Methanotrophs, methanogens, and microbial community structure in livestock slurry surface crusts. Microbiome of slurry surface crusts

Livestock manure stores are significant sources of atmospheric methane (CH4). However, crusts forming at the surface of liquid manure (slurry) during storage have been shown to harbor methane-oxidizing bacteria (MOB), suggesting there is a potential for mitigation of CH4 emissions from the slurry. So far, the biological basis for CH4 metabolism in surface crusts is largely unknown. Using denaturing gradient gel electrophoresis (DGGE) and Tag-encoded FLX amplicon pyrosequencing, this study investigated the microbial community in four surface crusts from cattle and swine slurries, with special focus on microorganisms involved in CH4 metabolism. All crusts had distinct structures of Type I and Type II MOB communities, and of other bacteria and archaea. MOB and methanogens were identified at genus level. The genera Methylobacter, Methylomicrobium, Methylomonas, and Methylosarcina of Type I, and Methylocystis of Type II, dominated the MOB community, whereas Methanocorpusculum was the predominant methanogen. Higher numbers of OTUs (operational taxonomic units) representing Type I than Type II MOB were found in all crust materials based on pyrosequencing and DGGE image analysis, indicating that Type I MOB are more diverse and abundant than Type II MOB in this environment. Potential CH4 oxidation was observed in cattle slurry crusts, but not in the present swine slurry crusts. The distinct methane-metabolizing dynamics suggest a link between microbial community composition and ecological functions.