Bioprocesses: what energy regimen for microorganisms ?

Two Irstea researchers have successfully established a link between energy balance and microbial growth, causing a small revolution in the scientific community. This is a relationship hitherto little understood, but one which could pave the way for many technological and ecological developments, especially in relation to bioprocesses. With the publication of their research in a prestigious scientific journal, the microbiology of bioprocesses is, little by little, unveiling its secrets.

They are so small, yet so greedy! Just like humans, bacteria feed on the energy contained in the food they ingest. The energy they ingest (for example in the form of waste) is not only used and dissipated, but can also be released in the form of chemical energy contained in different molecules (methane, hydrogen, ethanol or even biomass) depending on the thermodynamic conditions of where they were placed!

We can therefore benefit from these little microscopic allies in treatment stations, biogas plants or composting processes, where engineers use them to clean, to make methane or to make compost.

These days, we know from experience that if you want to make compost from waste you must aerate it, while if you want to produce methane you must instead prevent air from entering the bioprocess. These operating strategies determine the conditions of the thermodynamic equilibrium within the bioprocess. Within these conditions, scientists can describe the microbial populations which take hold and the chemical reactions that take place. What is happening however, in the mechanism that drives microbial communities, in all their diversity, to systematically express the same functional properties according to the thermodynamic equilibrium they are subjected to?

A small revolution in the scientific community: Two Irstea researchers have explored this mechanism by attempting to better understand the link between the growth of microorganisms and the energy available. They have thus been able to reveal and demonstrate a thermodynamic equation for microbial growth. A top-ranking publication has recently confirmed their research. Now, a bit of explanation is probably in order.

Energy, the key to the microbial engine

"For a long time, we have observed purifying biomasses self-organizing themselves in these systems in relation to energy principles," explains Théodore Bouchez, head of the BIOMIC team based in the Irstea Antony center's microbiological bioprocess laboratory. The existence of a thermodynamic principle of growth was obvious to anyone who cared to see it. All that was needed was to express and demonstrate this. The idea of how to do this developed in Bouchez's mind over several years: "It was a somewhat left-field and risky idea because of the very unusual nature of the work to be done." Essentially, there are already empirical models of microbial growth, but the speed/power relationship had thus far not been studied. "We had to rebuild something, and select or even invent relevant concepts for representing our problem adequately." A risky approach.

With the arrival in 2010 of Elie Desmond-Le Quéméner, a post-doctoral researcher, the project could really take flight. Diving into long-standing theoretical work, the two researchers had to reformulate the relationship between the (chemical) energy available and the division of a individual microbe. From this they could then infer the statistical distribution that governs the development of a microbial population, consisting of a set of individual microbes, depending on the spatial distribution of energy in an environment.

Finally in 2013, the two researchers were be able to demonstrate a microbial growth equation, which was then published in the renowned scientific journal The ISME-Journal [1]. This demonstration called on theories of statistical physics, something not often seen at Irstea, and published even less: "This is the first time in the BIOMIC team that we have undertaken purely theoretical work, even if the motivation for it was not just an intellectual exercise. It is the high potential for application in bioprocesses that led us to ask these questions, but for this we had to go back to basics," explains Bouchez.

Activation energy & predictions

In order to develop their thermodynamic model for microbial growth, the two researchers have built on the work of their predecessors, primarily in chemistry and the concept of activation energy: namely the link between the speed of chemical reactions and energy released in collisions between molecules. But does that which applies to chemistry also apply to biology ?

While chemists describe meetings between molecules that are roughly the same size, our researchers are describing encounters between "big" microorganisms and "small" molecules. "With this difference in scale, we had to divide up the space to better understand the behavior of microbes: thus each researcher studied a portion of the space.The concept of "microorganism harvest volume" then appears. After a few twists and turns, the two researchers were finally able to theoretically express the energy available to each microbe for division, by using thermodynamic balance sheets prepared by other teams, and were also able to express how these microbes were affected by the frequency distribution of molecules in the medium.

All it was missing was experimental validation: "The strength of a theory is in bringing together previously unconnected elements, and making new predictions." How ? The answer lay right before their eyes, in their Irstea laboratory: "We analyzed the microbial isotopic fractionation (the distribution of isotopes of an element), with a good, well-developed analytical method. It was the perfect place to test the hypotheses of our theory," says Desmond-Le Quéméner.

The model was used to create predictions, which were then verified using experimental data, such as data on the way microbes would use a heavy or light molecule, depending on the energy variations of the reactions involved. "So our theory has identified exceptions to a universally known and acknowledged rule: that microbes prefer molecules containing 12 carbon atoms to those containing 13 atoms. We are the first to show, in accordance with some early experimental data, that there are situations in which they prefer carbon 13." Clearly, the microbes do not distinguish between the carbon atoms, but respond differently to the chemical energy contained in the carbon molecules. "This is perfect, because our model takes that energy into account !"

Although published, the theory remains incomplete: a thesis has been announced that will continue the work. But already, future applications are emerging: "As part of the BIORARE project [2], we could use this model to test microbial cultures in electrolyzers by controlling the energy supplied to the microorganisms," explains Bouchez. "In fact we are reproducing this universal physical link between the invested energy and velocity (or growth) obtained at the microbial level," finishes Desmond-Le Quéméner. "We can then choose whether a relatively fast or energetically efficient microbial engine is preferable."

Towards predictive ecological engineering ?

A small revolution is looming, and is already being positively echoed on social networks, mainly through the Twitter accounts of American scientists. "By introducing theoretical concepts and applying the thermodynamic principles that govern the growth of microorganisms, we hope to lay the groundwork for the engineering of microbial ecosystems that can actually be predictive: in other words, engineering that takes full account of the capacity of these ecological systems for self-organization. Currently we cannot model bioprocesses," concludes Bouchez. "To get there, we need to make the link between ecological dynamics and optimization of their underlying energy flows, questions that have always been particularly sensitive in bioprocesses."

In other words a speed/power relationship, intrinsically linked to the evolution of living systems and the fact that some populations can survive or not in a given environment. Other ecological developments should then follow. "This is a fundamental issue for the entire natural world." Microbes are just one step forward.

For more information

[1] Desmond-Le Quéméner, E. & Bouchez, T., A thermodynamic theory of microbial growth. The ISME Journal, 2014.

[2] The BIORARE project, financed through the Investments for the Future Programme AAP Biotechnologies and Bioresources (2011-2016). Irstea is the leader in the use of the microbial electrosynthesis technique for treating waste and organic matter.