All columns were sectioned for biomass analysis on day 300
when column operation ceased. The following segments as
measured from the column inlet were removed and transferred
aseptically to sterile 15 mL polypropylene tubes (BD
Falcon, Franklin Lakes, NJ): 0e2, 2e3, 11e13, 18e20, 27e28,
28e30 cm. Samples were stored at 80 C until further analysis.
After thawing, samples were split into two 15 mL tubes.
Sterile liquid mineral medium (4 mL) was added to each tube
containing the column sand samples. Tubes were vortexed for
10 s and sonicated for 5 min with a Bransonic tabletop ultrasonic
cleaner model 1501 (40 kHz, 70 W, Branson Ultrasonic
Corporation, Danbury, CT) to disrupt biofilms and lyse cells.
Samples were then centrifuged at 4000 rpm for 5 min to
remove sand and particles generated during sonication.
Supernatants from duplicate tubes were combined into one
tube that served as the sample source for the protein assay
(analyzed in duplicate). Sand remaining in the tubes was
washed three times with ultra pure water and dried at 105 C
for 24 h in pre-weighed aluminum weigh boats. Sand samples
were cooled in a dessicator before being weighed. Protein
measurements were normalized to dry sand weight and are
reported as the mean of duplicate samples plus or minus one
standard deviation in mg protein per g dry sand. A Micro BCA
Protein Assay Kit (Thermo Fisher Scientific, Waltham, MA)
was employed according to the manufacturer’s instructions
using an Ultrospec 3100 Pro UV/Vis spectrophotometer
(Amersham Biosciences). Briefly, an albumin standard curve
was made ranging from 0 to 200 mg/mL protein. After mixing samples (1 mL) with the kit’s “working reagent” (1 mL) in test
tubes, the solutions were incubated at 60 C for 1 h. Standards
and samples were then analyzed with a spectrophotometer at
562 nm.