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.

Temperature-Phased Conversion of Acid Whey Waste Into Medium-Chain Carboxylic Acids via Lactic Acid: No External e-Donor

“…Genomic DNA was extracted using the PowerSoil-htp 96 Well Soil DNA Isolation kit (MO BIO Laboratories, Carlsbad, CA, USA) according to the protocol of the manufacturer. The DNA amplification protocol was described previously, 44 with the following exceptions: Mag-Bind RxnPure Plus magnetic beads solution (Omega Biotek, Norcross, GA, USA) was used instead of Mag-Bind E-Z Pure, and 50 ng of DNA per sample was pooled instead of 100 ng. Sequencing on the Illumina MiSeq platform was performed at the Cornell University Biotechnology Resource Center (Ithaca, NY, USA).…”

Waste Conversion into n-Caprylate and n-Caproate: Resource Recovery from Wine Lees Using Anaerobic Reactor Microbiomes and In-line Extraction

“…Genomic DNA was extracted using the PowerSoil DNA isolation kit (MO BIO Laboratories Inc., Carlsbad, CA, USA). Modifications to the protocol included utilization of custom bead tubes containing a mixture of 300 mg of 0.1-mm diameter and 100 mg of 0.5-mm diameter silica/zirconia beads (Hospodsky et al, 2010) and physical cell lysis with bead-beating at 3450 oscillations/min for 45 s. The DNA amplification protocol was performed according to Regueiro et al (2015) with the following exceptions: (1) Mag-Bind RxnPure Plus magnetic beads solution (Omega Biotek, Norcross, GA, USA) were used instead of Mag-Bind E-Z Pure; and (2) only 20 ng DNA per sample were pooled instead of 100 ng. QIITA 1 was used for initial processing of the sequencing data.…”

“…Community analysis, including beta diversity, was performed as described previously (Regueiro et al, 2015) with the following exceptions: (1) the alpha diversity was calculated using the Shannon diversity index (Shannon, 1948) rather than Chao1; and (2) the Pearson correlation coefficient was calculated for samples from Phase II with the functions cor and cor.test in the R stats package (R Core Team, 2013). At a significance level of p < 0.05 and n = 7, the relative abundance of an OTU would be positively correlated with the MCC productivity if the Pearson r was greater than 0.754.…”

Bacterial community dynamics in long‐term operation of a pilot plant using aerobic granular sludge to treat pig slurry

“…The Variance Inflation Factors (VIF) were studied to evaluate if the constraints were redundant . Non‐significant or redundant parameters were discarded until all the constraining variables in the db‐RDA were significant ( P > 0.05) and non‐redundant (VIF score < 10) . In addition, to analyse the alpha diversity, the sample libraries were rarefied using the vegan package in R , via rarefaction function and calculation of Shannon‐Weaver index.…”