Effect of common bean (Phaseolus vulgaris L.) on the community composition of ammonia-oxidizing bacteria in soil previously cultivated with Medicago sativa

The community composition of ammonia-oxidizing bacteria (AOB) was studied during four stages of plant development in soil cultivated with Phaseolus vulgaris in comparison to unplanted soil, using an alfisol previously harboring the legume Medicago sativa. Denaturing gradient gel electrophoresis (DGGE) patterns of 16S rRNA gene and clone libraries of the same gene suggested that bacteria related to Nitrosospira cluster 3 were dominant in both planted and unplanted soil. Bacteria related to Nitrosomonas cluster 8 (Nitrosomonas communis cluster) were found at all times in planted soil, but appeared only randomly in unplanted soil. Analysis of PCR products of the gene encoding the alpha-subunit of ammonia monooxygenase (amoA) by DGGE and clone libraries only detected Nitrosospira cluster 3-like organisms, but failed to detect sequences related to Nitrosomonas. The results suggest that P. vulgaris does not affect the dominant members of AOB communities (Nitrosospira cluster 3), but could have an effect on the prevalence of Nitrosomonas cluster 8 in this type of legume-planted alfisol.