Manure treatments that reduce microbiological load

Although live animals are the focus of livestock farming, the process of raising stock for food is not fundamentally different to any other manufacturing process.  In essence, raw materials in the form of young animals, water and feed are converted over time to finished livestock.  A major waste product of the farming process is livestock manure, and like any other process waste, it has to be disposed of in a manner which does not cause chemical or biological pollution of the environment.  Traditionally, livestock wastes have been cost-effectively disposed of by spreading onto agricultural land.  For some soil types, it has been claimed that there are benefits in terms improved soil structure.  It is without question that short-term quantifiable increases to the soil concentrations of fertilizer chemicals can occur as a consequence of waste spreading.  However, after the Second World War, livestock farming in Western Europe became greatly more intensive (Strauch and Ballarini, 1994).  Consequently, it became apparent that unless care was taken to restrict the masses of waste being spread, eutrophication (pollution with chemicals such as phosphorus and nitrates from the waste) of watercourses could occur.  Since the effects of chemical contamination are highly visible, initial efforts to contain the pollution associated with the land spreading of livestock wastes focused on reducing chemical damage to the environment.  Unfortunately however, it became apparent in the 1990s that consideration of chemical pollution in isolation from biological (and in particular microbiological) damage was not an effective strategy. Frequently, what is good for reducing chemical pollution, promotes enhanced microbiological survival.  Furthermore, what is effective for rapidly reducing microbiological populations causes increased chemical contamination (particularly of the air).  Hutchison et al. 2005 likens the chemical and microbiological considerations of manure disposal to a see-saw with chemistry on one side of the pivot and microbiology on the other.  What is done to reduce the pollution from one end of the see-saw, causes increases to the other side of the pivot.  Table 1 below shows in more detail how some common manure disposal and treatment processes impact on chemical and microbiological concerns.

Table 1  Common manure disposal and treatment processes their impact on chemical and microbiological pollution concerns


Effect on chemical pollution

Effect on microbiological pollution

Turning FYM heaps

Enhanced air pollution

Reduced microbial survival

Stirring slurry tanks

Enhanced air pollution

Reduced microbial survival

Heating slurry

Enhanced air pollution

Reduced microbial survival

Injection of slurry into soil

Reduced chemical pollution

Enhanced microbial survival

Band spreading of slurry

Reduced chemical pollution

Enhanced microbial survival

Leaving 1 week between FYM spreading and soil incorporation

Enhanced chemical pollution

Reduced microbial survival

There are a number of balanced and effective treatment methods which can be used to rapidly and cost-effectively lower the numbers of microorganisms in manures prior to their disposal by land spreading without significantly impacting on chemical pollution.  However, its is stressed that it is unlikely that any of the treatments listed below will reduce bacterial counts to below the detection limits of standard microbiological test protocols.  The treatments below will all make a significant impact on the microbiological risks associated with waste disposal by land spreading.  Please note that there are additional concerns (and laws) relating particularly to nitrate pollution of water courses, and greenhouse gas emissions during treatment that should be considered in conjunction with the microbiological advantages of manure treatment prior to disposal.

Simple storage

Pathogens contained within livestock manures will decline naturally with time.  Given enough time, even without active treatment, all of the microbes contained within a batch of waste will disappear.  The principal challenge to farmers relating to manure storage in the UK is the number and capacity of manure storage they have.  In order for pathogen populations to decline, the manure has to be batch stored without further introductions of waste (which contain fresh nutrients and more microorganisms).  In the UK, most farms only have a single slurry store.  That means batch storing of slurry for periods long enough to cause meaningful pathogen decline is unlikely.  It is more likely that FYM heaps can be stored as discrete batch piles, although prevention of pollution from heap leachate and vermin control mean such practices are rare in practice.  Simple batch storage for 6 months to 1 year is an exceptionally safe method for the treatment of manure which has very limited impact on greenhouse gas emissions or watercourse pollution.

Aerobic digestion

There is some evidence to suggest that active aeration of both slurry and farmyard manure (FYM) decreases pathogen levels compared with non-aerated slurry.  A 90% reduction in Salmonella numbers occurred in between 2 and 4 weeks in anaerobically stored cattle slurry.  A similar reduction was achieved in less than 2 days when the slurry was aerated (Jones and Matthews, 1975). Aeration also reduced the numbers of Campylobacter in dairy slurry (Stanley et al., 1998).  Aeration of farm-scale slurry tanks stored in winter increased temperatures to between 19oC and 40oC over ambient temperature thereby reducing Salmonella levels by over 99% in 2-5 weeks for cattle slurry contaminated with Salmonella Infantis. A similar effect was observed for pig slurry contaminated with S. Typhimurium, Yersinia, Listeria, faecal coliforms, enterococci and coliphages (Heinonen-Tanski et al. 1998). 

It is estimated that up to 10% of pig slurry in the UK is aerobically treated, but few installations exist to treat cattle slurry (Williams, 1989). The design of aeration systems varies enormously, although most systems have a degree of control over running time and cost. A number of agitation systems using relatively small amounts of air to mix slurry at intervals have been installed, but are unlikely to achieve effective oxygenation throughout all of the stored slurry. Therefore, there is no guarantee that existing systems would achieve the conditions required to achieve effective pathogen control.  As for anaerobic digestion, the majority of the livestock industry is excluded on a cost basis from installing effective aeration equipment.

One of the simplest and most cost-effective treatments that can reduce bacterial populations in livestock wastes is the composting of FYM.  At its simplest, the process involves arranging the waste material in heaps or windrows (cigar-shaped heaps) and periodically aerating the wasted by turning it.  If required, water is added to prevent excessive drying of the waste.  The simple process initially encourages bacterial proliferation which in turn generates metabolic heat inside the heaps.  The temperatures achieved can exceed 65oC which is high enough to cause bacterial death.  There is a danger that human pathogens on the outer edges of composting heaps are ineffectively killed because the temperatures there are lower than those achieved in the centre of the heap.  The most cost effective way to combat this hazard is periodic targetted turnings to redistribute the bacteria in these outer locations to a more central position for a second heating phase. Chai et al. (2009) report that composted manure on one farm contained lower numbers of campylobacters compared with unmanaged manure on another farm of similar age and in a similar location. 

Figure 1  Elongated heaps of farmyard manure (FYM) can be cost-effectively treated by turning and watering periodically to promote heating which causes effective bacterial kill

Anaerobic digestion

Anaerobic digestion involves the breakdown of the organic compounds in livestock waste (principally slurries) in the absence of oxygen (Figure 2).  Effective digestion typically takes around one month.  The effectiveness of anaerobic digestion at reducing pathogen numbers has been found to depend largely on temperatures achieved in the slurry (Bendixen 1999). A study of pathogen reduction in 10 large-scale Danish Biogas plants indicated that for mesophilic (mid temperature) systems, pathogen reduction was modest (around 10x or 100x reduction), whereas thermophilic (high temperature) plants were capable of achieving a x10000 reduction (Bendixen 1999). Similar investigations in Germany confirmed that either a thermophilic process or pasteurisation at 70oC for one hour was necessary to inactivate pathogens (Böhm et al. 1999). These findings mirror closely those of UK surveys on mesophilic digestion of sewage sludge where an average log10 reduction of two units was observed (UKWIR 1999 a, b). A study on the inactivation of viruses in animal slurries concluded that fermentation at or above 55oC was the most important factor, and that thermophilic processes were also likely to kill the majority of viruses (Pesaro et al 1999).  

Figure 2  A schematic diagram demonstrating the operation of an anaerobic digestion tank. (Image is provided courtesy of the Holly WasteWater Treatment Plant)

Whilst anaerobic digestion is proven technology which has been available for 30 years, uptake in the UK has been minimal and restricted to enthusiastic farmers or those sites with specific factors, such as the need for odour control or a direct need for the biogas produced. Initial setup costs are the initial barrier to implementation.  A study carried out in 1993 indicated that there were less than 50 digesters in the whole of the UK of which only 23 were confirmed to be functional at the time. Since then, a small number of additional digesters have been installed but significant numbers of the original 43 have fallen into poor repair.  The digesters no longer in use includes the large pilot-model digester at Hanford Farms (Dorset) which harvested the biogas generated as a side product and used it to supply electricity to the National Grid.  It is challenging to setup and operate a thermophilic anaerobic digestion, which would be required to provide a complete solution to the problem of human pathogens in slurry.  Furthermore, the significant capital costs involved in equipping farms with digesters would be difficult for the livestock industry to finance given the low profitability upon which most units operate. Based on the volumes of livestock slurry produced (Pain, 1998) for individual farm scale digesters the total UK capital investment required would be around £1,300 million for cattle slurry and £100 million for pig slurry. 

Lime treatment

Calcium hydroxide (lime) is widely used in the UK as a soil pH neutraliser in those areas that have a strongly acidic soil (e.g. parts of the Scottish Highlands).  However, lime can also be used to treat animal wastes, reducing pathogen numbers (Derbyshire and Brown, 1979; Mohaibes and Heinonen-Tanski, 2004).  Manure liming also has an advantage of reducing odours associated with wastes before their disposal. The advantages of lime treatment are that resultant can be easily disposed of, and it is inexpensive, and it would be already in use as a slurry stabilisation treatment, so reducing the requirements for developing a new treatment plant for pathogen control (Haas et al., 1995).


Chai, L.C., Ghazali, F.M., Bakar, F.A., Lee, H.Y., Suhaimi, L.R.A., Talib, S.A., Nakaguchi, Y., Nishibuchi, M. and Radu, S. (2009) Occurrence of thermophilic Campylobacter spp. contamination on vegetable farms in Malaysia. Journal of Microbiology and Biotechnology 19, 1415-1420. 

Derbyshire, J. B. and Brown, E. G. 1979. The inactivation of viruses in cattle and pig slurry by aeration or treatment with calcium hydroxide. J. Hygiene 82, 293–299.

Mohaibes, M. and Heinonen-Tanski, H. (2004) Aerobic thermophilic treatment of farm slurry and food wastes. Bioresource Technology 95, 245–254

Strauch,D. and Ballarini,G. 1994. Hygienic aspects of the production and agricultural use of animal wastes. Journal of Veterinary Medicine Series B-Zentralblatt fur Veterinarmedizin Reihe B-Infectious Diseases and Veterinary Public Health 41, 176-228.  (reference is too old to be available electronically).