Phylogeny of the Rhizobium–Allorhizobium–Agrobacterium clade supports the delineation of Neorhizobium gen. nov.

Mousavi, Seyed Abdollah; Österman, Janina; Wahlberg, Niklas; Nesme, Xavier; Lavire, Céline; Vial, Ludovic; Paulín, Lars; Lajudie, Philippe de; Lindström, Kristina

doi:10.1016/j.syapm.2013.12.007

Cited by 196 publications

(98 citation statements)

References 39 publications

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“…Interestingly, the theoretical RPs spectrum of R. giardinii bv. giardinii H152 T appeared to be more similar to those of Ensifer than Rhizobium strains, a finding consistent with the unclear phylogenetic position of H152 T reported previously (Laguerre et al 2001;Mousavi et al 2014;Ormeño-Orrillo et al 2015). Closely related strains, such as the Ensifer medicae (#45 to 50) and Ensifer meliloti (#51 to 60) isolates, formed two compact clusters clearly separated from other Ensifer members by Ensifer arboris (#41) (see also Supplementary Fig.…”

Section: Using Deduced Ribosomal Proteins As Markers For Maldi-tof Mssupporting

confidence: 88%

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Ziegler

Pothier

Ardley

et al. 2015

Appl Microbiol Biotechnol

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Accurate identification of soil bacteria that form nitrogen-fixing associations with legume crops is challenging given the phylogenetic diversity of root nodule bacteria (RNB). The labor-intensive and time-consuming 16S ribosomal RNA (rRNA) sequencing and/or multilocus sequence analysis (MLSA) of conserved genes so far remain the favored molecular tools to characterize symbiotic bacteria. With the development of mass spectrometry (MS) as an alternative method to rapidly identify bacterial isolates, we recently showed that matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) can accurately characterize RNB found inside plant nodules or grown in cultures. Here, we report on the development of a MALDI-TOF RNB-specific spectral database built on whole cell MS fingerprints of 116 strains representing the major rhizobial genera. In addition to this RNB-specific module, which was successfully tested on unknown field isolates, a subset of 13 ribosomal proteins extracted from genome data was found to be sufficient for the reliable identification of nodule isolates to rhizobial species as shown in the putatively ascribed ribosomal protein masses (PARPM) database. These results reveal that data gathered from genome sequences can be used to expand spectral libraries to aid the accurate identification of bacterial species by MALDI-TOF MS.

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Section: Using Deduced Ribosomal Proteins As Markers For Maldi-tof Mssupporting

confidence: 88%

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Ziegler

Pothier

Ardley

et al. 2015

Appl Microbiol Biotechnol

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“…We recently showed that Agrobacterium fabrum, a species of the Agrobacterium tumefaciens species complex (20)(21)(22), has several species-specific regions in the genome, including the SpG8-1b region containing 15 different genes named atu1409 to atu1423. This region confers on A. fabrum the ability to degrade FA, since a mutant with the region deleted was no longer able to degrade the compound (23).…”

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confidence: 99%

Analysis of Hydroxycinnamic Acid Degradation in Agrobacterium fabrum Reveals a Coenzyme A-Dependent, Beta-Oxidative Deacetylation Pathway

Campillo

Renoud

Kerzaon

et al. 2014

Appl Environ Microbiol

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gThe soil-and rhizosphere-inhabiting bacterium Agrobacterium fabrum (genomospecies G8 of the Agrobacterium tumefaciens species complex) is known to have species-specific genes involved in ferulic acid degradation. Here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme A (feruloyl-CoA), 4-hydroxy-3-methoxyphenyl-␤-hydroxypropionyl-CoA, 4-hydroxy-3-methoxyphenyl-␤-ketopropionyl-CoA, vanillic acid, and protocatechuic acid. The genes atu1416, atu1417, and atu1420 have been experimentally shown to be necessary for the degradation of ferulic acid. Moreover, the genes atu1415 and atu1421 have been experimentally demonstrated to be essential for this degradation and are proposed to encode a phenylhydroxypropionyl-CoA dehydrogenase and a 4-hydroxy-3-methoxyphenyl-␤-ketopropionic acid (HMPKP)-CoA ␤-keto-thiolase, respectively. We thus demonstrated that the A. fabrum hydroxycinnamic degradation pathway is an original coenzyme A-dependent ␤-oxidative deacetylation that could also transform p-coumaric and caffeic acids. Finally, we showed that this pathway enables the metabolism of toxic compounds from plants and their use for growth, likely providing the species an ecological advantage in hydroxycinnamic-rich environments, such as plant roots or decaying plant materials.

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“…Furthermore, Fig. 1 also shows that strain PC004 T is separated from a recently established genus, Neorhizobium (Mousavi et al, 2014). Therefore, we propose that strain PC004 T is the member of the genus Rhizobium.…”

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confidence: 60%

Rhizobium puerariae sp. nov., an endophytic bacterium from the root nodules of the medicinal plant Pueraria candollei var. candollei

Boonsnongcheep

Prathanturarug

Takahashi

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan A Gram-stain-negative, rod-shaped, motile bacterium, PC004 T , was isolated from root nodules of the Thai medicinal plant Pueraria candollei var. candollei. 16S rRNA gene sequence analysis indicated that the strain is phylogenetically related to species in the genus Rhizobium, showing highest similarity (96.6 %) with Rhizobium mesosinicum HAMBI 3194 T . The phylogenetic tree reconstructed based on 16S rRNA gene sequences showed that strain PC004 T forms a cluster with Rhizobium petrolearium KCTC 23288 T . Based on atpD, gyrB and recA gene sequences, strain PC004 T also showed low similarity (,90 %) to reference strains. These phylogenetic data indicate that PC004 T may represent a novel species. Strain PC004 T also exhibited low DNA-DNA relatedness with R. mesosinicum HAMBI 3194 T (8.2 %) and R. petrolearium KCTC 23288 T (26.3 %). The DNA G+C content of strain PC004 T was 64 mol%, which is within the range reported for the genus Rhizobium. The major fatty acid of PC004 T was C 18 : 1 v7c with minor amounts of C 16 : 0 , C 16 : 0 3-OH, C 18 : 0 3-OH, C 18 : 1 2-OH, C 19 : 0 cyclo v8c and summed feature 2. The strain was able to grow at pH 12 and with up to 2 % (w/v) NaCl. Strain PC004 T did not nodulate five tested legumes and the nifH and nodC genes were not detected by PCR. Based on the physiological, chemotaxonomic and phenotypic data from this study, strain PC004 T represents a novel species of the genus Rhizobium, for which the name Rhizobium puerariae sp. nov. is proposed; the type strain is PC004 T (5BCC 73740 T 5NBRC 110722 T ).

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Phylogeny of the Rhizobium–Allorhizobium–Agrobacterium clade supports the delineation of Neorhizobium gen. nov.

Cited by 196 publications

References 39 publications

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

Analysis of Hydroxycinnamic Acid Degradation in Agrobacterium fabrum Reveals a Coenzyme A-Dependent, Beta-Oxidative Deacetylation Pathway

Rhizobium puerariae sp. nov., an endophytic bacterium from the root nodules of the medicinal plant Pueraria candollei var. candollei

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