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Title: MULTI-LOCUS SEQUENCE TYPING (MLST), A BASIS FOR THE POPULATION ANALYSIS OF MEDICAGO-NODULATING RHIZOBIA.

Author
item Van Berkum, Peter
item Elia, Patrick
item EARDLY, BERTRAND - PENN STATE

Submitted to: Journal of Bacteriology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2006
Publication Date: 5/25/2006
Citation: Van Berkum, P.B., Elia, P.E., Eardly, B.D. 2006. Multi-locus sequence typing (mlst), a basis for the population analysis of medicago-nodulating rhizobia. Journal of Bacteriology. 188:5570-5577.

Interpretive Summary: Soil bacteria known as rhizobia form a symbiosis with legume crops such as soybean and alfalfa. In symbiosis, these rhizobia extract nitrogen gas from the atmosphere and convert it into a form that the plants use for growth. This results in efficient crop production since growers need not apply fertilizer, which saves money and prevents pollution of the environment. Management of the symbiosis is at sowing by inoculation of the seeds with rhizobia using precise formulations of the bacteria. Precise formulations are used because most strains of rhizobia only have a poor to moderate ability to provide their crop legume with sufficient nitrogen to realize full productivity. In achieving precise formulations the problem is that the collection of rhizobial germplasm and its subsequent evaluation for efficiency has been haphazard because no adequate methods are available to accurately identify rhizobia strains. A method is described that addresses this limitation using rhizobia strains that form symbioses with alfalfa and related plant species. By applying this method, a precise identification of strains is possible. This permits informed decisions to be made in choosing strains for evaluation and for subsequent use in legume incoculation. The method also has application in the management of rhizobial germplasm resource collections and in quality control of inoculants, important to industry and regulatory agencies.

Technical Abstract: MultiLocus Sequence Typing (MLST), a sequence-based method to characterize bacterial genomes, was used to examine the genetic structure in a large collection of Medicago-nodulating rhizobial strains. This is the first study where MLST has been applied in conjunction with e-Burst analysis to determine the population genetic structure of non-pathogenic bacteria recovered from the soil environment. Sequence variation was determined in 10 chromosomal loci of 231 strains that predominantly originated from southwest Asia. Genetic diversity for each locus ranged from 0.351 to 0.819 and the strains examined were allocated to 91 different allelic profiles or sequence types (STs). The genus Medicago is nodulated by at least two highly divergent groups of rhizobia among which the degree of genetic exchange is limited. The potential application of MLST for linking symbiotic phenotype with the allelic profiles of extrachromosomal elements rather than the chromosome was considered.