Warming, eutrophication (nutrient fertilization) and brownification (increased loading of allochthonous organic matter) are three global trends impacting lake ecosystems. However, the independent and synergistic effects of resource addition and warming on autotrophic and heterotrophic microorganisms are largely unknown.  In this study, we investigate the independent and interactive effects of temperature, dissolved organic carbon (DOC, both allochthonous and autochthonous), and nitrogen (N) supply, in addition to the effect of spatial variables, on the composition, richness, and evenness of prokaryotic and eukaryotic microbial communities in lakes across elevation and N deposition gradients in the Sierra Nevada mountains of California, USA. We found that both prokaryotic and eukaryotic communities are structured by temperature, terrestrial (allochthonous) DOC and latitude. Prokaryotic communities are also influenced by total and aquatic (autochthonous) DOC, while eukaryotic communities are also structured by nitrate. Additionally, increasing N availability was associated with reduced richness of prokaryotic communities, and both lower richness and evenness of eukaryotes. We did not detect any synergistic or antagonistic effects as there were no interactions among temperature and resource variables. Together, our results suggest that (a) organic and inorganic resources, temperature, and geographic location (based on latitude and longitude) independently influence lake microbial communities; and (b) increasing N supply due to atmospheric N deposition may reduce richness of both prokaryotic and eukaryotic microbes, likely by reducing niche dimensionality.  Our study provides insight into abiotic processes structuring microbial communities across environmental gradients and their potential roles in material and energy fluxes within and between ecosystems.

Between June and August 2015, thirty-four Sierra Nevada lakes containing fish were sampled across a 904 m elevation gradient (2433-3337 m), encompassing lakes in the montane (below 2450 m), subalpine (2450-2900 m) and alpine zones (2900 m and above). The lakes were also sampled across a latitudinal N deposition gradient spanning Yosemite National Park (YOSE), Inyo National Forest (INYO), and Sequoia National Park (SEKI). Latitude and Longitude data are provided in degrees and UTM, as well as Lake Chain Number (LCN), which indicates relative positioning of lakes connected by surface flow along a linear chain (ie. higher vs. lower in watershed) to account for connectivity between lakes sharing the same basin. The lakes encompassed a 10.2°C temperature gradient (8.7-18.9°C), 805.7 μM DOC gradient (68.8-874.5 μM) and 2.6 μM NO₃^- gradient (0.0044-2.6 μM). The lakes ranged 0.5–21 hectares in surface area and 1.8 to 40.8 m in depth. All lakes were oligotrophic (chl-a ≤ 3.33 µg l⁻¹) and have similar geologic and chemical characteristics as they are situated on granite and granodiorite bedrock.

Water samples from the epilimnion (surface to 1m depth) were collected at each lake for biological and chemical analyses. At the deepest point in each lake, in situ depth profiles of physico-chemical data were taken using a YSI probe (YSI Incorporated, Yellow Springs, Ohio, USA). However, pH data were not reliable due to a faulty pH probe and have been excluded from this study. Water samples were collected with a 1 m integrated tube sampler and filtered through 63 μm mesh to remove zooplankton, then processed for chlorophyll-a (chl-a); nitrogen and phosphorus in particulate organic matter (POM); total nitrogen (TN); total phosphorus (TP); dissolved nitrate (NO₃^-); and dissolved organic carbon (DOC).

From UV-vis absorbance and EEMs data, we calculated two indices of DOC quality: the freshness index (β:α) and specific UV absorption (SUVA). Freshness Index (FrI) is a ratio of emission intensity at 380 nm to that of the region between 420 and 435 nm at an excitation of 310 nm and is reflective of recently produced algal organic matter (Parlanti et al., 2000). SUVA is a DOC-normalized index of aromaticity calculated as UV absorbance at 254 nm/[(DOC(mg/L) x path length (0.01 m)] (Weishaar et al., 2003). Therefore, Freshness Index increases with autochthonous carbon production whereas SUVA increases with allochthonous carbon production.

There are missing values for TP because many samples were below detection limit (indicated as '<detection') and missing values for NO₃^- are indicated as 'NA'. Lakes higher in the basin have lower LCN values (eg. 1 is headwater lake), and LCN values of 0 indicate that lakes are not connected to others in the basin.