Geomicrobiology

The Geomicrobiology laboratory at the Department of Earth and Environmental Sciences specializes in quantifying microbial metabolic fluxes and redox dynamics within environmental samples such as sediments, soils, and rocks. A methodological cornerstone is DNA Stable Isotope Probing (DNA-SIP), which allows researchers to identify active microorganisms by tracking the incorporation of stable isotopes into their genetic material. Combined with density gradient ultracentrifugation and quantitative PCR, this enables the precise determination of microbial abundance and functional activity.

To analyze metabolic processes, the facility provides dedicated RNA clean hoods for transcriptomics and advanced GC-MS systems for measuring gas concentrations of hydrogen, methane, and carbon dioxide, including their isotopic signatures. The infrastructure also supports anaerobic enrichment and cultivation to simulate specific environments, such as ferruginous analog oceans. This is complemented by fiber-optic oxygen sensing and UV/VIS spectrophotometry for real-time monitoring of microbial respiration and redox status. Consequently, the lab offers a comprehensive analytical pipeline from molecular biology to the quantitative assessment of biogeochemical cycles.

Anaerobic chamber for enrichment and cultivation of anaerobic microorganisms and early earth ferruginous analog ocean experiments.

A density gradient fractionation system (left side) for DNA stable isotope probing experiments and a ultracentrifuge (right side) for creating density gradients in order to separate stable isotope labeled DNA.

Gas chromatograph - mass spectrometer setup for measuring gases H2, CO2, CH4 and production of 13CO2, 13CH4, and 15N2 from stable isotope labeling experiments.

RNA dedicated clean hoods for extracting RNA and producing cDNA, free of external DNA contamination.

DNA stable isotope probing

Room: D U113
Contact person: Bill Orsi
Description: A density gradient fractionation system (left side from above photo) for DNA stable isotope probing experiments.

Density gradient centrifugation

Room: D U113
Contact person: Bill Orsi
Description: Optima Max TL ultracentrifuge (right side from above photo) for creating density gradients in order to separate stable isotope labeled DNA.

Quantitative PCR

Room: A 014
Contact person: Bill Orsi
Device: CFX Connect Real-Time PCR Detection System
Description: Quantifying gene copies from microbial communities as a measure of microbial abundance in environmental samples (sediment, soil, water, and rock)

Transcriptomics

Room: A 014
Contact person: Bill Orsi
Description: RNA dedicated clean hoods for extracting RNA and producing cDNA, free of external DNA contamination. Additional equipment for sample lysis prior to transcriptome prep, including FastPrep 5G homogenizer are available."

Spectrophotometer

Room: A 014
Contact person: Bill Orsi
Device: GENESYS™ 40/50 VIS- und
UV/VIS-Spektralphotometer.
Description: Measuring the growth of microbial cultures over time, as well as measuring dissolved
iron (Fe2+) concentrations using the ferrozine assay.

Fiber optic O2 mesurements

Room: A 014
Contact person: Bill Orsi
Device: Fibox-4 (from PreSens)
Description: Measuring O2 in liquid and gas samples, as a measure of microbial respiration and redox status in environmental samples and experiments.

MilliQ water purifier

Room: A 014
Contact person: Bill Orsi
Description: Producing purified water that is filtered through a charcoal filter, 0.2 µm membrane, and disinfected using UV. The purified water is used for DNA and RNA extractions, enzymatic assays, media preparation, and all molecular microbiology work.

Gas chromatography – mass spectrometry

Room: D U113
Contact person: Bill Orsi
Description: Gas chromatograph - mass spectrometer setup (GCMS-QP2020 NX, Shimadzu) is connected to headspace sampler and autosampler for measuring gases H2, CO2, CH4. The instrument is also set up for measuring production of 13CO2, 13CH4, and 15N2 from stable isotope labeling experiments. An internal split allows
for pre-separation of corrosive H2S, permitting measurements from sulfidic samples.