Taxonomic note
Description of Xenorhabdus khoisanae sp. nov., the symbiont of the entomopathogenic nematode Steinernema khoisanae
Tiarin Ferreira1, Carol A. van Reenen2, Akihito Endo2, Cathrin Spröer3, Antoinette P. Malan1, Leon M.T. Dicks2*
1
Department of Conservation Ecology and Entomology, University of Stellenbosch, Private Bag X1, 7602 Matieland, South Africa
2
Department of Microbiology, University of Stellenbosch, Private Bag X1, 7602 Matieland, South Africa
3
DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
*Corresponding author: Leon M.T. Dicks
Tel.: +27-21-8085849; fax: +27-21-8085846; e-mail: LMTD@sun.ac.za
Running title: Description of Xenorhabdus khoisanae sp. nov.
Summary
Bacterial strain SF87, and additional strains SF80, SF362 and 106-C, isolated from the nematode Steinernema khoisanae, are non-bioluminescent Gram-negative bacteria that share many of the carbohydrate fermentation reactions recorded for the type strains of previously described Xenorhabdus spp. Based on the 16S rRNA gene sequence data, strain SF87 is 98% related to Xenorhabdus hominickii. Nucleotide sequences of strain SF87 obtained from the
recA, dnaN, gltX, gyrB and infB genes showed 96 to 97% similarity with Xenorhabdus
miraniensis. However, strain SF87 shares only 52.7% DNA homology with the type strain of
X. miraniensis by DNA-DNA hybridization analysis, confirming that it belongs to a different
species. Strains SF87, SF80, SF362 and 106-C are phenotypically similar to X. miraniensis and X. beddingii, except that they do not produce acid from esculin. Xenorhabdus khoisanae sp. nov. is proposed as a new species of the genus Xenorhabdus (type strain SF87T, DSM 25463T, ATCC BAA-2406T).
16S rDNA
Neighbour-joining
0.01 X. khoisanae 106-C (JX623972) X. khoisanae SF362 (JX623978) X. khoisanae SF87T (HQ142625) X. khoisanae SF80 (JX623966) X. hominickii DSM 17903T (DQ211719) X. koppenhoeferi DSM 18168T (DQ205450) X. japonica DSM 16188T (D78008) X. vietnamensis DSM 22392T (DQ205447) X. innexi DSM 16336T (AJ810292) X. stockiae DSM 17904T (DQ202309) X. ehlersii DSM 16337T (AJ810294) X. budapestensis DSM 16342T (AJ810293) X. kozodoii DSM 17907T (DQ211716) X. bovienii DSM 4766T (AY278673) X. ishibashii DSM 22670T (GQ149086) X. griffiniae DSM 17911T (DQ211710) X. poinarii DSM 4768T (D78010) X. indica DSM 17382T (AM040494) X. mauleonii DSM 17908T (DQ211715) X. szentirmaii DSM 16338T (AJ810295) X. miraniensis DSM 17902T (DQ211713) X. doucetiae DSM 17909T (DQ211709) X. romanii DSM 17910T (DQ211717) X. nematophila DSM 3370T (AY278674) X.magdalenensis DSM 24915T (HQ877464) X. cabanillasii DSM 17905T (AY521244) X. beddingii DSM 4764T (AY278675)P. asymbiotica subsp. asymbiotica DSM15149T(NR_036851)
96.2 99.7
79.4 100
16S rDNA
Maximum-likelihood
0.1 X. khoisanae SF362 (JX623978) X. khoisanae SF80 (JX623966) X. khoisanae SF87T (HQ142625) X. khoisanae 106-C (JX623972) X. hominickii DSM 17903T (DQ211719) X. koppenhoeferi DSM 18168T (DQ205450) X. japonica DSM 16188T (D78008) X. vietnamensis DSM 22392T (DQ205447) X. doucetiae DSM17909T (DQ211709) X. innexi DSM 16336T (AJ810292) X. stockiae DSM 17904T (DQ202309) X. budapestensis DSM 16342T (AJ810293) X. ehlersii DSM 16337T (AJ810294) X. kozodoii DSM 17907T (DQ211716) X. bovienii DSM 4766T (AY278673) X. griffiniae DSM 17911T (DQ211710) X. ishibashii DSM 22670T (GQ149086) X. poinarii DSM 4768T(D78010) X. indica DSM 17382T (AM040494) X. mauleonii DSM 17908T (DQ211715) X. romanii DSM 17910T (DQ211717) X. miraniensis DSM 17902T (DQ211713) X. szentirmaii DSM 16338T (AJ810295) X.magdalenensis DSM 24915T (HQ877464) X. nematophila DSM 3370T (AY278674) X. cabanillasii DSM 17905T (AY521244) X. beddingii DSM 4764T (AY278675)P. asymbiotica subsp. asymbiotica DSM 15149T(NR_036851)
99.0
97.0
76.0
82.0
recA
0.1 X. griffiniae DSM 17911T (FJ823399) X. ehlersii DSM 16337T (FJ823398) X. ishibashii DSM 22670T (JQ348906) X. vietnamensis DSM 22392T (FJ823401) X. japonica DSM 16522T (FJ823400) X. doucetiae DSM 17909T (FJ823402) X. romanii DSM 17910T (FJ823403) X. magdalenensis DSM 24915T (JF798401) X. kozodoii DSM 17907T (FJ823404) X. poinarii DSM 4768T (FJ823409) X. khoisanae SF87T (AB685736) X. khoisanae SF80 (JX623967) X. khoisanae 106-C (JX623973) X. khoisanae SF362 (JX623979) X. miraniensis DSM 17902T (FJ823414) X. beddingii DSM 4764T (FJ823415) X. hominickii DSM 17903T (FJ823410) X. szentirmaii DSM 16338T (FJ823416) X. koppenhoeferi DSM 18168T (FJ823413) X. nematophila DSM 3370T (FN667742) X. mauleonii DSM 17908T (FJ823417) X. bovienii DSM 4766T (FJ823426) X. indica DSM 17382T (FJ823421) X. budapestensis DSM 16324T (FJ823418) X. cabanillasii DSM 17905T (FJ823422) X. stockiae DSM 17904T (FJ823425) X. innexi DSM 16336T (FJ823423)P.asymbiotica subsp. asymbiotica DSM15149T (FJ862017)
73.5 100 84.4 100 100 87.2 98.8 98.4 98.5 83.2 95.7
dnaN
0.1 X. griffiniae DSM 17911T (FJ831449) X. ehlersii DSM16337T (FJ831448) X. ishibashii DSM 22670T (JQ348908) X. vietnamensis DSM 22392T (FJ831452) X. japonica DSM 16522T (FJ831453) X. kozodoii DSM 17907T (FJ831445) X. romanii DSM 17910T (FJ831451) X. magdalenensis DSM 24915T (JF798399) X. doucetiae DSM 17909T (FJ831450) X. poinarii DSM 4768T (FJ831454) X. khoisanae SF87T (AB685733) X. khoisanae 106-C (JX623974) X. khoisanae SF80 (JX623968) X. khoisanae SF362 (JX623980) X. miraniensis DSM 17902T (FJ831459) X. beddingii DSM 4764T (FJ831460) X. nematophila DSM 3370T (NC_014228) X. koppenhoeferi DSM 18168T (FJ831457) X. szentirmaii DSM 16338T (FJ831458) X. mauleonii DSM 17908T (FJ831464) X. hominickii DSM 17903T (FJ831461) X. bovienii DSM 4766T (FJ831465) X. indica DSM 17382T (FJ831470) X. cabanillasii DSM 17905T (FJ831472) X. budapestensis DSM 16324T (FJ831474) X. stockiae DSM 17904T (FJ831477) X. innexi DSM 16336T (FJ831475)P. asymbiotica subsp. asymbiotica DSM 15149T (FJ831491)
77.8 100 100 91.0 96.0 100 100 98.1 99.5 90.5 81.8 95.9 91.7 Fig 4S
gltX
0.1 X. budapestensis DSM 16324T (FJ840517) X. indica DSM 17382T (FJ840520) X. cabanillasii DSM 17905T (FJ840521) X. stockiae DSM 17904T (FJ840524) X. innexi DMS 16336T (FJ840522) X. bovienii DSM 4766T (FJ840516) X. hominickii DSM 17903T (FJ840509) X. khoisanae SF87T (AB685734) X. khoisanae SF80 (JX623969) X. khoisanae 106-C (JX623975) X. khoisanae SF362 (JX623981) X. miraniensis DSM 17902T (FJ840505) X. beddingii DSM 4764T (FJ840506) X. griffiniae DSM 17911T (FJ840496) X. ehlersii DSM16337T (FJ840495) X. ishibashii DSM 22670T (JQ348909) X. kozodoii DSM 17907T (FJ840492) X. doucetiae DSM 17909T (FJ840497) X. romanii DSM 17910T (FJ840498) X. magdalenensis DSM 24915T (JF798400) X. vietnamensis DSM 22392T (FJ840502) X. japonica DSM 16522T (FJ840503) X. poinarii DSM 4768T (FJ840499) X. nematophila DSM 3370T (FN667742) X. koppenhoeferi DSM 18168T (FJ840504) X. szentirmaii DSM 16338T (FJ840508) X. mauleonii DSM 17908T (FJ840507)P. asymbiotica subsp. asymbiotica DSM 15149T (FJ844929)
82.7 100 100 94.9 99.8 100 97.4 96.3 96.1 92.4 100 100 99.8 99.3
gyrB
0.1 X. khoisanae SF87T (AB685735) X. khoisanae 106-C (JX623976) X. khoisanae SF80 (JX623970) X. khoisanae SF362 (JX623982) X. miraniensis DSM 17902T (EU934520) X. hominickii DSM 17903T (EU934517) X. beddingii DSM 4764T (EU934516) X. romanii DSM 17910T (EU934515) X. szentirmaii DSM 16338T (EU934534) X. mauleonii DSM 17908T (EU934533) X. nematophila DSM 3370T (FN667742) X. koppenhoeferi DSM 18168T (EU934532) X. vietnamensis DSM 22392T (EU934514) X. japonica DSM 16522T (EU934513) X. griffiniae DSM 17911T (EU934525) X. ehlersii DSM 16337T (EU934524) X. ishibashii DSM 22670T (JQ348907) X. kozodoii DSM 17907T (EU934521) X. doucetiae DSM 17909T (EU934526) X. magdalenensis DSM 24915T (JF798402) X. cabanillasii DSM 17905T (EU934537) X. budapestensis DSM 16342T (EU934535) X. indica DSM 17382T (EU934538) X. stockiae DSM 17904T (EU934542) X. innexi DSM 16336T (EU934540) X. bovienii DSM 4766T (EU934527) X. poinarii DSM 4768T (EU934543)P. asymbiotica subsp. asymbiotica DSM 15149T (AY278494)
100 100 100 97.8 100 99.5 97.7 80.3 94.2 95.0 85.9 100 99.9 86.4 Fig 6S
infB
0.1 X. doucetiae DSM 17909T (JF798406) X. romanii DSM 17910T (JF798407) X. magdalenensis DSM 24915T (JF798403 ) X. kozodoii DSM 17907T (JF798411) X. ehlersii DSM 16337T (JF798404) X. ishibashii DSM 22670T (JQ348910) X. griffiniae DSM 17911T (JF798405) X. vietnamensis DSM 22392T (JF798408) X. japonica DSM 16522T (JF798409) X. poinarii DSM 4768T (JF798410) X. khoisanae 106-C (JX623977) X. khoisanae SF87T (JX623984) X. khoisanae SF80 (JX623971) X. khoisanae SF362 (JX623983) X. miraniensis DSM 17902T (JF798412) X. beddingii DSM 4764T (JF798413) X. hominickii DSM 17903T (JF798414) X. koppenhoeferi DSM 18168T (JF798417) X. nematophila DSM 3370T (FN667742) X. szentirmaii DSM 16338T (JF798416) X. mauleonii DSM 17908T (JF798415) X. cabanillasii DSM 17905T (JF798420) X. budapestensis DSM 16342T (JF798419) X. indica DSM 17382T (JF798421) X. stockiae DSM 17904T (JF798423) X. innexi DSM 16336T (JF798422) X. bovienii DSM 4766T (JF798418)P. asymbiotica subsp. asymbiotica ATCC 43949 (FM162591)
85.4 100 100 95.3 100 97.9 99.4 75.2 96.7 100 82.2 76.3 76.0 100 100
Fig. 1S. Phylogenetic relationship of strains SF87T, SF80, 106-C and SF362 to known
Xenorhabdus spp. based on 16S rRNA gene sequences. The tree was constructed by the
neighbour-joining method. Photorhabdus asymbiotica subsp. asymbiotica was used as an outgroup species. Bootstrap percentages above 70% are given at branching points. The scale bar indicates 10% sequence divergence.
Fig. 2S. Phylogenetic relationship of strains SF87T, SF80, 106-C and SF362 to known
Xenorhabdus spp. based on the 16S rRNA gene sequences. The tree was constructed by the
maximum-likelihood method. Photorhabdus asymbiotica subsp. asymbiotica was used as an outgroup species. Bootstrap percentages above 70% are given at branching points. The scale bar indicates 10% sequence divergence.
Fig. 3S. Phylogenetic relationship of strains SF87T, SF80, 106-C and SF362 to known
Xenorhabdus spp. based on recA gene sequences. The tree was constructed by the
neighbour-joining method. Photorhabdus asymbiotica subsp. asymbiotica was used as an outgroup species. Bootstrap percentages above 70% are given at branching points. The scale bar indicates 10% sequence divergence.
Fig. 4S. Phylogenetic relationship of strains SF87T, SF80, 106-C and SF362 to known
Xenorhabdus spp. based on dnaN gene sequences. The tree was constructed by the
neighbour-joining method. Photorhabdus asymbiotica subsp. asymbiotica was used as an outgroup species. Bootstrap percentages above 70% are given at branching points. The scale bar indicates 10% sequence divergence.
Fig. 5S. Phylogenetic relationship of strains SF87T, SF80, 106-C and SF362 to known
Xenorhabdus spp. based on gltX gene sequences. The tree was constructed by the
neighbour-joining method. Photorhabdus asymbiotica subsp. asymbiotica was used as an outgroup species. Bootstrap percentages above 70% are given at branching points. The scale bar indicates 10% sequence divergence.
Fig. 6S. Phylogenetic relationship of strains SF87T, SF80, 106-C and SF362 to known
Xenorhabdus spp. based on gyrB gene sequences. The tree was constructed by the
neighbour-joining method. Photorhabdus asymbiotica subsp. asymbiotica was used as an outgroup species. Bootstrap percentages above 70% are given at branching points. The scale bar indicates 10% sequence divergence.
Fig. 7S. Phylogenetic relationship of strains SF87T, SF80, 106-C and SF362 to known
Xenorhabdus spp. based on infB gene sequences. The tree was constructed by the
neighbour-joining method. Photorhabdus asymbiotica subsp. asymbiotica was used as an outgroup species. Bootstrap percentages above 70% are given at branching points. The scale bar indicates 10% sequence divergence.
