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This is a complicated issue, and one that is becoming increasingly important as more and more people look at recycling and reusing their wastewater.
The textbook answer is that the use of untreated effluent in agriculture is potentially hazardous and requires careful handling plus restrictions on the type of crops irrigated and the use of the crop products (as per the revised 2005 WHO Guidelines for the safe use of wastewater, excreta and greywater. Volume 2: Wastewater use in agriculture). I have extracted a few of the relevant sections from this long and wordy document, and copied them below this email.
The WHO note that the greatest health risks are associated with crops that are eaten raw - for example salad crops, especially if they are root crops (e.g. radishes and onions) - or crops that grow close to the soil (e.g. lettuce, courgettes). In addition, crops that have irregular surface properties (e.g. hairy, sticky, creviced, or rough) protect pathogens from exposure to radiation and make them more difficult to wash off with rain or post-harvest washing. The amount of water each crop holds is also an important factor: one study found that lettuce retains 10.8ml of irrigation water, whereas a cucumber retains only 0.36ml (i.e. only 3% the volume retained by the lettuce). Obviously, the more irrigation water retained the more likely the contamination.
A practical response is that untreated effluent is a valuable and nutrient-rich commodity in many developing countries, and that few poor communities (or individuals) are willing to follow the restrictive guidelines advocated by the WHO (and few local authorities have the resources to treat wastewater or enforce environmental regulations). In particular, those coming into contact with raw wastewater are usually reluctant to wear the required protective boots, gloves and clothing, particularly in hot climates; and smallholder farmers are often unwilling to stop growing the high value fruit and vegetables that are most at risk of contamination.
Relevant approaches (as detailed in the attached Water Policy Briefing from the International Water Management Institute) include:
Improved crop selection and irrigation practices Selecting crops that are suitable for wastewater irrigation (often low value grains and fodder crops) and using irrigation techniques that prevent direct contact with untreated wastewater (e.g. drip irrigation; 'bed and furrow' cultivation).
Preventive medical care programs Provide anti-helminthic (deworming) medication to farmers (and their families) exposed to untreated wastewater.
Improved post-harvest handling Washing and improved storage of harvested vegetables.
Conjunctive management of wastewater and other water supplies Because wastewater has a low/negligible cost, farmers tend to overwater, which needlessly increases the environmental and health risks (as well as wasting valuable nutrients). Where alternative water sources are available, the blending of wastewater and other water supplies allows expansion of the irrigated area (potentially allowing more people to benefit) and more efficient use of the nutrient-rich wastewater.
Educating farmers and awareness-raising among consumers and authorities Farmers (and others) should be aware of the risks that they face, and would benefit from knowledge of the basic hygiene-related precautions that they could take to avoid infection and prevent the spread of gastro-intestinal diseases to their families. A program that educates consumers about the need to wash thoroughly fruits and vegetables before use would also be beneficial.