Effect of mesophilic anaerobic digestion on the resistome profile of dairy manure

Virome and metagenomic sequencing reveal the impact of microbial inoculants on suppressions of antibiotic resistome and viruses during co-composting

Co-composting with exogenous microbial inoculant, presents an effective approach for the harmless utilization of livestock manure and agroforestry wastes. However, the impact of inoculant application on the variations of viral and antibiotic resistance genes (ARGs) remains poorly understood, particularly under varying manure quantity (low 10 % vs. high 20 % w/w). Thus, employing virome and metagenomic sequencing, we examined the influence of Streptomyces-Bacillus Inoculants (SBI) on viral communities, phytopathogen, ARGs, mobile genetic elements, and their interrelations. Our results indicate that SBI shifted dominant bacterial species from Phenylobacterium to thermotropic Bordetella, and the quantity of manure mediates the effect of SBI on whole bacterial community. Major ARGs and genetic elements experienced substantial changes with SBI addition. There was a higher ARGs elimination rate in the composts with low (∼76 %) than those with high manure (∼70 %) application. Virus emerged as a critical factor influencing ARG dynamics. We observed a significant variation in virus community, transitioning from Gemycircularvirus- (∼95 %) to Chlamydiamicrovirus-dominance. RDA analysis revealed that Gemycircularvirus was the most influential taxon in shaping ARGs, with its abundance decreased approximately 80 % after composting. Collectively, these findings underscore the role of microbial inoculants in modulating virus communities and ARGs during biowaste co-composting.

Fate of florfenicol and linezolid resistance genes and their bacterial hosts during two waste treatment models in swine feedlots

Florfenicol resistance genes (FRGs) are widely present in livestock farms. The aim of this study was to evaluate the removal efficiencies of FRGs as well as the relationships between FRGs, mobile genetic elements (MGEs) and bacterial communities during the natural drying (ND) and anaerobic digestion (AD) processes of manure treatment in swine farms by combining bacterial isolation, quantitative PCR and metagenomic approaches. Solid manure showed a higher abundance of FRGs than fresh manure and was the main contamination source of fexA and fexB in ND farms, whilst biogas slurry displayed a lower abundance of FRGs than the wastewater in AD farms. Moreover, fresh manure and wastewater showed a high abundance of optrA, and wastewater was the main contamination source of cfr in both ND and AD farms. Both optrA/fexA-positive enterococci and cfr/fexA-positive staphylococci were mainly isolated along the farms' treatment processes. The cfr-positive staphylococci were highly prevalent in wastewater (57.14 % - 100 %) and may be associated with nasal-derived cfr-positive porcine staphylococci. An increased abundance of Enterococcus, Jeotgalibaca and Vagococcus in the bacterial community structures may account for the high optrA abundance in wastewater and Jeotgalibaca may be another potential host of optrA. Furthermore, the abundance of FRG-related MGEs increased by 22.63 % after the ND process and decreased by 66.96 % in AD farms. A significant correlation was observed between cfr and ISEnfa4, whereas no significance was found between optrA and IS1216E, although IS1216E is the predominant insertion sequence involved in the transfer of optrA. In conclusion, manure and wastewater represented independent pollution sources of FRGs in swine farms. Associated MGEs might play a key role in the transfer and persistence of FRGs. The AD process was more efficient in the removal of FRGs than the ND method, nevertheless a longer storage of slurry may be required for a complete removal.

National Greenhouse Gas Emission Reduction Potential from Adopting Anaerobic Digestion on Large-Scale Dairy Farms in the United States

Waste-to-energy systems can provide a functional demonstration of the economic and environmental benefits of circularity, innovation, and reimagining existing systems. This study offers a robust quantification of the greenhouse gas (GHG) emission reduction potential of the adoption of anaerobic digestion (AD) technology on applicable large-scale dairy farms in the contiguous United States. GHG reduction estimates were developed through a robust life cycle modeling framework paired with sensitivity and uncertainty analyses. Twenty dairy configurations were modeled to capture important differences in housing and manure management practices, applicable AD technologies, regional climates, storage cleanout schedules, and methods of land application. Monte Carlo results for the 90% confidence interval illustrate the potential for AD adoption to reduce GHG emissions from the large-scale dairy industry by 2.45-3.52 MMT of CO2-eq per year considering biogas use only in renewable natural gas programs and as much as 4.53-6.46 MMT of CO2-eq per year with combined heat and power as an additional biogas use case. At the farm level, AD technology may reduce GHG emissions from manure management systems by 58.1-79.8% depending on the region. Discussion focuses on regional differences in GHG emissions from manure management strategies and the challenges and opportunities surrounding AD adoption.

Bacterial diversity and resistome analysis of drinking water stored in cisterns from two First Nations communities in Manitoba, Canada

The microbiological content of water is an ongoing concern in First Nations communities in Canada. Many communities lack water treatment plants and continue to be under drinking water advisories. However, lack of access to treatment plants is only a part of the problem as poor water distribution systems also contribute to the failure to provide safe drinking water. Here, we studied the microbial diversity and antibiotic resistome from water stored in cisterns from two First Nations communities in Manitoba, Canada. We found that the cistern water contained a high number of bacteria and showed the presence of diverse antimicrobial resistance genes. Interestingly, the bacterial diversity and antimicrobial resistance genes varied considerably from that of the untreated source water, indicating that the origin of contamination in the cistern water came from within the treatment plant or along the delivery route to the homes. Our study highlights the importance of proper maintenance of the water distribution system in addition to access to water treatment facilities to ensure a supply of safe water to First Nations communities in Canada.IMPORTANCEThe work described addresses a critical issue in First Nations communities in Canada-the microbiological content of water. Many of these communities lack access to water treatment plants and frequently experience drinking water advisories. This study focused on the microbial diversity and antibiotic resistome in water stored in cisterns within two First Nations communities in Manitoba, Canada. These findings reveal that cistern water, a common source of drinking water in these communities, contains a high number of bacteria and a wide range of antimicrobial resistance genes. This highlights a serious health risk as exposure to such water can lead to the spread of drug-resistant infections, posing a threat to the well-being of the residents.

Developing a sorptive material of cadmium from pyrolysis of hen manure

A large amount of manure is generated from concentrated animal feeding operations (CAFOs), leading to serious environmental issues and hazardous risks from pathogens, such as methicillin-resistant Staphylococcus aureus. Therefore, developing an effective method for manure disposal is essential. Thus, in this study, we suggest the use of CO2 in pyrolysis of hen manure (HM) as an effective method to convert the carbon in HM into syngas (especially carbon monoxide (CO)). HM was used and tested as the model compound. From the results of thermo-gravimetric analysis, the decarboxylation of CaCO3 in HM in the presence of N2 was realized at temperatures ranging from 638 to 754 °C. The Boudouard reaction was observed at ≥ 664 °C in the presence of CO2. Despite the lack of occurrence of the Boudouard reaction, more CO formation was observed in the presence of CO2 at ≥ 460 °C. This was deemed as a homogeneous reaction induced by CO2. Considering the high Ca content of HM, HM biochar in N2 and CO2 were used as adsorbent for removal of Cadmium (Cd), which is toxic heavy metal. The adsorption capacities of HM_N2 and HM_CO2 were 302.4 and 95.7 mg g-1, respectively. The superior performance of HM_N2 is mainly attributed to the presence of Ca(OH)2, which provides favorable (alkaline) conditions for precipitation and ion exchange. Our results indicate the environmental benefits from using CO2. Specifically, CO2 (representative greenhouse gas) converted into fuel. Given this, pyrolysis of HM in the presence of CO2 was achieved at ≤ 640 °C, and the atmospheric condition should be switched from CO2 to N2 at ≥ 640 °C to ensure the decarboxylation of CaCO3.

Characterisation of synthesised trimetallic nanoparticles and its influence on anaerobic digestion of palm oil mill effluent

The augmentation of biogas production can be achieved by incorporating metallic nanoparticles as additives within anaerobic digestion. The objective of this current study is to examine the synthesis of Fe-Ni-Zn and Fe-Co-Zn trimetallic nanoparticles using the co-precipitation technique and assess its impact on anaerobic digestion using palm oil mill effluent (POME) as carbon source. The structural morphology and size of the synthesised trimetallic nanoparticles were analysed using a range of characterization techniques, such as X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), Scanning electron microscopy (SEM), and Energy-dispersive X-ray spectroscopy (EDX) . The average size of Fe-Ni-Zn and Fe-Co-Zn were 19-25.5 nm and 19.1-30.5 nm respectively. Further, investigation focused on examining the diverse concentrations of trimetallic nanoparticles, ranging from 0 to 50 mgL-1. The biogas production increased by 55.55% and 60.11% with Fe-Ni-Zn and Fe-Co-Zn trimetallic nanoparticles at 40 mgL-1 and 20 mgL-1, respectively. Moreover, the lowest biogas of 11.11% and 38.11% were found with 10 mgL-1 of Fe-Ni-Zn and Fe-Co-Zn trimetallic nanoparticles. The findings of this study indicated that the trimetallic nanoparticles exhibited interactions with anaerobes, thereby enhancing the degradation process of palm oil mill effluent (POME) and biogas production. The study underscores the potential efficacy of trimetallic nanoparticles as a viable supplement for the promotion of sustainable biogas generation.

A Review on Performance Improvement of Anaerobic Digestion Using Co-Digestion of Food Waste and Sewage Sludge

Anaerobic co-digestion (AcoD) is a vital technology in the decarburization of the economy because of its ability to process organic waste, recover nutrients, and create biogas as a sustainable biofuel all at the same time. This attribute also makes this technology a viable partner in pursuing a circular economic model. However, the poor biogas output of typical substrates like sewage sludge and animal manure and the hefty installation costs limit its viability. This review paper with literature analysis provides a good grasp of the anaerobic co-digesting process with diverse food digestion methods. In this survey, we have analyzed the Anaerobic Digestion of water waste, food waste, and animal manure and the anaerobic co-digestion of animal waste with water waste and food waste with water waste. This analysis demonstrates that anaerobic co-digestion produces more methane biogas than anaerobic digestion. Also, it has been shown that by adjusting the ratio of food and animal waste to water waste, we can produce more methane. In the future, we would like to supplement anaerobic co-digestion by altering the proportion of different wastes that are mixed with water waste in order to increase methane production.

Exploring resistomes and microbiomes in pilot-scale microalgae-bacteria wastewater treatment systems for use in low-resource settings

Antibiotic resistance genes (ARGs) released into the environment are an emerging human and environmental health concern, including ARGs spread in wastewater treatment effluents. In low-to-middle income countries (LMICs), an alternate wastewater treatment option instead of conventional systems are low-energy, high-rate algal ponds (HRAP) that use microalgae-bacteria aggregates (MABA) for waste degradation. Here we studied the robustness of ARG removal in MABA-based pilot-scale outdoor systems for 140 days of continuous operation. The HRAP system successfully removed 73 to 88 % chemical oxygen demand and up to 97.4 % ammonia, with aggregate size increasing over operating time. Fourteen ARG classes were identified in the HRAP influent, MABA, and effluent using metagenomics, with the HRAP process reducing total ARG abundances by up to 5-fold from influent to effluent. Parallel qPCR analyses showed the HRAP system significantly reduced exemplar ARGs (p < 0.05), with 1.2 to 4.9, 2.7 to 6.3, 0 to 1.5, and 1.2 to 4.8 log-removals for sul1, tetQ, blaKPC, and intl1 genes, respectively. Sequencing of influent, effluent and MABAs samples showed associated microbial communities differed significantly, with influent communities by Enterobacteriales (clinically relevant ARGs carrying bacteria), which were less evident in MABA and effluent. In this sense, such bacteria might be excluded from MABA due to their good settling properties and the presence of antimicrobial peptides. Microalgae-bacteria treatment systems steadily reduced ARGs from wastewater during operation time, using sunlight as the energetic driver, making them ideal for use in LMIC wastewater treatment applications.

Developing a biogas centralised circular bioeconomy using agricultural residues - Challenges and opportunities

Anaerobic digestion (AD) can be used as a stand-alone process or integrated as part of a larger biorefining process to produce biofuels, biochemicals and fertiliser, and has the potential to play a central role in the emerging circular bioeconomy (CBE). Agricultural residues, such as animal slurry, straw, and grass silage, represent an important resource and have a huge potential to boost biogas and methane yields. Under the CBE concept, there is a need to assess the long-term impact and investigate the potential accumulation of specific unwanted substances. Thus, a comprehensive literature review to summarise the benefits and environmental impacts of using agricultural residues for AD is needed. This review analyses the benefits and potential adverse effects related to developing biogas-centred CBE. The identified potential risks/challenges for developing biogas CBE include GHG emission, nutrient management, pollutants, etc. In general, the environmental risks are highly dependent on the input feedstocks and resulting digestate. Integrated treatment processes should be developed as these could both minimise risks and improve the economic perspective.

Characterization of Escherichia coli and Other Enterobacterales Resistant to Extended-Spectrum Cephalosporins Isolated from Dairy Manure in Ontario, Canada

Extended-spectrum cephalosporins (ESCs) resistance genes, such as bla_CTX-M, bla_CMY, and bla_SHV, have been found regularly in bacteria from livestock. However, information on their distribution in dairy cattle in Canada and on the associated genome sequences of ESC-resistant Enterobacterales is sparse. In this study, the diversity and distribution of ESC-resistant Escherichia coli throughout manure treatments in six farms in Southern Ontario were assessed over a one-year period, and their ESC-resistance plasmids were characterized. The manure samples were enriched using selective media. The resulting isolates were screened via polymerase chain reaction for bla_CTX-M, bla_CMY, and bla_SHV. No E. coli carrying bla_SHV were detected. Escherichia coli (n = 248) carrying bla_CTX-M or bla_CMY underwent whole-genome sequencing using an Illumina MiSeq/NextSeq. These isolates were typed using multilocus sequence typing (MLST) and their resistance gene profiles. A subset of E. coli (n = 28) were sequenced using Oxford Nanopore Technologies. Plasmids were assembled using Unicycler and characterized via the resistance genes pattern, replicon type, plasmid MLST, phylogenetic analysis, and Mauve alignments. The recovery of ESC-resistant Enterobacterales (18 species, 8 genera) was drastically reduced in manure outputs. However, multiple treatment stages were needed to attain a significant reduction. 62 sequence types were identified, with ST10, ST46, ST58, ST155, ST190, ST398, ST685, and ST8761 being detected throughout the treatment pipeline. These STs overlapped with those found on multiple farms. The ESC-resistance determinants included CTX-M-1, -14, -15, -17, -24, -32, -55, and CMY-2. The plasmids carrying bla_CTX-M were more diverse than were the plasmids carrying bla_CMY. Known "epidemic plasmids" were detected for both bla_CTX-M and bla_CMY. IMPORTANCE The increase in antimicrobial resistance is of concern for human and animal health, especially when resistance is conferred to extended-spectrum cephalosporins, which are used to treat serious infections in both human and veterinary medicine. Bacteria carrying extended-spectrum cephalosporin resistance genes, including bla_CTX-M and bla_CMY, are frequently found in dairy manure. Manure treatment influences the loads and diversity of bacteria, including those carrying antimicrobial resistance genes, such as Enterobacterales and Escherichia coli. Any bacteria that survive the treatment process are subsequently applied to the environment. Enterobacterales carrying bla_CTX-M or bla_CMY can contaminate soil and crops consumed by humans and animals, thereby increasing the potential for antimicrobial resistance genes to integrate into the human gut microflora through horizontal gene transfer. This furthers the dissemination of resistance. Therefore, it is imperative to understand the effects manure treatments have on ESC-resistance in environmentally applied manure.

Digestate from Agricultural Biogas Plants as a Reservoir of Antimicrobials and Antibiotic Resistance Genes-Implications for the Environment

Antimicrobials and antibiotic resistance genes (ARGs) in substrates processed during anaerobic digestion in agricultural biogas plants (BPs) can reach the digestate (_D), which is used as fertilizer. Antimicrobials and ARGs can be transferred to agricultural land, which increases their concentrations in the environment. The concentrations of 13 antibiotics in digestate samples from biogas plants (BPs) were investigated in this study. The abundance of ARGs encoding resistance to beta-lactams, tetracyclines, sulfonamides, fluoroquinolones, macrolide-lincosamide-streptogramin antibiotics, and the integrase genes were determined in the analyzed samples. The presence of cadmium, lead, nickel, chromium, zinc, and mercury was also examined. Antimicrobials were not eliminated during anaerobic digestion. Their concentrations differed in digestates obtained from different substrates and in liquid and solid fractions (ranging from 62.8 ng/g clarithromycin in the solid fraction of sewage sludge digestate to 1555.9 ng/L doxycycline in the liquid fraction of cattle manure digestate). Digestates obtained from plant-based substrates were characterized by high concentrations of ARGs (ranging from 5.73 × 10² copies/g_DcfxA to 2.98 × 10⁹ copies/g_Dsul1). The samples also contained mercury (0.5 mg/kg dry mass (dm)) and zinc (830 mg/kg dm). The results confirmed that digestate is a reservoir of ARGs (5.73 × 10² to 8.89 × 10¹⁰ copies/g_D) and heavy metals (HMs). In addition, high concentrations of integrase genes (10⁵ to 10⁷ copies/g_D) in the samples indicate that mobile genetic elements may be involved in the spread of antibiotic resistance. The study suggested that the risk of soil contamination with antibiotics, HMs, and ARGs is high in farms where digestate is used as fertilizer.

Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion

Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6')-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6')-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.

Anaerobic membrane bioreactor for carbon-neutral treatment of industrial wastewater containing N, N-dimethylformamide: Evaluation of electricity, bio-energy production and carbon emission

The feasibility of anaerobic membrane bioreactor (AnMBR) for the treatment of N, N-dimethylformamide (DMF)-containing wastewater was theoretically compared with the conventional activated sludge (CAS) process in this study. The electricity consumption and expenditure, bio-energy production and CO₂ emission were investigated using the operational results of a lab-scale AnMBR operated in a long-term operation. The AnMBR was capable of producing bio-methane from wastewater and generated 3.45 kWh/m³ of electricity as recovered bio-energy while the CAS just generated 1.17 kWh/m³ of electricity from the post-treatment of excessive sludge disposal. The large quantity of bio-methane recovered by the AnMBR can also be sold as sustainable bioresource for the use of household natural gas with a theoretical profit gain of 29,821 US$/year, while that of the CAS was unprofitable. The AnMBR was also demonstrated to significantly reduce the carbon emission by obtaining a theoretical negative CO₂ production of -2.34 kg CO₂/m³ with the recycle of bio-energy while that for the CAS was 4.50 kg CO₂/m³. The results of this study demonstrate that the AnMBR process has promising potential for the carbon-neutral treatment of high-strength DMF-containing wastewater in the future.

Impact of mesophilic anaerobic digestion and post-treatment of digestates on the transfer of conjugative antimicrobial resistance plasmids

Manure is a major source of antimicrobial-resistant bacteria and resistance genes carried by mobile genetic elements such as plasmids. In France, the number of on-farm biogas plants has increased significantly in recent years. Our study investigated the impact of mesophilic anaerobic digestion (AD) and the post-treatment of digestates on the fate of conjugative plasmids, along with their potential transfer of antimicrobial resistance. Samples of raw manure, digestates and post-treated digestates were collected from three on-farm biogas plants. Conjugative plasmids were captured using the Escherichia coli CV601 recipient strain and media supplemented with rifampicin and kanamycin - to which the recipient strain is resistant - and tetracycline, sulfamethoxazole, gentamicin, trimethoprim, amoxicillin, cefotaxime, ciprofloxacin or colistin. Putative transconjugants were identified and characterised by disc diffusion and whole genome sequencing. The results showed that the antimicrobial resistance genes transferred from the different matrices conferred resistance to tetracyclines, sulphonamides, trimethoprim, and/or streptomycin. Transconjugants were obtained from raw manure samples but not from digestates or post-digestates, suggesting that mesophilic AD processes may produce fewer conjugative plasmids potentially able to be transferred to Enterobacterales.

Fate and exposure risk of florfenicol, thiamphenicol and antibiotic resistance genes during composting of swine manure

Livestock manure is an important source of antibiotic resistance genes (ARGs) spreading to the environment, posing a potential threat to human health. Here, we investigated the dissipation of florfenicol (FF) and thiamphenicol (TAP), and their effects on the bacterial community, mobile genetic elements (MGEs), and ARGs during composting. The results indicated that FF and TAP dissipated rapidly in compost, with half-life values of 5.1 and 1.6 d, respectively. However, FF could not be completely removed during composting. The FF and TAP residues in manure could reduce the elimination of ARGs and MGEs during composting, and had a negative effect on the physicochemical factors of the compost. Significant correlations were found between floR and intI1, indicating that floR in manure may more easily diffuse to the soil environment. Meanwhile, the presence of FF in manure could increase the abundance of floR. Network analysis showed that Proteobacteria and Firmicutes were the dominant bacterial communities and important potential pathogen hosts carrying ARGs. The predicted environmental concentration of FF in the soil was over 100 μg kg^-1, which indicates that FF poses a potential risk to the natural environment, and we verified this result through field experiments. The results showed that FF dissipated in the soil after it migrated from manure to soil. In contrast, TAP in manure posed lower environmental risk. This study highlights that changed in composting conditions may control the rate of removal of ARGs. Further studies are needed to investigate the best environmental conditions to achieve a faster degradation of FF and a more comprehensive elimination of ARGs during composting.

Substrate complexity affects the prevalence and interconnections of antibiotic, metal and biocide resistance genes, integron-integrase genes, human pathogens and virulence factors in anaerobic digestion

Anaerobic digestion (AD) is widely used to treat livestock manure that harbors diverse pollutants (resistance genes (ARGs), metal/biocide resistance genes (MBRGs), integron-integrase genes, human pathogens and pathogen virulence factors (VFs)). However, the interplays of these pollutants and the effects of substrate complexity on pollutants in AD are elusive. This study investigated the dynamics of these pollutants and bacterial communities during AD of swine manure, by metatranscriptomic sequencing and amplicon sequencing of 16 S rRNA and 16 S rRNA gene. The pollutant profiles and bacterial communities differed across AD processes, nevertheless with consistent dominance of ARGs of multi-drugs, tetracycline, aminoglycoside and rifamycin, MBRGs of multi-biocides, multi-metals, copper and arsenic, the integron-integrase gene intI1, potential pathogens of Escherichia coli, Streptococcus gallolyticus and Clostridium perfringens, VFs involved in pathogen adherence, and bacterial phyla of Firmicutes, Bacteroidetes and Proteobacteria. Reduced substrate complexity (replacing a part of swine manure, a complex substrate, with a simple substrate, apple waste or fructose) decreased the prevalence and stochastic turnover of ARGs and MBRGs. Network analyses revealed decreased interplays among pollutants under reduced substrate complexity. Our findings provide a mechanical understanding of diverse pollutants dynamics during AD, and reveal the importance of substrate complexity in controlling prevalence and interplays of pollutants.

Carbon-neutral treatment of N, N-dimethylformamide-containing industrial wastewater by anaerobic membrane bioreactor (AnMBR): Bio-energy recovery and CO2 emission reduction

High-strength industrial wastewater containing approximately 2000 mg/L of N, N-dimethylformamide (DMF) was treated by the anaerobic membrane bioreactor (AnMBR) during a long-term operation with the concept of carbon neutrality in this study. Bio-methane was recovered as bio-energy or bio-resource from DMF-containing wastewater along with the CO₂ emission reduction. The results are clear evidence of the feasibility of carbon-neutral treatment of DMF-containing wastewater by the AnMBR. With an effective degradation under the organic loading rate of 6.53 COD kg/m³/d at the HRT of 12 h, the AnMBR completely covered the energy consumption during long-term operation by saving electricity of 4.16 kWh/m³ compared with the conventional activated sludge process. The CO₂ emission of the AnMBR was just 1.06 kg/m³, remarkably reducing 1.45 kg/m³ of CO₂. The treatment of DMF-containing wastewater by the AnMBR perfectly realized the goal of carbon neutrality, and was considered as an alternative to the conventional activated sludge process.

A meta-analysis reveals that operational parameters influence levels of antibiotic resistance genes during anaerobic digestion of animal manures

Anaerobic digestion (AD) has shown the potential to reduce the numbers and types of antibiotic-resistance genes (ARG) present in animal manures. However, the variability of the results has limited the ability to draw solid conclusions. To address this issue, we performed a series of meta-analyses to evaluate how AD of pig, cattle, and dairy manures affects ARG levels and how different parameters, such as temperature, pH, digestion times, and the addition of other substances (e.g., solids, antibiotics) influence ARG changes. Twenty studies with enough details on changes in ARG levels during the AD process were identified and used for the meta-analyses. The results suggested that AD could significantly reduce ARG levels regardless of the conditions of the process. Also, thermophilic AD was more effective than mesophilic AD at reducing ARGs, although this difference was only significant for pig manures. The results also suggested that long digestion times (>50 days) yielded better ARG reduction rates, and that the addition of solids from an external source (co-digestion) negatively affected the efficiency of ARG reduction. In general, the results suggested that ARG changes during AD could be linked to the abundance and activity of hydrolytic communities.

Response behavior of antibiotic resistance genes to zinc oxide nanoparticles in cattle manure thermophilic anaerobic digestion process: A metagenomic analysis

This work investigated the metagenomics-based behavior of antibiotic resistance genes (ARGs) during cattle manure anaerobic digestion with zinc oxide nanoparticles (ZnO NPs) that are commonly used as animal feed additives. The 6.6% decrease in total ARGs abundance while remained unchanged ARGs diversity with ZnO NPs (5 mg/g total solid), suggested ZnO NPs may mitigate ARGs risk by abundance. Also, ZnO NPs affected ARGs with mechanisms specifically of antibiotic inactivation and antibiotic target change, and declined potential hosts' abundance (bacterial genus Ruminiclostridium, Riminococcus, and Paenibacillus) which mainly contributed to the decreased ARGs' abundance. Besides, microbial chemotaxis decreased by 17% with ZnO NPs compared to that without nanoparticles indicated a depression on potential hosts, who could develop the mechanism to adapt to altered digestion conditions, which probably inhibited the ARGs' propagation. These findings are important to promote understanding of the potential ARGs risks in treatments of livestock wastes containing animal feed additives.

From gut to mud: dissemination of antimicrobial resistance between animal and agricultural niches

With increasing reports on antimicrobial resistance (AMR) in humans, animals and the environment, we are at risk of returning to a pre-antibiotic era. Therefore, AMR is recognized as one of the major global health threats of this century. Antibiotics are used extensively in farming systems to treat and prevent infections in food animals or to increase their growth. Besides the risk of a transfer of AMR between the human and the animal sector, there is another yet largely overlooked sector in the One Health triad. Human-dominated ecosystems such as agricultural soils are a major sink for antibiotics and AMR originating from livestock farming. This review summarizes current knowledge on the prevalence of AMR at the interface of animal and agricultural production and discusses the potential implications for human health. Soil resistomes are augmented by the application of manure from treated livestock. Subsequent transfer of AMR into plant microbiomes may likely play a critical role in human exposure to antibiotic resistance in the environment. Based on the knowledge that is currently available we advocate that more attention should be paid to the role of environmental resistomes in the AMR crisis.

In situ analysis of antibiotic resistance genes in anaerobically digested dairy manure and its subsequent disposal facilities

The metagenomic and quantitative polymerase chain reaction approaches were combined to evaluate the profiles of ARGs and plasmids in anaerobically digested dairy manure in situ and reveal the persistence and elevation of typical ARGs and plasmids in its subsequent disposal facilities in CAFOs, respectively. Our results indicated that the typical ARGs and plasimd were mainly sul2, mefa, tetm-01, tetm-02, tetw, aph3iiia, and clostridioides difficile strain 12,038 plasmid unnamed in CAFOs, some of which greatly enriched in AD residue after its storage, especially sul1 and sul2. Meantime, the AD slurry recycling introduced the bacteria carrying ARGs into soil, especially Romboutsia genus, which greatly enriched sul2, tetm-01, tetm-02, aphiiia, and mefa. In the present study, ARGs occurrence, persistence and distribution were understood through in situ analysis of their profiles during dairy manure AD treatment and subsequent disposals in CAFOs, which are helpful for controlling the potential environmental risks from dairy manure recycling.

The potential of dairy manure and sewage management pathways towards a circular economy: A meta-analysis from the life cycle perspective

The global dairy farming sector has markedly expanded and intensified over the past decades due to the growing demand for milk and dairy products. The interest in implementing life cycle assessments of various manure and sewage management (MSM) strategies is increasing on a global scale, which is motivated by the concerns of environmental degradation caused by unsustainable MSM and growing awareness of circular economy. Life cycle thinking concept has been widely introduced to favor the comparative studies of different MSM strategies, with the aim of identifying suitable MSM strategies and formulating related policies. This meta-analysis presented comparative results of publicly available dairy MSM pathways, including waste-to-energy, composting, recycling, and other management pathways, aiming to explore potential benefits towards a circular economy. Results showed a consensus that waste-to-energy pathway significantly reduced global warming, eutrophication, and ecotoxicity potential. More specifically, the comparative performances of various detailed technologies belonging to a specified pathway were analyzed. Results indicated that anaerobic mono-digestion decreased global warming and eutrophication remarkably; its integrated management technologies reduced global warming considerably and an obvious decrease in eutrophication potential was observed. It revealed that most of current MSM strategies had limited potential and uncertain consequences to reduce environmental impacts and costs. In terms of influence factors, besides the intrinsic factor (pathway type), key extrinsic determinants including location, country income level, and farm scale were proved to affect mitigation potential of some specific impacts. Overall, it is necessary for the scientific community and policy-makers to focus on more possible trade-offs of different life cycle performances towards sustainability and circularity.

Enhanced control of sulfonamide resistance genes and host bacteria during thermophilic aerobic composting of cow manure

Traditional composting has already shown a certain effect in eliminating antibiotic residues, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs). It is worth noting that the rebounding of ARGs and the succession of the bacterial community during conventional aerobic composting are still serious threats. Considering the probable risk, improved and adaptable technologies are urgently needed to control antibiotic resistance efficiently. This study monitored how thermophilic aerobic composting affected the ARGs, as well as the bacterial diversity during the composting of cow manure spiked with sulfamethoxazole (SMX) at different concentrations. Results showed that the degradation of SMX was enhanced during thermophilic aerobic composting (control > SMX25 > SMX50 > SMX100) and was no longer detected after 20 days of composting. High temperature or heat significantly stimulated the rebounding of certain genes. After 35 days, the abundance of detected genes (sul2, sulA, dfrA7, and dfrA1) significantly decreased (p < 0.05) in control and antibiotic-spiked treatments, except for sul1. The addition of three concentrations of SMX elicited a sharp effect on bacterial diversity, and microbial structure in SMX25 led to significant differences with others (p < 0.05). The network analysis revealed more rigorous interactions among ARGs and abundant genera, suggesting that the host of ARGs potentially increased at low concentrations of SMX. Especially, genera g_norank_f__Beggiatoaceae, Ruminiclostridium, Caldicoprobacter, g_norank_o_MBA03, Hydrogenispora, and Ruminiclostridium_1 were major potential hosts for sul1. In conclusion, the rebounding of ARGs could be intermitted partially, and more efficient control of antibiotic resistance could be achieved in the thermophilic composting compared to conventional methods.

Changes and distributions of antibiotic resistance genes in liquid and solid fractions in mesophilic and thermophilic anaerobic digestion of dairy manure

This study mainly explored the changes and distributions of antibiotic resistance genes (ARGs) in liquid fraction (L_F) and solid fraction (S_F) in anaerobic digestion (AD) of dairy manure. After mesophilic and thermophilic AD, the copy numbers of ARGs in L_F decreased by 0.06-1.80 logs while those in S_F increased by 0.08-7.85 logs, suggesting the enrichment of ARGs in S_F. Statistical analysis elucidated that high total solids promoted the enrichment of ARGs in S_F. The increased abundances of genera such as Ruminofilibacter, Treponema and Sphaerochaeta in S_F were responsible for the enrichment of most ARGs. These insights demonstrated the digested solid had the potential risks to promote the spread of ARGs in the environment, and the digested solid of livestock manure should be post-treated before the application.

Response of Microbial Community to Induced Failure of Anaerobic Digesters Through Overloading With Propionic Acid Followed by Process Recovery

In order to effectively use microbial-based strategies to manage anaerobic digesters, it is necessary to distinguish between community shifts that are part of the natural dynamic of the system and shifts caused by environmental or operational disturbances. The objective of this research study was to evaluate the significance of changes in the microbial community of anaerobic digesters during failure in correlation to operational parameters such as an organic acid overload. Five continuously stirred 0.5 L reactors were set-up as semi-continuously-fed, mesophilic dairy manure digesters with a 30-day hydraulic retention time. After a 120-day stabilization period, two digesters were kept as controls, while the organic loading rates in the triplicate set were increased step-wise to ultimately provide a shock-load leading to failure using propionic acid spikes. Acidosis resulting in near cessation of biogas and termination of methane production occurred between 4 and 7 weeks, after which all the digesters continued to be fed only dairy manure. The shock loading of propionic acid led to an accumulation of mainly acetate and propionate, with low levels of iso-butyrate, butyrate, iso-valerate, and valerate. High-throughput Illumina sequencing of the V4 region of the bacterial and archaeal 16S rRNA gene in digester samples showed a significant change in the microbial community composition during propionic acid overload, followed by a return to the original composition with regular feedstock. Bacterial genera whose relative abundance decreased during the inhibition stage included Sedimentibacter, Syntrophomonas, TSCOR003.O20, and Marinilabiaceae, while the relative abundance of Lachnospiraceae, Ruminococcus, Mogibacteriaceae, Pyramidobacter, and Bacteroides increased. The relative abundance of dominant methanogens, Methanosarcina and Methanobacterium, although initially resistant, were decreased (from 91.71 to 12.14% and from 2.98 to 0.73%, respectively) during inhibition, while Methanobrevibacter and Methanosphaera that were prominent in the manure feedstock increased from 17.36 to 79.45% and from 0.14 to 1.12%, respectively. Shifts in bacterial and archaeal compositions, back to their pre-shock steady state after failure, highlight the digester's microbial resilience and recovery potential.

Manure as a Potential Hotspot for Antibiotic Resistance Dissemination by Horizontal Gene Transfer Events

The increasing demand for animal-derived foods has led to intensive and large-scale livestock production with the consequent formation of large amounts of manure. Livestock manure is widely used in agricultural practices as soil fertilizer worldwide. However, several antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria are frequently detected in manure and manure-amended soils. This review explores the role of manure in the persistence and dissemination of ARGs in the environment, analyzes the procedures used to decrease antimicrobial resistance in manure and the potential impact of manure application in public health. We highlight that manure shows unique features as a hotspot for antimicrobial gene dissemination by horizontal transfer events: richness in nutrients, a high abundance and diversity of bacteria populations and antibiotic residues that may exert a selective pressure on bacteria and trigger gene mobilization; reduction methodologies are able to reduce the concentrations of some, but not all, antimicrobials and microorganisms. Conjugation events are often seen in the manure environment, even after composting. Antibiotic resistance is considered a growing threat to human, animal and environmental health. Therefore, it is crucial to reduce the amount of antimicrobials and the load of antimicrobial resistant bacteria that end up in soil.