## 3 Results
### NGS Approach for Elucidation of Eukaryotes Biodiversity in the Compost  
The NGS analysis of the sequenced 148,049 eukaryotic amplicons showed that in the initial phase of active degradation, the thermophilic fungal community was composed mainly of phyla the _Ascomycota_ (89.96%) and _Basidiomycota_ (3.36%). At the same time, in the mesophilic community, _Ascomycota_ was less abundant, with 77.97% representation, while the _Basidiomycota_ distribution was higher (Figure 4A). In both kinds of habitats, fungi of the class _Sordariomycetes_ were at almost equal amounts of approximately 66.79-67.20%. These fungi participate most actively in both phases of organic matter degradation in composting. _Pezizomycetes_ were represented by 12-18% of the fungi, with a slight advantage over thermophilic ones (Figure 4B). We have a greater difference between the two phases in the case of the _Agaricomycetes_ class, where the mesophilic representatives are 21.7%, and the thermophilic ones are 13.2%. The distribution of fungal genera is presented in Figure 5 and Supplementary Figure S2. The fungi from genera _Psathyrella_ were the dominant populations in themesophilic habitats (35.91%), while in the thermophilic environment the abundance decreased by nine to 4.08% (Figure 5A,B). It seems that most of _Psathyrella_ populations are mesophilic, as their representation was strongly reduced at a lower temperature. The three further most dominant fungal genera were _Chuetomidium_, _Mortierella_, and _Cheilymenia_. _Chaetomidium_ increased to 20.11% in the 37.2 \({}^{\circ}\)C pile, dramatically reducing the population deep in the compost mound to 0.65%. Similarly, the abundance of _Cheilymenia_ decreased to 4.76% at 58.1 \({}^{\circ}\)C. However, the amount of _Mortierella_ was increased in thermophilic habitats by 32.5% compared to with the mesophilic ones, reaching 22.91%. Furthermore, _Thielavia_ sp. was predominant in the inner part of the compost pile, representing almost 55% of all genera where conditions were thermophilic. Both of them represented more than 78% of all thermophilic genera. With increasing depth and temperature, Penicillium and Verticillium frequency increased. Numerous mesophilic fungi such as _Acremonium_, _Fusarium_, _Microscus_, _Trichoderma_, and _Verticillium_ proliferate during the cooling and curing phases. Many of the fungi we found are known to be widespread saprophytes on soil and dead plant tissue [23]. They occur in compost, given their ability to produce cellulolytic enzymes [24]. \begin{table}
\begin{tabular}{c c c c c c c} \hline \hline
**Sample** & **[PERSON]** & **Simpson** & **Chao1** & **ACE** & \begin{tabular}{c} **Goods** \\ **Coverage** \\ \end{tabular} & \begin{tabular}{c} **PD Whole** \\ **Tree** \\ \end{tabular} \\ \hline \
\begin{tabular}{c} Compost \\ at 37.2 \({}^{\circ}\)C \\ \end{tabular} & 10.417 & 0.994 & 2623.109 & 2638.908 & 0.987 & 209.132 \\
\begin{tabular}{c} Compost \\ at 58.1 \({}^{\circ}\)C \\ \end{tabular} & 6.972 & 0.889 & 1654.224 & 1775.459 & 0.990 & 126.207 \\ \hline \hline \end{tabular}
\end{table} 
Table 3: The range of \(\alpha\)-diversity values in the compost samples. Figure 4: Microbial community composition with the number of OTUs identified by MG-RAST at the phylum level (**A**) and class level (**B**). Unassembled reads annotated on MG-RAST were analyzed using the classification tool based on RDP (97% identity; the e-value cutoff of 10,230) and MSNR (60% identity; the e-value cutoff of 1025) with a minimum alignment length of 50 bp. The figure displays the taxonomic distribution for the 10 most abundant phyla and classes. Figure 5: Analysis of taxonomic annotation with the number of OTUs identified by MG-RAST. (**A**) Mesophilic and (**B**) thermophilic habitats. Area of sector means respective proportion of different OTU annotation results in percent.