Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation

• DOI: 10.1128/msystems.00038-18
• Publication Date: 2018-08-13T07:14:59Z
• Authors: Andrea Söllinger; Alexander Tøsdal ...; Morten Poulsen; Samantha Joan Noel; Mia Bengtsson; Jörg Bernhardt; Anne Louise Fryde...; Peter Lund; Katharina Riedel; Christa Schleper; Ole Højberg; Tim Urich
• Keywords: Methanogen

Ruminant livestock is a major source of the potent greenhouse gas methane. The complex rumen microbiome, consisting bacteria, archaea, and microbial eukaryotes, facilitates anaerobic plant biomass degradation in cow rumen, leading to methane emissions. Using an integrated approach combining multidomain quantitative metatranscriptomics with volatile fatty acid (VFA) profiling, we aimed at obtaining most comprehensive picture active microbiome during feed date. Bacterial, archaeal, eukaryotic biomass, but also emissions VFA concentrations, increased drastically within hour after intake. mRNA profiling revealed dynamic response carbohydrate-active enzyme transcripts, transcripts involved production methanogenesis. While relative abundances functional did not mirror observed processes, such as emissions, transformation abundance per gram fluid echoed ruminant processes. composition was highly individual, with, e.g., ciliate, Neocallimastigaceae, Prevotellaceae, Succinivibrionaceae, Fibrobacteraceae differing between cows. Microbiome individuality accompanied by inter- intradomain multifunctional redundancy among members degradation. This likely enabled robust performance process each rumen. Neocallimastigaceae ciliates contributed unexpectedly large share for cellulose- hemicellulose-degrading enzymes, respectively. Methyl-reducing CO2-reducing methanogens were positively correlated Methanomassiliicoccales switched from methanol methylamines electron acceptors, Methanosphaera became dominating methanol-reducing methanogen. study first time linked meta-omics processes holistic insights into contribution all IMPORTANCE animals, cows, live tight symbiotic association microorganisms, allowing them on otherwise indigestible food sources. Methane produced end product ruminants emitted atmosphere, making animals anthropogenic sources newly developed analysis, here identified bacterial, key players short-term dynamics subsequent These novel might pave way ecologically economically sustainable mitigation strategies, much needed times global climate change.