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Section: Application Domains

Interpretation of molecular techniques in microbial ecology

Dynamical studies of bioreactors as used in waste-water treatment are hampered by the lack of measurement techniques to assess the microbial community structure. Typically only global system variables (biomass and substrate densities, gas production, etc) are measured, so that the community dynamics as such cannot be followed in any detail. Nevertheless, it is commonly believed that monitoring the microbial composition in bioreactors is crucial for their performances (in terms of efficiency and stability). Accurate, rapid and inexpensive techniques to estimate microbial community properties are therefore of crucial importance.

Molecular fingerprinting techniques seem to be good candidates to fill this gap. They are based on a small region (so-called 16S ribosomal DNA) present in all bacterial genomes. This region is relatively constant over many generations (compared to other parts of the genome), so that it can be used as a signature of a bacterial species. The fingerprinting protocol then consists in, first, extracting all the DNA of the microbial community, next, selecting and amplifying the genomic region of interest (using the PCR (polymerase chain reaction) technique), and finally, separating the PCR products belonging to different species by electrophoresis migration. Compared to other molecular techniques (such as cloning/sequencing), fingerprinting is rapid and inexpensive, and therefore well suited to follow microbial community dynamics.

A quantitative interpretation of fingerprints is however troublesome. Under the assumption that all species are perfectly separated in the migration step, the fingerprinting profile would consist of a succession of sharp rays, each one corresponding to a species, and with ray heights proportional to the abundance of the corresponding species. In this ideal scenario, the complete community structure could be read off from the profile. Unfortunately, due to biases in the different experimental steps (DNA extraction + PCR amplification + electrophoresis migration), real profiles are composed of a number of peaks, all with more or less the same width, where some species can occasionally contribute several peaks, and with peak heights only approximately proportional to the species abundance. Moreover, as soon as the community is somehow diverse, different peaks overlap each other, resulting in a complex profile.

Although one cannot hope to recuperate the complete community structure from such complex profiles, partial community information is still encoded in them. Our objective is to develop quantitative methods to extract this information from the profiles. Given a single profile, the genetic diversity of the microbial community is contained in the fingerprint. In recent years, we have developed an accurate diversity estimator; the corresponding patent has now been published [45] . Given a sequence of profiles, additional information can be obtained by comparing successive profiles. Once this information is extracted, it can be coupled to mathematical models describing the dynamics of microbial communities. We are investigating how to tackle this signal processing problem.


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