## 2 Materials and Methods
### Gross Primary Production
The rate of change in DO for containers that were stored in dark chambers (also placed in the near-shore water to minimize changes to ambient water temperatures) represented CR, which we report as a negative number, given that it is a rate of decline in DO. Light incubations that are exposed for too long may form bubbles when oxygen leaves the dissolved state (resulting in a dampened DO measurement in light incubations). We therefore adapted our sampling periods in the field to avoid this. Specifically, we found that incubation periods of 30-60 min for rocks were appropriate for measuring substantial metabolic rates in both light and dark treatments, while minimizing bubble formation. Gross primary production was calculated as NEP minus (negative) CR. Changes in the DO concentration were measured using a Yellow Springs Instruments (YSI) DO probe, calibrated prior to each deployment. The metabolic rates that were measured in each chamber were calculated according to the water volume (measured carefully with a graduated cylinder, accounting for displacement by the rocks), and converted from volumetric to surface area rates by multiplying the total rates by the upper-exposed surface area of each incubated rock. This was calculated by wrapping the upper-exposed surface of each rock in aluminum foil and weighing the dried foil in our laboratory, and finally comparing the weight of that foil with the weight of the aluminum foil of the known surface area. The metabolic rates are furthermore converted to carbon units assuming photosynthetic and respiratory quotients (PQ and RQ) of 1. Although the lake PQ and RQ values may vary between lakes, they are often close to 1 [40; 41]. To correct for phytoplankton production in the lake water during the rock incubation experiments, we deployed two \"control\" chambers containing only lake water, in order to measure the water-column aquatic metabolism rates. Given the lower rates of aquatic metabolism, longer incubation periods of 1-2 h were adopted in the water-only treatments. However, as the water column concentrations of chl \(a\) in Bear Lake tend to be extremely low,we anticipated that incubation experiments of water alone might not provide suitable data for calculating water-column metabolism rates via changes in dissolved oxygen. Therefore, we collected one liter of water from each site and sampling campaign, which we filtered and analyzed in the laboratory to determine the ambient water chl \(a\) concentrations at our sampling sites. The chl \(a\) concentrations were measured in 95% ethanol using a Turner 10 AU fluorometer [42], either within 24 h of sampling, or else within two weeks if the samples were immediately frozen. Phytoplankton production (P, mg C m\({}^{-3}\) d\({}^{-1}\)) was subsequently estimated as 10.3 x chl \(a\) (mg m\({}^{-3}\))\({}^{1.19}\)[43]. As we expected differences in GPP between the FAB and non-FAB communities to be primarily apparent as GPP rates that were expressed relative to periphyton chl \(a\) concentrations on rocks, we took additional steps to measure the rock periphyton chl \(a\) concentrations. Immediately following the incubation experiments, periphyto was scrubbed from each rock using a metal periphyto brush, transferred to a glass-fiber filter, and transported to our laboratory in a dark cooler with ice packs for analyzing the chl \(a\) concentrations (following the same method described above). We recognized that the irregular sampling structure (including separate campaigns for stable isotope analysis measurements and GPP measurements) introduced potential uncertainties in precisely matching the GPP rates to the results of stable isotope analyses. We also recognize that asymmetries within the GPP-specific campaigns (with unmatched sampling frequencies of FAB and non-FAB sites) are not ideal for comparing aquatic metabolism rates in these two communities.