Ammonia-oxidizing archaea and ammonium concentration as drivers of nitrification in a protected freshwater lake

Nitrification rates and ammonia-oxidizer functional gene abundance were measured in the water column of Lake Lacawac, Pennsylvania, USA, a freshwater lake on a nature sanctuary that allowed an investigation with minimal human impacts. Nitrification is a 2-step process consisting of ammonia oxidation followed by nitrite oxidation. Recent studies have shown that these 2 nitrification steps may be uncoupled and respond in different ways to environmental conditions. Additionally, the relative contribution of ammonia-oxidizing archea (AOA) vs ammonia-oxidizing bacteria (AOB) to nitrification rates varies widely across aquatic systems. To determine how nitrification rates are related to environmental parameters and the ammonia-oxidizing community in a nearly pristine environment, rates and gene abundance were measured over multiple seasons where in-situ environmental conditions varied. Rates of ammonia and nitrite oxidation were measured separately and summed to calculate total nitrification rates ranging from 1 to 568 nM/d. Ammonia oxidation rates generally outpaced nitrite oxidation rates, and rates of both ammonia and nitrite oxidation were higher at depth (10 m) compared with near-surface and mid water column. Ammonia oxidation, nitrite oxidation, and total nitrification rates were all strongly, positively correlated with in-situ [NH4+] (Kendall’s τ > 0.35, p < 0.02). AOB ammonia monooxygenase (amoA) gene copy numbers were generally greater than AOA amoA. However, AOB gene copy numbers were not correlated with any ammonia oxidation or total nitrification rates, whereas AOA abundance was positively correlated with both ammonia oxidation and total nitrification rates (Kendall’s τ > 0.41, p < 0.01). A Bayesian generalized additive model, which accounted for sampling month, indicated that total nitrification rates were best explained by AOA and [NH4+]. Thus, substrate concentration and AOA likely play key roles in regulating rates of nitrification in this small, nearly pristine freshwater lake. These reported relationships between rates of ammonia and nitrite oxidation (and, thus, total nitrification), in-situ environmental parameters, and the ammonia-oxidizer community in a protected environment establish a reference for evaluating the impact of a changing environment on mesotrophic lake water quality.