As the world’s population grows, the associated increase in waste production becomes a significant challenge that requires more effective management strategies. Approximately 11.2 billion tonnes of solid waste is generated globally each year. Surprisingly, more than half of this global waste comes from food waste alone. The expected increase in waste generation from two billion tonnes in 2016 to 3.4 billion tonnes in 2050 highlights a major concern. The amount of waste we produce (even without the projected increase) is a growing problem to manage. The direct impact of waste on the environment and climate change cannot be ignored. The natural decomposition of organic components in this waste accounts for around 5% of total global greenhouse gas emissions. This is why the European Commission is making a special effort to reduce the impact of waste through various strategies, such as recycling. One of the outlined targets is to reach the overall recycling target of 65% of municipal waste by 2035, in addition to the need to provide further incentives to improve the separate collection and biological treatment of bio-waste at European level. It is therefore of the utmost importance to use all available methods to reduce the environmental impact of organic waste and to significantly improve the organic matter cycle.

The two main ways of treating bio-waste are composting and anaerobic digestion. The main difference between the two is that the former is an aerobic process. Composting is an environmentally friendly way to reduce organic waste while producing a nutrient-rich fertiliser that can help improve soil properties. In addition, composting can play a significant role in reducing environmental and climate impacts by reducing methane emissions and overall carbon footprint, which, along with improving soil health, is one of the objectives defined in the EU’s Farm to Fork Strategy. However, compost production is not without risk. The main risk is that some seeds, pests and/or pathogens may survive the treatment processes due to pest resistance or treatment process failures. The risk associated with the use of biowaste of plant origin is identified in European and Mediterranean Plant Protection Organisation Phytosanitary procedure (EPPO PM 3/66) and minimum treatment process requirements are recommended to eliminate most pests. Following the recommended guidelines for composting plant material can help to reduce the risks associated with pathogens. On the other hand, if not well monitored and controlled, these waste reuse practices can have disastrous consequences in terms of the spread of pests. To test the successfulness of the procedure, EPPO PM 3/66 suggests the use of indicator organisms, such as stable tobacco mosaic virus (TMV). Leaves infected with TMV should be placed in the biowaste and after composting those leaves should be used for mechanical inoculation of susceptible Nicotiana species and symptom development should be monitored.

During the composting process, the entire quantity of material to be treated should be exposed to temperatures of 60°C or higher for several days (usually 3 days) or a temperature of at least 55°C for longer periods (e.g. a continuous period of 2 weeks). Material for composting comes from a variety of sources, such as animal manure, crop residues, food processing waste, municipal biosolids and waste from households and some industries, and the main risk to plant production is from agricultural and horticultural bio-waste, which can be infected with plant pathogens. The temperatures reached during the composting procedure, in theory, should eliminate most of the pests (pathogens, seeds, insects), however, solid evidences that some pests may survive treatment process have been provided by several research groups. Residues of solanaceous plants can be particularly dangerous in this respect, as they are hosts to some of the most notorious heat-resistant viruses, such as TMV. In addition to heat tolerance of some pests, the reason why some pests can survive composting could be connected to the failures in the treatment procedures. Occurrence of dry pockets in composting heaps is probably the main cause of pathogen survival. At the moment, plant health professionals do not advise the use of compost from infested residues in susceptible crops. In the Pest Risk Assessment for tomato brown rugose virus (ToBRFV, Tobamovirus, Virgaviridae) which is the biggest problem in the production of solanaceous crop worldwide, is noted that composting may be insufficient for the secure inactivation of the virus. Therefore, Slovenian Ministry of Agriculture, Forestry and Food in the “Emergency measures plan for tomato brown rugose fruit virus (ToBRFV) in the Republic of Slovenia” forbids the use of compost from infected plants in the case of suspected ToBRFV infection (to fertilise ToBRFV host plants). In addition, due to uncertainties regarding the survival of ToBRFV in soil as described in the EPPO pest risk assessment, the use of ToBRFV-infested substrate/soil for the cultivation of ToBRFV host plants is prohibited for one year. To clarify this epidemiological aspect, it is therefore of utmost importance to provide more experimental data on the survival of viruses/viroids in soil/growing substrate and on their potential to be transmitted to growing plants. Besides some viruses that are known for their notorious stability, plant infecting viroids are also known for their high tolerance to thermal inactivation. As an example, under experimental conditions, the hop stunt viroid (HSVd) was still able to infect plants after heat treatment for 10 min at 140°C. Due to the complexity of the composting process and the variety of organic waste it contains, it is crucial that the risk assessment verifies the effectiveness of waste treatments carried out in laboratories, testing stations or produce processing plants.

Another product derived from compost material that can be used to mitigate plant pathogens is compost tea. Compost teas are seen as a natural remedy against plant pathogens and a potential alternative to the use of common synthetic fungicides in response to the increasing need for environmentally friendly agriculture, food safety and sustainability in agriculture. Compost tea is a fermented liquid organic preparation usually of mature compost with tap water in a ratio of 1:5 or 1:10 (v/v) with or without aeration and optionally with nutrient additives. The uncertainty associated with the potential transfer of resistant environmentally stable plant pathogens through the use of compost tea has not been assessed. There are also no recommendations for the use of compost tea in the EU nor in the EPPO.

One of the novel and innovative approaches to break down low-value organic matter and convert it into high-value fertiliser is insect-mediated bioconversion. This process takes place in large-scale insect farming, which has emerged in recent years as a promising measure to address prevalent socio-environmental issues, requiring less land and water while producing lower greenhouse gas emissions compared to the conventional production. Although insect farming is primarily focused on protein and fat production, the rearing residues produced can be used as high-value organic fertiliser and can contribute significantly to farm profitability. These residues include excreta, exuviae, undigested substrates and dead insects and are commonly referred to as insect frass. Insect frass can be produced by various insects that are used to produce high quality protein ingredients in animal feeds, among which saprophytic insects such as the black soldier fly (Hermertia illucens L.) have promising potential. The use of frass fertilisers can have many benefits, such as contributing nutrients to the soil, adding biomolecules and microorganisms that promote plant growth, and increasing tolerance to abiotic stresses and resistance to pathogens and pests through the presence of various compounds and microorganisms. Current research on insect frass is mainly focused on identifying the promising benefits of its use, but potential phytosanitary risks shouldn’t be neglected and they can present a significant uncertainty during pest risk assessment process. Therefore, the EU Commission has established a detailed definition of insect frass and placed it in the same group as processed animal manure to increase product safety and reduce potential health hazards from pathogens in insect products. This Regulation introduces the first hygiene standards for insect frass, requiring farmers to heat-treat frass at a temperature of 70°C for at least 60 minutes. Temperatures higher than 70°C have not been considered because the energy requirements for potential pre-treatments may be too high to be practical. To date, only limited studies have been carried out to investigate the effect of heat treatment on black soldier fly larvae, showing a reduction in bacterial pathogens such as Enterobacteriaceae, Salmonella and Clostridium perfringens below the detection limit. The potential risk of transmission of highly stable plant pathogenic viruses and viroids through insect frass has not yet been investigated.

Due to their physical and biological properties, the viruses/viroids with the highest survival risk in organic waste fertilisers also have a high epidemic potential. Therefore, the survival of even minute amounts of a particular virus/viroid can lead to serious epidemics in susceptible crops that may not be contained. Closing the knowledge gaps on the potential epidemiology of viruses/viroids in organic waste fertilisers can therefore lead to a reliable pest risk assessment and consequently provide us with better means to contain further spread. The most important step in these management strategies is the timely and accurate detection of certain pests on which control measures will be based. Recent advances in high-throughput sequencing (HTS) techniques allow simultaneous non-targeted detection of the presence of nucleic acids from any organism present in a sample, including distant variants and uncharacterised organisms. Also, economically very important plant viruses as well as quarantine viruses can be detected by HTS without an a priori information on the infectious status of the sample. In comparison, when using targeted methods, we need different tests for each pathogen or a few similar pathogens, requiring significant input of resources, personnel and time. Therefore, in recent years significant efforts have been made to obtain the guidelines for the implementation of HTS in the diagnostics of plant pathogens (35, 36). In this regard, since organic waste fertilisers can be composed of residues of mixed and often unknown origin, untargeted methods, such as HTS, seems especially suitable for investigation of viral presence in such matrices. The adaptation of the HTS method for screening for viruses and viroids in organic waste fertilisers may be of utmost importance for decision making with regard to the risk assessment of the use of these types of fertilizers.

The project will address important research questions about the risks associated with plant viruses and viroids when using fertilisers made from organic waste. Specifically, our aims are:

• To develop an efficient method for the detection of plant pathogenic viruses and viroids in organic waste fertilisers. Since the composition of the matrix can significantly influence the retention of viral particles, the development of suitable isolation methods represents the first major aim in our study. In addition to targeted detection methods for the monitoring of plant pathogenic viruses and viroids, such as PCR-based methods, we are also planning to introduce and validate a non-targeted HTS approach.
• To investigate the virome of various organic waste fertilisers, including insect frass, which has been particularly understudied in this regard. This data will allow us to better assess whether the use of such fertilisers could pose a potential risk to agriculture and horticulture in terms of plant viruses and viroids.
• To determine the persistence of selected stable viruses and viroids in organic waste fertilisers and in growing substrate. We will assess the persistence of virus/viroid-infected plant material in insect frass and compare this with the efficiency of degradation during the composting process under strictly controlled conditions with defined substrate and inoculum concentrations and with degradation in the growing substrate alone.