Band pattern data from Gammaproteobacteria-group specific DGGE

• Other Authors: BOWMAN, JOHN (hasPrincipalInvestigator), POWELL, SHANE (hasPrincipalInvestigator), POWELL, SHANE (processor), RIDDLE, MARTIN J. (hasPrincipalInvestigator), Australian Antarctic Data Centre (publisher)
• Format: Dataset
• Language: unknown
• Published: Australian Antarctic Data Centre
• Subjects: environment; CONTAMINANT LEVELS/SPILLS; EARTH SCIENCE; HUMAN DIMENSIONS; ENVIRONMENTAL IMPACTS; OIL SPILLS; EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > BENTHIC; COMMUNITY STRUCTURE; BIOSPHERE; ECOLOGICAL DYNAMICS; COMMUNITY DYNAMICS; denaturing gradient gel electrophoresis; benthic microbiota; gammaproteobacteria; microbial community structure; oil contamination; CONTINENT > ANTARCTICA > Windmill Islands; O'Brien Bay; GEOGRAPHIC REGION > POLAR; Antarctic; The Antarctic; Lanes; Antarc*; Antarctica
• Online Access: https://researchdata.ands.org.au/band-pattern-gammaproteobacteria-specific-dgge/701813; https://doi.org/10.4225/15/55CD35AAF186A; https://data.aad.gov.au/metadata/records/SRE4_gammaproteobacteriaDGGE; http://nla.gov.au/nla.party-617536

Samples are from the SRE4 experiment - an in situ experiment to determine fate and effects of different types of oils in the Antarctic marine environment. For details see: Powell S.M., Snape I., Bowman J.P., Thompson B.A.W., Stark J.S., McCammon S.A., Riddle M.J. 2005. A comparison of the short term effects of diesel fuel and lubricant oils on Antarctic benthic microbial communities. Journal of Experimental Marine Biology and Ecology 322:53-65. Samples were analysed by denaturing gradient gel electrophoresis (DGGE) with primers specific for the Gammaproteobacteria. Samples used were from Time2 (1 year) Initial: T-1C; T-1E Control: T2C SAB treatment: T2S PCR conditions: Primers: GAMFC: CGC CCG CCG CGC CCC GCG CCC GGC CCG CCG CCC CCG CCC GGG TTA ATC GGA ATT ACT GG GAMR: GGT AAG GTT CTT CGC GTT GCA T 50 ul (micro litre) reactions with HotStar (qiagen) mix, 5ul Q solution, 10 pmol (pico mol) each primer and 20 ng (nano gram) template DNA cycling: 94C 15 minutes 35 cycles of: 94C 1 minutes 55C 1 minutes 72C 1 minutes 72C 20 minutes DGGE was performed using D-Code system (BioRad). Gel: 8% acryloamide, 30 - 65% denaturant with 2 cm stacking gel 1 x TAE, 60 degrees C, 80V 16 hours Gel was pre-run for 20 minutes and lanes were flushed out after 15 minutes. Gel was stained with Sybrgold. Image captured using Storm Phosphorimager and ImageQuant v5.2 software (.gel files). The image files are called 151105#2.gel and 151105.tif Band pattern results are in gammadgge.xls. The first column is the band position (or band name) and the remaining columns are samples with the first row being the sample name. The numbers indicates how many times the band appeared for that sample out of 2 DGGE runs. This work was completed as part of ASAC projects 1228 and 2201 (ASAC_1228, ASAC_2201).