Abstract
Solfataric mud sediment samples were analyzed from two hot springs of North Sikkim district of the Sikkim Himalayas, located at the north-eastern region of Indian Himalayan Geothermal Belt. Old Yume Samdung hot spring (OYS) and New Yume Samdung hot spring (NYS) are located 4500m above the mean sea level and are one of the highest located hot springs of Sikkim. OYS hot spring had more abundance of archaea than the NYS hot spring. The solfataric mud sediments of NYS had 0.03% and OYS had 1.06% archaeal reads of the whole microbiome. Both the samples were dominated by Euryarchaeota (NYS~85%; OYS~95%) followed by few representatives from Crenarchaeota (NYS~12%; OYS~3%) and Thaumanarchaeota (NYS~2%; OYS~1%). Based on abundance, Methanocaldococcus, Pyrococcus, Archaeoglobus, Methanobacter, and Thermococcus were the predominant genera in both the hot springs. Functional protein reads for Crenarchaeota were found among the orders of Desulfurococcales, Sulfolobales and Thermoproteales; whereas reads for the order Nanoarchaeales belonging to Nanoarchaeota phylum and orders Cenarchaeales; Nitrosopumilales from phylum Thaumarchaeota were present in the samples. Functional metagenomics revealed the methanogens of the hot springs. There were no functional genes detected for methanogenesis in NYS, whereas in the case of OYS it was abundantly present in various orders of Euryarchaeota - Methanobacteriales, Methanococcales, Methanopyrales, and Methanosarcinales. Three types of methanogenesis were found – aceticlastic, methylotrophic and hydrogenotrophic in the OYS metaarchaeome. Methanopyrus kandleri, Methanosarcina acetivorans, Methanothermobacter marburgensis, Methanothermobacter thermautotrophicus, and Methanocaldococcus jannaschii were the dominant methanogens found in the metaarchaeome, based on their functional proteins for methanogenesis.
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References
Adam PS, Borrel G, Brochier-Armanet C et al (2017) The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME J 11(11):2407–2425. https://doi.org/10.1038/ismej.2017.122
Aouad M, Borrel G, Brochier-Armanet C et al (2019) Evolutionary placement of Methanonatronarchaeia. Nat Microbiol 4(4):558–559. https://doi.org/10.1038/s41564-019-0359-z
Auchtung TA, Takacs-Vesbach CD, Cavanaugh CM (2006) 16S rRNA phylogenetic investigation of the candidate division "Korarchaeota". Appl Environ Microbiol 72(7):5077–5082. https://doi.org/10.1128/AEM.00052-06
Baker BJ (2013) Dick GJ (2013) Omic approaches in microbial ecology: charting the unknown. Microbe 8:353–359
Balch WE, Fox GE, Magrum LJ et al (1979) Methanogens: reevaluation of a unique biological group. Microbiol Rev 43(2):260–296
Barns SM, Fundyga RE, Jeffries MW et al (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci USA 91(5):1609-1613. https://doi.org/10.1073/pnas.91.5.1-609
Barns SM, Delwiche CF, Palmer JD et al (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA 93(17):9188–9193. https://doi.org/10.1073/pnas.9-3.17.9188
Berghuis BA, Yu FB, Schulz F et al (2019) Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. Proc Natl Acad Sci USA 116(11):5037–5044. https://doi.org/10.1073/pnas.1815631116
Boone DR, Whitman WB, Koga Y (2001) "Order III. Methanosarcinales ord. nov." In: Bergey's Manual of Systematic Bacteriology, 2nd ed., vol. 1 (The Archaea and the deeply branching and phototrophic Bacteria) (D.R. Boone and R.W. Castenholz, eds.), Springer-Verlag, New York p. 268.
Borsodi AK, Anda D, Makk J et al (2018) Biofilm forming bacteria and archaea in thermal karst springs of Gellért Hill discharge area (Hungary). J Basic Microbiol 58(11):928–937. https://doi.org/10.1002/jobm.201800138
Brochier-Armanet C, Boussau B, Gribaldo S et al (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6(3):245–252. https://doi.org/10.1038/nrmicro1852
Burggraf S, Heyder P, Eis N (1997) A pivotal Archaea group. Nature 385(6619):780. https://doi.org/10.1038/385780-a0
Castelle CJ, Banfield JF (2018) Major new microbial groups expand diversity and alter our understanding of the tree of life. Cell 172(6):1181–1197. https://doi.org/10.1016/j.cell.2018.02.016
Chen LX, Méndez-García C, Dombrowski N et al (2018) Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. ISME J 12(3):756–775. https://doi.org/10.1038/s41396-017-0002-z
Chouari R, Le Paslier D, Daegelen P et al (2005) Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester. Environ Microbiol 7(8):1104–1115. https://doi.org/10.1111/j.1462-2920.2005.00795.x
Das S, Sherpa MT, Sachdeva S et al (2012) Hot springs of Sikkim (Tatopani): A Socio medical conjuncture which amalgamates religion, faith, traditional belief and tourism. Asian Acad Res J SocSci Human 1:80–93
Das S, Kumari A, Sherpa MT et al (2020) Metavirome and its functional diversity analysis through microbiome study of the Sikkim Himalayan hot spring solfataric mud sediments. Curr Res Microbial Sci. https://doi.org/10.1016/j.crmicr.2020.05.002
Dridi B, Henry M, Richet H et al (2012) Age-related prevalence of Methanomassiliicoccus luminyensis in the human gut microbiome. APMIS 120(10):773–777. https://doi.org/10.1111/j.1600-0463.2012.02899.x
Elkins JG, Podar M, Graham DE et al (2008) A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci USA 105(23):8102–8107. https://doi.org/10.1073/pnas.0801980105
Enzmann F, Mayer F, Rother M et al (2018) Methanogens: biochemical background and biotechnological applications. AMB Express 8:1. https://doi.org/10.1186/s13568-017-0531-x
Evans PN, Boyd JA, Leu AO et al (2019) An evolving view of methane metabolism in the Archaea. Nat Rev Microbiol 17(4):219–232. https://doi.org/10.1038/s41579-018-0136-7
Fillol M, Auguet JC, Casamayor EO et al (2016) Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage. ISME J 10(3):665–677. https://doi.org/10.1038/ismej.2015.143
Fortney NW, He S, Converse BJ et al (2018) Investigating the composition and metabolic potential of microbial communities in Chocolate Pots hot springs. Front Microbiol 9:2075. https://doi.org/10.3389/fmicb.2018.02075
Golyshina OV, Toshchakov SV, Makarova KS et al (2017) 'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ. Nat Commun 8(1):60. https://doi.org/10.1038/s41467-017-00104-7
Golyshina OV, Bargiela R, Toshchakov SV et al (2019) Diversity of "Ca. Micrarchaeota" in two distinct types of acidic environments and their associations with Thermoplasmatales. Genes (Basel) 10(6):461. https://doi.org/10.3390/genes100-60461
Gomez-Silvan C, Leung MHY, Grue KA et al (2018) A comparison of methods used to unveil the genetic and metabolic pool in the built environment. Microbiome 6:71. https://doi.org/10.1186/s40168-018-0453-0
Ghilamicael AM, Budambula NLM, Anami SE et al (2017) Evaluation of prokaryotic diversity of five hot springs in Eritrea. BMC Microbiol 17(1):203. https://doi.org/10.1186/s12866-017-1113-4
Harris RL, Lau MCY, Cadar A et al (2018) Draft Genome Sequence of "Candidatus Bathyarchaeota" Archaeon BE326-BA-RLH, an uncultured denitrifier and putative anaerobic methanotroph from South Africa's deep continental biosphere. Microbiol Resour Announc 7(20):e01295–18. https://doi.org/10.1128/MRA.01295-18
Hjorleifsdottir S, Skirnisdottir S, Hreggvidsson GO et al (2001) Species composition of cultivated and noncultivated bacteria from short filaments in an Icelandic hot spring at 88 degrees C. Microb Ecol 42(2):117–125. https://doi.org/10.1007/s002480000110
Hoedt EC, Cuív PÓ, Evans PN et al (2016) Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids. ISME J 10(10):2376–2388. https://doi.org/10.1038/ismej.2016.41
Huang Q, Dong CZ, Dong RM et al (2011) Archaeal and bacterial diversity in hot springs on the Tibetan Plateau China. Extremophiles 15(5):549–563. https://doi.org/10.1007/s00792-011-0386-z
Huang Q, Jiang H, Briggs BR et al (2013) Archaeal and bacterial diversity in acidic to circumneutral hot springs in the Philippines. FEMS Microbiol Ecol 85(3):452–464. https://doi.org/10.1111/1574-6941.12134
Huber R and Stetter KO (2001) "Order I. Methanopyrales ord. nov." In: Bergey's Manual of Systematic Bacteriology, 2nd ed., vol. 1 (The Archaea and the deeply branching and phototrophic Bacteria) (D.R. Boone and R.W. Castenholz, eds.), Springer-Verlag, NewYork p. 353.
Huber H, Hohn MJ, Rachel R et al (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417(6884):63–67. https://doi.org/10.1038/417063a
Hyatt D, Chen GL, Locascio PF et al (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119 https://doi.org/10.1186/1471-2105-11-119
Iino T, Tamaki H, Tamazawa S, et al (2013) Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov and Methanomassiliicoccales ord nov, for a methanogenic lineage of the class Thermoplasmata. Microbes Environ 28(2):244-250. https://doi.org/10.1264/jsme2.me12189
Itoh T, Suzuki KI, Nakase T (2002) Vulcanisaeta distributa gen nov., sp nov., and Vulcanisaeta souniana sp nov., novel hyperthermophilic, rod-shaped crenarchaeotes isolated from hot springs in Japan. Int J Syst Evol Microbiol 52(Pt 4):1097–1104. https://doi.org/10.1099/00207713-52-4-1097
Jarett JK, Džunková M, Schulz F et al (2020) Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. ISME J. https://doi.org/10.1038/s41396-020-0705-4
Jurgens G, Glöckner F, Amann R et al (2000) Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization(1). FEMS Microbiol Ecol 34(1):45–56. https://doi.org/10.1111/j.1574-6941.2000.tb00753.x
Kambura AK, Mwirichia RK, Kasili RW et al (2016) Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya. BMC Microbiol 16(1):136. https://doi.org/10.1186/s12866-016-0748-x
Kim J, Kim MS, Koh AY et al (2016) FMAP: Functional mapping and analysis pipeline for metagenomics and metatranscriptomics studies. BMC Bioinform 17:1-8. https://doi.org/10.1186/s12859-016-1278-0
Koonaphapdeelert S, Aggarangsi P, Moran J (2020) Biomethane in domestic and industrial applications. In: Biomethane. Green energy and technology. Springer, Singapore. https://doi.org/10.1007/978-981-13-8307-6_5
Lang K, Schuldes J, Klingl A et al (2015) New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus Methanoplasma termitum”. Appl Environ Microbiol 81(4):1338–1352. https://doi.org/10.1128/AEM.03389-14
Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–6. https://doi.org/10.1093/nar/gkh152
Laso-Pérez R, Wegener G, Knittel K et al (2016) Thermophilic archaea activate butane via alkyl-coenzyme M formation. Nature 539(7629):396–401. https://doi.org/10.1038/nat-ure20152
Lu J, Breitwieser FP, Thielen P et al (2017) Bracken: estimating species abundance in metagenomics data. Peer J Comput Sci 3:e104. https://doi.org/10.7717/peerj-cs.104
MacGregor BJ, Moser DP, Alm EW et al (1997) (1997) Crenarchaeota in Lake Michigan sediment. Appl Environ Microbiol 63:1178–1181
Mahato NK, Sharma A, Singh Y et al (2019) Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics. Arch Microbiol 201(3):377–388. https://doi.org/10.1007/s00203-018-01616-6
Mardanov AV, Gumerov VM, Beletsky AV et al (2011) Complete genome sequence of the thermoacidophilic crenarchaeon Thermoproteus uzoniensis 768–20. J Bacteriol 193(12):3156–3157. https://doi.org/10.1128/JB.-00409-11
Mirete S, de Figueras CG, González-Pastor JE (2011) Diversity of Archaea in Icelandic hot springs based on 16S rRNA and chaperonin genes. FEMS Microbiol Ecol 77(1):165–175. https://doi.org/10.1111/j.1574-6941.2011.01095.x
Najar IN, Sherpa MT, Das S et al (2018) Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry. Sci Total Environ 637-638:730–745. https://doi.org/10.1016/j.scitotenv.2018.05.037
Najar IN, Sherpa MT, Das S et al (2020) Bacterial diversity and functional metagenomics expounding the diversity of xenobiotics, stress, defense and CRISPR gene ontology providing eco-efficiency to Himalayan Hot Springs. FunctIntegr Genomic. https://doi.org/10.1007/s10142-019-00723-x
Nurk S, Meleshko D, Korobeynikov A et al (2017) metaSPAdes: a new versatile metagenomic assembler. Genome Res 27:824–834. https://doi.org/10.1101/gr.213959.116
Panda AK, Bisht SS, De Mandal S et al (2016) Bacterial and archeal community composition in hot springs from Indo-Burma region North-east India. AMB Express 6(1):111. https://doi.org/10.1186/s13568-016-0284-y
Patel RK, Jain M (2012) NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS One 7:e30619. https://doi.org/10.1371/journal.pone.0030619
Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394. https://doi.org/10.1146/annurev.micro.57.030502.090759
Reeves EP, McDermott JM, Seewald JS (2014) The origin of methanethiol in midocean ridge hydrothermal fluids. Proc Natl Acad Sci USA 111(15):5474–5479. https://doi.org/10.1073/pnas.1-400643111
Reigstad LJ, Jorgensen SL, Schleper C (2010) Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka. ISME J 4(3):346–356. https://doi.org/10.1038/ismej.2009.126
Reysenbach AL, Ehringer M, Hershberger K (2000) Microbial diversity at 83 degrees C in Calcite Springs, Yellowstone National Park: another environment where the Aquificales and "Korarchaeota" coexist. Extremophiles 4(1):61–67. https://doi.org/10.1007/s007920050008
Roy C, Rameez MJ, Haldar PK et al (2020) Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau. Sci Rep 10:5917. https://doi.org/10.1038/s41598-020-62797-z
Rozanov AS, Bryanskaya AV, Ivanisenko TV et al (2017) Biodiversity of the microbial mat of the Garga hot spring. BMC Evol Biol 17(Suppl 2):254. https://doi.org/10.1186/s12862-017-1106-9
Sakai S, Imachi H, Hanada S et al (2008) Methanocella paludicola gen. nov, sp nov, a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord nov. Int J Syst Evol Microbiol 58(Pt 4):929-936. https://doi.org/10.1099/ijs.0.65571-0
Sakai HD, Kurosawa N (2019) Complete genome sequence of the Sulfodiicoccus acidiphilus strain HS-1T, the first crenarchaeon that lacks polB3, isolated from an acidic hot spring in Ohwaku-dani, Hakone Japan. BMC Res Notes 12(1):444. https://doi.org/10.1186/s13104-019-4488-5
Sharma N, Kumar J, Abedin MM et al (2020) Metagenomics revealing molecular profiling of community structure and metabolic pathways in natural hot springs of the Sikkim Himalaya. BMC Microbiol 20(1):246. https://doi.org/10.1186/s12866-020-01923-3
Skirnisdottir S, Hreggvidsson GO, Hjörleifsdottir S (2000) Influence of sulfide and temperature on species composition and community structure of hot spring microbial mats. Appl Environ Microbiol 66(7):2835–2841. https://doi.org/10.1128/aem.66.7.2835-2841.2000
Song ZQ, Wang FP, Zhi XY et al (2013) Bacterial and archaeal diversities in Yunnan and Tibetan hot springs China. Environ Microbiol 15(4):1160–1175. https://doi.org/10.1111/1462-2920.12025
Spear JR, Walker JJ, McCollom TM et al (2005) Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proc Natl Acad Sci USA 102(7):2555–2560. https://doi.org/10.1073/pnas.0409574102
St John E, Liu Y, Podar M et al (2019) A new symbiotic nanoarchaeote (Candidatus Nanoclepta minutus) and its host (Zestosphaera tikiterensis gen nov, sp nov) from a New Zealand hot spring. Syst Appl Microbiol 42(1):94–106. https://doi.org/10.1016/j.syapm.2018.08.005
Staley JT, Caetano-Anollés G (2018) Archaea - First and the co-evolutionary diversification of domains of life. Bioessays 40(8):e1800036. https://doi.org/10.1002/bies.201800036
Takai K, Sako Y (1999) A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol Ecol 28:177–188
Tatusov RL, Fedorova ND, Jackson JD et al (2003) The COG database: an updated version includes eukaryotes. BMC Bioinform 4:41. https://doi.org/10.1186/1471-2105-4-41
Wagner T, Wegner CE, Kahnt J et al (2017) Phylogenetic and structural comparisons of the three types of methyl coenzyme M reductase from Methanococcales and Methanobacteriales. J Bacteriol 199(16):e00197–17. https://doi.org/10.1128/JB.00197-17
Wang S, Dong H, Hou W et al (2014) Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province China. Sci. Rep 4:7479. https://doi.org/10.1038/srep07479
Wheeler TJ, Eddy SR (2013) nhmmer: DNA homology search with profile HMMs. Bioinformatics 29:2487–2489. https://doi.org/10.1093/bioinformatics/btt403
Wilkie AC (2008) Biomethane from biomass, biowaste and biofuels. In Bionergy; Wall JD, Harwood CS, Deamin AL (Eds.); ASM Press: Washingston, DC, USA, 2008; pp. 195–215.
Williams TA, Szöllősi GJ, Spang A et al (2017) Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proc Natl Acad Sci USA 114(23):E4602–E4611. https://doi.org/10.1073/pnas.1618463114
Wood DE, Lu J, Langmead B (2019) Improved metagenomic analysis with Kraken 2. Genome Biol 20:257. https://doi.org/10.1186/s13059-019-1891-0
Wu YW, Simmons BA, Singer SW (2016) MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32:605-607. https://doi.org/10.1093/bioinformatics/btv638
Vanwonterghem I, Evans PN, Parks DH et al (2016) Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat Microbiol 1:16170. https://doi.org/10.1038/nmicrobiol.2016.170
Yasir M, Qureshi AK, Srinivasan S et al (2020) Domination of filamentous anoxygenic phototrophic bacteria and prediction of metabolic pathways in microbial mats from the Hot Springs of Al Aridhah. Folia Biol (Praha) 66(1):24–35
Zhang CL, Hedlund BP, Meng J (2011) Diversity of Archaea in terrestrial hot springs and role in ammonia oxidation. In Handbook of Molecular microbial ecology II, F.J. de Bruijn (Ed.). https://doi.org/10.1002/9781118010549.ch37
Acknowledgements
SD would like to thank DST INPIRE, Department of Science and Technology, Govt. of India, for providing the INSPIRE FELLOWSHIP (IF130091) for research work. SD acknowledges the support of Dr. Pulakesh Das (ChemDraw analysis) and Bionivid Technology, India for its technical assistance with microbiome analysis. The authors heartily thank and express their most sincere gratitude to Forest, Environment and Wildlife Management Department, Govt. of Sikkim, Sikkim Police and North Sikkim administration, for granting research permission, kind cooperation and support during the field work.
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The work was funded by the Department of Biotechnology, Ministry of Science of Technology, Government of India (BT/PR25092/NER/95/1009/2017).
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SD and NT conceived and designed the study; SD, MTS and INN did the field survey; SD curated the data; interpreted the results and wrote the manuscript; NT edited the manuscript.
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Das, S., Sherpa, M.T., Najar, I.N. et al. Prevalence of methanogens in the uncultured Sikkim hot spring solfataric mud archaeal microbiome. Environmental Sustainability 3, 453–469 (2020). https://doi.org/10.1007/s42398-020-00133-x
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DOI: https://doi.org/10.1007/s42398-020-00133-x