Sampling locations (white circles) in Yosemite National Park displayed on 10 m resolution elevation data from the United States Geological Survey National Elevation Dataset (http://nationalmap.gov/).

<p>Inset: location of Yosemite shown as the green shaded area within the state of California.</p

Lake elevation plotted against longitude for the nine lakes sampled in this study.

<p>Lake elevation plotted against longitude for the nine lakes sampled in this study.</p

Variation in lake nutrient concentrations versus elevation for (A) phosphate (PO₄^3-), (B) ammonium (NH₄⁺), (C) nitrite (NO₂^-), and (D) nitrate (NO₃^-).

<p>Vertical axes show nutrient concentrations in nanomolar (nM) plotted on a logarithmic scale, and colors denote month of sampling. Note that some samples have highly similar nutrient concentrations and fall nearly on top of one another.</p

Bi-plot of redundancy analysis of bacterial community composition.

<p>Color key denotes different lakes, and arrows denote biplot scores for the constraining variables. The grey box encompasses 17 samples that fall within a narrow range of each other and are not visually distinguishable on the bi-plot; this includes 1–2 samples from every lake except Middle Sunrise and Upper Cathedral Lake. One sample from Middle Sunrise Lake with extremely high AOB <i>amoA</i> gene abundance is not shown, as it falls much farther along the RDA1 and RDA2 axes.</p

Lake names, elevation, depth, and average nutrient concentrations.

<p>Lake names, elevation, depth, and average nutrient concentrations.</p

Boxplot comparison of calculated ¹⁵NH₄⁺ oxidation rates measured in Lower Cathedral and Lower Gaylor lakes.

<p>The vertical axis shows ¹⁵NH ⁺ oxidation rates (pmol L⁻¹ D⁻¹). The blue bars represent dark bottle incubations that were incubated under zero-light conditions, while the orange bars represent samples that were exposed to ambient light over a 24-hour cycle during in-situ incubation at the sampling site. The dashed line notes the detection limit. In these plots, the box denotes the mean plus and minus one standard deviation; the line within the box represents the median value; and lines extending above and below the box span the full range of the data.</p

Boxplot comparison of number of <i>amoA</i> genes per milliliter (genes mL⁻¹) for (A) ammonia-oxidizing archaea (AOA) and (B) ammonia-oxidizing bacteria (AOB).

<p>The vertical axes (logarithimic scale) denote the number of genes mL⁻¹; the horizontal axes represent the elevation of the sampling sites, and are ordered from lowest elevation (Harden Lake) to highest elevation (Upper Gaylor Lake). In these plots, the box denotes the mean plus and minus one standard deviation; the line within the box represents the median value; and lines extending above and below the box span the full range of the data. Outliers were defined as sample values 1.5 times larger than the upper quartile and are represented by green and blue circles.</p