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Thermoplasmata and Nitrososphaeria as dominant archaeal members in acid mine drainage sediment of Malanjkhand Copper Project, India

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Abstract

Acid mine drainage (AMD) harbors all three life forms in spite of its toxic and hazardous nature. In comparison to bacterial diversity, an in-depth understanding of the archaeal diversity in AMD and their ecological significance remain less explored. Archaeal populations are known to play significant roles in various biogeochemical cycles within the AMD ecosystem, and it is imperative to have a deeper understanding of archaeal diversity and their functional potential in AMD system. The present study is aimed to understand the archaeal diversity of an AMD sediment of Malanjkhand Copper Project, India through archaea specific V6 region of 16S rRNA gene amplicon sequencing. Geochemical data confirmed the acidic, toxic, heavy metal-rich nature of the sample. Archaea specific V6-16S rRNA gene amplicon data showed a predominance of Thermoplasmata (BSLdp215, uncultured Thermoplasmata, and Thermoplasmataceae) and Nitrososphaeria (Nitrosotaleaceae) members constituting ~ 95% of the archaeal community. Uncultured members of Bathyarchaeia, Group 1.1c, Hydrothermarchaeota, and Methanomassiliicoccales along with Methanobacteriaceae, Methanocellaceae, Haloferaceae, Methanosaetaceae, and Methanoregulaceae constituted the part of rare taxa. Analysis of sequence reads indicated that apart from their close ecological relevance, members of the Thermoplasmata present in Malanjkhand AMD were mostly involved in chemoheterotrophy, Fe/S redox cycling, and with heavy metal resistance, while the Nitrososphaeria members were responsible for ammonia oxidation and fixation of HCO3− through 3-hydroxypropionate/4-hydroxybutyrate cycle at low pH and oligotrophic environment which subsequently played an important role in nitrification process in AMD sediment. Overall, the present study elucidated the biogeochemical significance of archaeal populations inhabiting the toxic AMD environment.

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Availability of data and materials

Amplicon sequences are submitted in NCBI under Bioproject number PRJNA479957. Accession numbers of the V6 and V4 regions of the sample were SRR12489631 and SRR7511722, respectively.

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Acknowledgements

Authors would like to thank the Department of Biotechnology, Govt. of India for funding the project (Grant ID BT/PR7533/BCE/8/959/2013) and MCP authority for sample collection. Authors thank the IIT Kharagpur for the in-house NGS facility (Ion S5 platform) through SGBSI challenge grant (IIT/SRIC/BT/ODM/2015-16/141). AG thanks Department of Biotechnology Govt. of India for DBT-JRF fellowship (DBT/2014/IITKH/113). AS thanks IIT Kharagpur for the Fellowship.

Funding

Authors would like to thank the Department of Biotechnology, Govt. of India for funding the project (Grant ID BT/PR7533/BCE/8/959/2013). Authors thank the IIT Kharagpur for the in-house NGS facility (Ion S5 platform) through SGBSI challenge grant (IIT/SRIC/BT/ODM/2015-16/141).

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  1. Environmental Microbiology and Genomics Laboratory, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India

    Abhishek Gupta, Anumeha Saha & Pinaki Sar

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  1. Abhishek Gupta
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Correspondence to Pinaki Sar.

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Gupta, A., Saha, A. & Sar, P. Thermoplasmata and Nitrososphaeria as dominant archaeal members in acid mine drainage sediment of Malanjkhand Copper Project, India. Arch Microbiol 203, 1833–1841 (2021). https://doi.org/10.1007/s00203-020-02130-4

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