Nitrogen cycling research

Nitrogen cycling is the “bread and butter” of the lab, and includes study of biogeochemistry (N cycling rates) and the ecology of relevant microbes. Most studies are in aquatic systems. Current projects include:

  1. Understanding the drivers of water column nitrification in aquatic ecosystems.

Nitrification, the microbial oxidation of ammonia (NH3) to nitrite (NO2) and/or nitrate (NO3), is a key link in the N cycle. We are interested in how rates of nitrification and communities of nitrifying microbes change over space and time in a variety of aquatic ecosystems. Much of this work started in the Francis Lab at Stanford (studying San Francisco Bay) and the Hollibaugh Lab at the University of Georgia (studying the coastal Atlantic Ocean). We are currently sampling a variety of rivers, creeks, and lakes in central New York to continue this work, and are particularly interested in how anthoropogenic N pollution from both urban sources (such as sewage and Combined Sewer Overflows) and rural sources (such as fertilizer runoff) is cycled in aquatic ecosystems. We are also working on a global analysis of nitrifier ecology in freshwaters.

Students involved: Smith, T. Kuts, K. Kuts, Marsh, Lohmann, Garrett, Dautovic, Okotie-Oyekan, Challenor, Menendez, Christie, Pettie, Greaney

Manuscripts: Hollibaugh et al. (in review); Rasmussen et al. 2021; Damashek, Tolar et al. 2019; Damashek & Francis 2018; Damashek et al. 2017; Damashek et al. 2016; Smith et al. 2016; Damashek et al. 2015

2.) Determining the role of dissolved organic N (DON) in nitrification.

Aquatic DON is studied less than inorganic N but has important roles in ecosystems. Recent evidence has shown that urea, a commond form of DON, often controls the growth and toxicity of “harmful algal blooms” (HABs), and some nitrifiers – including diverse bacteria and archaea – can take urea up into their cells, break it down, and oxidize the resulting NH3. There has been further speculation that some ammonia oxidizers may be capable of using more complex DON compounds as energy sources. Previous work in the Hollibaugh Lab at the University of Georgia focused on understanding the role of polyamines in marine nitrification, particularly whether common ammonia-oxidizing archaea are capable of using polyamines as their sole energy source. Currently, we are studying urea cycling in freshwater ecosystems in central New York, with a focus on urea oxidation rates and microbial competition for urea. Recently we have been collaborating with the Geier Lab at Colgate University to test novel ways to measure N isotopes, which we hope will facilitate rapid rate measurements for future projects.

Students involved: Smith, LaFramboise, T. Kuts, Okotie-Oyekan

Manuscripts: Damashek, Bayer et al. (in review), Hollibaugh et al. (in review), Damashek, Tolar et al. 2019

3) Determining patterns of N2-fixation across the freshwater-marine continuum

This project is the lab’s first foray into N2-fixation, a biological process by which N2 gas in converted to inorganic NH3 and thus enters the biosphere. We are primarily focusing on studying the biodiversity of N2-fixing microbes at inter-ecosystem scales. This work is a massive collaboration with the Fulweiler Lab at Boston University, the Marcarelli Lab at Michigan Technological University, the Scott Lab at Baylor University, and many others associated with the Aquatic N2-Fixation Research Coordination Network.