Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns

Avontuur, Juanita R.; Palmer, Marike; Beukes, Chrizelle W.; Chan, Wai; Tasiya, Taponeswa; Zyl, Elritha Van; Coetzee, Martin Petrus Albertus; Stępkowski, Tomasz; Venter, Stephanus N.; Steenkamp, Emma Theodora

doi:10.1016/j.ympev.2021.107338

Cited by 343 publications

(9 citation statements)

References 103 publications

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“…This notion is consistent with its broad genetic diversity, exemplified by the rapid rate of novel species descriptions in the last decade (Delamuta et al, 2012;Grönemeyer and Reinhold-Hurek, 2018). Recent genomic studies showed that the genus is characterized by a number of deep divergences that has given rise to seven well-supported clades that are commonly referred to as supergroups (Avontuur et al, 2022(Avontuur et al, , 2019. Most of the described Bradyrhizobium species form part of the so-called B. japonicum supergroup, which has been recovered from a wide range of continents and climatic zones (Avontuur et al, 2019).…”

Section: Introductionsupporting

confidence: 66%

Bradyrhizobium Xenonodulans Sp. Nov. Isolated from Nodules of Australian Acacia Species Invasive to South Africa

Venter

Claassens

Beukes

et al. 2023

Preprint

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Section: Introductionsupporting

confidence: 66%

Bradyrhizobium Xenonodulans Sp. Nov. Isolated from Nodules of Australian Acacia Species Invasive to South Africa

Venter

Claassens

Beukes

et al. 2023

Preprint

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“…The use of ANI has been reported to be problematic for delineating boundaries between borderline species due to inconsistencies in results generated across different platforms and a lack of standardization [2, 36, 41]. Based on the established ANI threshold of 95–96 % for species circumscription [18, 42, 43], our tests (Table S3) show similar inconsistencies in the results generated by four different ANI implementations.…”

Section: Genome Analysesmentioning

confidence: 59%

“…The genus Bradyrhizobium is a diverse group of species that includes economically important bacteria capable of forming nitrogenfixing symbioses with agricultural legumes such as soybeans [e.g., [2][3][4][5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

Strains of Bradyrhizobium barranii sp. nov. associated with legumes native to Canada are symbionts of soybeans and belong to different subspecies (subsp. barranii subsp. nov. and subsp. apii subsp. nov.) and symbiovars (sv. glycinearum and sv. septentrionale)

Bromfield

Cloutier

Wasai-Hara

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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Four bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soils of legumes native to Canada were previously identified as a novel Bradyrhizobium lineage consisting of symbiovars (sv.) glycinearum and septentrionale. Our purpose was to verify the taxonomic status of these strains using phylogenetic, genomic and phenotypic analyses. Multiple phylogenetic analyses including analysis of 51 full-length ribosome protein subunit (rps) gene sequences confirmed placement of the novel strains in a highly supported lineage distinct from named Bradyrhizobium species with B. japonicum USDA 6T as the closest relative. The results of genomic and phylogenomic analyses based on digital DNA–DNA hybridization and genome blast distance phylogeny showed that novel strains in comparisons with type strains of closest relatives were below the established threshold (70 %) for species delineation. Moreover, the novel strains were divided into two subspecies clusters based on the established threshold of 79 %. The genomes of strains 144S4T, 323S2, 1S5 and 38S5T have sizes of 11 399 526, 11 474 152, 10580853 and 10 530 141 bp with DNA G+C contents of 63.1, 63.0, 63.4 and 63.3 mol%, respectively. These strains possess symbiosis islands harbouring key nodulation, nitrogen-fixation and type III secretion system genes as well as abundant insertion sequences and between two and four putative plasmids. Strains 144S4T and 323S2 (sv. glycinearum) are effective with regard to nitrogen fixation in symbiotic association with soybeans whereas strains 1S5 and 38S5T (sv. septentrionale) are ineffective. Data for morphological, physiological and symbiotic characteristics complement the sequence-based results. The data presented here support the description of a new species and two new subspecies for which the names Bradyrhizobium barranii sp. nov. subsp. barranii subsp. nov. (sv. glycinearum) and Bradyrhizobium barranii sp. nov. subsp. apii subsp. nov. (sv. septentrionale) are proposed with strain 144S4T (=LMG 31552T=HAMBI 3722T) as the species type strain and type strain of subsp. barranii subsp. nov., and strain 38S5T (=LMG 31556T=HAMBI 3721T) as the type strain of subsp. apii subsp. nov.

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“…The genetic segments responsible for this diversity directly affect evolutionary outcomes and are targeted by diverse evolutionary pressures. Bradyrhizobium isolates have rather big genomes ranging from 5 to 11M, with an average size of 8.6M (Ormeño-Orrillo and Martínez-Romero, 2019; Avontuur et al, 2022;Jin et al, 2022b;Claassens et al, 2023;Lafay et al, 2023;Zhang et al, 2023). Nevertheless, the range of GSs within the genus remains unknown.…”

Section: Genome Size Of Bradyrhizobiummentioning

confidence: 99%

Genetic diversity into a novel free-living species of Bradyrhizobium from contaminated freshwater sediment

Zhang,

Jin,

Zhuo

et al. 2023

Front. Microbiol.

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A free-living Bradyrhizobium strain isolated from a contaminated sediment sample collected at a water depth of 4 m from the Hongze Lake in China was characterized. Phylogenetic investigation of the 16S rRNA gene, concatenated housekeeping gene sequences, and phylogenomic analysis placed this strain in a lineage distinct from all previously described Bradyrhizobium species. The sequence similarities of the concatenated housekeeping genes support its distinctiveness with the type strains of the named species. The complete genome of strain S12-14-2 consists of a single chromosome of size 7.3M. The strain lacks both a symbiosis island and important nodulation genes. Based on the data presented here, the strain represents a new species, for which the name Bradyrhizobium roseus sp. nov. is proposed for the type strain S12-14-2T. Several functional differences between the isolate and other published genomes indicate that the genus Bradyrhizobium is extremely heterogeneous and has functions within the community, such as non-symbiotic nitrogen fixation. Functional denitrification and nitrogen fixation genes were identified on the genomes of strain S12-14-2T. Genes encoding proteins for sulfur oxidation, sulfonate transport, phosphonate degradation, and phosphonate production were also identified. Lastly, the B. roseus genome contained genes encoding ribulose 1,5-bisphosphate carboxylase/oxygenase, a trait that presumably enables autotrophic flexibility under varying environmental conditions. This study provides insights into the dynamics of a genome that could enhance our understanding of the metabolism and evolutionary characteristics of the genus Bradyrhizobium and a new genetic framework for future research.

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Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns

Cited by 343 publications

References 103 publications

Bradyrhizobium Xenonodulans Sp. Nov. Isolated from Nodules of Australian Acacia Species Invasive to South Africa

Bradyrhizobium Xenonodulans Sp. Nov. Isolated from Nodules of Australian Acacia Species Invasive to South Africa

Strains of Bradyrhizobium barranii sp. nov. associated with legumes native to Canada are symbionts of soybeans and belong to different subspecies (subsp. barranii subsp. nov. and subsp. apii subsp. nov.) and symbiovars (sv. glycinearum and sv. septentrionale)

Genetic diversity into a novel free-living species of Bradyrhizobium from contaminated freshwater sediment

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