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Hyporheic zone waters were sampled 8 cmand 15 cm below the sediment–water interface at site 1 using a polyvinyl chloride (PVC) pipe, PP tubing, and 50 mL syringes. Field parameters were measured with a Thermo Scientific Orion Star A329 pH/temp/conductivity probe. Samples were placed on ice in a cooler for transport to the laboratory for immediate processing and preservation. All water samples were filtered with 0.45 mm Whatman filters and a subset of waters was filtered with 0.22 mm filters in the laboratory. Samples for analysis by Inductively Coupled Plasma were preserved to a pH # 2 with ultrapure nitric acid by adding between 0.5 and 1 mL to each sample. The hyporheic zone waters and related surface waters were analyzed as total water (unfiltered and digested with ultrapure nitric acid), less than 0.45 mm, and less than 0.22 mm. Lab blanks and two quality control (QC) standards were used during analysis, one at a concentration of 25% of the highest calibration standard and one at a concentration of 75% of the highest calibration standard. The latter QC standard (75% of the highest calibration standard) was checked every 15 samples to monitor potential instrument drift. A total of eighty sediment samples were collected with a hand trowel (cleaned between each use with DI water) and placed in gallon plastic bags for transport to the laboratory at: an ore outcrop (site A, Fig. 1); weathered sediment below the ore (site B, Fig. 1); and, in the stream bank and stream bed at sites _6 to 10 with repeat sediments collected at sites 1 to 10. Sediment cores of the hyporheic zone were collected in 1 1/14 inch PVC pipes at site 1. Sediments were dried overnight in an oven at 80 deg. C prior to use. Homogenized sediment samples were digested in duplicate for analysis using 1 gram of sediment and aqua regia [2 mL HNO3 and 6 mL hydrochloric acid (HCl, 34– 37% by mass, trace metal grade)]. The extracted solution from the sediment digestion was measured as described in the next subsection to determine extractable elemental concentration amenable to reaction with aqua regia. The grain size in the stream bank and bed ranged from silt/clay to sand. Bulk sediment analysis was performed using X-ray fluorescence with a Rigaku ZSX with a rhodium X-ray tube that can be operated from 200 to 4000 watts (End window, Rh-anode, 4 kW, 60 kV) that delivers rapid quantitative determination of major and minor atomic elements, from beryllium (Be) through uranium (U), in a wide variety of sample types with minimal standards. The software is ZSX Primus II that performs both qualitative and quantitative analysis. X-ray diffraction (XRD) was performed on the ore sample (location A), stream bed sediments from site 1 and site 9 using a Rigaku Smart Lab X-ray diffraction (XRD) using Cu Ka radiation with a scintillation detector and a graphite monochromator, to obtain information on the crystallinity, mineral structure, and normalized approximate percent amount of mineral phases present in the sediment samples. The XRD data were analyzed using Jade® software. An X-ray Photoelectron Spectrometer (XPS) was used to acquire the near surface (<10 nm) elemental composition and oxidation states. A monochromatic Al source was used at 150 W power to obtain Fe 3p high resolution spectra from top _4 nm of the surface. Au reference powder was used to calibrate the spectra. Shirley background was used to process the spectra. Quantification utilized sensitivity factors that were provided by the manufacturer. A 70% Gaussian/30% Lorentzian (GL (30)) line shape was used for the curve fittings. Constraints used in curve fitting were in correspondence with our previous study.2 Qualitative X-ray mapping of epoxy-mounted polished ore samples was performed on a JEOL 8200 electron microprobe. Maps were acquired at 20 kV accelerating voltage and 30 nA beam current utilizing stage mapping at 2 mm steps (pixel) and 100 ms dwell time per pixel. The K-a X-ray lines for Mg, P, S, K, Ca, Ti, V, and Fe; the L-a line of As; and the M-a line of U were mapped on 5 separate wavelength dispersive spectrometers (2 passes per map area) simultaneously with the K-a lines for Al and Si on an energy dispersive spectrometer. A backscattered electron image was also acquired on each map area. The JEOL software utilizes a free shape map process in which undesirable areas, such as epoxy, may be excluded from the overall map; therefore map sizes varied according to the size of particles mapped. Loss on ignition was performed to determine the organic matter content in sediments by heating porcelain crucibles in a muffle furnace at 550 _C for one hour, cooling, and weighing empty crucibles. Sediment and water samples collected from site 1 during the March sampling event were processed for microbial community analysis. Sediment was scooped into a sterile centrifuge tube using a flame sterilized spatula. Microorganisms in water were concentrated by filtering the water sample through a sterile mixed cellulose-ester filter membrane with 0.22 mm pores. Samples were stored in the field on ice in a cooler and were immediately frozen (_20 _C) in the lab within 8 hours after collection, which is acceptable as per the results in Lauber et al. (2010). Total community DNA was extracted from the sediment and the water filter using an UltraClean® Soil DNA Isolation Kit (MO BIO). We contracted MR DNA® laboratory to amplify and sequence 16S rRNA genes in the samples. The laboratory amplified DNA over 30 cycles of PCR using the Hot- StarTaq Plus Master Mix Kit (Qiagen) under the following conditions: 94 _C for 3 minutes, followed by 28 cycles of 94 _C for 30 seconds, 53 _C for 40 seconds and 72 _C for 1 minute. Following the final cycle, the reaction sequence included an elongation step at 72 C for 5 minutes. Reaction mixtures used universal primers 519F (GTGCCAGCMGCCGCGGTAA) and 806R (GGACTACVSGGGTATCTAAT) to cover the variable region V4 of the 16S rRNA gene. After amplification, the laboratory verified amplification success using electrophoresis, pooled samples together in equal proportions, and purified using calibrated Ampure XP beads. The pooled and purified PCR product was used to prepare a DNA library by following the Illumina TruSeq DNA library preparation protocol. Paired-end 2 250 sequencing was performed on an Illumina MiSeq system following manufacturer guidelines. We processed sequencing data using QIIME v. 1.8.0. We first split samples according to barcodes and filtered the sequences to remove low-quality reads (script: split_libraries.py). Next, we generated operational taxonomic unit (OTU) tables at 97% similarity and evaluated taxonomy with uclust (script: pick_de_novo_otus.py). The method used the Greengenes reference dataset release 13_8; and assigned the most detailed lineage description shared by at least 90% of the sequences within each OTU. Lastly, we removed singletons and created taxonomy tables (scripts: filter_otus_from_otu_table.py, summarize_taxa_through_plots.py).