Genome-informed Bradyrhizobium taxonomy: where to from here?

Avontuur, Juanita R.; Palmer, Marike; Beukes, Chrizelle W.; Chan, Wai; Coetzee, Martin Petrus Albertus; Blom, Jochen; Stępkowski, Tomasz; Kyrpides, Nikos C.; Woyke, Tanja; Shapiro, Nicole; Whitman, William B.; Venter, Stephanus N.; Steenkamp, Emma Theodora

doi:10.1016/j.syapm.2019.03.006

Cited by 69 publications

(75 citation statements)

References 112 publications

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“…The Generation time (h) in YM broth 8-9 8-9 9-10 >20 11-12 >6 Growth at: 1.0% NaCl (Fig. 3) showed that the tested L. anagyroides nodule isolates were members of the Bradyrhizobium genus with affinity to strains referred to as the B. jicamae supergroup (Avontuur et al 2019). The previous studies have shown that the B. jicamae supergroup strains are relatively rare and their geographic range covers mainly hot and arid areas all over the world (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…In fact, due to the growing availability of genomes for rhizobia, MLSA has now been superseded by ANI comparisons between genomes, which has been proven to be adequate for taxonomic purposes (de Lajudie et al 2019). Nevertheless, MLSA supports many phylogenetic relationships recovered in the genome-based phylogeny for Bradyrhizobium (Avontuur et al 2019). Unfortunately, there is no defined MLSA threshold to identify bacteria at the species or genus level in rhizobia, in contrast to some other groups of bacteria, e.g.…”

Section: Discussionmentioning

confidence: 99%

“…Bradyrhizobium communities are also abundant in many soils where legumes are absent, often acting as endophytes of different plants (Vanlnsberghe et al 2015). The studies have revealed that the genus Bradyrhizobium is separated into seven lineages, including symbiotic as well non-symbiotic bacteria (Avontuur et al 2019;Ormeño-Orrillo and Martínez-Romero 2019). A large number of species in Bradyrhizobium has been recognized, however the list of species in this genus will probably be still growing due to the rapid development of molecular tools and the huge diversity of this genus (Stępkowski et al 2018;de Lajudie et al 2019).…”

Section: Introductionmentioning

confidence: 99%

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Bradyrhizobia associated with Laburnum anagyroides, an exotic legume grown in Poland

Sajnaga

Jach

2020

Symbiosis

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We isolated 18 rhizobial strains from root nodules of a leguminous shrub Laburnum anagyroides (common laburnum) grown in Southeast Poland as an exotic plant. With the use of BOX-PCR fingerprinting, the isolates were clustered into 2 main groups and one separate lineage, which was congruent with the ITS-RFLP results. The phylogenetic trees constructed based on 16S rRNA and combined atpD, dnaK, glnA, and recA gene sequence data separated the representative strains into three evolutionary lineages within the Bradyrhizobium jicamae supergroup, with Bradyrhizobium algeriense and Bradyrhizobium valentinum as the closest relatives. The nodA and nifH gene phylogenies proved that the L. anagyroides symbionts carry a symbiotic gene variant known as Clade IV, representing the symbiovar retamae. Phenotypic characteristics of the isolates and reference strains are also reported. Our study of the rhizobia nodulating L. anagyroides growing in Poland complements earlier few findings on the symbiotic associations of this Genisteae species.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Bradyrhizobia associated with Laburnum anagyroides, an exotic legume grown in Poland

Sajnaga

Jach

2020

Symbiosis

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“…1). The exception was Bradyrhizobium lablabi HAMBI 3052 T , which is a member of the Bradyrhizobium jicamae supergroup according to the new genome-based taxonomy of bradyrhizobia proposed by Avontuur et al [53]. The test strains were placed in 11 lineages (clades A-K) with high posterior probability (PP=1.00).…”

Section: Phylogenetic Distribution Of Denitrifying Bradyrhizobiamentioning

confidence: 99%

Competition for electrons favors N₂O reduction in denitrifyingBradyrhizobium isolates

Yuan

Mania

Mousavi

et al. 2020

Preprint

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The legume-rhizobium symbiosis accounts for the major part of the biological N2 fixation in agricultural systems. Despite their lower need for synthetic nitrogen fertilizers, legume-cropped fields are responsible for substantial N2O emissions. Several economically important legumes fix N2 through symbiosis with bacteria belonging to the genus Bradyrhizobium. Many bradyrhizobia are also denitrifiers, and inoculation of legumes with N2O-reducing strains has been suggested to mitigate N2O emissions. Here, we analyzed the phylogeny and denitrification capacity of Bradyrhizobium strains, most of them isolated from peanut nodules. All performed at least partial denitrification, but only 37% were complete denitrifiers. This group shared a common phenotype with a strong preference for N2O- over NO3--reduction. We tested if this could be due to low quantities of NO3- reductase (periplasmic Nap) but found that Nap was more abundant than N2O reductase (Nos). This corroborates a recently proposed mechanism that the electron pathway from quinols to Nos via the cytochrome bc1 complex outcompetes that to Nap via the membrane-bound NapC. We propose that this applies to all organisms which, like many bradyrhizobia, carry Nos and Nap but lack membrane-bond NO3- reductase (Nar). Supporting this, Paracoccus denitrificans, which has Nap and Nar, reduced N2O and NO3- simultaneously.

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“…), and L. uliginosus have been shown to be nodulated by closely related bradyrhizobia that are in the same cross-inoculation group [9,16,17]. The genus Bradyrhizobium comprises highly diversified bacteria, with 39 described species thus far [18][19][20], including some photosynthetic strains [21][22][23]. The 16S rRNA gene is very conserved within this genus and, like the symbiotic genes, has been shown to be laterally transmitted [24,25].…”

Section: Introductionmentioning

confidence: 99%

Diversity, Phylogeny and Plant Growth Promotion Traits of Nodule Associated Bacteria Isolated from Lotus parviflorus

et al. 2020

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Lotus spp. are widely used as a forage to improve pastures, and inoculation with elite rhizobial strains is a common practice in many countries. However, only a few Lotus species have been studied in the context of plant-rhizobia interactions. In this study, forty highly diverse bacterial strains were isolated from root nodules of wild Lotus parviflorus plants growing in two field locations in Portugal. However, only 10% of these isolates could nodulate one or more legume hosts tested, whereas 90% were thought to be opportunistic nodule associated bacteria. Phylogenetic studies place the nodulating isolates within the Bradyrhizobium genus, which is closely related to B. canariense and other Bradyrhizobium sp. strains isolated from genistoid legumes and Ornithopus spp. Symbiotic nodC and nifH gene phylogenies were fully consistent with the taxonomic assignment and host range. The non-nodulating bacteria isolated were alpha- (Rhizobium/Agrobacterium), beta- (Massilia) and gamma-proteobacteria (Pseudomonas, Lysobacter, Luteibacter, Stenotrophomonas and Rahnella), as well as some bacteroidetes from genera Sphingobacterium and Mucilaginibacter. Some of these nodule-associated bacteria expressed plant growth promotion (PGP) traits, such as production of lytic enzymes, antagonistic activity against phytopathogens, phosphate solubilization, or siderophore production. This argues for a potential beneficial role of these L. parviflorus nodule-associated bacteria.

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Genome-informed Bradyrhizobium taxonomy: where to from here?

Cited by 69 publications

References 112 publications

Bradyrhizobia associated with Laburnum anagyroides, an exotic legume grown in Poland

Bradyrhizobia associated with Laburnum anagyroides, an exotic legume grown in Poland

Competition for electrons favors N₂O reduction in denitrifyingBradyrhizobium isolates

Diversity, Phylogeny and Plant Growth Promotion Traits of Nodule Associated Bacteria Isolated from Lotus parviflorus

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Genome-informed Bradyrhizobium taxonomy: where to from here?

Cited by 69 publications

References 112 publications

Bradyrhizobia associated with Laburnum anagyroides, an exotic legume grown in Poland

Bradyrhizobia associated with Laburnum anagyroides, an exotic legume grown in Poland

Competition for electrons favors N2O reduction in denitrifyingBradyrhizobium isolates

Diversity, Phylogeny and Plant Growth Promotion Traits of Nodule Associated Bacteria Isolated from Lotus parviflorus

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Competition for electrons favors N₂O reduction in denitrifyingBradyrhizobium isolates