Downloaded from www.microbiologyresearch.org by IP: 54.70.40.11 On: Tue, 20 Nov 2018 04:59:42 Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria Kelly P. Williams 1 and Donovan P. Kelly 2 Correspondence Donovan Kelly D.P.Kelly@warwick.ac.uk 1 Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA 2 School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK The order Acidithiobacillales was previously assigned to the class Gammaproteobacteria. Recent analyses have indicated that this order actually lies outside all the proteobacterial classes, as a sister group to the combined classes Betaproteobacteria and Gammaproteobacteria. We now confirm this result with multiprotein phylogenetic analysis of all the available genomes of members of the order Acidithiobacillales and representatives of all available bacterial orders, and propose the new proteobacterial class, Acidithiobacillia, with the type order Acidithiobacillales, comprising the families Acidithiobacillaceae and Thermithiobacillaceae with the type genus Acidithiobacillus. The phylum Proteobacteria has its taxonomic origin as the ‘purple bacteria’, defined as four bacterial groups (alpha, beta, gamma and delta), which were classified by their 16S rRNA gene sequence structures (Woese, 1987). The phylum was formally established, also using phylogenetic analysis of 16S rRNA gene sequences, by Garrity et al. (2005a), with five constituent classes containing all known Gram-negative bacteria, Alphaproteobacteria, Betaproteo- bacteria, Gammaproteobacteria, Deltaproteobacteria and Epsilonproteobacteria. Subsequently a sixth class was proposed, the ‘Zetaproteobacteria’, although this name is not yet validly published (Emerson et al., 2007; McAllister et al., 2011). Recent molecular analyses using complete multigenome/multiprotein alignment studies have made possible more in-depth probing of these class delineations (Williams et al., 2007, 2010; Yutin et al., 2012). These have confirmed the internal coherence of the classes Alphaproteobacteria and Gammaproteobacteria, enabled further taxonomic dissection within these classes, and support the exclusion of the ‘Zetaproteobacteria’ from the Gammaproteobacteria. We now confirm the exclusion also of the order Acidithiobacillales from the class Gammaproteobacteria, as a new class of proteobacteria. The order Acidithiobacillales currently comprises the two families of Order II of the class Gammaproteobacteria, as defined by Garrity et al. (2005b, c). The type genus of the type order is the genus Acidithiobacillus Kelly and Wood 2000 emend. Hallberg et al. 2010, with Acidithiobacillus thiooxidans as the type species (Waksman & Joffe 1922; Kelly & Wood 2000, 2005a). Four other species of the family Acidithiobacillaceae are currently recognized: Acidithiobacillus ferrooxidans, Acidithiobacillus caldus, Acidithiobacillus albertensis and Acidithiobacillus ferrivorans. The second family is the family Thermithiobacillaceae, currently with a single genus and species, Thermithio- bacillus tepidarius (Garrity et al., 2005b, d; Kelly & Wood, 2005b). The phylogenetic relationships of T. tepidarius and the species of the genus Acidithiobacillus have been conjectural since the proteobacterial classes were defined on the basis of rRNA signatures (Lane et al., 1992; Woese et al., 1984a, b, 1985). Lane et al. (1992) placed T. tepidarius, Acidithio- bacillus thiooxidans and Acidithiobacillus ferrooxidans close to the beta–gamma root in the class Betaproteobacteria, but placed another putative Acidithiobacillus ferrooxidans strain (m-1) in the class Gammaproteobacteria. When the taxonomy of the thiobacilli was rationalized, T. tepidarius and the species of the genus Acidithiobacillus were reassigned to the class Gammaproteobacteria (Kelly & Wood, 2000), with the exception of strain m-1 which was reclassified as Acidiferrobacter thiooxydans in the gamma- proteobacterial family Ectothiorhodospiraceae (Hallberg et al., 2011). Woese et al. (1984b, 1985) identified 8– 12 nt signature sequences in the 16S rRNA gene that were unique to the species of the classes Betaproteobacteria and Gammaproteobacteria considered by them. One of these (AAAAACCUUACC, found in 100 % of members of the class Betaproteobacteria, but absent from members of the class Gammaproteobacteria) was found (as AACCUUACC) in all species of the genus Acidithiobacillus and in T. tepidarius; and another (AAACUCAAAUG, unique to the class Gammaproteobacteria) was also found (as AAACU- CAAA) in species of the genera Acidithiobacillus and Two supplementary tables are available with the online version of this paper. International Journal of Systematic and Evolutionary Microbiology (2013), 63, 2901–2906 DOI 10.1099/ijs.0.049270-0 049270 G 2013 IUMS Printed in Great Britain 2901