Distribution and diversity of rhizobia associated with wild soybean (Glycine soja Sieb. &amp; Zucc.) in Northwest China

Zhao, Liang; Fan, Miaochun; Zou, Dehui; Yang, Ruiping; Zhang, Feilong; Xu, Lin; Wei, Xiuli; Shen, Yali; Wei, Gehong

doi:10.1016/j.syapm.2014.05.011

Cited by 31 publications

(24 citation statements)

References 49 publications

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“…This makes MALDI-TOF MS and the rhizobia-specific module an ideal replacement for the demanding and expensive sequencing of partial 16S rRNA or AFLP/RFLP analyses that have been performed to identify and determine the diversity of microsymbionts of wild legumes in recent large-scale studies (Aserse et al 2013;Safronova et al 2014;Yang et al 2013;Zhao et al 2014). In the economically important field of symbiotic nitrogen fixation in agricultural systems, knowledge of the biodiversity of rhizobia and of local populations is important for the design of successful inoculation strategies (Lindström et al 2010).…”

Section: Discussionmentioning

confidence: 99%

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: Discussionmentioning

confidence: 99%

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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“…; Zhao et al . ). Alfalfa plants mainly nodulate with Ensifer meliloti strains with very similar nodulation genes in different geographical regions and soil types (van Berkum et al .…”

Section: Introductionmentioning

confidence: 97%

“…Previous studies of the interactions between plant roots and microbial communities in the rhizosphere have found that nodule-forming legumes are different from other plants due to their symbiosis with diverse bacteria (rhizobia) in Alphaproteobacteria and Betaproteobacteria (Weir 2016). Specific associations between legume species and rhizobial species are determined by symbiotic genes on both sides but are also regulated by soil conditions (Mendes et al 2014;Yan et al 2014;Zhao et al 2014;Saini et al 2015). Depending on the soil conditions, soya bean plants can nodulate with various species in the genera Bradyrhizobium, Ensifer and Rhizobium, in which certain lineages of nodulation genes have been defined (Wu et al 2011;Yan et al 2014;Zhao et al 2014).…”

Section: Introductionmentioning

confidence: 99%

“…Specific associations between legume species and rhizobial species are determined by symbiotic genes on both sides but are also regulated by soil conditions (Mendes et al 2014;Yan et al 2014;Zhao et al 2014;Saini et al 2015). Depending on the soil conditions, soya bean plants can nodulate with various species in the genera Bradyrhizobium, Ensifer and Rhizobium, in which certain lineages of nodulation genes have been defined (Wu et al 2011;Yan et al 2014;Zhao et al 2014). Alfalfa plants mainly nodulate with Ensifer meliloti strains with very similar nodulation genes in different geographical regions and soil types (van Berkum et al 2006(van Berkum et al , 2010Alias-Villegas et al 2015).…”

Section: Introductionmentioning

confidence: 99%

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Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments

et al. 2017

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The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soya bean and alfalfa were analysed using high-throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments - the nodule endosphere, root endosphere, rhizosphere and root zone - as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged to Ensifer for alfalfa and Ensifer-Bradyrhizobium for soya bean. The nonsymbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.

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“…Phytopathogenic strains may cause crown gall disease which is mainly determined by the presence of tumor-inducing (Ti) plasmid in their genome, while strains harboring root-inducing (Ri) plasmid are the causal agents of hairy root disease [8,24]. It is recently reported that Agrobacterium strains may carry symbiotic (Sym) plasmid and have nodulating activity on legume plants [7,41]. They have been also identified as an opportunistic human pathogens responsible for nosocomial infections [2] and are widely used in biotechnology to produce genetically modified plants [36].…”

mentioning

confidence: 99%

Agrobacterium arsenijevicii sp. nov., isolated from crown gall tumors on raspberry and cherry plum

Kuzmanović

Puławska

Prokić

et al. 2015

Systematic and Applied Microbiology

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Distribution and diversity of rhizobia associated with wild soybean (Glycine soja Sieb. & Zucc.) in Northwest China

Cited by 31 publications

References 49 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

Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments

Agrobacterium arsenijevicii sp. nov., isolated from crown gall tumors on raspberry and cherry plum

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