International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016

Lajudie, Philippe M. de; Young, J. Peter W.

doi:10.1099/ijsem.0.002144

Cited by 28 publications

(17 citation statements)

References 89 publications

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“…and the means by which the new genera were initially described has caused skepticism. This was also evident from the minutes of the International committee on systematics of prokaryotes subcommittee for the taxonomy of Rhizobium and Agrobacterium , which discussed this subject during the 12th Nitrogen fixation Conference held in Budapest, Hungary on 25 August 2016 [ 10 ]. The subcommittee stated their position as “Research efforts directed towards robust characterization and taxonomy of Burkholderia s.l.…”

Section: Introductionmentioning

confidence: 99%

Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae

Santos

Palmer

Chávez-Ramírez

et al. 2018

Genes

218

148

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Burkholderia sensu lato is a large and complex group, containing pathogenic, phytopathogenic, symbiotic and non-symbiotic strains from a very wide range of environmental (soil, water, plants, fungi) and clinical (animal, human) habitats. Its taxonomy has been evaluated several times through the analysis of 16S rRNA sequences, concantenated 4–7 housekeeping gene sequences, and lately by genome sequences. Currently, the division of this group into Burkholderia, Caballeronia, Paraburkholderia, and Robbsia is strongly supported by genome analysis. These new genera broadly correspond to the various habitats/lifestyles of Burkholderia s.l., e.g., all the plant beneficial and environmental (PBE) strains are included in Paraburkholderia (which also includes all the N2-fixing legume symbionts) and Caballeronia, while most of the human and animal pathogens are retained in Burkholderia sensu stricto. However, none of these genera can accommodate two important groups of species. One of these includes the closely related Paraburkholderia rhizoxinica and Paraburkholderia endofungorum, which are both symbionts of the fungal phytopathogen Rhizopus microsporus. The second group comprises the Mimosa-nodulating bacterium Paraburkholderia symbiotica, the phytopathogen Paraburkholderia caryophylli, and the soil bacteria Burkholderia dabaoshanensis and Paraburkholderia soli. In order to clarify their positions within Burkholderia sensu lato, a phylogenomic approach based on a maximum likelihood analysis of conserved genes from more than 100 Burkholderia sensu lato species was carried out. Additionally, the average nucleotide identity (ANI) and amino acid identity (AAI) were calculated. The data strongly supported the existence of two distinct and unique clades, which in fact sustain the description of two novel genera Mycetohabitans gen. nov. and Trinickia gen. nov. The newly proposed combinations are Mycetohabitans endofungorum comb. nov., Mycetohabitans rhizoxinica comb. nov., Trinickia caryophylli comb. nov., Trinickia dabaoshanensis comb. nov., Trinickia soli comb. nov., and Trinickia symbiotica comb. nov. Given that the division between the genera that comprise Burkholderia s.l. in terms of their lifestyles is often complex, differential characteristics of the genomes of these new combinations were investigated. In addition, two important lifestyle-determining traits—diazotrophy and/or symbiotic nodulation, and pathogenesis—were analyzed in depth i.e., the phylogenetic positions of nitrogen fixation and nodulation genes in Trinickia via-à-vis other Burkholderiaceae were determined, and the possibility of pathogenesis in Mycetohabitans and Trinickia was tested by performing infection experiments on plants and the nematode Caenorhabditis elegans. It is concluded that (1) T. symbiotica nif and nod genes fit within the wider Mimosa-nodulating Burkholderiaceae but appear in separate clades and that T. caryophylli nif genes are basal to the free-living Burkholderia s.l. strains, while with regard to pathogenesis (2) none of the Mycetoh...

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Section: Introductionmentioning

confidence: 99%

Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae

Santos

Palmer

Chávez-Ramírez

et al. 2018

Genes

218

148

View full text Add to dashboard Cite

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“…Although each group was recently classified into new prokaryotes genera (PBE species belong to the Paraburkholderia genus [ 22 ], BGG species belong to the Caballeronia genus [ 23 ], while BCC species remain in the Burkholderia genus), some authors still disagree with that classification [ 21 , 24 ]. In fact, the International Committee on Systematics of Prokaryotes, Subcommittee for the Taxonomy of Rhizobium and Agrobacterium have recently stated the needed for a more conclusive approach to unravel the taxonomy of the Burkholderia genus [ 25 ]. Clearly, a more robust analysis is needed to define a robust taxonomy into this bacterial genus.…”

Section: Introductionmentioning

confidence: 99%

Biodiversity of cultivable Burkholderia species in Argentinean soils under no-till agricultural practices

et al. 2018

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No-tillage crop production has revolutionized the agriculture worldwide. In our country more than 30 Mha are currently cultivated under no-till schemes, stressing the importance of this management system for crop production. It is widely recognized that soil microbiota is altered under different soil managements. In this regard the structure of Burkholderia populations is affected by soils management practices such as tillage, fertilization, or crop rotation. The stability of these structures, however, has not been evaluated under sustainable schemes where the impact of land practices could be less deleterious to physicochemical soils characteristics. In order to assess the structure of Burkholderia spp. populations in no-till schemes, culturable Burkholderia spp. strains were quantified and their biodiversity evaluated. Results showed that Burkholderia spp. biodiversity, but not their abundance, clearly displayed a dependence on agricultural managements. We also showed that biodiversity was mainly influenced by two soil factors: Total Organic Carbon and Total Nitrogen. Results showed that no-till schemes are not per se sufficient to maintain a richer Burkholderia spp. soil microbiota, and additional traits should be considered when sustainability of productive soils is a goal to fulfil productive agricultural schemes.

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“…With the help of alternative markers and multilocus sequence analysis (MLSA) (Stepkowski et al, 2005 ; Vinuesa et al, 2005b ), species delineation became more feasible. Now the number of validly published bradyrhizobial species is rapidly increasing since 2012 (Figure 1 ) and currently counting 42 validly published species, more than half of which have been published since 2014 (Parté, 2014 ; de Lajudie and Young, 2017 ). Approximately one third of the described species originates from South America, one third from other regions, and a large number from China, while only few originate from SSA (Figure 1 ).…”

Section: Global Species Discovery Of Bradyrhizobium mentioning

confidence: 99%

“… Increase of described species of the genus Bradyrhizobium with time. Data includes all species officially listed (Parté, 2014 ; de Lajudie and Young, 2017 ), and the effectively, but not validly, published species “ B. arachidis ,” “ B. valentinum ,” “ B. brasilense ,” “ B. sacchari ,” “ B. centrolobii ,” “ B. macuxiense ,” and “ B. shewense ” (Wang et al, 2013 ; Durán et al, 2014 ; Aserse et al, 2017 ; da Costa et al, 2017 ; de Matos et al, 2017 ; Michel et al, 2017 ). …”

Section: Global Species Discovery Of Bradyrhizobium mentioning

confidence: 99%

Diversity of Bradyrhizobia in Subsahara Africa: A Rich Resource

Grönemeyer

Reinhold‐Hurek

2018

Front. Microbiol.

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Making use of biological nitrogen fixation (BNF) with pulses and green manure legumes can help to alleviate nitrogen deficiencies and increase soil fertility, problems faced particularly in smallholder agriculture in Subsahara Africa (SSA). The isolation of indigenous rhizobia provides a basis for the formulation of rhizobial inoculants. Moreover, their identification and characterization contribute to the general understanding of species distribution and ecology. Here we discuss global species discovery of Bradyrhizobium spp. Although recently the number of validly published Bradyrhizobium species is rapidly increasing, their diversity in SSA is not well-represented. We summarize the recent knowledge on species diversity in the Bradyrhizobium yuanmingense lineage to which most SSA isolates belong, and their biogeographic distribution and adaptations. Most indigenous rhizobia appear to differ from species found on other continents. We stress that an as yet hidden diversity may be a rich resource for inoculant development in future. As some species are exceptionally temperature tolerant, they may be potential biofertilizer candidates for global warming scenarios.

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International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016

Cited by 28 publications

References 89 publications

Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae

Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae

Biodiversity of cultivable Burkholderia species in Argentinean soils under no-till agricultural practices

Diversity of Bradyrhizobia in Subsahara Africa: A Rich Resource

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