Microbial Diversity of a Disused Copper Mine Site (Parys Mountain, UK), Dominated by Intensive Eukaryotic Filamentous Growth

Abstract

The Parys Mountain copper mine (Wales, UK) contains a wide range of discrete environmental microniches with various physicochemical conditions that shape microbial community composition. Our aim was to assess the microbial community in the sediments and overlying water column in an acidic mine drainage (AMD) site containing abundant filamentous biogenic growth via application of a combination of chemical analysis and taxonomic profiling using 16S rRNA gene amplicon sequencing. Our results were then compared to previously studied sites at Parys Mt. Overall, the sediment microbiome showed a dominance of bacteria over archaea, particularly those belonging to Proteobacteria (genera Acidiphilium and Acidisphaera), Acidobacteriota (subgroup 1), Chloroflexota (AD3 cluster), Nitrospirota (Leptospirillum) and the uncultured Planctomycetota/CPIa-3 termite group. Archaea were only present in the sediment in small quantities, being represented by the Terrestrial Miscellaneous Euryarchaeota Group (TMEG), Thermoplasmatales and Ca. Micrarchaeota (Ca. Micracaldota). Bacteria, mostly of the genera Acidiphilium and Leptospirillum, also dominated within the filamentous streamers while archaea were largely absent. This study found pH and dissolved solutes to be the most important parameters correlating with relative proportions of bacteria to archaea in an AMD environment and revealed the abundance patterns of native acidophilic prokaryotes inhabiting Parys Mt sites and their niche specificities.

A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota

“…Thirteen MAGs associated with Thermoplasmatales were discovered by us, and phylogenomic research reveals that these archaea are very diverse. Thermoplasmatales archaea are present in acid mine drainage sites all over the world, including Parys Mountain, United Kingdom [42,43], Los Rueldos, Spain [44], and Richmond mine at Iron Mountain, United States [45,46]. Additionally, Thermoplasmatales were discovered in water samples from the Kamchatka Peninsula and Kunashir Island in Russia [47] as well as the Tenorio Volcano National Park in Costa Rica [48].…”

“…It is important to note that bacteria from the phyla Actinomycetota and Pseudomonadota were also discovered in the Parys Mountain in the UK [42,43] and Tenorio Volcano National Park in Costa Rica [48]. Additionally, algae from the Chlorophyceae family were present in Parys Mountain [43], whereas acidophilic algae from the Cyanidiaceae family were found in the Los Azufres geothermal area.…”

Evolutionary patterns of archaea predominant in acidic environment

“…Furthermore, “E-plasma” representatives were shown to be present across the depth of sediment of acidic stream (up to 25 cm) on Parys Mt site in numbers varying from 0.5 to 15% of prokaryotic SSU rRNA gene amplicon reads [ 5 ]. Besides, archaea of this phylotype were shown to inhabit other sites across Parys Mt [ 6 ].…”