Delineation of Paraburkholderia tuberum sensu stricto and description of Paraburkholderia podalyriae sp. nov. nodulating the South African legume Podalyria calyptrata

Mavima, Lazarus; Beukes, Chrizelle W.; Palmer, Marike; Meyer, Sofie E. De; James, Euan K.; Maluk, Marta; Muasya, Muthama; Avontuur, Juanita R.; Chan, Wai; Venter, Stephanus N.; Steenkamp, Emma Theodora

doi:10.1016/j.syapm.2022.126316

Cited by 7 publications

(6 citation statements)

References 108 publications

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“…Interestingly, these species contain strains able to fix nitrogen and nodule mimosoid legumes of South and Central America, which also led to their classification into the symbiovar sv. atlantica ( Mavima et al, 2022 ).…”

Section: Resultsmentioning

confidence: 99%

“…While glanders is primarily a horse disease, melioidosis may affect humans and other animals ( Godoy et al, 2003 ). Furthermore, distinct rhizobial Paraburkholderia species can establish a beneficial symbiotic relationship and form root nodules for nitrogen fixation in different legume species ( Mavima et al, 2022 ). The species mentioned above are hardly distinguished by the evaluation of 16S rRNA or recA gene sequences, highlighting the importance of using genome metrics to differentiate closely related species.…”

Section: Introductionmentioning

confidence: 99%

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Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species

Bach,

Volpiano,

Sant’Anna

et al. 2023

Genet. Mol. Biol.

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The taxonomy of Burkholderia sensu lato (s.l.) has been revisited using genome-based tools, which have helped differentiate closely related species. Many species from this group are indistinguishable through phenotypic traits and 16S rRNA gene sequence analysis. Furthermore, they also exhibit whole-genome Average Nucleotide Identity (ANI) values in the twilight zone for species circumscription (95-96%), which may impair their correct classification. In this work, we provided an updated Burkholderia s.l. taxonomy focusing on closely related species and give other recommendations for those developing genome-based taxonomy studies. We showed that a combination of ANI and digital DNA-DNA hybridization (dDDH) applying the universal cutoff values of 95% and 70%, respectively, successfully discriminates Burkholderia s.l. species. Using genome metrics with this pragmatic criterion, we demonstrated that i) Paraburkholderia insulsa should be considered a later heterotypic synonym of Paraburkholderia fungorum; ii) Paraburkholderia steynii differs from P. terrae by harboring symbiotic genes; iii) some Paraburkholderia are indeed different species based on dDDH values, albeit sharing ANI values close to 95%; iv) some Burkholderia s.l. indeed represent new species from the genomic viewpoint; iv) some genome sequences should be evaluated with care due to quality concerns.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species

Bach,

Volpiano,

Sant’Anna

et al. 2023

Genet. Mol. Biol.

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“…The phylogenetic analysis based on the 16S rRNA gene (Fig. 2) showed that all isolated strains grouped within the species P. atlantica that has recently been separated from the South African species P. tuberum (Paulitsch et al 2020;Mavima et al 2021Mavima et al , 2022. Five strains (W3, W33, W38, W47 and W48) were selected and phylogenetically analyzed by multilocus sequence analysis (MLSA) of the concatenated sequences from 16S rRNA, recA, and gyrB genes.…”

Section: Discussionmentioning

confidence: 99%

Paraburkholderia atlantica is the main rhizobial symbiont of Mimosa spp. in ultramafic soils in the Brazilian Cerrado biome

Neto

Ribeiro²,

Fernandes‐Júnior³

et al. 2022

Plant Soil

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were characterized for their nodulation capacity on M. pudica and common bean, and their tolerance to Ni in culture medium. Bacteria were also partially identified by their 16S rRNA gene sequences. In addition, recA, gyrB, nodC and nifH genes from five representative isolates were sequenced for phylogenetic studies. Results In situ detection indicated the exclusive presence of Paraburkholderia sp. within the nodules. This identification was confirmed for most of the isolates by the analysis of their 16S rRNA gene sequences. All isolates identified as Paraburkholderia sp. were able to effectively nodulate M. pudica, but those tested in common bean produced ineffective

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“…Using both ANI and dDDH, Wekesa et al [ 17 ] characterized two high-efficiency Kenyan common bean-nodulating rhizobia. While investigating the taxonomic status of 31 rhizobial isolates from the root nodules of diverse South African legume hosts, a Papilionoideae isolate previously identified as Paraburkholderia tuberum was found to be a new species and consequently renamed Paraburkholderia podalyriae after performing average nucleotide identity [ 161 ].…”

Section: Methods Used In Rhizobia Characterization In Africamentioning

confidence: 99%

Distribution, Characterization and the Commercialization of Elite Rhizobia Strains in Africa

Wekesa

Jalloh

John

et al. 2022

IJMS

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Grain legumes play a significant role in smallholder farming systems in Africa because of their contribution to nutrition and income security and their role in fixing nitrogen. Biological Nitrogen Fixation (BNF) serves a critical role in improving soil fertility for legumes. Although much research has been conducted on rhizobia in nitrogen fixation and their contribution to soil fertility, much less is known about the distribution and diversity of the bacteria strains in different areas of the world and which of the strains achieve optimal benefits for the host plants under specific soil and environmental conditions. This paper reviews the distribution, characterization, and commercialization of elite rhizobia strains in Africa.

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Delineation of Paraburkholderia tuberum sensu stricto and description of Paraburkholderia podalyriae sp. nov. nodulating the South African legume Podalyria calyptrata

Cited by 7 publications

References 108 publications

Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species

Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species

Paraburkholderia atlantica is the main rhizobial symbiont of Mimosa spp. in ultramafic soils in the Brazilian Cerrado biome

Distribution, Characterization and the Commercialization of Elite Rhizobia Strains in Africa

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