Some organic waste can be used directly as amendments in agricultural soils, especially animal manure; crop residue, such as cereal straw; and pruning residue, among others. For instance, vines are traditionally incorporated into vineyard soils in Spain. Manure, which is a collective term for excretions of different animal species in combination with straw and other plant materials but also livestock feed residues, improves soil properties through increased organic carbon and nutrients in soils. However, organic matter in manure may be quickly degraded because of its low carbon-to-nitrogen ratio [6]. Similarly, returning straw to the soil takes advantage of the large contents of organic carbon to improve soil physical and chemical properties, for instance porosity and bulk density [7], benefitting the growth of crops, but it may also have negative effects caused by organic acids production during decomposition [8]. In addition, the high C/N ratio hinders soil organic matter formation due to the lack of adequate nutrient supply. The same reason might lead to limited nutrient supply to plants when straw is applied alone to soils.

While the benefits of direct application of organic waste are many, not all should be applied directly to soil. In some cases, there are potential risks associated with their composition and transformation processes in soils, such as the leaching of readily available nutrients, especially nitrogen in form of nitrate, into the groundwater [9]. Other materials such as manure can also benefit from previous transformation processes to be converted into amendments better suited for soil application, even if their direct application is feasible.

Composting is a process of biological decomposition and the stabilization of organic matter under aerobic conditions through the action of diverse microorganisms. Although composting is a method that has been used since ancient times for waste transformation and soil fertilization, scientific studies about its fundamentals have only begun to be published in the past four decades. Several methods and systems for composting have been developed, varying in scale and purpose from home-made systems in individual households, over medium-sized, on-site reactors operated by farmers, to large, high-tech systems used by professional producers. The fundamental physical, chemical and biological and aspects of composting are always the same despite different techniques, and knowledge about the interactions and dependence of factors and competing forces within a composting matrix have recently been investigated. These include the suitability of different feedstocks and amendments as well as their adequate composition, porosity and free air space, moisture control, energy balance as well as substrate degradability, decomposition and stabilization [10,11]. This process has three typical phases. The first one is a moderate-temperature (mesophilic) phase and after a few days, a high temperature of over 60 °C is reached (thermophilic phase). This phase is very important to eliminate pathogenic bacteria and seeds. Finally, the last phase is the maturation stage, leading to the final stabilized organic matter.

Composting allows us to stabilize organic residues before application to soil avoiding crop damage that can come from highly biodegradable fresh residues, but it also allows to blend materials that are not easily composted alone. Animal manure is typically composted to improve its properties [12], as well as plant-derived materials such as pruning residues [13], cereal crop residue [14], grape marc and other winery waste [15,16], olive pomace [17] or fruit and vegetable waste [18]. These organic residues are also commonly treated by co-composting processes using more than one feedstock (Table 1). The final product of this biological process is compost, a stabilized substrate rich in organic matter, free of pathogens and plant seeds, which is suitable to be added to the soil as an organic fertilizer. Composted organic residues are typically used in agriculture and horticulture, as well as to produce topsoil for landscaping or land restoration activities, including phytoremediation [19].

A similar technique is vermicomposting, which is a decomposition process involving microorganisms and earthworms. A disadvantage of vermicomposting is that it does not reach high temperatures [20], lacking the proper elimination of pathogens and seeds. Therefore, vermicomposting should not be used alone. Instead, vermicomposting and traditional composting should be combined, beginning with a partial pre-composting followed by a finishing stage of vermicomposting [21].

Charred organic material has been added to soil in ancient agricultural systems all over the world [36], in addition to the Terra Preta phenomenon [37], precedents of the current use of biochar as soil amendment. Agro-industrial residues employed preferentially for biochar production are wood, sawdust and crop residues, including straw and woody materials such as pruning residues. Biochar is produced by the thermal treatment (>400 °C) of organic materials, e.g., by pyrolysis or gasification under oxygen-deficient conditions. Different technologies are available for biochar production: these include charcoal stacks, the traditional way of converting wood to charcoal [38]; rotary kilns, which are cylindrical-shaped pyrolizers, externally heated, where biomass is moving continually via rotating spirals. The Pyreg process is a patented pyrolysis characterized by biomass allothermic gasification. Wood gasifiers produce biochar in a fixed-bed, downdraft, open core, compact gasifier with the main purpose of electricity production; they are normally fed with pure and clean wood rather than on agricultural organic residues. Preferred technologies are pyrolisis systems and gasification because of emissions free of toxic compounds and the beneficial use of released energy, e.g., for electricity production or heating purposes [38].

Biochar has been proven to increase soil organic carbon, nutrient availability, and water holding capacity over a long time period and to sequester carbon [39,40]. Biochar affects crops and soils differently [38], and its addition to soil should be additionally considered as a strategy to mitigate the negative effects of climate change [40,41].

Anaerobic digestion is a biological process in which organic matter is decomposed and stabilized in the absence of oxygen. As a result of the decomposition under anerobic conditions, a gas mixture known as biogas is produced, containing essentially methane (50–75%) and carbon dioxide (30–40%), which can be used to generate heat or electricity as a substitute for fossil fuels [42]. Therefore, anaerobic digestion allows the conversion of organic waste into a renewable source of energy. This technology is very useful for those agricultural waste with high moisture, and in particular for liquid manure.

In addition to biogas, the anaerobic digestion of agricultural waste also products digestate, a by-product that can be used as a soil amendment [43]. However, digestate should undergo a composting/stabilization stage before application to soil for easier management and an efficient agronomic use as fertilizer [44], in order to reduce odors, ammonia emission and risk of nutrient leaching. Digestate has been applied to soil proving good fertilizer value, increasing soil organic carbon and stimulating soil biological activity [45,46].

Finally, advantages and disadvantages of the options presented for organic waste use on soil are summarized in Table 2.