Microbial Ecology

, Volume 69, Issue 1, pp 13–24 | Cite as

Spatiotemporal Relationships Between the Abundance, Distribution, and Potential Activities of Ammonia-Oxidizing and Denitrifying Microorganisms in Intertidal Sediments

  • Jason M. Smith
  • Annika C. Mosier
  • Christopher A. FrancisEmail author
Microbiology of Aquatic Systems


The primary objective of this study was to gain an understanding of how key microbial communities involved in nitrogen cycling in estuarine sediments vary over a 12-month period. Furthermore, we sought to determine whether changes in the size of these communities are related to, or indicative of, seasonal patterns in fixed nitrogen dynamics in Elkhorn Slough—a small, agriculturally impacted estuary with a direct connection to Monterey Bay. We assessed sediment and pore water characteristics, abundance of functional genes for nitrification (bacterial and archaeal amoA, encoding ammonia monooxygenase subunit A) and denitrification (nirS and nirK, encoding nitrite reductase), and measurements of potential nitrification and denitrification activities at six sites. No seasonality in the abundance of denitrifier or ammonia oxidizer genes was observed. A strong association between potential nitrification activity and the size of ammonia-oxidizing bacterial communities was observed across the estuary. In contrast, ammonia-oxidizing archaeal abundances remained relatively constant in space and time. Unlike many other estuaries, salinity does not appear to regulate the distribution of ammonia-oxidizing communities in Elkhorn Slough. Instead, their distributions appear to be governed over two different time scales. Long-term niche characteristics selected for the gross size of archaeal and bacterial ammonia-oxidizing communities, yet covariation in their abundances between monthly samples suggests that they respond in a similar manner to short-term changes in their environment. Abundances of denitrifier and ammonia oxidizer genes also covaried, but site-specific differences in this relationship suggest differing levels of interaction (or coupling) between nitrification and denitrification.


Denitrification Dissolve Inorganic Nitrogen Ammonia Oxidizer amoA Gene Potential Nitrification 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors would like to thank Darcy McRose, Helen Chen, Alyson Santoro, Daniel Keymer, Nicholas Nidzieko, Nate Clark, and Angela Primavera for the assistance with sample collection and data acquisition. This work was supported in part by National Science Foundation grants MCB-0604270 and OCE-0847266 to C.A.F.

Supplementary material

248_2014_450_MOESM1_ESM.docx (244 kb)
ESM 1 (DOCX 244 kb)


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Jason M. Smith
    • 1
    • 2
  • Annika C. Mosier
    • 1
    • 3
  • Christopher A. Francis
    • 1
    Email author
  1. 1.Department of Environmental Earth System Science Stanford UniversityStanfordUSA
  2. 2.Monterey Bay Aquarium Research InstituteMoss LandingUSA
  3. 3.Department of Integrative BiologyUniversity of ColoradoDenverUSA

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