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Phylogenetic Analysis of Burkholderia Species by Multilocus Sequence Analysis

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Phylogenetic Analysis of Burkholderia Species by Multilocus Sequence Analysis Curr Microbiol DOI 10.1007/s00284-013-0330-9 Phylogenetic Analysis of Burkholderia Species by Multilocus Sequence Analysis Paulina Estrada-de los Santos • Pablo Vinuesa • Lourdes Martı´nez-Aguilar • Ann M. Hirsch • Jesu´s Caballero-Mellado Received: 11 August 2012 / Accepted: 21 January 2013 Ó Springer Science+Business Media New York 2013 Abstract Burkholderia comprises more than 60 species bacterial species. The group B comprises the B. cepacia of environmental, clinical, and agro-biotechnological rel- complex (opportunistic human pathogens), the B. pseudo- evance. Previous phylogenetic analyses of 16S rRNA, mallei subgroup, which includes both human and animal recA, gyrB, rpoB, and acdS gene sequences as well as pathogens, and an assemblage of plant pathogenic species. genome sequence comparisons of different Burkholderia The distinct lineages present in Burkholderia suggest that species have revealed two major species clusters. In this each group might represent a different genus. However, it study, we undertook a multilocus sequence analysis of 77 will be necessary to analyze the full set of Burkholderia type and reference strains of Burkholderia using atpD, species and explore whether enough phenotypic features gltB, lepA, and recA genes in combination with the 16S exist among the different clusters to propose that these rRNA gene sequence and employed maximum likelihood groups should be considered separate genera. and neighbor-joining criteria to test this further. The phy- logenetic analysis revealed, with high supporting values, Abbreviations distinct lineages within the genus Burkholderia. The two MLSA Multilocus sequence analysis large groups were named A and B, whereas the B. rhi- BCC Burkholderia cepacia complex zoxinica/B. endofungorum, and B. andropogonis groups ML Maximum likelihood consisted of two and one species, respectively. The group NJ Neighbor-joining A encompasses several plant-associated and saprophytic Introduction Electronic supplementary material The online version of this article (doi:10.1007/s00284-013-0330-9) contains supplementary The genus Burkholderia,ab-proteobacteria group, was material, which is available to authorized users. created to accommodate seven species from the Pseudo- P. Estrada-de los Santos (&) Á P. Vinuesa Á L. Martı´nez-Aguilar Á monas ribosomal RNA group II [51, 89]. Eventually, many J. Caballero-Mellado more species were described and included in this new Centro de Ciencias Geno´micas,Universidad Nacional Auto´noma de genus. Others were removed or reclassified, such as Me´xico, Ap. Postal 565-A, Cuernavaca, Morelos, Mexico e-mail: [email protected] Burkholderia pickettii (now Ralstonia pickettii) and B. solanacearum (now Ralstonia solanacearum)[90], or P. Estrada-de los Santos B. cocovenenans, which was a synonym of B. gladioli [17, Departamento de Microbiologı´a, Escuela Nacional de Ciencias 41] and B. vandii, a synonym of B. plantarii [17]. Cur- Biolo´gicas, I.P.N., Prolongacio´n de Carpio y Plan de Ayala, Mexico, D.F., Mexico rently, Burkholderia comprises more than 60 species, which are distributed in diverse habitats. For example, A. M. Hirsch several species are important components of the rhizo- Department of Molecular, Cell and Developmental Biology, sphere [22]. Others have been found in water, plant roots, Molecular Biology Institute, University of California, Los Angeles, 621 Charles E. Young Drive South, or legume nodules, or can be opportunistic pathogens Los Angeles, CA 90095-1606, USA zon plants or humans [22, 77]. Among the pathogenic 123 P. Estrada-de los Santos et al.: Phylogenetic Analysis of Burkholderia Species Burkholderia, B. mallei and B. pseudomallei are extremely lepA, and recA, combined with the 16S rRNA gene important because they are the etiologic agents of known sequence, to explore the positioning of the Burkholderia diseases such as glanders and melioidosis, respectively species in a phylogenetic analysis. In this report, we [10, 87]. The Burkholderia cepacia complex (BCC; 17 present evidence that the genus Burkholderia is composed species up to now) is another important group that includes of distinctly different phylogenetic lineages. many opportunistic pathogens, which may be found in patients with cystic fibrosis [38]. In 2001, two reports presented a totally different view of Materials and Methods Burkholderia. First, the genus was rich in nitrogen-fixing species [28], and second, several nitrogen-fixing species Bacterial Strains were found to nodulate legume plants [48]. This last fea- ture was striking because previously legumes were thought A set of Burkholderia species was analyzed by MLSA. to be nodulated only by a-proteobacteria. Today, eight Several species with sequenced genomes were also chosen Burkholderia species that elicit effective nodule formation for the analysis. The set of Burkholderia species analyzed on legume roots have been reported and more are in the included a total of 77 Burkholderia species, 51 type species pipeline awaiting description [37, 46]. Recently, strains and 26 reference species. Additionally, type and reference from B. fungorum were found to nodulate Phaseolus strains from Cupriavidus (3) and Ralstonia (4) species were vulgaris, although ineffectively [30]. included. A list of strains used in this study is presented in As the number of described Burkholderia species has Additional file 1. increased, 16S rRNA sequence analyses have revealed two sub-lineages within the genus [8, 37, 53, 54, 58]. These two atpD, gltB, lepA, and recA Gene Sequencing groups have been recovered with different phylogenetic reconstruction methods using 16S rRNA sequences [52], The housekeeping genes were randomly selected based on Multilocus sequence analysis (MLSA) with gyrB and rpoB the BCC MLST Database (http://pubmlst.org/bcc/). The genes sequences [2] or seven housekeeping genes [63], or following set of primers was designed to obtain DNA recA gene sequences [73]. A phylogenetic analysis of the fragments in the range of 850–1,100 bp. These DNA acdS gene in Burkholderia species also revealed the same fragments were more than twice as long as the ones used in two clusters [49]. One of these sub-lineages contains the MLST for the BCC because we wished to retrieve more BCC opportunistic human pathogens, some environmental information for the phylogenetic analysis. For the ATP species, the B. pseudomallei group, as well as plant path- synthase beta chain (atpD), the primers atpD-F2 (50- ogenic species, which have been also detected in human CCACCAGCACAAGCCGCT-30) and atpD-R (50-ATCCG infections [43, 60, 86]. The other sub-lineage comprises CTCGTCGTCGGCG-30) were used. For the glutamate soil, water, and plant-associated species, which thrive in synthase large subunit (gltB), the primers gltB-F (50- rhizospheres, live as endophytes, or nodulate legumes. CTGCGCTCGAAGATCAAGCAGGG-30) and gltB-R (50- Many species are diazotrophs and so far, evidence for TGCGCACCGGCTGGATGAACG-30) were utilized. For pathogenicity is lacking, although a few reports exist of the GTP binding protein (lepA), the primers lepA-F2 (50- single strains of B. xenovorans, B. tropica, and B. fungo- TGGTTCGACAACTACGTCGG-30) and lepA-R (50-AT- rum that were isolated from animal or human clinical CAGCATGTCGACCTTCAC-30) were employed, and for samples [18, 24, 35]. Additionally, the phylogenetic anal- recombinase A (recA), BUR1 and BUR2 primers were ysis of 617 genes, from the Burkholderia core genome, used [52]. The PCR was performed as described previously demonstrated that the BCC–B. pseudomallei–plant patho- [28]. The DNA fragments on each strand were sequenced gen group was clearly separated from the cluster of envi- with the primers used in the initial PCR amplification by ronmental species [69]. Macrogen (www.macrogen.com). The housekeeping genes Not only MLSA but also Multilocus sequence typing from some Burkholderia species were retrieved from the (MLST) have been used for epidemiologic and population NCBI Genome Database (http://www.ncbi.nlm.nih.gov/ genetics studies, delineation of species, and assignment of sites/entrez?db=genome). The accession numbers are pro- strains to defined bacterial species in Burkholderia [2, 40, vided in Additional file 1 and displayed on the phyloge- 80, 82]. Different housekeeping genes have been useful for netic trees. this purpose and an MLST database exists for BCC members (http://pubmlst.org/bcc/). Phylogenetic Inference In view of these findings, we performed MLSA of a set of Burkholderia species (77 Burkholderia type and refer- Data processing and phylogenetic analyses were performed ence species) using four housekeeping genes, atpD, gltB, as described elsewhere [77]. In brief, nucleotide sequences 123 P. Estrada-de los Santos et al.: Phylogenetic Analysis of Burkholderia Species of the housekeeping genes were translated and aligned B. pseudomallei group, and the plant pathogenic species. using Muscle 3.57 [25]. The resulting multiple-sequence Burkholderia andropogonis, B. rhizoxinica, and B. endo- alignments of proteins were used as masks to generate the fungorum were placed at the edge of group A. A distance corresponding nucleotide codon alignments using custom analysis (using MEGA version 5) of the 16S rRNA Perl scripts. Individual alignments were concatenated using sequences from group A and B, B. rhizoxinica/B. endo- ad hoc Perl scripts. Models of nucleotide substitution were fungorum and B. andropogonis was carried out. The selected by the Akaike information criterion, using analysis showed a larger dissimilarity
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