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,dnaNandgltX) to investigate the phylogeny of the generaPhotorhabdusandXenorhabdus(entomopathogenic bacteria associated with nematodes of the generaHeterorhabditisandSteinernema, 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 ofPhotorhabdus luminescenssubsp.thracensistoPhotorhabdus temperatasubsp.thracensiscomb. nov. (type strain CIP 108426T=DSM 15199T). We found that, within the genusXenorhabdus, strains or isolates that shared less than 97 % nucleotide identity (NI), calculated on the concatenated sequences of the four gene fragments (recA,gyrB,dnaNandgltX) encompassing 3395 nucleotides, did not belong to the same species. Thus, at the 97 % NI cutoff, we confirm the current 20 species of the genusXenorhabdusand propose the description of a novel species,Xenorhabdus vietnamensissp. nov. (type strain VN01T= CIP 109945T=DSM 22392T). Within each of the three current species of the genusPhotorhabdus,P. asymbiotica,P. luminescensandP. temperata, strains or isolates which shared less than 97 % NI did not belong to the same subspecies. Comparisons of the four gene fragments plus therplBgene fragment analysed separately led us to propose four novel subspecies:Photorhabdus luminescenssubsp.caribbeanensissubsp. nov. (type strain HG29T=CIP 109949T=DSM 22391T),P. luminescenssubsp.hainanensissubsp. nov. (type strain C8404T= CIP 109946T=DSM 22397T),P. temperatasubsp.khaniisubsp. nov. (type strain C1T=NC19T=CIP 109947T=DSM 3369T), andP. temperatasubsp.tasmaniensissubsp. nov. (type strain T327T= CIP 109948T=DSM 22387T).