organism: hydrocarbon metagenome
description: A sediment sample from tailings pond 5A operated by Suncor was collected in July 2009 from a depth of 1.5 ft below the surface. The sample jar was filled to the lid to limit oxygen diffusion. The sample was transported to the University of Calgary and stored under anaerobic conditions without hydrogen (90% N2, 10%CO2) at room temperature. The inoculum that seeded all biofilms was tailings sludge (loosely packed sediments). The tailings sludge sample was diluted 2 fold with sterile double distilled water to serve as the inoculum for all biofilms. Biofilms were grown on the Calgary Biofilm Device (CBD). Wells were replenished with fresh growth medium every 24 and 48 hours for aerobic and anaerobic growth respectively.  Anaerobic biofilms were grown under atmospheric conditions of 90%N2 and 10% CO2/H2 mix.  Microaerobic biofilms were grown in a candle jar and replenished with fresh growth medium every 72 hours. Total genomic DNA was extracted from 250 mg of the starting sludge inoculum. DNA from biofilms was extracted using 2 biofilm pegs per extraction and an isolation kit optimized for the type of sample. DNA was extracted using MO Bio Power Soil™ DNA isolation kit  (Carlsbad CA) for aerobic and microaerobic biofilm samples and the MP Bio Soil DNA Extraction™ kit (Solon, OH) with bead beating step for anaerobic biofilms and the sludge inoculum.