On Land

Lab bottles (© Max Planck Institute for Marine Microbiology, K. Matthes)

The human eye is unable to recognize things smaller than 0.2 mm. At the Max Planck Institute for Marine Microbiology, we study micro-organisms from the environment that are many times smaller – some of them measure only 500–1000 nm. Light microscopes are used to detect these microbes. However, individual structures in the cells can be visualized only with special microscopes.

Moreover, when microbes live together with each other or with animals, everything involves small molecules. From nutrition to communication, proteins, lipids, and the like are almost always involved. We look at these molecules in order to gain insight into the processes both within and between cells.

For this, we use various devices in our laboratories.



Confocal laser scanning microscope

The confocal laser scanning microscope is our workhorse for detecting specific fluorescence signals. The main task of a confocal microscope is to display as accurate an image of minute objects as possible. It allows a more detailed view of the microbes than a standard light microscope. More…

Transmission Electron Microscope (TEM) with EDX detector

The TEM is a microscope that allows us to take images of biological samples, at a significantly higher resolution and magnification than common light microscopes. TEM enables our scientists to visualize particularly small structures at Nanometer scale such as viruses, or bacterial and eukaryotic cells and their substructures like the membrane or small organelles. More...

Environmental scanning electron microscope

When examining and imaging very small objects, such as marine microorganisms, one very quickly reaches the limits of optical microscopy. To be able to image these organisms, the application of scanning electron microscopy is the next step. Our scanning electron microscope is equipped with various detectors for image generation and analysis. More...

Su­per­res­ol­u­tion mi­cro­scopy - Stimulated Emission Depletion (STED)

Su­per­res­ol­u­tion mi­cro­scopy al­lows us to visu­al­ize mi­cro­struc­tures be­low the dif­frac­tion limit. Our latest su­per­res­ol­u­tion in­stru­ment is based on the Stimulated Emission Depletion (STED) tech­nique. The Ab­berior In­stru­ments easy3D STED can provide a lat­eral res­ol­u­tion be­low 25 nm and a 3D res­ol­u­tion of up to 60 nm. The in­stru­ment in­cludes the meth­odes pulsed-STED, gated-STED, and RES­Cue STED. It is the first STED mi­cro­scope with MIN­FIELD tech­nique on the com­mer­cial mar­ket.

More information on our device can be found here, at the Department of Molecular Ecology

More information on the function can be found here... (Link to the MPI for Biophysical Chemistry)

Video (Youtube): Stefan Hell explains superresolution and STED

Auto­mated Mi­cro­scopy and Cell Count­ing

We de­veloped an im­age ac­quis­i­tion and eval­u­ation sys­tem for the auto­mated mi­cro­scopic eval­u­ation of com­par­at­ively simple samples, i.e. the count­ing of bac­terial cells in sus­pen­sion that are filtered and im­mob­il­ized on mem­brane fil­ters. For this we have de­veloped a ro­bust com­pu­ter­ized fo­cus­sing sys­tem that com­bines a pro­pri­et­ary auto­fo­cus with cus­tom tex­ture para­met­ers, feed­back loops for im­age con­trast max­im­a­tion, and de­cisions on im­age con­tent dur­ing ac­quis­i­tion. The sys­tem is cap­able of ex­clud­ing in­ap­pro­pri­ate or badly fo­cussed mi­cro­scopic fields prior to eval­u­ation without op­er­ator in­ter­ac­tion with high re­li­ab­il­ity. More...

Fully motorized and software controlled microscope used for automated high-throughput microbial cell enumeration. (© Max Planck Institute for Marine Microbiology, A. Ellrott)

Mass spectrometers

Na­no­s­ca­le Se­con­da­ry Ion Mass Spec­tro­me­ter (Na­no­SIMS)

It is big, silver, and looks rather complicated. But it works wonders. With its help, we can watch micro-organisms at work. The NanoSIMS is a mass spectrometer with special optics that enable impressive spatial resolution. We can thus observe things that are only about 50 nm in size. We use it to study structures and processes inside bacterial cells. More...

MALDI imaging mass spectrometry

MALDI imaging mass spectrometry is an imaging method for analysing chemical compounds and their spatial distribution in a sample. It can be used to identify where certain compounds are located in a sample. Scientists can use this information to draw conclusions about how the metabolism of the mussel works. More…

High performance liquid chromatograph with mass spectrometry (HPLC-MS)

A high-performance liquid chromatograph, coupled to a mass spectrometer, is among the most sensitive instruments available to science. The HPLC-MS allows it to separate mixtures of substances into their components and to measure the molecular masses of these components very precisely. More...



Gas chromatograph with mass spectrometry (GC-MS)

A gas chromatograph can be used to analyze volatile compounds. The connected mass spectrometer serves to determine which substances are contained in the sample and how much of each substance is present.

Ultrahigh-resolution mass spectrometry

The Re­search Group for Mar­ine Geo­chem­istry has a Fourier-Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR-MS) at its disposal, which offers ul­trahigh-res­ol­u­tion mass spec­tro­metry for our re­search. It is the most power­ful tech­nique to mo­lecu­larly char­ac­ter­ize com­plex or­ganic mix­tures, such as DOM, whose com­pos­i­tion is still largely un­known. We can de­term­ine the mass of an in­di­vidual mo­lecule with a pre­ci­sion of one ten-thou­sandth of a Dalton, which is less than the mass of an elec­tron. This level of pre­ci­sion is re­quired to identify in­di­vidual mo­lecules in sea­wa­ter.

This special mass spectrometer is located at the In­sti­tute for Chem­istry and Bio­logy of the Mar­ine En­vir­on­ment of the University Oldenburg (ICBM) and is used by the Research Group Marine Geochemistry, which is a Bridge Group between the ICBM and the Max Planck Institute for Marine Microbiology. The ICBM is the only in­sti­tu­tion in the mar­ine sci­ences world­wide that hosts such unique mass spec­tro­meter.

More information is available at the departments page of the Group Marine Geochemistry and at the homepage of the ICBM.


Fourier transform ion cyclotron resonance mass spectrometer (©Carl von Ossietzky Universität Oldenburg)

Other instruments and techniques


A chemostat is a cul­tiv­a­tion biore­act­or, which closely mimic the en­vir­on­ments that mi­croor­gan­isms live in – in the labor­at­ory, un­der con­trolled con­di­tions. That al­lows us to cul­ture en­vir­on­ment­ally-rel­ev­ant mi­croor­gan­isms to study their physiolo­gical and bio­chem­ical prop­er­ties in mo­lecu­lar de­tail. More...

Chemostat (©Max Planck Institute for Marine Microbiology, B. Kartal)

Flow Cytometry

Gen­e­ral­ly, flow cy­to­metry is the mea­su­re­ment of sin­gle cells in a wa­ter jet. At the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy, we use flow cy­to­metry rou­ti­nely to quan­ti­fy cell num­bers pi­co­plank­ton sam­ples and cell cul­tu­res. Fur­ther, cells mee­ting pre­de­fi­ned pro­per­ties can be sor­ted with high speed in high pur­ity for fur­ther mo­lecu­lar bio­lo­gical ana­ly­sis. More...

Raman spectrometer and atomic force microscope

The Raman spectrometer is used to investigate material properties. The great advantage of the device is that it allows non-destructive and non-contact measurement. Furthermore, only very small amounts of a biological sample are needed. More...


Any solid material in air or liquids can be examined using atomic force microscopy. This is a great advantage for biological samples because they will not dry out and thus retain their shape. Information on the surface structure can be determined in the nanometre range. More...


The Microsensor Group stud­es mi­cro­bial eco­logy in a wide range of en­vir­on­ments: seep sys­tems, deep-sea and coastal sed­i­ments, coral reefs, an­oxic lakes, mi­cro­bial mats, an­imal-as­so­ci­ated mi­crobes and more. The re­search is highly di­verse, en­com­passing themes of pho­to­syn­thesis, ni­tro­gen and sul­fur cyc­ling, cal­ci­fic­a­tion, hab­itat map­ping, eco­sys­tem pro­ductiv­ity and cell physiology. Most themes in­volve the study of the func­tion­ing of in­tact mi­cro­bial com­mu­nit­ies with non-in­vas­ive meth­ods that al­low as dir­ect an ob­ser­va­tion as pos­sible. To this end, we de­velop, con­struct and use mi­cro­sensors for labor­at­ory and in-situ meas­ure­ments. These tiny sensors, typ­ic­ally made of ex­truded glass, have tip sizes in the or­der of 5-50 μm and can rap­idly meas­ure chem­ical fluxes caused by cells.These mi­cro­sensors are also ap­plied to­wards meas­ur­ing eco­sys­tem fluxes with the eddy co­v­ari­ance tech­nique.

Video: Microsensors: How they are made (Link to youtube)

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