Vimac,

We have thought about this issue and reached the conclusion that understanding the process at the genome level is not very useful.  In anaerobic digestion you are dealing with an ecosystem that is dynamically altering itself to adapt to its environment.  The microbes are swapping DNA material between themselves to achieve survival.  Anaerobic digestion involves thousands of species of microbes including bacteria, yeast, anaerobic fungi, protozoa, etc.  All of theses species are needed to make the reaction work.  Most of these microbes can not be isolated as their dependence upon another species.  We have shown a more productive approach is to manage the system, not try to manage each microbe. 

That said we have been able to alter an anaerobic process by the introduction of select species of microbes that are compatible with the ecosystem.  This enables us to shift the production of acids from the low valued material of acetic acid to higher value buteric and hexanoic acids. Essentially we find compatible microbes and let nature take its course.  As one engineer put it, " in this process, you are either at the table or on the table".

If it's hard for you to cultivate and simulate the process in lab, then metagenomics or single-cell sequencing are perhaps the only approaches you have.  If you just focus on anaerobic digestion, you may want to try Geochip. Also, don't forget to extract the total RNA. Metatransciptonomics may give you better understanding of the genes invovled in this process.

hey,

investigate metagenomics in biogas process can only give your overall view of microbial ecology in anaerobic process in my eye, but if you can connect functional microorganisms in ad such as methanogens or syntrophic acetate oxidation bacteria with stable carbon isotopic fingerprinting of produced biogas seems can trace microbial community shift and somehow useful for process control. for more details you can check  this latest article using GCIRMS for process anticipation http://www.sciencedirect.com/science/article/pii/S0960852414008736 or papers from Dr. Frank Keppler's group using laser absorption spectroscopy for real time detection. good luck!

Hi all, thanks for the answers.

My question is more focused on whether it is useful to use metagenomics to increase a process, in this case the anaerobic digestion. I myself work in this topic but I have the feeling that all the information obtained with metagenomics / transcriptomics is useful for a better understanding of the process but not to increase the actual performance of the reactor. I still haven't seen or found any paper where this knowledge has actually been used to improve the process.

I think that both metagenomics / transcriptomics are useful to understand a process but I still don't see any real application.

It is different from direct manipulation of strains or microorganisms where you can see a direct output by increasing or decreasing the desired product. 

Metagenomics are useful in improving the anaerobic digestion.

Vimac,

We have thought about this issue and reached the conclusion that understanding the process at the genome level is not very useful.  In anaerobic digestion you are dealing with an ecosystem that is dynamically altering itself to adapt to its environment.  The microbes are swapping DNA material between themselves to achieve survival.  Anaerobic digestion involves thousands of species of microbes including bacteria, yeast, anaerobic fungi, protozoa, etc.  All of theses species are needed to make the reaction work.  Most of these microbes can not be isolated as their dependence upon another species.  We have shown a more productive approach is to manage the system, not try to manage each microbe. 

That said we have been able to alter an anaerobic process by the introduction of select species of microbes that are compatible with the ecosystem.  This enables us to shift the production of acids from the low valued material of acetic acid to higher value buteric and hexanoic acids. Essentially we find compatible microbes and let nature take its course.  As one engineer put it, " in this process, you are either at the table or on the table".

My simple opinion: we need to further investigate about the real involvement of microorganisms in the process. The use of sequences collected by metagenomics to carry out fluorescence in situ hybridization for me is essential. 

in my opinion it is more useful proteomics

Dear Vimac,

My opinion is that you can't directly use the microbial community composition as an influencing factor during a process optimization approach, however, none the less having a close monitoring strategy regarding the shift in the microbial populations (especially those directly involved in the desired fermentation products) as well as the followed metabolic pathways is crucial for the overall optimization strategy. So I think that metagenomics/metatranscriptomics approaches are essential not just to better understand the involved biological processes, but also as an integrated part of the optimization strategy when used as objective functions and process control tools.

We just published a paper in "Biotechnology for Biofuels" entitled: "Revealing the factors influencing a fermentative biohydrogen production process using industrial wastewater as fermentation substrate" (it should appear in the following weeks) in which you will find more details regarding this approach.

Hope this helped.

Cheers

The question posed has not addressed the issue of the conditions of the substrate.  Is it homogenous and sterile, at what volumes are being considered for conversion. 

My thought is to start with enrichment experiment and ideally use C13-labelled substrate, and track community changes over time by Next-gen sequencing. Hopefully, you can get a high efficient microbial system for anaerobic digestion and understand the process, and ultimately design a high-performance synthetic microbial consortia for your purpose.

Three points are here:  1) firstly, the enrichment culture will simplify your community but keep the useful/functional microbes dominant and remain in the community; 2)  you can get microbial interaction data through correlation analysis of community DNA across time, which will help understand the process and identify the dominant microbes responsible for the process;  3) Stable isotope labelled substrate will help track the potential pathway of microbial functions / process.     

PS: metagenomics here means amplicon sequencing.  However, shotgun sequencing of community RNA or DNA will help find the useful and functional genes and their relative abundance in the community. This might be helpful to identify the rate-limiting genes for the process.  

I think you need to consider you are proposing is to go from a homogenous, sterile environment to a non-homogenous, non-sterile feedstock and operate under non-sterile conditions. 

If the desired output is methane, then consider isolating the methanogenic bacteria, propagating the bacteria and strengthen their resistance to the conditions that are adverse to their survival.

From my humble point of view if depend on substrates. In a biotreatment for example the process is defined by pollutants. In this case little or nothing can be done. In natural environments could serve to define some enrichment, but this is not always successful because you can not control all the factors.

If you are looking to use a single microbe, then Ms Sanabria is correct.  If you use a microbial ecosystem that  has been adapted to consume the specific waste, then you can address the waste.

We have demonstrated that the ecosystem approach can address a broad range of organic wastes.  The range from food waste, brewers grain, sewer cake, short fibers from a paper mill, to news print.

Using metagenomics Mr Edward?

Yes metagenomics makes sense... in a multi-species system all you probably would observe is the state of affairs at a point in time.... unless there are stable conditions such as a homogenous feedstock, under constant temperature, with appropriately uniform extraction of the microbial wastes produced, the microbes will alter their DNA configuration to adapt to the changes in the environment by swapping DNA between species.... assuming this is correct, how much usable information can be gained by snapshots that reflect past conditions, which may not be predictive of the system changes occurring.  The other issue we have observed is there is a periodicity inherent in a multi-species system.  Again, this raises the question as to just what is occurring... is it due to adaption, periodicity, or something else occurring within the ecosystem.  We have learned that focusing on to small a details does not provide the information needed to manage the whole ecosystem... we have been very successful with a macro approach.