Abstract
Chilas and Hunza areas, located in the Main Mantle Thrust and Main Karakoram Thrust of the Himalayas, host a range of geochemically diverse hot springs. This Himalayan geothermal region encompassed hot springs ranging in temperature from 60 to 95 °C, in pH from 6.2 to 9.4, and in mineralogy from bicarbonates (Tato Field), sulfates (Tatta Pani) to mixed type (Murtazaabad). Microbial community structures in these geothermal springs remained largely unexplored to date. In this study, we report a comprehensive, culture-independent survey of microbial communities in nine samples from these geothermal fields by employing a bar-coded pyrosequencing technique. The bacterial phyla Proteobacteria and Chloroflexi were dominant in all samples from Tato Field, Tatta Pani, and Murtazaabad. The community structures however depended on temperature, pH, and physicochemical parameters of the geothermal sites. The Murtazaabad hot springs with relatively higher temperature (90–95 °C) favored the growth of phylum Thermotogae, whereas the Tatta Pani thermal spring site TP-H3-b (60 °C) favored the phylum Proteobacteria. At sites with low silica and high temperature, OTUs belonging to phylum Chloroflexi were dominant. Deep water areas of the Murtazaabad hot springs favored the sulfur-reducing bacteria. About 40% of the total OTUs obtained from these samples were unclassified or uncharacterized, suggesting the presence of many undiscovered and unexplored microbiota. This study has provided novel insights into the nature of ecological interactions among important taxa in these communities, which in turn will help in determining future study courses in these sites.
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs00248-017-0930-1/MediaObjects/248_2017_930_Fig1_HTML.gif)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs00248-017-0930-1/MediaObjects/248_2017_930_Fig2_HTML.gif)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs00248-017-0930-1/MediaObjects/248_2017_930_Fig3_HTML.gif)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs00248-017-0930-1/MediaObjects/248_2017_930_Fig4_HTML.gif)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs00248-017-0930-1/MediaObjects/248_2017_930_Fig5_HTML.gif)
Similar content being viewed by others
References
Cai L, Ye L, Tong AH, Lok S, Zhang T (2013) Biased diversity metrics revealed by bacterial 16S pyrotags derived from different primer sets. PLoS One 8:e53649. doi:10.1371/journal.pone.0053649
Blank CE, Cady SL, Pace NR (2002) Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park. Appl. Environ. Microbiol. 68:5123–5135
Hou W, Wang S, Dong H, Jiang H, Briggs BR, Peacock JP, Huang Q, Huang L, Wu G, Zhi X, Li W, Dodsworth JA, Hedlund BP, Zhang C, Hartnett HE, Dijkstra P, Hungate BA (2013) A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing. PLoS One 8:e53350. doi:10.1371/journal.pone.0053350
Liu L, Salam N, Jiao JY, Jiang HC, Zhou EM, Yin YR, Ming H, Li WJ (2016) Diversity of culturable thermophilic actinobacteria in hot springs in Tengchong, China and studies of their biosynthetic gene profiles. Microb. Ecol. 72:150–162
Deng Y, Cui X, Hernandez M, Dumont MG (2014) Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan plateau revealed by 16S rRNA pyrosequencing. PLoS One 9:e103115. doi:10.1371/journal.pone.0103115
Lau MC, Aitchison JC, Pointing SB (2009) Bacterial community composition in thermophilic microbial mats from five hot springs in Central Tibet. Extremophiles 13:139–149
Kumar M, Yadav AN, Tiwari R, Prasanna R, Saxena AK (2014) Deciphering the diversity of culturable thermotolerant bacteria from Manikaran hot springs. Ann. Microbiol. 64:741–751
Wang S, Hou W, Dong H, Jiang H, Huang L, Wu G, Zhang C, Song Z, Zhang Y, Ren H, Zhang J, Zhang L (2013) Control of temperature on microbial community structure in hot springs of the Tibetan plateau. PLoS One 8:e62901. doi:10.1371/journal.pone.0062901
Yim LC, Hongmei J, Aitchison JC, Pointing SB (2006) Highly diverse community structure in a remote central Tibetan geothermal spring does not display monotonic variation to thermal stress. FEMS Microbiol. Ecol. 57:80–91
Hedlund BP, Reysenbach AL, Huang L, Ong JC, Liu Z, Dodsworth JA, Ahmed R, Williams AJ, Briggs BR, Liu Y, Hou W, Dong H (2015) Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China. Front. Microbiol. 6:157. doi:10.3389/fmicb.2015.00157
Song ZQ, Zhi XY, Li WJ, Jiang HC, Zhang CL, Dong HL (2009) Actinobacterial diversity in hotsprings in Tengchong (China), Kamchatka (Russia), and Nevada (USA). Geomicrobiol. J. 26:256–263
Song ZQ, Chen JQ, Jiang HC, Zhou EM, Tang SK, Zhi XY, Zhang LX, Zhang CL, Li WJ (2010) Diversity of Crenarchaeoto in terrestrial hot springs in Tengchong, China. Extremophiles 14:287–296
Kubo K, Knittel K, Amann R, Fukui M, Matsuura K (2011) Sulfur-metabolizing bacterial populations in microbial mats of the Nakabusa hot spring, Japan. Syst. Appl. Microbiol. 34:293–302
Tekere M, Lötter A, Olivier J, Jonker N, Venter S (2013) Metagenomic analysis of bacterial diversity of Siloam hot water spring, Limpopo, South Africa. Afr. J. Biotechnol. 10:18005–18012
Dodsworth JA, Hungate BA, Hedlund BP (2011) Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea. Environ. Microbiol. 13:2371–2386
Bohorquez LC, Delgado-Serrano L, Lopez G, Osorio-Forero C, Klepac-Ceraj V, Kolter R, Junca H, Baena S, Zambrano MM (2012) In-depth characterization via complementing culture-independent approaches of the microbial community in an acidic hot spring of the Colombian Andes. Microb. Ecol. 63:103–115
Delgado-Serrano L, Lopez G, Bohorquez LC, Bustos JR, Rubiano C, Osorio-Forero C, Junca H, Baena S, Zambrano MM (2014) Neotropical Andes hot springs harbor diverse and distinct planktonic microbial communities. FEMS Microbiol. Ecol. 89:56–66
Skirnisdottir S, Hreggvidsson GO, Hjorleifsdottir S, Marteinsson VT, Petursdottir SK, Holst O, Kristjansson JK (2000) Influence of sulfide and temperature on species composition and community structure of hot spring microbial mats. Appl. Environ. Microbiol. 66:2835–2841
Spear JR, Walker JJ, Pace NR (2005) Hydrogen and primary productivity: inference of biogeochemistry from phylogeny in a geothermal ecosystem. In: Inskeep W, McDermott T (eds) Geothermal biology and geochemistry in Yellowstone National Park Bozeman, MT. Montana State University, Thermal Biology Institute, pp. 113–128
Unsworth LD, van der Oost J, Koutsopoulos S (2007) Hyperthermophilic enzymes − stability, activity and implementation strategies for high temperature applications. FEBS J. 274:4044–4056
Mirete S, Morgante V, González-Pastor JE (2016) Functional metagenomics of extreme environments. Curr. Opin. Biotechnol. 38:143–149
Leis B, Angelov A, Mientus M, Li H, Pham VT, Lauinger B, Bongen P, Pietruszka J, Gonçalves LG, Santos H (2015) Identification of novel esterase-active enzymes from hot environments by use of the host bacterium Thermus thermophilus. Front. Microbiol. 6:275. doi:10.3389/fmicb.2015.00275
Berelson WM, Corsetti FA, Pepe-Ranney C, Hammond DE, Beaumont W, Spear JR (2011) Hot spring siliceous stromatolites from Yellowstone National Park: assessing growth rate and laminae formation. Geobiology 9:411–424
Zaigham NA, Nayyar ZA, Hisamuddin N (2009) Review of geothermal energy resources in Pakistan. Renew. Sust. Energ. Rev. 13:223–232
Mohanrao MM, Singh DP, Kanika K, Goyal E, Singh AK (2016) Deciphering the microbial diversity of Tattapani water spring using metagenomic approach. Int. J. Agri. Sci. Res. 6:371–382
Huang Q, Dong CZ, Dong RM, Jiang H, Wang S, Wang G, Fang B, Ding Z, Niu L, Li X (2011) Archaeal and bacterial diversity in hot springs on the Tibetan Plateau, China. Extremophiles 15:549–563
Bakht MS (2000) An overview of geothermal resources of Pakistan. Proc World Geotherm Congr, pp.:77–83
Javed MM, Zahoor S, Sabar H, Haq IU, Babar ME (2012) Thermophilic bacteria from the hot springs of Gilgit (Pakistan). J. Anim. Plant. Sci. 22:83–87
Ahmad M, Akram W, Hussain SD, Sajjad MI, Zafar MS (2001) Origin and subsurface history of geothermal water of Murtazabad area, Pakistan-an isotopic evidence. Appl. Radiat. Isot. 55:731–736
APHA (1985) Standard methods for the examination of water and wastewater. American Public Health Association, USA, Washington, DC
Nickson RT, McArthur JM, Shrestha B, Kyaw-Myint TO, Lowry D (2005) Arsenic and other drinking water quality issues, Muzaffargarh District, Pakistan. Appl. Geochem. 20:55–68
Stumm W, Morgan JJ, Drever JI (1996) Aquatic chemistry. J. Environ. Qual. 25:1162
White DE, Brannock W, Murata K (1956) Silica in hot-spring waters. Geochim. Cosmochim. Acta 10:27–59
Hur M, Kim Y, Song HR, Kim JM, Choi YI, Yi H (2011) Effect of genetically modified poplars on soil microbial communities during the phytoremediation of waste mine tailings. Appl. Environ. Microbiol. 77:7611–7619
Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537–7541
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J. Mol. Biol. 215:403–410
Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 62:716–721
Hamady M, Lozupone C, Knight R (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 4:17–27
Sharp CE, Martinez-Lorenzo A, Brady AL, Grasby SE, Dunfield PF (2014) Methanotrophic bacteria in warm geothermal spring sediments identified using stable-isotope probing. FEMS Microbiol. Ecol. 90:92–102
Dedysh SN, Khmelenina VN, Suzina NE, Trotsenko YA, Semrau JD, Liesack W, Tiedje JM (2002) Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. Int. J. Syst. Evol. Microbiol. 52:251–261
Tsubota J, Eshinimaev B, Khmelenina VN, Trotsenko YA (2005) Methylothermus thermalis gen. nov., sp. nov., a novel moderately thermophilic obligate methanotroph from a hot spring in Japan. Int. J. Syst. Evol. Microbiol. 55:1877–1884
Merkel AY, Podosokorskaya OA, Sokolova TG, Bonch-Osmolovskaya EA (2016) Diversity of methanogenic archaea from the 2012 terrestrial hot spring (Valley of Geysers, Kamchatka). Microbiology 85:342–349
Borsodi AK, Szirányi B, Krett G, Márialigeti K, Janurik E, Pekár F (2016) Changes in the water quality and bacterial community composition of an alkaline and saline oxbow lake used for temporary reservoir of geothermal waters. Environ. Sci. Pollut. Res. Int. 23:17676–17688
Elshahed MS, Senko JM, Najar FZ, Kenton SM, Roe BA, Dewers TA, Spear JR, Krumholz LR (2003) Bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring. Appl. Environ. Microbiol. 69:5609–5621
Castenholz RW (2015) Portrait of a geothermal spring, Hunter’s hot springs, Oregon. Life 5:332–347
Nübel U, Bateson MM, Madigan MT, Kühl M, Ward DM (2001) Diversity and distribution in hypersaline microbial mats of bacteria related to Chloroflexus spp. Appl. Environ. Microbiol. 67:4365–4371
Tripathy S, Padhi SK, Mohanty S, Samanta M, Maiti NK (2016) Analysis of the metatrancriptome of microbial communities of an alkaline hot sulfur spring revealed different gene encoding pathway enzymes associated with energy metabolism. Extremophiles 20:525–536
Kanoksilapatham W, Psomsup P, Keawram P, Cuecas A, Portillo MC, Gonzalez JM (2016) Fervidobacterium thailandense sp. nov., a novel extreme thermophilic bacterium isolated from a hot spring in northern Thailand. Int. J. Syst. Evol. Microbiol. doi:10.1099/ijsem.0.001463
Cai J, Wang Y, Liu D, Zeng Y, Xue Y, Ma Y, Feng Y (2007) Fervidobacterium changbaicum sp. nov., a novel thermophilic anaerobic bacterium isolated from a hot spring of the Changbai Mountains, China. Int. J. Syst. Evol. Microbiol. 57:2333–2336
Islam T, Jensen S, Reigstad LJ, Larsen O, Birkeland NK (2008) Methane oxidation at 55 degrees C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc. Natl. Acad. Sci. U. S. A. 105:300–304
Khadem AF, Pol A, Wieczorek A, Mohammadi SS, Francoijs KJ, Stunnenberg HG, Jetten MS, Op den Camp HJ (2011) Autotrophic methanotrophy in verrucomicrobia: Methylacidiphilum fumariolicum SolV uses the Calvin-Benson-Bassham cycle for carbon dioxide fixation. J. Bacteriol. 193:4438–4446
Sharp CE, Stott MB, Dunfield PF (2012) Detection of autotrophic verrucomicrobial methanotrophs in a geothermal environment using stable isotope probing. Front. Microbiol. 3:303. doi:10.3389/fmicb.2012.00303
Hugenholtz J, Ljungdahl LG (1990) Metabolism and energy generation in homoacetogneic clostridia. FEMS Microbiol. Rev. 7:383–389
Sokolova TG, Kostrikina NA, Chernyh NA, Tourova TP, Kolganova TV, Bonch-Osmolovskaya EA (2002) Carboxydocella thermautotrophica gen. nov., sp. nov., a novel anaerobic, CO-utilizing thermophile from a Kamchatkan hot spring. Int. J. Syst. Evol. Microbiol. 52:1961–1967
Stackebrandt E (2014) The family Gracilibacteraceae and transfer of the genus Lutispora into Gracilibacteraceae. The Prokaryotes, Firmicutes and Tenericutes, pp. 149–151
Nakagawa T, Fukui M (2002) Phylogenetic characterization of microbial mats and streamers from a Japanese alkaline hot spring with a thermal gradient. J. Gen. Appl. Microbiol. 48:211–222
Cava F, Zafra O, da Costa MS, Berenguer J (2008) The role of the nitrate respiration element of Thermus thermophilus in the control and activity of the denitrification apparatus. Environ. Microbiol. 10:522–533
Mishima M, Iwata K, Nara K, Matsui T, Shigeno T, Omori T (2009) Cultivation characteristics of denitrification by thermophilic Geobacillus sp. strain TDN01. J. Gen. Appl. Microbiol. 55:81–86
Otaki H, Everroad RC, Matsuura K, Haruta S (2012) Production and consumption of hydrogen in hot spring microbial mats dominated by a filamentous anoxygenic photosynthetic bacterium. Microbes Environ. 27:293–299
Cox A, Shock EL, Havig JR (2011) The transition to microbial photosynthesis in hot spring ecosystems. Chem. Geol. 280:344–351
Liu Z, Klatt CG, Wood JM, Rusch DB, Ludwig M, Wittekindt N, Tomsho LP, Schuster SC, Ward DM, Bryant DA (2011) Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat. ISME J. 5:1279–1290
Miller SR, Strong AL, Jones KL, Ungerer MC (2009) Bar-coded pyrosequencing reveals shared bacterial community properties along the temperature gradients of two alkaline hot springs in Yellowstone national park. Appl. Environ. Microbiol. 75:4565–4572
Kambura AK, Mwirichia RK, Kasili RW, Karanja EN, Makonde HM, Boga HI (2016) Bacteria and archaea diversity within the hot springs of Lake Magadi and little Magadi in Kenya. BMC Microbiol. 16:136. doi:10.1186/s12866-016-0748-x
Sharma N, Vyas G, Pathania S (2013) Culturable diversity of thermophilic microorganisms found in hot springs of northern Himalayas and to explore their potential for production of industrially important enzymes. Sch. Acad. J. Biosci. 1:165–178
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc. Natl. Acad. Sci. U. S. A. 103:12115–12120
Kamruzzaman M, Udden SMN, Cameron DE, Calderwood SB, Nair GB, Mekalanos JJ, Faruque SM (2010) Quorum-regulated biofilms enhance the development of conditionally viable, environmental Vibrio cholerae. Proc. Natl. Acad. Sci. U. S. A. 107:1588–1593
Acknowledgements
This work was supported by the Key Project of International Cooperation of Ministry of Science and Technology (MOST) (No. 2013DFA31980), National Natural Science Foundation of China (No. 31470139), Yunnan Provincial Natural Science Foundation (2013FA004), China Postdoctoral Science Foundation Grant (No. 2016M602566), and Visiting Scholar grant of State Key Laboratory of Biocontrol, Sun Yat-Sen University (No. SKLBC14F02). W-J Li was also supported by the Hundred Talents Program of Chinese Academy of Sciences and Guangdong Province Higher Vocational Colleges and Schools Pearl River Scholar Funded Scheme (2014).
Author information
Authors and Affiliations
Corresponding authors
Electronic supplementary material
Supplementary Figure S1
(PDF 172 kb)
Supplementary Figure S2
(PDF 308 kb)
Supplementary Figure S3
(PDF 497 kb)
Supplementary Figure S4
(PDF 35 kb)
Supplementary Figure S5
(PDF 45 kb)
Supplementary Figure S6
(PDF 192 kb)
Supplementary Table S1
(XLSX 112 kb)
Supplementary Table S2
(PDF 95 kb)
Supplementary Table S3
(PDF 95 kb)
Supplementary Table S4
(PDF 95 kb)
Supplementary Table S5
(PDF 89 kb)
Supplementary Table S6
(PDF 93 kb)
Supplementary Table S7
(PDF 85 kb)
Rights and permissions
About this article
Cite this article
Amin, A., Ahmed, I., Salam, N. et al. Diversity and Distribution of Thermophilic Bacteria in Hot Springs of Pakistan. Microb Ecol 74, 116–127 (2017). https://doi.org/10.1007/s00248-017-0930-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00248-017-0930-1