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Background  The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8–18 °C), extremely low pH (1.7) and high concentrations of soluble iron and other metal cations.    Results  Metagenomic and SSU rRNA amplicon sequencing of DNA from Parys Mountain revealed a significant proportion of archaea affiliated with  Euryarchaeota,  which accounted for ca. 67% of the community. Within this phylum, potentially new clades of  Thermoplasmata  were overrepresented (58%), with the most predominant group being “E-plasma”, alongside low-abundant  Cuniculiplasmataceae , ‘Ca. Micrarchaeota’ and ‘Terrestrial Miscellaneous Euryarchaeal Group’ (TMEG) archaea, which were phylogenetically close to  Methanomassilicoccales  and clustered with counterparts from acidic/moderately acidic settings. In the sediment, archaea and  Thermoplasmata  contributed the highest numbers in V3-V4 amplicon reads, in contrast with the water body community, where  Proteobacteria ,  Nitrospirae ,  Acidobacteria  and  Actinobacteria  outnumbered archaea. Cultivation efforts revealed the abundance of archaeal sequences closely related to  Cuniculiplasma divulgatum  in an enrichment culture established from the filterable fraction of the water sample. Enrichment cultures with unfiltered samples showed the presence of  Ferrimicrobium acidiphilum ,  C .  divulgatum , ‘ Ca . Mancarchaeum acidiphilum Mia14’, ‘ Ca . Micrarchaeota’-related and diverse minor (&lt; 2%) bacterial metagenomic reads.    Conclusion  Contrary to expectation, our study showed a high abundance of archaea in this extremely acidic mine-impacted environment. Further, archaeal populations were dominated by one particular group, suggesting that they are functionally important. The prevalence of archaea over bacteria in these microbiomes and their spatial distribution patterns represents a novel and important advance in our understanding of acidophile ecology. We also demonstrated a procedure for the specific enrichment of cell wall-deficient members of the archaeal component of this community, although the large fraction of archaeal taxa remained unculturable. Lastly, we identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within  Thermoplasmata  with yet unclear functional roles in the ecosystem.    Electronic supplementary material  The online version of this article (10.1186/s40168-019-0623-8) contains supplementary material, which is available to authorized users.

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity