Waste: research key to microbe wars

We thought we knew all there was to know about waste water treatment plants or anaerobic digestion units, bioprocesses that are rapidly expanding. However, the microbial drivers at work during decomposition and waste recovery have still more secrets to reveal. It was enough to stimulate the curiosity of researchers at Irstea, who have opened the “black box” of bioprocesses to investigate more closely. They have recently made surprising discoveries, published in 2 high-ranking scientific journals: The ISME-Journal [1] and Plos One [2], with the aim of improving and offering new management methods to advance waste recovery processes.

The end of microbial "black boxes" ?

Waste decomposition and recovery (what to do with it, for what purpose) is based on a series of reactions catalysed by microorganisms. The problem is that these very diverse microorganisms are difficult to grow and it was only in the early 1990s that new molecular biology techniques were developed. "We were then able to describe these microorganisms using their molecular identities, without having to cultivate them", explains Théodore Bouchez, head of the BIOMIC team at the Bioprocesses microbiology laboratory at Irstea's Hydrosystems and Bioprocesses (HBAN) research unit. "However, we then had to move beyond this descriptive phase and understand the functions of these microorganisms." New methods were therefore developed and have revealed the metabolic capacity of microbial groups found in pollution control bioprocesses.

Using a microorganism’s identification card, researchers were able to move onto omic approaches: observing microorganisms at a group and ecosystem level to include their interactions (which proteins are present, which microorganism produced them, which metabolic pathway was used to transform the molecules etc.). This is a real log, full of information, which puts an end to the current status of microbial "black box".

Laboratory pilot bioprocesses (1 L and 200 L) to study anaerobic decomposition phenomena (anaerobic digestion) in household waste © Irstea

Laboratory pilot bioprocesses (1 L and 200 L) to study anaerobic decomposition phenomena (anaerobic digestion) in household waste © Irstea Measuring gas emissions during lixiviate recirculation in a waste storage facility © Irstea

From laboratory pilot to storage facility.

Left and centre: Laboratory pilot bioprocesses (1 L and 200 L) to study anaerobic decomposition phenomena (anaerobic digestion) in household waste © Irstea

Right: Measuring gas emissions during lixiviate recirculation in a waste storage facility © Irstea

Microbial war and laboratory taylorisation

Supported by these new tools, Irstea researchers focused on cellulose, a macromolecule abundantly found in organic waste and whose recovery requires a stream of proteins, all synthesised by a complex microbe community. The team managed to characterise a large number of these proteins (published in The ISME-Journal): "This was a unique level of description that provided us with a global view", notes Théodore Bouchez. By observing the decomposition of cellulose, the researchers pinpointed new processes.

  • The most unexpected discovery: there is a type of "microbe war" within these communities. Researchers did not expect to find significant activity around nitrogen, which is not found in high quantities in cellulose. Why ? At the heart of the recovery process, "good" microbes synthesise proteins (enzymes) that they use to surround the cellulose in order to decompose the insoluble substrate. However, it would seem that "nasty" microbes take advantage of this mass of available proteins to feed and reproduce, to the detriment of the good microbes that are working towards pollution control. "This could be one of the reasons for a drop in bioprocess performance. No one had seen this before. The hypothesis is there and needs to be proven." These interactions, whether positive or negative, are the foundations of bioprocess operations, which is why it is important to identify and understand them
  • The data also suggests a "taylorisation" of work between the various microbe groups: "Some are more specialised in decomposing cellulose, including crystalline zones, while others are more focused on decomposing hemicellulose. Work gets divided between the two." This resembled a proper microbe society that mirrors our own.

The BIOMIC team has also performed remarkable work on visualising the function of microorganisms (published in Plos One) with methodological developments to the SIMSISH technique. They managed to measure the incorporation of isotopically marked substrates into microorganisms. This method allows the precise function of microorganisms to be traced throughout decomposition changes, highlighting what they have eaten, etc.…

We were another step closer to understanding bioprocesses.

Towards ecological bioprocess engineering ?

What will happen once we improve our understanding of microbial drivers ? We will have to develop new drivers. To this end, researchers need engineering tools with models to simulate various configurations and imagine the processes of the future. "For a long time, we focused on empiricism, we tested this and that", notes Théodore Bouchez, head of the BIOMIC team at Irstea. "Our aim now is to move towards ecological engineering: engineering that explicitly takes into account the interactions within a microbial ecosystem in order to make the most of the properties of adaptation, resistance and energy optimisation of microbe communities to maximise the performance of the bioprocesses. Currently, the models used to describe microbe reactions to various stages of the bioprocess have not been updated with new data or knowledge. We therefore have to create new cross-disciplinary models."

In the meantime, Irstea scientists continue their research, particularly into microbial electrosynthesis [3]. What is this process ? Instead of giving microbes glucose, for example, to make them grow and express certain properties, researchers give them an electrical current. Microbes eat the electrons along with CO2 and use the energy from the current to produce interesting molecules (ethanol etc.). This will allow researchers to define a development strategy for future biorefineries. Microorganisms are precious allies!

LABE: 500 m2 dedicated to microbial drivers

© IrsteaThe Environmental Bioprocess Research Laboratory (LABE) is an Irstea project that has been hotly anticipated by its teams.

Covering an area of around 500m2, it will include a technological hall and analysis laboratories. These facilities, scheduled to be ready by 2015 at the Anthony site, will offer a continuum of activities ranging from setting up experiments to analysing their operation. Aims for the scientific teams: contributeto the creation of operational waste biorefineries to produce renewable energies (biogas, bioethanol etc.)

Consult the two online publications of the BIOMIC team : The ISME-Journal (paid access) and Plos One.

For further information


[1] Lü, F., et al., “Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity”. The ISME Journal, August 2013. In collaboration with INRA-Micalis de Jouy en Josas and Tongji University in Qhanghai, China.

[2] Chapleur, O., et al., “SIMSISH technique does not alter the apparent isotopic composition of bacterial cells”. Plos One, November 2013. In collaboration with the Ion Microscopy Laboratory at the Institut Curie at Orsay.

[3] 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 this technique for treating waste and organic matter.