Phylogeny of Photorhabdus and Xenorhabdus based on universally conserved protein-coding sequences and implications for the taxonomy of these two genera. Proposal of new taxa: X. vietnamensis sp. nov., P. luminescens subsp. caribbeanensis subsp. nov., P. luminescens subsp. hainanensis subsp. nov., P. temperata subsp. khanii subsp. nov., P. temperata subsp. tasmaniensis subsp. nov., and the reclassification of P. luminescens subsp. thracensis as P. temperata subsp. thracensis comb. nov.

Abstract

We used the information from a set of concatenated sequences from four genes (recA, gyrB, dnaN and gltX) to investigate the phylogeny of the genera Photorhabdus and Xenorhabdus (entomopathogenic bacteria associated with nematodes of the genera Heterorhabditis and Steinernema, respectively). The robustness of the phylogenetic tree obtained by this multigene approach was significantly better than that of the tree obtained by a single gene approach. The comparison of the topologies of single gene phylogenetic trees highlighted discrepancies which have implications for the classification of strains and new isolates; in particular, we propose the transfer of Photorhabdus luminescens subsp. thracensis to Photorhabdus temperata subsp. thracensis comb. nov. (type strain CIP 108426T =DSM 15199T). We found that, within the genus Xenorhabdus, strains or isolates that shared less than 97 % nucleotide identity (NI), calculated on the concatenated sequences of the four gene fragments (recA, gyrB, dnaN and gltX) encompassing 3395 nucleotides, did not belong to the same species. Thus, at the 97 % NI cutoff, we confirm the current 20 species of the genus Xenorhabdus and propose the description of a novel species, Xenorhabdus vietnamensis sp. nov. (type strain VN01T = CIP 109945T =DSM 22392T). Within each of the three current species of the genus Photorhabdus, P. asymbiotica, P. luminescens and P. temperata, strains or isolates which shared less than 97 % NI did not belong to the same subspecies. Comparisons of the four gene fragments plus the rplB gene fragment analysed separately led us to propose four novel subspecies: Photorhabdus luminescens subsp. caribbeanensis subsp. nov. (type strain HG29T =CIP 109949T =DSM 22391T), P. luminescens subsp. hainanensis subsp. nov. (type strain C8404T = CIP 109946T =DSM 22397T), P. temperata subsp. khanii subsp. nov. (type strain C1T =NC19T =CIP 109947T =DSM 3369T), and P. temperata subsp. tasmaniensis subsp. nov. (type strain T327T = CIP 109948T =DSM 22387T).

Description of Xenorhabdus khoisanae sp. nov., the symbiont of the entomopathogenic nematode Steinernema khoisanae

“…Biolog GN microplate reactions indicated that strain SF87 T utilized N-acetylglucosamine, DL-lactic acid, bromosuccinic , Kuwata et al (2012), Lengyel et al (2005), Nishimura et al (1994), Somvanshi et al (2006), Tailliez et al (2006Tailliez et al ( , 2010Tailliez et al ( , 2012 and Thomas & Poinar (1979). +, Carbohydrate utilized; 2, not utilized; W, weak reaction; V, variable reaction.…”

“…Lee & Stock (2010) analysed the 16S rRNA gene and two housekeeping genes, phosphoserine aminotransferase and recA, while Tailliez et al (2010Tailliez et al ( , 2012 and Kuwata et al (2013) used the genes recA, dnaN, gltX, gyrB and infB. In this study, partial recA, dnaN, gltX, gyrB and infB gene sequences of strains SF87 T , SF80, SF362 and 106-C were analysed using the neighbour-joining method.…”

“…In addition to 16S rRNA gene sequence analysis, several recent studies have adopted a multi-gene approach to distinguish between Xenorhabdus species (Kuwata et al, 2013;Lee & Stock, 2010;Tailliez et al, 2010Tailliez et al, , 2012. Lee & Stock (2010) analysed the 16S rRNA gene and two housekeeping genes, phosphoserine aminotransferase and recA, while Tailliez et al (2010Tailliez et al ( , 2012 and Kuwata et al (2013) used the genes recA, dnaN, gltX, gyrB and infB.…”

“…Isolates were initially identified by amplifying the 16S rRNA gene using primers as described by Brunel et al (1997). Based on previous phylogenetic studies, the recombinase A (recA), DNA polymerase III beta chain (dnaN), glutamyl-tRNA synthetase catalytic subunit (gltX), DNA gyrase subunit B (gyrB) and initiation factor B (infB) genes were amplified with primers recA1(F) and recA2(R), dnaN1(F) and dnaN2(R), gltX1(F) and gltX2(R), 8SF_gyrB(F) and 9Rev_gyrB(R), and infB1(F) and infB2(R), respectively (Tailliez et al, 2010(Tailliez et al, , 2012). An initial denaturation step of 94 u C for 4 min was used, followed by 35 cycles of 94 u C for 1 min, the appropriate temperature for each primer pair for 30 s and 72 u C for 1 min.…”

Photorhabdus heterorhabditis sp. nov., a symbiont of the entomopathogenic nematode Heterorhabditis zealandica

“…caribbeanensis and Photorhabdus luminescens subsp. hainanensis (Tailliez et al, 2010), Photorhabdus luminescens subsp. kayaii (Hazir et al, 2004), Photorhabdus luminescens subsp.…”