Systems Biology of Natural Microbial Assemblages - SysBioNaMa

Institution CRP Gabriel Lippmann
Autres partenaire(s) University of Vienna , Free University of Bruxelles , Lawrence Berkeley National Laboratory
Du : 01/01/2010
Au : 31/12/2014
Budget : 1 112 617,00€
Contact(s) : Wilmes Paul

Progress Summary 2009

Microbial consortia facilitate life on Earth and provide essential services to mankind. Organismal and functional diversity within complex microbial communities remains largely unknown. However, microbial ecology is currently undergoing a technology-driven revolution. The application of molecular tools, from community genomic to post-genomic functional approaches, is providing unprecedented insights into the genetic and physiological dynamics in situ. Such information is crucial for the dependable exploitation of essential microbiological resources in the future. Biological wastewater treatment represents a ubiquitous biotechnological process.

However, limited fundamental knowledge regarding the underlying microbiology and biochemistry is preventing efficient, reliable and predictable process operation. Furthermore, wastewater represents a valuable energy commodity that is currently not being harnessed comprehensively. Here we propose a systems biology approach to study microbial biofilm assemblages that form the backbone of biological wastewater treatment systems and that may be exploited for bioenergy production. This integrative approach employing imaging, genomics, transcriptomics, proteomics, metabolomics and bioinformatics will facilitate the high-resolution characterization of these microbial communities and allow the systematic study of complex interactions.

A particular emphasis of the analyses will be on within-population genetic and functional heterogeneity and how this fine-scale variation contributes to process performance (ecosystem functioning). The proposed research project will involve a multi-phasic approach focusing on (A) laboratory-scale moving bed biofilm reactors (MBBRs) and (B) a full-scale system. (A) MBBRs will be operated within the laboratory setting analogously to full-scale systems. They will allow for controlled experimental conditions and, hence, facilitate targeted high-density enrichments of populations of interest. Cultures inoculated with stable isotope-labeled substrates (lipids) will be subjected to comprehensive chemical analyses and phylogenetic surveys {rRNA gene amplification followed by high-throughput sequencing and imaging [nanometer-scale secondary ion mass spectrometry, electron microscopy and confocal laser scanning microscopy]}. Enrichment and axenic cultures of highest interest will be subjected to a comprehensive suite of molecular analyses. Fine-scale selection of populations of interest will be carried out using laser-microdissection of biofilm thin-sections followed by downstream analyses.

The systems-level data will be integrated using relevant bioinformatic methodologies. (B) The approaches applied to the laboratory-scale MBBR communities will be expanded to a full-scale wastewater treatment system. Phylogenetic surveys will contrast the microbial communities in the laboratory- and full-scale systems. Differences in community structure and resulting functional manifestations will be monitored closely over space and time. Furthermore, hypotheses generated from experiments in the laboratory-scale MBBRs will be tested using this system. Where appropriate, the high-resolution molecular data will be integrated into existing wastewater treatment dynamic simulation models. Insights gained through this project will provide much needed fundamental understanding of microbial community and population dynamics within wastewater treatment biofilms.

Together with knowledge regarding complex metabolic transformations and transactions, this knowledge will be applied to optimization and modeling strategies for current biological wastewater treatment processes. Furthermore, the proposed project will highlight new avenues for the exhaustive exploitation of wastewater’s full bioenergy potential. Finally, the techniques and methodologies developed in this project will be applicable to a broad range of other mixed microbial communities.