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.
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 =NC19(T) =CIP 109947T =DSM 3369T), and P. temperata subsp. tasmaniensis subsp. nov. (type strain T327T =CIP 109948T =DSM 22387T).
INRA and Université Montpellier 2, Unité d'Ecologie Microbienne des Insectes and Interactions hôte-Pathogène, F-34000 Montpellier, France.
Patrick
P
Tailliez
INRA and Université Montpellier 2, Unité d'Ecologie Microbienne des Insectes and Interactions hôte-Pathogène, F-34000 Montpellier, France.
Christine
C
Laroui
INRA and Université Montpellier 2, Unité d'Ecologie Microbienne des Insectes and Interactions hôte-Pathogène, F-34000 Montpellier, France.
Nadège
N
Ginibre
INRA and Université Montpellier 2, Unité d'Ecologie Microbienne des Insectes and Interactions hôte-Pathogène, F-34000 Montpellier, France.
Armelle
A
Paule
INRA and Université Montpellier 2, Unité d'Ecologie Microbienne des Insectes and Interactions hôte-Pathogène, F-34000 Montpellier, France.
Sylvie
S
Pagès
INRA and Université Montpellier 2, Unité d'Ecologie Microbienne des Insectes and Interactions hôte-Pathogène, F-34000 Montpellier, France.
Noël
N
Boemare
D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D008969:Molecular Sequence Data; D009348:Nematoda / Q000382:microbiology*; D020637:Photorhabdus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D020593:Xenorhabdus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S