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I'm working on a project where I need to find certain cellulolytic bacteria. I was looking at this list :

How could I selectively separate one of the bacteria types that I had in mind from that list? So how would I have to extract the bacteria from the compost?

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up vote 3 down vote accepted

A first (and obvious) approach is the use of cellulose agar in order to isolate all the celluloltic bacteria in the sample. Be careful, however, since the nutrient requirements of some of those microbes may be higher and then they won't grow with only cellulose (they may need some other compounds, like a nitrogen source). Be careful with fungi, too.

If you have the proper equipment, it would be ideal to extract DNA and analyze the environmental rRNA 18s sequences. With this, you should be able to know if your bacteria is present in your sample. If so, proceed with the previous steps.

Once you had a set of suspected colonies, you must proceed with more specific culture media (wich would depend of the exact bacteria you're looking for. For example, if you're looking for Clostridium, you should try to grow your sample in an anaerobic jar and test the ability to reduce sulphur). With this approach, you may reach a point where you can't differenciate similar species. At this point, mollecular characterization is the best option, with the use of rRNA 18s again. Note that the mollecular approach, while relative expensive, can be performed in every step, so you can combine cultures and DNA analyses at will.

Lastly, if you're looking for an specific bacteria, it would be useful to know wich one is, so the community can give you more accurate responses.

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Thanks - as for your last question : I'm not sure which species I would like to separate, because I don't know which bacteria are available in my compost heap... – user2606722 Sep 10 '13 at 16:08
you can also just take some compost and boil it and then use it as a medium for an agar. if you want to optimize for a particular sort of refuse that might be better.. – shigeta Sep 10 '13 at 16:34
thanks - I'll use your advice too! – user2606722 Sep 10 '13 at 17:14
and - before I forget - Where in the compost heap should I look for bacteria? (the bottom or middle?) – user2606722 Sep 10 '13 at 18:08
Be careful with the boiling. First, endospores can survive the process if it hasn't done properly. And second, the heat may cause some undesired reactions, changing the composition. – Miguel Ángel Naranjo Ortiz Sep 10 '13 at 19:28

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