Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: Do the different methods provide similar results?

@article{citeulike:2758424, abstract = {Bacterial communities of four arable soils - pelosol, gley, para brown soil, and podsol brown soil - were analysed by fingerprinting of 16S rRNA gene fragments amplified from total DNA of four replicate samples for each soil type. Fingerprints were generated in parallel by denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), and single strand conformation polymorphism (SSCP) to test whether these commonly applied techniques are interchangeable. PCR amplicons could be separated with all three methods resulting in complex ribotype patterns. Although the fragments amplified comprised different variable regions and lengths, DGGE, T-RFLP and SSCP analyses led to similar findings: (a) a clustering of fingerprints which correlated with soil physico-chemical properties, (b) little variability between the four replicates of the same soil, (c) the patterns of the two brown soils were more similar to each other than to those of the other two soils, and (d) the fingerprints of the different soil types revealed significant differences in a permutation test, which was recently developed for this purpose.}, author = {Smalla, Kornelia and Oros-Sichler, Miruna and Milling, Annett and Heuer, Holger and Baumgarte, Susanne and Becker, Regina and Neuber, Gabriele and Kropf, Siegfried and Ulrich, Andreas and Tebbe, Christoph C. }, citeulike-article-id = {2758424}, doi = {10.1016/j.mimet.2007.02.014}, journal = {Journal of Microbiological Methods}, keywords = {dgge, sscp, trflp}, month = {June}, number = {3}, pages = {470--479}, posted-at = {2008-05-05 18:08:50}, priority = {2}, title = {Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: Do the different methods provide similar results?}, url = {http://dx.doi.org/10.1016/j.mimet.2007.02.014}, volume = {69}, year = {2007} }

TY - JOUR ID - citeulike:2758424 L3 - citeulike-article-id:2758424 TI - Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: Do the different methods provide similar results? JF - Journal of Microbiological Methods VL - 69 IS - 3 SP - 470 EP - 479 N2 - Bacterial communities of four arable soils - pelosol, gley, para brown soil, and podsol brown soil - were analysed by fingerprinting of 16S rRNA gene fragments amplified from total DNA of four replicate samples for each soil type. Fingerprints were generated in parallel by denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), and single strand conformation polymorphism (SSCP) to test whether these commonly applied techniques are interchangeable. PCR amplicons could be separated with all three methods resulting in complex ribotype patterns. Although the fragments amplified comprised different variable regions and lengths, DGGE, T-RFLP and SSCP analyses led to similar findings: (a) a clustering of fingerprints which correlated with soil physico-chemical properties, (b) little variability between the four replicates of the same soil, (c) the patterns of the two brown soils were more similar to each other than to those of the other two soils, and (d) the fingerprints of the different soil types revealed significant differences in a permutation test, which was recently developed for this purpose. KW - dgge KW - sscp KW - trflp AU - Smalla, Kornelia AU - Oros-Sichler, Miruna AU - Milling, Annett AU - Heuer, Holger AU - Baumgarte, Susanne AU - Becker, Regina AU - Neuber, Gabriele AU - Kropf, Siegfried AU - Ulrich, Andreas AU - Tebbe, Christoph PY - 2007/06// UR - http://dx.doi.org/10.1016/j.mimet.2007.02.014 ER -