Molecular Microbiology Laboratories

GFZ Helmholtz Centre for Geosciences

last updated: April 21, 2025

About the Laboratory

Molecular Microbiology Laboratories

GFZ Helmholtz Centre for Geosciences

@ Section 3.6 Geomicrobiology

This Laboratory is part of:

GeoBioLab – Helmholtz Laboratory for Integrated Geological and Biological Research laboratory complex
Networks: Geo.X

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Visit us on our website in DE / EN

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Description

Molecular microbial ecology is crucial for understanding the role of microorganisms in ecosystems, as it provides insights into microbial diversity, interactions, and functions at the molecular level. Our labs utilize advanced techniques for environmental DNA and RNA isolation but also DNA sequencing, metagenomics, and enumeration of microbial cells to uncover the genetic and metabolic capabilities of microbes in all kinds of natural environments. This knowledge is vital for addressing global challenges such as climate change, soil health and development, the sustainable utilization of the underground and the exploration of the limits of life.

The Molecular Microbiology Laboratories focus on

I) Environmental DNA and RNA Isolation and Purification

II) Environmental Genomics and Transcriptomics

III) Enumeration of Microbial Cell and Gene Copy Numbers

IV) Stable Isotope Probing

V) S1 Facility for Genetically Modified Organisms

VI) Separation of eDNA (external DNA) and iDNA (internal DNA).

Instruments

DNA/RNA Extraction Kit
A fluorometer is an instrument that measures the amount of fluorescent radiation produced by a sample exposed to monochromatic radiation. Additional information available at "http://gcmd.gsfc.nasa.gov/cgi-bin/createsensorsupweb" [Summary provided by NOAA] (Source: Global Change Master Directory (GCMD). 2023. GCMD Keywords, Version 16.3 [...] )
Fluorometer
Fluorimeter
Homogenizer
PCR Cycler
Thermal Cycler, Thermal PCR Cycler
qPCR Cycler
PCR Workstation
Fluorescence illumination and observation is the most rapidly expanding microscopy technique employed today, both in the medical and biological sciences, a fact which has spurred the development of more sophisticated microscopes and numerous fluorescence accessories. Epi-fluorescence, or incident light fluorescence, has now become the method of choice in many applications and comprises a large part of this tutorial. We have divided the fluorescence section of the primer into several categories to make it easier to organize and download. Please follow the links below to navigate to points of interest. Introductory Concepts - Fluorescence is a member of the ubiquitous luminescence family of processes in which susceptible molecules emit light from electronically excited states created by either a physical (for example, absorption of light), mechanical (friction), or chemical mechanism. Generation of luminescence through excitation of a molecule by ultraviolet or visible light photons is a phenomenon termed photoluminescence, which is formally divided into two categories, fluorescence and phosphorescence, depending upon the electronic configuration of the excited state and the emission pathway. Fluorescence is the property of some atoms and molecules to absorb light at a particular wavelength and to subsequently emit light of longer wavelength after a brief interval, termed the fluorescence lifetime. The process of phosphorescence occurs in a manner similar to fluorescence, but with a much longer excited state lifetime. Anatomy of the Fluorescence Microscope - In contrast to other modes of optical microscopy that are based on macroscopic specimen features, such as phase gradients, light absorption, and birefringence, fluorescence microscopy is capable of imaging the distribution of a single molecular species based solely on the properties of fluorescence emission. Thus, using fluorescence microscopy, the precise location of intracellular components labeled with specific fluorophores can be monitored, as well as their associated diffusion coefficients, transport characteristics, and interactions with other biomolecules. In addition, the dramatic response in fluorescence to localized environmental variables enables the investigation of pH, viscosity, refractive index, ionic concentrations, membrane potential, and solvent polarity in living cells and tissues. Additional information available at: "http://micro.magnet.fsu.edu/primer/techniques/fluorescence/ fluorhome.html" (Source: Global Change Master Directory (GCMD). 2023. GCMD Keywords, Version 16.3 [...] )
Fluorescence Microscope
UV-VIS Spectrophotometer
Gel Documentation System
Gel Doc Systems, Gel Image System, Gel Imager
Electrophoresis Device
Bioanalyzer
Gel Electrophoresis Device

Analytical Methods

Next generation sequencing methods require a DNA library preparation prior to processing. (Own definition)
DNA Library Preparation
A fluorometer is an instrument that measures the amount of fluorescent radiation produced by a sample exposed to monochromatic radiation. Additional information available at "http://gcmd.gsfc.nasa.gov/cgi-bin/createsensorsupweb" [Summary provided by NOAA]
A fluorometer is an instrument that measures the amount of fluorescent radiation produced by a sample exposed to monochromatic radiation. Additional information available at "http://gcmd.gsfc.nasa.gov/cgi-bin/createsensorsupweb" [Summary provided by NOAA] (Source: NASA; UUID: e904c3c7-0111-4d09-bb01-2b7bea9b4d3f) Own comment: For Bioanalytics a fluorometer is used to measure quantity and quality of DNA. (Source: Global Change Master Directory (GCMD). 2023. GCMD Keywords, Version 16.3 [...] )
Fluorometry
Fluorescence Spectroscopy, Fluorimetry
DNA Isolation
DNA/RNA Isolation, Homogenization
DNA Extraction
Determination of nucleotide sequence (the DNA primary structure). (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
DNA Sequencing
Cytogenetic technique used to detect and localize the presence or absence of specific DNA sequences on chromosomes. It uses fluorescent probes that only bind to those parts of the chromosome with which they show a high degree of sequence complementarity. Note: FISH is often used for finding specific features in DNA for use in genetic counselling, medicine, and species identification. FISH can also be used to detect and localize specific RNA targets (mRNA, lncRNA and miRNA) in cells, circulating tumor cells, and tissue samples. In this context, it can help define the spatial-temporal patterns of gene expression within cells and tissues. (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
FISH - Fluorescent In Situ Hybridization
CARD-FISH, Fluorescence In Situ Hybridization
Determination of nucleotide sequence (the DNA primary structure). Note: Next-generation sequencing refers to non-Sanger-based high-throughput DNA sequencing technologies where millions of DNA strands can be sequenced in parallel. (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
NGS - Next Generation Sequencing
Massive Parallel Sequencing, Second Generation Sequencing
Laboratory technique for rapid amplification and pre-determination of regions of double-stranded DNA using DNA polymerase. (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
PCR - Polymerase Chain Reaction
DNA Amplification, DNA Enrichment
Polymerase chain reaction to quantify target nucleotide sequences of interest. (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
qPCR - Quantitative Polymerase Chain Reaction
DNA Amplification, DNA Enrichment, Quantitative PCR
Fluorescence illumination and observation is the most rapidly expanding microscopy technique employed today, both in the medical and biological sciences, a fact which has spurred the development of more sophisticated microscopes and numerous fluorescence accessories. Epi-fluorescence, or incident light fluorescence, has now become the method of choice in many applications and comprises a large part of this tutorial. We have divided the fluorescence section of the primer into several categories to make it easier to organize and download. Please follow the links below to navigate to points of interest. Introductory Concepts - Fluorescence is a member of the ubiquitous luminescence family of processes in which susceptible molecules emit light from electronically excited states created by either a physical (for example, absorption of light), mechanical (friction), or chemical mechanism. Generation of luminescence through excitation of a molecule by ultraviolet or visible light photons is a phenomenon termed photoluminescence, which is formally divided into two categories, fluorescence and phosphorescence, depending upon the electronic configuration of the excited state and the emission pathway. Fluorescence is the property of some atoms and molecules to absorb light at a particular wavelength and to subsequently emit light of longer wavelength after a brief interval, termed the fluorescence lifetime. The process of phosphorescence occurs in a manner similar to fluorescence, but with a much longer excited state lifetime. Anatomy of the Fluorescence Microscope - In contrast to other modes of optical microscopy that are based on macroscopic specimen features, such as phase gradients, light absorption, and birefringence, fluorescence microscopy is capable of imaging the distribution of a single molecular species based solely on the properties of fluorescence emission. Thus, using fluorescence microscopy, the precise location of intracellular components labeled with specific fluorophores can be monitored, as well as their associated diffusion coefficients, transport characteristics, and interactions with other biomolecules. In addition, the dramatic response in fluorescence to localized environmental variables enables the investigation of pH, viscosity, refractive index, ionic concentrations, membrane potential, and solvent polarity in living cells and tissues. Additional information available at: "http://micro.magnet.fsu.edu/primer/techniques/fluorescence/ fluorhome.html"
Fluorescence illumination and observation is the most rapidly expanding microscopy technique employed today, both in the medical and biological sciences, a fact which has spurred the development of more sophisticated microscopes and numerous fluorescence accessories. Epi-fluorescence, or incident light fluorescence, has now become the method of choice in many applications and comprises a large part of this tutorial. We have divided the fluorescence section of the primer into several categories to make it easier to organize and download. Please follow the links below to navigate to points of interest. Introductory Concepts - Fluorescence is a member of the ubiquitous luminescence family of processes in which susceptible molecules emit light from electronically excited states created by either a physical (for example, absorption of light), mechanical (friction), or chemical mechanism. Generation of luminescence through excitation of a molecule by ultraviolet or visible light photons is a phenomenon termed photoluminescence, which is formally divided into two categories, fluorescence and phosphorescence, depending upon the electronic configuration of the excited state and the emission pathway. Fluorescence is the property of some atoms and molecules to absorb light at a particular wavelength and to subsequently emit light of longer wavelength after a brief interval, termed the fluorescence lifetime. The process of phosphorescence occurs in a manner similar to fluorescence, but with a much longer excited state lifetime. Anatomy of the Fluorescence Microscope - In contrast to other modes of optical microscopy that are based on macroscopic specimen features, such as phase gradients, light absorption, and birefringence, fluorescence microscopy is capable of imaging the distribution of a single molecular species based solely on the properties of fluorescence emission. Thus, using fluorescence microscopy, the precise location of intracellular components labeled with specific fluorophores can be monitored, as well as their associated diffusion coefficients, transport characteristics, and interactions with other biomolecules. In addition, the dramatic response in fluorescence to localized environmental variables enables the investigation of pH, viscosity, refractive index, ionic concentrations, membrane potential, and solvent polarity in living cells and tissues. Additional information available at: "http://micro.magnet.fsu.edu/primer/techniques/fluorescence/fluorhome.html" (Source: NASA; UUID: 35dc5fc4-4c96-44d9-8710-0e99e00201c8) (Source: Global Change Master Directory (GCMD). 2023. GCMD Keywords, Version 16.3 [...] )
Fluorescence Microscopy
UV-VIS Spectrophotometry
UV-VIS Spectroscopy
Gel Documentation
Gel Imaging
Electrophoresis
Automated Electrophoresis
Separation technique used to separate or fractionate proteins and larger peptides according to their relative molecular mass using an electric field in polyacrylamide gel (PAGE). (Source: IUPAC; https://doi.org/10.1515/iupac.90.0262)
Gel Electrophoresis

Laboratory Keywords

In addition to the instruments and analytical methods listed above, these keywords help to describe the work done in the laboratory. This may include the type of samples, standard materials, specific preparative or analytical methods and specific instrument characteristics.

Disciplines

Interdisciplinary > Biology/Ecosystems Science > Geomicrobiology
Geomicrobiology
Interdisciplinary > Biology/Ecosystems Science > Microbial Studies
Microbial Studies

The Research Network for Geosciences in Berlin and Potsdam

Molecular Microbiology Laboratories

GFZ Helmholtz Centre for Geosciences

About the Laboratory

Molecular Microbiology Laboratories

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Description

Instruments

Analytical Methods

Laboratory Keywords

Disciplines

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