Effects of different animal waste treatment technologies on detection and viability of porcine enteric viruses

Biodigestion System Made of Polyethylene and Polystyrene Insulator for Dog Farm (on the Example of the Republic of Chile)

Anaerobic digestion is a system that can have a high environmental impact through the use of different wastes to obtain biogas and its consequent use for the generation of renewable energy. The objective of this study was to implement a polyethylene biodigester, using polystyrene for thermal insulation in a dog kennel, using canine feces collected in the same place during a period of 5 months to obtain biogas and energy. The results indicated that biogas production started on day 30 and stopped during the winter period with low temperatures; therefore, from day 54 onwards, equine manure was added to continue producing biogas. Although biogas was obtained, the biodigester did not function optimally, due to the fact that the materials used in its construction did not provide efficient insulation from the low external temperatures; the low C/N ratio of the canine feces, which led to a reduction in the processing of the methanogenic bacteria; and the low amount of feces collected for use. In general, the use of a biodigester can provide a tool for the biological processing and management of organic waste, yielding a cumulative source of renewable energy and ensuring environmental safety.

Using agro-industrial wastes for the cultivation of microalgae and duckweeds: Contamination risks and biomass safety concerns

Aquatic organisms, such as microalgae (Chlorella, Arthrospira (Spirulina), Tetrasselmis, Dunalliela etc.) and duckweed (Lemna spp., Wolffia spp. etc.) are a potential source for the production of protein-rich biomass and for numerous other high-value compounds (fatty acids, pigments, vitamins etc.). Their cultivation using agro-industrial wastes and wastewater (WaW) is of particular interest in the context of a circular economy, not only for recycling valuable nutrients but also for reducing the requirements for fresh water for the production of biomass. Recovery and recycling of nutrients is an unavoidable long-term approach for securing future food and feed production. Agro-industrial WaW are rich in nutrients and have been widely considered as a potential nutrient source for the cultivation of microalgae/duckweed. However, they commonly contain various hazardous contaminants, which could potentially taint the produced biomass, raising various concerns about the safety of their consumption. Herein, an overview of the most important contaminants, including heavy metals and metalloids, pathogens (bacteria, viruses, parasites etc.), and xenobiotics (hormones, antibiotics, parasiticides etc.) is given. It is concluded that pretreatment and processing of WaW is a requisite step for the removal of several contaminants. Among the various technologies, anaerobic digestion (AD) is widely used in practice and offers a technologically mature approach for WaW treatment. During AD, various organic and biological contaminants are significantly removed. Further removal of contaminants could be achieved by post-treatment and processing of digestates (solid/liquid separation, dilution etc.) to further decrease the concentration of contaminants. Moreover, during cultivation an additional removal may occur through various mechanisms, such as precipitation, degradation, and biotransformation. Since many jurisdictions regulate the presence of various contaminants in feed or food setting strict safety monitoring processes, it would be of particular interest to initiate a multi-disciplinary discussion whether agro-industrial WaW ought to be used to cultivate microalgae/duckweed for feed or food production and identify most feasible options for doing this safely. Based on the current body of knowledge it is estimated that AD and post-treatment of WaW can lower significantly the risks associated with heavy metals and pathogens, but it is yet unclear to what extent this is the case for certain persistent xenobiotics.

Monitoring Survivability and Infectivity of Porcine Epidemic Diarrhea Virus (PEDv) in the Infected On-Farm Earthen Manure Storages (EMS)

In recent years, porcine epidemic diarrhea virus (PEDv) has caused major epidemics, which has been a burden to North America’s swine industry. Low infectious dose and high viability in the environment are major challenges in eradication of this virus. To further understand the viability of PEDv in the infected manure, we longitudinally monitored survivability and infectivity of PEDv in two open earthen manure storages (EMS; previously referred to as lagoon) from two different infected swine farms identified in the province of Manitoba, Canada. Our study revealed that PEDv could survive up to 9 months in the infected EMS after the initial outbreak in the farm. The viral load varied among different layers of the EMS with an average of 1.1 × 10⁵ copies/ml of EMS, independent of EMS temperature and pH. In both studied EMS, the evidence of viral replication was observed through increased viral load in the later weeks of the samplings while there was no new influx of infected manure into the EMS, which was suggestive of presence of potential alternative hosts for PEDv within the EMS. Decreasing infectivity of virus over time irrespective of increased viral load suggested the possibility of PEDv evolution within the EMS and perhaps in the new host that negatively impacted virus infectivity. Viral load in the top layer of the EMS was low and mostly non-infective suggesting that environmental factors, such as UV and sunlight, could diminish the replicability and infectivity of the virus. Thus, frequent agitation of the EMS that could expose virus to UV and sunlight might be a potential strategy for reduction of PEDv load and infectivity in the infected EMS.

Utility of specific biomarkers to assess safety of swine manure for biofertilizing purposes

Swine production is an important economic activity in Brazil, and there is interest in the development of clean production mechanisms to support sustainable agro-industrial activities. The biomass derived from swine manure has good potential to be used as a biofertilizer due to its high nutrient concentration. However, the land application of manure should be based on safety parameters such as the presence of pathogens that can potentially infect animals and people. This study was designed to assess the presence of porcine circovirus-2 (PCV2), porcine adenovirus (PAdV), rotavirus-A (RV-A) and Salmonella spp. in liquid manure, as well the infectivity of two genotypes of circovirus-2 (PCV2a and PCV2b) present in liquid manure. Three swine farms were evaluated: 1) a nursery production farm (manure analyzed before and after anaerobic biodigestion), 2) a grow-finish production farm (analyzed before and after anaerobic biodigestion), and 3) a second grow-finish production farm (raw manure-affluent). PCV2, PAdV and RV-A were present before and after anaerobic biodigestion (either affluent or effluent) at all farms. Salmonella spp. were detected at farm 1 (affluent and effluent) and farm 3 (raw manure-affluent) but not farm 2 (affluent and effluent). When the ability of the anaerobic biodigestion process to reduce viral concentration was evaluated, no significant reduction was observed (P>0.05). Both the PCV2a and PCV2b genotypes were detected, suggesting viral co-infection in swine production. The results revealed infectious PCV2 even after anaerobic biodigestion treatment. The presence of Salmonella spp. and enteric viruses, especially infectious PCV2, in the final effluent from the anaerobic biodigester system suggests that the process is inefficient for pathogen inactivation. Due to the prevalence and infectivity of PCV2 and considering the successful use of molecular methods coupled to cell culture for detecting infectious PCV2, we suggest that this virus can be used as a bioindicator in swine manure treatment systems to check the efficiency of pathogen inactivation and ensure the production of safe biofertilizers from swine manure.

Detection of hepatitis E virus (HEV) through the different stages of pig manure composting plants

Hepatitis E virus (HEV) is an increasing cause of acute hepatitis in industrialized countries. The aim of this study was to evaluate the presence of HEV in pig manure composting plants located in Spain. For this purpose, a total of 594 samples were taken in 54 sampling sessions from the different stages of composting treatment in these plants as follows: slurry reception ponds, anaerobic ponds, aerobic ponds, fermentation zone and composting final products. HEV was detected by reverse transcription polymerase chain reaction (RT-nested PCR) in four (80%) of five plants studied, mainly in the first stages of the process. HEV was not detected in any final product (compost) sample, destined to be commercialized as a soil fertilizer, suggesting that composting is a suitable method to eliminate HEV and thus, to reduce the transmission of HEV from pigs to humans.

Performance of two swine manure treatment systems on chemical composition and on the reduction of pathogens

Swine effluents must be correctly handled to avoid negative environmental impacts. In this study, the profiles of two swine manure treatment systems were evaluated: a solid-liquid separation step, followed by an anaerobic reactor, and an aerobic step (System 1); and a biodigester followed by serial lagoons (System 2). Both systems were described by the assessment of chemical, bacterial and viral parameters. The results showed that in System 1, there was reduction of chemicals (COD, phosphorus, total Kjeldhal nitrogen - TKN - and NH(3)), total coliforms and Escherichia coli; however, the same reduction was not observed for Salmonella sp. Viral particles were significantly reduced but not totally eliminated from the effluent. In System 2, there was a reduction of chemicals, bacteria and viruses with no detection of Salmonella sp., circovirus, parvovirus, and torque teno virus in the effluent. The chemical results indicate that the treated effluent can be reused for cleaning swine facilities. However, the microbiological results show a need of additional treatment to achieve a complete inactivation for cases when direct contact with animals is required.

The fecal virome of pigs on a high-density farm

Swine are an important source of proteins worldwide but are subject to frequent viral outbreaks and numerous infections capable of infecting humans. Modern farming conditions may also increase viral transmission and potential zoonotic spread. We describe here the metagenomics-derived virome in the feces of 24 healthy and 12 diarrheic piglets on a high-density farm. An average of 4.2 different mammalian viruses were shed by healthy piglets, reflecting a high level of asymptomatic infections. Diarrheic pigs shed an average of 5.4 different mammalian viruses. Ninety-nine percent of the viral sequences were related to the RNA virus families Picornaviridae, Astroviridae, Coronaviridae, and Caliciviridae, while 1% were related to the small DNA virus families Circoviridae, and Parvoviridae. Porcine RNA viruses identified, in order of decreasing number of sequence reads, consisted of kobuviruses, astroviruses, enteroviruses, sapoviruses, sapeloviruses, coronaviruses, bocaviruses, and teschoviruses. The near-full genomes of multiple novel species of porcine astroviruses and bocaviruses were generated and phylogenetically analyzed. Multiple small circular DNA genomes encoding replicase proteins plus two highly divergent members of the Picornavirales order were also characterized. The possible origin of these viral genomes from pig-infecting protozoans and nematodes, based on closest sequence similarities, is discussed. In summary, an unbiased survey of viruses in the feces of intensely farmed animals revealed frequent coinfections with a highly diverse set of viruses providing favorable conditions for viral recombination. Viral surveys of animals can readily document the circulation of known and new viruses, facilitating the detection of emerging viruses and prospective evaluation of their pathogenic and zoonotic potentials.

Fate and transport of zoonotic, bacterial, viral, and parasitic pathogens during swine manure treatment, storage, and land application

Members of the public are always somewhat aware of foodborne and other zoonotic pathogens; however, recent illnesses traced to produce and the emergence of pandemic H1N1 influenza virus have increased the scrutiny on all areas of food production. The Council for Agricultural Science and Technology has recently published a comprehensive review of the fate and transport of zoonotic pathogens that can be associated with swine manure. The majority of microbes in swine manure are not zoonotic, but several bacterial, viral, and parasitic pathogens have been detected. Awareness of the potential zoonotic pathogens in swine manure and how treatment, storage, and handling affect their survival and their potential to persist in the environment is critical to ensure that producers and consumers are not at risk. This review discusses the primary zoonotic pathogens associated with swine manure, including bacteria, viruses, and parasites, as well as their fate and transport. Because the ecology of microbes in swine waste is still poorly described, several recommendations for future research are made to better understand and reduce human health risks. These recommendations include examination of environmental and ecological conditions that contribute to off-farm transport and development of quantitative risk assessments.

Inactivation of murine norovirus 1 and Bacteroides fragilis phage B40-8 by mesophilic and thermophilic anaerobic digestion of pig slurry

Mesophilic (37 degrees C) and thermophilic (52 degrees C) anaerobic digestion of pig slurry induced at least a 4-log decrease in murine norovirus 1, used as a surrogate virus for porcine norovirus, after 13 and 7 days, respectively. Bacteroides fragilis phage B40-8, employed as a universal viral model, was lowered by 2.5 log after 7 days. The viral titer declined due to temperature and matrix effects.

Removal of viruses and indicators by anaerobic membrane bioreactor treating animal waste

Appropriate treatment of agricultural waste is necessary for the protection of public health in rural areas because land-applied animal manure may transmit zoonotic disease. In this study, we evaluated the potential of using a pilot anaerobic membrane bioreactor (AnMBR) to treat agricultural waste. The AnMBR system, following a conventional complete mix anaerobic digester (CMAD), achieved high removals of biological and chemical agents. The mean log(10) removals of Escherichia coli, enterococci, Clostridium perfringens, and coliphage by the AnMBR were 5.2, 6.1, 6.4, and 3.7, respectively, and for the CMAD were 1.5, 1.2, 0.1, and 0.5, respectively. Compared with other indicators, coliphage was observed most frequently and had the highest concentration in effluent samples. Bovine adenoviruses and bovine polymaviruses (BPyV) were monitored in this study using nested PCR methods. All of the CMAD influent and CMAD effluent samples were positive for both viruses, and three AnMBR effluent samples were BPyV positive. The mean removals of total Kjeldahl nitrogen, total phosphate, chemical oxygen demand, total solids, and volatile solids by the entire system were 31, 96, 92, 82, and 91%, respectively, but there was no removal of ammonium. When the AnMBR was operated independent of the CMAD, AnMBR achieved similar E. coli and enterococci removals as the combined CMAD/AnMBR system. The high quality of effluent produced by the pilot AnMBR system in this study demonstrated that such systems can be considered as alternatives for managing animal manure.