Using geochemical indicators to distinguish high biogeochemical activity in floodplain soils and sediments, Science of the Total Environment: Dataset
Data associated with analysis of sediment samples collected in the East River watershed and Rifle floodplain sites, CO. Samples were collected and analyzed as part of two student MS theses at Colorado School of Mines (Kenwell and Prugue) over a time period ranging from 2012 to 2015. Analyses include total organic carbon, leachable Fe and Mn, and total microbial DNA; all analyses performed at Colorado School of Mines. Methods: Samples were collected from core during a drilling campaign at the Rifle Site. Samples were collected every 1.5 m. At the East River site soil and sediment samples were collected using hand-augered bulk density sampler. Collected samples were stored at -20C until analysis. Samples were thawed in an anaerobic chamber and subsampled for extractions and DNA analysis. Samples for DNA analysis were freeze-dried, the remaining sample was oven dried and ground to 0.991 cm for TOC and leaching analysis. TOC analysis was performed on duplicate samples using a CM 5014 Coulometer (UIC, Joliet, IL, USA). Two chemical extractions were performed: hydroxylamine (HA) extraction of Fe and Mn adapted from Lovley et al., 1987 and synthetic precipitation (ppt) leaching adapted from EPA method 1312 (EPA, 1994) . For theHA extraction 3g of wet sediment was mixed with 150 mL of 0.5 N HCl in one bottle and another 3 g of sediment was mixed with 150 mL of 0.25 N hydroxylamine hydrochloride in 0.5 N HCl. Extraction were performed for 24 hours at room temperature after which samples of the liquid were removed and filtered to 0.45 micron and analyzed by ICP-AES. HA-reducible iron and manganese concentrations were determined by difference between the two extractions. For ppt leaches, a 60:40 sulfuric:nitric acid mixture was added to Milliq water to a pH of 4.2 and combined with sediment in a 20:1 mass ratio of acid to sediment. The extraction was performed for 18 hours at room temperature after which the samples of the liquid were removed and filtered to 0.45 micron and analyzed by ICP-AES. DNA was sampled from sediment using a PowerSoil DNA Isolation Kit and extractions were performed according to manufactured instuctions with one adjustment, a 1 minute bead beating replaced the 10 minute vortexing step. Extracted DNA was stored at -20C. Quantitative PCR was performed in triplicate on a Roche LightCycler 480 system and working curves were created by amplifying environmental samples with primers and bead purifying them with Agencourt AMPure XP. Analysis was performed with a Qubit 2.0 Fluorometer and Qubit dsDNA High Sensitivity Assay Kit with results converted to copies using the URI Genomics and Sequencing Center converter (Staroscik, 2004). Additional method details can be found in Kenwell et al., 2016. Lovley, D.R., Phillips, E.J.P. (1987). Rapid assay for microbially reducible ferric iron in aquatic sediments. Applied and Environmental Microbiology, 53(7), 1536-1540. Staroscik, A. (2004). Calculator for determining the number of copies of a template. URI Genomics & Sequencing Center. <http://cels.uri.edu/gsc/cndna.html>. EPA. (1994). Method 1312: Synthetic precipitation leaching procedure.
- Research Organization:
- Watershed Functionality Scientific Focus Area
- Sponsoring Organization:
- U.S. Department of Energy Office of Science Office of Biological and Environmental Research
- DOE Contract Number:
- DEAC0205CH11231
- OSTI ID:
- 1506944
- Country of Publication:
- United States
- Language:
- English
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