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  4. Department of Biogeochemistry
  5. Biogeochemistry Group


Research in the Biogeochemistry Department focuses on microbiological and geochemical processes that control bioactive element cycling in the marine environment. We employ geochemical, microbiological, modeling, molecular and single-cell techniques to study the environmental regulation of these processes, and their effects on the global biogeochemical cycles. Our goal is to provide fundamental insights into microbial mediated processes in the Ocean that ultimately affect Ocean chemistry, biology and climate, and vital input for models used to predict potential future changes resulting from human activities.

Current News

From nitrogen biogeochemistry to method development…..three new manuscripts featuring young post-doctoral researchers Hannah Marchant and Wiebke Mohr.
The biogeochemistry of sandy sediments – especially in regards to nitrogen cycling is an ongoing research topic within the Biogeochemistry Department. Anthropogenic activities continue to pollute our coastal seas with nitrate and the functioning of sandy sediments as natural bioreactors which remove these nitrate inputs is still poorly understood. Recent research carried out by Hannah Marchant (see photo below left) in the nearby Wadden Sea, unravels the fate of nitrate after it enters the sediment. In all seasons denitrification was shown to be the main source of N-loss in both oxic and anoxic sediments, however the important role of DNRA and intracellular storage of nitrate by organisms within the sediment was also uncovered. The nitrate respiration supported by intracellularly stored nitrate increases the N-loss in intertidal sediments by up to 20 %, further increasing the important role these sediments have in removing anthropogenic nitrate.

The cold, lonely life of a Wadden Sea intertidal sediment researcher (photo: H. Marchant)

The dry, dusty oligotrophic coastline just outside Mindelo, São Vicente, Cabo Verde (photo: W. Mohr)

The physiology of the recently discovered symbiosis between a widely distributed, N2-fixing cyanobacterial group (group A or UCYN-A) and a eukaryotic algae has now been further characterized by former Ph.D. student Andreas Krupke and co-workers from the MPI and the GEOMAR (Helmholtz-Centre for Ocean Research, Kiel). The manuscript highlights the importance of Saharan dust as a source of iron and/or phosphorus for N2 fixation by the UCYN-A in the subtropical Northeast Atlantic (see photo above right). The symbiosis persists even under changing nutrient conditions suggesting an obligate association that might play an important role in the global carbon and nitrogen cycles. (ISME Journal Dec 2014)

Collaborators from Harvard University and Wiebke Mohr have developed a new method (reported in Analytical Chemistry), called P-SIF (Protein Stable Isotope Fingerprinting), which aims at linking the identity of microbial organisms to their function in mixed microbial communities. The method relies on the extraction of cellular proteins that are subsequently separated by multidimensional chromatography and analyzed for their carbon stable isotope ratio as well as the identity and origin of the proteins.

Congratulations to Hannah Marchant....
...on the successful defense of her doctoral dissertation on March 27th in Geosciences at the University of Bremen. Her doctoral dissertation colloquium was entitled:
The coastal sand filter and its role as a biocatalyst of nitrogen transformations
A MarMic student, Hannah did both her Masters and doctoral research in Biogeochemistry and will continue as a post-doc in our group.

Congratulations to Jessika Füssel....
...on the successful defense of her doctoral dissertation on March 27th in Geosciences at the University of Bremen. Her doctoral dissertation colloquium was entitled:
Nitrite Oxidation in Oceanic Oxygen Minimum Zones.
A MarMic student, Jessika did both her Masters and doctoral research in Biogeochemistry and is now working in the Project SeaPump at MARUM

The strange behavior of porous particles at interfaces

Arzhang Khalili and colleagues have found a remarkable effect while studying porosity of different porous materials near fluid-porous interfaces, which could affect the way scientists assess the interfacial heat and mass transfer.
Usually, a constant value for porosity known as bulk porosity is taken, even when the porous medium is attached to a free fluid. However, the researchers found that the porosity undergoes a spatial variation, since the volume fraction of the solid matrix near the interface region differs from that in the core. For the first time, the authors present an analytically derived relation for the variation of porosity with depth below an interface, which is published in the Journal of Chemical Engineering Science. The quantification of porosity by laboratory experiments and numerical modeling matched well with the analytical prediction. Arzhang Khalili points out that although variable porosity has been mentioned in literature, a functional relationship had remained illusive. “Surprisingly, this relation was found to be applicable to porosity variations of the non-granular porous layers such as biofilms and microbial mats”.

New Biogeochemistry Publications in the Proceedings of the National Academy of Science (PNAS)

Scientists from the Biogeochemistry Group have published three articles within the last month in the highly renowned journal Proceedings of the National Academy of Science. All three publications concern links between biogeochemical processes and eludating Earth history. In the first, Sergio Contreras (Biogeochemistry alumnus now at the University of Pittsburgh) and co-workers detail the effects of glacial-interglacial oceanographic perturbations on biogeochemical processes occuring in deeply buried sediments in the deep biosphere. In the second paper, Marcel Kuypers joins on a paper by Owen et al. that uses stable sulfur isotopes to constrain the extent of sulfide-rich basins during the Cretaceaous. Tim Lyons, the principal investigator of the project at the U. California, Riverside, has been a frequent guest as a Hansa Science Fellow in our group. Finally, Ben Brunner (Biogeochemistry alumnus, now on his way to a faculty position at the University of Texas, El Paso) and Sergio Contreras, along with collaborators from the Biogeochemistry Group, the Radboud University of Nijmegen and University of Basel, have explored the nitrogen isotope systematics of the anaerobic ammonium oxidation process, which should help in deciphering the N isotope story recorded over geological time in marine sediments.

New on viral-bacterial interactions....

Former Biogeochemistry student Abdul Sheik and co-workers from the MPI and the Royal Netherlands Institute of Sea Research (NIOZ) have just published in The ISME Journal an article entitled Responses of the coastal bacterial community to viral infection of the algae Phaeocystis globosa. The research, arising from his doctoral research, reveals a "novel role of viruses in theleakage or excretion of algal biomass upon infection, which provides an additional ecological niche for specific bacterial populations and potentially redirects carbon availability. " Abdul is now working as a post-doc at the Eco-Systems Biology Research Group,Luxembourg Centre for Systems Biomedicine (LCSB).

Insights into N2 Fixation with Single Cell techniques.....

Andreas Krupke, Nicullina Musat, Marcel Kuypers and Rachel Foster along with Molecular Ecology colleagues Bernhard Fuchs and Rudi Amann have pulbished a new paper in Systematic and Applied Microbiology on N2 fixation by unicellular cyanobacteria populations of Cape Verde. It includessome spectacular nanoSIMs imaging and
FISH images of the uncultivated unicellular group A by Andreas and Niculina.

Controls on Nitrogen Fluxes in the Oxygen Minimum Zone off Peru

Biogeochemistry Group members Tim Kavelage, Gaute Lavik, Phyllis Lam, Sergio Contreras and Marcel Kuypers, together with colleagues from GEOMAR (Kiel, Germany) and IMARPE (Lima, Peru) have published an article in Nature Geoscience. Through extensive shipboard experimentation they have been able to link fixed nitrogen loss from the Peru Upwelling to carbon export.
See News on the MPI homepage for more information and also the informative News and Views article written by Bo Thamdrup.

Sulfur as an intermediate in anaerobic oxidation of methane

Biogeochemistry Group members Jana Milucka, Tim Ferdelman, Daniela Franzke and Marcel Kuypers are lead authors on a recent article in Nature, where new results and a new model for sulfate-dependent anaerobic oxidation of methane appeared.
See News on MPI homepage for more information.

Milucka, J, T.G. Ferdelman, L. Polerecky, D. Franzke, G. Wegener, M. Schmid, I. Lieberwirth, M. Wagner, F. Widdel, M.M.M Kuypers. 2012. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature, 491, 541-546, doi: 10:1038/nature11656.

Polysulfide formation during oxidation and reduction of sulfur by Beggiatoa sp.

Many sulfide-oxidizing bacteria store large amounts of sulfur intra- or extracellularly but the chemical nature of this stored sulfur has long been debated. By analyzing living cells of Beggiatoa sp. with Raman microscopy, Jasmine Berg and colleagues show that the composition of intracellular sulfur in these bacteria changes under different ecophysiological conditions(Berg et al. published online this month in Applied & Environmental Microbiology) . The authors propose that polysulfides represent a universal pool of bio-available sulfur during sulfur oxidation and reduction. Further oxidation of sulfur occurred simultaneously with sulfide oxidation and led to accumulation of high concentrations of sulfate inside the bacterial cells.

See the following press releases for more information:

Cyclic 100 ka (glacial-interglacial) migration of sub-seafloor redox zonation on the Peruvian shelf. Sergio Contreras, Patrick Meister, Bo Liu, Xavier Prieto-Mollar, Kai-Uwe Hinrichs, Arzhang Khalili, Timothy G. Ferdelman, Marcel M. M. Kuypers, and Bo Barker Jørgensen. Proceedings of the National Academy of Sciences 2013, doi:10.1073/pnas.1305981110/-/DCSupplemental

Sulfur isotopes track the global extent and dynamics of euxinia during Cretaceous Oceanic Anoxic Event 2
Jeremy D. Owens, Benjamin C. Gill, Hugh C. Jenkyns, Steven M. Bates, Silke Severmann, Marcel M. M. Kuypers, Richard G. Woodfine, and Timothy W. Lyons
Proceedings of the National Academy of Sciences 2013,

Nitrogen isotope effects induced by anammox bacteria
Benjamin Brunner, Sergio Contreras, Moritz F. Lehmann, Olga Matantseva, Mark Rollog, Tim Kalvelage, Gabriele Klockgether, Gaute Lavik, Mike S. M. Jetten, Boran Kartal, and Marcel M. M. Kuypers
Proceedings of the National Academy of Sciences 2013,

Congratulations to Andreas Krupke....
...on the successful defense of his doctoral dissertation on Octorber 2nd in Geosciences at the University of Bremen. His doctoral dissertation colloquium was entitled:
The role of unicellular cyanobacteria in nitrogen fixation and assimilation in subtropical marine waters.
A MarMic student, Andreas did both his Masters and doctoral research in Biogeochemistry, but also spent long and fruitful hours working together with scientists in the Molecular Ecology Department.

Congratulations to Inigo Müller....
...on the successful defense of his doctoral dissertation on March 19th in Geosciences at the University of Bremen. His doctoral dissertation was entitled The pivotal role of sulfite species in shaping the oxygen isotope composition of sulfate: new insights from a stable isotope perspective. Inigo's research was within the DFG sponsored MARUM Project Area: Geo-Biosphere Interactions.

Congratulations to Nguyen Manh Thang....
...on the successful defense of his doctoral dissertation on February 11th in Geosciences at the University of Bremen. His doctoral dissertation was entitled Biogeochemical controls on carbon and sulfur cycling in Baltic Sea sediments. Thang's research was part of the EU Bonus Project Baltic Gas.

Congratulations to Abdul Sheik....
...on the successful defense of his doctoral dissertation on December 10th in Geosciences at the University of Bremen. His doctoral colloqium was entitled Viruses in the microbial loop from a single cell point of view. Abdul Sheik

New online!  publications from doctoral students Sarah Sokoll, Nguyen Manh Thang, and other MPI colleagues

Sarah Sokoll, Moritz Holtappels, Phyllis Lam, Gavin Collins, Michael Schlüter, Gaute Lavik and Marcel M. M. Kuypers (2012) Benthic nitrogen loss in the Arabian Sea off Pakistan. Frontiers in Microbiology, doi: 10.3389/fmicb.2012.00395.

Thang, N.M., V. Brüchert, M. Formolo, G. Wegener, L. Ginters, B.B. Joergensen, T.G. Ferdelman. 2012. The impact of sediment and carbon fluxes on the biogeochemitry of methane and sulfur in littoral Baltic Sea Sediments (Himmerfjaerden, Sweden). Estuaries and Coasts, doi: 10.1007/s12237-012-9557-0.

Congratulations to Sarah Sokoll....
...on the successful defense of his doctoral dissertation on November 20th in Geosciences at the University of Bremen on Nutrient Cycling in the Sub-Euphotic Water Column and Benthic Boundary Layer .
Sarah did both her Masters and Doctoral research in Biogeochemistry and spent many productive days at sea with scientists from MARUM Project GB1.