Chapter five: Environmental pollution and pathogen control

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Environmental pollution
The need for decontamination
The role of blogas in improving rural development, environment and ecology.


Environmental pollution

The rapid growth of the world population in the past decades has resulted in two factors that are particularly relevant to us here: increased urban wastes and the intensification of agriculture.

The first has led to the creation of toxic wastelands; the second to an increase in agricultural waste products, which represent wasted resources, as well as leaching pesticides and chemical fertilizers into the soil. Both of them contribute to a new menace, whose scale is giving rise to a crisis that is on a par with the food production crisis of the 50s and 60s: the contamination of water, both surface sources and ground water. In many parts of the world, a shortage of drinking water is an actual problem, or threatens to become one very soon. It is worth noting that this problem is not dependent on the state of the affected country's development.

It is not our purpose here to discuss questions of water conservation, but to point to the contribution that anaerobic digestion can make towards a solution to the problem of land and water pollution.

The conversion of wastes to harmless and useful products can provide at least a partial answer to urban pollution, while at the same time relieving the pressure on ground water threatened by pollution. The replacement of chemical fertilizers, soil conditioning and the recycling of waste products represent the contribution of the rural sector. Fewer harmful substances will leach into the soil, and from there into sources of drinking water, while the water holding properties of the soil will be improved, saving irrigation water and thereby reducing seepage. It is, of course, well established that agriculture must limit itself to wastewater for irrigation, but even this wastewater must, in the long run, be treated to render it less pathogenic.

While the present state of development of anaerobic digestion does not offer a complete solution to land and water pollution, it already provides a partial answer, and may be the key to the solution of a problem that has overtaken that of food shortage on a world-wide scale, now and in the immediate future.


The need for decontamination

Waste products of farms, such as animal and human manures, straw and cotton wastes, as well as wastes of cattle and pig slaughtering (the manure of animals in the pre-slaughter period, the contents of the intestinal tract and other organic solids) are highly contaminated with pathogenic microorganisms and are therefore hazardous to animals and humans. When examined, pathogenic microorganisms are frequently found in the excrete of farm animals, and include enteric bacteria, fungal spores, parasite eggs and some hardy viruses. Through the practices of waste disposal by land application, these microorganisms may contaminate equipment, soil and surface water. The transmissions of pathogens present a potential threat to the health of farm workers and consumers, as well as farm animals. Prophylactic treatments, such as medication and sanitation, can help control pathogens. However, these treatments are increasingly expensive, and decreasingly effective, because drug resistance can develop in microorganisms. A mute treatment process is needed that will destroy pathogens and consequently protect environmental health. This is important, not only in the Developing Countries, where sanitary practices are inadequate, but also in the Developed Countries where animal production is so intensive that animal wastes are generated at high rates (Klinger 1986; White 1982; Shih 1988). Several papers and guidelines have been published, concerning different methods of handling manure and environmental hazards, by the FAO Network on Animal Waste Utilization.

Slaughterhouses are, inter alia, terminal stations for diseased animals. Usually sufficient care is taken to avoid a health risk to consumers of the animal products themselves, but very few precautionary measures are reported in the literature (Grant 1980) to avoid the spread of infective agents through these solid wastes. The waste of slaughterhouses is usually flushed into the municipal sewage purification system (Irmer and Belting 1984), where it creates a severe problem, due to the very high biological oxygen demand (BOD) and chemical oxygen demand (COD). Some authors consider that a slaughterhouse which processes 100 head of cattle daily produces sewage with BOD equivalent to a town of 40,000 50,000 people (Klinger 1986).

This is where a decontamination method to safeguard environmental health is necessary, particularly when dealing with a food producing establishment. Anaerobic methanogenic fermentation is an attractive method for this purpose, as it converts the waste materials into useful products. Changes in the microbiological content of the fermented material, and uses of the residual materials are discussed here.

Strict hygienic measures have to be taken in order to protect human health in the operation of slaughterhouses. Intestinal content, particularly rumen contents and the excreta of the animals, create a nuisance for sewage purification systems. Anaerobic methanogenic thermophilic digestion (Klinger and Marchaim 1987) has proved itself, not only as a process which converts part of this material into useful substances, but also as a decontamination process. The anaerobic thermophilic process reduced coliforms by 6 - 7 logarithmic units, and Salmonellae to below the regular detection level. In several cases, Salmonellae were present in the material loaded into the digester, but was reduced to below the detection level by the thermophilic fermentation.

Anaerobic digestion is both a resource and an environmental biotechnology. In the treatment of animal waste, it produces biogas as an energy source, while the digested slurry is used as a fertilizer or a feed. It decomposes organic waste to reduce environmental pollution and also destroys pathogenic microorganisms, protecting human and animal health. The multiple benefits of the system have been demonstrated on the basis of diverse waste digesters, both at North Carolina State University (Steinsberger & Shih 1984; Steinsberger et al. 1987; Shih 1987b; Shih 1988; Jiang et al. 1988), and on some Kibbutzim in Israel. By integrating the multiple benefits around the technology, a concept was proposed of holistic farming, as a new agricultural ecosystem (Marchaim 1983; Shih 1985; Shih 1987a). However, holistic farming on a large scale in Developing Countries is yet to be assessed and implemented.

The results of a series of studies, conducted in several countries to establish the role of poultry and cow waste digesters in the control of different types of microbial pathogens, are reported. The fate of pathogenic microorganisms, including Salmonellae, faecal coliforms, fungi , protozoan oocysts and viruses, in poultry waste anaerobic digesters has been studied (Shih 1988). The digesters were operated in the laboratory at thermophilic (50C) and mesophyllic (35C) temperatures. When comparing the influent (manure slurry) and effluent samples, it was found that faecal coliforms including Salmonellae were completely destroyed in the 50C digester in 24 furs, and reduced by 50 - 70% at 35C. Reductions of fungi were close to 100% at 50C and 95% at 35C. The digesters were inoculated with oocysts of Eimeria tenella. After 24 furs, oocysts were recovered and tested in vitro for sporulation and for infectivity, in young chicks. The thermophilically treated oocysts lost all their infectivity, while the mesophylically treated remained 40% infective. Marek's disease virus (MDV) was incubated anaerobically with digester fluid at 50C. After 24 furs, isolation of MDV was attempted by centrifugation and its presence tested for by DNA hybridization with 32p-labelled MDV gene probe, prepared from a gene library, cloned in plasma-cd pBR328. No MDV DNA was detected by dot-blot hybridization. Evidently MDV were destroyed, and its DNA disappeared. In conclusion, a broad spectrum of microbial pathogens can be destroyed by anaerobic digestion, especially at thermophilic temperatures. Although the pathogens studied were related to poultry diseases, it is believed that the digestion process will also kill pathogens causing human diseases.

Enteric bacteria: Many pathogenic bacteria, including Salmonellae, Enterobacterium, were found associated with poultry, pig and cow waste samples (Alexander et al. 1968; Kraft et al. 1969; Smith et al. 1978; Shih 1988; Klinger and Marchaim 1987). These bacteria in poultry waste can be a source of contamination of poultry houses, equipment and runoff water (Kraft et al. 1969; Coker 1983; Khaleel et al. 1980; Thelin & Gifford 1983). It is of great concern that the contamination can be carried over to the final poultry product destined for consumers. The reduction of these pathogenic bacteria on the farm will not only protect the health of a poultry farm environment, but also protect the health of consumers by reducing the incidence of food contamination.

Shih (1988) compared the effects of mesophyllic (35C) and thermophilic (50C) poultry waste digesters on faecal coliforms including Salmonellae. Fresh manure samples collected from a commercial egg farm were used to prepare the slurry for daily feeding of laboratory digesters. The digester influent (manure slurry) and effluent were sampled and the most probable number of Salmonella was examined (McCoy 1962). No bacterial growth on the plate was detected from the effluent of a thermophilic digester, but numerous colonies of presumptive coliforms were observed from that of a mesophyllic digester (Shih 1988). In the influent, there was an average of 1.9x105 presumptive total coliforms and 14.4 Salmonellae per 100 ml. In the effluents, there were 6.5x104 coliforms (66% reduction) and 7.0 Salmonellae (51% reduction) per 100 ml from the mesophyllic digester, but none at all were detected from the thermophilic digester.

For the examination of cow manure and slaughterhouse wastes, microbial counts were performed according to a standard method (Klinger et al. 1986). The following parameters were calculated and analyzed: total aerobic mesophyllic bacteria (TAM); total anaerobic mesophyllic bacteria (TAnM); total aerobic thermophilic bacteria (TAT); total coliform bacteria; sulphite reducing clostridia (S. Red. Cl.), and the presence of Salmonellae. Counts of bacteria were performed in duplicate. The figures presented in Table 5.1 are the mean of decimal logarithms of two counts each. Thermophilic anaerobic fermentation was selected to treat slaughterhouse wastes, because it was hoped to eliminate Salmonellae and reduce pathogenic bacteria populations. As evident from Table 5.1, there was a reduction of several orders of magnitude in coliform bacteria and, in most cases, total elimination of Salmonellae. Where fermentation was unstable or incomplete, an immediate increase of coliforms occurred, and in some cases survival of Salmonellae was observed. Few changes were observed in other bacterial parameters examined. Sulphite reducing clostridia usually survived in up to 103 colony forming units (CFU) per ml.

This material was also examined for its bacterial population after a month of composting. Bacterial content was similar to that of slurry (Table 5.1), but in all cases except one no Salmonellae were detected, and coliforms were reduced to below the detection level. In the one exceptional sample, a positive reaction for Salmonella was found in the fresh Peatrum used for the mushroom production.

Table 5.1: Changes in bacterial population before and after AMTD of rumen content and cow manure loaded into pilot plant.


Logarithms of bacterial count

Material loaded

Digested Slurry output

mean upper lower mean upper lower
T.A.M 6.41 7.70 5.95 5.87 6.00 5.78
T.A.T. 5.66 5.84 5.30 5.11 6.84 <5.00
T.An.M. 7.04 7.48 5.60 5.69 7.00 5.00
S.Red.Cl. 2.78 3.48 2.30 <2.00 3.00 <1.00
Coliforms 6.38 6.86 5.30 <2.30 3.00 <1.00
pH 7.10 7.50 6.50 7.46 7.60 7.20

Fungi: Many moulds, including both pathogenic and toxigenic ones, have been found in poultry, cow, pig and other wastes. They are the species of Asperaillus, Penicillium, Candida, Fusarium, Mucor, etc. Fungal spores and mouldy feeds are the main sources of contaminations. Little work has focused on the fate of fungi in animal waste treatment processes, but they were found in various sludges and effluents from municipal waste treatment plants (Butler 1960; Cooke 1965b). Two studies demonstrated that decreased crop yields could be traced to phytopathogenic fungi in sewage water used to irrigate the fields (Butler 1960; Cooke 1971). Only one study was reported on seeding pathogenic fungus into an anaerobic digester and following its viability. A 99% loss of the viability of the spore of Fusarium oxysporum was detected after 28 hours in a mesophyllic anaerobic digester (Turner et al. 1983).

In Shih's laboratory the effects of mesophyllic and thermophilic anaerobic poultry waste digesters on the resident fungi in poultry manure were studied (Woollens 1987). Destruction of fungi and fungal spores during digestion was assessed by comparing colony counts of influent and effluent of the digester. The numbers of fungi or fungal spores in the influent varied from sample to sample, but they were all drastically reduced in both digesters. In the mesophyllic digester, the reduction rate averaged 95%, and in the thermophilic digester, 99.8%.

Protozoa Parasitic protozoa, nematodes, cestodes and helminths are also of concern in waste treatment. Most of these organisms have a life cycle that includes a stage in which they are resident in the animal gut, and are thus often present in animal waste. Generally speaking, the cysts of the protozoa such as Entamoeba and Gtardia are inactivated by anaerobic digestion. The eggs of parasites such as Ascaris, Toxocara, Toxascaris and Trichuris are more resistant (Leftwich et al. 1981; Black et al. 1982; Coker 1983; Olsen 1984). The effectiveness of anaerobic digestion in destroying cysts and eggs is dependent on time and temperature. Anaerobic digestion can retard egg development, due to the lack of oxygen. Increasing temperature enhances the destruction or inactivation of parasite eggs. Anaerobic treatment at 60C for land application was recommended (Hays 1977). In China an improvement in public health in some rural areas has been reported, after a large number of digesters were installed in the 70s (Zhao 1985).

TABLE 5.2: Decrease of Fungal Counts in Digested Poultry Waste



Influent Effluent (%)
Exp. 1 5,386 235 96.6
2 4,586 403 91.2
3 13,314 396 97.0
Exp. 1 1,529 1 99.9
2 1,671 10 99.4
3 386 0 100.0

Coccidiosis caused by the protozoan Eimeria species is one of the most prevalent diseases of poultry. An important factor in the epidemiology of coccidiosis is the survival of oocysts which are shed in the excrete of infected hosts. A waste treatment process which destroys oocysts will interrupt the life cycle of coccidia, and thus prevent the disease (Fayer and Reid 1982). The effects of mesophyllic and thermophilic anaerobic digestion on the survival and infectivity of the oocysts of Eimeria tenella were studied by Shih (1985, 1988) and Lee and Shih (1988). Active oocysts, collected from the faecal contents of infected chicks, were found to be badly damaged after thermophilic (50C) digestion: unable to sporulate and non-infective to young chicks. On the other hand, oocysts after mesophyllic digestion were still moderately infective.

Viruses Viral pathogens present a formidable challenge to the development of waste treatment processes. Human enteric viruses are nearly always present in sewage, and remain active in many conventional-treatments (Ward & Ashley 1976). One can predict that viruses affecting animals are present in animal waste, though little work has been done in this area. Some viruses, in their free form, are able to remain active in nature for long periods. Viruses also migrate freely in ground water. There is a potential for ground water contamination resulting from land application of waste material. Several studies have shown that human viruses such as Coxsachievirus, Poliovirus, Echovirus, and several other enteric viruses are substantially inactivated during anaerobic treatment, especially at thermophilic temperatures (Ward and Ashley 1976; Eisenhardt et al. 1977; Berg and Berman 1980). ard and Ashley (1976) listed four major factors involved in viral inactivation. They are temperature, ammonia concentration, pH, and presence of ionic detergents. The propensity of viruses to adsorb to solids in wastes is a major protective factor and prolongs their survival time when subjected to treatment processes. As anaerobic digesters are applied in agricultural waste treatment, more investigations should be conducted to determine the fate of animal viruses in these systems. Diagnostic methods for MDV infection, for instance, have been developed in some laboratories (Pyrzak and Shih 1987; Xi et al. 1986).


The role of blogas in improving rural development, environment and ecology.

In China, anaerobic digestion is an important way of making use of biomass resources, achieving a number of benefits through biogas technology, in the production of energy, the protection of the environment and improvement of the ecology. China's use of biogas technology has attracted attention in many other countries.

A biogas digester connected with a latrine and pigsty was developed in 1973, and since then many such digesters have been built in rural areas of China. Manure flows into the digester automatically, reducing exposure and loss into the air and improving environmental sanitation. Human excrete are also washed from the latrine, directly into the biogas digester. An effective way has been found to solve the problems of environmental sanitation of cities and rural areas, through biogas technology. Before biogas systems were constructed, the hygienic and sanitary conditions in the countryside were poor, in general; there was garbage, manure, pieces of straw and stalks in the farmers' courtyards, mosquitoes and flies, with occasional epidemics, which seriously threatened the health of farmers. After the building of digesters, these wastes were all put into digesters for anaerobic fermentation and gas production. In rural areas, a small digester, connected with the latrine and pigsty, was recommended and popularized. This kind of digester is a vertical cylindrical type: most of them are 6 - 8m3 in volume. The retention time of slurry in the digester may be more than 30 days. In addition, there are digesters with capacity of hundreds of m3 in a few state farms. An experimental latrine connected with a three-stage type biogas digester was designed and constructed in Mianyang City, Sichuan Province. By adding new sanitary installations, the latrine was freed from flies, pupae and offensive odours. (Den Ke-yun et al. 1988). The reduction in egg population in the effluent was about 95.3%. The fatality rate of Ascaris eggs was 93.7% in the effluent, 65.2% in the buffer tank, and 12.5% in the slide ditch. Colititer was 10-7-10-5 in effluent. The result of killing parasite eggs was much better than that in an ordinary latrine, used as a control.

It is clear from the foregoing that great benefit can be obtained from the control of pathogens by fermentation; and that the anaerobic process is considerably more effective then aerobic fermentation.

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