Molecular detection of nifH gene-containing Paenibacillus in the rhizosphere of sorghum (Sorghum bicolor) sown in Cerrado soil

To develop a polymerase chain reaction (PCR)-based approach for the detection of nifH gene-containing Paenibacillus in environmental samples. The primers, nifHPAENf and nifHPAENr, were designed and tested with DNA from: (i) strains of different nitrogen-fixing Paenibacillus species, (ii) strains of other nitrogen-fixing genera and (iii) rhizosphere of sorghum sown in Cerrado soil amended with either 12 or 120 kg ha(-1) of nitrogen fertilizer. All nitrogen-fixing Paenibacillus strains tested and the DNA samples from rhizosphere soil were amplified when these primers were used, generating a 280 bp fragment. When the PCR products obtained from both sorghum rhizospheres were cloned and sequenced, the majority of the clones analysed could be identified as Paenibacillus durus. Moreover, a greater diversity in the nifH sequences could be observed in the rhizosphere treated with a high amount of nitrogen fertilizer. Nitrogen fertilization slightly influenced the structure of the nifH gene-containing Paenibacillus community in sorghum rhizospheres cultivated in Cerrado soil. The PCR detection method developed is adequate to assess the presence of nifH gene-containing Paenibacillus in the environment and can be used in future to determine the ecological role of this group of micro-organisms for the nitrogen input to the plants.