Diversity of Paenibacillus spp. in the rhizosphere of four sorghum (Sorghum bicolor) cultivars sown with two contrasting levels of nitrogen fertilizer assessed by rpoB-based PCR-DGGE and sequencing analysis.
The diversity of Paenibacillus species was assessed in the rhizospheres of four cultivars of sorghum sown in Cerrado soil amended with two levels of nitrogen fertilizer (12 and 120 kg/ha). Two cultivars (IS 5322-C and IS 6320) demanded the higher amount of nitrogen to grow, whereas the other two (FBS 8701-9 and IPA 1011) did not. Using the DNA extracted from the rhizospheres, a Paenibacillus-specific PCR system based on the RNA polymerase gene (rpoB) was chosen for the molecular analyses. The resulting PCR products were separated into community fingerprints by DGGE and the results showed a clear distinction between cultivars. In addition, clone libraries were generated from the rpoB fragments of two cultivars (IPA 1011 and IS 5322-C) using both fertilization conditions, and 318 selected clones were sequenced. Analyzed sequences were grouped into 14 Paenibacillus species. A greater diversity of Paenibacillus species was observed in cultivar IPA 1011 compared with cultivar IS 5322-C. Moreover, statistical analyses of the sequences showed that the bacterial diversity was more influenced by cultivar type than nitrogen fertilization, corroborating the DGGE results. Thus, the sorghum cultivar type was the overriding determinative factor that influenced the community structures of the Paenibacillus communities in the habitats investigated.
Instituto de Microbiologia Prof Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
Marcia Reed Rodrigues
MR
Coelho
Fabio Faria
FF
Da Mota
Newton Portilho
NP
Carneiro
Ivanildo Evódio
IE
Marriel
Edilson
E
Paiva
Alexandre Soares
AS
Rosado
Lucy
L
Seldin
D044822:Biodiversity; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel; D005308:Fertilizers / Q000382:microbiology*; D006094:Gram-Positive Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000378:metabolism*; D009691:Nucleic Acid Denaturation; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology*; D016133:Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D045868:Sorghum / Q000382:microbiology*
D004269:DNA, Bacterial; D005308:Fertilizers; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit; D009584:Nitrogen