Genetic diversity of resident soil rhizobia isolated from nodules of distinct hairy vetch (Vicia villosa Roth) genotypes

Abstract

Follow this and additional works at: https://digitalcommons.unl.edu/usdaarsfacpub Mothapo, N.V.; Grossman, J.M.; Maul, J. E.; Shi, W.; and Isleib, T., "Genetic diversity of resident soil rhizobia isolated from nodules of distinct hairy vetch (Vicia villosa Roth) genotypes" (2013). Publications from USDA-ARS / UNL Faculty. 1168. a b s t r a c tHairy vetch (Vicia villosa Roth, HV) 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 affect genetic diversity of resident Rlv. Soil samples were collected from within farmers' fields at Graham, Cedar Grove and Ivanhoe sites in North Carolina and pairs of genetically similar hairy vetch genotypes used as trap hosts. A total of 519 Rlv strains were isolated from six paired field soils, 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 and redundancy analysis showed rhizobial diversity to vary greatly within and between fields, with over 30 BOX banding patterns 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. Site was found to be the main driver of isolate diversity overall, explaining 57%, of the total variation among rhizobia occupying HV nodules, followed by history of hairy vetch cultivation. Evidence of a HV host genotype influence on the populations of rhizobia that infect hairy vetch was also observed, with plant genotype explaining 12.7% of the variation among all isolates. Our results show that second to site, HV cultivation history was the most important driver of rhizobial nodule community structure and increases the genetic diversity of resident Rlv in soils.

Intercropped red beet and radish with green bean affected microbial communities and nodulation by indigenous rhizobia

“…Similarly, in addition to high specificity between hairy vetch and R. leguminosarum biovar viciae, nifH-PCR is used for rhizobia confirmation during investigation of large number of isolates (Mothapo et al 2013). However, two Bacillus isolates from radish rhizosphere yielded several products of unexpected sizes.…”

Drivers of promiscuous soybean associated rhizobia diversity in un-inoculated soil in Malawi

“…In these cases, both types of colonies were selected and cultured separately. All isolated colonies were confirmed as being symbiotic nitrogen fixing rhizobia by amplifying nifH genes as described in Mothapo et al (2013). Colonies that did not test positive for a nifH gene were not included in the analysis.…”

“…The resulting cell suspensions were used as template for PCR reactions. Genomic fingerprinting was conducted using the repetitive extragenic primer BOX A1R (Versalovic et al 1994), in a 25 μl reaction as described by Mothapo et al (2013). Resulting products were visualized after gel electrophoresis in a 25 cm gel containing 3 % agarose and ethidium bromide run for 5 min at 300 V followed by 18 h at 80 V, and imaged using UV light.…”

“…Rhizobia were extracted from soil using the host-plant trap method described previously (Mothapo et al 2013). Briefly, seeds of soybean variety TGx 1740-2F were sterilized by immersing in 3 % NaClO for 4 min and then rinsing 5 times in sterile water.…”

“…The number of nodule-forming isolates usually increases the longer a soil is exposed to a particular host-legume crop (Elkins et al 1976;Mothapo et al 2013;Nkot et al 2008). Additionally, the use of commercial inoculants can lead to an increase in diversity through the introduction of novel strains and genetic material (Loureiro et al 2007).…”