ena-STUDY-AALBORG UNIVERSITY-18-02-2019-12:44:45:955-660
Investigating the response of digester metagenomes to various short-chain fatty acids using genome-centric metatranscriptomics
Short-chain fatty acid (SCFA) degradation is an essential step that occurs across methanogenic environments, and is usually catalyzed by SCFA-oxidizing bacteria in syntrophy with methanogens. Current knowledge of this functional guild is mainly based on isolated or enriched syntrophs due to past methodological limitations. However, it is unclear whether these reference organisms reflect the true ecological properties and in situ activities of the syntrophs that predominate in full-scale systems. Here we describe novel, metabolically versatile bacterial species playing key roles in SCFA oxidation which were ubiquitous in full-scale anaerobic sludge digesters. A genome-guided metatranscriptomic approach was employed, with 198 metagenome-assembled genomes (MAGs) generated from the microbiome of two digesters. The transcriptomic response of individual MAG was studied after stimulation with low concentration of acetate, propionate, or butyrate, to identify the positively responsive members. Such responding MAGs included one bacterium of the family Pelotomaculaceae, and two bacteria of the class Desulfomonilia, which encoded complete propionate or butyrate beta-oxidation pathways that were significantly upregulated under propionate or butyrate stimulation, respectively. These three SCFA oxidizers were detected in most of the 38 investigated digesters, and encoded unique genomic features compared with the well-characterized populations, including the metabolic pathways for phosphite oxidation, nitrite, or sulfate reduction.
Short-chain fatty acid (SCFA) degradation is an essential step that occurs across methanogenic environments, and is usually catalyzed by SCFA-oxidizing bacteria in syntrophy with methanogens. Current knowledge of this functional guild is mainly based on isolated or enriched syntrophs due to past methodological limitations. However, it is unclear whether these reference organisms reflect the true ecological properties and in situ activities of the syntrophs that predominate in full-scale systems. Here we describe novel, metabolically versatile bacterial species playing key roles in SCFA oxidation which were ubiquitous in full-scale anaerobic sludge digesters. A genome-guided metatranscriptomic approach was employed, with 198 metagenome-assembled genomes (MAGs) generated from the microbiome of two digesters. The transcriptomic response of individual MAG was studied after stimulation with low concentration of acetate, propionate, or butyrate, to identify the positively responsive members. Such responding MAGs included one bacterium of the family Pelotomaculaceae, and two bacteria of the class Desulfomonilia, which encoded complete propionate or butyrate beta-oxidation pathways that were significantly upregulated under propionate or butyrate stimulation, respectively. These three SCFA oxidizers were detected in most of the 38 investigated digesters, and encoded unique genomic features compared with the well-characterized populations, including the metabolic pathways for phosphite oxidation, nitrite, or sulfate reduction.