Estuaries and Coasts

, Volume 39, Issue 4, pp 1050–1071 | Cite as

Variable Nitrification Rates Across Environmental Gradients in Turbid, Nutrient-Rich Estuary Waters of San Francisco Bay

  • Julian Damashek
  • Karen L. Casciotti
  • Christopher A. FrancisEmail author


Understanding rates of nitrogen cycling in estuaries is crucial for understanding their productivity and resilience to eutrophication. Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, links reduced and oxidized forms of inorganic nitrogen and is therefore an important step of the nitrogen cycle. However, rates of nitrification in estuary waters are poorly characterized. In fall and winter of 2011–2012, we measured nitrification rates throughout the water column of all major regions of San Francisco Bay, a large, turbid, nutrient-rich estuary on the west coast of North America. Nitrification rates were highest in regions furthest from the ocean, including many samples with rates higher than those typically measured in the sea. In bottom waters, nitrification rates were commonly at least twice the magnitude of surface rates. Strong positive correlations were found between nitrification and both suspended particulate matter and ammonium concentration. Our results are consistent with previous studies documenting high nitrification rates in brackish, turbid regions of other estuaries, many of which also showed correlations with suspended sediment and ammonium concentrations. Overall, nitrification in estuary waters appears to play a significant role in the estuarine nitrogen cycle, though the maximum rate of nitrification can differ dramatically between estuaries.


Nitrification Biogeochemistry Ammonia oxidation Ammonium Nitrogen Estuary 



We are grateful to the crews of the R/V Polaris and the R/V Questuary, as well as Jim Cloern, Tara Schraga, and the rest of the USGS Water Quality of San Francisco Bay group for enabling our participation in cruises and assisting with sample collection. Jason Smith assisted in cruise planning and sample collection onboard the Questuary and, along with Matt Forbes, Carly Buchwald, and Brian Peters, gave valuable help with isotopic measurements. Jim Cloern also provided useful advice in modeling SPM concentrations for Questuary sites. Carol Kendall and her group at USGS, particularly Sara Peek, kindly provided preliminary ammonium isotope data prior to publication. Thoughtful comments from two anonymous reviewers, as well as discussions with Alex Parker and Bradley Tolar, greatly improved this manuscript. This work was funded by National Science Foundation Biological Oceanography grant OCE-0847266 (to Chris Francis), and additional salary support came from the 2014–2015 Stanford-USGS Fellowship (to Julian Damashek).

Supplementary material

12237_2016_71_Fig6_ESM.jpg (530 kb)
Supp. Fig. 1

Cleveland dotplots of each environmental variable. Values are shown on the x-axes, while samples are displayed in random order along the y-axes. Clear outliers were identified in nitrite and SPM (JPG 530 kb)

12237_2016_71_MOESM1_ESM.eps (2.4 mb)
High resolution image (EPS 2456 kb)
12237_2016_71_Fig7_ESM.jpg (170 kb)
Supp. Fig. 2

Delta outflow (Dayflow) data for water year 2011-2012. Sampling dates in this study are marked by red crosses above the Dayflow data (JPG 170 kb)

12237_2016_71_MOESM2_ESM.eps (1.3 mb)
High resolution image (EPS 1309 kb)
12237_2016_71_MOESM3_ESM.pdf (351 kb)
Supp. Table 1 Environmental data from San Francisco Bay waters. a Modeled SPM concentrations (PDF 350 kb)


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Copyright information

© Coastal and Estuarine Research Federation 2016

Authors and Affiliations

  • Julian Damashek
    • 1
  • Karen L. Casciotti
    • 1
  • Christopher A. Francis
    • 1
    Email author
  1. 1.Department of Earth System ScienceStanford UniversityStanfordUSA

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