Abstract
Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic nitrification, is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.
Highlights
In the past century, widespread synthetic ammonia production has profoundly perturbed the global nitrogen (N) cycle (Erisman et al, 2008)
All nutrients were lowest at station EMP0046, located at the southern tip of Franks Tract, a shallow tidal lake connected to the San Joaquin River (Lucas et al, 2002)
The high abundance of ammonia-oxidizing bacteria (AOB) in this river, combined with elevated potential nitrification www.frontiersin.org rates, suggested AOB may be driving nitrification in the benthic regions of the Delta most directly affected by anthropogenic NH+4 pollution
Summary
Widespread synthetic ammonia production has profoundly perturbed the global nitrogen (N) cycle (Erisman et al, 2008). In well-mixed rivers and estuaries, these N loss pathways are typically active only within anoxic sediments, and provide an ecological N sink by converting fixed N to nitrogen gas (N2). In this way, microbes provide a tremendous “ecosystem service” by shuttling N out of aquatic ecosystems and back to the atmosphere
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