Estuaries and Coasts

, Volume 41, Issue 3, pp 626–660 | Cite as

Microbial Nitrogen Cycling in Estuaries: From Genes to Ecosystem Processes

  • Julian Damashek
  • Christopher A. FrancisEmail author


Nitrogen (N) is one of the primary nutrients required to build biomass and is therefore in high demand in aquatic ecosystems. Estuaries, however, are frequently inundated with high concentrations of anthropogenic nitrogen, which can lead to substantially degraded water quality. Understanding drivers of biogeochemical N cycling rates and the microbial communities responsible for these processes is critical for understanding how estuaries are responding to human development. Estuaries are notoriously complex ecosystems: not only do individual estuaries by definition encompass gradients of salinity and other changing environmental conditions, but differences in physical parameters (e.g., bathymetry, hydrodynamics, tidal flushing) lead to a tremendous amount of variability in estuarine processes between ecosystems, as well. Here, we review the current knowledge of N cycling processes in estuaries carried out by bacteria and archaea, including both biogeochemical rate measurements and molecular characterizations of N cycling microbial communities. Particular attention is focused on identifying key environmental factors associated with distinct biogeochemical or microbial regimes across numerous estuaries. Additionally, we describe novel metabolisms or organisms that have recently been discovered but have not yet been fully explored in estuaries to date. While the majority of research has been conducted in the benthos, we also describe data from estuarine water columns. Understanding both the common patterns and the differences between estuaries has important implications for how these critical ecosystems respond to changing environmental conditions.


Nitrogen Biogeochemistry Microbial ecology Functional gene Nutrient cycling 



This work was funded by National Science Foundation Biological Oceanography grant OCE-0847266 (to Chris Francis), with additional salary support from the 2014-2015 Stanford-USGS Fellowship (to Julian Damashek).


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© Coastal and Estuarine Research Federation 2017

Authors and Affiliations

  1. 1.Department of Earth System ScienceStanford UniversityStanfordUSA
  2. 2.Department of Marine SciencesUniversity of GeorgiaAthensUSA

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