A novel strategy to extract specific phylogenetic sequence information from community T-RFLP.
Cultivation-independent analyses of soil microbial community structures are frequently used to describe microbiological soil characteristics. Semi-automated terminal restriction fragment length polymorphism (T-RFLP) analyses yield high-resolution genetic profiles of highly diverse soil microbial communities and hold great potential for use in routine soil quality monitoring. A serious limitation of T-RFLP analyses has been the inability to reliably affiliate observed terminal restriction fragments (T-RF) to phylogenetic groups. In the study presented here, we were able to overcome this limitation of T-RFLP. With a combination of adapter ligation, fragment size selection, and re-amplification with adapter site specific PCR, we were able to isolate a T-RF-fraction of a narrow size-range containing a T-RF that was significantly more abundant in heavy metal amended soils. Cloning the size-selected T-RF fraction allowed for the efficient isolation of clones containing this specific T-RF. Sequence determination and phylogenetic inference in RDP-II affiliated the sequence to unclassified cyanobacteria. Specific primer design and PCR amplification from bulk soil DNA allowed for independent confirmation of the results from bacterial T-RFLP and T-RF cloning. Our results show that specific T-RFs can be efficiently isolated and identified, and that the adapter ligation approach holds great potential for genetic profiling and for identification of community components of interest.
Molecular Ecology, Agroscope FAL Reckenholz, Swiss Federal Research Station for Agroecology and Agriculture, Zurich, Switzerland. franco.widmer@fal.admin.ch
Franco
F
Widmer
Martin
M
Hartmann
Beat
B
Frey
Roland
R
Kölliker
D001483:Base Sequence; D000458:Cyanobacteria / Q000235:genetics* / Q000302:isolation & purification; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D019003:Deoxyribonuclease HpaII / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
D017931:DNA Primers; D004269:DNA, Bacterial; D019003:Deoxyribonuclease HpaII