[en] Microbial communities are strongly shaped by the niche breadths of their constituent populations. However, a detailed understanding of microbial niche ecology is typically lacking. Integrated multi-omic analyses of host- or environment-derived samples offer the prospect of resolving fundamental and realised niches in situ. In turn, this is considered a prerequisite for niche engineering in order to drive an individual population or a community towards a specific phenotype, e.g., improvement of a biotechnological process.
Here, we sampled floating islets on the surface of an activated sludge tank in a time-series spanning 51 time-points over 14 months. Multi-omics datasets (metagenomics, metatranscriptomics, metaproteomics, and (meta-)metabolomics) were generated for all time-points. Leveraging nucleotide sequencing data, we analyzed the community structure and reconstructed genomes for specific populations of interest. Moreover, based on their metabolic potential, three major groups emerged, serving as proxies for their respective fundamental niches . Time-resolved linkage of the proteomic and transcriptomic data to the reconstructed genomes revealed a fine-grained picture of niche realization. In particular, environmental factors (temperature, metabolites, oxygen) were significantly associated with gene expression of individual populations. Furthermore, we subjected the community to controlled oxygen conditions (stable or dynamic) in a bioreactor experiment and measured the transcriptomic response. Our results suggest short-term adaptations of populations of interest with respect to lipid metabolism, among other pathways.
In conclusion, our work demonstrates how longitudinal multi-omic datasets can be integrated in order to further our understanding of microbial niche ecology within a biotechnological process with potential applications beyond waste water treatment.
Research center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Eco-Systems Biology (Wilmes Group)
HEROLD, Malte ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
NARAYANASAMY, Shaman ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) ; Megeno Sarl, Luxembourg
MARTINEZ ARBAS, Susana ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
MULLER, Emilie ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) ; Université de Strasbourg > Equipe Adaptations et Interactions Microbiennes
KLEINE-BORGMANN, Anna Luise ; University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit
LEBRUN, Laura ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
ROUME, Hugo ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) ; French National Institute for Agricultural Research > MetaGenoPolis
SHEIK, Abdul ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Bessarab, Irina; Singapore Centre for Environmental Life Sciences
Williams, Rohan; Singapore Centre for Environmental Life Sciences
Gillece, John; The Translational Genomics Research Institute
Schupp, Jim; The Translational Genomics Research Institute
Keim, Paul; The Translational Genomics Research Institute
Jäger, Christian ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Hoopmann, Michael; Institute for Systems Biology - ISB
Li, Sujun; University of Indiana > School of Informatics and Computing
Tang, Haixu; University of Indiana > School of Informatics and Computing
HEINTZ, Anna ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) ; German Centre for Integrative Biodiversity Research (iDiv)
MAY, Patrick ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
LACZNY, Cedric Christian ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
WILMES, Paul ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)