A Metagenomic Assessment of Soil Microbial Communities in a Coal Mine Spoil Dump Under Reclaimed Vegetation in La Guajira, Colombia

Recovery of belowground microbial biodiversity is important for soil restoration after mining exploitation. We aimed to compare microbial communities of a mine rehabilitation site to those with native vegetation. Community structure and metabolic potential of soil microbial communities were analyzed in an inactive open-pit coal mine located in northeastern Colombia using GeoChip and high-throughput sequencing techniques. Sites included (1) a spoil dump closed in 2010 with a mix of mesquite trees and native vegetation, and (2) a native dry forest next to the mining area. Most samples had an alkaline pH, high sulfur, zinc, and magnesium contents, and high cation exchange capacity as well as low calcium content. A total of 61,384 bacterial amplicon sequence variants (ASVs) and 402 Eukarya ASVs were obtained. Overall, the most abundant bacterial/archaeal phyla (0.1%) were Acidobacteria, Actinobacteria, Bacteroidetes, and Chlorolexi. The fungal genus Cladosporium dominated all treatments, while Volutella was observed only in the inactive dump. Bacterial alpha diversity was surprisingly higher in the inactive spoil dump than in the forest, while fungal alpha diversity was similar between that treatment and the native dry forest. Fungal genera might be more sensitive to the different treatments, as their abundances were highly influenced by their location compared to bacterial genera. There were no significant differences regarding the metabolic potential of bacterial communities. The GeoChip 5.0S analysis showed that the native dry forest had a higher number of genes related to C, N, P, and Z cycles, metal homeostasis, and organic remediation.

Automated summary

The study compared microbial communities in a mine rehabilitation site and an area with native vegetation. It was found that while bacterial diversity was higher in the rehabilitation site, fungal genera were more sensitive to different treatments. Additionally, microbial communities in the native dry forest had more genes related to carbon, nitrogen, phosphorus, and zinc cycles, metal homeostasis, and organic remediation.