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Setting up a Home Laboratory for Microscopy

Found in: Howto, Labwork, Techniques

The home laboratory provides a safe working environment for microscopic investigations.

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Why a home lab?

For someone who wants to observe ready-made permanent slides or an occasional pond water sample, a fully equipped home laboratory may not be necessary and somewhat of an overkill. In this case it is sufficient to find a reasonably dust-free place to store and operate the microscope. The microscope can then be unpacked as required. For someone wants to prepare slides, perform microtoming and staining procedures, the issue may be somewhat different and space as well as equipment requirements are higher. As so often the case, it depends very much on the type of work that needs to be done.

The advantages of a dedicated lab can be summarized in a few points:

  • Safe working environment – You need to protect family members, furniture and your own health from the chemicals that you use.
  • Convenience and comfort – A dedicated work place does not require you to pack and unpack the chemicals and equipment that you use.
  • Equipment safety – Microscopes should not be moved around too much – there is the danger that you drop them on your toes. This may hurt your microscope… 🙂
  • Specimen quality – A proper work place makes it easier to produce (nearly) dust-free specimens. There is also less hassle.
  • Fun – It’s simply more fun to work in an environment which has been designed accordingly. After all, it’s a hobby.

Be cautious about growing bacteria

There are several legal issues that you must be aware of if you intend to furnish a “wet” laboratory for microbiological work. If you want to grow (unidentified) bacteria in Petri dishes and culture medium, then you are already working in an elevated Biohazard Level 2 (out of 4 levels). You simply do not know if you are growing a pathogen or not. Even Level 1 laboratories must adhere to certain safety standards and decontamination procedures. Level 2 is even more stringent.

Now, what does this mean for the amateur microscopist? The answer is: do not enrich and grow unidentified bacteria. Even the enrichment and growth of bacteria that belong to the lowest Biohazard Level (level 1), such as E. coli and B. subtilis, may not be permitted, because a home is (legally) not considered a laboratory. And how do you want to obtain these known microorganisms? Cell culture collections such as the DSMZ (Deutsche Sammlung für Mikroorganismen und Zellkulturen) in Germany or the ATCC (American Type Culture Collection) may not even send samples to private individuals. Microbiological work may be prohibited even in school laboratories, because they do not possess the appropriate license to conduct microbiological work. They generally also do not possess the appropriate equipment in order to conduct safe work. The legal situation may differ from country to country, naturally, but I would not take the risk. Proper microbiological work also requires you to use a gas Bunsen burner, an additional hazard source.

As a side note: properly observing bacteria requires you to use a phase contrast microscope, something that not all amateur microscopists have available. Personally I also think that there are more interesting samples to observe than bacteria.

Microorganisms to observe

The amateur microscopist should not despair, there are many safe microorganisms, including bacteria that can be observed. My advice: go for microorganisms that can be found growing on fresh food:

  • Joghurt – This is a good source of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus salivarius subsp. thermophilus.
  • Cheese – Roquefort cheese, including other blue cheeses, can serve as a source for molds. Camembert cheese is a source for the moulds Penicillium candidum and Penicillium camemberti.
  • Pond water samples and water from a home aquarium – These are good sources for a wide variety of ciliates, water fleas and algae. What about safety? Can you take a swim in the pond? Be aware that keeping pond water samples for extended periods of time in a jar may result in the water to turn foul. Unfriendly microorganisms may start to grow and I would be more cautious.
  • Yeast – Also safe. Can be grown in a petri dish.

The requirements of setting up a microscopy work place

  • Place for the microscope – The scope should have its own place and ideally it should not be necessary to pack and unpack the instrument. The table should be extremely stable to minimize vibrations. It should be easily cleanable with water to remove dust. There should be drawers for storing microscopic tools, slides and mounting media.
  • Place for chemicals – You need a safe place to store the chemicals. You must be able to lock away the substances to protect them from kids. The place should also allow for containment and easy cleaning, in case there are spills. I once dropped a small bottle of iodine solution on our wood floor. The top layer of the wood floor had to be polished away because the solution ate its way into the wood, staining it red.
  • Family friendliness – This one is often overlooked. I once got into trouble with my family because I wanted to store fly maggots and earth worms for dissection in the kitchen refrigerator. I did not even dare to ask if it is OK to modify the living room to accommodate a work bench for the microscope. The living room cupboards are also taboo for chemicals, also due to safety considerations. After all, children might be around.
  • Dust-free environment – Often a difficult thing to achieve. Electronic equipment likes to attract dust due to static electricity. This dust can be quite interesting to observe under the microscope, but in most cases it is a serious nuisance, greatly decreasing the quality of microscopic images.
  • A place for storing water samples – Pond water samples should not be stored in direct sunlight. This may cause overheating and (if there are few algae in the sample) a reduction in oxygen. The water can turn foul.
  • Running water and sink – This is needed for cleaning the equipment and for disposing (permitted) solutions. Note, that some wastes must be collected and disposed separately.
  • Work bench – You need some space for staining and preparing the slides. Some stains can be very aggressive and will irreversibly stain wood and other organic materials. Make sure that the work bench is easily cleanable.
  • Ventilation – You need fresh air if you work with volatile solvents such as alcohol.

Equipment of a microbiology lab

Some amateurs (or teachers) may be interested in growing safe microorganisms such as yeast. It still needs to be mentioned that contaminations of the culture medium can be a health hazard. For people who want to equip a wet lab, the following equipment is necessary. You may also want to read the post: What accessories should be bought?.

  • An autoclave – This is a pressure cooker. Used for sterilizing equipment and nutrient media. It is also used to kill off microorganisms on petri dishes before they are discarded.
  • An incubator – This device allows for the control of the temperature. Petridishes with microorganisms can be placed into the incubator. This one is not always necessary. If the room temperature is too low, microorganisms may simply take longer to grow.
  • Flowing water and a sink – Used for cleaning and washing. This one is pretty self-explanatory.
  • Gas – The gas flame is used for sterilization and to minimize the risk of contamination when making the agar plates. It is also used to heat-fix the microorganisms on the slide.
  • A shaker – This one is only needed if one intends to grow microorganisms in liquid medium. The shaking ensures that the liquid medium is supplied with oxygen from the air.
  • Inoculation loop – For picking up colonies of microorganisms
  • Nutrient media and agar – They supply the food to the microorganisms. The agar is used to solidify the medium.
  • Petridishes – It contains the agar nutrient media.
  • Parafilm – For sealing off the petri dishes.
  • Various stains and reagents – These are used for fixing and staining the specimens.
  • Miscellaneous – Materials such as gloves, alcohol for disinfection etc. are also needed
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