Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

Environmental Microbiome - Tập 15 - Trang 1-21 - 2020
Irena Maus1, Michael Klocke2, Jaqueline Derenkó2, Yvonne Stolze1, Michael Beckstette3, Carsten Jost2, Daniel Wibberg1, Jochen Blom4, Christian Henke5, Katharina Willenbücher2, Madis Rumming5, Antje Rademacher2, Alfred Pühler1, Alexander Sczyrba1,5, Andreas Schlüter1
1Bielefeld University, Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld, Germany
2Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
3Helmholtz Centre for Infection Research, Microbial Infection Biology / Experimental Immunology, Braunschweig, Germany
4Department Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Giessen, Germany
5Faculty of Technology, Bielefeld University, Bielefeld, Germany

Tóm tắt

Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37 °C) and thermophilic (55 °C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted. In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and / or acetogenesis. An integrated -omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass.

Tài liệu tham khảo

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