Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., two novel B. cepacia complex species causing onion sour skin

Leandro S Velez; Flávia F Aburjaile; Antonio R G Farias; Ana D B Baia; Willams J Oliveira; Adriano M F Silva; Ana M Benko-Iseppon; Vasco Azevedo; Bertram Brenig; Jong H Ham; Elineide B Souza; Marco A S Gama

doi:10.1016/j.syapm.2023.126415

Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., two novel B. cepacia complex species causing onion sour skin

Syst Appl Microbiol. 2023 May;46(3):126415. doi: 10.1016/j.syapm.2023.126415. Epub 2023 Mar 11.

Affiliations

¹ Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil.
² Preventive Veterinary Medicine Departament, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
³ Center of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.
⁴ Department of Genetics, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil.
⁵ Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
⁶ Department of Molecular Biology of Livestock, Institute of Veterinary Medicine, Georg August University Göttingen, 37077 Göttingen, Germany.
⁷ Department Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, United States.
⁸ Department of Biology, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil.
⁹ Department of Agronomy, Universidade Federal Rural de Pernambuco, Recife, PE 52171-900, Brazil. Electronic address: marco.gama@ufrpe.com.br.

PMID: 36933352
DOI: 10.1016/j.syapm.2023.126415

Abstract

Two putative novel Burkholderia cenocepacia lineages found in the semi-arid region of north-east Brazil causing onion sour skin were studied using genomic approaches to determine their taxonomic position. Four strains belonging to one novel lineage (CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171) and one strain (CCRMBC51) belonging to another novel lineage had their whole genome sequenced to carry out taxogenomic analyses. The phylogenomic tree built using the type (strain) genome server (TYGS) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 into the same clade, while grouped the strain CCRMBC51 separately. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analysis showed values above 99.21 % and 93.2 %, respectively, among the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171, while ANI and dDDH values between these strains and the strain CCRMBC51 were below 94.49 % and 56.6 %, respectively. All these strains showed ANI and dDDH values below 94.78 % and 58.8 % concerning type strains of the B. cepacia complex (Bcc) species. The phylogenetic maximum likelihood tree constructed based on the multilocus sequence analysis of core genes (cMLSA) clustered the strains CCRMBC16, CCRMBC33, CCRMBC74, and CCRMBC171 and the strain CCRMBC51 in two exclusive clades, which did not cluster with any known species of the Bcc. Therefore, combined data from TYGS, ANI, dDDH, and cMLSA demonstrated that the strains represent two novel species of the Bcc, which we classified as Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov., and proposed the strains CCRMBC74^T (=IBSBF 3371 ^T = CBAS 905 ^T) and CCRMBC51^T (=IBSBF3370^T = CBAS 904 ^T) as type strains, respectively.

Keywords: Allium cepa; Burkholderia semiarida sp. nov.; Burkholderia sola sp. nov.; Novel species; Onion diseases; Taxogenomic approach.

MeSH terms

Bacterial Typing Techniques
Burkholderia* / genetics
DNA
DNA, Bacterial / genetics
Fatty Acids
Nucleic Acid Hybridization
Onions / genetics
Phylogeny
RNA, Ribosomal, 16S / genetics
Sequence Analysis, DNA

Substances

RNA, Ribosomal, 16S
DNA
DNA, Bacterial
Fatty Acids