Project description:The anaerobic digestion microbiomes has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and phenotypics, in their ability to reflect the full-scale anaerobic digestion microbiome. The phenotypic fingerprinting reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and phenotypic traits, yielded certain similar features yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, phenotypic fingerprinting is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.
Project description:Aspergillus oryzae is used in solid-state fermentation (SSF) to produce plant-based foods. To this end, the substrate is inoculated with spores of this fungus. So far, the effect of inoculum size on SSF with A. oryzae has primarily focused on the production of specific enzymes. Therefore, the aim of this study was to examine the impact of inoculum size on the full secretome, combined with enzyme activity assays, assessment of colonization, substrate degradation, and sporulation. To this end, A. oryzae was grown for 7 days on whole yellow pea (Pisum sativum). Fluorescence microscopy with a GFP-expressing A. oryzae strain showed that peas had been colonized externally and internally, irrespective of inoculum size. Yet, the highest inoculum size resulted in a stronger pea biomass reduction when compared to the lowest inoculum size. By contrast, sporulation decreased with increasing inoculum size. Notably, proteomics revealed no effect of inoculum size on the protein profiles of aqueous extracts of the colonized peas. Amylases and proteases were the most abundant secreted proteins, which was consistent with their high activity in the aqueous extracts. Proteomics also identified β-1,3-glucanases and chitinases, indicating hyphal lysis. Indeed, 10–19% of the fungal proteins detected in the aqueous extracts lacked signal peptides. These data contribute to our understanding of colonization of substrates by A. oryzae and may be used to optimize SSF with this food grade fungus.
