NGS-Based Metagenomics Depicting Taxonomic and Functional Insights into North-Western Himalayan Hot Springs

Sharma N, Kumar J, Abedin M, Sahoo D, Pandey A, Rai AK, Singh SP (2020) Metagenomics revealing molecular profiling of community structure and metabolic pathways in natural hot springs of the Sikkim Himalaya. BMC Microbiol 20:1–17. https://doi.org/10.1186/s12866-020-01923-3

Article  CAS  Google Scholar 

Shu WS, Huang LN (2022) Microbial diversity in extreme environments. Nat Rev Microbiol 20:219–235. https://doi.org/10.1038/s41579-021-00648-y

Article  CAS  PubMed  Google Scholar 

Kumar J, Sharma N, Singh SP (2023) Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings. Environ Sci Pollut Res 30:50864–50882. https://doi.org/10.1007/s11356-023-25893-x

Article  CAS  Google Scholar 

Wani AK, Akhtar N, Sher F, Navarrete AA, Américo-Pinheiro JHP (2022) Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems. Arch Microbiol 204:144. https://doi.org/10.1007/s00203-022-02757-5

Article  CAS  PubMed  Google Scholar 

Giovanella P, Vieira GA, Otero IVR, Pellizzer EP, de Jesus FB, Sette LD (2020) Metal and organic pollutants bioremediation by extremophile microorganisms. J Hazard Mater 382:121024. https://doi.org/10.1016/j.jhazmat.2019.121024

Article  CAS  PubMed  Google Scholar 

Ferone M, Gowen A, Fanning S, Scannell AG (2020) Microbial detection and identification methods: bench top assays to omics approaches. Compr Rev Food Sci Food Saf 19:3106–3129. https://doi.org/10.1111/1541-4337.12618

Article  PubMed  Google Scholar 

Aigle A, Prosser JI, Gubry-Rangin C (2019) The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers. Environ Microbiome 14:1–10. https://doi.org/10.1186/s40793-019-0342-6

Article  CAS  Google Scholar 

Xu J (2006) Invited review: microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15:1713–1731. https://doi.org/10.1111/j.1365-294X.2006.02882.x

Article  CAS  PubMed  Google Scholar 

Garza DR, Dutilh BE (2015) From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cell Mol Life Sci 72:4287–4308. https://doi.org/10.1007/s00018-015-2004-1

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M (2008) Metagenomics approaches in systems microbiology. FEMS Microbiol Rev 33:236–255. https://doi.org/10.1111/j.1574-6976.2008.00152.x

Article  CAS  PubMed  Google Scholar 

Pandey A, Dhakar K, Sharma A, Priti P, Sati P, Kumar B (2015) Thermophilic bacteria that tolerate a wide temperature and pH range colonize the Soldhar (95 °C) and Ringigad (80 °C) hot springs of Uttarakhand, India. Ann Microbiol 65:809–816. https://doi.org/10.1007/s13213-014-0921-0

Article  CAS  Google Scholar 

Colman DR, Feyhl-Buska J, Robinson KJ, Fecteau KM, Xu H, Shock EL, Boyd ES (2016) Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs. FEMS Microbiol Eco 92:9. https://doi.org/10.1093/femsec/fiw137

Article  CAS  Google Scholar 

Ismail AR, Kashtoh H, Baek KH (2021) Temperature-resistant and solvent-tolerant lipases as industrial biocatalysts: biotechnological approaches and applications. Int J Biol Macromol 187:127–142. https://doi.org/10.1016/j.ijbiomac.2021.07.101

Article  CAS  PubMed  Google Scholar 

Sellek GA, Chaudhuri JB (1999) Biocatalysis in organic media using enzymes from extremophiles. Enzyme Microb Technol 25:471–482. https://doi.org/10.1016/S0141-0229(99)00075-7

Article  CAS  Google Scholar 

Robinson PK (2015) Enzymes: principles and biotechnological applications. Essays Biochem 59:1. https://doi.org/10.1042/Fbse0590001

Article  PubMed  PubMed Central  Google Scholar 

Park S, Lee B, Park K (2017) Extremophilic carbohydrate active enzymes (CAZymes). J Nutr Health Food Eng 7:230–237. https://doi.org/10.15406/jnhfe.2017.07.00230

Article  Google Scholar 

Schmid A, Dordick JS, Hauer B, Kiener A, Wubbolts M, Witholt B (2001) Industrial biocatalysis today and tomorrow. Nature 409:258–268. https://doi.org/10.1038/35051736

Article  CAS  PubMed  Google Scholar 

Kaushal G, Kumar J, Sangwan RS, Singh SP (2018) Metagenomic analysis of geothermal water reservoir sites exploring carbohydrate-related thermozymes. Int J Biol Macromol 119:882–895. https://doi.org/10.1016/j.ijbiomac.2018.07.196

Article  CAS  PubMed  Google Scholar 

Mahato NK, Sharma A, Singh Y, Lal R (2019) Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics. Arch Microbiol 201:377–388. https://doi.org/10.1007/s00203-018-01616-6

Article  CAS  PubMed  Google Scholar 

Fowler CMR, Tunnicliffe V (1997) Hydrothermal vent communities and plate tectonics. Endeavour 21:164–168. https://doi.org/10.1016/S0160-9327(97)01040-5

Article  Google Scholar 

Li D, Luo R, Liu CM, Leung CM, Ting HF, Sadakane K et al (2016) MEGAHIT v1. 0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102:3–11. https://doi.org/10.1016/j.ymeth.2016.02.020

Article  CAS  PubMed  Google Scholar 

Mikheenko A, Saveliev V, Gurevich A (2016) MetaQUAST: evaluation of metagenome assemblies. Bioinform 32:1088–1090. https://doi.org/10.1093/bioinformatics/btv697

Article  CAS  Google Scholar 

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

Article  CAS  Google Scholar 

Buchfink B, Xie C, Huson D (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59–60. https://doi.org/10.1038/nmeth.3176

Article  CAS  PubMed  Google Scholar 

El Hadidi M, Ruscheweyh HJ, Huson D (2013) Improved metagenome analysis using MEGAN5. In: InJoint 21st annual international conference on intelligent systems for molecular biology (ISMB) and 12th European conference on computational biology (ECCB)

Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

Article  CAS  PubMed  PubMed Central  Google Scholar 

Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T et al (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:206–214. https://doi.org/10.1093/nar/gkt1226

Article  CAS  Google Scholar 

Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (2014) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:490–495. https://doi.org/10.1093/nar/gkt1178

Article  CAS  Google Scholar 

Skirnisdottir S, Hreggvidsson GO, Hjorleifsdottir S, Marteinsson VT, Petursdottir SK, Holst O et al (2000) Influence of sulfide and temperature on species composition and community structure of hot spring microbial mats. Appl Environ Microbiol 66:2835–2841. https://doi.org/10.1128/AEM.66.7.2835-2841.2000

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sahay H, Yadav AN, Singh AK, Singh S, Kaushik R, Saxena AK (2017) Hot springs of Indian Himalayas: potential sources of microbial diversity and thermostable hydrolytic enzymes. 3 Biotech. https://doi.org/10.1007/s13205-017-0762-1

Article  PubMed  PubMed Central  Google Scholar 

Uribe-Lorio L, Brenes-Guillen L, Hernandez-Ascencio W, Mora-Amador R, Gonzalez G, Ramirez-Umana CJ et al (2019) The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica. Microbiologyopen 8:1–26. https://doi.org/10.1002/mbo3.893

Article  CAS  Google Scholar 

Power JF, Carere CR, Lee CK, Wakerley GLJ, Evans DW, Button M et al (2018) Microbial biogeography of 925 geothermal springs in New Zealand. Nat Commun 9:2876. https://doi.org/10.1038/s41467-018-05020-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Purcell D, Sompong U, Yim LC, Barraclough TG, Peerapornpisal Y, Pointing SB (2007) The effects of temperature, pH, and sulphide on the community structure of hyperthermophilic streamers in hot springs of Northern Thailand. FEMS Microbiol Ecol 60:456–466. https://doi.org/10.1111/j.1574-6941.2007.00302x

Article  CAS  PubMed  Google Scholar 

Lopez-Lopez O, Knapik K, Cerdán ME, González-Siso MI (2015) Metagenomics of an alkaline hot spring in Galicia (Spain): microbial diversity analysis and screening for novel lipolytic enzymes. Front Microbiol 6:1291

Article  PubMed  PubMed Central  Google Scholar 

Knapik K, Becerra M, González-Siso MI (2019) Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios hot spring in Spain. Sci Rep 9:11195

Article  PubMed  PubMed Central  Google Scholar 

DeCastro ME, Doane MP, Dinsdale EA, Rodríguez-Belmonte E, González-Siso MI (2021) Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases. Sci Rep 11:101

留言 (0)

沒有登入
gif