Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa

Ricu Claassens; Stephanus N Venter; Chrizelle W Beukes; Tomasz Stępkowski; Wai Y Chan; Emma T Steenkamp

doi:10.1016/j.syapm.2023.126452

Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa

Syst Appl Microbiol. 2023 Sep;46(5):126452. doi: 10.1016/j.syapm.2023.126452. Epub 2023 Aug 18.

Authors

Ricu Claassens¹, Stephanus N Venter¹, Chrizelle W Beukes², Tomasz Stępkowski³, Wai Y Chan⁴, Emma T Steenkamp⁵

Affiliations

¹ Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa.
² The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
³ Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Poland.
⁴ Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa; Right to Care, Centurion, Gauteng, South Africa.
⁵ Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, Gauteng, South Africa. Electronic address: emma.steenkamp@up.ac.za.

PMID: 37634485
DOI: 10.1016/j.syapm.2023.126452

Abstract

A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (B. cosmicum 58S1^T, B. betae PL7HG1^T, B. ganzhouense CCBAU 51670 ^T, B. cytisi CTAW11^T and B. rifense CTAW71^T) resulted in values well below 95-96%. We further performed phenotypic tests which revealed that there are high levels of intraspecies variation, while an additional analysis of the nodA and nifD loci indicated that the symbiotic loci of the strains are closely related to those of Bradyrhizobium isolates with an Australian origin. Strain 14AB^T (=LMG 31415 ^T = SARCC-753 ^T) is designated as the type strain of the novel species for which we propose the name Bradyrhizobium xenonodulans sp. nov.

Keywords: Acacia; Bradyrhizobium; Genealogical concordance; South Africa; nodA.

MeSH terms

Acacia* / genetics
Australia
Bradyrhizobium*
DNA, Bacterial / genetics
Genes, Bacterial / genetics
Nucleic Acid Hybridization
Phylogeny
RNA, Ribosomal, 16S / genetics
Root Nodules, Plant
Sequence Analysis, DNA
South Africa

Substances

RNA, Ribosomal, 16S
DNA, Bacterial