References:

  1. Mbachu AE, Chukwura EI, Amalachukwu M. Role of microorganisms in the degradation of organic pollutants: a review. Energy Environ Eng. 2020;7(1):1-11.[Google Scholar]
  2. Bodor A, Bounedjoum N, Vincze GE, Erdei J, Palagyi A, Kovacs K, et al. Challenges of unculturable bacteria: environmental perspectives. Rev Environ SciBiotechnol. 2020;19(1):1–22.[ResearchGate]
  3. Kazarina A, Wiechman H, Sarkar S, et al. Recovery of 679 metagenome-assembled genomes from different soil depths along a precipitation gradient. Sci Data. 2025; 12:521.[PubMed]
  4. Harris JK, Kelley ST, Pace NR. New perspective on uncultured bacterial phylogenetic division OP11. Appl Environ Microbiol. 2004;70(2):845-849.[PubMed]
  5. Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J ClinMicrobiol. 2007;45(9):2761-2764 .[PubMed] [ResearchGate]
  6. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991 Jan;173(2):697-703..[PubMed]
  7. Smets W, Leff JW, Bradford MA, McCulley RL, Lebeer S, Fierer N. A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing. Soil BiolBiochem. 2016; 96:145-151.[Google Scholar]
  8. Sanders ER. Aseptic laboratory techniques: plating methods. J Vis Exp. 2012;(63): e3064.[PubMed].
  9. Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M. Improved culturability of soil bacteria and isolation in pure culture using liquid serial dilution. Appl Environ Microbial. 2002;68(5):2391-2396..[PubMed]
  10. Lee PY, Costumbrado J, Hsu CY, Kim YH. Agarose gel electrophoresis for the separation of DNA fragments. J Vis Exp. 2012;(62):3923. .[PubMed]
  11. Kharel Sitaula R,Janani MK, Madhavan HN , Biswas J. Outcome of polymerase chain reaction (PCR) analysis in 100 suspected cases of infectious uveities. J Ophthalmic Infect. 2018;8(1):2.[PubMed]
  12. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol. 2008;74(8):2461-2470.[Google Scholar] [PubMed]
  13. Hanke M, Wink M. Direct sequencing of PCR products using exonuclease I and shrimp alkaline phosphatase. BioTechniques. 1994;17(5):858-860.
  14. Swerdlow H, Gesteland R. Capillary gel electrophoresis for rapid, high-resolution DNA sequencing. Nucleic Acids Res. 1990;18(6):1415-1419.[PubMed]
  15. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22 b(22):4673-4680..[PubMed]
  16. Altschul SF, Gish W, Miller W, Myers E.W, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–410.[PubMed]
  17. Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. MolBiolEvol. 1987;4(4):406-425.[PubMed]
  1. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 1985;39(4):783-791.[PubMed]
  2. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J MolEvol. 1980;16(2):111-120.[PubMed]
  3. Tamura K, Stecher G, Kumar S. MEGA 11: Molecular Evolutionary Genetics Analysis Version 11. MolBiolEvol. 2021; 38(7):3022-3027.[PubMed]
  4. Delbari AS, Kulkarni DK, Saptarshi PG. Heavy metal contamination in soils along highways near Pune, India. Int J PollutAbat Technol. 2012;1(1):35-39. [Research Gate]
  5. Patturajan V, Jaybhaye RG, Shouche Y. Effect of shifting cultivation on soil health and microbial diversity in BhorTaluka of Pune District. Indian J Nat Sci. 2021 Aug;12(67):33102-33110.[  Research Gate]
  6. Allison SD, Martiny JB. Resistance, resilience, and redundancy in microbial communities. ProcNatlAcadSci U S A. 2008 Aug 12;105 Suppl 1:11512-9.[PubMed]
  7. Murphy CL, Sheremet A, Dunfield PF, Spear JR, Stepanauskas R, Woyke T, et al. Genomic analysis of the yet-uncultured Binatota reveals broad methylotrophic, alkane-degradation, and pigment production capacities. mBio. 2021;12 (3):e00985-21.[PubMed]
  8. Bhattacharya S, Panda AK. In silico analysis of phylogeny, structure, and function of enzymes from uncultured soil bacteria. BMC Microbiol. 2021;21(1):89.[PubMed]
  9. Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol. 2003;69(12):7210-5.[PubMed]