Kraut-Cohen, J., Institute of Soil, Water and Environmental Science, Agricultural Research Organization, The Volcani Center, P.O Box 6, Bet Dagan, Israel
Tripathi, V., Institute of Soil, Water and Environmental Science, Agricultural Research Organization, The Volcani Center, P.O Box 6, Bet Dagan, Israel
Chen, Y., Department of Food Quality and Safety, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
Gatica, J., Institute of Soil, Water and Environmental Science, Agricultural Research Organization, The Volcani Center, P.O Box 6, Bet Dagan, Israel, Department of Soil and Water Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
Volchinski, V., Department of Food Quality and Safety, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
Sela, S., Department of Food Quality and Safety, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
Weinberg, Z., Department of Food Quality and Safety, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
Cytryn, E., Institute of Soil, Water and Environmental Science, Agricultural Research Organization, The Volcani Center, P.O Box 6, Bet Dagan, Israel

Ensiling is a feed preservation method of moist forage crops that generally depends on naturally developing lactic acid bacteria to convert water-soluble carbohydrates into organic acids. While bacterial community dynamics have been previously assessed in bench-scale and pilot ensiling facilities, almost no studies have assessed the microbiomes of large-scale silage facilities. This study analyzed bacterial community composition in mature silage from bunker silos in three commercial production centers as related to pH, organic matter, volatile fatty acid composition, and spatial distribution within the ensiling bunker. It revealed significant physicochemical differences between “preserved” regions situated in the center and along the walls of the silage bunkers that were characterized by high concentrations of lactic acid and other volatiles and pH values below 5, and “spoiled” regions in the corners (shoulders) of the bunkers that had low lactic acid concentrations and high pH values. Preserved silage was dominated (>90 %) by lactic acid bacteria and characterized by high similarity and low taxonomic diversity, whereas spoiled silage had highly diverse microbiomes with low abundances of lactic acid bacteria (<5 %) that were sometimes characterized by high levels of Enterobacteriaceae. Spatial position had a much stronger impact on the microbial community composition than feedstock type, sampling date, or production center location supporting previous studies demonstrating that ecology and not geography is a major driver of environmental microbiomes. © 2016, Springer-Verlag Berlin Heidelberg.