The Bulletin of Bismis

The Bulletin of BISMiS Published by Bergey’s International Society for Microbial Systematics Volume 2, part 1 – July 2011 The Bulletin of BISMiS Published by Bergey’s International Society for Microbial Systematics ISSN 2159-287X Editorial Board Director of the Editorial Office: William B. Whitman, Athens, GA, USA Editor: James T. Staley, Seattle, WA, USA Associate Editor: Paul A. Lawson, Norman, OK, USA Editorial Board Members: Hans-Jürgen Busse, Jongsik Chun, Paul De Vos, Michael Goodfellow, Brian P. Hedlund, Peter Kämpfer, Wolfgang Ludwig, Bruce J. Paster, Fred A. Rainey, Ken-ichiro Suzuki, Martha E. Tujillo, William G. Wade, Naomi L. Ward and William B. Whitman Managing Editor: Aidan C. Parte, Sudbury, MA, USA Publisher and Editorial Office Bergey’s International Society for Microbial Systematics Department of Microbiology 527 Biological Sciences Building University of Georgia Athens, GA 30602-2605 USA email: [email protected] Copyright The copyright in this publications belongs to Bergey’s International Society for Microbial Systematics (BISMiS). All rights reserved. This work may not be translated or copied in whole or in part without the written permis- sion of the publisher (BISMiS), 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 or dissimilar methodology now known or hereafter developed is forbidden. The use in this publica- tion of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. © 2011 Bergey’s International Society for Microbial Systematics On the cover Opening ceremony of the Inaugural Meeting of BISMiS in Beijing, May 2011. The Bulletin of BISMiS Contents of Volume 2, part 1 Opinion Recommendations for a new bacterial species description based on analyses of the unrelated genera Aeromonas and Arcobacter 1 María José Figueras, Roxana Beaz-Hidalgo, Luis Collado and Antonio Martínez- Murcia What is a bacterial species? I will know it when I see it 17 Micah I. Krichevsky Report Report of the Inaugural Meeting of Bergey’s International Society for Microbial Systematics in Beijing, China, 19—23 May 2011 25 Autobiographies Microbial systematics, “weaving threads into cloth” 33 Kazuo Komagata My career as a curator of microbial cultures 61 Tian-shen Tao Appendix Bergey’s International Society for Microbial Systematics Constitution and Bylaws 83 The Bulletin of BISMiS (2011), Volume 2, part 1, pp. 1–16 Recommendations for a new bacterial species description based on analyses of the unrelated genera Aeromonas and Arcobacter María José Figueras1, Roxana Beaz-Hidalgo1, Luis Collado2 and Antonio Martínez- Murcia3 Assigning a strain or a group of strains to a new bacterial species and describing it formally requires at least its phenotypic characterization in order to establish its distinctiveness from existing species and 16S rRNA gene sequences and DNA–DNA reassociation results with closely related species (classi- cally those with 16S rRNA similarities >97%). More recently Multilocus Sequence Analysis (MLSA) has been proposed as a potential alternative for DNA hybridization. These are common requirements for species in all genera, irrespective of how different they are. In the present study, the advantages and disadvantages of each of these requirements is reviewed and analyzed using two unrelated bacterial genera Aeromonas (Gammaproteobacteria) and Arcobacter (Epsilonproteobacteria) as models with some additional examples from their close neighbors Vibrio and Campylobacter. The genus Aeromo- nas, defined in 1943, is considered to have a complex taxonomy because it includes a tight group of species (and several subspecies) with 16S rRNA gene similarities ranging from 96.9 to 100%, some of which have required reclassification. In contrast, the genus Arcobacter, was defined 20 years ago (1991) from members of the genus Campylobacter, and the presently known species show 16S rRNA gene similarities ranging from 92.1 to 98.9%, and none of the species have required reclassification. Therefore, while the similarity of the 16S rRNA gene cannot be used to delineate closely related species of Aeromonas, this is still an excellent tool for Arcobacter, something that may change in the near future with the addition of new species. Several specific topics are discussed, such as the number of isolates needed to define a new bacterial species, the molecular approaches used for recognizing new species and the procedure for validly publishing a new species name. In addition, the need for developing genus-specific guidelines for describing new bacterial species, recommendations for avoiding common errors in the laboratory, and a species definition for prokaryotes in the 21st century are pre- sented. Emphasis is placed on the two factors that govern the proper description of new bacterial species, the precision of the performance of experimental work and the correct interpretation of results. Introduction bacterial species (Stackebrandt et al., 2002) generating a homogeneous approach of universal application (Rosselló- The reliable identification of bacterial strains as belonging Móra and Amann, 2001; Schleifer, 2009; Tindall et al., to a known or a new species requires a robust taxonomy. 2010). A new species description should include as many The “ad hoc committee for the re-evaluation of the species strains as possible, phenotypic diagnostic properties, anal- definition in bacteriology” (CSDB) has settled the criteria ysis of 16S rRNA gene sequences and if there is a similar- and methods to be applied for defining and describing new ity with closely related species above 97% (Stackebrandt and Goebel, 1994) or 98.7–99.0% (Stackebrandt and Eb- Contact details ers, 2006) DNA–DNA hybridization (DDH) results. Ad- 1Unitat de Microbiologia. Departament de Ciènces Médiques Bà- ditional recommendations include the analysis of the se- siques, Facultat de Medicina I Ciències de la Salut. IISPV. Univer- quences of at least five housekeeping genes (Multilocus sitat Rovira i Virgili, Reus, Spain. Sequence Analysis, MLSA) and DNA typing methods for 2Institute of Microbiology, Faculty of Sciences, Universidad Aus- tral de Chile, Valdivia, Chile. establishing inter- and intra-specific genomic relatedness. 3Molecular Diagnostics Center and Universidad Miguel Hernández. All these criteria for defining species have been extensive- Orihuela, Alicante, Spain. ly reviewed in other studies (Rosselló-Móra and Amann, 2001; Schleifer, 2009; Tindall et al., 2010). Corresponding author: María José Figueras - mariajose.figueras@ urv.cat More recently, information derived from whole genome © BISMiS 2011 1 Recommendations for a new bacterial species description sequences or indexes derived from them, such as the Aver- cusses the need for developing genus-specific guidelines age Nucleotide Identity (ANI; Konstantinidis et al., 2006) for describing new bacterial species, makes recommenda- and the Maximal Unique Matches (MUM; Deloger et al., tions for avoiding common laboratory errors and presents a 2009) have been envisaged as alternatives to replace DDH proposal for a species definition for prokaryotes in the 21st in the near future (Ritcher and Rosselló-Móra, 2009; Tindall century. et al., 2010). In addition, faster sequencing techniques such as pyrosequencing, which relies on the detection of pyro- Advantages and disadvantages of the phosphate release on nucleotide incorporation rather than requirements for new bacterial species’ chain termination with dideoxynucleotides (Petrosino et al., descriptions - analysis of the unrelated 2009; Ritcher and Rosselló-Móra, 2009) are also available genera Aeromonas and Arcobacter now. Phenotypic methods This paper presents current criteria and boundaries for defining new bacterial species emphasizing their advantages and Phenotypic characterization includes morphological and disadvantages (Table 1) and describing how they have been physiological properties and chemical composition (using applied to two unrelated bacterial genera Aeromonas and standardized techniques) and leads to a set of diagnostic Arcobacter (with examples from their close neighbors Vib- tests for species’ identification and discrimination (Ros- rio and Campylobacter). The use and importance of MLSA selló-Móra and Amann, 2001; Stackebrandt et al., 2002; today as an alternative technique for replacing DDH will be Schleifer, 2009; Tindall et al., 2010). A new species cannot underlined with specific examples. be described unless it can be differentiated from known species by at least one phenotypic property (Wayne et al., 1987; The genus Aeromonas described in 1943 (Martin-Carnahan Rosselló-Móra and Amann, 2001). Disadvantages (Table 1) and Joseph, 2005), which now includes 26 species and 8 include the lack of reproducibility (due to poor precision, subspecies (Table 2), was originally proposed on the basis different methodologies, different strain response etc.) the of only phenotypic characters from bacteria recognized as large number of tests and the specialized skills needed (Ros- early as 1891 and has evolved through advances in taxo- selló-Móra and Amann, 2001). Some of these disadvantages nomic techniques. In contrast, the genus Arcobacter, was cannot be attributed to the phenotypic methods per se but to created in 1991 when molecular techniques

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