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Soil Community Analysis Using DGGE of 16S rDNA Polymerase Chain Reaction Products

^a Dep. of Agronomy, Purdue Univ., West Lafayette, IN, 47907-1150 USA
^b Dep. of Microbiology, Bergen Univ., Jahnebakken 5, N-5020 Bergen, Norway

View larger version (68K): [in a new window]   Fig. 1 Denaturing gradient gel electrophoresis gel of Bacteria 16S rDNA polymerase chain reaction (PCR) products (Bases 338 to 518 relative to the E. coli rRNA sequence) amplified from USA (Lanes 2–6) and Norwegian (Lanes 7–8) soil-DNA extracts. Gel gradient ranging from 30 to 55% denaturant. Lane 1, marker (PCR products from top to bottom, Pseudomonas putida, Acinetobacter sp. ADP1, Comamonas acidovorans ATCC 15668, E. coli DH5, Alcaligenes sp. BR40, C. testosteroni); Lane 2, PAH (700 mg kg-1)–contaminated soil; Lane 3, no-till corn field; Lane 4, no-till soybean field; Lane 5, plowed corn field; Lane 6, plowed soybean field; Lane 7, fallow field; Lane 8, pastureland. Arrows indicate the dominant populations (Lane 2) and regions of greater band intensity that characterize the community structure (Lanes 3, 4 and 7). Minus signs indicate intense bands not seen in Lanes 4–6 but present in Lane 3

View larger version (114K): [in a new window]   Fig. 2 Denaturing gradient gel electrophoresis gel of Bacteria 16S rDNA polymerase chain reaction products (Bases 968 to 1406 relative to the E. coli rRNA sequence) amplified from USA (Lanes 1–4) and Norwegian (Lanes 5–6) soil-DNA extracts. Gel gradient ranging from 30 to 55% denaturant. Lane 1, no-till corn field; Lane 2, no-till soybean field; Lane 3, plowed corn field; Lane 4, plowed soybean field; Lane 5, fallow field; Lane 6, pastureland

View larger version (73K): [in a new window]   Fig. 3 Denaturing gradient gel electrophoresis (DGGE) gel of Archaea 16S rDNA polymerase chain reaction products (Bases 340 to 534 relative to the E. coli rRNA sequence) amplified from USA (Lanes 1–4) and Norwegian (Lanes 5–6) soil DNA extracts. Gel gradient ranging from 30 to 55% denaturant. Lane 1, no-till corn field; Lane 2, no-till soybean field; Lane 3, plowed corn field; Lane 4, plowed soybean field; Lane 5, fallow field; Lane 6, pastureland. Arrows mark each of the 11 different populations detected by DGGE, as determined by the distance the products migrated in the gel. Band A is present in all the soils. Bands B and C are common to all the Indiana soils (Lanes 1–4). Band E was unique to soils under no-till cultivation in Indiana (Lanes 1 and 2). Band D was present in some soils from Indiana and Norway, but its presence did not correlate with any agronomic treatments