Biogeochemistry of marine sediments

The ocean floor is covered with sediments ranging from a few meters to more than 10 km thickness. Biological, geological, chemical and physical processes within marine sediments shape the composition of the natural environment. We study the cycles of chemical elements such as carbon, nitrogen and sulfur and their interaction with microorganisms.

Microorganisms in marine sediments derive energy by transferring electrons to a variety of external electron acceptors depending on their availability and energy yield and the availability of a suitable organic carbon substrate. Using a multitude of techniques we conduct direct measurements of microbially mediated transformation rates of specific compounds such as sulfate, iron and nitrogen. We measure the solid phase concentrations and isotopic signature of key elements and of the dissolved compounds in the interstitial water. This allows us to describe the partitioning of microbially mediated pathways of carbon mineralization and to model reaction rates throughout the sediment column. Our research takes us from the organic rich coastal sediments, over the continental shelf and into the nutrient-poor sediments of the deep oceans, and ranges from the very young to millions of years old deposits.

Carbon mineralization

The total microbial respiration in sediments can in principle be determined from either the consumption of electron acceptors or from the production of CO2. Due to slow conversion of large pools it is generally not possible to determine concentration changes over time directly on deeply buried sediments. We develop new modeling approaches combining reverse modeling of porewater profiles, direct rate measurements based on radiotracers, and natural isotopic signature. In addition we have developed a D:L-amino acid racemization model by which it is possible to quantify living microbial biomass and necromass, turnover times of these pools as well as the carbon oxidation rate. We have a keen interest in microbial processes that linger on at extremely slow rates across immense time spans in deeply buried deposits.

Microbially mediated turnover of volatile fatty acids

Short chain volatile fatty acids, primarily acetate, are the link between fermenters and terminal oxidizers in marine sediments. We developed a new method based on Two-Dimensional Ion Chromatography Mass Spectrometry (2D-IC-MS) for analyzing formate, acetate, propionate, butyrate, and lactate at in situ levels in marine porewater. The 2D-IC-MS is also a valuable tool in isotope tracer studies because it allows us to monitor substrate concentrations and isotopic enrichment. We wish to resolve the kinetic and thermodynamic constraints that control the concentration of volatile fatty acids, and thereby determine the division of the energy liberated during mineralization of organic carbon between the fermenters and the oxidizers.

Cryptic sulfur cycling

The traditional view of marine geomicrobiology is that the sediment column is divided into compartments of different electron acceptor utilization. According to theory, a more energy efficient respiration excludes less efficient pathways by depleting the electron donors below the threshold for energy conservation for organisms with less efficient metabolism. This produces a characteristic sequence where oxygen is respired in the first few millimeter, then nitrate, manganese, iron, and sulfate. The organic matter below the penetration depth of sulfate is consumed by methane producing organisms. Nevertheless, the population of sulfate reducing organisms is about as high in the metanogenic zone as in the sulfate reducing zone. We investigate this phenomenon under the assumption that sulfate is continuously produced by oxidation of sulfide with ferric iron in the metanogenic zone, and that this sulfate is immediately consumed by an active population of sulfate reducing microorganisms. We study the turnover of sulfate based on radiotracer techniques and natural stabile isotopes as well as the natural populations from environmental RNA and DNA; and we study the metabolic capability of high affinity sulfate reducers.

Sulfur cyclling and isotopes

The sulfur cycle in marine sediments is a globally significant process that remineralizes part of the Earth’s annual primary production and plays an important role in the recycling not only of carbon but also of nutrients and minerals to the oceans. Sulfate respiring microorganisms, living in the anoxic part of marine sediments are the driver of this cycle. They utilize the large pool of electron acceptor available as sulfate to oxidize organic matter deposited and buried in the seabed and in doing so, produce energy for cell maintenance and growth. The byproducts of their metabolism are inorganic carbon and sulfide. Modelling of sulfate consumption rates in sediments, as well as measurements in-situ with radioactive tracers have been used in order to understand the different parameters controlling the sulfur cycle in marine sediments. The two approaches, while sound, often give very different results because the sulfur cycle often is affected by site-specific environmental conditions and other sulfur metabolism present in the seabed.

Stable isotopes can be a useful tool for the study of a variety of microbially-mediated processes within marine sediments.  Isotopes, which are ‘versions’ of an element with a different number of neutrons in the nucleus, do not necessarily react at the same rate in various chemical and biological reactions. Therefore, measuring the ratio of various isotopes and how it changes over the course of a chemical or biological reaction provides independent information about the nature of the reaction. A particularly powerful tool for studying the sulfur cycle in marine sediments is the coupling of stable sulfur, oxygen and carbon isotopes. These measurements provide a good constraint on the depth distribution and location of the biogeochemical processes because of their metabolic-specific isotopic discriminations. The center for geomicrobiology is currently working on coupling the traditional methods of monitoring sulfate reduction, with the metabolically-active tracers to better understand how marine sediments utilize sulfur.


  • Røy H., H. S. Weber, I. H. Tarpgaard, T. G. Ferdelman, and B. B. Jørgensen (2014). Determination of dissimilatory sulfate reduction rates in marine sediment via radioactive 35S tracer, Limnology and Oceanography: Methods 12: 196-211.
  • Glombitza, C., J. Pedersen, H. Røy & B.B. Jørgensen (2014). Direct analysis of volatile fatty acids in marine sediment porewater by two-dimensional ion chromatography-mass spectrometry. Limnology and Oceanography: Methods, 12: 455-468.
  • Arnold G. L., B. Brunner, I. A. Müller and H. Røy (2014). Modern applications for a total sulfur reduction distillation method - what's old is new again, Geochemical Transactions. 15:4
  • Holmkvist, L., A. Kamyshny Jr., V. Brüchert, T. Ferdelman & B.B. Jørgensen (2014). Sulfidization of lacustrine glacial clay upon Holocene marine transgression (Arkona Basin, Baltic Sea). Geochimica et Cosmochimica Acta, 142: 75-94.
  • Røy, H., Kallmeyer, J., Adhikari, R. R., Pockalny, R., Jørgensen, B. B. & S D'Hondt (2012). Aerobic Microbial Respiration in 86-Million-Year-Old Deep-Sea Red Clay, Science, vol. 336, s. 922-925.
  • Karsten Alexander Lettmann, Natascha Riedinger, Ronny Ramlau, Nina Knab, Michael Ernst Böttcher, Arzhang Khalili, Jörg-Olaf Wolff, Bo Barker Jørgensen (2012). "Estimation of biogeochemical rates from concentration profiles: A novel inverse method", Estuarine, Coastal and Shelf Science, Volume 100, 26–37.