Development and application of a multilocus sequence analysis method for the identification of genotypes within genus Bradyrhizobium and for establishing nodule occupancy of soybean (Glycine max L. Merr)

Authors: Van Berkum, Peter; Elia, Patrick; Song, Qijian; EARDLY, BERTRAND - Pennsylvania State University

Submitted to: Molecular Plant-Microbe Interactions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2011
Publication Date: 3/15/2012
Citation: Van Berkum, P.B., Elia, P.E., Song, Q., Eardly, B. 2012. Development and application of a multilocus sequence analysis method for the identification of genotypes within genus Bradyrhizobium and for establishing nodule occupancy of soybean (Glycine max L. Merr). Molecular Plant-Microbe Interactions. 25(3):321-330.

Interpretive Summary: Certain crops called legumes, important to North American agriculture, require bacteria to be associated with their root systems in order to produce nitrogen for growth and production. One of these crops is soybean that originally came from the Far East. So the problem is how to find the best bacteria to help soybeans grow since the bacteria that evolved with this crop did not necessarily come to North America when the plants were brought here. In this work we wanted to find out if we could measure differences in the genes of the bacteria to tell them apart and then develop a database for their future recognition. To develop the technique, we first used bacterial cultures that were obtained long ago and that are kept in a collection. Then we obtained cultures from plants other than soybean to determine if they were very different or very similar to the bacteria of soybean. Finally, we examined the structures on the roots of plants called nodules where the bacteria live with the soybean plant. To be able to do examine the bacteria in the nodule we developed a method to extract the DNA of the bacteria directly from the plant tissue. We found that the soybean bacteria varied, but differences in most cases were not associated with the legume plant species of origin. In a few cases the variation we found was related to the geogrophic origin of the bacteria. From the database we can choose different bacteria to measure how well they provide the soybean plant with nitrogen. Also, we shall be able in the future to measure factors affecting the bacteria such as the variety of the crop that is grown. This information will be valuable to companies who sell these bacteria for crops. Also, geneticists will find this information useful in their studies to determine how these bacteria can change the growth of crop plants.

Technical Abstract: A Multilocus Sequence Typing (MLST) method based on allelic variation of 7 chromosomal loci was developed for characterizing genotypes within the genus Bradyrhizobium. With the method 29 distinct multilocus genotypes (GTs) were identified among 191 culture collection soybean strains. The occupancy of 347 nodules taken from uninoculated field-grown soybean plants also was determined. The bacteroid genotypes were either the same or were closely related to genotypes identified among strains in the culture collection. Double nodule occupancy estimates of 2.9% were much lower than values published based on serology. Of the 347 nodules examined, 337 and 10 were occupied by B. japonicum and B. elkanii, respectively. The collection strains within the species B. japonicum and B. elkanii also were compared with Bradyrhizobium cultures from other legumes. In many cases the observed genotypes were more strongly influenced by their geographic origin than by their trap hosts of isolation. In other cases there were no apparent relationships with either the legume or geographic source. The MLST method that was developed should be a useful tool in determining the influence of geographic location, temperature, season, soil type, and host plant cultivar on the distribution of genotypes of Bradyrhizobium.