The assessment of microbial composition in mining environments is of growing interest because microorganisms are essential for the resilience of disturbed ecosystems (30, 31, 32). Displacement and accumulation of soils and rocks exposed to weathering cause significant physicochemical changes that alter the composition and functionality of these communities (33). This study aimed to comprehensively compare the microbial communities of different soil types and pit ecosystems in the context of an open pit mine.
All Shannon indices of soil samples showed a high bacterial richness, higher than that of fungi. For both types of microorganisms, Shannon indices were lower in engineered soils compared to topsoil and pristine soil. Pit samples had a lower value than soils for both bacteria and fungi. Similar to soils, Shannon indices were higher for bacteria than for fungi, with the exception of the gray pit (GP), which shows a predominance of a few species. The water sample (WP) showed the highest diversity, with microorganisms present in soils and pits, highlighting the role of water in transporting microorganisms from one ecosystem to another (34). Similarly, the Chao1 indices were higher in the soil samples than in the pits for bacterial and fungal communities, both indices indicating that the soils generally had higher microbial diversity than the pits, probably due to the greater complexity of the soils in terms of nutrient availability, physicochemical variations, and the possibility of interaction with other microorganisms (35). On the contrary, pyroclastic pits are considered extreme ecosystems; they are poor in nutrients, exposed to UV radiation and to the formation of acidic waters that limit the growth of most microorganisms (36).
Taxonomic analyses revealed dominant phyla such as Proteobacteria, Acidobacteria, and Actinobacteria in the soils. These results are consistent with previous studies highlighting the adaptability of these phyla to mining-impacted soils (37, 38). In contrast, the pit bacteria were predominantly Proteobacteria, a phylum known to prevail in extreme conditions such as heavy metal exposure and nutrient deficiency in pit ecosystems (39).
Some extremophilic bacteria such as the nitrifying acidophilic bacteria Nitrosovibrio and the sulfur compound producers Holophaga or the soil stabilizer Acidobacterium predominated in topsoil and pristine soil (40, 41). Technosoils harbored Bacteroides and Acidovorax, which are uncommon in natural soils, indicating anthropogenic influence (42). The revegetated technosoils (TCP) showed the highest diversity with genera such as Thiobacillus, Anaeromyxobacter, Geobacter, and Geothrix which are associated with bioremediation and revegetation processes (43, 44, 45). It is suggested that their abundance is related to the introduction of amendments and soil revegetation (46).
Among the pit microbiota, Pseudomonas was predominant in oxidized rock (POD, POW) and HR samples. Pseudomonas is able to colonize even the most hostile environments due to its adaptability and resistance to contaminants (47, 48, 49). Other genera such as Burkholderia or Serratia were highly abundant in gray pits (GP) and HR respectively. These ubiquitous bacteria are also involved in organic matter degradation, shows metal resistance and nitrogen fixation in mine tailings (50, 51). Pit water (WP) shows diverse bacteria such as Acinetobacter and Rhodanobacter, that contribute to soil mineralization and denitrification in acidic environments (52).
Few studies have analyzed the fungal community structure of environments impacted by mining activities, with Basidiomycota and Ascomycota being the dominant phyla (53, 54). Here we observed that Ascomycota dominated pristine soil and topsoil, followed by Basidiomycota while Basidiomycota outnumbered Ascomycota in freshly prepared or vegetated technosoil (55).
The pristine soil fungal community was dominated by saprophytic genera such as Archaeorhizomyces, Mortierella and Sphaerosporella that grow in the soil and around roots (56, 57, 58). Coprinellus is another saprophytic fungus that has been reported only on technosoils. This ligninolytic genus has been associated with wood degradation, especially pine which is one of the components of technosoils (59, 60). At the pit level, fungal genera showed large variation among samples.
The Bray-Curtis indices in the soils revealed 2 important lessons; (1) that a clear differentiation in bacteria and fungi was observed between soils with and without amendments. (2), within the unamended soils, it is observed that the pristine soil is separated from the topsoils, and therefore, these soils have lost many characteristics of their original state. This should be contrasted with the profound physico-chemical changes that these soils undergo when displaced and piled, with the death and degradation of macro-organisms that are buried, with the lack of oxygen, light and water. To restore these soils in an effective way, pristine soils should be considered as a reference and could serve as a source of inoculation of important microorganisms for the restoration process, which have been lost or are scarce in the areas to be rehabilitated (54, 61).
For pits, the Bray-Curtis index reflected how fungi are directly influenced by; (1) moisture conditions (wet pit POW - water collected WP, different from dry pit POD), (2) different rock compositions and/or sulfur content, and (3) disturbance caused by traffic (HR). No clear pattern of similarity in the prokaryotic communities could be observed or matched with the above characteristics. We can speculate that the variation of similarities between clusters of bacterial and fungal communities is due to the "extreme" environment represented by these pits, exposed to dust, weathering, lack of nutrients, solar radiation and extreme pH, among others (35). It is also very likely that the variations in microbial community structures observed in our study are also influenced by micro-variations in the mineral composition of the pit (62, 63, 64). Due to their extension and verticality, remediation options for pits are more limited than for soils. A strategy combining the inoculation of pit ubiquitous microorganisms with amendments would promote the formation of a stable protective biofilm to prevent the formation of acidic water and heavy metal drainage.