Pathogen Pathways – Best management practices
1. Executive summary
This report describes the key pathways by which faecal microbes are transferred from farm animals to waterways, that were identified in the Pathogen Transmission Routes Research Program (and related studies). Additionally, Best Management Practice (BMP) guidelines are presented with which to reduce the faecal contamination of waterbodies. The key findings are summarised as follows:
Faecal contamination of freshwaters can arise through the deposition of faeces by grazing animals directly into waterways. This ‘direct’ deposition can occur when dairy cows cross streams as a herd to or from the milking shed, and through sporadic incursions by grazing cattle into unfenced waterways adjoining pasture. Indirect pathways whereby microbes are ultimately transferred to waterways via the flow of water over the surface of the land (surface runoff) or down through the soil horizons (subsurface flow) are also important.
Direct deposition associated with herd crossings is a major pathogen transmission route and hence bridging streams intersected by farm raceways should markedly improve stream water quality.
Sporadic incursions by cattle have been shown to deliver a faecal contamination burden broadly comparable to some ‘indirect’ pathways (e.g., via tile drainage and surface runoff). Permanent fencing is the most stringent measure with which to prevent sporadic incursions. Provided the fence is set back from the bank, this not only prevents direct deposition to the channel, but also contamination from faecal deposits in riparian areas close to the stream. Furthermore, a vegetated riparian buffer strip (RBS) can entrap microbes washed downslope by surface runoff (an indirect pathway). Guidelines for optimal riparian buffer design are provided within this report with respect to the entrapment of faecal bacteria. These account for the influence of soil type, slope angle and the degree of bacterial attachment (to soil and faecal material) upon entrapment efficiency. Alternatives to permanent fencing exist that can potentially reduce the input of faecal material to waterways. These include the provision of alternative sources of water, shade and shelter. However, their effectiveness has yet to be tested in the New Zealand pastoral landscape.
Surface runoff is an important transmission pathway. In hill-country, surface runoff often converges with subsurface flow to form wetlands. Cattle are attracted to the smaller shallower of these wetlands for grazing, resulting in direct deposition of faecal material onto them. The wetlands drain into waterways and consequently deliver a high number of faecal microbes, particularly during rain events. Therefore, fencing smaller wetlands to exclude livestock will improve water quality.
On some soils, a significant volume of surface runoff can be generated on dairy pasture despite the presence of subsurface drains. In these location RBS are likely to be a worthwhile mitigation measure.
Soil type, timing, volume, location and technique are all key factors in the optimal irrigation of effluent, with respect to minimising the loss of microbes (and other pollutants) to waterways. Ideally, irrigation should occur when the volume to be applied does not exceed the water storage capacity of the soil, with effluent being stored until such soil moisture conditions arise. This ‘deferred irrigation’ can markedly reduce pollutant transfer to waterways, through a reduction or elimination of subsurface artificial drain flows and surface runoff. The technique requires sufficient effluent storage capacity and the measurement or prediction of soil moisture on a daily basis. Advanced Pond Systems provide an alternative to the land application of dairy shed effluent and provide effluent of appreciably higher microbial quality than the traditional two-stage oxidation ponds.
With irrigation of water, as with effluent irrigation, the identification of appropriate soil type, timing, volume, location and technique are also key factors. Accounting for the soil moisture deficit when determining the volume of water to be applied will reduce flows to, and hence microbial contamination of, groundwater. Spray irrigation results in less bypass flow and hence less microbial contamination of groundwater than the border strip technique.
Soil type is a key factor in the transfer of faecal microbes to waterways. The ability of a given soil to attenuate microbes is strongly dependent upon the degree to which water can infiltrate and, the degree to which infiltrating water bypasses the fine pores (that filter microbes) of the soil matrix. The avoidance of, or a reduction in, grazing and irrigation upon poorly drained soils characterised by potentially high bypass flow and the generation of surface runoff, are appropriate management practices that are likely to lead to improvements in bacterial water quality.
The identification of appropriate (and conversely, inappropriate) locations for livestock grazing can lead to a reduction in faecal contamination of waterways. Water quality improvements can be realised from fencing stock out of ephemeral streams, wetlands, seeps, and riparian paddocks prone to saturation. During prolonged spells of wet weather, improved water quality may result through the relocation of stock from paddocks to feed or wintering pads, and herd homes.
Some microbial transmission pathways and potential mitigation measures remain untested or poorly understood. Recommendations for further research are provided and include: an analysis of the cost-effectiveness and social implications of each mitigation measure; assessment of the impact of off-stream sources of water, shade and shelter for cattle, as alternatives to the permanent fencing of streams; an improved understanding of the factors that influence cattle attraction to water, this would help to prioritise the management of waterways, including ephemeral streams and wetlands; further evaluation of the entrapment of microbes in riparian buffer strips encompassing a range of soil, slope and vegetation types (including forested buffers); an improved understanding of the attachment of microbes to particulates, since this process strongly influences microbial entrainment in surface runoff and hence entrapment in buffer strips; evaluation of the effectiveness of constructed wetlands, vegetated drains and farm ponds in attenuating microbes within drain flows.
In addition to the evaluation of BMPs, broader issues relating to faecal contamination of waterways are of significant importance. Firstly, the role of water in explaining reported rates of human zoonotic infection in New Zealand, notably by Campylobacter, remains poorly understood. Waterways may play an important role as a vector for pathogens in the environment, causing re-infection of animals in farms downstream, and maintaining a general background level of pathogens on pastoral land. Identifying causes of human infection therefore requires that water as a pathogen vector or indirect cause needs to be better understood. Furthermore, the tracing of pathogen strains that cause infection and re-infection of grazing cattle is of high priority and would help to explain the persistence of some pathogens in the pastoral landscape. Finally, limited overseas evidence is available to link productivity of cattle with the microbial quality of their drinking water. Given the potential significance of this issue, New Zealand based studies are desirable.
Contact for Enquiries
Phil Journeaux
Manager
North Island Regions
Sector Performance Policy
MAF Policy
Private Bag 3123
Hamilton
NEW ZEALAND
Phone: +64 7 957 8313
Fax: +64 7 957 8315
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