Nitrification in Mono Lake, California: Activity and community composition during contrasting hydrological regimes Stephen A. Carini 1 and Samantha B. Joye 2 Department of Marine Science, University of Georgia, Athens, Georgia 30602-3636 Abstract Rates of nitrification, geochemical variables, and the associated ammonia oxidizer microbial community were investigated in the water column of Mono Lake, California, between August 2002 and August 2003. Ammonia oxidation rates were measured using a 15 N isotope tracer technique. 16S ribosomal deoxyribonucleic acid, functional gene, and fluorescence in situ hybridization (FISH) analyses were used to characterize the ammonia oxidizer population. Peak ammonia oxidation activity occurred consistently between 12 and 14 m; the maximum integrated rate was observed in November 2002. The ammonia-oxidizing bacterial (AOB) community exhibited sequences most closely related to halo and/or alkaline tolerant Nitrosomonas-like sequences. The observed phylogeny represented a significant shift from previously documented AOB community composition and was coincident with Mono Lake’s transition from monomixis to meromixis. Samples were also analyzed for ammonia- oxidizing archaea (AOA). FISH analysis revealed a substantial population of Crenarchaeota, the phylum encompassing all known AOA; however, no archaeal ammonia monooxygenase (amoA) sequences were detected. Unrealistic AOB cell-specific nitrification rates strongly indicate the possibility of a missing nitrification source, and correlations between nitrification rates, geochemical variables, and crenarchaeal and AOB abundance also indicate a significant AOA contribution to nitrification. However, the lack of verifiable archaeal amoA genes leaves open the question of whether AOA contribute to nitrification in Mono Lake. Mono Lake is an alkaline (pH 9.8), saline (68– 79 g kg 21 ) lake located just east of the Sierra Nevada range in northern California (38uN, 119uW). Like many closed-basin lakes, Mono Lake’s hydrological regime alternates between periods of meromixis and monomixis depending on interannual variations of freshwater inflow (Melack and Jellison 1998). The prevailing hydrological mixing regime affects water column fluxes and resulting mixolimnetic ammonia (NH 3 ) concentrations. During monomictic periods, fall turnover replenishes the mixolim- nion with nutrient-rich deep water. During meromictic periods, the development of a steep salinity gradient (chemocline) isolates a portion of bottom water (monimo- limnion) and prevents seasonal holomixis (Romero et al. 1998). The development of a persistent chemocline in 1995 produced an extended period of meromixis and resulted in the accumulation of high concentrations of NH 3 in the monimolimnion and chronic nitrogen (N) limitation in the mixolimnion (Melack and Jellison 1998). Ammonia con- centrations exert a major control on nitrification rates (Ward 1986), and, thus, changes in mixing regimes may affect nitrification activity. Nitrification, an aerobic, chemolithotrophic process that converts ammonia (NH 3 ) to nitrate (NO { 3 ) via nitrite (NO { 2 ), plays a key role in N cycling in aquatic environments (Ward 1986; Hastings et al. 1998; Joye et al. 1999). The products of nitrification (e.g., NO { 3 and NO { 2 ) may serve as substrates for denitrifiers or anaerobic ammonia oxidizers, thus removing bioavailable N from the system through N gas evolution (Jenkins and Kemp 1984; Codispoti and Christensen 1985; Mulder et al. 1998). In alkaline ecosystems, however, nitrification may curtail the loss of fixed N via NH 3 volatilization by converting NH 3 to NO { 2 and NO { 3 (Joye et al. 1999). Ammonia volatilization is a critical aspect of the N cycle in Mono Lake as a result of the lake’s low external N inputs, high internal nutrient recycling rates (Jellison et al. 1993), and strong N limitation of phytoplankton primary production (Jellison and Melack 1993). Mono Lake nitrification was investigated just prior to and again shortly after the transition from monomixis to meromixis in 1995–1996. Significant ammonia oxidation rates and a viable ammonia-oxidizing bacterial (AOB) population were documented throughout the oxic water column in April and July 1995 (Joye et al. 1999; Ward et al. 2000). Subsequent phylogenetic analyses during early meromixis (August 1997 and April 1998) did not detect any AOB sequences using the original Ward et al. (2000) protocols or with a wide variety of general and nitrifier- specific 16S ribosomal deoxyribonucleic acid (rDNA) and functional gene primers, denaturing gradient gel electro- phoresis (DGGE), and clone library analyses (Hovanec 1998). The AOB population was presumed to be below 1 Present address: Marine Science Institute, University of Texas, Port Aransas, Texas 78373. 2 Corresponding author (mjoye@uga.edu). Acknowledgments Field laboratory facilities, limnological hydrographic data processing, and other logistical support were provided by R. Jellison, S. Roll, and the Sierra Nevada Aquatic Research Laboratory (MCB 99-77901). We thank J. T. Hollibaugh and G. LeCleir for assistance with sample collection; T. Hollibaugh for use of the FMBIO imaging system; T. Hovanec for providing unpublished 1997 and 1998 nutrient data; K. Kalentera for providing archaeal amoA positive PCR controls; B. Binder for epifluorescent microscope use; M. Beman, C. Francis, and D. Erdner for helpful discussions; and three anonymous reviewers for providing comments that substantially improved the manuscript. This work was supported by National Science Foundation grant MCB 99-77886. Limnol. Oceanogr., 53(6), 2008, 2546–2557 E 2008, by the American Society of Limnology and Oceanography, Inc. 2546