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Location: Sustainable Agricultural Systems Laboratory

Title: Genetic diversity of resident soil rhizobia isolated from nodules of distinct hairy vetch genotypes

item Mothapo, Nape
item Maul, Jude
item Shi, Wei
item Isleib, Thomas
item Grossman, Julie

Submitted to: Applied Soil Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2012
Publication Date: 2/1/2013
Citation: Mothapo, N.V., Maul, J.E., Shi, W., Isleib, T., Grossman, J.M. 2013. Genetic diversity of resident soil rhizobia isolated from nodules of distinct hairy vetch genotypes. Applied Soil Ecology. 64:201-213.

Interpretive Summary: One goal of designing sustainable farming systems is to balance the inputs required for profitable production with exports of yield or biomass. By taking a mass balance approach farmers and land managers can reduce the potential for loss of nutrients, which can become pollutants in near-by streams and rivers. A strategy for improving nutrient use efficiency and reducing off farm inputs is to maximize the proportion of nitrogen in the system derived from bacterial symbiosis with legume plants in the cropping rotation. Biological nitrogen fixation is carried out by soil bacteria (rhizobia) that form symbiotic relationships with legume plants and can account for as much as 100% of the nitrogen required by the growing plant. Although biological nitrogen fixation is extremely important to farmers, little is known about the diversity and nitrogen-fixing efficiency of indigenous rhizobia species found in any agricultural soil that has had a history of legume growth. This study used a combination of classic microbiological techniques as well as molecular facilitated “fingerprinting” techniques to assess the diversity and nitrogen fixing efficiency of rhizobia species isolated from plant hosts (Vicia villosa) with known genetic relationships to each other. Knowledge of the hosts relationship to other host in the study allowed us to isolate the host genetic effects on successful infection and symbiosis with the legume. We were able to determine that plant host genetic context accounted for 40% of the composition of the community of rhizobial symbionts isolated from nodule re-capture cultures. We also found that host plants varied in their ability to form symbiosis with a diverse range of potential rhizobia symbionts. This work lays the ground work for determining the genetic factors present in a host that sets limitations for rhizobia in their symbiotic relationships with legumes. This work also suggests that the approach of inoculating a host with a pre-made cocktail of rhizobia may not be as effective as exploiting host controls on rhizobia/legume symbiosis. Results from this study will assist researchers attempting to improve agricultural nitrogen use efficiency and eventually the sustainability and profitability of farming operations throughout the nation.

Technical Abstract: Hairy vetch (Vicia villosa Roth) is widely grown as a legume cover crop throughout the U.S.A., with biological nitrogen fixation (BNF) through symbiosis with Rhizobium leguminosarum biovar viciae (Rlv) being one of the most sought after benefits of its cultivation. This study determined if HV cultivation history and plant genotype have an effect on the genetic diversity of resident Rlv. Soil samples were collected from within farmers’ fields at Graham, Cedar Grove and Ivanhoe sites in North Carolina. Pairs of genetically similar Hairy vetch genotypes were organized into five groups that were genetically dissimilar from each other. Each genotype was used as a trap host, with a total of 519 Rlv strains isolated from soil dilutions of six paired fields, three with and three without histories of HV cultivation. A total of 46 strains failed to PCR-amplify the nifH gene; however nodC PCR amplification of these nifH-negative strains resulted in amplification of 22 of the strains. Repetitive element polymerase chain reaction (rep-PCR) with BOX-A1R primer showed that diversity of rhizobia varied greatly within and between fields. Over 30 BOX banding patterns were obtained across the six fields. Cluster analysis of BOX-PCR banding patterns resulted in 36 genetic groups of Rlv at a similarity level of 70%, with 15 of the isolates from fields with HV history not belonging to any of the clusters. The largest cluster comprised 96 strains, 86 of which were from the Cedar Grove. Rlv tended to group based on site from which they were isolated, and within a site by field history. Hairy vetch genotypes appeared to have a significant effect on diversity of Rlv isolated from nodules but to much less a degree than site and field history. Our results show that HV cultivation history is the most important driver of the structure of the rhizobia nodule community and increases the genetic diversity of resident Rlv in soils, but even among distinct soils and cultivation histories an underlying plant genotype control on nodule occupancy can be observed.