Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage

Abstract

Acid mine drainages are characterized by their low pH and the presence of dissolved toxic metallic species. Microorganisms survive in different microhabitats within the ecosystem, namely water, sediments, and biofilms. In this report, we surveyed the microbial diversity within all domains of life in the different microhabitats at Los Rueldos abandoned mercury underground mine (NW Spain), and predicted bacterial function based on community composition. Sediment samples contained higher proportions of soil bacteria (AD3, Acidobacteria), as well as Crenarchaeota and Methanomassiliicoccaceae archaea. Oxic and hypoxic biofilm samples were enriched in bacterial iron oxidizers from the genus Leptospirillum, order Acidithiobacillales, class Betaproteobacteria, and archaea from the class Thermoplasmata. Water samples were enriched in Cyanobacteria and Thermoplasmata archaea at a 3–98% of the sunlight influence, whilst Betaproteobacteria, Thermoplasmata archaea, and Micrarchaea dominated in acid water collected in total darkness. Stalactites hanging from the Fe-rich mine ceiling were dominated by the neutrophilic iron oxidizer Gallionella and other lineages that were absent in the rest of the microhabitats (e.g., Chlorobi, Chloroflexi). Eukaryotes were detected in biofilms and open-air water samples, and belonged mainly to clades SAR (Alveolata and Stramenopiles), and Opisthokonta (Fungi). Oxic and hypoxic biofilms displayed higher proportions of ciliates (Gonostomum, Oxytricha), whereas water samples were enriched in fungi (Paramicrosporidium and unknown microbial Helotiales). Predicted function through bacterial community composition suggested adaptive evolutive convergence of function in heterogeneous communities. Our study showcases a broad description of the microbial diversity across different microhabitats in the same environment and expands the knowledge on the diversity of microbial eukaryotes in AMD habitats.

Untapped microbial composition along a horizontal oxygen gradient in a Costa Rican volcanic influenced acid rock drainage system

“…Members from this group have been previously detected in the sediments of other AMD habitats like Rio Tinto (Sánchez-Andrea et al . 2011) or Los Rueldos mercury underground mine in Spain (Mesa et al . 2017), and it has been suggested that they could have an important role in the oxidation of iron and sulfur compounds (Mesa et al .…”

“…2011) or Los Rueldos mercury underground mine in Spain (Mesa et al . 2017), and it has been suggested that they could have an important role in the oxidation of iron and sulfur compounds (Mesa et al . 2017).…”

Metagenome assembled genomes of novel taxa from an acid mine drainage environment

“…Here, we presented MAGs from four such phyla -the Dormibacterota, the Elusimicrobiota, the Eremiobacterota, and the Patescibacteria. Elusimicrobiota have also been found in AMD environments across the globe including in Spain (70,72), France (29), and Svalbard (73), but it is not abundant in these environments. The only cultivated taxa from this phylum are strictly anaerobic (74)(75)(76).…”

Seasonal blooms of neutrophilic Betaproteobacterial Fe(II) oxidizers and Chlorobi in iron-rich coal mine drainage sediments

“…Currently, most photoferrotrophic isolates have originated from either freshwater sediment and lakes or marine sediments (Bryce et al 2018). The occurrence of Chlorobi has been reported in 16S rRNA gene sequencing surveys of acid mine drainage (Volant et al 2014;Mesa et al 2017) and soils impacted by circumneutral mine drainage (Pereira, Vicentini and Ottoboni 2014) though at low abundance (<1%). It is possible that the high relative abundance for Chlorobi-affiliated OTUs at Ynysarwed represents a previously overlooked microbial metabolism in circumneutral mine drainage that can greatly impact pollutant turnover.…”