Whole-genome-based revisit of Photorhabdus phylogeny: proposal for the elevation of most Photorhabdus subspecies to the species level and description of one novel species Photorhabdus bodei sp. nov., and one novel subspecies Photorhabdus laumondii subsp. clarkei subsp. nov.

Machado, Ricardo A. R.; Wüthrich, Daniel; Kuhnert, Peter; Arce, Carla C. M.; Thönen, Lisa; Ruiz, Celia; Zhang, Xi; Robert, Christelle A. M.; Karimi, Javad; Kamali, Shokoofeh; Ma, Juan; Bruggmann, Rémy; Erb, Matthias (2018). Whole-genome-based revisit of Photorhabdus phylogeny: proposal for the elevation of most Photorhabdus subspecies to the species level and description of one novel species Photorhabdus bodei sp. nov., and one novel subspecies Photorhabdus laumondii subsp. clarkei subsp. nov. International journal of systematic and evolutionary microbiology, 68(8), pp. 2664-2681. Society for General Microbiology SGM 10.1099/ijsem.0.002820

[img] Text
2018_IntJSystEvolMicrobiol_002820.pdf - Published Version
Restricted to registered users only
Available under License Publisher holds Copyright.

Download (9MB) | Request a copy

Bacterial symbionts are crucial for the infectivity and success of entomopathogenic nematodes as biological control agents. The current understanding of the symbiotic relationships is limited by taxonomic uncertainties. Here, we used whole-genome sequencing and traditional techniques to reconstruct the phylogenetic relationships between all described Photorhabdus species and subspecies as well as 11 newly isolated symbiotic bacteria of Heterorhabditis nematodes, including the unreported bacterial partner of H. beicherriana. In silico DNA–DNA hybridization, orthologous average nucleotide identity and nucleotide sequence identity of concatenated housekeeping genes scores were calculated and set into relation with current cut-off values for species delimitation in bacteria. Sequence data were complemented with biochemical and chemotaxonomic markers, and ribosomal protein fingerprinting profiles. This polyphasic approach resolves the ambiguous taxonomy of Photorhabdus and lead to the proposal for the elevation of most of them into a higher taxon and the creation of several new taxa: 15 new species, one of which is newly described: Photorhabdus bodei sp. nov. (type strain LJ24-63T=DSM 105690T=CCOS 1159T) and the other 14 arise through the proposal of elevating already described subspecies to species, and are proposed to be renamed as follows: Photorhabdus asymbiotica subsp. australis as Photorhabdus australis sp. nov., Photorhabdus luminescens subsp. akhurstii as Photorhabdus akhurstii sp. nov., Photorhabdus luminescens subsp. caribbeanensis as Photorhabdus caribbeanensis sp. nov., Photorhabdus luminescens subsp. hainanensis as Photorhabdus hainanensis sp. nov., Photorhabdus luminescens subsp. kayaii as Photorhabdus kayaii sp. nov., Photorhabdus luminescens subsp. kleinii as Photorhabdus kleinii sp. nov., Photorhabdus luminescens subsp. namnaonensis as Photorhabdus namnaonensis sp. nov., Photorhabdus luminescens subsp. noenieputensis as Photorhabdus noenieputensis sp. nov., Photorhabdus luminescens subsp. laumondii as Photorhabdus laumondii sp. nov., Photorhabdus temperata subsp. cinerea as Photorhabdus cinerea sp. nov., Photorhabdus temperata subsp. khanii as Photorhabdus khanii sp. nov., Photorhabdus temperata subsp. stackebrandtii as Photorhabdus stackebrandtii sp. nov., Photorhabdus temperata subsp. tasmaniensis as Photorhabdus tasmaniensis sp. nov., and Photorhabdus temperata subsp. thracensis as Photorhabdus thracensis sp. nov. In addition, we propose the creation of two new subspecies, one of which arises through the reduction of rank: Photorhabdus laumondii subsp. laumondii comb. nov. (basonym: P. luminescens subsp. laumondii ) and the second one is newly described: Photorhabdus laumondii subsp. clarkei subsp. nov. (type strain BOJ-47T=DSM 105531T=CCOS 1160T). Finally, we propose to emend the description of three species, which results from the proposal of elevating three subspecies to the species status: Photorhabdus asymbiotica , Photorhabdus temperata and Photorhabdus luminescens , formerly classified as Photorhabdus asymbiotica subsp. asymbiotica , Photorhabdus temperata subsp. temperata and Photorhabdus luminescens subsp. luminescens , respectively.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Department of Infectious Diseases and Pathobiology (DIP) > Institute of Veterinary Bacteriology
08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS)
08 Faculty of Science > Department of Biology > Bioinformatics

UniBE Contributor:

Ruiz Machado, Ricardo Alberto; Wüthrich, Daniel; Kuhnert, Peter; Marques Arce, Carla Cristina; Thönen, Lisa Paulina; Ruiz, Celia; Zhang, Xi; Robert, Christelle Aurélie Maud; Bruggmann, Rémy and Erb, Matthias

Subjects:

500 Science > 580 Plants (Botany)
600 Technology > 630 Agriculture

ISSN:

1466-5026

Publisher:

Society for General Microbiology SGM

Language:

English

Submitter:

Peter Alfred von Ballmoos-Haas

Date Deposited:

12 Jun 2018 13:52

Last Modified:

05 Aug 2018 01:32

Publisher DOI:

10.1099/ijsem.0.002820

PubMed ID:

29877789

Uncontrolled Keywords:

isDDH, Heterorhabditis, reclassification, phylogenomics, polyphasic classification, whole-genome sequencing, OrthoANI, Photorhabdus

BORIS DOI:

10.7892/boris.117147

URI:

https://boris.unibe.ch/id/eprint/117147

Actions (login required)

Edit item Edit item
Provide Feedback