I am planing to compare the microbial diversity of each stage during anaerobic digestion and also attempt to isolate microbes responsible for each stage. Is there any better way to know which stage of digestion so I could collect sample in the right time. I am going to measure the methane concentration from the digester as well so I will consider the methane production out of my digestion.
Its a good question and I am not sure If my answer would be still valid and helpful since it comes after almost 2 years, but I think the best way would be to create difined medium conditions. So instead of using complex media use different media in which you know all components. In addition radioactive labled target substrates could help in the identification of the degradation products. I hope this answer comes not to late and gives an idea of how to solve the problem.
You could use techniques like GC and LC to sample the extracellular metabolites. This would help give you some idea of what stage the digester is in. Then you could sample the community to see what bugs are active at that time point. I hope this helps!
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