Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations

Mousavi, Seyed Abdollah; Willems, Anne; Nesme, Xavier; Lajudie, Philippe de; Lindström, Kristina

doi:10.1016/j.syapm.2014.12.003

Cited by 228 publications

(115 citation statements)

References 44 publications

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“…It was proposed to retain the genus Agrobacterium to accommodate predominantly phytopathogenic species. This recommendation was supported by multilocus sequence analysis of plant-associated members of the Rhizobiaceae (Mousavi et al, 2014(Mousavi et al, , 2015 and the analysis of wholegenome averaged nucleotide identity of the family members that have been sequenced thus far (Ormeno-Orrillo et al, 2015). Furthermore, Mousavi et al (2014Mousavi et al ( , 2015 proposed reclassifying several Rhizobium species in the novel genera Pararhizobium and Neorhizobium and the revived genus Allorhizobium.…”

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confidence: 97%

“…This recommendation was supported by multilocus sequence analysis of plant-associated members of the Rhizobiaceae (Mousavi et al, 2014(Mousavi et al, , 2015 and the analysis of wholegenome averaged nucleotide identity of the family members that have been sequenced thus far (Ormeno-Orrillo et al, 2015). Furthermore, Mousavi et al (2014Mousavi et al ( , 2015 proposed reclassifying several Rhizobium species in the novel genera Pararhizobium and Neorhizobium and the revived genus Allorhizobium. Based on this approach, further strains currently ascribed to the genus Rhizobium were identified that may represent as yet undescribed genera within the family Rhizobiaceae (Mousavi et al, 2015;Ormeno-Orrillo et al, 2015), and therefore further splitting of the genus can be expected that is not reflected in the 16S rRNA gene phylogeny.…”

mentioning

confidence: 97%

“…Furthermore, Mousavi et al (2014Mousavi et al ( , 2015 proposed reclassifying several Rhizobium species in the novel genera Pararhizobium and Neorhizobium and the revived genus Allorhizobium. Based on this approach, further strains currently ascribed to the genus Rhizobium were identified that may represent as yet undescribed genera within the family Rhizobiaceae (Mousavi et al, 2015;Ormeno-Orrillo et al, 2015), and therefore further splitting of the genus can be expected that is not reflected in the 16S rRNA gene phylogeny. Furthermore, this splitting based on genomic data is mostly unsupported by phenotypic differences that allow the differentiation of these genera on the basis of significant physiological or chemotaxonomic features.…”

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confidence: 99%

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Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.

Behrendt

Kämpfer

Glaeser

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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In the context of studying the bacterial community involved in nitrogen transformation processes in arable soils exposed to different extents of erosion and sedimentation in a long-term experiment (CarboZALF), a strain was isolated that reduced nitrate to nitrous oxide without formation of molecular nitrogen. The presence of the functional gene nirK, encoding the respiratory copper-containing nitrite reductase, and the absence of the nitrous oxide reductase gene nosZ indicated a truncated denitrification pathway and that this bacterium may contribute significantly to the formation of the important greenhouse gas N 2 O. Phylogenetic analysis based on the 16S rRNA gene sequence and the housekeeping genes recA and atpD demonstrated that the investigated soil isolate belongs to the genus Rhizobium. The closest phylogenetic neighbours were the type strains of Rhizobium. subbaraonis and Rhizobium. halophytocola. The close relationship with R. subbaraonis was reflected by similarity analysis of the recA and atpD genes and their amino acid positions. DNA-DNA hybridization studies revealed genetic differences at the species level, which were substantiated by analysis of the whole-cell fatty acid profile and several distinct physiological characteristics. Based on these results, it was concluded that the soil isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium azooxidifex sp. nov. proposed.

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confidence: 97%

mentioning

confidence: 97%

mentioning

confidence: 99%

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Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.

Behrendt

Kämpfer

Glaeser

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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“…Allorhizobium, Neorhizobium, Rhizobium and Pararhizobium has been suggested recently (Mousavi et al, 2014(Mousavi et al, , 2015.…”

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confidence: 99%

“…anhuiense' CCBAU 23252 (99.7 %), followed by R. leguminosarum USDA 2370 T (98.6 %), R. sophorae CCBAU 03386 T , R. phaseoli ATCC 14482 T , R. fabae CCBAU 33202 T and R. pisi DSM 30132 T (98.3 %), R. laguerreae FB206 T (97.8 %) and R. etli CFN 42 T (97.7 %) ( Table 1). All of these species are members of the recently revised genus Rhizobium (Mousavi et al, 2014(Mousavi et al, , 2015. Taking the threshold of 97 % similarity for species delineation (Graham et al, 1991), all these species were closely related rhizobia and 16S rRNA gene sequence analysis was unable to differentiate them clearly.…”

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confidence: 99%

Rhizobium acidisoli sp. nov., isolated from root nodules of Phaseolus vulgaris in acid soils

Román‐Ponce

Zhang

Vásquez-Murrieta

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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Two Gram-negative, aerobic, non-motile, rod-shaped bacterial strains, FH13 T and FH23, representing a novel group of Rhizobium isolated from root nodules of Phaseolus vulgaris in Mexico, were studied by a polyphasic analysis. Phylogeny of 16S rRNA gene sequences revealed them to be members of the genus Rhizobium related most closely to 'Rhizobium anhuiense' CCBAU 23252 (99.7 % similarity), Rhizobium leguminosarum USDA 2370 T (98.6 %), and Rhizobium sophorae CCBAU 03386 T and others (j98.3 %). In sequence analyses of the housekeeping genes recA, glnII and atpD, both strains formed a subclade distinct from all defined species of the genus Rhizobium at sequence similarities of 82.3-94.0 %, demonstrating that they represented a novel genomic species in the genus Rhizobium. Mean levels of DNA-DNA relatedness between the reference strain FH13 T and the type strains of related species varied between 13.0¡2.0 and 52.1¡1.2 %. The DNA G+C content of strain FH13 T was 63.5 mol% (T m ). The major cellular fatty acids were 16 : 0, 17 : 0 anteiso, 18 : 0, summed feature 2 (12 : 0 aldehyde/unknown 10.928) and summed feature 8 (18 : 1v7c). The fatty acid 17 : 1v5c was unique for this strain. Some phenotypic features, such as failure to utilize adonitol, L-arabinose, D-fructose and D-fucose, and ability to utilize D-galacturonic acid and itaconic acid as carbon source, could also be used to distinguish strain FH13 T from the type strains of related species. Based upon these results, a novel species, Rhizobium acidisoli sp. nov., is proposed, with FH13 T (5CCBAU 101094 T 5HAMBI 3626 T 5LMG 28672 T ) as the type strain.

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Nitrogen Fixation

Newton

2015

Kirk-Othmer Encyclopedia of Chemical Technology

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About 80% of the Earth's atmosphere is made up of nitrogen gas (N 2 ), but nitrogen is most often the limiting nutrient for agricultural productivity, because neither plants nor animals can use it directly. It must first be fixed into either ammonium or nitrate. Only the simplest life forms, bacteria and archaea, can produce ammonium from N 2 using the enzyme called nitrogenase. N 2 is also fixed by nonbiological processes, which contribute equally to the total annual fixation rate. In fact, without commercial fertilizers, the human population could not be supported. This article first describes the major industrial processes and their shortcomings, emphasizing the dominant Haber‐Bosch process. Then, an overview of the various biological nitrogen‐fixing systems, both free‐living and symbiotic organisms, focusing on the agriculturally important legume– Rhizobium symbiosis is provided. Nitrogenase is detailed and analyzed next with sections on its evolution, biosynthesis, composition and structure, regulation, and catalytic mechanism, the last of which is now beginning to be understood in some detail. The penultimate section describes attempts to duplicate either the reactivity or the structure of nitrogenase in chemical systems, some of which have achieved limited catalytic capability. Finally, the last section attempts to highlight both the important strides made and the problems that remain. These include limiting losses of applied fertilizer to ground water and atmosphere; careful matching of inoculant with cultivar; reducing fossil fuel energy inputs to fertilizer production; manipulating plant colonization and symbiosis development to produce new pairings; and simplifying the biological process for transfer to other organisms.

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Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations

Cited by 228 publications

References 44 publications

Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.

Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.

Rhizobium acidisoli sp. nov., isolated from root nodules of Phaseolus vulgaris in acid soils

Nitrogen Fixation

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