## 2 Materials and Methods
### Calculating Procedures
#### 2.5.2 Effect of Water Quality Constituents on Crop Yield and Quality
The approach adopted in IrrigWQ for evaluating the effect of plant nutrients on irrigation water is to estimate both the quantity of NPK that will be added through irrigation and the contribution their addition will make to NPK removal by a specific crop (indirectly, the crop nutrient requirement). The situation wherein inadvertent nutrient additions through irrigation are relatively low compared to crop requirements is considered to be \"Ideal\" because, under these conditions, it is easier to accommodate the additional nutrients as part of normal nutrient management practices, and the additional nutrients may be viewed as only beneficial. However, as inadvertent nutrient additions increase, it becomes more difficult to manage the negative effects associated with higher fertiliser applications. Nutrient additions of less than 10% of crop removal are considered to be ideal, while additions in excess of 50% are considered to be unacceptable. * Risk of microbial contamination from consuming crops  
The main concern about the presence of human pathogens in irrigation water is the risk this poses to food safety (crop quality) when crops destined for human consumption are contaminated during irrigation. This also has implications for compliance with food safety regulations. The deposition of pathogens during irrigation is of particular concern for fruits and vegetables that are consumed raw or with minimal processing. _E. coli_ is used in IrigWQ as an indicator of microbial pathogens, recognizing that levels of _E. coli_ are much higher than those of microbial pathogens and are, thus, more easily determined. Norovirus is recognized as the most common agent of viral diarrhoea transmitted by irrigation water and by irrigated fresh produce consumed raw and is, thus, used as a proxy to estimate the risk of human infections caused by the microbial contamination of irrigation water. The risk of norovirus infection per person per year is estimated from _E. coli_ counts per 100 mL, using a dose-response look-up table [22], which gives the risk of norovirus infection per person per year when consuming lettuce irrigated with water containing different _E coli_ concentrations. The calculated risk of exposure is, thus, based on total annual _E. coli_ intake. For crops consumed raw other than lettuce, the annual intake is calculated from the volume of irrigation water retained by the crop (in comparison to that retained by lettuce) and how much of the crop is consumed on an annual basis. Whether a crop is wetted by irrigation and the volume of water retained is determined by the irrigation system and anatomy of the crop. IrigWQ output reports the risk of infection by human pathogens in irrigation water, as the number of excess infections per thousand persons p.a. The threshold value of 3 excess infections per 1000 people p.a. separating the _Acceptable_ and _Tolerable_ fitness-for-use categories represents the geometric mean of the risks \(10^{-3}\) and \(10^{-2}\). The geometric mean is used, as the distribution of risk is usually log-normal or similar (rather than normal, in which case the arithmetic mean would best describe the central tendency)
* Qualitative crop damage by atrazine  
Herbicides are the most widely applied class of pesticides and, in view of the photovoltaic risk they pose to non-target/sensitive crops, are more likely to be of concern to irrigation farmers than the possibility of irrigation water being the source of unacceptable pesticide residues in or on produce. However, they need to be present in concentrations that are toxicologically relevant to pose a risk of phyto-toxicity. Although this risk also appears to be low based on the available evidence, for the sake of completeness, it was decided to consider herbicides as one of the suitability indicators for inclusion in IrigWQ. After glyphosate, atrazine is the most widely used herbicide in South Africa [10]. Since atrazine is highly mobile compared to glyphosate, with a significantly longer half-life, atrazine was selected as the herbicide to consider in IrigWQ.