Hi Bastien,

Antibiotics are efficient to counterselect bacteria: you can use a cocktail with several, like chloranphenicol and streptomycin etc. For Archaea, I guess that in your reactor you mostly (have in not only) methanogens. Thus I suggest you use bromoethanesulfonate to specifically inhibits mathanogens growth. I used it for similar purpose and it worked well. here is a publication about that:

http://dx.doi.org/10.1016/j.ijhydene.2009.11.114, How to Cite or Link Using DOI

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Hi, thanks for your answer. I will definitively try the conditions mentioned in the paper, but I expose my reactors to high oxygen levels (8 mg/L). Shouldn´t this inhibit methanogens?

Another approach to answer your question is this technique called stable isotope probing (SIP): http://www.ncbi.nlm.nih.gov/pubmed/17446886

Essentially, you spike your media with an isotope such as C13 - in your case, you may want to have C13 xenobiotic compounds (there are companies that will produce virtually any chemical with C13). As the microbes degrade the labeled food, they incorporate the heavier C13 into their DNA. You can then extract the DNA, run it over a CsCl gradient and get different fractions of "active degraders" and "inactive degraders". You can then use your primer sets to look at the relative ratios of bacteria:archaea in each fraction to see who is really degrading the the compounds. We prefer to perform 16s rRNA sequencing on the fractions to get specific species responsible for the degradation.

It's a nice system because it rules out a lot of the issues with selective media. However, I have found these types of organisms to grow best in selective media in the agar-slant system rather than on plates.

Also, I would definitely expect methanogens to be dying off in 8mg/L O2 - but they can survive in anaerobic pockets of organic material - depending on the density of your sludge. Some are surprisingly aerotolerant when grown with the proper symbionts that scavenge O2 quickly. However, as Gael mentioned, BESA should also prevent growth of methanogenic archaea.

Hi, Bastian

You just want to identify the microorganisms present in the reactor, or selects them and continue to operate the reactor degrading the xenobiotic compound?

For the identification of the organism a technique that I really like is the pyrosequencing, both for bacteria and for Archaea, this technique is very interesting when using inocula with a very large diversity of microorganisms.

In question of degradation of your compost be aware that many of these microorganisms (bacteria and Archaea) involved in the degradation of xenobiotics compounds work in cooperation, where the product of the metabolism of a species is used as substrate (carbon source or electron donor) to another, so if you separate some of these microorganisms, you can not find the removal efficiency of the compound you want.

How long you have been running your bioreactor? If it has been running long enough chances that all the currently present microoganisms are actively participating in the degradation pathway, as otherwise they would diminish. Now I'm not sure about selective antibiotics that would inhibit one group but not the other. You need to search the literature of such antibiotics. But you could you Florecence in situ hybridization (FISH) by tagging your 16s primers of the archea and bacteria differently to visualize each of the groups simuntanously.

You could, however, using FISH, target some potential functional metabolic genes, and at the same time, target the 16s genes of the archea and bacteria all in different dye colors. This way, you can visually see which group is doing what.

Hope that helps,

Regards

You could also physically separate Archaea from FISH probe labelled Bacteria using a flow cytometer. So take you sample add a bacteria specific probe then flow sort.

There is much information about archaea inhibition. N1-guanyl-1, 7-diaminoheptane (GC7), an efficient inhibitor of archaeal and eukaryote cell growth.