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Aquatic Microbial Ecology

Aquatic Microbial Ecology

The primary production of our aquatic ecosystems is governed by the supply of essential nutrients, of which nitrogen is one of the most important. The microbiology section has been heavily involved in the study of transformations of nitrogen compounds in sediments and planktonic  environments. We have developed and are still developing new techniques for these studies, many of which are based on use of stable nitrogen isotope or sensors that can detect various N-compounds, and we combine these process and microenvironmental analyses with state-of-the-art molecular ecology techniques. We are also studying other important biological transformations in nature, such as those of hydrogen, sulfur compounds, and methane. Some parts of the oceans have extensive water masses with low-oxygen or anoxic water masses, and we investigate primary production and respiratory processes associated with these waters.

Researchers in the field:

- Andreas Schramm              - Anja Kamp

- Emilio Garcia-Robledo         - Lars Peter Nielsen

- Niels Peter Revsbech          - Nils Risgaard-Petersen

- Signe Høgslund                  - Xianzhe Gong

Nitrogen transformations

Sediments (and also terrestrial soils) are important environments for both ammonium and nitrite oxidation and for dissimilatory reductions of nitrate to N2 gas or ammonium by denitrification, anammox  and Dissimilatory Nitrate Reduction to Ammonium (DNRA). The processes may occur in the sediment itself, but may also be mediated by bacteria associated with fauna or plants. Some eukaryotic unicellular organisms such as foraminifera, gromids and diatoms have been shown to accumulate huge concentrations of nitrate and denitrify (foraminifera) or do DNRA (diatoms). Much of our understanding about the nitrogen transformations in sediments stem from the use of microsensors, of which sensors for nitrous oxide, nitrite and nitrate have been developed in our laboratories. In collaboration with colleagues from University of Southern Denmark we also study nitrogen cycling associated with the so-called oxygen minimum zones found at various locations in the oceans, and here we in particulate investigate how very low oxygen concentrations affect the cycling.


Oxygen respiration and photosynthesis

Sediment oxygen consumption and photosynthesis by sediment-associated microorganisms have been studied extensively by use of microsensors for oxygen and pH. Lately an ultra-sensitive oxygen (STOX) sensor developed in our laboratories have made it possible to study these processes also in oceanic oxygen minimum zones, which are of particular interest as a large part of the marine N-loss through denitrification and anammox occurs in these environments . It is possible to directly measure respiration and photosynthesis rates of < 1 nmol L-1 h-1 by use of the new sensor and by optical sensors developed in collaboration with the Technical University of Graz. We have worked in the oxygen minimum zones off Chile, Peru, Ecuador and Mexico, and also in the Bay of Bengal and the fjord of Golfo Dulce in Costa Rica. The expression of genes for various terminal oxidases and N-cycling enzymes in ocean water and pure cultures of bacteria is studied as a function of oxygen concentration and previous exposure to oxygen.


Transformations of hydrogen, sulfur, and methane

Hydrogen is a key intermediate in anaerobic degradation of organic compounds, and we have studied the formation and consumption of hydrogen in cyanobacterial mats from Danish coastal regions and from hot springs of Yellowstone National Park. The study of hydrogen dynamics was enabled by the development of a sulfide-insensitive hydrogen microsensor. A major part of the hydrogen consumption occurs by sulfate reduction, but methanogenesis also contributes. The hydrogen microsensor is also used extensively in our biotechnological projects. The emission of greenhouse gasses including methane and nitrous oxide have been studied in soil, manure, and in marine communities associated with marine fauna.


Key publications

Nielsen LP (1992) Denitrification in sediment determined from nitrogen isotope pairing. FEMS Microbiology Ecology 86: 357-362

Risgaard-Petersen N, Langezaal AM, Ingvardsen S, Schmid MC, Jetten MSM, Op den Camp HJM, Derksen JWM, Pina-Ochoa E, Eriksson SP, Nielsen LP, Revsbech NP, Cedhagen T, van der Zwaan GJ (2006) Evidence for complete denitrification in a benthic foraminifer. Nature 443: 93-96

Tiano, L, E. Garcia-Robledo, T. Dalsgaard, T, A.H. Devol, B.B.Ward, O. Ulloa, D.E. Canfield, and N.P. Revsbech. 2014. Oxygen distribution and aerobic respiration in the north and south eastern tropical Pacific oxygen minimum zones. Deep Sea Res. Part 1: 94: 173-183.

Svenningsen, N.B., Heisterkamp, I.M., Sigby-Clausen, M., Larsen, L.H., Nielsen, L.P.; Stief, P., Schramm, A. 2012. Shell biofilm nitrification and gut denitrification contribute to emission of nitrous oxide by the invasive freshwater mussel Dreissena polymorpha (Zebra mussel). Appl. Env. Microbiol., 78: 4505-4509.

Nielsen, D.Aa., Schramm, A.; Nielsen, L.P., Revsbech, N.P. 2013. Seasonal methane oxidation potential in manure crusts.  Appl. Env. Microbiol. 79: 407-410.

Stief, P., M. Poulsen, L.P. Nielsen, H. Brix, and A. Schramm. 2009. Nitrous oxide emission by aquatic macrofauna. Proc. Nat. Acad. Sci. USA, 106: 4296-4300


External Collaborators

> B.B. Ward, Princeton University                        > B. Thamdrup, Univ. of Southern Denmark

> D.E. Canfield, Univ. of Southern Denmark         > D.M. Ward, Montana State University

> M. Kühl, University of Copenhagen                   > R. Glud, Univ. of Southern Denmark

> O. Ulloa, Univ. of Concepcion, Chile                  > A.H. Devol, University of Washington


Rosette of Niskin bottles equipped with standard CTD and in situ STOX sensors for the measurement of trace oxygen concentrations along the water column. The water collected in the Niskin bottles were used for laboratory experiments with the low-oxygen waters of the oxygen minimum zone.
Microsensor measurements in hot springs of Yellowstone National Park


Light incubation of sub-oxic seawater for the measurement of photosynthesis in water from an Oxygen Minimum Zone (OMZ) by the use of STOX and optical sensors.