ARS | Publication request: Application of Multilocus Sequence Typing To Study the Genetic Structure of Megaplasmids in Medicago-Nodulating Rhizobia

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 31, 2009
Publication Date: February 15, 2010
Citation: Van Berkum, P.B., Elia, P.E., Eardly, B.D. 2010. Application of Multilocus Sequence Typing To Study the Genetic Structure of Megaplasmids in Medicago-Nodulating Rhizobia. Applied and Environmental Microbiology. 76:3967-3977.

Interpretive Summary: Certain crops, referred to a Legumes which include beans, peas, and alfalfa, require bacteria to be associated with their roots in order to take nitrogen from the air for crop growth via a process called nitrogen fixation. Many of these crops originally came from other countries. So the problem is how to find the best bacteria to help these plants grow since the bacteria that evolved with the crops did not necessarily come to the U.S. when the crops were introduced. In this work we wanted to find out how to determine the best combination of crop and bacteria. We looked at DNA of the bacteria associated with alfalfa and found that the alfalfa plant can exert selection pressure on the bacteria to become better at fixing nitrogen. This information helps us find the best bacteria-crop combination to promote growth of alfalfa plants. This information will be valuable to companies who sell these bacteria for crops. Also, evolutionary biologists will find this information useful in their studies to determine how bacteria evolve.

Technical Abstract: A multilocus sequence typing (MLST) analysis was used to examine the relatedness and distribution of genotypic variants of the two large extrachromosomal replicons in Medicago-nodulating rhizobia (Sinorhizobium meliloti and S. medicae). One goal was to develop a strategy for the characterization of these replicons through the use of a combination of partial- and full-length gene sequences in over 200 strains of S. meliloti. A second goal was to assess the extent of recombination in these replicons. The diversity of these replicons was high, as was evident by the presence of 161 and 177 allelic profiles or Sequence types (STs) for pSymA and pSymB, respectively. Strong localized linkage disequilibrium was revealed between certain pSymA loci, e.g., nodC and nifD. Although the cause of the LD was uncertain, it could be explained by either the proximity of these loci on the pSymA replicon or host selection for epistatic fitness. On a finer scale, it appeared that certain nodC alleles have a history of intragenic recombination, with smaller recombinant fragments nested within larger clonal segments. This arrangement is consistent with the clonal frames model proposed by Milkman and Bridges (1990, Genetics 126:505-517).