Anaerobic and molecular microbiology

About

The Anaerobic and Molecular Microbiology Laboratory at ISBB 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

Projects

Like fish out of water? Elucidating the ecophysiology of upland-soil methanogens through cultivation and omics methods. (GA ČR projekt č. 22-34650S, 2022-)
Microbes on mountain tops: how rhizosphere microbes help plants cope with climate changes in stressful and rapidly changing environments of Himalayas. (GA ČR projekt č. 1-04987S, 2021-2024)
With a little help from my friends: understanding the roles and importance of the millipede gut microbiome. (GA ČR projekt č. 19-24309Y, 2019-2021)
Who eats whom and when? Zooming-in on alternative energy transfer pathways in planktonic food webs of hypertrophic shallow lakes. (GA ČR projekt č. 19-16554S, 2019-2021)
Functional and transcriptomic analysis of leaf litter digestion by millipedes: Role of microorganisms and digestive enzymes. (GA ČR projekt č. 17-22572S, 2017-2019)
Citizen Science : Teatime4Schools (2018-2019)
Evrona Nature Reserve Oil Contamination Ecological Monitoring Program (Israel, 2018-2022)