Integrated omics of wastewater lipid accumulating microbial consortia

We are studying microbial populations within biological wastewater treatment plants with a special interest on lipid accumulating bacterial populations. These populations are naturally enriched in biological wastewater treatment systems and may be harnessed for the conversion of mixed lipid substrates (wastewater) into biodiesel. We explicitly aim to elucidate the genetic blueprints and the functional relevance of specific populations within the community. We are focusing on within-population genetic and functional heterogeneity, trying to understand how fine-scale variations contribute to differing lipid accumulating phenotypes. Insights from this project will help us understand at a fundamental level the functioning of microbial ecosystems; and in a concrete level, help us improve optimization and modeling strategies for current and future biological wastewater treatment processes.

Collaborators: Paul Keim and Lance Price (TGen North, Flagstaff, Arizona, USA)

Funding: FNR ATTRACT programme "SysBioNaMA"; FNR AFR PDR programme grant MetaLABpop; FNR COREJunior programme grant “LEGeLis”; FNR CORE programme grant “GoMiCo”

Publications:

Muller E. E. L., Glaab E., May P., Vlassis N. and Wilmes P. (2013) Condensing the omics fog of microbial communities. Trends in Microbiology 21:325-333 (doi: 10.1016/j.tim.2013.04.009).

Muller E.E.L., Pinel N., Laczny C., Hoopmann M.R., Lebrun L.A., Roume H., May P, Hicks N.D., Liu C.M., Price L.B., Gillece J., Guignard C., Schupp J.M., Vlassis N., Moritz R.L., Baliga N., Keim P.S., Wilmes P. (2014) Community integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nature Communications 5:5603 (doi: 10.1038/ncomms6603).

Roume H., Heintz-Buschart A., Muller E.E.L., May P., Satagopam V.P., Laczny C., Narayanasamy S., Lebrun L., Hoopmann M., Schupp J., Gillece J., Hicks N., Engelthaler D., Sauter T., Keim P.S., Moritz R.L., Wilmes P. (2015) Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. npj Biofilms and Microbiomes, 1:15007 (doi: 10.1038/npjbiofilms.2015.7).

Sheik A.R., Muller E.E.L., Audinot J.-N., Lebrun L.A., Grysan P., Guignard C., Wilmes P.* (2016) In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella. The ISME Journal 10:1274-1279 (doi: 10.1038/ismej.2015.181).

Muller E.E.L., Widder S., Faust K., Herold M., Martinez Arbas S., Wilmes P.* (2018) Using metabolic networks to resolve ecological properties of microbiomes. Current Opinion in Systems Biology 8:73-80 (doi: 10.1016/j.coisb.2017.12.004).

Genomics of isolated lipid accumulating bacteria

Here we are reconstructing the genomes of bacteria isolated from our model wastewater lipid accumulating communities. The lack of appropriate reference genomes continues to hamper the integration of community-level multi-omic data (e.g., metagenomic, metatranscriptomic, metaproteomic, etc.) from all but the most heavily studied microbial ecosystems. To address this limitation, we have sequenced the genomes of Candidatus Microthrix parvicella, a model lipid-accumulating bacterium, and a first isolate from the Zooglea genus. We are currently working on sequencing 130 additional isolates. The genome sequences will help us improve our assembly and read-recruitment analyses of community sequence data. Coupled with phenotypic characterisation of these organisms, they will also give us insights into the biology of the dominant members of lipid accumulating communities in biological wastewater treatment plants.

Collaborators: Paul Keim and Lance Price (TGen North, Flagstaff, Arizona, USA)

Funding: FNR ATTRACT programme "SysBioNaMA"

Publications:

Muller E.E.L., Pinel N., Gillece J.D., Schupp J.M., Price L.B., Engelthaler D.M., Levantesi C., Tandoi V., Luong K., Baliga N.S., Korlach J., Keim P.S., Wilmes P. (2012) Genome sequence of “Candidatus Microthrix parvicella” Bio17-1, a long-chain-fatty-acid-accumulating filamentous Actinobacterium from a biological wastewater treatment plant. Journal of Bacteriology 194(23):6670-6671 (doi: 10.1128/JB.01765-12).

Muller E.E.L., Narayanasamy S., Zeimes M., Laczny C.C., Lebrun L.A., Herold M., Hicks N.D., Gillece J.D., Schupp J.M., Keim P., Wilmes P. (2017) First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ. Standards in Genomic Sciences 12:64 (doi: 10.1186/s40793-017-0274-y).

Improving the bioleaching of chalcopyrite by multiscale modelling using metatranscriptomics, metaproteomics and imaging data

Environmentally friendly techniques, such as biomining, must be developed to meet the increased European demand for metals. Biomining exploits acidophilic microorganisms for the recovery of metals from sulphide ores in tanks, heaps and dumps. In this project, biofilm formation of moderately thermophilic bioleaching bacteria, Acidithiobacillus caldus, Leptospirillum ferriphilum and Sulfobacillus thermosulfidooxidans on chalcopyrite surfaces are studied with the aim of improving the leaching of copper. Since a unique feature of the experimental setup is the use of well-defined microbial communities of limited diversity and known cultivation conditions, it is possible to establish and test novel approaches for measuring and modelling mixed-microorganism biofilm formation processes.

Collaborators: Mark Dopson, Stephan Christel (Linneaus University Kalmar), Ansgar Poetsch (Ruhr Universitaet Bochum), Wolfgang Sand, Mario Vera (Universitaet Duisburg Essen), Igor Pivkin, Antoine Buetti-Dinh (Università della Svizzera italiana)

Publications:

Christel S., Herold M., Bellenberg S., Buetti-Dinh A., El Hajjami M., Pivkin I.V., Sand W., Wilmes P., Poetsch A., Vera M., Dopson M. (2018) Weak iron oxidation by Sulfobacillus thermosulfidooxidans maintains a favorable redox potential for chalcopyrite bioleaching. Frontiers in Microbiology 9:3059 (doi: 10.3389/fmicb.2018.03059).

Bellenberg S., Buetti-Dinh A., Galli V., Ilie O., Herold M., Christel S., Boretska M., Pivkin I.V., Wilmes P., Sand W., Vera M., Dopson M. (2018) Automated microscopic analysis of metal sulfide colonization by acidophilic microorganisms. Applied and Environmental Microbiology, 84:e01835-18 (doi: 10.1128/AEM.01835-18).

Buetti-Dinh A., Galli V., Bellenberg S., Ilie O., Herold M., Christel S., Boretska M., Pivkin I.V., Wilmes P., Sand W., Vera M., Dopson M. (2019) Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition. Biotechnology Reports in press (doi: 10.1016/j.btre.2019.e00321).

Funding: EU ERASysApp grant “SysMetEx” 

Microbial populations underpining anaerobic digestion processes

Advances towards efficiency improvement of the anaerobic digestion process (AD) for biogas production is often quoted to be dependent on two major key subjects of research (1) an in depth understanding of the structure and dynamics of the microbial populations involved in the process, and (2) the development of online monitoring tools to better predict process dysfunction occurring during inadequate organic loading rate. We are applying our integrated omics methodology to obtain detailed insights into the microbial ecology and microbial community dynamics of the anaerobic digestion process in relation to reactor design and feeding regime. We hope to identify biomarkers which will prove helpful for real-time performance monitoring of AD plants.

Collaborator: Philippe Delfosse and Magdalena Calusinka (Luxembourg Institute of Science and Technology)

Publications:

Calusinska M., Goux X., Fossépré M., Muller E.E.L., Wilmes P., Delfosse P. (2018) A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems. Biotechnology for Biofuels, 11:196 (doi: 10.1186/s13068-018-1195-8).

Broeksema B., Calusinska M., McGee F., Winter K., Bongiovanni F., Goux X., Wilmes P., Defosse P., Ghoniem M. (2017) ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins. BMC Bioinformatics 18:233 (doi: 10.1186/s12859-017-1653-5).

Funding: FNR CORE programme grant “GASPOP”; FNR COREJunior programme grant “CLOMICS”