Microbial diversity at remediated former gold and copper mines and the metal tolerance of indigenous microbial strains

Abstract

Metamorphic Devonian rocks in the northern Moravian Jeseník district (Czech Republic) contain non-vein polymetallic, copper, and gold deposits. Sulfide leaching following previous mining activities has caused significant chemical and physical alterations in the local environment, resulting in biological process shifts. Here, we present a detailed microbiological survey of the Zlaté Hory mine and its adjacent features, including tailings, sediments, and treated mine water. In addition, we isolated metal-tolerant bacteria and fungi as potential candidates for the bioremediation of mine wastewater. Microbial community analysis revealed differences driven by environmental conditions. Acidotolerant consortia, for example, Gallionella sp. and Ferrovum sp., were mainly detected in the acidic shaft outflow (pH 3.07, conductivity 1,351 µS.cm^-1). Subsequent treatment and pH neutralization led to the presence of metal-tolerant heterotrophs, including fungi, despite elevated heavy metal concentrations. Notably, the highest microbial diversity was observed in drainage water with low metal content. These findings suggest that physicochemical factors, such as pH and metal/metalloid concentration, play a pivotal role in shaping environmental microbiomes and influencing community composition. Furthermore, while biogeochemical processes (e.g., Fe(II) oxidation, sulfide precipitation, metal immobilization) may already be contributing to natural mine water remediation, unfavorable equilibria in the iron cycle caused by acidification could be compensated for through bioremediation using beneficial microorganisms, such as Variovorax or Arthrobacter isolates.IMPORTANCEMicroorganisms play a crucial role in the biogeochemical cycles of elements, for example, carbon and sulfur, and metals. As ubiquitous ecosystem components, they have a significant influence on most processes on Earth. Investigating microbial diversity is essential for understanding these processes, particularly in extreme environments such as mining sites. Microorganisms from mining sites often develop resistance to harsh conditions, including high concentrations of heavy metals and acidity. In addition, certain microbes can metabolize or transform toxic substances, contributing to the remediation of other contaminated environments. As mining activities persist or legacy sites degrade, microbial data become invaluable for predicting long-term environmental impacts and informing sustainable management practices.

Keywords: acid mine drainage; bioremediation; metal-tolerant microorganisms; polymetallic ore; tailing site.

Fig 1

Schematic overview of the two campaigns of sampling in the former Zlaté Hory mining site (A) and water treatment plant (B).

Fig 2

Alpha diversity (A and C) and PCoA (B and D) of bacterial communities in water (A and B) and solid (C and D) samples, based on data from sequencing analysis using the 16S rRNA primer targeting bacteria.

Fig 3

Relative abundance of bacterial phyla based on sequencing of the 16S rRNA gene in water (A) and solid (B) samples.

Fig 4

Alpha diversity (A and C) and PCoA (B and D) of bacterial communities in water (A and B) and solid (C and D) samples based on data from sequencing analysis using ITS rRNA primer targeting fungi.

Fig 5

Relative abundance of fungal genera as detected by sequencing of the ITS rRNA in the water (A) and solid samples (B).

Fig 6

Detection of metal localization, determined by STEM-HAADF and growth curves for selected strains and metals. (A) Micrograph of culture #4 incubated with 1 mM Zn(NO₃)₂ (scale bar = 1 µm), inset = zinc nanoparticles (scale bar = 500 nm). (B) Micrograph of culture #20 incubated with 2 mM Cu(NO₃)₂ (scale bar = 1 µm). (C) Micrograph of culture #14 incubated with 2 mM Zn(NO₃)₂ (scale bar = 1 µm). (D) Micrographs of culture #21 incubated with 2 mM Cu(NO₃)₂ (scale bar = 1 µm).