Flow Cytometry

Flow Cytometer (© Max-Planck-Institut für Marine Mikrobiologie, K. Matthes)
Our Flow Cytometer BD Influx Mariner (© Max Planck Institute for Marine Microbiology, K. Matthes)

What is 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 in pi­co­plank­ton sam­ples and cell cul­tu­res. Fluor­es­cent pig­ments like chlo­ro­phyll and ca­ro­te­no­ids cha­rac­te­ris­tic for ma­ri­ne cya­no­bac­te­ria and mi­cro­al­gae are de­tec­ted as well as fluo­re­scent dyes spe­ci­fic for DNA, pro­te­ins and other cel­lu­lar com­pounds of mi­cro­or­ga­nisms like cell mem­branes. Fur­ther, cells mee­ting pre­de­fi­ned pro­per­ties can be sor­ted with high speed in high pur­ity for fur­ther mo­lecu­lar bio­lo­gical ana­ly­sis.

Flow cyto­metry com­ple­ments the mo­lecu­lar bio­lo­gical tool­box to study mi­croor­gan­isms. Its ca­pa­city of fast ana­lysis of thou­sands of cells per second and the sim­ul­tan­eous re­cord­ing of mul­tiple para­met­ers makes flow cyto­metry a stand­ard tool in plank­ton re­search. In ad­di­tion flow cyto­met­ric cell sort­ing (FACS) en­ables the phys­ical sep­ar­a­tion and en­rich­ment of well-defined cell pop­u­la­tions without prior cul­tiv­a­tion. 

At the MPI in Bremen, Flow Cytometry is a research group. In this group we con­tinu­ously im­prove our flow cyto­metry meth­ods and com­bine them with new mo­lecu­lar bio­lo­gical ap­proaches to gain deeper in­sights into the eco­lo­gical role of mi­crobes in a range of di­verse mar­ine hab­it­ats.

How does Flow Cytometry work?

Durchfluss-Zytometrie (©Max-Planck-Institut für Marine Mikrobiologie, B. Fuchs)
Principle of flow cytometric analysis and sorting
(© Max Planck Institute for Marine Microbiology, B. Fuchs)

In flow cytometry, the liquid sample containing the cells is injected into the middle of a continuously flowing water jet (also called sheath fluid). The water jet is then tapered to a diameter of less than 1/10 of a millimetre using a nozzle. The enclosed cells are thus focused into the centre of the water jet and exit the nozzle like beads on a string. The precisely aligned cells pass the laser beam individually at the observation point and can thus be excited by the laser light. Depending on the size and staining of the cell, the light signals from the cells are focused through lenses (not shown) onto the detectors, where they are converted into electrical signals and further fed into software on the computer.

In sorting mode, the cells can also be separated according to certain properties. To do this, the researchers set conditions that the cells must fulfil. The nozzle oscillates in high-frequency oscillations, which causes the water jet to break off into defined droplets below the observation point. If a cell that meets the specified parameters is detected, the corresponding cell is electrically charged with its droplet. The charged droplets with the cells are deflected according to their charge (positive or negative) and land in a reaction vessel. Shown here is a two-way sorter that can sort two populations simultaneously.

We currently have three different flow cytometers at the Institute. They differ for example in size, sensitivity, and capability. All three can be transported and are suitable for use on board research vessels. Further information is available on the department page of the Flow Cytometry Group.

Flow Cytometry in action

We combine several methods for the specific enrichment of bacteria: (1) Using FISH, we fluorescently label a specific bacterial species of our Helgoland water sample. (2) Based on that signal, cells are sorted. (3) The DNA of that enrichment is sequenced and further analyzed. (© Max Planck Institute for Marine Microbiology, A. Grieb)
We combine several methods for the specific enrichment of bacteria: (1) Using FISH, we fluorescently label a specific bacterial species of our Helgoland water sample. (2) Based on that signal, cells are sorted. (3) The DNA of that enrichment is sequenced and further analyzed. (© Max Planck Institute for Marine Microbiology, A. Grieb)

Analysis of unknown microbes

Marine microbes like to play hide and seek. Some bacteria often appear in samples but do not grow in the lab. At the same time, they are too few to be discovered via genetic analysis.

The idea to solve this problem: As we have a flow cyto­meter with a cell sort­ing sys­tem in our re­search group, the idea arised to se­lect the cells be­fore se­quen­cing the DNA. That way, the di­versity is re­duced and the rare spe­cies can no longer hide. Thus, the sci­ent­ists used the FISH-method to la­bel DNA sec­tions of the mi­crobes with fluor­es­cent dyes to de­tect and sort the bac­teria they were in­ter­ested in. However, they faced two chal­lenges: Firstly, a very bright FISH sig­nal was needed for the de­tec­tion and sort­ing of tar­geted cells us­ing flow cyto­metry. Secondly, suf­fi­cient un­im­paired DNA ma­ter­ial was re­quired for high qual­ity gen­ome se­quen­cing.

A team around the scientist Anissa Grieb, to­gether with re­search­ers from the Joint Gen­ome In­sti­tute, tested how this could work. At the end, they suc­ceeded by us­ing a re­cently de­veloped ver­sion of the FISH-method, the hy­brid­iz­a­tion chain re­ac­tion (HCR)-FISH. First, they op­tim­ized this pro­ced­ure with pure cul­tures in the labor­at­ory and af­ter­wards used it on the en­vir­on­mental samples, which had been taken off the coast of Hel­go­land. 

 

 

Who uses Flow Cytometry?

It is mainly used by scientists of the department Molecular Ecology. However, it is also open to all other scientists of the institute as well as to external researchers in the context of collaborative projects.

Contact

Group Leader

Flow Cytometry Research Group

PD Dr. Bernhard Fuchs

MPI for Marine Microbiology
Celsiusstr. 1
D-28359 Bremen
Germany

Room: 

2222

Phone: 

+49 421 2028-9350

PD Dr. Bernhard Fuchs
 
 
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