For the practical course lecture: Methods in Aquatic Microbial Ecology

Skills to be acquired in this module

The students learn to…

·       analyze bacterial substrates at ambient concentrations such as dissolved amino acids and carbohydrates by high performance liquid chromatography (HPLC).

·       determine bacterial cell numbers by flow cytometry and epifluorescence microscopy and to analyze these data by image analysis.

·       extract bacterial DNA from water and sediment samples.

·       amplify bacterial genes by specific primers and PCR.

·       assess bacterial communities by culture-independent methods such as denaturing gradient gel electrophoresis and next generation sequencing.

·       present and discuss scientific results.

·       write a scientific protocol.

The students gain competences in:

·       Understanding how to analyze dissolved substrates of heterotrophic aquatic bacterial communities by state of the art approaches.

·       How to assess the abundance of aquatic bacterial communities by state of the art approaches.

·       Analyzing the composition of bacterial communities by PCR-based culture-independent approaches.

The course starts with a lecture introducing basic issues of aquatic microbial ecology with an emphasis on methodological aspects. This lecture is completed before the practical work starts.

During the practical course of a block of two weeks the participants carry out analyses and experiments on:

·       determining the concentration of dissolved organic substrates (amino acids, carbohydrates),

·       the abundance of bacterial communities in aquatic systems

·       the composition of bacterial communities in environmental samples by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA targeted gene fragments.

The main emphasis is on analyses and approaches of bacterial communities in the water column.

Lecture notes, available on Stud.IP

Will be announced during the course.

One assessment of examination: Portfolio (seminar presentation, written protocol)

Protocol (100 %), seminar presentation (no mark). Active participation (Active and documented participation in practical courses (labs, exercises, seminars, field trips) and courses. These include e.g. the delivery of exercises, writing a lab report or seminar presentations according to the advice of the course supervisor.)