High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream

Abstract

Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0–20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by “E-plasma,” “A-plasma,” other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.

Microbial Community Diversity Dynamics in Acid Mine Drainage and Acid Mine Drainage-Polluted Soils: Implication on Mining Water Irrigation Agricultural Sustainability

“…For example, Thermoplasmatales dominates AMD from Dabaoshan Mine (Guangdong Province, China) (Lu et al, 2010). Distaso et al (2020) and Korzhenkov et al (2019) also recently reported higher representation of archaea Thermoplasmatales across all depths in oxic and low-pH sediment layers underlying an acidic stream in Parys Mountain (Mynydd Parys) AMD habitat in the UK, indicating contribution of these organisms to carbon, and probably to iron and sulfur cycles in this ecosystem. Gupta et al (2021) also reported the dominant archaeal communities in AMD sediment of Malanjkhand Copper Project, India as Thermoplasmata, Nitrososphaeria, Bathyarchaeia, Hydrothermarchaeota, Methanomassiliicoccales, Methanobacteriaceae, Methanocellaceae, Haloferaceae, Methanosaetaceae, and Methanoregulaceae.…”

“…According to Edwards et al (2000), about 75% of AMD produced results from microbial activity. Under the extremophilic AMD environment, acidophilic microbial communities belonging to Bacteria, Archaea, and Eukarya domains dominates, with members of phylum Proteobacteria, Nitrospira, Actinobacteria, Firmicutes, and Acidobacteria being the dominant bacterial taxa (Mesa et al, 2017;Lukhele et al, 2019;Distaso et al, 2020), as well as iron/sulfur-oxidizing microbes such Leptospirillum ferrooxidans, Ferrovum, Acidothiobacillus occurring in an environmentally dependent biogeographic pattern (Kuang et al, 2013(Kuang et al, , 2016Wang et al, 2019b). In addition, a large number of rare taxa constituting a "rare biosphere" in the microbial community that may perform crucial function in AMD ecosystems have been reported (Luo et al, 2020b).…”

Physiological, Genomic and Transcriptomic Analyses Reveal the Adaptation Mechanisms of Acidiella bohemica to Extreme Acid Mine Drainage Environments

“…Acid mine drainage is an extreme acid environment and low pH will threaten the growth of microorganisms ( Rothschild and Mancinelli, 2001 ; Huang et al, 2016 ; Distaso et al, 2020 ). In order to adapt to acid stress, microorganisms will form a series of defense mechanisms to regulate intracellular pH, K + , and Na + concentration.…”

Thermophilic carboxylesterases from hydrothermal vents of the volcanic island of Ischia active on synthetic and biobased polymers and mycotoxins

“…The purified barcoded amplicons were quantified by Qubit™ dsDNA BR Assay Kit (Life Technologies, USA), pooled in equimolar amounts and sequenced on Illumina MiSeq™ platform (Illumina Inc., San Diego, CA, USA) using paired-end 250 bp reads at the Centre for Environmental Biotechnology (Bangor, UK). Sequencing reads were processed and analysed as previously described (38). All statistical analysis was conducted using R programming environment (39) prcomp function and in-house scripts for graphical design.…”