The biodiversity of beneficial microbe-host mutualism: the case of rhizobia

Lindström, Kristina; Murwira, Mazvita; Willems, Anne; Altier, Nora

doi:10.1016/j.resmic.2010.05.005

Cited by 125 publications

(92 citation statements)

References 78 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). Identification of RNB to strain level offers the possibility of using MALDI-TOF MS in diagnostic tests, for example, in ecological studies to test the ability of inoculant strains to compete with naturalized soil populations of rhizobia (Denton et al 2002).…”

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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“…The occurrence of a wide variety of strains increases the chance for a legume host to find a compatible rhizobium in any soil. All the commercial strains originate in indigenous rhizobial pools which represent an important resource to isolate and characterize new local rhizobial strains that could lead to the improvement of commercial strains [11].…”

Section: Discussionmentioning

confidence: 99%

“…Castro-Sowinski et al [1] reported that there are millions of hectares of crops inoculated with a variety of rhizobial strains in South America. The inoculants are comprised of commercial strains, which are not adapted to local pedo-climatic conditions compared with indigenous rhizobial strains [11]. The isolation and characterization of native rhizobia could lead to improvement in the manufacture of commercial inoculants and crop production.…”

Section: Introductionmentioning

confidence: 99%

RAPD-inferred genetic variability of some indigenousRhizobium leguminosarumisolates from red clover (Trifolium pratenseL.) nodules

Stefan

Roșu

Stedel

et al. 2015

Acta Biologica Hungarica

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The application of commercial rhizobial inoculants to legume crops is proving to be an alternative to synthetic fertilizer use. The challenge for sustainable agriculture resides in the compatibility between crop, inoculants and environmental conditions. The evaluation of symbiotic efficiency and genetic diversity of indigenous rhizobial strains could lead to the development of better inoculants and increased crop production. The genetic variability of 32 wild indigenous rhizobial isolates was assessed by RAPD (Random Amplified Polymorphic DNA). The strains were isolated from red clover (Trifolium pratense L.) nodules from two distinct geographical regions of Northern and Eastern Romania. Three decamer primers were used to resolve the phylogenetic relationships between the investigated isolates. Cluster analysis revealed a high diversity; most strains clustered together based on their geographical location.

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“…It is important to clarify that this classification is based on taxonomically important strains that may not necessarily be important reference strains for legume growth improvement. Rhizobial strains commonly used in inoculants have good field performance and stability of symbiotic properties in culture, but are not necessarily well documented or used in taxonomy or molecular biology studies (Lindström et al, 2010). The legumerhizobia association is specific (each rhizobial strain establishes a symbiosis with only a limited set of host plants and vice versa).…”

Section: Rhizobia: the Master Microbementioning

confidence: 99%

Legume Crops, Importance and Use of Bacterial Inoculation to Increase Production

Morel¹,

Braña²,

Castro‐Sowinski³

2012

Crop Plant

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The biodiversity of beneficial microbe-host mutualism: the case of rhizobia

Cited by 125 publications

References 78 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

RAPD-inferred genetic variability of some indigenousRhizobium leguminosarumisolates from red clover (Trifolium pratenseL.) nodules

Legume Crops, Importance and Use of Bacterial Inoculation to Increase Production

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