# A Snapshot of the Microbiome of a Portuguese Abandoned Gold Mining Area
## 3 Results and Discussion  
### Microbiome Diversity and Community Structural Organization  
The microbiome analysis was achieved by sequencing the V3/V4 hypervariable regions and the ITS2 subregion with the Illumina MiSeq(r) sequencing platform. Tables 1 and 2 highlight the metabarcoding statistical data obtained and the diversity indexes calculated for each sample considered during the course of this study. For bacteria, a total of 70,685 reads were obtained, with the OTU number determined for each sample fluctuating between 889 (mine) and 1679 (control). Complementarily, for fungi, 185,740 reads were obtained, with the OTU number determined for each sample fluctuating between 254 (tailings) and 684 (control). Based on the aforementioned results, it was evident that fungi constituted the most abundant group at these sites. By examining the obtained Chao1, sobs and the coverage values, it can be verified that for both taxonomic groups, their diversity was successfully recovered and analyzed. Complementarily, when considering the results obtained for the biodiversity indexes, the values demonstrated the existence of a relatively high bacterial and fungal diversity in all sites. For both cases, the uppermost diversity values were verified in the control, while the lowest were verified in the mine for bacteria and in the tailings for fungi. High evenness levels were observed for bacteria and intermediary for fungi, pointing towards the presence of a relatively homogenous bacterial taxa distribution and the presence of some dominant fungal taxa among the studied areas. In parallel, the results also revealed the detection of 2575 OTUs for bacteria and 1039 for fungi across all samples. For bacteria, 262 OTUs were common to all sites, with the largest unique OTU number being found in the control (829), followed by the tailings (426) and the mine (333) (Figure 2). On the other hand, for fungi, 31 OTUs were found in all samples, with the largest unique OTU number being found in the control (468), followed by the mine (210) and the tailings (124) (Figure 2). The results obtained for the PCA analysis can be verified in Supplementary Figures S1 and S2. For bacteria, the control and tailings samples clustered somewhat closer together, thus indicating a more similar composition and distribution while also implying that their structural diversity is less exclusive to either of these sites. Additionally, it could also be verified that the majority of the OTUs clustered in a somewhat dispersed pattern when taking into account the different samples. In contrast, for fungi, all the samples clustered \begin{table}
\begin{tabular}{c c c c c c c c c} \hline \hline
**Sample** & **nseqs** & **Coverage** & **Chao1** & **Sobs** & **Shannon** & **Shannoneven** & **Simpson** & **Simpsonen** \\ \hline
**Control (P1)** & 28,226 & 0.994 & 1,785,009 & 1679 & 6282 & 0.846 & 0.006 & 0.099 \\
**Tailings (P2)** & 15,845 & 0.988 & 1,366,039 & 1256 & 5911 & 0.828 & 0.009 & 0.084 \\
**Mine (P3)** & 26,614 & 0.995 & 1,018,000 & 889 & 5244 & 0.772 & 0.015 & 0.073 \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Metabarcoding statistical data and biodiversity indexes obtained for bacteria. \begin{table}
\begin{tabular}{c c c c c c c c} \hline \hline
**Sample** & **nseqs** & **Coverage** & **[PERSON]** & **[PERSON]** & **[PERSON]** & **[PERSON]** & **[PERSON]** & **[PERSON]** \\ \hline
**Control (P1)** & 46,115 & 0.999 & 7,055,769 & 684 & 44,333 & 0.6791 & 0.034 & 0.043 \\
**Tailings (P2)** & 91,776 & 1.000 & 2,707,143 & 254 & 24,392 & 0.4405 & 0.172 & 0.023 \\
**Mine (P3)** & 47,849 & 0.999 & 383,625 & 369 & 36,553 & 0.6184 & 0.061 & 0.044 \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Metabarcoding statistical data and biodiversity indexes obtained for fungi. Figure 2: Venn diagrams displaying the number of shared bacterial and fungal OTUs across samples. in a more heterogeneous manner, indicating a dissimilar composition and distribution and pointing out that their structural diversity is somewhat more restricted to each site.