An economically important problem in microbial ecology concerns the efficacy of rhizobial inoculants for the formation of nitrogen-fixing root nodules on legume crop plants such as soybean, alfalfa, and clover. Some strains of rhizobia can increase symbiotic nitrogen fixation under controlled conditions. However, attempts to improve nitrogen fixation under agricultural conditions with such strains often fail, usually as a result of the presence of indigenous rhizobia limiting nodulation by the inoculum strains. This problem is referred to as the Rhizobium competition problem, and molecular genetics is being used to address the problem from two perspectives. First, the host specificity of rhizobia is being characterized with the long term goal of developing strains that can nodulate a very strain-specific host-legume genotype. Second, the genetic basis of competitiveness in several strains is being examined. Genetic determinants of nodulation competitiveness have been isolated and mechanisms for their stable integration into the genome of superior nitrogen-fixing strains have been developed. Several phenotypes have been identified as playing an important role in nodulation competitiveness including antibiosis, motility, speed of nodulation, cell-surface characteristics, and nodulation efficiency. Several solutions to this problem are likely to result from these strategies and will be useful for certain legumes in specific locations.

The genetic diversity among 20 field isolates of Bradyrhizobium japonicum serogroup 123 was examined by using restriction endonuclease digestions, one-dimensional sodium dodecyl sulfate-polyacrylamide gel electro-phQresis of total cell proteins, Southern hybridization analysis of nif and nod genes, and intrinsic antibiotic resistance profiles. All of the isolates were previously separated into three broad nodulation classes (low, medium, and high) based on their ability to form symbioses with specific soybean genotypes. Results of our studies indicate that there is a relationship between these three genotype-specific nodulation classes and groupings that have been made based on genomic DNA digestion patterns, sodium dodecyl sulfate-protein profiles, and Southern hybridizations to a nipHD gene probe. Intrinsic antibiotic resistance profiles and nodAB gene hybridizations were not useful in determining interrelationships between isolates and nodulation classes. Southern hybridizations revealed that two of the isolates had reiterated nod genes; however, there was no correlation between the presence of extra nodAB genes and the nodulation classes or symbiotic performance on permissive soybean genotypes. Hybridizations with the nif gene probe indicated that there is a relationship among serogroup, nodulation class, and the physical organization of the genome.

Fast-growing, acid-producing soybean rhizobia were examined to determine their biochemical relatedness to each other, to typical slow-growing Rhizobium japonicum strains, and to other fast-growing species of Rhizobium. Although both the fast-and slow-growing soybean rhizobia were positive for catalase, urease, oxidase, nitrate reductase, and penicillinase, the fast-growing strains grouped with other fast-growing species of Rhizobium in that they tolerated 2% NaCl, were capable of growth at pH 9.5, utilized a large variety of carbohydrates (notably disaccharides), and produced serum zones in litmus milk. In addition, these fastgrowing strains were similar to other fast-growing species of Rhizobium in that they produced appreciable levels of P-galactosidase and nicotinamide adenine dinucleotide phosphate-linked 6-phosphogluconate dehydrogenase but had no detectable hydrogenase activity. The fast-growing soybean rhizobia share symbiotic host specificity with Brudyvhizobium japonicum, but appear to be related biochemically to the other fast-growing species of Rhizobium.

Better understanding of process controls over nitrous oxide (N2O) production in urine-impacted ‘hot spots’ and fertilizer bands is needed to improve mitigation strategies and emission models. Following amendment with bovine (Bos taurus) urine (Bu) or urea (Ur), we measured inorganic N, pH, N2O, and genes associated with nitrification in two soils (‘L’ and ‘W’) having similar texture, pH, C, and C/N ratio. Solution-phase ammonia (slNH3) was also calculated accounting for non-linear ammonium (NH4+) sorption capacities (ASC). Soil W displayed greater nitrification rates and nitrate (NO3−) levels than soil L, but was more resistant to nitrite (NO2−) accumulation and produced two to ten times less N2O than soil L. Genes associated with NO2− oxidation (nxrA) increased substantially in soil W but remained static in soil L. Soil NO2− was strongly correlated with N2O production, and cumulative (c-) slNH3 explained 87% of the variance in c-NO2−. Differences between soils were explained by greater slNH3 in soil L which inhibited NO2− oxidization leading to greater NO2− levels and N2O production. This is the first study to correlate the dynamics of soil slNH3, NO2−, N2O and nitrifier genes, and the first to show how ASC can regulate NO2− levels and N2O production.