Microbial Nitrogen and Phosphorus Cycling in Stream Ecosystems

The biogeochemical cycling of nitrogen (N) and phosphorus (P) in streams has received significant scientific attention due to their status as primary limiting nutrients for aquatic primary production. Microbes play a particularly crucial role in the nitrogen cycle, leveraging its multiple oxidation states to transform its bioavailability. Certain microbe-mediated processes introduce bioavailable nitrogen into the stream system, while others permanently remove it. The management of these nutrients is critical because their export from streams is a leading cause of eutrophication in downstream lakes and coastal oceans. Consequently, the capacity of stream biota to retain and transform nutrients directly impacts broader water quality.

The nitrogen cycle is complex and involves several key, interdependent microbial processes, each performed by organisms with specific physiological abilities (Figure 3). These transformations are driven by metabolic needs such as nutrient acquisition and energy generation. Importantly, these processes require distinct redox conditions, meaning they do not occur simultaneously in the same physical location within the stream. This spatial separation is a fundamental aspect of stream nutrient dynamics, influenced by factors from the hypotheic zone to surface biofilms.

Figure 3. Critical microbial-mediated steps in the nitrogen cycle

Denitrification: A Critical Nitrogen Removal Pathway. Denitrification is an anaerobic process mediated primarily by facultatively anaerobic heterotrophic bacteria. It has been extensively studied due to its capacity for the dissimilatory reduction of nitrate to dinitrogen gas, effectively removing nitrogen from the aquatic system. This process is a vital ecosystem service, as high nitrate concentrations in streams often drive eutrophication. While denitrification rates are frequently measured without characterizing the underlying bacterial community, understanding the sequence of biochemical steps is essential. If the final reduction step is incomplete due to the absence of the nitrous oxide reductase enzyme, the potent greenhouse gas nitrous oxide is produced instead of harmless nitrogen gas.

The environmental drivers of denitrification are well-established and include concentrations of nitrate, the amount and type of organic carbon, oxygen levels, temperature, pH, and the presence of specific enzyme inhibitors. In stream ecosystems, nitrate concentration is consistently identified as the primary driver. A seminal study by Mulholland et al. found that nitrate concentrations and water discharge were the most important variables positively correlated with denitrification rates across a variety of streams. This is evident in agriculturally impacted streams, which typically exhibit both high nitrate concentrations and consequently high denitrification rates.

Nitrification and Nitrogen Fixation. Nitrification is the aerobic process performed by chemoautotrophic bacteria that oxidizes ammonia to nitrate. This process is often coupled with denitrification, as the nitrate produced by nitrifiers becomes the primary substrate for denitrifiers. However, nitrifying bacteria in streams can be outcompeted for ammonia by heterotrophic bacteria when labile carbon is readily available, which can throttle the entire nitrogen transformation pathway. This competition highlights the tight coupling between carbon and nitrogen cycles in these ecosystems.

Nitrogen fixation is another key microbial process, performed by certain bacteria and cyanobacteria, which converts atmospheric dinitrogen gas into bioavailable ammonia. While the occurrence of noxious blooms of nitrogen-fixing cyanobacteria is a greater concern in eutrophic lakes, the process is still relevant in streams. Arguably, light limitation in forested headwater streams often restricts cyanobacterial growth, leading to relatively fewer studies on stream nitrogen fixation. Nevertheless, this process can be critically important in certain systems, such as in desert streams of the southwestern US, where studies have shown moderately high rates of nitrogen fixation seasonally.

The Role of Phosphorus in Stream Limitation.Although phosphorus does not undergo the same suite of microbial-mediated redox transformations as nitrogen, it is often the primary limiting nutrient for algal growth in freshwater environments. The impacts of phosphorus on stimulating algal blooms are widely documented, and its management is a cornerstone of eutrophication control strategies. It is also possible for ecosystems to experience N and P co-limitation, where both nutrients simultaneously constrain primary production. A meta-analysis of stream data by Dodds et al. concluded that both nitrogen and phosphorus are potentially limiting in stream ecosystems, emphasizing the need for a dual-nutrient management strategy to effectively protect water quality from algal blooms.