Methods:
NDS Design
After being soaked in deionized water for 3 days, a plastic petri dish is used to fill the large opening of 3-inch terra cotta flowerpots (Fairchild et al. 1985). Agar solutions containing the nitrate treatments, low medium and high and constant phosphate are added to the pot through the small hole (n=96). The small hole is plugged using a stopper.
Constructed streams
At the University of Michigan Biological Station Stream Lab, water will be pumped from Maple River into 55-gallon tanks. Salt (NaCl) will be added to the tanks to create each concentration: ambient, low, medium, and high. Conductance in each stream will be monitored to ensure consistent salinity. A total of 6 trials will be completed for each condition, with a total of 96 streams. Streams will be at least 6”x6”.
Sample collection
Each pot within a stream is randomly assigned a collection day (14, 21, 28, 35). Pots are placed into the stream with the collection area facing toward the flow of water. On collection days, pots are removed from the stream and collection area is scraped using a razor blade and a hard-bristled toothbrush and placed into a collection jar with deionized water.
DNA Sequencing
Samples are added to CTAB extraction buffer and incubated at 60°C for an hour (Haddad et al. 2014). After cooling to room temperature, 1ml of chloroform:isoamyl alcohol is added and stirred for 15 minutes. The solution is centrifuged for 10 minutes at 12000 rpm. The supernatant is moved to a new test tube and chloroform:isoamyl alcohol is added again. The final supernatant is moved to another test tube with isopropanol at -20°C for 1 hour. This is centrifuged at 12000 rpm at 4°C for 10 minutes. Sample is washed with 70% ethanol, then dissolved in TE buffer. Samples are then sent to UMN for 16s and 18s sequencing.