris Actinobacteria Actinobacteria Brevibacillus limnophilus Firmicutes Bacilli Bryantella formatexigens Firmicutes Clostridia Caldilinea aerophila Chloroflexi Anaerolineae Caldithrix abyssi Deferribacteres Deferribacteres Caminibacter profundus Proteobacteria Epsilonproteobacteria Cellulomonas xylanilytica Actinobacteria Actinobacteria Cellulophaga pacifica Bacteroidetes Flavobacteria Chryseobacterium miricola Bacteroidetes Flavobacteria Corynebacterium nigricans Actinobacteria Actinobacteria Corynebacterium suicordis Actinobacteria Actinobacteria Deinococcus indicus Deinococcus-Thermus Deinococci Desulfatibacillum aliphaticivorans Proteobacteria Deltaproteobacteria Desulfofaba fastidiosa Proteobacteria Deltaproteobacteria Desulfofaba hansenii Proteobacteria Deltaproteobacteria Dialister invisus Firmicutes Clostridia Ensifer arboris Proteobacteria Alphaproteobacteria Ensifer fredii Proteobacteria Alphaproteobacteria Ensifer kostiensis Proteobacteria Alphaproteobacteria Ensifer kummerowiae Proteobacteria Alphaproteobacteria Ensifer medicae Proteobacteria Alphaproteobacteria Ensifer meliloti Proteobacteria Alphaproteobacteria Ensifer saheli Proteobacteria Alphaproteobacteria Ensifer terangae Proteobacteria Alphaproteobacteria Ensifer xinjiangensis Proteobacteria Alphaproteobacteria 6 Bergey’s Manual of Systematic Bacteriology, 2nd Edition Rank Taxon Phylum Class Erysipelothrix inopinata Firmicutes Mollicutes Flavobacterium degerlachei Bacteroidetes Flavobacteria Flavobacterium frigoris Bacteroidetes Flavobacteria Flavobacterium micromati Bacteroidetes Flavobacteria Fulvimarina pelagi Proteobacteria Alphaproteobacteria Gillisia limnaea Bacteroidetes Flavobacteria Haloferax lucentense Euryarchaeota Halobacteria Halomonas axialensis Proteobacteria Gammaproteobacteria Halomonas hydrothermalis Proteobacteria Gammaproteobacteria Halomonas neptunia Proteobacteria Gammaproteobacteria Halomonas sulfidaeris Proteobacteria Gammaproteobacteria Halorubrum terrestre Euryarchaeota Halobacteria Herbaspirillum lusitanum Proteobacteria Betaproteobacteria Hespellia porcina Firmicutes Clostridia Hespellia stercorisuis Firmicutes Clostridia Hongiella halophila Bacteroidetes Sphingobacteria Hongiella mannitolivorans Bacteroidetes Sphingobacteria Hongiella ornithinivorans Bacteroidetes Sphingobacteria Hydrogenimonas thermophila Proteobacteria Epsilonproteobacteria Hylemonella gracilis Proteobacteria Betaproteobacteria Idiomarina loihiensis Proteobacteria Gammaproteobacteria Kerstersia gyiorum Proteobacteria Betaproteobacteria Kitasatospora kifunensis Actinobacteria Actinobacteria Kitasatospora putterlickiae Actinobacteria Actinobacteria Lactobacillus kitasatonis Firmicutes Bacilli Lactobacillus paracollinoides Firmicutes Bacilli Leptotrichia goodfellowii Fusobacteria Fusobacteria Leptotrichia hofstadii Fusobacteria Fusobacteria Leptotrichia shahii Fusobacteria Fusobacteria Leptotrichia wadei Fusobacteria Fusobacteria Luteococcus sanguinis Actinobacteria Actinobacteria Marinobacter excellens Proteobacteria Gammaproteobacteria Marinobacter lutaoensis Proteobacteria Gammaproteobacteria Marinospirillum insulare Proteobacteria Gammaproteobacteria Mesonia algae Bacteroidetes Flavobacteria Methanocalculus chunghsingensis Euryarchaeota Methanomicrobia Methanocaldococcus indicus Euryarchaeota Methanococci 7 Taxonomic Outline of the Procaryotes Rank Taxon Phylum Class Methanoculleus submarinus Euryarchaeota Methanomicrobia Methanogenium marinum Euryarchaeota Methanomicrobia Methanomethylovorans hollandica Euryarchaeota Methanomicrobia Methylocella tundrae Proteobacteria Alphaproteobacteria Microbacterium ulmi Actinobacteria Actinobacteria Microtetraspora malaysiensis Actinobacteria Actinobacteria Mycobacterium caprae Actinobacteria Actinobacteria Mycobacterium montefiorense Actinobacteria Actinobacteria Mycoplasma ovis Firmicutes Mollicutes Nitratireductor aquibiodomus Proteobacteria Alphaproteobacteria Nocardia asiatica Actinobacteria Actinobacteria Nocardia inohanensis Actinobacteria Actinobacteria Nocardia neocaledoniensis Actinobacteria Actinobacteria Nocardia niigatensis Actinobacteria Actinobacteria Nocardia tenerifensis Actinobacteria Actinobacteria Nocardia yamanashiensis Actinobacteria Actinobacteria Nocardioides aquiterrae Actinobacteria Actinobacteria Nocardiopsis aegyptia Actinobacteria Actinobacteria Nocardiopsis alkaliphila Actinobacteria Actinobacteria Oceanicaulis alexandrii Proteobacteria Alphaproteobacteria Oceanisphaera litoralis Proteobacteria Gammaproteobacteria Ottowia thiooxydans Proteobacteria Betaproteobacteria Paenibacillus favisporus Firmicutes Bacilli Parasporobacterium paucivorans Firmicutes Clostridia Petrotoga mexicana Thermotogae Thermotogae Phytoplasma ulmi Firmicutes Mollicutes Planococcus maitriensis Firmicutes Bacilli Planococcus maritimus Firmicutes Bacilli Planococcus rifietoensis Firmicutes Bacilli Polaromonas naphthalenivorans Proteobacteria Betaproteobacteria Promicromonospora pachnodae Actinobacteria Actinobacteria Propionicimonas paludicola Actinobacteria Actinobacteria Pseudomonas rhizosphaerae Proteobacteria Gammaproteobacteria Pseudonocardia chloroethenivorans Actinobacteria Actinobacteria Psychrobacter okhotskensi Proteobacteria Gammaproteobacteria Ralstonia syzygii Proteobacteria Betaproteobacteria Rhabdochlamydia porcellionis Chlamydiae Chlamydiae 8 [...]... Methanothermobacter thermoflexus comb nov is proposed in Volume 1 of Bergey s Manual of Systematic Bacteriology, 2nd Ed Methanothermobacter thermophilus comb nov is proposed in Volume 1 of Bergey s Manual of Systematic Bacteriology, 2nd Ed 14 Bergey s Manual of Systematic Bacteriology, 2nd Edition Methanothermobacter marburgensis VP Wasserfallen et al 2000 – Marburg, X15364, Mb.tautotr | DSM 2133 | OCM 82 Methanothermobacter... halotolerans Actinobacteria Actinobacteria Caldanaerobacter subterraneus pacificus Firmicutes Clostridia Caldanaerobacter subterraneus subterraneus Firmicutes Clostridia Caldanaerobacter subterraneus tengcongensis Firmicutes Clostridia Caldanaerobacter subterraneus yonseiensis Firmicutes Clostridia Lactobacillus kefiranofaciens kefiranofaciens Firmicutes Bacilli Lactobacillus kefiranofaciens kefirgranum... class within the phylum 40 These species appear as multiple branches in the RDP, suggesting the possibility of at least three or more families This pattern is also seen in PCA plots, where the four genera are well separated along the second dimension, suggesting the possibility of deep branches 41 Note that a subculture of the type strain is only deposited in one public collection or may otherwise... Thermococcales and Archaeaoglobales NCBI currently lists those taxa within the Methanomicrobiales and Methanosarcinales as orders incertae sedis We tentatively ascribe these orders to the class Methanomicrobia based on priority 16 Bergey s Manual of Systematic Bacteriology, 2nd Edition Methanoculleus olentangyi VP (Corder et al 1988) Maestrojuán et al 1990 . Manual of Systematic Bacteriology, 2ndEd. 13 Methanothermobacter thermophilus comb. nov. is proposed in Volume 1 of Bergey s Manual of Systematic Bacteriology, 2ndEd. 14 Bergey s Manual of Systematic. Firmicutes. 2 Bergey s Manual of Systematic Bacteriology, 2nd Edition In the unabridged version of the outline that includes species names and associated information, proposals for new combinations. Trust as a preliminary step in organizing the con- tent of the second edition of Bergey s Manual of System- atic Bacteriology (the Systematics). The primary objec- tive was to devise a classification