# A Snapshot of the Microbiome of a Portuguese Abandoned Gold Mining Area
## 3 Results and Discussion
### Microbiome Diversity and Community Structural Organization
Furthermore, it should be noted that various distinct OTUs clustered in a more assembled pattern with each of the considered samples for this taxonomic group. Taken together, these results highlight that the overall microbiome diversity of the Escadia Grande mining area decreases inside the mine itself and at the tailings. However, bacterial and fungal diversity and distribution are affected differently, as prokaryotes displayed a relatively homogeneous taxa distribution with the lowest diversity found in the mine interior, while fungi exhibited the presence of some dominant taxa, with the lower diversity found at the tailings. Moreover, despite some commonality and the recognition that each site harbors a distinct microbial community, the data also underscores a further notorious site-specific nature of the fungal communities. In general, As, aluminum (AI), potassium (K), silicon (Si), chromium (Cr), mercury (Hg) and Pb concentrations, soil pH and total organic carbon, as well as vegetation density and the specific plant species, have been pinpointed as critical factors influencing the prokaryotic community diversity and structure in similar environments [27; 30; 32; 33; 34; 35; 36]. Moreover, it is also known that less-polluted soils exhibit increased microbial diversities and more complex community structures [30; 32]. On the other hand, fungal communities' structures are known to be more similar across tailings deposits regardless of vegetation density. Moreover, fungal richness increases in a tailor-made trend with contamination level, and biodiversity is not related to the concentrations of inorganic toxicants [29]. As such, the results obtained during the course of this work are in accordance with the literature, showing that the polluted soils from the mining area shape the microbiome diversity. Additionally, our findings suggest that the presence of highly dense fern vegetation in the tailings (see Section 3.2 below for details) and the higher humidity in the mine interior may contribute to the contrasting lower fungal and bacterial diversities verified, respectively. Conversely, the lower diversities observed for a specific group of organisms at these sites might result from the documented increase in the other group, influenced by the specific settings of the location. In other words, the increase in bacterial richness in tailings was likely influenced by the presence of vegetation [35], coupled with a decrease in fungal diversity. Similarly, the observed increase in fungal diversity in the mine is likely influenced by factors such as mine settings (e.g., darkness, acidic environment) and the impact of flooding water, coupled with a decrease in bacterial abundance and richness [39]. The biodiversity results obtained from the metabarcoding analyses are presented in Figures 3 and 4 and Supplementary Files S1-S6. In general, at the Phylum level for bacteria, the control was largely dominated by _Proteobacteria_ (22%), _Plantomycetota_ (15%), _Acidobacterriota_ (14%), _Bacteroidota_ (10%) and _Actinobacterriota_ (8%); the tailings were largely dominated by _Acidobacterriota_ (22%), _Chloroflexi_ (16%), _Proteobacteria_ (15%), _Plantomycetota_ (12%) and _Actinobacterriota_ (7%); and lastly, the mine was largely dominated by _Acidobacterriota_ (22%), _Chloroflexi_ (19%), _Proteobacteria_ (18%), _Actinobacterriota_ (15%) and _Plantomycetota_ (13%). At the family level, the great majority of reads were assigned to families: _Sphingomonadaceae_ (8%), WD2101 soil group (8%), _Chitinophagaceae_ (7%), _Chthoniobacteraceae_ (5%) and _Gemmatimonadaceae_ (3%) in the control samples; _Bryobacteraceae_ (10%), _Kedonobacteraceae_ (6%), WD2101 soil group (6%), unclassified WPS-2 (Candidatus phylum _Eremiobacterota_) (6%) and an additional WPS-2 family (6%) in the tailings; and _Gemmataceae_ (9%), _Pseudonocardiace_ (9%), _Ktedonobacteraceae_ (8%), _Acidobacteriaceae_ (Subgroup 1) (7%) and _Acetobacteraceae_ (6%) in the mine.