Methods

Mikroben (© Max-Planck-Institut für Marine Mikrobiologie, A. Esken)

We are always looking for exciting knowledge about individual microbes, but also about entire ecosystems. The ge­netic ma­ter­ial of mi­crobes, their DNA, for example con­ceals a lot of in­form­a­tion about their life­style and abil­it­ies. To ana­lyze microbes in detail, to get to the bottom of their DNA, their enzymes, their biochemical capabilities, we use many different methods. Here we present some of the methods we use at our institute.

Analysis of marine sugars

Every bac­terium, every mi­croor­gan­ism has its very own en­zymes – its own tools – in or­der to cut poly­sac­char­ides. We can use such en­zymes to meas­ure sugar mo­lecules in the sea. The bac­terial en­zymes are re­spons­ible for the break­ing down of sugar com­pounds. They break the large, com­plex poly­sac­char­ides into small, simple mono­sac­char­ide units. These simple sug­ars are easier to meas­ure than poly­sac­char­ides. More...

Analysis of microbial metabolism

In focus are the en­zymes in­volved in the con­ver­sion of min­er­als and gases. They are pro­teins that or­ches­trate strange re­ac­tions highly chal­len­ging for chem­ists. We have to ex­tract these en­zymes, and sort them out from other pro­teins by us­ing the nat­ive puri­fic­a­tion. We then pierce the mo­lecu­lar secret of their re­ac­tion by look­ing at them with X-ray crys­tal­lo­graphy, which means that we have to crys­tal­lize the en­zymes, and use X-ray to get their pic­tures. More...

Metagenomics

With the help of meta-genomics, it is possible to analyse an environmental sample (i.e. a mixture of the most diverse organisms as they live together in the environment) and find out which organisms live in this environment as well as which genes – and thus metabolic pathways, interactions, and defence strategies – predominate. More...

Fluor­es­cence In Situ Hy­brid­isa­tion (FISH)

Mi­croor­gan­isms can barely be dis­tin­guished from each other based on their ap­pear­ance. Nev­er­the­less, every cell has its own fin­ger­print that is typ­ical for the spe­cies – its ge­netic ma­ter­ial. A case for FISH, Fluor­es­cence In Situ Hy­brid­isa­tion. It se­lect­ively visu­al­izes cer­tain sec­tions of the ge­netic ma­ter­ial of in­di­vidual cells. Un­der the mi­cro­scope, these cells are then made to glow. FISH im­ages of mi­croor­gan­isms look like a starry sky, but one with many dif­fer­ent col­ours. Our ques­tion is: What is shin­ing where? With FISH, we can pre­cisely identify the or­gan­isms in our samples. More...

Cultivation and Isolation of Microorganisms

We di­lute the cells with sterile sea­wa­ter dir­ectly after sampling to isol­ate in­di­vidual cells and in­cub­ate for long times to get slowly grow­ing bac­teria. The com­bin­a­tion of phys­ical isol­a­tion into hun­dreds of cul­tures, suf­fi­cient time to grow and mo­lecu­lar tools to ana­lyze en­rich­ment cul­tures still needs the per­fect me­dium for the mi­croor­gan­ism of in­terest. A per­fect me­dium provides all nu­tri­ents at non-toxic con­cen­tra­tions, ideally in a per­man­ent con­tinu­ous-fed mode at mi­cro­molar con­cen­tra­tion, like in nature. More...

 
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