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Rhizobium sophorae, Rhizobium laguerreae, and two novel Rhizobium genospecies associated with Vicia sativa L. in Northwest China

Aims To identify the rhizobia nodulating Vicia sativa in Northwestern China and to estimate their geographic distribution. Methods Rhizobia trapped with V. sativa plants from soils at six sites in the northwest of China were classified into genotypes by PCR-based restriction fragment length polymorp... Full description

Journal Title: Plant and soil 2019-06-26, Vol.442 (1-2), p.113-126
Main Author: Zhang, Junjie
Other Authors: Shang, Yimin , Peng, Shanshan , Chen, Wenfeng , Wang, Entao , de Lajudie, Philippe , Li, Benyin , Guo, Chen , Liu, Chunzeng
Format: Electronic Article Electronic Article
Language: English
Subjects:
RNA
Publisher: Cham: Springer International Publishing
ID: ISSN: 0032-079X
Link: https://hal.inrae.fr/hal-02619697
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recordid: cdi_hal_primary_oai_HAL_hal_02619697v1
title: Rhizobium sophorae, Rhizobium laguerreae, and two novel Rhizobium genospecies associated with Vicia sativa L. in Northwest China
format: Article
creator:
  • Zhang, Junjie
  • Shang, Yimin
  • Peng, Shanshan
  • Chen, Wenfeng
  • Wang, Entao
  • de Lajudie, Philippe
  • Li, Benyin
  • Guo, Chen
  • Liu, Chunzeng
subjects:
  • Agricultural sciences
  • Biomedical and Life Sciences
  • Cluster analysis
  • Correlation analysis
  • Ecology
  • Gene polymorphism
  • Genes
  • Genotypes
  • Geographical distribution
  • Life Sciences
  • Marine resources conservation
  • Phylogenetics
  • Phylogeny
  • Plant Physiology
  • Plant Sciences
  • Polymorphism
  • RecA protein
  • Regular Article
  • Restriction fragment length polymorphism
  • Rhizobium laguerreae
  • RNA
  • rRNA 16S
  • rRNA 23S
  • Salinity
  • Soil acidity
  • Soil chemistry
  • Soil pH
  • Soil Science & Conservation
  • Soils
  • Spacer
  • Strains (organisms)
  • Vegetal Biology
  • Vicia sativa
ispartof: Plant and soil, 2019-06-26, Vol.442 (1-2), p.113-126
description: Aims To identify the rhizobia nodulating Vicia sativa in Northwestern China and to estimate their geographic distribution. Methods Rhizobia trapped with V. sativa plants from soils at six sites in the northwest of China were classified into genotypes by PCR-based restriction fragment length polymorphism (RFLP) of 16S–23S rRNA intergenic spacer (IGS) and 16S rRNA genes, and phylogenetic analyses of housekeeping (16S rRNA, recA , atpD ) and symbiotic genes were performed for the representative strains. Soil physicochemical characteristics were recorded and canonical correlation analysis was performed to examine the correlations between soil features and distribution of rhizobial genotypes. Results A total of 202 rhizobial isolates were discriminated by RFLP analyses into 15 IGS types and a single 16S rRNA type, which were identified as Rhizobium by 16S rRNA gene phylogeny and as four clusters by multilocus sequence analysis (MLSA). Cluster 1 covering 86 strains and 7 IGS types prevalent in all sites was identified as Rhizobium laguerreae ; cluster 2 was R. sophorae with 18 strains in 2 IGS types found in the site Q-GD. Each of cluster 3 and cluster 4 contained three IGS types representing two novel Rhizobium genospecies specific to Gansu Province and Shanxi Province, respectively. Four nodC phylogenetic clades were defined among the isolates. Conclusions R. sophorae , R. laguerreae , and two novel Rhizobium genospecies with diverse symbiotic genotypes are associated with Vicia sativa L. in Northwest China. Their biogeographic patterns are mainly directed by soil pH and salinity. This is the first study on the diversity of rhizobia nodulating Vicia sativa in China.
language: eng
source:
identifier: ISSN: 0032-079X
fulltext: no_fulltext
issn:
  • 0032-079X
  • 1573-5036
url: Link


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titleRhizobium sophorae, Rhizobium laguerreae, and two novel Rhizobium genospecies associated with Vicia sativa L. in Northwest China
creatorZhang, Junjie ; Shang, Yimin ; Peng, Shanshan ; Chen, Wenfeng ; Wang, Entao ; de Lajudie, Philippe ; Li, Benyin ; Guo, Chen ; Liu, Chunzeng
creatorcontribZhang, Junjie ; Shang, Yimin ; Peng, Shanshan ; Chen, Wenfeng ; Wang, Entao ; de Lajudie, Philippe ; Li, Benyin ; Guo, Chen ; Liu, Chunzeng
descriptionAims To identify the rhizobia nodulating Vicia sativa in Northwestern China and to estimate their geographic distribution. Methods Rhizobia trapped with V. sativa plants from soils at six sites in the northwest of China were classified into genotypes by PCR-based restriction fragment length polymorphism (RFLP) of 16S–23S rRNA intergenic spacer (IGS) and 16S rRNA genes, and phylogenetic analyses of housekeeping (16S rRNA, recA , atpD ) and symbiotic genes were performed for the representative strains. Soil physicochemical characteristics were recorded and canonical correlation analysis was performed to examine the correlations between soil features and distribution of rhizobial genotypes. Results A total of 202 rhizobial isolates were discriminated by RFLP analyses into 15 IGS types and a single 16S rRNA type, which were identified as Rhizobium by 16S rRNA gene phylogeny and as four clusters by multilocus sequence analysis (MLSA). Cluster 1 covering 86 strains and 7 IGS types prevalent in all sites was identified as Rhizobium laguerreae ; cluster 2 was R. sophorae with 18 strains in 2 IGS types found in the site Q-GD. Each of cluster 3 and cluster 4 contained three IGS types representing two novel Rhizobium genospecies specific to Gansu Province and Shanxi Province, respectively. Four nodC phylogenetic clades were defined among the isolates. Conclusions R. sophorae , R. laguerreae , and two novel Rhizobium genospecies with diverse symbiotic genotypes are associated with Vicia sativa L. in Northwest China. Their biogeographic patterns are mainly directed by soil pH and salinity. This is the first study on the diversity of rhizobia nodulating Vicia sativa in China.
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subjectAgricultural sciences ; Biomedical and Life Sciences ; Cluster analysis ; Correlation analysis ; Ecology ; Gene polymorphism ; Genes ; Genotypes ; Geographical distribution ; Life Sciences ; Marine resources conservation ; Phylogenetics ; Phylogeny ; Plant Physiology ; Plant Sciences ; Polymorphism ; RecA protein ; Regular Article ; Restriction fragment length polymorphism ; Rhizobium laguerreae ; RNA ; rRNA 16S ; rRNA 23S ; Salinity ; Soil acidity ; Soil chemistry ; Soil pH ; Soil Science & Conservation ; Soils ; Spacer ; Strains (organisms) ; Vegetal Biology ; Vicia sativa
ispartofPlant and soil, 2019-06-26, Vol.442 (1-2), p.113-126
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descriptionAims To identify the rhizobia nodulating Vicia sativa in Northwestern China and to estimate their geographic distribution. Methods Rhizobia trapped with V. sativa plants from soils at six sites in the northwest of China were classified into genotypes by PCR-based restriction fragment length polymorphism (RFLP) of 16S–23S rRNA intergenic spacer (IGS) and 16S rRNA genes, and phylogenetic analyses of housekeeping (16S rRNA, recA , atpD ) and symbiotic genes were performed for the representative strains. Soil physicochemical characteristics were recorded and canonical correlation analysis was performed to examine the correlations between soil features and distribution of rhizobial genotypes. Results A total of 202 rhizobial isolates were discriminated by RFLP analyses into 15 IGS types and a single 16S rRNA type, which were identified as Rhizobium by 16S rRNA gene phylogeny and as four clusters by multilocus sequence analysis (MLSA). Cluster 1 covering 86 strains and 7 IGS types prevalent in all sites was identified as Rhizobium laguerreae ; cluster 2 was R. sophorae with 18 strains in 2 IGS types found in the site Q-GD. Each of cluster 3 and cluster 4 contained three IGS types representing two novel Rhizobium genospecies specific to Gansu Province and Shanxi Province, respectively. Four nodC phylogenetic clades were defined among the isolates. Conclusions R. sophorae , R. laguerreae , and two novel Rhizobium genospecies with diverse symbiotic genotypes are associated with Vicia sativa L. in Northwest China. Their biogeographic patterns are mainly directed by soil pH and salinity. This is the first study on the diversity of rhizobia nodulating Vicia sativa in China.
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authorZhang, Junjie ; Shang, Yimin ; Peng, Shanshan ; Chen, Wenfeng ; Wang, Entao ; de Lajudie, Philippe ; Li, Benyin ; Guo, Chen ; Liu, Chunzeng
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atitleRhizobium sophorae, Rhizobium laguerreae, and two novel Rhizobium genospecies associated with Vicia sativa L. in Northwest China
jtitlePlant and soil
stitlePlant Soil
date2019-06-26
risdate2019
volume442
issue1-2
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issn0032-079X
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abstractAims To identify the rhizobia nodulating Vicia sativa in Northwestern China and to estimate their geographic distribution. Methods Rhizobia trapped with V. sativa plants from soils at six sites in the northwest of China were classified into genotypes by PCR-based restriction fragment length polymorphism (RFLP) of 16S–23S rRNA intergenic spacer (IGS) and 16S rRNA genes, and phylogenetic analyses of housekeeping (16S rRNA, recA , atpD ) and symbiotic genes were performed for the representative strains. Soil physicochemical characteristics were recorded and canonical correlation analysis was performed to examine the correlations between soil features and distribution of rhizobial genotypes. Results A total of 202 rhizobial isolates were discriminated by RFLP analyses into 15 IGS types and a single 16S rRNA type, which were identified as Rhizobium by 16S rRNA gene phylogeny and as four clusters by multilocus sequence analysis (MLSA). Cluster 1 covering 86 strains and 7 IGS types prevalent in all sites was identified as Rhizobium laguerreae ; cluster 2 was R. sophorae with 18 strains in 2 IGS types found in the site Q-GD. Each of cluster 3 and cluster 4 contained three IGS types representing two novel Rhizobium genospecies specific to Gansu Province and Shanxi Province, respectively. Four nodC phylogenetic clades were defined among the isolates. Conclusions R. sophorae , R. laguerreae , and two novel Rhizobium genospecies with diverse symbiotic genotypes are associated with Vicia sativa L. in Northwest China. Their biogeographic patterns are mainly directed by soil pH and salinity. This is the first study on the diversity of rhizobia nodulating Vicia sativa in China.
copCham
pubSpringer International Publishing
doi10.1007/s11104-019-04168-w