Composting is defined as a bio-oxidative process involving the mineralization and partial humification of the organic matter, leading to a stabilised final product, free of phytotoxicity and pathogens and with certain humic properties, which can be used to improve and maintain soil quality and fertility [25]. Composting of animal manures has been traditionally carried out by the farmers after manure collection for better handling, transport and management [6]. Frequently, the wastes were heaped up and very little attention was paid to the process conditions (aeration, temperature, ammonia loss, etc.) and using rudimentary methodology.

From a microbial viewpoint continuous composting processes may be described as a sequence of continuous cultures, each of them with their own physical (temperature), chemical (the available substrate), and biological (i. e., the microbial community composition) properties and feedback effects. These changes make it difficult to study the process, which is virtually impossible to simulate in the laboratory since temperature, moisture, aeration, etc., are directly related to the surface/volume ratio. However, in general, composting may be described as a four-phase process in which the energy-rich, abundant and easily degradable compounds like sugars and proteins are degraded by fungi and bacteria (referred to as primary decomposers) during an initial phase called the mesophilic phase (25-40 °C). Although there exists a competition between both microbial groups regarding the easily available substrates, fungi are very soon outcompeted because the maximum of specific growth rates of bacteria exceed those of fungi by one order of magnitude [26]. The importance of bacteria (with the exception of Actinobacteria) during the composting process has long been neglected, probably because of the better visibility of mycelial organisms. A review on the microbial groups involved in the first mesophilic phase is given by [27]. Provided that mechanical influences (like turning) are small, compost fauna including earthworms, mites and millipedes may also act as catalysts, thereby contributing to the mechanical breakdown and offering an intestinal habitat for specialized microorganisms. The contribution of these animals may be negligible or, as in the special case of vermicomposting, considerable (see section 2.2). The number of mesophilic organisms in the original substrate is three orders of magnitude higher than the number of thermophilic organisms; however, the activity of primary decomposers induces a temperature rise and in turn, mesophilic microbiota is, along with the remaining easily degradable compounds, degraded by the succeeding thermophiles. The temperature rise continues to be fast and accelerates up to a temperature of about 62 °C during this second phase of composting, known as the thermophilic phase.

When a temperature exceeding 55 °C is reached in a compost pile, fungal growth is usually inhibited and the thermophilic bacteria and Actinobacteria are the main degraders during this peak-heating phase. Moreover, oxygen supply affects fungi to a greater extent than bacteria, and even in force-aerated systems, temporary anoxic conditions may occur. Hence, fungi play a negligible role during this phase, except for the composting of lignocellulosic residues. Bacteria of the genus Bacillus are often dominant when the temperature ranges from 50 to 65 °C. Moreover, members of the Thermus/Deinococcus group have been found in biowaste composts [28] with an optimum growth between 65 and 75 °C. A number of autotrophic bacteria that obtain their energy by the oxidation of sulfur or hydrogen have been isolated from composts [28]. Their temperature optimum is at 70-75 °C and they closely resemble Hydrogenobacter strains, which were previously found in geothermal sites. Furthermore, obligate anaerobic bacteria are also common in composts, but up to now, there is still a gap of knowledge concerning this microbial group. It is believed that the longer generation times of archaea, in comparison with bacteria, made the archaea unsuitable for the rapidly changing conditions in the composting process. Nevertheless, in recent works, and using the right tools, a considerable number of cultivable (Methanosarcina termophila, Methanothermobacter sp., Methanobacterium formicicum, among others) and yet uncultivated archaea have been detected in composting processes [29-30].

The final temperature increase may exceed 80 °C and it is mainly due to the effect of abiotic exothermic reactions in which temperature-stable enzymes of Actinobacteria might be involved. Such high temperatures are crucial for compost hygienisation in order to destroy human and plant pathogens, and kill weed seeds and insect larvae [31]. The disadvantage of temperatures exceeding 70 °C is that most mesophiles are killed, and therefore the recovery of the decomposer community is retarded after the temperature peak. The inoculation with matter from the first mesophilic stage might, however, solve this problem.

When the activity of thermophilic organisms ceases due to the exhaustion of substrates, the temperature starts to decrease. This constitutes the beginning of the third stage of composting, called the cooling phase or second mesophilic phase. It is characterised by the recolonisation of the substrate with mesophilic organisms, either originating from surviving spores, through the spread from protected microniches, or from external inoculation. During this phase there is an increased number of organisms with the ability to degrade cellulose or starch, such as the bacteria Cellulomonas, Clostridium and Nocardia, and fungi of the genera Aspergillus, Fusarium and Paecilomyces [27]. Finally, during the maturation phase, the ratio of fungi to bacteria increases due to the competitive advantage of fungi under conditions of decreasing water potential and poorer substrate availability. Compounds that are not further degradable, such as lignin-humus complexes, are formed and become predominant. Some authors have proposed a fifth composting phase, known as the curing phase (or storage phase), during which the physico-chemical parameters do not change, but changes in microbial communities still occur [32]. Therefore, the chemical and microbial changes that the substrate undergoes during the different phases of the composting process will largely determine the stability and degree of maturity of the end product and in turn, its safe use as an organic amendment. There exists a wide range of parameters that have been proposed to evaluate compost stability/maturity, as shown in the next section.