Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities

Abstract

Microscopic eukaryotes are known to have important ecosystem functions, but their diversity in most environments remains vastly unexplored. Here we analyzed an 18S rRNA gene library from a subsurface ironand sulfur-oxidizing microbial community growing in highly acidic (pH < 0.9) runoff within the Richmond Mine at Iron Mountain (northern California). Phylogenetic analysis revealed that the majority (68%) of the sequences belonged to fungi. Protists falling into the deeply branching lineage named the acidophilic protist clade (APC) and the class Heterolobosea were also present. The APC group represents kingdom-level novelty, with <76% sequence similarity to 18S rRNA gene sequences of organisms from other environments. Fluorescently labeled oligonucleotide rRNA probes were designed to target each of these groups in biofilm samples, enabling abundance and morphological characterization. Results revealed that the populations vary significantly with the habitat and no group is ubiquitous. Surprisingly, many of the eukaryotic lineages (with the exception of the APC) are closely related to neutrophiles, suggesting that they recently adapted to this extreme environment. Molecular analyses presented here confirm that the number of eukaryotic species associated with the acid mine drainage (AMD) communities is low. This finding is consistent with previous results showing a limited diversity of archaea, bacteria, and viruses in AMD environments and suggests that the environmental pressures and interplay between the members of these communities limit species diversity at all trophic levels.

Quantification of Tinto River Sediment Microbial Communities: Importance of Sulfate-Reducing Bacteria and Their Role in Attenuating Acid Mine Drainage

“…Both Ferroplasma and Thermoplasma are usually found in bioleaching operations at lower pH (around 2) and at much higher iron and sulfate concentrations than those prevailing in Río Tinto sediments (13). Although algae, ciliates, flagellates, amoebae, and fungi have been reported in the water column and the biofilms of the Río Tinto (1,5), no Eukarya probe signal was detected by CARD-FISH; therefore, Bacteria seem to fully dominate the anoxic sediment layers of Tinto River. When genus-specific probes were applied, a pronounced variability was detected between the two sampling sites.…”

Assessing Biomineral Formation by Iron‐oxidizing Bacteria in a Circumneutral Creek

“…These processes commonly occur simultaneously upon mixing of iron-rich, anoxic groundwater with oxygen-rich surface water (Druschel et al 2008). Iron biomineral formation from microbially mediated processes has been identified in diverse aqueous environments, including acid mine drainage sites (Colmer et al 1950;Baker et al 2009;Johnson and Hallberg 2015), hydrothermal vents (Emerson et al 1999;Peng et al 2011;Toner et al 2012), and circumneutral pH surface waters (Emerson and Moyer 1997;Duckworth et al 2009;Emerson et al 2010;Fleming et al 2014). In many circumneutral pH waters, abiotic oxidation is in direct competition with neutrophilic iron oxidizing bacteria (FeOB), organisms that exist at oxic-anoxic interfaces and have metabolic capabilities that promote rapid iron oxidation (Druschel et al 2008).…”

In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis

“…The extreme physico-chemical characteristics of AMDs make these environments hostile for most of the living cells (Leblanc et al, 1996;Baker et al, 2009). Nevertheless, it is now well established that the microbial communities they harbor are well adapted and can have a decisive impact on the evolution of such ecosystems (Tichy et al, 1998;Das et al, 2009).…”