## 1 Introduction  
A considerable amount of bio-waste is constantly produced in Bulgaria. Some of the waste ends up in landfills, contrary to the EC Waste Framework Directive and the goals set for the member states to reduce the landfill of biodegradable waste [1]. Biowaste composting is an aerobic process of recycling organic substances and turning them into valuable products for soil and plants [2, 3]. The quality of such end-products depends on many different factors. The degradation of biopolymers and simpler organic molecules is carried out by aerobic microorganisms with correctly implemented technology. Until a decade ago, the study of quantitative and qualitative indicators of this microflora was carried out by many indirect and less direct techniques. With the development of new technologies and next-generation sequencing (NGS), it is possible to reveal the participating microorganisms, prokaryotes and eukaryotes, and their quantity, abundance, metabolic abilities, etc. [4]. In addition, in-depth research of microbial diversity would allow for better control over how composting proceeds.  
According to different authors [5, 6], the temperature of composting is essential to estimate the final quality and applicability of compost. High temperatures can kill pathogensin compost and promote the degradation of organic matter [7]. Generally, the composting process could be separated into different phases or stages depending on temperature [8]. [PERSON] and co-authors [9] determined four composting stages based on the temperature--mesophilic, thermophilic, cooling, and maturing. Various scientists analyzed the dynamics and composition of the microbial population during the composting of various types of organic wastes [10; 11; 12]. Diverse traditional methods (culture-dependent) have been used for decades to study bacterial diversity in composting [13]. Recently, researchers have developed various molecular biological techniques to build detailed information linked to microbial community composition during composting time. Some methods are clone library, DNA fingerprinting, qPCR or investigative microarrays [14; 15; 16]. The 16S rRNA sequence-based molecular technique has become a valuable method to identify the specific microorganisms in compost and soil samples [17; 18].  
Investigations related to microbial diversity of composting are often very detailed and are related to a specific group of prokaryotes, for example, to the nitrogen cycle, nitrifying and denitrifying bacterial communities [3]. Other researchers are studying changes in the dynamics of bacterial communities in compost and their metabolic functions [19]. In addition, [PERSON] and collaborators [20] investigated the diversity of prokaryotes and eukaryotes and the relationship of community structure to physicochemical parameters of habitats. The recovery of biowaste through composting depends on many factors, and the comparison between research papers is sometimes indirect due to the different factors in different studies. These differences are related to both waste types and environmental factors. These are some reasons that research on the structure and functions of microbial communities in composting is extremely limited, insufficient and not diverse. We know that different microclimatic conditions create opportunities for the development of different prokaryotic communities with a similar metabolic profile occupying the same ecological niche. Since high throughput sequencing technology has been applied to composting, the investigations are now based on both qualitative and quantitative determination of microorganisms and reveal their numbers and metabolic abilities. In this sense, the main objective of the present study was to reveal the existing difference in prokaryotic diversity of composting of biowastes in thermophilic and mesophilic phases of two sites in South Bulgaria using the metagenomic approach.