Manure hygiene


From Catherine Roy, agr. M.Sc.
Project Manager – Agronomy

Anaerobic biological treatment makes it possible to raw manure by deodorization, stabilization, and dehydration, as well as to sanitize the co-products derived from the initial manure into digestate resulting from biomethanization (MAPAQ, 2020). Temperature, pH, residence time, volatile fatty acids, bacterial species, nutrient availability as well as the initial quantity of pathogens are parameters that can influence the growth of pathogens in anaerobic biological treatment (Sahlström et al. 2003).

Temperatures above 40oC cause a reduction in the growth rate of pathogenic bacteria and many viruses (Sahlström et al. 2003). In mesophilic anaerobic biological treatment, the temperature is maintained at this approximate temperature range, which provides a hygienizing environment against several pathogens. In addition, the longer the retention time inside the digesters, the greater the limitation on the growth of pathogens, and with higher digestate pH, conditions become less favorable for the growth of pathogens. Digestate has a higher pH than the initial feedstock inputs due to production of H+ ions in initial biodigestion stages which is then consumed by methanogenic bacteria to form biomethane, which overall limits the growth of pathogens in the digestate.

In BioÉnertek projects, the mesophilic anaerobic biological treatment has retention times of 40 and 80 days for slurry and solid manure respectively in the digesters, maintained at approximately 40oC (mesophilic). These retention times are supported by hygienization periods presented in literature review effectiveness of anaerobic digestion in the manure sanitation process (Table 1). In mesophilic biomethanation, in addition to the temperature which plays a role on the growth of pathogens, this heat range increases the competition between methanogenic bacteria and pathogens for nutrients, which can help to reduce the latter (Smith et al. 2005).


The study by Coelho et al. (2018), demonstrated that out of 11 mesophilic anaerobic digestion units in the United Kingdom and Ireland, only 1 sample contained Salmonella spp and this at a very low concentration (7 CFU/10g of fresh weight). E. Coli was also found in only 2 samples in very low concentrations, which demonstrates the sanitizing effect of mesophilic biomethanation. In the study by Pandey et al. (2011), to obtain a reduction of more than 90% in the survival rate of E. Coli, the manure must be in mesophilic condition (42°C) for 20 days in an anaerobic digester. Smith et al. (2005) concluded that a residence time of 35 days reduced E. Coli by up to 5.8 log10 at 35oC and 5.7 log10 at 42oC in 9 days. A disappearance below the detection threshold for E. Coli is observed in several other studies in mesophilic anaerobic conditions between 1.8 and 64 days (Olsen et al. 1987; Watcharasukarn et al. 2009; Pandey et al. 2011; Varel et al. 2012; Manyi-Loh et al. 2014, etc.). Regarding coliforms, Varel et al. (2012) demonstrated that these bacteria could have a reduction of up to 3-4 Log10 with a residence time of 3 days in pig and bovine slurry in mesophilic conditions.

Clostridium-type sporulating bacteria are heat resistant. These are bacteria that are found naturally in soil. The studies by Fröschle et al. (2015) and Bagge et al. (2005) demonstrate similar quantities of Clostridium between the initial manure and the digestate. However, in the study by Watcharasukarn et al. (2009), they observed a small reduction of 1.35 log10 after a residence time of 15 days of manure in mesophilic anaerobic condition for Clostridium perfringens and suggest in their discussion to increase the residence time above 20 days and keep the temperature above 70oC in order to obtain a higher log10 reduction.

Mycobacterium avium subsp. paratuberculosis (MAP) is no longer countable after 28 days of retention time in the digesters in the study by Olsen et al. (1985), and after 24 hours in thermophilic mode (≥ 50◦C).


According to Bötner and Behlsam (2012), temperature is the parameter with the greatest impact on animal viruses. In mesophilic conditions, we are talking about a few hours before the viruses are inactivated for porcine enteroviruses (McKain and Hobson, 1987). The longest decimal reduction time is for PPV (porcine parvovirus), requiring 8 days at 55°C and 21 weeks at 35°C to be fully inactivated.

As for highly Pathogenic Avian Influenza virus, it all depends on the strains. In general, this virus is very sensitive to heat, pH, organic matter content, salinity, etc. For the H9N2 strain, 37°C ensures inactivation between 3 to 5 days (Davidson et al. 2010). For H5N1, the inactivation time is approximately 50 days at 30°C (Paek et al. 2010).

The African swine fever virus is highly susceptible to heat. Turner et al. (1998) demonstrate that the viral population declines from 50°C in 24 hours and in a few minutes at 60°C. However, the implementation of good biosecurity management on the farm is essential.

According to Lund et al. 1996, bovine enterovirus needs 23 hours in mesophilic conditions (35oC) and 30 minutes in thermophilic conditions (55oC) to reach the minimum detection threshold in the digestate.


As for parasites, no traces of helminths, cestodes or protozoa were found in the inputs or in the digestate during the mesophilic methanization process in the study by Bonetta et al. (2014). In the study by Pecson et al. (2007), the objective was to count Ascaris suum eggs in biologically treated wastewater. This accounted for a reduction below the detection threshold for a residence time of 12 days at 40oC. In the study by Lee et al. 1988, we see a reduction of the sporulating effect of Eimeria tenella in chicken manure in thermophilic anaerobic digestion (50oC).

Tableau 1

Quantity of pathogens observed in the final product of different biological anaerobic treatments, according to several studies.


It’s a common practice for farms to utilize slurry or manure from external sources to fulfill the nutrient requirements of their fields. The name of the farm which exports the effluent, the type of manure, the quantity and the analyzes in N, P2O5 and K2O are elements present in the Agri-environmental Fertilization Plan (AEFP) are applied to each farm’s fields, including the importation of slurry or manure to supplement nutrients.

Producers’ increasing acquisition and leasing of land have raised the demand for slurry and manure. Consequently, many agricultural producers seek these materials from neighboring farms, leading to the transportation of effluents from one farm to another and posing contamination risks. The quality of the input is pivotal in fostering the growth of pathogenic bacteria, whether it’s the original manure or the resulting digestate. If the initial quality is poor, the output after the anaerobic biological treatment process will likely be subpar or even absent. It underscores the crucial role of robust biosecurity practices at the farm level.


Recontamination of digestate may occur in post-digestion pasteurization processes due to the absence of competition with other bacteria. This absence can encourage the growth of external pathogens, as observed in studies like that by (Bagge et al. in 2005). The return of the digestates to the ground must therefore be done with the same good hygiene practices as the spreading of raw effluents: no grazing before 21 days on plots having received digestate, do not eat or drink on the site of spreading, implement a health control plan on the methanization units.


We can conclude that the mesophilic anaerobic biological treatment of manure and slurry makes it possible to limit the growth of many pathogens, including E.Coli, fecal coliforms, Salmonella spp., particularly because of the high temperature, even in mesophilic conditions ( ± 40oC) and the residence time, the scientific literature can prove it. In addition, the pH of the final result, the competition against methanogenic bacteria (responsible for the production of biogas) and other microorganisms are also parameters influencing the content of these pathogens in the final product (Sahlström et al. 2003). Certain viruses such as porcine parvovirus disappear in a few hours in thermophilic conditions, which should represent a few days in mesophilic conditions (Jiang et al. 2020). Many other studies demonstrate the positive effects of anaerobic digestion on manure hygienization (notably Lin et al. 2022).

We must also keep in mind that agricultural producers import and export slurry and manure with their neighbors (regulated by the PAEF), which was and will always be part of daily life given the deficit in organic fertilizers on certain farms.

The retention times of slurry and liquid manure from BioÉnertek anaerobic biological treatment are long enough to sufficiently reduce the most common pathogenic bacteria, several viruses and even parasites. Conditions are unfavorable for the growth of pathogens in mesophilic conditions, and producers each follow their biosecurity plan to the letter in order to minimize the incidence of pathogens on the farm. On the farm, we must remember that pathogen means disease, and disease means loss of income. Producers know this and are aware of this subject. 


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Bonetta, Si, Ferretti, E., Bonetta, Sa, Fezia, G. and E. Carraro. 2011. Microbiological contamination of digested products from anaerobic co‐digestion of bovine manure and agricultural by‐products. Appl Microbiol. 53, 552–557.

Coelho, J.J., Prieto, M.L., Dowling, S., Hennessy, A., Casey, I., Woodcock, T. and N. Kennedy. 2018. Physical-chemical traits, phytotoxicity and pathogen detection in liquid anaerobic digestates. Waste Manag. 78, 8–15.

Davidson, I., S. Nagar, R. Haddas, M. Ben-Shabat, N. Golender, E. Lapin, A. Altory, L. Simanov, I. Ribshtein, A. Panshin and S. Perk. 2010. Avian Influenza Virus H9N2 Survival at Different temperatures and pHS. Avian Diseases. 54(1 Suppl):725-8.

Kearney, T.E., Larkin, M.J., Frost, J.P. and P.N. Levett. 1993. Survival of pathogenic bacteria during mesophilic anaerobic digestion of animal waste. J Appl Bacteriol. 75, 215–219.

M.R. and J.C. Shih. 1988. Effect of anaerobic digestion on oocysts of the protozoan Eimeria tenella. Appl Environ Microbiol. 54(10):2335-41.

Lin, M., Aijie, W., Lijuan R., Wei, Q., Simon, M.W. and D. Renjie. 2022. Challenges of pathogen inactivation in animal manure through anaerobic digestion: a short review, Bioengineered. 13:1, 1149-1161.

Lund, B., Jensen, V.F., Have, P. and B. Ahring. 1996. Inactivation of virus during anaerobic digestion of manure in laboratory scale biogas reactors. Antonie van Leeuwenhoek. 69:25–31.

Manyi-Loh, C.E., Mamphweli, S.N., Meyer, E.L., Okoh, A.I., Makaka, G., and M. Simon. 2014. Inactivation of selected bacterial pathogens in dairy cattle manure by mesophilic anaerobic digestion (Balloon type digester). Int J Environ Res Public Health. 11(7):7184–7194.

McKain, N. and P.N. Hobson. 1987. A note on the destruction of procine enteroviruses in anaerobic digestions. Biol Wastes. 22:147-155.

Monteith, H., Shannon, E. and J. Derbyshire. 1986. The inactivation of a bovine enterovirus and a bovine parvovirus in cattle manure by anaerobic digestion, heat treatment, gamma irradiation, ensilage and composting. Journal of Hygiene. 97(1):175-184.

Olsen, J.E. and H.E. Larsen. 1987. Bacterial decimation times in anaerobic digestions of animal slurries. Biological Wastes. 21(3):153–168.

Paek, M.R., Lee, Y.J., Yoon, H., Kang, H.M., Kim, M.C., Choi, J.G., Jeong, O.M., Kwon, O.S., Moon, O.K., Lee, S.J. and J.H. Kwon. 2010. Survival rate of H5N1 highly pathogenic avian influenza viruses at different temperatures. Poultry Science 89 :1647–1650.

Pandey, P.K. and M.L. Soupir. 2011. Escherichia coli inactivation kinetics in anaerobic digestion of dairy manure under moderate, mesophilic and thermophilic temperatures. Amb Express. 1(1):18.

Park, J.H., Cheong, H.K., Son, D.Y., Kim, S.U. and C.M. Ha. 2010. Perceptions and behaviors related to hand hygiene for the prevention of H1N1 influenza transmission among Korean university students during the peak pandemic period. BMC Infect Dis. 10. 222.

Pecson, B., Barrios, J., Jiménez, B. and K. Nelson. 2007. The effects of temperature, pH, and ammonia concentration on the inactivation of Ascaris eggs in sewage sludge. Water research. 41. 2893-902.

Sahlstrom, L., 2003. A review of survival of pathogenic bacteria in organic waste used in biogas plants. Bioresour. Technol. 6.

Smith, S.R., Lang N.L., Cheung K.H.M. and K. Spanoudaki. 2005. Factors controlling pathogen destruction during anaerobic digestion of biowastes. Waste Manag. 25 (4):417–425.

Sorlini, C., Allievi, L., Ranalli, G., Ferrari, A. 1987. A note on the removal of fecal bacteria in cattle slurry after different farm and laboratory treatments. Biol. Wastes. 22:39–47.

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Varel, V.H., Wells, J.E., Shelver, W.L., Rice, C.P., Armstrong, D.L. and D.B. Parker. 2012. Effect of anaerobic digestion temperature on odour, coliforms and chlortetracycline in swine manure or monensin in cattle manure. J Appl Microbiol. 112(4):705–715.

Watcharasukarn, M., Kaparaju, P., Steyer, J.P., Krogfelt, K.A. and I. Angelidaki. 2009. Screening Escherichia coli, enterococcus faecalis, and Clostridium perfringens as indicator organisms in evaluating pathogen-reducing capacity in biogas plants. Microb Ecol. 58(2):221–230.

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