It would be helpful to know what magnification is used for the photos.  For a biogas facility, I would expect there to be a range of different microbes and the photos tend to show that.  Identifying them is not a trivial task, and the microscopic examination will not be very useful.  You would need to do selective media plating and/or genetic profiling.

Dear William, thank you for your response!

I took the images with 40x objective, then I assume the magnification should be 400x, right? I uploaded the image again with scalbars of 50um. I was told this liquid should help to improve the efficiency of biogas facility and save raw material by adding it to the facility on a daily basis. However, it seems not the case since my friend has been using it for nearly 9 months and he does not see any improvement and they are quite expensive.

As a biologist I am just curious about what is in the mysterious liquid and want to help my friend out. I can only do culture if they are not anaerobic organism, so maybe I can't help my friend very much...

Attached file shows microbial gropes involved in the anaerobic digestion. Hydrolysis (step 1) is normally done by heterotrophic microorganisms which can live in aerobic, anoxic and anaerobic environment.

Since its 400X magnification, bacteria are usually not visible as large as it is seen in this image. I have worked with both yeast/ fungus and metanogenic consortia, the observed microbes seems to be wild yeast/yeast or fungus, on basis of size and morphology . But what are they doing during methane production?what was ur substrate for methane production (liquid was brownish) and how are you maintaining anaerobic condition is imp. Yeast can grow anaerobically in sugars. Methanoges and other bacteria are very small point size with size of around 5 um.

Hi, Mustafa, thank you for your reply! my first impression was also yeast, but I have never seen yeast budding in the way like a chain... then I googled the pictures of methane bacteria and found some morphological similarity... 

As showed in Talib's figure, I think yeast can participate the hydrolytic fermentation procedure, because the substrates of biogas production are corn, animal feces, sugar beet and liquid manure.

dear Trik, thank you very much for your information!

Dear Chen, depending on your magnification and size they cannot be methanogen. Certain wild yeast or yeast in stressful conditions do form such structure called pseudomycelium structure.

And obviously the reason for the presence of yeast is the substrate is sugary substrate.

For curious reason, i think the number are too high. Are you getting good methane yield?

Because 1) yeast grow at low pH. while during acidogenesis the pH does go low, during methanogenesis, it increases to pH 7. 

2) the end product of yeast fermentation is usually and majorly ethanol. Yup other bacterias can reduce it to acids but at higher conc it can inhibit the process.

Just a curious thought though.

And i also want to ask is whether are you using wastewater of the above mentioned substrate or direct substrats?

Dear Mustafa, thank you for your answer! I am afraid that I can not answer your question. I have no idea what my friend's business, but I can ask him... but he is farmer running the biogas facility, I can at least him about pH value. as far as I know, they do not use waste water.

could be streptokokkus (because it forms long lines; E.coli usually makes little heaps...), but you should get it tested (Micrology Dept.) and have antibiotics testing if you want to get rid of it.

Are you sure that these are bacteria and not fungi- candida?

Dear Prof. Wissinger, thank you very much for your suggestion! Streptococcus are usually 0,5–2,0 µm, it is hard to see under 400x magnification. my scalebars are 50µm. But I think I can use penicillin to test it.

Dear Prof. Klingel, what an honor to get your attention! yes, I'd rather believe it is some kind of yeast. it seems doing yeast culture can make the question more clear...

yes, also possible but I think these particles are rather fungi than bacteria

In order to know if these are bacteria you should try growing them on some general medium like nutritive agar. You can get this already formulated and just add steril destilled water and agar. Once you have UFC´s you could use a Gram dye in order to see if they are Gram + or -. Knowing the genera would take more work. I understand you can know if they are methane bacteria through DGGE.

It looks like yeast.

Possibly, with this biomass the methanogen process are not efficient.  Also It's possible that biomass come from a first phase (hydrolysis-acidogenic) of a two phase methanogenic process.  Particulary, if the biomass sludge is brown, that seem to be a failed process or an acidogenic phase (low pH, low CH4, high organic acids...).  Take a smell of the biomass sludge, if It smell volatil fatty acid (butyric, lactic, acetic, swine manure or ???...) that indicate the methanogen process is failed (possibly overload of substrate).

Yann       

It would be advisable to place the scale bar inside fotos. Otherwise, not so easy to see the size of cells.

Dear Dr. Galushko, thank you for your reply! maybe you have missed my post. I put an image with scale bar in the second answer.

Dear all, I did culture with 2xYT medium without antibiotics. after 72 hours cultivation I got OD 2.0 as I had measured with the liquid I inoculated from. after checking under the microscope, I am pretty sure that they are yeast. the only strange thing is why the brown liquid pH is 2.7, while my grow culture pH is 8.4?

Dear Chen, I have checked and I see your second message about scale bar but I could not find image with the scale bar in it (no attachment).

pH in your biogas facility is indeed low - meaning that probably that was fermentation occurring with various fatty acids production. At such pH many methanogens could not survive.