PEEIR
Pacific Estuarine Ecosystem Indicator Research Consortium
Controls on Microbial Nitrogen
Cycling in Coastal Estuaries
Issue
Nutrients, especially nitrogen (N), strongly influence
the productivity and environmental quality of coastal
estuaries. Upland development and human activity
have increased nitrogen loading into coastal zones
by as much as 50% during the past century, and
eutrophication has become an increasingly serious
problem worldwide. It is thus critical to understand
the environmental and biological controls on the
cycling of nitrogen, which is predominately mediated
by microbial processes such as N fixation, nitrification
and denitrification (see Figure 1). Ammonium (NH4+),
resulting from soil microbial nitrogen fixation and
organic decomposition, is oxidized during nitrification
to NO2- and then to NO3-. Denitrification, on the other
hand, reduces oxidized N to nitrogen gases, and is the
only means to permanently remove fixed nitrogen from
a system.
Given the extreme importance of nitrogen cycling
in coastal estuaries, there have been many studies
regarding nitrogen budgets in estuaries, its import
from the uplands, and storage and export into the open
ocean (Link to Nitrogen Isotopes). However, nutrient
budget models often rely on estimating the microbial
contribution using “black boxes,” whereas effective
management relies on understanding and working with
the controlling processes. This work investigated the
underlying controls on microbial nitrogen processing
including biophysical controls, microbial community
compositional influences, environmental effects,
and pollutant-microbial interactions. The goal was
to provide estuarine ecosystem managers useful
information towards managing nitrogen loading and
eutrophication of estuaries and coastal waters.
Approach and Rationale
Our approach was to characterize both the
physicochemical and the biological aspects of N cycling,
and also the interactions between them. Linking
the environmental traits and the biological entities
in the environment thus provides a more accurate
and complete understanding of N cycling in coastal
estuaries.

The estuaries were characterized physically and
chemically by quantifying nitrogen species, organic
matter, and rates of nitrification and denitrification.
Microbial communities responsible for the processes
were characterized via molecular tools: DNA extraction,
PCR, terminal restriction fragment length polymorphism
(TRFLP), and clone library analysis.
Findings and Impact
•
Rocky biofilms exhibited both higher nitrification
and denitrification rates as compared to intertidal
sediments.
•
Denitrification preferentially occurred in particleattached microbial communities, and the attached
communities possessed a higher denitrification capacity
on a per cell basis as compared to free-living denitrifiers.
•
Differences in environmental factors
(physicochemical characteristics including pollutants)
led to the selection of particular ammonia oxidizing
bacteria, different functional communities, and different
N-cycling rates.
•
Denitirification potential was postively related
to organic carbon content and the abundance of
denitrifiers.
A research partnership between University of California, Davis, Bodega Marine Laboratory
and University of California, Santa Barbara
Funded by U.S. EPA Science To Achieve Results (STAR) EAGLE Program Grant No. R82867601
PEEIR
Pacific Estuarine Ecosystem Indicator Research Consortium
Applications
Given that N-cycling processes exhibit spatial
heterogeneity or even “hot spots” in the estuarine systems,
coastal managers can use the tools herein to identify
local regions of concern and to focus human and financial
efforts. For example, if managers intend to use a wetland
to ameliorate excessive nitrate loading from uplands, they
can increase the residence time of the nitrate input into
the local “hot spot” to increase overall nitrate removal.
Similarly, information on the environmental factors can
be used for a more accurate estimation of N-cycling
conditions in a salt marsh so that managers can more
effectively evaluate the marsh’s buffering capacity during
storm events.
Publications
Cao, Y. and Holden, P.A. submitted. Significance of
particle-attached microbial communities in salt
marsh denitrification,.
Magalhaes, C., Bano, N. , Wiebe, W.J., Bordalo, A.
A. and Hollibaugh, J.T. submitted. Nitrous oxide
reductase genes (nosZ) dynamics in intertidal rocky
biofilms and sediments of the Douro River Estuary
(Portugal), and relation with N-biogeochemistry .
Fig. 1. Conceptual diagram of nitrogen cycling in coastal regions.
Contact Names
Patricia Holden, [email protected]
Donald Bren School of Environmental Science & Management,
University of California, Santa Barbara;
James Hollibaugh, [email protected]
Department of Marine Sciences, University of Georgia, Athens
Contributing Investigator:
Yiping Cao, University of California, Santa Barbara
A research partnership between University of California, Davis, Bodega Marine Laboratory
and University of California, Santa Barbara
Funded by U.S. EPA Science To Achieve Results (STAR) EAGLE Program Grant No. R82867601