title: Temporal and spatial assessment of microbial communities in commercial silages from bunker silos.
abstract: 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.
authors.affiliation: Institute of Soil, Water and Environmental Science, Agricultural Research Organization, The Volcani Center, P.O Box 6, 50250, Bet Dagan, Israel.
authors.forename: J
authors.initials: J
authors.lastname: Kraut-Cohen
authors.affiliation: Institute of Soil, Water and Environmental Science, Agricultural Research Organization, The Volcani Center, P.O Box 6, 50250, Bet Dagan, Israel.
authors.forename: V
authors.initials: V
authors.lastname: Tripathi
authors.affiliation: Department of Food Quality and Safety, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel.
authors.forename: Y
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Institute of Soil, Water and Environmental Science, Agricultural Research Organization, The Volcani Center, P.O Box 6, 50250, 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.
authors.forename: J
authors.initials: J
authors.lastname: Gatica
authors.affiliation: Department of Food Quality and Safety, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel.
authors.forename: V
authors.initials: V
authors.lastname: Volchinski
authors.affiliation: Department of Food Quality and Safety, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel.
authors.forename: S
authors.initials: S
authors.lastname: Sela
authors.affiliation: Department of Food Quality and Safety, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel.
authors.forename: Z
authors.initials: Z
authors.lastname: Weinberg
authors.affiliation: Institute of Soil, Water and Environmental Science, Agricultural Research Organization, The Volcani Center, P.O Box 6, 50250, Bet Dagan, Israel. eddie@volcani.agri.gov.il.
authors.forename: E
authors.initials: E
authors.lastname: Cytryn
mesh_terms: D044822:Biodiversity; D050260:Carbohydrate Metabolism; D002241:Carbohydrates; D018556:Crops, Agricultural / Q000378:metabolism; D004755:Enterobacteriaceae / Q000302:isolation & purification; D005285:Fermentation; D059014:High-Throughput Nucleotide Sequencing; D019344:Lactic Acid; D007778:Lactobacillus / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D064307:Microbiota / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012820:Silage / Q000382:microbiology*
chemical_list: D002241:Carbohydrates; D012336:RNA, Ribosomal, 16S; D019344:Lactic Acid
keywords: Bacteria; Feedstock; Fermentation; Lactobacillus; Microbial diversity; Microbiome; Silage