Skip to end of metadata
Go to start of metadata

Theoretical background

The aim of the sediment group on the cruise He 376 with the research vessel Heinke of the research institute AWI was to sample the sediment and the microorganisms living in it in certain areas of the North sea, where organic matter deposition rates are high. Here the following was to be investigated:

  • The reduction sequence in the marine sediments
  • The reactivity of iron in marine sediments
  • The potential influence of dissimilatory bacteria on the reduction of iron
  • Anaerobic oxidation of methane

The focus was on sampling a site with high depositional rates of organic matter and therefore long reduction sequences in the surface sediments at the bottom of the ocean. Those areas are mostly shallow areas with large nutrient and organic matter input from river tributaries, like in the North Sea the Weser or Elbe tributary. Since there has been a lot of previous research in the North Sea such areas were known from previous cruises and therefore selected.

Biogeochemical zonation of marine sediments:

The deposition of organic matter and the degradation of the same on the ground leads to a typical zonation of the first few meters of marine sediments. The first few centimeters of the sediment are mostly oxic. Here aerobic respiration leads to the degradation of organic matter. This zone can be partially extended into the following suboxic zone by burrowing animals and the resulting bioturbation. Microorganisms play an important role in these processes, since they get involved in the oxidation of the organic matter and that way gain energy. The most favored electron acceptor is oxygen. But oxygen only penetrates through the first few centimeters of sediment, such that in the suboxic zone other oxidants get involved. The sequence starts in the oxic zone with oxygen respiration, then in the suboxic zone it goes on with nitrate reduction, manganese reduction and iron reduction. In the anoxic zone sulfate reduction takes over, followed by anaerobic reduction of methane and last methanogenesis. This process can generally be observed in the pore water chemistry of a sediment core sample. Since the drill cores were taken in the North Sea, a shallow marine environment with high deposition rates, the oxic zone can be expected to be only a few millimeters or centimeters deep. The suboxic zone is less important, since nitrate, manganese and iron are less available in the sediment. The concentrations of sulfate in seawater are high, approximately 29 mmol/l. Therefore sulfate reduction is the more important type of organic carbon oxidation. It can usually be traced a few meters down into the sediment. Below methane is formed as a stable end product of the carbon degradation sequence.

The reactivity of iron in marine sediments

Iron (Fe) has two valence states: oxidized ferric iron (Fe(III)) and reduced ferrous iron (Fe(II)). There are biotic and abiotic reactions influencing the iron cycle. The biotic ones include assimilation by the uptake of iron by certain organisms like magneto tactic bacteria and phytoplankton and dissimilation, the gain of energy from the reduction of Fe(III). Iron is used as an oxidant, an electron acceptor here. Thermodynamic and kinetic conditions influence abiotic reactions occurring. Those include the redox-reactions leading to precipitation and dissolution of iron minerals. On their surfaces sorption and desorption can lead to the precipitation and release of trace metals and phosphate. Major input of iron into the oceans comes from rivers. Iron has a short residence time of only 100 to 200 years, its concentration still stays about the same in the deeper ocean, around 0.6 nM (Johnson et al. 1997). Iron organic complexes seem to play an important role in the distribution of dissolved iron, since organic ligands with a binding capacity of 0.6 nM have been found (Rue and Bruland 1995; Wu and Luther 1995). Iron oxides can as well be dissolved by protons, ligands and reductants. Since the conditions in the ocean are mostly neutral to slightly alkaline proton-promoted dissolution in iron bearing minerals can be neglected. Ligands dissolve iron oxides by primary surface complexation on the iron oxide, by which the bond between oxygen and iron is weakened. Then the detachment of the ligand follows.
Primary surface complexation and the electron transfer from the reductant to the ferric iron, after which the Fe2+ is detached is reductive dissolution e.g. by HS-. All these processes and the initial thermodynamic and kinetic conditions in the water column as well as in the sediment influence the reactivity of iron.

The influence of bacteria on the reactivity of iron

Some microorganisms are capable of producing siderophores to make dissolved iron more bioavailable. Those siderophores are chelators that complex iron out of a solid phase. The microorganisms excrete these siderophores, which then form a complex with the ferric iron (Fe(III)). The complexed iron is transported into the cell, where it is reduced under the influence of enzymes. The iron is subsequently released from the siderophore and the siderophore is excreted again to start the process from the beginning. This process has been observed in phytoplankton (Trick et al. 1983) and bacteria (Trick 1989). In some iron poor regions of the ocean this process plays an important role for the availability of iron to microorganisms. Dissimilatory iron reduction is the reduction of iron in the presence of enzymes, while the bacteria are in direct contact with the solid phase (Munch and Ottow 1982). There are many different pathways: fermentative Fe3+ reduction, sulfur oxidizing Fe3+ reduction, hydrogen-oxidizing Fe3+ reduction, organic acid oxidizing Fe 3+ reduction and aromatic compound oxidizing Fe 3+ reduction. These processes play an important role in the degradation of organic matter with ferric iron (Fe(III)) as an electron acceptor (Loveley 1991). By hydrolyzation the organic matter is degraded into sugars, amino acids, fatty acids and aromatic compounds, which are then available for the dissimilatory iron reduction.

Anaerobic oxidation of methane (AOM)

Anaerobic oxidation of methane is a very important process in marine sediments (Martens and Berner 1974). Methane is oxidized biologically in the absence of oxygen at the interphase of sulfate and methane. The organisms responsible for this are one issue being investigated with the gravity cores taken on this cruise. Underneath the sulfate reduction zone carbon mineralization occurs via methanogenesis. Anaerobic archaea produce the methane (Whitman et al. 1999). In marine sediments the sources of methane formation are splitting of acetate and reduction of carbon dioxide by hydrogen. Since the amount of energy obtained is quite low, sulfate reducing bacteria and methanogenic archaea therefore compete for the same compounds, like acetate and hydrogen. Methanogenesis therefore only occurs on large scale, when all sulfate has been depleted (Martens and Berer 1974). This is one large difference of marine sediments compared to river or lake sediments, where sulfate concentrations are much lower and there is little competition. The sulfate-methane transition (SMT) is the reaction zone within which methane is oxidized. This methane originates below the sulfate zone and diffuses upward. Here sulfate as well as methane is consumed. It is the contact zone between carbon dioxide, methane and its reducing character and sulfate, a very good electron acceptor and is therefore bio geochemically very important. The methane is oxidized to carbon dioxide. As a result of this the sulfate reduction as well as the methane oxidation have their highest rates in this zone.


The methods used to take the final sediment samples and the pore water samples can be split into two types of methods. The methods used to retrieve the sediment including the pore water from the bottom of the North Sea and the methods used to obtained the final data from the sediment core.

Sampling methods

To sample the sediment three different devices were used: A box corer, a multi/mini corer and the gravity corer. Each of them is used for a different type of sample. All of them can only be deployed, when the ship is hovering over a constant point on the ocean floor. This is most important for the gravity corer. If a gravity corer hits the ground with an angle, not exactly vertical or the corer is lowered too fast, the result can be a “banana”, a bent corer. If the gravity corer hits soft ground with too much momentum, the gravity corer can get stuck in the sediment and it might not be possible to retrieve it. Generally the corer moves at 0.3m/s. In muddy environments it needs to be lowerd slowly to avoid anchoring. In sandy environments, on the other hand, it needs to be lowered quickly to ensure proper entry into the sediment. Weather conditions have to be considered as well, when taking a core. In rough waters it is much more difficult for the captain to keep the ship hovering exactly over a specific spot on the sea floor and one should therefore take notes on the weather conditions, especially the wind speed and how much the ship subsequently had to maneuver. When examining the core for the first time right after it was pulled on to the deck, the smell or the absence of a typical smell should be taken note of as well. This smell is most likely hydrogen sulfide (H2S) escaping from the sediment, which is an indicator for sulfate reduction.

The box corer

The box corer consists of a metal base frame and a box in the middle of it. This box rams into the ground when the corer hits the ground due to its weight and gravitational acceleration, because it is detached from the frame. So when the tension is released from the cable, with which it is deployed from the research vessel, it keeps going down. Once the box corer is pulled up again, strain is applied to the cable and the catch is released, which keeps the core inside the box. The box itself is metal outside and has a plastic lining inside. When the corer is back on deck, it is set above two wooden planks on a plastic basin. And the catch is removed. Then the sample drops into the plastic basin. Here a picture is taken in which a ruler and a sign with the cruise number, the sample number and the date are held next to the sample. The box corer is a relatively simple device used mostly to get a rough impression of the sediment. It has the advantage that the surface of the sediment is sampled as well on a large area, such that all flora and fauna from the bottom are brought up as well. The disadvantages are the fact that no water is sampled and the core only consists of the top ~ 30 centimeters. Depending on the grain size and the organic content of the sediment, the sequence of the sample might be lost either at the ground of the ocean, when the core is taken, or on deck, when it is released. This is usually the case for large grain sizes and low organic content. Once the core is on deck further small samples are taken with syringes to later analyse for the physical properties. The physical properties include properties, such as the grain size distribution, the wet bulk density, the dry bulk density and the porosity. The syringes are pushed into the core at each of the different layers and about the same amount of sediment, approximately five milliliters, is taken from each layer. The content of the syringe is then preserved in a polyethylene tube and labeled with cruise number, sample number and date. If the core is very soft there is a second method to sample the different layers. A petri dish is used to take a little bit of each layer of sediment, closed and labeled like the tubes. When labeling the Petri dishes or tubes it is important to write the order and the depth in centimeters down as well. The rest of the core is usually described quickly and cut open with a putty knife before it disintegrates. The remains are then flushed over board while cleaning the deck. If however the core disintegrates right away when being released from the box corer, no sequence is preserved and no samples can be taken from different layers. Still a bulk sample is taken. Since the heavier particles sink down to the bottom of the basin, moving with the hands through the sediment water mix is useful to find larger rock fragments or maybe bottom dwelling organisms.

The multi/mini corer

The multi/mini corer consists of a metal base frame and a variable number of see-through plastic tubes, a wire, with which it is deployed and a catch for each tube, similar to the box corer. It is deployed in the same way as the box corer and the catches work the same way. They snap closed and produce a vacuum in the tube. The tubes are approximately 50 cm long. Preservation of the first few centimeters of the sediment depends on the momentum of the corer. When hitting the ground, some of the flora and fauna and the bottom water above the ground are sampled by the multi/mini corer. The tubes preserve the sequence no matter how coarse grained the sediment or low the content of organic matter. The tubes are emptied by taking them out of the base frame one by one and sliding them slowly over a plastic pole with a winding. The winding is designed such that one 360° turn corresponds to one centimeter. The bottom water can be sampled first. Then the sediment comes up. After each full turn, one centimeter of the core sticks up from the tube and can be cut off with a putty knife and then put into a petri dish, which is labeled with the cruise number, sample number and depth or sequence. That way each part of the core can later be analyzed separately in the lab.

The gravity corer

The gravity corer is designed to sample down to greater depths, approximately five meters down into the sediment, corresponding to around 10,000 years back in time depending on depositional rates. The disadvantage is that the corer is very heavy and difficult to handle (700kg). Apart from that the first few centimeters of sediment are lost when this device comes down to the bottom of the ocean with too much momentum. This can mean that the last few thousand years might be lost as well as the oxic-anoxic interphase. It consists of the “head”, a wire with which it is deployed, the metal pipe and a core catcher. The head is simply contains all the weight which is needed to push the corer into the sediment. The metal pipe has a plastic lining, which is pulled out afterwards and within which the core is stored and partially analyzed. The core catcher, just like the plastic lining, is attached just before the gravity corer is used. It is pushed over the metal pipe and then fixed by putting greased nails into the space between pipe and catcher such that the pressure will keep it in place. The core catcher works like a metal fyke. The core can only move in one direction, into the tube. It is prevented from sliding back out when the gravity corer is pulled back up and out of the sediment. When the core is pulled up on to deck the plastic tube is cut into five one meter pieces, which are stuffed with plastic bags in case there is further space at either of the ends. Beforehand at the bottom of each piece a sediment sample of five milliliters is taken with a syringe and dropped into twenty milliliters of preliminary prepared NaCl saturated solution. Then the glass bottle is closed air-tight with a metal cap. That way the methane from the sediment exsolves from the solution and accumulates in the top of the bottle. The gas can later be analyzed for methane content with a gas chromatograph in the lab. Since the volume of the bottle, fifty milliliters, the volume of the sediment, five milliliters and the volume of the solution, twenty milliliters are known, the volume of the gas can be computed easily. Then with the results of the gas chromatography, the methane content of the sediment can be computed. Each piece is labeled with a number, one at the bottom at the deepest piece up to five on the shallowest piece. Additionally the cruise number and the sample number are noted down on the core, as well as bottom and top. Then plastic caps are pushed over the ends and taped air-proof. In case the core is not full up to the top, the empty part is cut off with a vibro saw.
The gravity corer, the multi/mini corer and the box corer are usually used in combination to obtain the best results.

Smear slides

One sampling method which is the same for all types of sediment corers is the smear slide. A smear slide is obtained by taking a minor amount of sediment from a layer with a tooth pick, sliding it with some water over a glass plate and letting it dry. Then some glue is applied and a second very thin glass plate is put on top. The smear slides of the different layers can then later be analyzed in the lab under a microscope. Like always appropriate labeling is very important.

Analytical methods

The gravity core

The one meter pieces are analyzed one by one starting with the surface sediment core in the lab. First, small two times two centimeter large holes are cut into the core every ten centimeters. This interval will increase with increasing depth. The top two meters have a smaller interval, since the sulphide reduction occurs in this part of the sediment and are therefore most interesting. The pH is measured and noted down. Then another sediment sample of five ml is taken with a syringe and dropped into a glass bottle which is filled with 20 ml of preliminary prepared NaCl saturated solution and closed quickly with a metal top, such that no gas can escape and it therefore accumulates in the top part of the bottle, because it is exsolved out of the liquid phase due to the saturation of the water with NaCl. Afterwards the first pore water is sampled using a syringe with a porous polymer (pore size ~0.1 µm) at the top through which the pore water has to pass before it enters the syringe such that only pore water and dissolved components can pass. The pore size is so small that even bacteria cannot pass. Once the syringe is filled with about 10 to 12 ml of pore water it is filled into a polyethylene bottle and labeled. Another syringe (red tape) is applied and more pore water is sampled with concentrated nitric acid inside the syringe such that the iron is kept in solution. Both samples will later be analyzed further in the lab, the first row of syringes for methylated sulfide methanes, potential precursors of methane and the second row (red tape) for iron content and speciation, since larger amounts of dissolved iron are supplied to the sediment and the pore water simultaneously with high organic matter deposition. The core is then closed again and stored at ~4 °C and anoxic conditions inside the core to keep the conditions as close as possible to the natural environment and stored horizontally, such that the sediment is not compressed. In general the cores are split into two halves by cutting them open on the long axis. One half is used for analysis in the lab and the other half is stored at low temperatures and air-proof, such that any results obtained from the analysis and potentially published and can later be reconfirmed.

Smear slides

The smear slides are analyzed under the microscope with transmitted and reflected light. Of interest here are the grain size, the shape, the surface and the type of material deposited. The sediment can be well sorted or ill sorted. The grains can be spherical or elongated and the surface can be well rounded or fuzzy. There can potentially be terrigenous sediments, biogenic, siliceous or carbonate ooze, organic material and micrometeorites. All these characteristics are described in the Results section of the report.

Data & Results

Station 002-2/Boxcore 1

Station 007-1/Boxcore 2

Station 007-4/Minicore 1

Station 014-1/Boxcore 3

Station 015-1/Boxcore 4

Smear Slides.pdf

H2S vs. Depth/ Gravity core 007

HS- vs. Depth/ Gravity core 007

SO4 vs. Depth/ Gravity core 007

H2S vs. Depth/ Gravity core 009

HS- vs. Depth/ Gravity core 009

SO4 vs. Depth/ Gravity core 009

*Data within the graphs is curtesy of Sabine Kasten


Organic Matter:

Deposition of organic matter depends on the distance from shore and the depth of the water. As the water becomes deeper less of the sinking particles actually reach the sea floor. Dark organic matter was noted in the first box core (sample 002-2) at a depth of 10.6m. Organic matter was also noted and visible in all of the other samples which were all taken between 28m and 34m water depth. Organic matter can be found in all of the samples because they were all taken in relatively shallow waters.

Shape of grains:

Well rounded grains indicate high levels of erosion and a long travel distance. Grains that are angular are most likely found close to their source, while grains that are rounded are found further from their source. The sediment samples which were analyzed were very mixed with larger angular clasts and other slightly more rounded ones. However, since no fully rounded grains were observed, the depositional environment was most likely close to the source. The occurrence of sand grains indicates proximity to the shore where fluvial input of sediments takes place. Usually only smaller particles make their way farther out into the ocean. In addition, sandy or coarse grained particles indicate high energy environments near tidal flats or where wave action takes place. Chipped off edges on many grains may be an indicator that there are many collisions between the grains, which would point to a high energy environment as well.


An Anomaly with Sample 015-1 was observed which may be due to a special depositional environment. We expected to find a normal fining upwards sequence with coarser grains more towards the bottom gradually fining upwards towards the surface. This was not the case. Instead a coarse grained middle layer was observed. This could be due to a series of depositional events, maybe moving sand dunes on the ocean floor depositing layers over top of each other. The normal depositional sequence was interrupted by input from some sort of sediment movement.

Sea stars:

Living organisms such as brittle sea stars can be used as an indicator for water quality as well as oxygen content in sediments. Many were observed in samples 014-1 and 015-1.


Smear slides exposed grains of various colors depending on the angle of incidence. These colors can be used to determine the type of grain. Rainbow colors could indicate quartz grains. This would be evidence for the materials’ terrigenous background. Black grains in all kinds of shapes were present throughout all samples. Since their color did not change in reflected light it can be speculated that it is organic material.

Graphs (Gravity core 007 and 009):

Both cores have very similar profiles. The H2S concentration of core 007  starts at 6mg /L right at the surface and increases to about 9.8 mg/L at a depth of 30cm  below the sea floor. From then on the concentration declines sharply until it is below detection limit at 80cm below the surface. The high concentrations observed at 30cm depth may indicate that we are in the anoxic zone where anaerobic oxidation of methane takes place.

H2S concentrations were generally higher for gravity core 009. The surface concentration exceeded the maximum concentration found at 30cm depth of 007 (9.8 mg/L). Gravity core 009’s H2S concentration peaked at a similar depth of 35cm at a value of 25 mg/L. It again decreased sharply to reach values below detection limit at approximately 1m below surface.

Sulfate peaks at the surface and then declines until around 50cm depth. Sulfate is almost completely consumed at a depth of around 30 to 35 cm. This consumption is driven by the process of anaerobic oxidation of methane (AOM) where methane diffusing upwards reacts with seawater sulfate (diffusing downwards into the sediment).


Up to this day, the results received have been limited. Therefore, it is not possible to draw all conclusions. It would also be of benefit to compare these findings with those of previous years. Then significant changes that may have occured could be denoted. In light of todays rapid transition in other locations all over the world, there may be some changes here too. This expedition sought to determine various constituents of the sediment and gather more information about processes which are occurring in these deeper sediments. Through the employment of various sampling techniques it was possible to obtain a rough overview on the sedimentary situation of the sea floor around Helgoland. It was shown that the sea floor is not a deserted uninhabited place, but rather a biome teeming with life and variety. Grain sizes and shapes were analysed and hypotheses regarding depositional environments were constructed. Other variables such as bioturbation and the concentration of Organic matter also played an important role in determining the depositional environments.  One can make in-depth deductions on the depositional environment of particular sediments with just a few mediums of research.

The most important instrument was the gravity corer. Upon closer analysis of the cores taken one could measure the methane content and pore water constituents. Pore water was extracted and later lab work was prepared, part of which can also be found in this report. Measurements, however, may not be so straightforward. There are many variables that may affect the outcome. The force of impact from the gravity corer creates a wave that destroys the top bit of sediment. It also compresses the sediment. Sulphate concentrations at the top of the cores are lower than sulphate concentrations in the North Sea which indicates that the upper 20cm to 30cm have been lost on impact of the core. This should be taken into account while analyzing the data.


  • Johnson, K.S., Gordon, R.M. and Coale, K.H., 1997.
    What controls dissolved iron concentrations in the
    world ocean? Marine Chemistry, 57: 137-161
  • Lovley, D.R., 1991. Dissimilatory Fe(III) and Mn(IV)
    reduction. Microbiological Reviews 55: 259-287
  • Martens, C.S., and Berner, R.A., 1974. Methane
    production in the interstitial waters of sulfatedepleted
    marine sediments. Science, 185: 1167-1169
  • Munch, J.C. and Ottow, J.C.G., 1982. Einfluß von
    Zellkontakt und Eisen(III)oxidform auf die bakterielle
    Eisenreduktion. Zeitschrift der Pflanzenernährung
    und Bodenkunde, 145: 66-77.
  • Rue, E.L. and Bruland, K.W., 1995. Complexation of
    Fe(III) by natural organic ligands in the Central North
    Pacific as determined by a new competitive ligand
    equilibration/ adsorptive cathodic stripping voltammetric
    method. Marine Chemistry, 50: 117-138
  • Schulz, Horst D., and Matthias Zabel eds. Marine geochemistry.  Berlin: Springer, 2006
  • Trick, C.G., Andersen, R.J., Gillam, A. and Harrison,
    P.J., 1983. Prorocentrin: An extracellular siderophore
    produced by the marine dinoflagellate Prorocentrum
    minimum. Science, 219: 306-308
  • Trick, C.G., 1989. Hydroxomate-siderophore production
    and utilization by marine eubacteria. Current Microbiology,
    18: 375-378
  • Whitman, W.B., Bowen, T.L., and Boone, D.R., 1999.
    The methanogenic bacteria. In: Dworkin, M., Balows,
    A., Trüper, H.G., Harder, W., and Schleifer, K.-H.
    (eds), The Prokaryotes, 3rd. Ed. Springer, New York
  • Wu, J. and Luther, G.W. III, 1995. Complexation of
    Fe(III) by natural organic ligands in the Northwest
    Atlantic Ocean by competitive ligand equilibration
    method and kinetic approach. Marine Chemistry,
    50: 159-177


  • No labels