title: Comparing the inhibitory thresholds of dairy manure co-digesters after prolonged acclimation periods: Part 2--correlations between microbiomes and environment.
abstract: Here, we studied the microbiome succession and time-scale variability of four mesophilic anaerobic reactors in a co-digestion study with the objective to find links between changing environmental conditions and the microbiome composition. The changing environmental conditions were ensured by gradual increases in loading rates and mixing ratios of three co-substrates with a constant manure-feeding scheme during an operating period longer than 900 days. Each co-substrate (i.e., alkaline hydrolysate, food waste, and glycerol) was co-digested separately. High throughput 16S rRNA gene sequencing was used to examine the microbiome succession. The alkaline hydrolysate reactor microbiome shifted and adapted to high concentrations of free ammonia, total volatile fatty acids, and potassium to maintain its function. The addition of food waste and glycerol as co-substrates also led to microbiome changes, but to a lesser extent, especially in the case of the glycerol reactor microbiome. The divergence of the food waste reactor microbiome was primarily linked to increasing free ammonia levels in the reactor; though, these levels remained below previously reported inhibitory levels for acclimated biomass. The glycerol reactor microbiome succession included an increase in Syntrophomonadaceae family members, which have previously been linked to long-chain fatty acid degradation. The glycerol reactor exhibited rapid failure and limited adaptation at the end of the study.
authors.affiliation: Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA; Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Rúa Lope Gómez de Marzoa s/n, E-15782 Santiago de Compostela, Spain.
authors.forename: Leticia
authors.initials: L
authors.lastname: Regueiro
authors.affiliation: Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Spirito
authors.affiliation: Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Joseph G
authors.initials: JG
authors.lastname: Usack
authors.affiliation: Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Denina
authors.initials: D
authors.lastname: Hospodsky
authors.affiliation: Chemistry Department, SUNY-Cortland, Cortland, NY 13045, USA.
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Werner
authors.affiliation: Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA. Electronic address: la249@cornell.edu.
authors.forename: Largus T
authors.initials: LT
authors.lastname: Angenent
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D001673:Biodegradation, Environmental; D018533:Biomass; D019149:Bioreactors; D002417:Cattle; D004269:DNA, Bacterial / Q000032:analysis; D003612:Dairying; D005735:Garbage; D005990:Glycerol / Q000378:metabolism; D008372:Manure / Q000032:analysis*; D008697:Methane / Q000032:analysis*; D064307:Microbiota; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D008372:Manure; D012336:RNA, Ribosomal, 16S; D008697:Methane; D005990:Glycerol
keywords: Ammonia; Bacteroidetes; Clostridia; Co-digestion; Volatile fatty acids