Decoding the microbial connectivity of livestock manure and anaerobic digestion (biogas) microbiomes
Final Report Abstract
In this project, we sampled and sequenced 36 different biogas plants and manure storage facilities including industrial-scale digesters, laboratory-scale fermenters and agricultural manure deposits. After we obtained all the sequencing results from the sequencing centers, we developed a strategy for quality control and a pipeline for an assembly based metagenomics approach. Especially the quality treatment posed some challenges which we had to overcome and delayed subsequent analysis. Moreover, we underestimated some of the computational challenges, for example re-basecalling of the ONT data, test assemblies to determine a reasonable assembly strategy, the final assemblies and the still ongoing task of the functional annotation of MAGs. We applied a read-based strategy first for taxonomic and functional microbiome profiling, since it is computationally less challenging. The examined biogas reactors showed substantial differences in their taxonomic composition and functional inventory, which was analyzed by dimension reduction methods. All samples with both ONT and Illumina data were successfully assembled using a newly developed nextflow based pipeline. MAGs were identified, dereplicated and abundance profiles as well as a co-occurrence network were created. Promising results were obtained that will be further analyzed for the purpose of publication. Taxa of the order DTU010 (class Limnochordia) and of the genus Methanoculleus were highly abundant in all examined biogas reactors from the CeBiTec samples and show large differences in their taxonomic profile at lower taxonomic levels. Additionally, the taxonomic profile in general is quite diverse across reactors which were fed with different substrates. We expect further insights when examining the functional inventory present in the analyzed microbiomes represented by reconstructed MAGs, which is an ongoing task, since the corresponding computations have not yet been completed. In conclusion, this project generated a highly valuable dataset for biogas plants and manure storage facilities/deposits, which lays the foundation for advances in the field of biogas microbiome research by means of metagenomics methods.
Publications
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Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics. Microorganisms, 11(10), 2412.
Hassa, Julia; Tubbesing, Tom; Maus, Irena; Heyer, Robert; Benndorf, Dirk; Effenberger, Mathias; Henke, Christian; Osterholz, Benedikt; Beckstette, Michael; Pühler, Alfred; Sczyrba, Alexander & Schlüter, Andreas
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Metagenomics-Toolkit: The Flexible and Efficient Cloud-Based Metagenomics Workflow featuring Machine Learning-Enabled Resource Allocation. openRxiv.
Belmann, Peter; Osterholz, Benedikt; Kleinboelting, Nils; Puehler, Alfred; Schlueter, Andreas & Sczyrba, Alexander
