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

Autor: Stepan V. Toshchakov, Rafael Bargiela, Alina V. Teplyuk, Olga V. Golyshina, Peter N. Golyshin, Aleksei A. Korzhenkov, David L. Jones, Manuel Ferrer, Huw Gibbard, Ilya V. Kublanov
Přispěvatelé: Royal Society (UK), Agencia Estatal de Investigación (España), Biotechnology and Biological Sciences Research Council (UK), European Commission, Government of the United Kingdom, Russian Science Foundation, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España)
Rok vydání: 2019
Předmět:
Zdroj: Digital.CSIC. Repositorio Institucional del CSIC
instname
Microbiome
Microbiome, Vol 7, Iss 1, Pp 1-14 (2019)
Popis: [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 (
[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.
The work of OVG, PNG and SVT was supported by the Royal Society UK-Russia Exchange Grant #IE 160224 (RFBR 16-54-10072 КО project). OVG and PNG acknowledge ERA Net IB2 Project MetaCat through UK Biotechnology and Biological Sciences Research Council (BBSRC) Grant BB/M029085/1 and the support of the Centre of Environmental Biotechnology Project funded by the European Regional Development Fund (ERDF) through the Welsh Government. RB and PNG acknowledge the support of the Supercomputing Wales project, which is part-funded by the European Regional Development Fund (ERDF) via the Welsh Government. The work of AAK and IVK was supported by the Russian Science Foundation grant # 18-44-04024. MF acknowledges grants PCIN-2014-107 (within ERA NET IB2 grant ERA-IB-14-030—MetaCat), PCIN-2017-078 (within the Marine Biotechnology ERA-NET (ERA-MBT) funded under the European Commission’s Seventh Framework Programme, 2013-2017, Grant agreement 604814), BIO2014-54494-R and BIO2017-85522-R from the Spanish Ministry of Economy and Competitiveness.
Databáze: OpenAIRE
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