## 2 Materials and Methods
### Gross Primary Production  
Three sampling campaigns to quantify rates of FAB and non-FAB gross primary production (GPP) were carried out in 2020 (in June, July, and October). Our first campaign (June) focused on the site where the FABs had first been identified and retrieved in 2019 (FAB; 41\({}^{\circ}\)54.942\({}^{\prime}\) N, 111\({}^{\circ}\)23.453\({}^{\prime}\) W), while subsequent campaigns sampled the FAB site, as well as a second site where minimal FAB occurrence was observed (non-FAB; 41\({}^{\circ}\)53.345\({}^{\prime}\) N, 111\({}^{\circ}\)17.468\({}^{\prime}\) W, Figure 1). Both sites are on the Utah side of the lake (featuring sewage systems, thus unlikely to have direct groundwater eutrophication from septic tanks), and both are far from the north end, where the lake is connected to the Bear River. During each field campaign, rocks and water samples were collected manually in the near-shore zone  
Figure 1: Bear Lake at the border of Idaho (ID) and Utah (UT) with infrastructure (red), major tributaries, and sampling locations of filamentous algae blooms at the western shore (FAB site) and non-filamentous algae at the eastern shore (non-FAB site). At the FAB site, aquatic plants (**A**) and rocks (**B**) were densely covered by filamentous algae during all sampling campaigns (October 2019; June, July, and October 2020; and June 2021), which mainly comprised _Cladophora glomenta_ (microscope image (**C**)). Periphyton on the rocky substrate at the non-FAB site (**D**,**E**) were dominated by various diatoms (_Epithemia, Gombonema, Cymbella;_ (**F**)). Photos by [PERSON] (non-FAB), [PERSON] (FAB) and [PERSON] (microscope). (from depths of ~0.1 to 0.15 m below the surface), minimizing physical disturbance to the rock surface (or filamentous algae growth on the rock). During each campaign, subsamples of filamentous algae from each site were also collected in plastic Falcon tubes and viewed under a microscope to identify the periphyton species present at a given site (permitting taxonomic comparisons with samples shipped to Berlin for stable isotope analyses, as described in Section 2.3). There is no universal standardized protocol for the measurement of GPP in benthic periphyton communities. All methods for measuring aquatic metabolism rates are associated with some errors [31; 32], and research focusing on benthic metabolism in particular has generally been more recent than research on planktonic dynamics [33]. Nevertheless, in situ measurements of changes in oxygen concentrations in sealed transparent benthic chambers or domes are a common method for assessing periphyton metabolism rates both in marine [34] and freshwater [35; 36] environments. We thus measured oxygen dynamics in sealed clear and dark chambers containing rocks with attached FAB (_Cladophora_) or non-FAB periphyton assemblages and exposed in the lake (in situ), as this general approach has also been applied to determine periphyton metabolism rates in other large lakes [37; 38]. This approach permits the direct measurement of benthic GPP for rocky littoral areas, and captures the effects of self-shading in dense FAB mats, which can play an important role in their seasonal growth patterns [39]. All the rocks (n = 12 in the first campaign; n = 6 per site in the second campaign; and n = 12 at the FAB and 6 at the non-FAB site in the third campaign) were incubated in the nearshore lake zone at ambient lake temperatures in 3 L watertight plastic (polycarbonate) chambers to undergo light-dark metabolism experiments, in order to measure the rates of gross primary production (GPP), net ecosystem production (NEP), and community respiration (CR) using changes in dissolved oxygen (DO) concentrations, following standard methods [30]. Each rock underwent both a light and dark treatment. Briefly, the rate of change in DO for a chamber that was exposed to ambient/full sunlight (in chambers that were exposed at the same near-shore depth that the rocks were collected from, ~10 to 15 cm below the water surface) represented NEP (the sum of GPP and CR).