Arctic Biogeochemistry

The benthic nitrogen cycle and denitrifying bacteria in arctic fjords

A fjord in the Svalbard islands field site
Some of the Fjords in the Svalbard Islands, like Kongsfjorden, have strong glacial input.
The R/V Farm and Captain Stig Henningsen at the dock in Ny Alesund.
A map showing the North Atlantic Current (NAC), West Spitsbergen Current (WSC), and East Spitsbergen Current (ESC) carrying water into the Arctic where it cools, sinks and becomes part of the North Atlantic Deep Water. Read more about these currents here.

Microbially-catalyzed nitrate reduction processes (denitrification; anammox; dissimilatory nitrate reduction to ammonium, DNRA) comprise the largest loss or output of nitrogen from the coastal ocean on a global scale. Though biogeochemical evidence has solidified the importance of these processes, the mechanisms and controls of nitrogen loss pathways are not well constrained. Temperature is a master physical variable that controls microbial metabolism. Surprisingly few studies have examined the effects of temperature on the rates and pathways of nitrogen loss.

The nitrogen cycle has now been altered by humans to a greater extent than any other biogeochemically-active element . In large portions of the U.S. and Europe, reactive nitrogen inputs are now an order of magnitude above those occurring prior to the 20th century. The relative increase in anthropogenic nitrogen fixation over the past 50 years has been at least five times greater than that observed in atmospheric CO2. The release of excess nitrogen into aquatic and marine ecosystems causes a suite of negative environmental and human health problems. Therefore, in order to effectively manage sensitive coastal environments, the factors controlling the input and output of nitrogen need to be better understood.

The majority of land-derived N is removed from coastal environments through denitrification, which is mediated by sedimentary microorganisms. Nitrogen may be removed by denitrification, the anaerobic microbial respiration of NO3- to gaseous end products (N2, N2O), anammox (anaerobic ammonium oxidation), or DNRA pathways. Temperature is well known to control the turnover of N in coastal marine sediments by both regulating the overall rates of metabolism of microbial communities and shifting the species composition of those communities. Such shifts in species composition may ultimately control whether nitrogen is lost from the ecosystem by defining the mechanism of nitrate respiration. Denitrification and anammox pathways result in a net loss of nitrogen from ecosystems, while DNRA results in the conservation of nitrogen. A shift in microbial communities toward DNRA with rising temperature would shunt nitrogen back into overlying waters, stimulate primary production, and potentially exacerbate coastal eutrophication.

The analysis of nitrate-respiring prokaryotes which catalyze nitrogen loss in marine sediments has thus far concentrated on studies of diversity, and the active community members have rarely been determined. We are employing cutting-edge nucleic acid-based methods that target functional genes encoding for enzymes involved in specific nitrogen transformations, thus allowing us to determine the “active” microorganisms involved in specific processes directly. A variety of functional genes in nitrate respiration pathways, such as nitrate reductase (narG, napA), nitrite reductases (nirS/K, nrfA), and the nitrous oxide reductase (nosZ) proteins, are useful target genes to monitor those bacteria capable of nitrate reduction in environmental samples. During sedimentary nitrate respiration, any microbial group possessing these genes may become active. In this project we are monitoring the active community using mRNA analysis of these target genes.

In polar regions, where sediments are permanently cold, temperature fluctuations resulting from global warming may have a large impact on biogeochemical processes such as the nitrogen cycle. This is particularly important in the Arctic ocean as much of the cold water in the global thermohaline current originates here. Our sampling locations near the Svalbard Islands lie on the eastern edge of the Fram Strait, which is the major deep-water passage between the Arctic Ocean and the North Atlantic. This area is important for the global transfer of heat, mass, and salt, meaning that benthic processes near Svalbard have the potential for widespread impacts globally. Understanding how biogeochemical process here respond to changes in temperature is critical for our understanding of the effects of climate change on the world’s oceans in general.

From the Kostka Lab:


  • Marcel Kuypers and Bo Barker Joergensen, Nutrient Group, Max Planck Institute for Marine Microbiology in Bremen, Germany.
  • Rudolf Amann, Molecular Ecology Group, Max Planck Institute for Marine Microbiology in Bremen, Germany.
  • Dr. Tom Gihring, former Ph.D. Student


T. M. Gihring, A. Canion, A. Riggs, M. Huettel, and J. E. Kostka. 2009. Denitrification in shallow, sublittoral Gulf of Mexico permeable sediments. Limnology and Oceanography (in review).

L. Chipman, D. Podgorski, S.J. Green, J.E. Kostka, W. Cooper, and M. Huettel. 2009. Decomposition of plankton-derived DOM in permeable coastal sediments. Limnology and Oceanography (in review).

T.M. Gihring, G. Lavik, M. Kuypers, and J.E. Kostka. 2009. Quantification of nitrogen removal from Arctic marine sediments and temperature regulation of microbial communities that mediate denitrification and anammox. Limnology and Oceanography (in review).

J. E. Kostka, T. M. Gihring, H. Mills, M. Huettel, J. E.E. van Beusekom, H. Gao, G. Lavik, and M. M.M. Kuypers. Nitrogen biogeochemistry of permeable sediments: temperature regulation of denitrification and anammox across a 50o latitudinal gradient (in preparation).

H. Gao, F. Schreiber, G. Collins, M. M. Jensen, J. E Kostka, G. Lavik, D. de Beer, H. Y. Zhou, M. M M Kuypers. 2009. Aerobic denitrification in permeable Wadden Sea sediment (in preparation).