Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study
-
Atif Khurshid Wani
,
Suhail Ahmad
,
Juliana Heloisa Pinê Américo-Pinheiro
,
Nazli Tizro
,
Reena Singh
Abstract
Background and Objectives: Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51′51′′N 75°32′07′′E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics.
Materials and Methods: In the present study, physiochemical parameters including temperature (65-75oC), pH (6. 9-8. 8), hardness (250 ppm), and mineral content was measured along with the microbial diversity using Illumina MiSeq metagenome-based 16s amplicon sequencing (V3-V4). The sequence reads were classified taxonomically into 31 phyla, 71 classes, 152 orders, 256 families, 410 genus, and 665 species. QIIME 2 (Quantitative Insights into Microbial Ecology), an extensible, powerful, and decentralized analytical tool, was used for taxonomic analysis.
Results: Bacteroidota (32. 57%) was the dominant phylum, Bacteroidia (32. 51%) the dominant class, Bacteroidales (16. 6%) the dominant order, and Lentimicrobiaceae (14. 23%) was the dominant family per the abundance analysis. Shannon (2. 28) and Chao 1 (87. 0) diversity indices support the existence of higher microbial diversity in RMHSK (50717 OTUs).
Conclusion: The microbial diversity of RMHSK is reported for the first time through a metagenomic study. Identification of microorganisms with characteristics that are relevant to industries.
1. Zimik HV, Farooq SH, Prusty P. Geochemical evaluation of thermal springs in Odisha, India. Environ Earth Sci 2017; 76: 593.
2. Singh HK, Thankappan A, Mohite P, Sinha SK, Chandrasekharam D, Chandrasekhar T. Geothermal energy potential of Tulsishyam thermal springs of Gujarat, India. Arab J Geosci 2018; 11: 1-11.
3. Dutta A, Gupta RK. Geochemistry and utilization of water from thermal springs of tawang and west Kameng Districts, Arunachal Pradesh. J Geol Soc India 2022; 98: 237-244.
4. Vaidya B, Nakarmi S. A qualitative study of patients’ beliefs and perception on medicinal properties of natural Hot Spring Bath for Musculoskeletal problems. J Environ Public Health 2020; 2020: 3694627.
5. Ahmad M, Akram W, Hussain SD, Sajjad MI, Zafar MS. Origin and subsurface history of geothermal water of Murtazabad area, Pakistan—isotopic evidence. Appl Radiat Isot 2001; 55: 731-736.
6. Amin A, Ahmed I, Salam N, Kim B-Y, Singh D, Zhi X-Y, et al. Diversity and distribution of thermophilic bacteria in Hot Springs of Pakistan. Microb Ecol 2017; 74: 116-127.
7. Sahoo RK, Gaur M, Das A, Singh A, Kumar M, Subudhi E. Comparative analysis of 16S rRNA Gene Illumina sequence for microbial community structure in diverse unexplored Hot Springs of Odisha, India. Geomicrobiol J 2017; 34: 567-576.
8. Tian J, Li Y, Zhou X, Pang Z, Li L, Xing L, et al. Geochemical characteristics of hydrothermal volatiles from southeast China and their implications on the tectonic structure controlling heat convection. Front Earth Sci 2021; 9: 786051.
9. Petersen IA, Meyer KM, Bohannan BJ. Meta-analysis reveals consistent bacterial responses to land use change across the tropics. Front Ecol Evol 2019; 7: 391.
10. Ji M, Kong W, Jia H, Delgado-Baquerizo M, Zhou T, Liu X, et al. Polar soils exhibit distinct patterns in microbial diversity and dominant phylotypes. Soil Biol Biochem 2022; 166: 108550.
11. Garcia-Lopez E, Rodriguez-Lorente I, Alcazar P, Cid C. Microbial communities in coastal glaciers and tidewater tongues of Svalbard archipelago, Norway. Front Mar Sci 2019; 5: 512.
12. Molina-Menor E, Gimeno-Valero H, Pascual J, Peretó J, Porcar M. High culturable bacterial diversity from a European desert: The Tabernas desert. Front Microbiol 2021; 11: 583120.
13. Ding J, Zhang Y, Wang H, Jian H, Leng H, Xiao X. Microbial community structure of deep-sea hydrothermal vents on the ultraslow spreading Southwest Indian Ridge. Front Microbiol 2017; 8: 1012.
14. Wani AK, Akhtar N, Sher F, Navarrete AA, Américo-Pinheiro JHP. Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems. Arch Microbiol 2022; 204: 144.
15. Wani AK, Rahayu F, Kadarwati FT, Suhara C, Singh R, Dhanjal DS, et al. Metagenomic screening strategies for bioprospecting enzymes from environmental samples. IOP Conf Ser Earth Environ Sci 2022; 974: 012003.
16. Valdez-Nuñez LF, Rivera-Jacinto MA. Thermophilic bacteria from Peruvian hot springs with high potential application in environmental biotechnology. Environ Technol 2022; 1-16.
17. Arora NK, Panosyan H. Extremophiles: applications and roles in environmental sustainability. Environ Sustain 2019; 2: 217-218.
18. Jorquera MA, Graether SP, Maruyama F. Editorial: Bioprospecting and biotechnology of extremophiles. Front Bioeng Biotechnol 2019; 7: 204.
19. Bonanomi G, Capodilupo M, Incerti G, Mazzoleni S, Scala F. Litter quality and temperature modulate microbial diversity effects on decomposition in model experiments. Community Ecol 2015; 16: 167-177.
20. Saha P, Chakrabarti T. Emticicia oligotrophica gen. nov., sp. nov., a new member of the family ‘Flexibacteraceae’, phylum Bacteroidetes. Int J Syst Evol Microbiol 2006; 56: 991-995.
21. Panda SK, Jyoti V, Bhadra B, Nayak KC, Shivaji S, Rainey FA, et al. Thiomonas bhubaneswarensis sp. nov., an obligately mixotrophic, moderately thermophilic, thiosulfate-oxidizing bacterium. Int J Syst Evol Microbiol 2009; 59: 2171-2175.
22. Köhler JM, Beetz N, Günther PM, Möller F, Schüler T, Cao J. Microbial community types and signature-like soil bacterial patterns from fortified prehistoric hills of Thuringia (Germany). Community Ecol 2020; 21: 107-120.
23. Wani AK, Chopra C, Singh R, Ahmad S, Américo-Pinheiro JHP. Mining microbial tapestry using high-throughput sequencing and In silico analysis of Trehalose synthase (TreS) derived from hot spring metagenome. Biocatal Agric Biotechnol 2023; 52: 102829.
24. Kelly CN, Schwaner GW, Cumming JR, Driscoll TP. Metagenomic reconstruction of nitrogen and carbon cycling pathways in forest soil: Influence of different hardwood tree species. Soil Biol Biochem 2021; 156: 108226.
25. Wani AK, Akhtar N, Naqash N, Rahayu F, Djajadi D, Chopra C, et al. Discovering untapped microbial communities through metagenomics for microplastic remediation: recent advances, challenges, and way forward. Environ Sci Pollut Res Int 2023; 30: 81450-81473.
26. Rupasinghe R, Amarasena S, Wickramarathna S, Biggs PJ, Chandrajith R, Wickramasinghe S. Microbial diversity and ecology of geothermal springs in the high-grade metamorphic terrain of Sri Lanka. Environ Adv 2022; 7: 100166.
27. Estaki M, Jiang L, Bokulich NA, McDonald D, González A, Kosciolek T, et al. QIIME 2 enables comprehensive end-to-end analysis of diverse microbiome data and comparative studies with publicly available data. Curr Protoc Bioinformatics 2020; 70(1): e100.
28. Fung C, Rusling M, Lampeter T, Love C, Karim A, Bongiorno C, et al. Automation of QIIME2 metagenomic analysis platform. Curr Protoc 2021; 1(9): e254.
29. Wani AK, Roy P, Kumar V, Mir TUG. Metagenomics and artificial intelligence in the context of human health. Infect Genet Evol 2022; 100: 105267.
30. Najar IN, Sherpa MT, Das S, Das S, Thakur N. Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry. Sci Total Environ 2018; 637-638: 730-745.
31. Peña-Ocaña BA, Ovando-Ovando CI, Puente-Sánchez F, Tamames J, Servín-Garcidueñas LE, González-Toril E, et al. Metagenomic and metabolic analyses of poly-extreme microbiome from an active crater volcano lake. Environ Res 2022; 203: 111862.
32. Kaur R, Rajesh C, Sharma R, Boparai JK, Sharma PK. Metagenomic investigation of bacterial diversity of hot spring soil from Manikaran, Himachal Pradesh, India. Ecol Genet Genom 2018; 6: 16-21.
33. Singh A, Subudhi E. Profiling of microbial community of Odisha hot spring based on metagenomic sequencing. Genom Data 2016; 7: 187-188.
34. D’Auria G, Artacho A, Rojas RA, Bautista JS, Méndez R, Gamboa MT, et al. Metagenomics of bacterial diversity in Villa Luz Caves with Sulfur Water Springs. Genes (Basel) 2018; 9: 55.
35. Mangrola AV, Dudhagara P, Koringa P, Joshi CG, Patel RK. Shotgun metagenomic sequencing based microbial diversity assessment of Lasundra hot spring, India. Genom Data 2015; 4: 73-75.
36. Wani AK, Akhtar N, Singh R, Chopra C, Kakade P, Borde M, et al. Prospects of advanced metagenomics and meta-omics in the investigation of phytomicrobiome to forecast beneficial and pathogenic response. Mol Biol Rep 2022; 49: 12165-12179.
37. Nearing JT, Douglas GM, Comeau AM, Langille MGI. Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches. PeerJ 2018; 6: e5364.
38. Jeong J, Yun K, Mun S, Chung W-H, Choi S-Y, Nam Y, et al. The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology. Sci Rep 2021; 11: 1727.
39. Torres-Ceron DA, Acosta-Medina CD, Restrepo-Parra E. Geothermal and mineralogic analysis of hot springs in the Puracé-La Mina sector in Cauca, Colombia. Geofluids 2019; 2019: 1-20.
40. Serbulea M, Payyappallimana U. Onsen (hot springs) in Japan--Transforming terrain into healing landscapes. Health Place 2012; 18: 1366-1373.
41. Chaudhuri B, Chowdhury T, Chattopadhyay B. Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India. Genom Data 2017; 12: 122-129.
42. Tessler M, Neumann JS, Afshinnekoo E, Pineda M, Hersch R, Velho LFM, et al. Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing. Sci Rep 2017; 7: 6589.
43. Sun L, Toyonaga M, Ohashi A, Tourlousse DM, Matsuura N, Meng X-Y, et al. Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov. Int J Syst Evol Microbiol 2016; 66: 2635-2642.
44. Thiel V, Garcia Costas AM, Fortney NW, Martinez JN, Tank M, Roden EE, et al. "Candidatus Thermonerobacter thiotrophicus,” a non-phototrophic member of the Bacteroidetes/Chlorobi with dissimilatory sulfur metabolism in hot spring mat communities. Front Microbiol 2019; 9: 3159.
45. Nazina TN, Lebedeva EV, Poltaraus AB, Tourova TP, Grigoryan AA, Sokolova DS, et al. Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov. Int J Syst Evol Microbiol 2004; 54: 2019-2024.
46. Verma JP, Jaiswal DK, Krishna R, Prakash S, Yadav J, Singh V. Characterization and screening of thermophilic Bacillus strains for developing plant growth promoting consortium from hot spring of Leh and Ladakh Region of India. Front Microbiol 2018; 9: 1293.
47. Panosyan H, Margaryan A, Birkeland N-K. Anoxybacillus karvacharensis sp. nov., a novel thermophilic bacterium isolated from the Karvachar geothermal spring in Nagorno-Karabakh. Int J Syst Evol Microbiol 2021; 71: 005035.
2. Singh HK, Thankappan A, Mohite P, Sinha SK, Chandrasekharam D, Chandrasekhar T. Geothermal energy potential of Tulsishyam thermal springs of Gujarat, India. Arab J Geosci 2018; 11: 1-11.
3. Dutta A, Gupta RK. Geochemistry and utilization of water from thermal springs of tawang and west Kameng Districts, Arunachal Pradesh. J Geol Soc India 2022; 98: 237-244.
4. Vaidya B, Nakarmi S. A qualitative study of patients’ beliefs and perception on medicinal properties of natural Hot Spring Bath for Musculoskeletal problems. J Environ Public Health 2020; 2020: 3694627.
5. Ahmad M, Akram W, Hussain SD, Sajjad MI, Zafar MS. Origin and subsurface history of geothermal water of Murtazabad area, Pakistan—isotopic evidence. Appl Radiat Isot 2001; 55: 731-736.
6. Amin A, Ahmed I, Salam N, Kim B-Y, Singh D, Zhi X-Y, et al. Diversity and distribution of thermophilic bacteria in Hot Springs of Pakistan. Microb Ecol 2017; 74: 116-127.
7. Sahoo RK, Gaur M, Das A, Singh A, Kumar M, Subudhi E. Comparative analysis of 16S rRNA Gene Illumina sequence for microbial community structure in diverse unexplored Hot Springs of Odisha, India. Geomicrobiol J 2017; 34: 567-576.
8. Tian J, Li Y, Zhou X, Pang Z, Li L, Xing L, et al. Geochemical characteristics of hydrothermal volatiles from southeast China and their implications on the tectonic structure controlling heat convection. Front Earth Sci 2021; 9: 786051.
9. Petersen IA, Meyer KM, Bohannan BJ. Meta-analysis reveals consistent bacterial responses to land use change across the tropics. Front Ecol Evol 2019; 7: 391.
10. Ji M, Kong W, Jia H, Delgado-Baquerizo M, Zhou T, Liu X, et al. Polar soils exhibit distinct patterns in microbial diversity and dominant phylotypes. Soil Biol Biochem 2022; 166: 108550.
11. Garcia-Lopez E, Rodriguez-Lorente I, Alcazar P, Cid C. Microbial communities in coastal glaciers and tidewater tongues of Svalbard archipelago, Norway. Front Mar Sci 2019; 5: 512.
12. Molina-Menor E, Gimeno-Valero H, Pascual J, Peretó J, Porcar M. High culturable bacterial diversity from a European desert: The Tabernas desert. Front Microbiol 2021; 11: 583120.
13. Ding J, Zhang Y, Wang H, Jian H, Leng H, Xiao X. Microbial community structure of deep-sea hydrothermal vents on the ultraslow spreading Southwest Indian Ridge. Front Microbiol 2017; 8: 1012.
14. Wani AK, Akhtar N, Sher F, Navarrete AA, Américo-Pinheiro JHP. Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems. Arch Microbiol 2022; 204: 144.
15. Wani AK, Rahayu F, Kadarwati FT, Suhara C, Singh R, Dhanjal DS, et al. Metagenomic screening strategies for bioprospecting enzymes from environmental samples. IOP Conf Ser Earth Environ Sci 2022; 974: 012003.
16. Valdez-Nuñez LF, Rivera-Jacinto MA. Thermophilic bacteria from Peruvian hot springs with high potential application in environmental biotechnology. Environ Technol 2022; 1-16.
17. Arora NK, Panosyan H. Extremophiles: applications and roles in environmental sustainability. Environ Sustain 2019; 2: 217-218.
18. Jorquera MA, Graether SP, Maruyama F. Editorial: Bioprospecting and biotechnology of extremophiles. Front Bioeng Biotechnol 2019; 7: 204.
19. Bonanomi G, Capodilupo M, Incerti G, Mazzoleni S, Scala F. Litter quality and temperature modulate microbial diversity effects on decomposition in model experiments. Community Ecol 2015; 16: 167-177.
20. Saha P, Chakrabarti T. Emticicia oligotrophica gen. nov., sp. nov., a new member of the family ‘Flexibacteraceae’, phylum Bacteroidetes. Int J Syst Evol Microbiol 2006; 56: 991-995.
21. Panda SK, Jyoti V, Bhadra B, Nayak KC, Shivaji S, Rainey FA, et al. Thiomonas bhubaneswarensis sp. nov., an obligately mixotrophic, moderately thermophilic, thiosulfate-oxidizing bacterium. Int J Syst Evol Microbiol 2009; 59: 2171-2175.
22. Köhler JM, Beetz N, Günther PM, Möller F, Schüler T, Cao J. Microbial community types and signature-like soil bacterial patterns from fortified prehistoric hills of Thuringia (Germany). Community Ecol 2020; 21: 107-120.
23. Wani AK, Chopra C, Singh R, Ahmad S, Américo-Pinheiro JHP. Mining microbial tapestry using high-throughput sequencing and In silico analysis of Trehalose synthase (TreS) derived from hot spring metagenome. Biocatal Agric Biotechnol 2023; 52: 102829.
24. Kelly CN, Schwaner GW, Cumming JR, Driscoll TP. Metagenomic reconstruction of nitrogen and carbon cycling pathways in forest soil: Influence of different hardwood tree species. Soil Biol Biochem 2021; 156: 108226.
25. Wani AK, Akhtar N, Naqash N, Rahayu F, Djajadi D, Chopra C, et al. Discovering untapped microbial communities through metagenomics for microplastic remediation: recent advances, challenges, and way forward. Environ Sci Pollut Res Int 2023; 30: 81450-81473.
26. Rupasinghe R, Amarasena S, Wickramarathna S, Biggs PJ, Chandrajith R, Wickramasinghe S. Microbial diversity and ecology of geothermal springs in the high-grade metamorphic terrain of Sri Lanka. Environ Adv 2022; 7: 100166.
27. Estaki M, Jiang L, Bokulich NA, McDonald D, González A, Kosciolek T, et al. QIIME 2 enables comprehensive end-to-end analysis of diverse microbiome data and comparative studies with publicly available data. Curr Protoc Bioinformatics 2020; 70(1): e100.
28. Fung C, Rusling M, Lampeter T, Love C, Karim A, Bongiorno C, et al. Automation of QIIME2 metagenomic analysis platform. Curr Protoc 2021; 1(9): e254.
29. Wani AK, Roy P, Kumar V, Mir TUG. Metagenomics and artificial intelligence in the context of human health. Infect Genet Evol 2022; 100: 105267.
30. Najar IN, Sherpa MT, Das S, Das S, Thakur N. Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry. Sci Total Environ 2018; 637-638: 730-745.
31. Peña-Ocaña BA, Ovando-Ovando CI, Puente-Sánchez F, Tamames J, Servín-Garcidueñas LE, González-Toril E, et al. Metagenomic and metabolic analyses of poly-extreme microbiome from an active crater volcano lake. Environ Res 2022; 203: 111862.
32. Kaur R, Rajesh C, Sharma R, Boparai JK, Sharma PK. Metagenomic investigation of bacterial diversity of hot spring soil from Manikaran, Himachal Pradesh, India. Ecol Genet Genom 2018; 6: 16-21.
33. Singh A, Subudhi E. Profiling of microbial community of Odisha hot spring based on metagenomic sequencing. Genom Data 2016; 7: 187-188.
34. D’Auria G, Artacho A, Rojas RA, Bautista JS, Méndez R, Gamboa MT, et al. Metagenomics of bacterial diversity in Villa Luz Caves with Sulfur Water Springs. Genes (Basel) 2018; 9: 55.
35. Mangrola AV, Dudhagara P, Koringa P, Joshi CG, Patel RK. Shotgun metagenomic sequencing based microbial diversity assessment of Lasundra hot spring, India. Genom Data 2015; 4: 73-75.
36. Wani AK, Akhtar N, Singh R, Chopra C, Kakade P, Borde M, et al. Prospects of advanced metagenomics and meta-omics in the investigation of phytomicrobiome to forecast beneficial and pathogenic response. Mol Biol Rep 2022; 49: 12165-12179.
37. Nearing JT, Douglas GM, Comeau AM, Langille MGI. Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches. PeerJ 2018; 6: e5364.
38. Jeong J, Yun K, Mun S, Chung W-H, Choi S-Y, Nam Y, et al. The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology. Sci Rep 2021; 11: 1727.
39. Torres-Ceron DA, Acosta-Medina CD, Restrepo-Parra E. Geothermal and mineralogic analysis of hot springs in the Puracé-La Mina sector in Cauca, Colombia. Geofluids 2019; 2019: 1-20.
40. Serbulea M, Payyappallimana U. Onsen (hot springs) in Japan--Transforming terrain into healing landscapes. Health Place 2012; 18: 1366-1373.
41. Chaudhuri B, Chowdhury T, Chattopadhyay B. Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India. Genom Data 2017; 12: 122-129.
42. Tessler M, Neumann JS, Afshinnekoo E, Pineda M, Hersch R, Velho LFM, et al. Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing. Sci Rep 2017; 7: 6589.
43. Sun L, Toyonaga M, Ohashi A, Tourlousse DM, Matsuura N, Meng X-Y, et al. Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov. Int J Syst Evol Microbiol 2016; 66: 2635-2642.
44. Thiel V, Garcia Costas AM, Fortney NW, Martinez JN, Tank M, Roden EE, et al. "Candidatus Thermonerobacter thiotrophicus,” a non-phototrophic member of the Bacteroidetes/Chlorobi with dissimilatory sulfur metabolism in hot spring mat communities. Front Microbiol 2019; 9: 3159.
45. Nazina TN, Lebedeva EV, Poltaraus AB, Tourova TP, Grigoryan AA, Sokolova DS, et al. Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov. Int J Syst Evol Microbiol 2004; 54: 2019-2024.
46. Verma JP, Jaiswal DK, Krishna R, Prakash S, Yadav J, Singh V. Characterization and screening of thermophilic Bacillus strains for developing plant growth promoting consortium from hot spring of Leh and Ladakh Region of India. Front Microbiol 2018; 9: 1293.
47. Panosyan H, Margaryan A, Birkeland N-K. Anoxybacillus karvacharensis sp. nov., a novel thermophilic bacterium isolated from the Karvachar geothermal spring in Nagorno-Karabakh. Int J Syst Evol Microbiol 2021; 71: 005035.
| Files | ||
| Issue | Vol 15 No 6 (2023) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v15i6.14132 | |
| Keywords | ||
| Hot spring; Metagenome; Taxonomy; High throughput DNA sequencing; Illumina sequencing | ||
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How to Cite
1.
Wani A, Ahmad S, Américo-Pinheiro JHP, Tizro N, Singh R. Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study. Iran J Microbiol. 2023;15(6):723-733.
