Faecal pathogens

Faecal matter from human sewage or animal waste contains pathogenic micro-organisms. The presence of faecal matter as pathogenic bacteria, viruses and protozoa in freshwater can be revealed by measuring faecal indicators, such as faecal coliforms, Escherichia coli (E.coli), faecal streptococci and enterococci (Davies-Colley et al., 2003). E.coli concentrations are used to measure drinking and recreational water standards. Adequate drinking water should have next to no E.coli present, but acceptable levels are higher for contact recreation (see Appendix C for guidelines). Faecal material can enter waterways through point source discharges from storm-water or sewage treatment (Ministry for the Environment, 2011b), animal processing plants (Donnison & Ross, 1999; Ferguson et al., 2003), and effluent pond discharges (Davies- Colley et al., 2003; Smith et al., 1993; Wilcock et al., 1999); as well as surface runoff from the land (Collins et al., 2007; Davies-Colley et al., 2003; Donnison & Ross, 1999; Environment Waikato, 2008) or subsurface flow (Ritchie & Donnison, 2010).

Pathogen levels in freshwater

Previous national studies have shown that faecal bacterial levels have been high throughout the country. In the period 2003-2007, E.coli concentrations exceeded the MfE/MoH contact recreation guidelines (550 E.coli/100 ml – see Appendix C) at about 75% of sites (Ballantine et al., 2010). The latest Ministry for the Environment indictor data (Ministry for the Environment, 2013f) for the suitability of swimming at 221 coastal and 204 freshwater sites nationwide showed that almost 70% of freshwater sites were unsafe for contact recreation at some point (Figure 5.3). Fifty per cent of sites are classed as poor or very poor and therefore should not be used for contact recreation, while 20% are classed as fair – described as sites that have potential sources of faecal material and water may be unsuitable for contact recreation after rainfall. These monitored sites are dedicated swimming spots (Ministry for the Environment, 2013f), situated in areas that are likely to have better water quality, such as forested streams. The poor performance of these areas does not give a promising outlook for streams in the rest of New Zealand.

Not surprisingly, when considering pastoral catchments E.coli concentrations are even higher.

E.coli concentrations frequently exceed guidelines for contact recreation in pastoral

catchments and are typically between two and 20 times higher than those in forested catchments (Davies-Colley et al., 2004; Larned et al., 2004). However, mixed results have been reported. Larned et al. (2004) found that E.coli guidelines for contact recreation were

Water 62 exceeded at 96% of 259 pastoral sites from 1998-2000, while Donnison et al. (2004) reported

only 28% of pastoral sites exceeded guideline levels.

Figure 5.3: Suitability for recreation grades at freshwater and coastal sites used for recreation around New Zealand assessed in 2013.

Data source: Ministry for the Environment (2013f). Note: No data was provided for sites in Auckland, Northland, Waikato or the West Coast regions.

Faecal matter from dairy farms

Dairy farms are likely to contribute a higher proportion of faecal contamination to waterways compared to other livestock types. Sheep faeces do have high concentrations of microbes but sheep do not enter water like cattle do (Ritchie & Donnison, 2010). Studies show dairy catchments have higher E.coli concentrations than average for lowland pastoral farming catchments (Collins, 2002; Davies-Colley & Nagels, 2002; Ministry for the Environment, 2009b). In Waikato intensive dairying areas, E.coli concentrations were exceeded at over 70% of sites tested for contact recreation (Collins, 2002). Likewise, median E.coli concentrations in five dairying catchment streams around New Zealand ranged from 290-1250 most probable number (MPN)/100 mL (Wilcock et al., 2007), 2-10 times the ANZECC guideline for contact recreation (median <126 E.coli/100 mL) (ANZECC, 2000). The five streams also had extreme (95 percentile) concentrations of E.coli that were 5-17 times the ANZECC ‘Red Alert’ value (>550/100 mL) (Wilcock et al., 2007).

Dairy farms in particular produce a large amount of faecal material. Cattle excrete 11-16 times a day and produce an average of 28-30 kg of faeces a day (Wilcock, 2006) One dairy cow is estimated to excrete faecal bacteria equivalent to between 14 (Environment Waikato, 2008) and 33 people (Figure 5.4) (Fleming & Ford, 2001). Given New Zealand’s dairy herd population of 6.5 million, this represents faecal bacteria concentrations equivalent to over 90 million and

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Freshwater Coastal Percen tage of site s Very poor Poor Fair Good Very good

Water 63 up to 215 million people. Solid waste from one dairy cow contains the equivalent amount of

nitrogen, phosphorus and total solids as 29, 30 and 44 humans respectively, while beef cow ratios are much smaller (Figure 5.4) (Fleming & Ford, 2001). Extending the waste measures to New Zealand’s entire dairy (6.5 million) and beef cattle (3.7 million) populations gives very high human population equivalents (Figure 5.5), compared to the relatively small human population of New Zealand.

Figure 5.4: Ratios of coliform bacteria, nitrogen, phosphorus and total solids in waste from dairy and beef cows to human equivalents.

Data source: Fleming and Ford (2001). Notes: Bars represent waste from one animal. Comparative data from sheep were not available from this data source.

Figure 5.5: Ratios of coliform bacteria, nitrogen, phosphorus and total solids in waste from the entire New Zealand dairy and beef cattle populations to human equivalents.

0 5 10 15 20 25 30 35 40 45 50

Coliform bacteria Nitrogen Phosphorus Total solids

A n im al to human rati o Measure

Dairy cows Beef cows

0 50 100 150 200 250 300 350

Coliform bacteria Nitrogen Phosphorus Total solids

To tal ani m al popul ati on to human e q uiva le n ts (m illion) Measure Dairy cows Beef cows

Water 64 Obviously due to the large amount of dairy excrement, large quantities of dairy shed effluent

water are produced from dairy farms. Dairy effluent contains mainly faeces, urine and wash- down water, but also comprises storm-water, spilled milk, soil and feed residue, detergents and other chemicals (Cameron & Trenouth, 1999). Estimations made over a decade ago (1997- 2000) of effluent water produced from New Zealand dairy farms were around 950 million cubic metres annually, of which about 59% was predicted to go to surface water (Flemmer & Flemmer, 2008). This amount would have undoubtedly increased since then and at the time was even deemed by the authors to be very imprecise. Furthermore, it also only accounts for the effluent from dairy shed operations, which is only a small proportion (5-15%) of the total waste produced by dairy cattle (Cameron & Trenouth, 1999). However, the total volume of dairy shed waste is likely to be larger than waste deposited on paddocks because of the large volume of water used to wash down dairy sheds.

Prior to the 1970s, dairy shed effluent was mainly discharged untreated into waterways. The wide spread adoption of on-farm oxidation treatment ponds saw effluent treated before discharge (Longhurst et al., 2000; Parliamentary Commissioner for the Environment, 2004). Regardless, pathogens often survived this process (Parliamentary Commissioner for the Environment, 2012). For this reason, land application of effluent became encouraged by regional councils (Cameron & Trenouth, 1999). However, some effluent is sprayed directly onto pastures without treatment (Cameron & Trenouth, 1999; Parliamentary Commissioner for the Environment, 2004). Even if two-pond treatment systems are used prior to discharge, pathogens can still be washed to water if the storage pond overflows, the effluent irrigator breaks down, or by irrigating on poorly drained and saturated soils (Parliamentary Commissioner for the Environment, 2012).

Regardless, the bulk of manure produced in New Zealand dairy systems is deposited directly to pasture from grazing cattle, of which is a significant source of faecal contaminants to freshwater (Davies-Colley et al., 2003; Davies-Colley et al., 2004; Donnison et al., 2004; Parliamentary Commissioner for the Environment, 2012; Wilcock, 2006; Wilcock et al., 2006; Wilcock et al., 1999). Overland flow and stock crossings have been found to generate the highest E.coli loadings to waterways in some instances (Wilcock, 2006). Concentrations are also high after rainfall as overland flow increases (Ritchie & Donnison, 2010). Direct deposition of faecal material to freshwater is common from stock grazing in or near water bodies or passing through streams and drains to and from the milking shed. Davies-Colley et al. (2004) found that dairy cows were 50 times more likely to defecate during stream crossings.

Water 65 Similarly, high E.coli counts were associated with dairy cow crossings in a Wellington region

stream (Perrie et al., 2012). Once faecal pathogens are excreted, they begin to die; therefore, concentrations are highest in fresh dung, and dark, moist, cool conditions are best for pathogen survival (Davies-Colley et al., 2003). In this regard, dung excreted directly in or near water-bodies poses the greatest threat of pathogen contamination.

Overland flow may be responsible for the largest proportion of annual catchment yields of faecal contamination. For example, modelling in the Toenepi catchment estimated that 80% of the faecal contamination occurred by overland flow (Ritchie & Donnison, 2010). Although, this modelling assumed that 90% of streams were fully fenced and effluent was treated and discharged from a two-pond system, so direct deposition into streams and contamination from dairy shed effluent were less likely to occur. Conversely, in the Bog Burn catchment (Southland), 78% of the total stream E.coli load from dairy farms was from direct drainage of irrigated dairy shed effluent onto mole-pipe drained land10, with overland flow, subsurface drainage and direct deposition of dung contributing 16%, 6% and 0.1% respectively (Monaghan et al., 2007). Within the whole catchment considering other land uses, irrigation of dairy shed effluent contributed approximately 65% of the E.coli generated and discharged to the Bog Burn Stream (Monaghan et al., 2007). These studies emphasise the importance of the management system in place in contributing to overall loads.

Stock exclusion and effluent management changes in some dairying catchments have not achieved contact recreation standards in waterways (Ritchie & Donnison, 2010). Riparian vegetation strips can prevent access to waterways as well as trap microbes being washed down-slope into streams (Collins et al., 2007; Monaghan et al., 2007). However, indicator bacteria can remain in farm run-off trapped in buffer strips and can be released to surface water in high flow events (Ritchie & Donnison, 2010). In addition, once in streams, faecal indicator bacteria can survive in bed sediments, and re-suspend in the water during flood events (Ritchie & Donnison, 2010).