Organic Geochemistry

Hinrichs Lab - Geomicrobiology Laboratory

Introduction

For the investigation of biogeochemical processes, we incubate microbes in cultures or environmental samples in the laboratory. In order to mimic conditions in the deep sea, it is crucial to provide the microorganisms with suitable atmosphere, temperature and pressure conditions.

Coy anaerobic chamber

Most of our samples come from anoxic environments. To avoid contamination from oxygen during laboratory incubation, samples need to be prepared in an oxygen-free environment. We are using the anaerobic flexible vinyl COY glove box to prepare and dispense sediment slurries anoxically.

Below are some specifications for this anaerobic chamber:
- Interior size of the chamber: W x D x H = 90 x 80 x 100 cm
- Interior size of the buffer chamber: W x D x H = 34 x 34 x 34 cm, door opening: W x H = 22.9 x 30.5 cm
- One pair of gloves
- Formation gas: 5% H₂ in N₂
- Pd-catalyst to reduced O₂ with H₂. The catalyst is regenerated on a weekly basis

Incubators

The natural habitats for microorganisms have a wide temperature range from lower than 0°C to higher than 100°C. To simulate their natural habitats, temperature control is an essential issue. Laboratory fridges are being used to simulate conditions lower than room temperature, whereas different heating facilities are utilized for generating higher temperatures.

These facilities include:
-A Memmert INE 400 incubator. Temperature range: +30°C to 70°C; natural convection or forced air circulation
-A Memmert IPP 800 incubator. Temperature range: +5 °C to 70 °C; fridge incubator with Peltier technology.
-A GFL 1083 shaking water bath. Temperature regulation: +10°C to 99.9°C; shaking frequency: 10 to 250 min-1
-A Heraeus heating and drying oven. Temperature: up to +300°C; with an air-circulation fan

High-pressure incubation equipment

Microorganisms in the deep ocean and marine sediment are experiencing pressure that is much higher than that at the Earth’s surface. Pressure will change the status of matter, particularly gas, making it difficult to simulate the in situ conditions using the conventional cultivation techniques. We have constructed in house two high-pressure systems for laboratory experiments.

High-pressure stainless steel tubing reactors

The stainless steel tubing reactors withstand pressure up to 200 bar, but offers no possibility for temperature regulation.

The liquid is pumped by the HPLC pump (back, middle) into the stainless steel tubing reactor (right), which is filled with testing materials and gas (photo: Yushih Lin, MARUM).

Pressure-temperature-gradient block

The pressure-temperature-gradient block allows to work at a pre-defined pressure and a range of temperatures that are adjusted with the help of a heating block.

The pressure-temperature-gradient block is equipped with polyoxymethylene incubation vessels that endure pressure up to 20 bar

The liquid saturated with gas in the saturation chamber (right) is being pumped by the two HPLC pumps (middle) into a polyoxymethylene incubation vessel, which sits in the aluminum temperature block (left) (photo: Yushih Lin, MARUM).

Autoclave

Most important of all: when working with samples from deep ocean or subseafloor sediment, you would not like to end up enriching microbes from your daily life! We use a Wolf Sanoclav LaM-3-20-MCS-J autoclave, which sterilizes laboratory equipments under conditions of either 140°C/2.7 bar or 121°C/1.2 bar. Sometimes a combustion oven is also used for sterilization as well as removal of organic matter.

Microcentrifuge

We use a microcentrifuge to separate small volumes of aqueous solutions and suspensions of different densities, e.g. cell cultures.

Eppendorf Centrifuge 5425, non-refridgerated, whisper-quiet, 24 places for 2mL vials.