Doctoral students gain insight into research methods

4 April 2022, by RTG2530

Photo: UHH/RTG2530/Stirn

The doctoral researchs of the RTG2530 are pipetting in the microbiology laboratory to isolate DNA from microogranism.

Microbiology, soil science and ecosystem modeling - the research fields involved in the RTG are methodologically very diverse and demanding. Therefore, the participating scientists of the RTG gave the PhD students an overview of important scientific methods that are applied in their research field.

Which microorganisms are found in the Elbe estuary? How many are present? And what role do they play in the global carbon cycle? These are the questions that microbiologists Prof. Dr. Wolfgang Streit and PhD student Luise Grueterich want to answer in their Research Training Group 2530 project. Last week, they gave the PhD students of the RTG an insight into their work and the methods used.

"Due to the limited time, we could not perform all steps of our usual investigations with the doctoral researches," says Prof. Wolfgang Streit. "However, we tried some important ones with them, namely isolation of bacterial DNA for analysis, polymerase chain reaction (PCR) and gel electrophoresis."

Microorganisms are so small that they are invisible to the eye. In addition, more than 99 percent of bacteria and archaea cannot be cultured. Nevertheless, molecular genetic methods can be used to identify these microorganisms. For this purpose, the doctoral researchers obtained the microorganism DNA directly from a sample of the Elbe estuary, amplified small parts of it using PCR and then separated them by length in the agarose gel during gel electrophoresis. This DNA was then sent to a genome analysis laboratory for sequence analysis. From the sequencing data, which is expected soon, the PhD students will be able to read which bacteria are in the sample.

PCR and gel electrophoresis are among the standard methods used in microbiology. Furthermore, the doctoral researchers learned about other standard methods of the participating research fields:

On the first day Prof. Dr. Lars Kutzbach introduced the doctoral researchers to methods of biogeochemistry and soil science. The PhD students excavated a soil pit, described the soil profile, and evaluated soil properties such as soil texture and structure as well as organic matter content.

As part of the presentation of aquatic and terrestrial ecology, Prof. Dr. Kai Jensen showed how to perform a vegetation analysis, i.e. plant species compositions. Prof. Dr. Kathrin Dausmann and Sina Remmers used humans and earthworms to explain how metabolic measurements work and how the energy content of food components is measured. Finally, Prof. Dr. Ralf Thiel guided the PhD students through the fish collection of the Leibniz Institute for the analysis of biodiversity change and Johanna Biederbick showed how plankton samples from the Elbe River are analyzed.

Ecosystem modeling is also part of the program. Prof. Dr. Philipp Porada will have the doctoral students create a simple ecosystem model that includes primary producers, consumers, dead organic matter and nutrients. In the process, they will also conduct sensitivity studies and analyze the results.

Dr. Andrej Fabrizius, Luise Grueterich and Prof. Dr. Wolfgang Streit presented the methods of molecular biology and microbiology with the isolation of DNA and its analysis in the laboratory, which is used to identify bacteria in soil samples. "We are confident that the results of the doctoral researchers match ours. Of course, Luise's studies have already given us a first insight into which bacteria are present in the soil of the estuary," says Prof. Streit. "We found many proteobacteria in the high and low marsh, but not in the pioneer zone. Unfortunately, we don't know why that is." The researchers suspect that the organisms have adapted to different living conditions, such as salinity, temperature and oxygen levels, and thus survive better in some habitats than others.

The microbiologists also found cyanobacteria, better known as blue-green algae, in the estuarine soil. Prof. Streit and Luise Grueterich have also been able to identify some environmental organisms from the phylum Bacteroidota, which primarily decompose plant materials and which researchers have only recently become familiar with. "We are still at the very beginning of our investigations," says Streit. "To answer our questions about the composition of the bacteria and their importance for material cycles, we need to collect and evaluate significantly more data in the coming years."