Detection and quantification of Paenibacillus polymyxa in the rhizosphere of wild barley (Hordeum spontaneum) with real-time PCR.
OBJECTIVE
To detect and quantify the plant drought tolerance enhancing bacterium Paenibacillus polymyxa in a collection of 160 Hordeum spontaneum rhizosphere samples at the 'Evolution Canyon' ('EC'), Israel.


RESULTS
PCR primers and a FAM-TAMRA probe (6-carboxyfluorescein, 6-carboxy-tetramethyl-rhodamine) targeting 16S rRNA genes were designed and used to detect and quantify the target strain. Two commercial kits, Bio101 Fast Spin and Mo Bio Ultra Clean Soil DNA, were tested for DNA isolation from the rhizosphere and surrounding soil. Population densities of P. polymyxa were studied in the rhizosphere of wild barley and surrounding soil from the contrasting climatic slopes at the 'EC' using the real-time PCR and culture based methods.


CONCLUSIONS
Paenibacillus polymyxa is one of the best established species in wild barley rhizosphere at the 'EC' slopes. With the real-time PCR assay we are able to detect 1 pg of DNA per PCR corresponding to 100 cells per ml. The results at the 'EC' correlate well to bacterial estimations by culture based methods.


CONCLUSIONS
Significantly higher P. polymyxa cell number was detected in the rhizosphere of arid 'African' microclimate indicating possible role of adaptive co-evolution with plants.
Timmusk
S
S
Department of Forest Mycology and Pathology, Uppsala BioCenter, SLU, Uppsala, Sweden. salme.timmusk@mykopat.slu.se
Paalme
V
V
Lagercrantz
U
U
Nevo
E
E
D015169:Colony Count, Microbial; D017931:DNA Primers / Q000235:genetics; D015342:DNA Probes / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D001467:Hordeum / Q000382:microbiology*; D057230:Limit of Detection; D008969:Molecular Sequence Data; D056507:Paenibacillus / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification*; D016133:Polymerase Chain Reaction / Q000379:methods; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012235:Rhodamines; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
C106141:6-carboxytetramethylrhodamine; D017931:DNA Primers; D015342:DNA Probes; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012235:Rhodamines