Microbial community dynamics of a sequentially fed anaerobic digester treating solid organic waste.

A 50-kg scale, high solids anaerobic digester (AD) comprising six sequentially fed leach beds with a leachate recirculation system was operated at 37°C for 88 weeks. The solid feedstock contained a constant fibre fraction (a mix of cardboard, boxboard, newsprint, and fine paper) and varying proportions of food waste. Previously, we reported on the stable operation of this digestion system, where significantly enhanced methane production from the fibre fraction was observed as the proportion of food waste increased. The objective of this study was to identify relationships between process parameters and the microbial community. Increasing food waste led to a large increase in the absolute microbial abundance in the circulating leachate. While 16S rRNA amplicons for Clostridium butyricum were most abundant and correlated with the amount of FW in the system and with the overall methane yield, it was more cryptic Candidatus Roizmanbacteria and Spirochaetaceae that correlated specifically with enhanced methane from the fiber fraction. A faulty batch of bulking agent led to hydraulic channeling, which was reflected in the leachate microbial profiles matching that of the incoming food waste. The system performance and microbial community re-established rapidly after reverting to better bulking agent, illustrating the robustness of the system.

Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard.

Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

Solid-State Anaerobic Digestion of Mixed Organic Waste: The Synergistic Effect of Food Waste Addition on the Destruction of Paper and Cardboard.

Full-scale anaerobic digestion processes for organic solid waste are common in Europe but are generally unaffordable in Canada and the United States because of inadequate regulations to restrict cheaper forms of disposal, particularly landfill. We investigated the viability of solid-state anaerobic digestion (SS-AD) as an alternative that reduces the costs of waste pretreatment and subsequent wastewater treatment. A laboratory SS-AD digester, comprising six 10 L leach beds and an upflow anaerobic sludge blanket reactor treating the leachate, was operated continuously for 88 weeks, with a mass balance based on chemical oxygen demand (COD) of 100 ± 2% (CODout/CODin). The feed was a mixture of fibers (cardboard, boxboard, newsprint, and fine paper) with varying amounts of food waste added. The process remained stable throughout. The addition of food waste caused a synergistic effect, raising methane production from the fiber mixture from a low of 52.7 L kg-1 COD fibersadded at no food waste, to 152 L kg-1 COD fibersadded at 29% food waste, an increase of 190%. Substrate COD destruction efficiency reached 65%, and the methane yield reached 225 L kg-1 CODadded at 29% food waste on a COD basis, with a solids retention time of 42 days. This performance was similar to that of a completely stirred tank reactor digesting similar wastes, but with much lower energy input. Multiple factors likely contributed to the enhanced fiber destruction, including the action of hydrolytic enzymes derived from fresh food waste and continuous leachate recirculation between leach beds of different ages.

Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker.

Motivation: Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data. Results: We evaluated the Metaxa2 Database Builder on 11 commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality. Availability and implementation: Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/. Supplementary information: Supplementary data are available at Bioinformatics online.

Reduction of antibiotic resistome and integron-integrase genes in laboratory-scale photobioreactors treating municipal wastewater.

Wastewater treatment systems receiving municipal wastewater are major dissemination nodes of antibiotic resistance genes (ARGs) between anthropogenic and natural environments. This study examined the fate of antibiotic resistome and class 1-3 integron-integrase genes in photobioreactors that were treating municipal wastewater diluted (70/30) with lake or tap water for the algal biomass production. A combined approach of metagenomic and quantitative (qPCR) analysis was undertaken. Municipal wastewater treatment in the photobioreactors led to reduced antibiotic resistome proportion, number of ARG subtypes, and abundances of individual ARGs in the bacterial community. The ARGs and intI1 gene abundances and relative abundances in the discharges of the photobioreactors were either comparable or lower than the respective values in the effluents of conventional wastewater treatment plants. The reduction of the resistome proved to be strongly related to the changes in the bacterial community composition during the wastewater treatment process as it was responding to rising pH levels caused by intense algal growth. Several bacterial genera (e.g., Azoarcus, Dechloromonas, and Sulfuritalea) were recognized as potential hosts of multiple antibiotic resistance types. Although the lake water contributed a diverse and abundant resistome and intI genes profile to the treatment system, it proved to be considerably more beneficial for wastewater dilution than the tap water. The diversity (number of detected resistance types and subtypes) and proportion of the antibiotic resistome, the amount of plasmid borne integron-integrase gene reads, and the abundances and relative abundances of the majority of quantified ARGs (aadA, sul1, tetQ, tetW, qnrS, ermB, blaOXA2-type) and intI1 gene as well as the amount of multi-resistance determinants were significantly lower in the discharges of photobioreactors where lake water was used to dilute wastewater.

Inorganic and organic fertilizers impact the abundance and proportion of antibiotic resistance and integron-integrase genes in agricultural grassland soil.

Soil fertilization with animal manure or its digestate may facilitate an important antibiotic resistance dissemination route from anthropogenic sources to the environment. This study examines the effect of mineral fertilizer (NH4NO3), cattle slurry and cattle slurry digestate amendment on the abundance and proportion dynamics of five antibiotic resistance genes (ARGs) and two classes of integron-integrase genes (intI1 and intI2) in agricultural grassland soil. Fertilization was performed thrice throughout one vegetation period. The targeted ARGs (sul1, tetA, blaCTX-M, blaOXA2 and qnrS) encode resistance to several major antibiotic classes used in veterinary medicine such as sulfonamides, tetracycline, cephalosporins, penicillin and fluoroquinolones, respectively. The non-fertilized grassland soil contained a stable background of tetA, blaCTX-M and sul1 genes. The type of applied fertilizer significantly affected ARGs and integron-integrase genes abundances and proportions in the bacterial community (p<0.001 in both cases), explaining 67.04% of the abundance and 42.95% of the proportion variations in the grassland soil. Both cattle slurry and cattle slurry digestate proved to be considerable sources of ARGs, especially sul1, as well as integron-integrases. Sul1, intI1 and intI2 levels in grassland soil were elevated in response to each organic fertilizer's application event, but this increase was followed by a stage of decrease, suggesting that microbes possessing these genes were predominantly entrained into soil via cattle slurry or its digestate application and had somewhat limited survival potential in a soil environment. However, the abundance of these three target genes did not decrease to a background level by the end of the study period. TetA was most abundant in mineral fertilizer treated soil and blaCTX-M in cattle slurry digestate amended soil. Despite significantly different abundances, the abundance dynamics of bacteria possessing these genes were similar (p<0.05 in all cases) in different treatments and resembled the dynamics of the whole bacterial community abundance in each soil treatment.