Fresh Produce tool glossary

A biological process used to treat wastewater by breaking down organic matter in the presence of oxygen. Naturally occurring bacteria feed on nutrients in the water, helping to reduce the level of dissolved and suspended solids. This method is commonly used in sewage and sludge treatment to lower pollution levels before the water is discharged or reused.

A biological process that breaks down biodegradable material in the absence of oxygen. Microorganisms decompose organic matter such as food waste, manure or sewage sludge, producing biogas, mainly methane, which can be captured and used as a renewable energy source. Commonly used in waste management and energy recovery.

A structured community of microorganisms, often of multiple species, that adhere to a surface and produce a protective matrix of substances such as exopolysaccharides. Biofilms are highly resistant to environmental stresses, including drying out and many cleaning or sanitising agents. In agriculture, they can form on equipment, irrigation systems, or fresh produce surfaces, making them a concern for hygiene and food safety.

A type of narrow well drilled into the ground to access groundwater, typically 5–10 cm in diameter. A pump is used to extract the water. Boreholes are commonly used in agriculture for irrigation, particularly where surface water is scarce. Water from boreholes often carries a lower microbiological risk than surface water, as it is naturally filtered through soil and rock layers, although this depends on local geology and borehole construction.

Brucella is a genus of bacteria that causes brucellosis, a zoonotic disease marked by symptoms such as fever, abdominal pain, diarrhoea, vomiting, weight loss, and liver dysfunction. Infection occurs through consumption of contaminated food (particularly unpasteurised dairy), direct contact with infected livestock or wildlife, or inhalation of contaminated aerosols. Brucella are intracellular pathogens, meaning they can survive inside human cells, making infections difficult to treat.

Capping refers to the formation of a hard crust on or near the soil surface, typically because of low rainfall, intense sunlight or strong winds. This crust can obstruct crop emergence and increase the risk of physical damage to crops during harvest. To mitigate this, water is sometimes applied pre-harvest to soften the soil. However, this practice can carry microbial risks, including splash-back contamination of crops if the water is not of suitable quality. Additionally, capped soil is more prone to surface runoff during rainfall, potentially transporting contaminants into nearby water sources.

Chemical water treatments are methods used to reduce or eliminate microbial contamination in irrigation water by creating conditions that are unfavourable for bacterial survival. These treatments use disinfectants such as chlorine, ozone, or hydrogen peroxide to destroy microorganisms.

In agriculture, these treatments can be valuable tools to improve the microbial safety of water used on fresh produce, helping to reduce the risk of contamination during irrigation. However, chemical treatments must be carefully managed, as excessive or inappropriate use can harm sensitive crops, affect soil health, or leave chemical residues on produce. Additionally, some chemicals may react with organic matter in the water, reducing their effectiveness or producing harmful by-products. Therefore, the choice and application of chemical treatments need to balance effective microbial control with crop safety and environmental considerations.

Citrobacter are a subgroup of the Enterobacteriaceae. The majority of strains are not pathogenic, and they rarely cause human illness. Citrobacter are widely dispersed in soils, waters and the waste from mammalian gastrointestinal tracts. The Enterobacteriaceae are an indicator of general hygiene of the environment used to grow and process crops.

Coliphages are viruses that specifically infect Escherichia coli (E. coli) bacteria. They are often used as indicators of viral contamination in water and food safety testing.

The process by which a microorganism establishes and grows a population within a new host or environment.

The first leaves that emerge from a germinating seed, often serving as a food source for the developing seedling before true leaves develop.

Cowpox is a zoonotic disease caused by the cowpox virus, transmitted from animals to humans. Human cases are very rare, although the UK experiences a higher incidence than continental Europe. Domestic cats and cattle udders are common sources of infection. In most cases, cowpox is self-limiting but can be severe or even fatal in immunocompromised individuals.

A specific step or stage in a food production or processing process where a hazard (biological, chemical, or physical) can be prevented, eliminated, or reduced to an acceptable level. Effective control at a CCP is essential to ensure food safety. Identifying and managing CCPs is a key part of food safety management systems such as HACCP (Hazard Analysis and Critical Control Points).

Cryptosporidium parvum is a protozoan parasite that causes gastroenteritis, diarrhoea and abdominal cramping in humans. It is commonly transmitted via contaminated water and is highly resistant to standard water treatments such as chlorination. In agricultural settings, surface water used for irrigation can become contaminated through faecal matter from livestock, particularly ruminants like cattle and sheep. The parasite is typically found as oocysts, durable, thick-walled spores capable of surviving in the environment for long periods. Where such water is used on fresh produce, there is potential for foodborne outbreaks.

Escherichia coli is a bacterium commonly found in the gastrointestinal tracts of mammals, birds, and reptiles. While most strains are harmless, some have acquired virulence factors that enable them to cause serious illness in humans. Of particular concern in fresh produce production are pathogenic strains of Shiga-toxin producing E. coli (STEC) such as E. coli O157. These strains produce Shiga toxin, a potent compound also associated with Shigella, as a result of infection by a Shiga toxin-encoding coliphage (stx-phage).
Pathogenic E. coli strains pose a significant food safety risk as they can be transmitted to fresh produce via contaminated water, inadequately composted manure, or contact with animal faeces. Although they typically cause little to no illness in animal hosts, they can lead to severe foodborne disease in humans. In food safety monitoring, generic E. coli is widely used as an indicator organism, since its presence suggests faecal contamination and an increased likelihood of pathogenic microorganisms being present.

Enterobacter is a genus within the Enterobacteriaceae family, which includes a broad group of bacteria commonly found in soil, water, and the intestines of animals. Although some Enterobacter strains can be opportunistic pathogens, typically causing infections in healthcare settings such as respiratory or urinary tract infections, food is rarely the source of infection. In agricultural contexts, Enterobacter species are part of the broader group known as coliforms, used as hygiene indicators. However, they do not typically grow at the higher incubation temperatures required to identify faecal coliforms. Their presence in irrigation water or produce environments may indicate general environmental contamination, rather than direct faecal pollution.

The Enterobacteriaceae are a large and diverse family of bacteria comprising over 30 genera, including both harmless and pathogenic species. While many members are commonly found in the intestines of humans and animals, some can also be isolated from soil, surface waters, and plants. In agricultural and food safety contexts, the presence of Enterobacteriaceae in test samples is used as a general indicator of environmental hygiene. Their detection on fresh produce may signal contamination from sources such as faecal material, insects, wildlife, soil, irrigation water, or plant surfaces, including some plant pathogens.

A term used to describe microorganisms capable of causing disease and damage to the cells lining the gastrointestinal tract of humans or other animals. Enteropathogenic organisms are often transmitted via contaminated food or water and are of particular concern in agricultural settings where produce may be exposed to faecal contamination or poor hygiene during handling and irrigation.

A weak solution of nutrients secreted or leaked from plant roots or other plant tissues. Root exudates can influence microbial activity in the soil, attracting both beneficial and harmful microorganisms, and may play a role in the transmission of soilborne pathogens in agricultural systems.

Faecal coliforms are a subgroup of the broader coliform group, which itself belongs to the Enterobacteriaceae family. The coliform group includes species such as Escherichia, Klebsiella, Citrobacter, Enterobacter, and Serratia. While many coliforms can be found in soil, water, and on plants, faecal coliforms are more closely associated with recent faecal contamination from warm-blooded animals. Faecal coliforms are identified by their ability to grow at elevated incubation temperatures (typically 44–45°C). This higher temperature selects for bacteria that have been recently deposited into the environment, because coliforms tend to lose their ability to grow at these warmer temperatures the longer they persist outside the host’s digestive tract.

In agricultural contexts, faecal coliforms serve as important indicators of microbial water quality, helping to assess the risk of contamination from animal waste in irrigation water or on produce. Typically, over 80% of the faecal coliform count is made up of E. coli, the most significant and commonly measured member of this group.

Many microorganisms that cause human illness are enteric pathogens, meaning they colonise the gastrointestinal tracts of animals and humans. These pathogens are shed in the faeces of infected hosts and can then be transferred to new hosts via the faecal oral route. This common transmission pathway involves the movement of pathogens from contaminated faecal material into the mouth of another individual.

In agricultural and food production settings, this can occur through various means, such as handling contaminated manure, irrigation water, or produce. In everyday life, common routes include infected individuals not washing their hands properly and subsequently contaminating surfaces like door handles, which can then transfer pathogens to others who touch them.

A mixture of livestock faeces and used bedding material. Typically, farmyard manure (FYM) contains more than 13% dry matter (w/w). Unless properly composted or treated, FYM can harbour microorganisms that pose a risk of causing illness in humans. Many pathogens can survive for extended periods in FYM, so effective treatment such as composting or pasteurisation is important to reduce microbial risks before application to land used for growing crops.

Filtration is a physical method used to reduce suspended solids in irrigation water. These approaches help improve water clarity and may lower microbial loads indirectly, as many pathogens adhere to particles that can be removed through these processes. Filtration passes the water through media such as sand or gravel to physically strain out remaining particulates.

While this treatment can significantly improve the physical quality of irrigation water, they do not disinfect it and is unlikely to eliminate microbial risks on its own. In fresh produce production, where water may contact edible parts of the crop, this method is best used as part of a broader strategy to manage contamination risks.

Fermentation is a metabolic process in which microorganisms convert nutrients into products such as organic acids, alcohol, combustible gases (like methane), or other useful compounds. This process is widely used in agriculture, for example in the production of silage, composting, and biogas generation.

Flocculation is a physical method used to reduce suspended solids in irrigation water. These approaches help improve water clarity and may lower microbial loads indirectly, as many pathogens adhere to particles that can be removed through these processes. Flocculation involves adding substances that cause fine particles to clump together into larger aggregates that settle more easily.

While this treatment can significantly improve the physical quality of irrigation water, they do not disinfect it and is unlikely to eliminate microbial risks on its own. In fresh produce production, where water may contact edible parts of the crop, this method is best used as part of a broader strategy to manage contamination risks

A fomite is an inanimate object or substance that has become contaminated with infectious agents (microorganisms) and can facilitate the transfer of contamination from one person or object to another.

The process of gathering mature crops from the field or growing area. Harvesting occurs when crops have reached the desired stage of growth or meet specific quality or size targets required by customers or market standards.

Heavy metal salts are compounds consisting of a heavy metal—such as lead, mercury, arsenic, or cadmium—and a salt ion like chloride, nitrite, or phosphate. In agricultural settings, these salts can originate from contaminated soils, fertilisers, pesticides, or irrigation water. Heavy metal salts can pose a health risk to humans due to their toxicity and potential to accumulate in crops.

Hepatitis A is a pathogenic virus that causes liver inflammation and illness in humans. Like many viruses, it has a narrow host range and infects only humans. Hepatitis A is transmitted exclusively through the faecal-oral route, via the faeces of infected individuals. The presence of Hepatitis A virus or infection in food handlers is a strong indicator of recent contamination with fresh human faecal matter, which poses a significant risk in food production and handling environments.

Hydroponics is a method of growing crops in mineral nutrient solutions without the use of soil. This soil-less cultivation allows precise control over nutrients and water, often resulting in faster growth and higher yields. Because the system is closed and controlled, hydroponics can reduce exposure to soil-borne pathogens, but water quality and system hygiene remain critical to prevent microbial contamination.

Hypochlorite is a compound containing chlorine and oxygen, commonly used as the active disinfecting agent in bleach. It is widely employed in agriculture and food production to sanitise water, equipment, and surfaces, helping to reduce microbial contamination. However, its effectiveness depends on concentration, contact time, and water quality.

The hypocotyl is the part of a seedling stem located between the cotyledons (seed leaves) and the root. It plays a crucial role in seedling development by elongating to push the cotyledons above the soil surface during germination.

Inoculation is the deliberate introduction of microorganisms, such as bacteria or fungi, onto a surface or growth medium to promote their growth and increase their numbers. In agriculture, inoculation is often used to introduce beneficial microbes to seeds, soil, or plants to enhance nutrient uptake or protect against pathogens. In research and food safety studies, inoculation is also used experimentally to introduce specific microorganisms into substrates or products, allowing their behaviour, survival, or potential risks in that environment to be assessed.

Irrigation is the controlled application of water to crops in quantities sufficient to meet their growth needs, supporting healthy development and optimal yields. Common methods include surface irrigation (flooding or furrows), sprinkler irrigation, and drip irrigation, each with different efficiencies and suitability depending on the crop and environment. Microbial risks associated with irrigation arise when water sources are contaminated with pathogens, which can then be transferred to crops, especially when water contacts edible parts. Proper management of irrigation water quality and application methods is essential to minimise the risk of crop contamination.

Leptospirosis is a zoonotic disease transmitted to humans through contact with soil or water contaminated by the urine of infected wild or domesticated animals. The causative bacteria belong to the genus Leptospira. In humans, infection typically causes flu-like symptoms such as headaches and muscle pain. More severe cases, known as Weil’s disease, involve liver damage, bleeding, and meningitis. Common animal carriers include cattle, pigs, dogs, and rodents, especially rats.

Listeria is a genus of closely related bacteria commonly found in soils and vegetation. Listeria species (spp.) testing is sometimes used as an indicator of conditions which would allow the growth of the pathogen Listeria monocytogenes.

Listeria monocytogenes

Listeria monocytogenes is the main Listeria species which causes illness in v humans, particularly vulnerable populations including pregnant women (where infection may cause miscarriage), the elderly, and immunocompromised individuals. Invasive human infections typically involve the bacteria multiplying in cerebrospinal fluid, leading to symptoms similar to meningitis. Milder, non-invasive listeriosis may occur as gastroenteritis in immunocompetent individuals and is thought to result from the consumption of high levels of the bacterium.

Listeria ivanovii

Listeria ivanovii is another species within this genus that primarily infects sheep, causing sepsis, enteritis, and abortion in ovine hosts. Human infection is rare but can occur, leading to serious illness.

Mesophiles are bacteria that grow within a temperature range of roughly between 15°C and 45°C. This group includes many microorganisms relevant to food safety and spoilage. Microbial testing often targets mesophiles because their growth range overlaps with common storage and handling temperatures, making them important indicators of product quality and hygiene.

Metabolic heat is the heat produced as a by-product when living organisms break down food and nutrients to generate energy. This heat can influence environmental conditions, such as temperature in compost heaps or stored crops, potentially affecting microbial activity and spoilage rates.

Microbiological testing involves analysing samples in a laboratory to detect and quantify microorganisms, including indicator bacteria and pathogens. It is commonly used to assess the safety and hygiene of water, soil, and fresh produce, as well as to evaluate the microbial safety of food handling and processing environments. This testing helps manage microbial risks in agricultural and food production settings.

This food safety approach involves using several stages or controls to reduce a foodborne hazard when no single critical control point (CCP) can completely manage the risk. Each ‘hurdle’ reduces the hazard to some extent, and together they lower the overall risk to an acceptable level. This strategy is applied in processes where absolute control of a hazard by one step is not possible.

Mycobacteria are a group of particularly robust bacteria, notable for their thick, waxy, and highly hydrophobic cell walls that allow them to survive outside a suitable host for extended periods. They are associated with a variety of diseases in humans, including Crohn’s disease (caused by Mycobacterium paratuberculosis), difficult-to-treat respiratory infections such as tuberculosis (caused by Mycobacterium tuberculosis) and, rarely, bovine tuberculosis (M. bovis). Common foodborne vectors include the consumption of unpasteurised milk from infected animals and the inhalation of aerosols containing Mycobacterium.

Newcastle disease is a zoonotic illness mainly spread from birds to humans, causing mild symptoms such as eye inflammation and flu-like effects. It is not usually a serious threat to human health.

In fresh produce production, wild and domestic birds can carry the virus and contaminate crops or irrigation water through their droppings, posing a food safety risk. Managing bird access to growing areas helps reduce this risk.

Animal manures contain high concentrations of nitrogen compounds, including nitrates. If manure is applied to land just before rain or in excessive amounts, nitrates can leach into nearby watercourses such as rivers and lakes. This can lead to poor water quality and encourage algal growth that depletes oxygen in the water, harming aquatic life.

Nitrate pollution can indirectly increase microbial risks by promoting conditions that support the survival and growth of certain pathogens in irrigation water or soil. Contaminated water used for irrigation may then transfer these pathogens onto crops, affecting food safety.

Osmosis is the movement of water across a natural or synthetic semi-permeable membrane, driven by differences in solute (such as salt or sugar) concentration on either side. Water generally moves from an area of low solute concentration to one of higher concentration to balance the concentrations. This process is important in plant water uptake and in maintaining cell health in fresh produce. Osmosis is also the underlying principle of reverse osmosis, a water treatment technique commonly used for desalination and purification.

An organism, such as a bacterium, virus, protozoa or fungus, that can cause disease in another organism, including humans, animals, or plants.

Phosphates are compounds containing phosphorus, commonly found in animal manures and fertilisers. Like nitrates, excessive phosphates can run off into watercourses, causing nutrient pollution that worsens water quality by promoting algal growth. Phosphate pollution can indirectly increase microbial risks by promoting conditions that support the survival and growth of certain pathogens in irrigation water or soil. Poor water quality can increase microbial risks to fresh produce if contaminated water is used for irrigation.

The phyllosphere is the above ground external surfaces of plants. Phyllospheres include leaf surfaces (called phylloplanes) and the surfaces of flowers (anthoplane), seed bodies (carpoplane) and stems (cauloplane).

Protozoa are single-celled, eukaryotic organisms. They occupy an evolutionary position between bacteria (prokaryotes) and simple multicellular life forms, such as algae. Many protozoa play important roles in ecosystems, including soil and water environments relevant to agriculture.

Reed beds are a physical and a biological method used to reduce suspended solids in irrigation water. These approaches help improve water clarity and may lower microbial loads indirectly, as many pathogens adhere to particles that can be removed through these processes.

Reed beds, also known as constructed wetlands, use rooted aquatic plants and the associated microbial communities in the root zone to trap solids and absorb nutrients.

Reed beds, also known as constructed wetlands, use rooted aquatic plants and the associated microbial communities in the root zone to trap solids and absorb nutrients.

While this treatment can significantly improve the physical quality of irrigation water, they do not disinfect it and is unlikely to eliminate microbial risks on its own. In fresh produce production, where water may contact edible parts of the crop, this method is best used as part of a broader strategy to manage contamination risks.

The rhizosphere is the narrow zone of soil immediately surrounding plant roots. It is enriched by nutrient-rich exudates released by the roots, which support the growth of a diverse community of microorganisms—some of which provide beneficial effects to the plant.

Salmonella is a complex genus of bacteria widely dispersed among mammals, birds, and reptiles. While many strains do not cause significant harm to their animal hosts, some serovars can infect humans, causing illness. Salmonella infections typically result in fever, gastroenteritis (including vomiting and diarrhoea), and sepsis. These bacteria are zoonotic agents, capable of transmitting from animals to humans.

Salmonella enterica is the principal species responsible for most human salmonellosis cases. It includes numerous serovars including Salmonella Enteritidis.

Salmonella Typhimurium is a serovar of Salmonella enterica and is notable for its ability to infect a broad range of hosts including humans, livestock, and wildlife. It can cause invasive infections where bacteria spread beyond the gut to other parts of the body, such as the bloodstream and cerebrospinal fluid.

A sanitiser is a chemical agent used to reduce or eliminate bacteria and other microorganisms from surfaces, equipment, and tools. Sanitisers are commonly employed in agricultural and food handling environments to reduce microbial contamination and minimise the risk of cross-contamination. They may work by disrupting cell membranes, denaturing proteins, or interfering with microbial metabolism. The effectiveness of a sanitiser depends on factors such as concentration, contact time, surface cleanliness, and the presence of organic matter. Common examples include chlorine-based compounds, quaternary ammonium compounds, and hydrogen peroxide.

Sedimentation is a physical method used to reduce suspended solids in irrigation water. These approaches help improve water clarity and may lower microbial loads indirectly, as many pathogens adhere to particles that can be removed through these processes. Sedimentation relies on gravity to allow heavier particles to settle out of the water.
While this treatment can significantly improve the physical quality of irrigation water, they do not disinfect it and is unlikely to eliminate microbial risks on its own. In fresh produce production, where water may contact edible parts of the crop, this method is best used as part of a broader strategy to manage contamination risks.

Serratia is a genus within the Enterobacteriaceae family, which includes both environmental and opportunistically pathogenic bacteria. While certain Serratia strains, most notably Serratia marcescens, can cause disease, infections are far more commonly associated with healthcare settings than with foodborne transmission. S. marcescens is often found in persistently damp environments, such as sinks, drains, and wet surfaces, where it can form distinctive, red-pigmented colonies.

Although Serratia is not typically a major concern in food safety, its presence, along with other Enterobacteriaceae, can indicate lapses in hygiene or sanitation in agricultural or processing environments. As such, members of this genus may serve as general environmental indicators for the cleanliness of surfaces or water used in the production and handling of fresh produce.

Slurry is a type of livestock waste, typically generated by cattle on specific diets, that has a watery consistency and a dry matter content of approximately 4% to 9% (w/v). It is favoured by some farmers because it can be efficiently collected in pits located beneath slatted flooring in livestock housing and is easily pumped for storage or field application. Slurry can be a significant source of nutrients for crops, but it may also carry microbial pathogens if not properly managed or treated.

A spore is a small, resilient reproductive or survival structure produced by certain fungi and bacteria. Spores are highly resistant to environmental stresses such as desiccation, heat, and chemical agents, including many sanitisers. They are typically formed in response to unfavourable conditions or nutrient scarcity. In agricultural settings, spores can persist in soil, water, or on surfaces for extended periods, sometimes decades, posing challenges for microbial control and sanitation.

In agriculture, storage refers to the containment of water in tanks, reservoirs, lagoons, or ponds for later use in irrigation or livestock operations. Stored water may originate from various sources, including rainwater harvesting, surface water abstraction, or treated wastewater. While storage improves control over water availability and timing, it also introduces potential microbial risks. Open-to-air storage systems, such as uncovered reservoirs or ponds, are particularly vulnerable to contamination from wildlife, insects, airborne particulates, and faecal matter, making them more likely to support pathogen survival and growth. In contrast, enclosed or covered storage systems help limit these risks by reducing exposure to contaminants. Regardless of the system used, regular monitoring and maintenance are essential to ensure that stored water remains microbiologically safe for agricultural use, especially when applied to fresh produce.

Streptococcus and Enterococcus are closely related genera of bacteria that have been investigated as alternative indicators of faecal pollution in water. Their use stems from differences in their prevalence in human versus animal waste. Human faecal material tends to contain a higher proportion of Enterococcus species as the dominant cocci, whereas animal faeces generally have greater numbers of Streptococcus. This distinction has led to attempts at using species profiles, or ratios between Enterococcus and Streptococcus, to identify the likely source of contamination.

Although this microbial source tracking strategy has shown some promise, it is not without limitations. One significant drawback is that Enterococcus and Streptococcus populations persist in the environment at different rates. Enterococci, while present in lower concentrations in animal manure, are generally more environmentally resilient than Streptococci. This uneven survival complicates the interpretation of ratios over time, particularly where pollution is not recent.

A similar approach involves comparing the ratio of faecal coliforms to faecal streptococci (the FC:FS ratio). A ratio greater than 4 typically indicates contamination of human origin, while a ratio less than 0.7 suggests animal-derived pollution. However, this method faces the same limitation: coliforms, streptococci and enterococci decline at different rates once in the environment, which can distort the original signal and lead to misinterpretation of the pollution source.

A test criterion is a limit or threshold, usually established by growers, food safety assurance schemes, or testing laboratories, that defines the maximum acceptable count of indicator bacteria in a sample. These criteria help determine whether irrigation water, soil amendments, or produce meet safety standards for use or sale, aiming to minimise microbial risks in agricultural production.

Thermal water treatments are methods used to reduce or eliminate microbial contamination in irrigation water by creating conditions that are unfavourable for bacterial survival. Thermal treatment typically involves heating the water to temperatures that kill or inactivate pathogens. In agriculture, these treatments can be valuable tools to improve the microbial safety of water used on fresh produce, helping to reduce the risk of contamination during irrigation.

Ultraviolet light (UV) is electromagnetic radiation with wavelengths between 200 nm and 400 nm. Exposure to UV radiation damages the DNA of microorganisms, leading to reductions in the number of viable bacteria and other pathogens.

In agriculture, UV light is increasingly used as a non-chemical method to disinfect irrigation water, helping to reduce microbial risks associated with waterborne pathogens on fresh produce. However, the effectiveness of UV treatment depends heavily on water quality, particularly its clarity, as suspended solids and cloudiness can significantly reduce UV penetration and therefore its disinfecting power. Proper water filtration before UV treatment is often necessary to ensure optimal microbial control.

Water application methods in agriculture include drip hoses, overhead sprinklers, rainguns, and buried porous pipes. Each method influences the potential microbial risk to crops, particularly fresh produce, in different ways.

Buried porous pipes apply water below the soil surface which reduces direct contamination of the crop surfaces but may still pose risks if the water carries pathogens that can persist in soil or be taken up by plant roots.
The choice of irrigation method should therefore consider the microbial quality of the water source, the type of crop, and the stage of crop development to minimise the risk of introducing human pathogens into the food chain. Proper water treatment and management practices are essential to reduce microbial risks associated with irrigation.

Drip irrigation delivers water directly to the soil near the plant roots, minimising contact between water and the edible parts of the crop. This reduces the risk of microbial contamination from irrigation water, making it one of the safer methods along with buried pipes when using water of uncertain microbial quality.

Overhead sprinklers and rainguns spray water over the entire plant canopy, including leaves, flowers, and fruit. This widespread wetting increases the likelihood that any pathogens present in the irrigation water, such as Escherichia coli, Salmonella, or Listeria, will be deposited directly onto the edible surfaces of the crops. This raises the microbial risk, especially if contaminated water is used or if conditions favour pathogen survival and growth.

Wildlife includes domestic and wild animals such as foxes, squirrels, and pests like rats (excluding insects). These animals can carry harmful pathogens like Salmonella, E. coli, and Listeria, which they shed in their faeces. Wildlife access to fields or water sources can contaminate fresh produce and irrigation water, increasing the risk of foodborne illness. Managing wildlife presence near crops is important to reduce microbial contamination risks.

Yersinia is a genus within the Enterobacteriaceae family. While most strains are non-pathogenic, some species can cause serious illnesses in humans, including bubonic plague, and have been associated with inflammatory bowel disease. In agriculture, the presence of Yersinia, like other Enterobacteriaceae, serves as an indicator of general hygiene and potential faecal contamination in environments where crops are grown and processed.

A zoonosis is a disease transmissible from animals to humans. In many cases, animals carry the infectious agent without showing symptoms, but when humans become infected, illness can result. Zoonotic diseases are important in agriculture because contact with livestock, wildlife, or contaminated environments can pose risks to farm workers and food safety.