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Thiobacillus Prosperus’ Huber and Stetter 1989 As Acidihalobacter Prosperus Gen International Journal of Systematic and Evolutionary Microbiology (2015), 65, 3641–3644 DOI 10.1099/ijsem.0.000468 Reclassification of ‘Thiobacillus prosperus’ Huber and Stetter 1989 as Acidihalobacter prosperus gen. nov., sp. nov., a member of the family Ectothiorhodospiraceae Juan Pablo Ca´rdenas,1,2,3 Rodrigo Ortiz,1,3 Paul R. Norris,4 Elizabeth Watkin5 and David S. Holmes1,2 Correspondence 1Departamento de Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, David S. Holmes Santiago, Chile [email protected] 2Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Santiago, Chile 3Laboratorio de Ecofisiologı´a Microbiana, Fundacion Ciencia & Vida, Santiago, Chile 4Environment and Sustainability Institute, University of Exeter, UK 5School of Biomedical Sciences, Curtin University, Perth, Australia Analysis of phylogenomic metrics of a recently released draft genome sequence of the halotolerant, acidophile ‘Thiobacillus prosperus’ DSM 5130 indicates that it is not a member of the genus Thiobacillus within the class Betaproteobacteria as originally proposed. Based on data from 16S rRNA gene phylogeny, and analyses of multiprotein phylogeny and average nucleotide identity (ANI), we show that it belongs to a new genus within the family Ectothiorhodospiraceae, for which we propose the name Acidihalobacter gen. nov. In accordance, it is proposed that ‘Thiobacillus prosperus’ DSM 5130 be named Acidihalobacter prosperus gen. nov., sp. nov. DSM 5130T (5JCM 30709T) and that it becomes the type strain of the type species of this genus. ‘Thiobacillus prosperus’ DSM 5130, is a halotolerant 2000) and the genus Acidithiobacillus was moved out of (growth with up to 0.6 M NaCl) acidophile (,pH 3) the class Gammaproteobacteria into the class Acidithiobacil- that was isolated from a geothermally heated seafloor at lia (Williams & Kelly, 2013). Porto di Levante, Vulcano, Italy (Huber & Stetter, 1989). Later studies, based on 16S rRNA phylogeny, suggested It was originally classified into the genus Thiobacillus as that ‘Thiobacillus prosperus’ was a member of the class ‘Thiobacillus prosperus’ on the basis of its phenotype and Gammaproteobacteria, with species of the family other classical criteria (sulfur-oxidizing, autotrophic, Ectothiorhodospiraceae asnearrelatives(Simmons& + Gram-stain-negative rods and with DNA G C content Norris, 2002). During a recent study of the classification of 64 mol%) (Huber & Stetter, 1989). However, the of Acidiferrobacter thiooxydans, a 16S rRNA-based phylo- genus name was potentially confusing because ‘Thiobacillus geny suggested a position for ‘Thiobacillus prosperus’asa prosperus’ exhibited insignificant DNA hybridization to member of the family Ectothiorhodospiraceae of the members of the genus Thiobacillus such as Thiobacillus fer- class Gammaproteobacteria (Hallberg et al., 2011). rooxidans, Thiobacillus thiooxidans, Thiobacillus neapolita- In addition, in a note in Bergey’s Manual of Systematic nus and Thiobacillus thioparus (Huber & Stetter, 1989). Bacteriology (Kelly et al., 2005), it was proposed that Thiobacillus ferrooxidans and Thiobacillus thiooxidans ‘Thiobacillus prosperus’ be removed from the genus Thio- were later reclassified as Acidithiobacillus ferrooxidans and bacillus, because of its close phylogenetic resemblance Acidithiobacillus thiooxidans, respectively (Kelly & Wood, (.95 % 16S rRNA gene sequence identity) with ‘Acidiha- lobacter aeolicus’(strainV65DSM 14174) and to ‘Acidi- Abbreviations: ANI, average nucleotide identity; COG, clusters of halobacter ferrooxidans’(strainV85DSM 14175). orthologous groups. However, despite its suggestive relationship with the The GenBank/EMBL/DDBJ accession number for the genome family Ectothiorhodospiraceae,‘Thiobacillus prosperus’ sequence of strain DSM 5130 is JQSG00000000. remains to be formally classified. Three supplementary tables and two supplementary figures are Recently, the draft genome sequence of ‘Thiobacillus available with the online Supplementary Material. prosperus’ was released (Ossandon et al., 2014) providing Downloaded from www.microbiologyresearch.org by 000468 G 2015 IUMS Printed in Great Britain 3641 IP: 82.45.151.19 On: Thu, 05 Nov 2015 15:40:09 J. P. Ca´rdenas and others an opportunity to re-evaluate its taxonomical position reconstructed using sequences obtained from the prokar- using phylogenomic strategies (Delsuc et al., 2005). yotic 16S rRNA database of NCBI-BLAST and aligned in MAFFT (Katoh & Standley, 2014). The phylogenetic tree A multi-locus phylogenomic tree was reconstructed, based was inferred using the maximum-likelihood method on a multiple alignment of concatenated sequences of 50 based on the Tamura–Nei model, defined as the most ribosomal protein families retrieved using COG (clusters appropriate model by ModelGenerator (Keane et al., of orthologous groups) classification from 95 proteobac- 2006). Tree reconstruction included the use of discrete teria (Tatusov et al., 2003). A list of the NCBI accession Gamma distribution and allowing some sites to be evolu- numbers for the genomes, including their taxonomical tionarily invariable (G+I+). data, and a list of the COG families used in the elaboration of the phylogenomic tree are provided, respectively, in A multi-locus phylogenomic tree was reconstructed from a Tables S1 and S2 (available in the online Supplementary multiple alignment of concatenated sequences of 50 riboso- Material). The alignment of the concatenated sequences mal protein families from 95 proteobacterial organisms was made using MAFFT (Katoh & Standley, 2014). including ‘Thiobacillus prosperus’ (Yutin et al., 2012). The A phylogenomic tree was reconstructed using the maxi- resulting full phylogenomic tree is shown in Fig. S1. The mum-likelihood method on PhyML version 3 using the region of the tree that includes ‘Thiobacillus prosperus’ LG model (Guindon et al., 2010); the latter was defined has been expanded for clarity (Fig. 1). ‘Thiobacillus pros- as the most appropriate model for the data using Model- perus’ is positioned within the family Ectothiorhodospira- Generator software (Keane et al., 2006). The phylogenomic ceae in the order Chromatiales of the class tree was reconstructed taking into account discrete esti- Gammaproteobacteria (Figs 1 and S1). This is consistent mated gamma values and amino acid frequencies (+G with its placement based on 16S rRNA gene phylogenetic +F), and the tree topology was optimized using a combi- analysis (Fig S2) and with a previously described 16S nation of the best results of nearest-neighbor interchange rRNA gene phylogenetic analysis (Hallberg et al., 2011). (NNI) and subtree pruning and regrafting (SPR) strategies Within the family Ectothiorhodospiraceae,‘Thiobacillus (Guindon et al., 2010). prosperus’ has the closest phylogenomic similarity with Average nucleotide identity (ANI) analysis was carried out the genus Ectothiorhodospira (Fig. 1). The genomic DNA using the ANI calculator (http://enve-omics.ce.gatech.edu/ of ‘Thiobacillus prosperus’ exhibits 64.5 mol% G+C con- ani/) (Goris et al., 2007). A list of ANI values obtained from tent (Ossandon et al., 2014), which is in agreement with a comparison of the ‘Thiobacillus prosperus’ genome against the range of 50.5–69.7 mol% DNA G+C for members of other sequenced members of the family Ectothiorhodospira- the family Ectothiorhodospiraceae (Imhoff, 2005). Also, ceae is provided in Table S3. consistent with the placement of ‘Thiobacillus prosperus’ close to the genus Ectothiorhodospira is the requirement A 16S rRNA sequence-based phylogenetic tree of for chloride for growth exhibited by both these groups organisms from the family Ectothiorhodospiraceae was (Davis-Belmar et al., 2008; Imhoff, 2005). 100 Thioalkalivibrio thiocyanoxidans ARh 4 (CP007029) 0.1 T 100 Thioalkalivibrio nitratireducens DSM 14787 (NC_019902) Thioalkalivibrio versutus AL 2T (402577*) 100 100 Thioalkalivibrio sp. K90mix (NC_013889) Thiorhodospira sibirica ATCC 700588T (AGFD00000000) 100 100 Ectothiorhodospira sp. PHS-1 (AGBG00000000) 100 Ectothiorhodospira haloalkaliphila ATCC 51935T (AJUE00000000) T 100 Acidihalobacter prosperus DSM 5130 (JQSG00000000) T 100 Thioalkalivibrio thiocyanodenitrificans ARhD 1 (AQZO00000000) Thioalkalivibrio sulfidiphilus HL-EbGr7 (NC_011901) Fig. 1. Phylogenetic position of Acidihalobacter prosperus gen. nov., sp. nov. (formerly ‘Thiobacillus prosperus’) in the family Ectothiorhodospiraceae within the order Chromatiales of the class Gammaproteobacteria based upon multi-locus concatena- tion of 50 ribosomal proteins. Results of the approximate likelihood ratio test returning x 2-based parametric branch support values are shown. Genome accession numbers for each organism are shown. The list of COGs used for tree elaboration is given in Table S2.The phylogenetic tree shown here is part of a more comprehensive phylogenomic analysis shown in Fig. S1. *Number corresponds to JGI project ID. Downloaded from www.microbiologyresearch.org by 3642 International Journal of Systematic and Evolutionary Microbiology 65 IP: 82.45.151.19 On: Thu, 05 Nov 2015 15:40:09 ‘Thiobacillus prosperus’ reclassification In addition, a phenotypic comparison between ‘Thioba- described by Goris and coworkers (2007) and implemented cillus prosperus’ and the genera Thioalkalivibrio and Acidi- at http://enve-omics.ce.gatech.edu/ani/, yielded ANI values ferrobacter belonging to the family Ectothiorhodospiraceae of 76–81 % between the ‘Thiobacillus prosperus’ genome is consistent with its placement in
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