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

Kanger, Kärt; Guilford, Nigel G H; Lee, HyunWoo; Nesbø, Camilla; Truu, Jaak; Edwards, Elizabeth A.

doi:10.1093/femsec/fiaa006

Cited by 31 publications

(8 citation statements)

References 94 publications

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“…A high-throughput qPCR (HT-qPCR) was used to quantify the ARGs and MGEs in soil samples. The array included 384 primers targeting ARGs (319) and MGEs (57); additionally, the taxonomic marker genes were included in the array ( Stedtfeld et al, 2018 ; Kanger et al, 2020 ; Pu et al, 2020 ). All reactions were performed in the Takara SmartChip real-time PCR system, as described previously.…”

Section: Methodsmentioning

confidence: 99%

“…All reactions were performed in the Takara SmartChip real-time PCR system, as described previously. Three technical replicates were performed for each sample, and a non-template negative control was included in each HT-qPCR run ( Kanger et al, 2020 ). A threshold cycle (Ct) of 31 was used as the detection limit, and only all three replicates with Ct lower than 31 were regarded as genes detected in that sample.…”

Section: Methodsmentioning

confidence: 99%

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Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields

Shen

Wang

et al. 2023

Front. Microbiol.

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The organic material amendment has been proven to change the soil antibiotic resistance genes (ARGs) profile, which may threaten human health through the food chain, but the effects and mechanisms of different organic materials on ARGs in paddy soils are less explored. In this study, a field experiment was set up with the treatments of conventional chemical fertilization (NPK) and common organic material amendment [rice straw (RS), swine manure (SM), and biochar (BC)] to explore the effects and mechanisms. In total, 84 unique ARGs were found across the soil samples with different organic material amendments, and they conferred resistance to the major antibiotic classes. Compared with NPK, SM significantly increased the detected number and relative abundance of ARGs. A higher detected number of ARGs than NPK was observed in BC, whereas BC had a lower relative abundance of ARGs than NPK. Compared with NPK, a detected number decrease was observed in RS, although abundance showed no significant differences. Compared with other treatments, a higher detected number and relative abundance of mobile genetic elements (MGEs) were observed in BC, indicating a higher potential for horizontal gene transfer. There were significantly positive relationships between the relative abundances of total ARGs and MGEs and the bacterial abundance. The network analysis suggested the important role of MGEs and bacterial communities in shaping the ARGs profile. Mantel test and redundancy analysis (RDA) suggested that soil carbon, nitrogen, and C/N were the major chemical drivers of the ARGs profile. The risk of ARGs spreading to the food chain should be considered when applying SM and biochar, which shifted the ARGs and MGEs profiles, respectively. Pre-treatment measures need to be studied to reduce the dissemination of ARGs in paddy fields.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields

Shen

Wang

et al. 2023

Front. Microbiol.

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“…ethanol and 5 M NaCl prior to sequencing (Kanger et al, 2020). The final DNA concentration was measured by Nanodrop (NanoDrop1000 Spectrophotometer, Thermo Fisher Scientific).…”

Section: Dna Extraction and Quantitative Polymerase Chain Reaction (Q...mentioning

confidence: 99%

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

Lee

Fitamo

Nesbø

et al. 2023

FEMS Microbiology Ecology

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A 50 kg-scale, high solids anaerobic digestor (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.

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“…We found that the α-diversity of ARGs were significantly higher in the HTR than in the NCR; the β-diversity in the HTR and MPR was also significantly different from that in the NCR (Figure 4). The most important sources of pollution in the HTR are also important reservoirs of ARGs, such as food waste, plastic bottles, and carton packaging (Yang et al, 2019;Kanger et al, 2020). High-protein foods, such as meat, can increase the diversity of ARGs during the decomposition process, thereby increasing the risk of their transmission and diffusion in the environment .…”

Section: Figurementioning

confidence: 99%

Anthropogenic disturbance promotes the diversification of antibiotic resistance genes and virulence factors in the gut of plateau pikas (Ochotona curzoniae)

et al. 2022

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The prevalence and transmission of antibiotic resistance genes (ARGs) and virulence factors (VFs) pose a great threat to public health. The importance of pollution in determining the occurrence of ARGs and VFs in wildlife is poorly understood. Using a metagenomic approach, this study investigates the composition and functional pathways of bacteria, ARGs, and VFs in the gut microbiome of Plateau pikas in regions of medical pollution (MPR), heavy tourist traffic (HTR), and no contamination (NCR). We found that the abundance of probiotic genera (Clostridium, Eubacterium, Faecalibacterium, and Roseburia) were significantly lower in the HTR. The metabolic pathways of replication and repair in the endocrine and nervous systems were significantly enriched in the MPR, whereas endocrine and metabolic diseases were significantly enriched in the NCR. The Shannon and Gini–Simpson α-diversity indices of ARGs were highest in the HTR, and there were significant differences in β-diversity among the three regions. The resistance of ARGs to glycopeptide antibiotics increased significantly in the MPR, whereas the ARGs for aminocoumarins increased significantly in the HTR. The diversity of mobile genetic elements (MGEs) was significantly higher in the MPR than in other regions. We observed a strong positive correlation between ARGs and pathogenic bacteria, and the network structure was the most complex in the MPR. There were significant differences in the β-diversity of VFs among the three regions. Medical pollution led to significant enrichment of fibronectin-binding protein and PhoP, whereas tourism-related pollution (in the HTR) led to significant enrichment of LPS and LplA1. Our study indicates that environmental pollution can affect the structure and function of gut microbes and disseminate ARGs and VFs via horizontal transmission, thereby posing a threat to the health of wild animals.

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

Cited by 31 publications

References 94 publications

Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields

Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields

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

Anthropogenic disturbance promotes the diversification of antibiotic resistance genes and virulence factors in the gut of plateau pikas (Ochotona curzoniae)

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