Anaerobic and Molecular Microbiology Laboratory

The laboratory is dedicated to the study of diversity of functional groups of organisms and their interactions in soil and sediment nitches differing in availability of oxygen.

Service Application

About

The Anaerobic and Molecular Microbiology Laboratory at SoWa covers all the aspects of work with anoxic environmental samples and anaerobic microorganisms.

Instrumentation

The Anaerobic and Molecular Microbiology Laboratory is fully equipped for anaerobic cultivations, microbiome and metagenome analysis, including an extraction facility for environmental DNA and RNA. For bioinformatic and statistical data analysis, the lab is equipped with a powerful computer server. In addition, we specialise in performing Stable Isotope Probing (SIP) and work in close collaboration with the IRMS lab of Dr Travis Meador for quantifying and measuring the isotopic signature of Volatile Fatty Acids (VFA), H2, CH4 and CO2.

For anoxic work:

  • Vinyl Anaerobic chamber (COY)
  • Anaerobic gassing manifold

For DNA/RNA extraction:

  • FastPrep-24™ 5G + CoolPrep Sample Holder (MP Biomedicals)
  • Centrifuge 5430R (Eppendorf)
  • c300 Chemi Blue light White light UV (Azure Biosystems)
  • Molecular lab facility (joint with the group of Dr. Alica Chroňáková): NanoDrop™ 2000 Spectrophotometer (ThermoFisher Scientific), Qubit 2.0 fluorometer (Invitrogen), Synergy™ 2 Multi-Mode Microplate Reader (BioTek Instruments), 2100 Bioanalyzer (Agilent technologies)

For data analysis:

  • Computer server CSE-825TQ-R740LPB with two AMD EPYC™ 7401P 24-core processors (total 48 cores) and 512GB of DDR4 SDRAM (Supermicro)

For gene and transcript quantification:

  • QX200™ AutoDG™ Droplet Digital™ PCR System (Bio-Rad)
  • T100 Thermal cycler (Bio-Rad), StepOnePlus Real-Time PCR (Applied Biosystems; joint with the group of Dr. Alica Chroňáková)

For stable isotope probing:

  • Ultracentrifuge Sorvall WX Ultra 100 (ThermoFisher Scientific)
  • Refractometer AR200 (Reichert technologies)

Services

  • Sample processing and incubation under anoxic conditions
  • Cultivation of microorganisms under anoxic conditions
  • DNA and RNA extraction from various environmental samples including soil and water samples (including also those with high humic content)
  • Microbiome analysis using targeted and untargeted metagenomics
  • Environmental gene and transcript quantification
  • DNA-, RNA- and PLFA- stable isotope probing

People

Name Role Phone Room Email
Dr Roey Angel Head of Laboratory +420 387 775 847 113 roey.angel@bc.cas.cz
RNDr. Eva Petrová Research assistant  +420 387 775 847 113 eva.petrova@bc.cas.cz
Dr. Ana Catalina Lara Rodriguez Postdoc 112 ana.lara@bc.cas.cz
Dr. Jolanta Niedzwiecka Postdoc 112 jniedzwiecka@prf.jcu.cz

Projects

  • Biological diversity
  • Functional and transcriptomic analysis of leaf litter digestion by millipedes: Role of microorganisms and digestive enzymes (GACR project No. 17-22572S)
  • With a little help from my friends: understanding the roles and importance of the millipede gut microbiome (GACR project No. 19-24309Y)
  • Who eats whom and when? Zooming-in on alternative energy transfer pathways in planktonic food webs of hypertrophic shallow lakes (GACR project No. 19-16554S)
  • Evrona Nature Reserve Oil Contamination Ecological Monitoring Program
  • Teatime4Schools

Contact

Head of lab
Dr. Roey Angel
Soil & Water Research Infrastructure and Institute of Soil Biology
Biology Centre CAS

Na Sádkách 7, Room 113
370 05 České Budějovice, Czechia

roey.angel@bc.cas.cz
+420 387 775 847

Lab manager
RNDr. Eva Petrová
eva.petrova@bc.cas.cz
+420 387 775 847