Techniques and methodology BGC

A wide range of techniques are being applied in our research, some of which are detailed below;

Hydrogen isotope analysis (GC-TC-irMS)

The hydrogen isotope ratio [= the relative deuterium content (δD) expressed in ‰ relative to standard mean ocean water (VSMOW, Vienna Standard Mean Ocean Water)] of water is depending on evaporation and precipitation. Water vapor contains relatively little deuterium (= low/more negative δD value) and the remaining water becomes enriched in deuterium (= high/more positive δD value). Seawater evaporates mostly at lower latitudes, close to the equator, there the seawater becomes enriched in deuterium, the water vapor is transported to higher latitudes, the poles, and rains out. The first rain close to the water vapor source is relatively enriched in deuterium, leaving water vapor that becomes more and more depleted in deuterium. Therefore, later rain, further away from the vapor source, will contain less and less deuterium. Freshwater from different locations on Earth will contain different relative amounts of deuterium, different δD values, depending on the distance from the water vapor source. These differences are used to determine the authenticity of different products, for instance, does Spanish wine originate from Spain or Greek olive oil from Greece etc.

At the NIOZ hydrogen isotopes are being used to reconstruct past climate and ocean currents. By measuring the hydrogen isotopic composition of plant material we can get an idea of the evaporation/ precipitation balance in the area where the plants are or were growing. By analyzing the specific plant derived chemical fossils extracted from sediment cores for their hydrogen isotopic composition we can reconstruct changes in precipitation versus evaporation in the past (for an extensive review see Sachse et al., 2012).

Since seawater not only becomes more enriched in deuterium when water evaporates, but also becomes more saline and freshwater contains relatively little deuterium, salinity and the δD value of seawater are correlated. Unfortunately we cannot measure the hydrogen isotopic composition of seawater from the past, but we can measure the δD value of chemical fossils specific for certain algae that lived in that water. From cultivation experiments it is clear that the hydrogen isotopic composition of algae is strongly correlated with the salinity of the water in which they were grown (Schouten et al. 2006). First because the δD value of the water is correlated with salinity, but also because algae build in more deuterium at higher salinities or in other words, algae fractionate less against deuterium when growing at higher salinities. The correlations between δD and salinity and biological fractionation and salinity can now be used to reconstruct salinities in the past (van der Meer et al., 2007) and therefore changes in ocean circulation.

Besides reconstructing climate and ocean circulation in the past, hydrogen isotope ratios of organic matter can also provide information on the metabolism of the organisms producing that organic material. For instance, organisms that use light as energy and CO2 as carbon source have a very different hydrogen isotope ration than organisms that use the oxidation of sulfide as energy and CO2 as carbon source and that is again very different from organisms using the oxidation of organic matter as energy and carbon source. Hydrogen isotope analysis could therefore potentially provide a metabolic fingerprint for different ecosystems, also those from the past.

In order to measure the hydrogen isotopic composition of organic matter it has to be converted into hydrogen gas (H2 or HD) and graphite at very high temperature (approximately 1450 °C). The graphite formed is also the catalyst for this reaction. Individual compounds first have to be extracted, cleaned and separated on a gas chromatography column before they can be converted to hydrogen gas and graphite in a high temperature conversion reactor.



Sachse, D., I. Billault, G.J. Bowen, Y. Chikaraishi, T. Dawson, S. Feakins, K.H. Freeman, C. Magill, F.A. McInerney, M.T.J. van der Meer, P. Polissar, R. Robins, J.P. Sachs, H.-L. Schmidt, A. Sessions, J. White, J.B. West & A. Kahmen (2012). Molecular paleohydrology: interpreting the hydrogen-isotopic composition of lipid biomarkers from photosynthesizing organisms. Annual Review of Earth and Planetary Sciences 40: 221-249.

Schouten, S., J. Ossebaar, K. Schreiber, M.V.M. Kienhuis, G. Langer, A. Benthien & J. Bijma (2006). The effect of temperature, salinity and growth rate on the stable hydrogen isotopic composition of long chain alkenones produced by Emiliania huxleyi and Gephyrocapsa oceanica. Biogeosciences 3: 113-119.

Van der Meer, M.T.J., M. Baas, W.I.C. Rijpstra, G. Marino, E.J. Rohling, J.S. Sinninghe Damsté & S. Schouten (2007) Hydrogen isotopic compositions of long-chain alkenones record freshwater flooding of the Eastern Mediterranean at the onset of sapropel deposition, Earth Planet. Sci. Lett. 262: 594-600.

GCTC-irMS Gaschromatograph-Thermal Conversion isotope ratio Mass Spectrometer
Gaschromatograph-Thermal Conversion isotope ratio Mass Spectrometer
Environmental Chemistry

Increasing numbers and amounts of polar organic contaminants (e.g., pesticides, pharmaceuticals, personal care products) are released into the environment. Chemical monitoring is essential for protecting the environment against possible adverse effects of these compounds. Passive sampling devices (PSDs) are powerful tools for monitoring the chemical status of water bodies because they yield estimates of time-integrated aqueous concentrations at low detection limits, and at relatively low costs, compared with batch water sampling. PSDs consist of a central sorption phase that is covered by a membrane. They are deployed for a period of several weeks to months.


Sampling device for polar organic contaminants


Contaminant uptake by PSDs is linearly proportional to their aqueous concentrations, but also depends on the environmental conditions during the deployment (e.g., water flow, temperature, salinity, pH). Our research focusses on understanding and quantifying the effect of these exposure conditions, and on developing methods for the in-situ calibration of PSD uptake rates, aiming to improve the accuracy and the precision of time-integrated aqueous concentrations of nonpolar and polar organic contaminants in marine monitoring programs.

 Working principle of a Polar Sampling Device (PSD)

Examples from the MEE department

The department of Marine Ecology uses as wide range of methods: from observations and monitoring to experiments, from field to lab applications and from classical benthos core sampling to state-of the art technologies. Here we illustrate just a few of our methodological approaches with some videos.


Experimental Shorebird Facility

At NIOZ we have built the Experimental Shorebird Facility (ESF) which is one of a kind, worldwide. In the ESF we are able to simulate a tidal environment, which allows controlled experiments on the behavioural ecology of shorebirds.

Red knot foraging experiment

This movie shows the experimental setup for a foraging experiment on Red Knots (Calidris canutus islandica). The experiment was designed to study patch departure decisions for red knots foraging in a patchy food environment. Foragers should not stay in a patch too long and waste time searching for that last prey item while other food patches have more to offer. On the other hand, foragers should not depart a patch too soon and leave many prey items behind. Depending on the density and distribution of food, one can calculate the optimal departure decision that foragers should use that maximises intake rate. We want to find out how and if red knots make optimal foraging decisions.

For this experiment we built 25 potential food patches. In each food patch we buried between 0 and 15 prey items. We videoed the trials to measure at which intake rates red knots depart a patch in search for patches with more food.

For information on this project see the website of Allert Bijleveld.

What lives in the open Wadden Sea

Next door unknown: What lives in the open Wadden Sea

Research cruise with the RV Navicula on the Wadden Sea, to discover what lives in the open Wadden Sea. By day and by night.

For more info: Lodewijk van Walraven & Vania Freitas

Plankton sampling

Plankton sampling with RV Luctor

A short movie about a plankton sampling cruise with the NIOZ RV Luctor. Including some underwater footage of plankton nets! The cruise was aimed at monitoring the invasive American comb jellyfish Mnemiopsis leidyi. What did we do, where did we go, what gear did we use?

For more info: Lodewijk van Walraven

Feeding behaviour of sea gooseberries Pleurobrachia pileus

Feeding behaviour of sea gooseberries Pleurobrachia pileus

Laboratory observations on the feeding behaviour of sea gooseberries using a special plankton chamber.

For more info: Lodewijk van Walraven



The 3D-dredge was developed by Magda Bergman and the NIOZ in-house technical support department. The dredge is designed to sample benthic macrofauna at low densities to be able to determine their population sizes. 

For more info: Magda Bergman

Gull goes feeding in Amsterdam (in Dutch)

Gull goes feeding in Amsterdam (in Dutch)

Example of the telemetry research done at NIOZ in cooperation with the University of Amsterdam. A gull with a transmitter on her back flew 300 km from Texel to Amsterdam to gather food for her chicks. From a Dutch TV programme called 'Natuur' Nederland van Boven. 

For more info: Kees Camphuysen 

SIBES sampling campaign

SIBES sampling campaign

An impression of the SIBES fieldwork on the Wadden Sea, in field season 2012.

For more info: Sander Holthuijsen


Examples from the GCO department

GCO applies a wide range of analytical techniques to determine the chemical composition of solid phase materials, be it calcareous coral structures or sediment fractions. These techniques include several non-destructive (semi-) quantitative approaches such as core scanners, as well as techniques that rely on the complete destruction of a solid phase and subsequent analysis of its composition. Our techniques and protocols are presented below. 

For further information, please contact Wim Boer.
ICP-MS (Thermo Scientific Element-2)
Application   Analyzing elemental composition of sediment and corals

Element-2 of Thermo Scientific.

SF ICP-MS is a combination of inductively coupled plasma (ICP) with a mass spectrometer (MS). The SF abbreviates 'Sector Field' which warrants a high resolution. ICPMS is a popular technique due to its many advantages, such as:

  • No matrix effects after dilution of >5000x resulting  in quantitative results.
  • Low limit of detection (ppt-ppb range).
  • Multi element capabilities.
  • Wide linear range (trace, minor and major elements in 1 run).
  • High sample throughput via a fast auto sampler (200 samples/day).
  • Ability to obtain isotopic information. 
   files/Fotos website editor/Onderzoek/geo/methods/ICP-MS.jpg
Analysis of sediments & corals  

At this moment our group uses the ICP-MS for analyzing:

  • 9 elements (Mg, Ca, Mn, Sr, Y, Ba, La, Pb and U) in tropical corals
  • 34 elements (Ag, Al, As, Ba, Be, Br, Ca, Cd, Co, Cr, Cu, Fe, Hg, K, Li, Mg, Mn, Mo, Ni, P, Pb, Rb, Ru, S, Sb, Se, Sn, Sr, Ti, U, V, Y, Zn, Zr) in sediments/traps.
  •  207Pb/206Pb and 208Pb/206Pb ratios in traps and sediment. 
Wim Boer
T 0222 369 386/394
@ wim.boer(at)nioz.nl
Sample preparation  

For every application a dissolution and dilution protocol is developed, a glassware set-up is chosen for the ICP (which spray chamber, nebulizer, pump-speed, etc) and an analytical method is developed (which elements, resolution, measurement time, etc). 

Discuss sample preparation with us prior to preparing your samples.

Here are some general remarks for preparing you samples:

The sample containers must be clean and dust free. Prepare your sample in a clean environment, and if possible in a laminar flow hood. Do not use any metals during collections or preparation of the sample. Use a ceramic mortar to grind the samples. When the samples have to be fractionated, use a nylon sieve, not a metal sieve. 

Amount of sample

  • 100 mg of ground sediment.
  • 1 mg of coral sample.
Sample dissolution and dilution  

Our sample dissolution and dilution methods are for:


Dissolve 1±0.3mg in 1±0.3 ml ultrapure 0.1M HNO3 in 5ml pots. Dissolve the coral using a Vortex mixer. Pipette a sub volume of 0.26ml into a 12ml autosampler tube. Dilute with 9.74ml of 0.1M HNO3. Preferable, the samples are measured on the same day.


Weight 100±5mg sediment in 30ml Savillex pots. Add 6,5ml concentrated. HNO3 (ultrapure)/HF (suprapure), 10:1. Add 1ml ultrapure HCl (conc) and 1ml perchloric acid to the samples. Heat a batch of 18 samples, 3 blanks and 3 standards at 125°C in an Analab hotblock  during 48 hours. Remove the matrix after heating at the lower station of the hotblock during 48 hours at the same temperature. Redissolve the sample with 20.00ml 1M HNO3. Pipette 0.4ml of subsample in a 50ml DigiPrep autosampler tube. Add 19.6ml 1M HNO3 with internal standards (scandium, indium and thallium). Measure the sample preferable within a few days.

For dissolving/diluting the samples yourselves, it is important to:

  • Use the highest quality Teflon containers (FEP, PFA).
  • Clean the sample containers. Put them in 8M HNO3 for at least 1 hour. Rinse them thoroughly with >17 MΩ water to remove all the acids. Dry them in a laminar flow hood.
  • Use preferable ultrapure HNO3 for dissolution. Other acids cause a lot of additional interferences in the mass spectra.
  • The end concentration must be 1-6% HNO3.
  • Total dissolved solids must be 
  • Use only high purity reagents (ultra grade, Teflon grade quality)
  • Use the highest purity water (>18.2 MΩ)
  • Prepare also a monitor standard.
  • Prepare a number of blanks.
  • The analytical solutions must be prepared shortly before a run.

The end solution can be 500 µl, but using a small volume of sample limits the number of elements that can be determined and/or the number of replicate analyses.

XRF core scanner (NIOZ-AVAATECH)
Application   Non destructive analysis of elemental composition of sediment cores
X-ray Fluorescence (XRF) Core Scanning is developed at the department of Marine Geology of the NIOZ for analysing the sediment composition in a fast and non-destructive way. The scanner is equipped with an Rh X-Ray source that covers the elements from Al through to Ba. We can analyse sediment cores up to 1500 cm length with a resolution down to 0.1 mm.
We developed new core scanning applications based on new insights and needs that evolved from our research, such as UV-luminesces for the analysing coral records. Both UV and visual light scans are performed with a CCD line scan camera that has an optical resolution of 70 µm.
   files/Fotos website editor/Onderzoek/geo/methods/corescanner.jpg
Analysis   Sample preparation is minimized to a cleaning of the core surface. We use a thin film (4 µm) to cover the core surface to avoid contamination of the measurement unit and desiccation of the sediment. The analysing time depends on sample resolution and the range of elements to be analysed. 
Rineke Gieles
T 0222 369 444/221
@ rieneke.gieles(at)nioz.nl



For a measurement request, please fill out these forms:
or contact 
Rineke Gieles
T 0222 369 444/221
@ rieneke.gieles(at)nioz.nl
Links & Literature  
XRF workshop 2010 & Workshop Report:
Tjallingii and workshop participants (2011). 2010 international workshop on XRF core scanning, PAGES news, Vol 19, No 2, July 2011. pages 90-91. [ pdf ]
Suggested Literature:
Jansen et al., 1998. CORTEX, a shipboard XRF-scanner for element analyses in split sediment cores. Marine Geology, 151: 143-153.
Richter et al., 2006. The Avaatech Core Scanner: Technical description and applications to NE Atlantic sediments. In: Rothwell, R.G. (Ed.), New ways of looking at sediment core and core data. Geological Society Special Publication, London, pp. 39-50.
Röhl, U., Abrams, L.J., 2000. High-resolution, downhole, andnondestructive core measurements from Site 999 and 1001 in the Caribbean sea: Application to the Late Paleocene Thermal Maximum, Proceedings of the Ocean Drilling Program, Scientific Results, pp. 191-203.
Tjallingii et al., 2007. Influence of the water content on X-ray fluorescence core scanning measurements in soft marine sediments. Geophysics, Geosystems, Geochemistry, 8(2): doi:10.1029/2006GC001393.
Weltje, G.J., Tjallingii, R., 2008. Calibration of XRF core scanners for quantitative geochemical logging of sediment cores: Theory and application. Earth and Planetary Science Letters, 274(3-4): 423-438.
Technical information: www.avaatech.com
Laser particle sizer (Coulter LS230 and a LS13320)
Application   Determine grain size distribution of complex particle mixtures
Equipment   We measure grain-size distributions of sediment and suspended matter via laser diffraction. We have two laser particle sizers at our disposal; a Coulter LS230 and a LS13320. They can measure particles with sizes from 0.04-2000 µm. The resolution of these instruments is relatively high in comparison with other instruments. The detection of the smallest particles in the range of 0.04-0.4 µm is performed by an additional detection technique (PIDS technology) involving multiple wave lengths of light. The amount of sample depends on the choice of the module. We have three modules (I) micro cuvet for very small (µg) amounts (II) small volume module (mg) (III) large volume module (g).
The large volume module of our CoulterLS230 is the standard module and requires 50 mg (clay) to 3000 mg (course sand) of freeze dried bulk sediments. If less material is available we use one of the smaller modules.
Our standard procedure for bulk sediments is as follows. Approximately 0.05-3 gram of freeze-dried sediment (weight is depending on grain size) is soaked in water and suspended (using either ultrasonic dispersion or boiling with NaPyP). These samples are passed through a 2 mm sieve and suspended in 1 liter water in the CoulterLS230. If necessary, the samples are diluted with water to yield a laser obscuration of 10%. The measured laser diffraction pattern is calculated into a particle-size distribution using a Mie model with a refractive index of 1.56 and adsorption coefficient of 0.2 for the solid phase. A high pump speed is used (50%), which means that, in combination with the internal sonification, there is very little chance of flocculation.
 Manager    Jan-Berend Stuut/Rineke Gieles
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Specific Surface Area (Micromeritics Tristar 3000)
Application   Determine the specific surface area of particles
Equipment   Our group uses a Micromeritics Tristar 3000, that can measure 3 samples at the same time. This kind of analyses requires a total degassed sample. We have a Micromeritics FlowPrep060 to degas our samples.
Wim Boer
T 0222 369 386/394
@ wim.boer(at)nioz.nl
    Meromictics SSA
Alpha Spectrometry (Canberra)
Application   210Pb analysis in sediment, traps and corals
Equipment   Our group has 12 alpha PIPS detectors (Canberra). These detectors have an active area of 600 mm2 and a resolution of 23 keV. Alpha spectrometry requires dissolution of sediment and a chemical purification. Our lab performs those steps for 210Pb analysis.
After measuring the grain size, we decide if 210Pb analyses are performed on bulk or fractionated samples.
We are able to measure 210Pb directly with gamma-spectrometry, but we prefer the more sensitive method of measuring it indirectly via its granddaughter 210Po with a half-life of 138.4 days. The advantage of alpha spectrometry is that our equipment can measure up to 12 samples in 1 or 2 days.
The analysis is normally performed 3-9 month after date of sampling to obtain total equilibrium between 210Pb and 210Po. For analysis, 100 - 500 mg of freeze-dried and ground sediment is spiked with 209Po and totally digested with 9 ml concentrated HNO3 and 3 ml concentrated HF in a microwave oven for 3 h. Subsequently, 2 ml 3.5% HClO4 is added and thereafter the acids are removed by evaporation. The resulting precipitate is re-dissolved in 5 ml concentrated HCl for 30 minutes and thereafter 40 ml 0.5M HCl (with 12 g/l boric acid), 4 ml NH4OH and 5 ml of 40 g/litre ascorbic acid (in 0.5M HCl) are added. Spontaneous deposition of Po-isotopes onto silver occurs at 80°C. This is done for 4 hours and the silver plates remain in solution overnight at room temperature to increase the deposition efficiency. The counting error (1s) is normally 3-7%.
Wim Boer
T 0222 369 386/394
@ wim.boer(at)nioz.nl
    files/Fotos website editor/Onderzoek/geo/methods/Spectrometrie GEO.jpg
Gamma Spectrometry (Canberra)
Application   Analyzing 234Th, 226Ra and 137Cs in sediment and traps.

Our group has three Canberra gamma detectors, (I) a low energy, (II) a coaxial and (III) a well type detector.

  1. The low energy detector has a 1000 mm2 active area, a diameter of 35.7 mm and a thickness of 20 mm. The detection range is from 10 to 1000 keV. The resolution for 57Co is 0.57 keV. The absolute efficiency is for a silicate matrix and a tube for 63 keV: 36 – 42% and for 609 keV: 4.3-4.6% (the range is for weights from 1.3.-1.7 gram).
  2. The coaxial detector has a diameter of 53 mm. The detection range is from 50-1200 keV and the resolution is 0.80 keV for 57Co. The absolute efficiency is for a silicate matrix and a Petri-dish of 5.5 cm diameter for 63 keV: 3.1 – 3.8% and for 609 keV: 2.3-2.6% (the range is for weights from 5-25 gram).
  3. The well type detector has a nominal volume of 140 cm3, a relative efficiency of 25%. The resolution for 57Co is 1.2 keV. The absolute efficiency is for a silicate matrix and a Petri-dish of 5.5 cm diameter for 63 keV: 9.2 – 11% and for 609 keV: 0.66-0.80% (the range is for weights from 5-25 gram).
For gamma spectrometry analyses a large quantity of sediment is preferred. This results in a shorter counting time. We prefer 5-20 gram of freeze dried sediment. For the well type detector 1 gram is sufficient.
To calculate mass accumulation rates or mixing rates from a210Pb profile, the supported 210Pb has to be subtracted from the total 210Pb.
The supported 210Pb can be determined by analyzing the226Ra activity with gamma spectrometry. This is done as follows.
226Ra is analyzed indirectly by counting the 214Pb lines (295 and 352 keV) and the 214Bi line (609 keV). 226Ra decays to 222Rn. This is a gas, therefore the containers has to be sealed. The sample can be counted after at least 1 month. The detector is calibrated with an external standard of a uranium ore mixed with a silicate matrix.
Box core or multi-core samples are normally used for 234Th analysis, to assess mixing rates.
The 234Th activity is measured either by counting the 92 keV gamma emission with a high-resolution coaxial germanium detector, or by counting the 63keV and 92 keV gamma emissions with a low energy detector. Samples from a single core are all measured with the same detector. Calibration is done by means of the external standard method. This standard is a uranium-ore diluted with a silica powder. Uranium is in secular equilibrium with all its daughters in this standard. Samples with excess thorium were re-analyzed after at least three months. Excess 234Th activity is decay corrected for the time elapsed between sample collectionand counting. The self-absorption correction factor can be measured according to the method of Cutshall (1983).
This isotope can be used to validate 210Pb mass accumulation rates.
The 137Cs activity can be measured with all three gamma detectors, but the coaxial detector is preferred. The 661 keV line is used and normally counted for 1-2 days. The detector is calibrated with a QCY48 standard, which is a mixture of different isotopes including 137Cs.
Wim Boer
T 0222 369 386/394
@ wim.boer(at)nioz.nl
    files/Fotos website editor/Onderzoek/geo/methods/Spectrometrie GEO.jpg