Microbial Treatment of Waste by Culture-Dependent and Culture-Independent Approaches: Opportunities and Challenges

  • Juhi Gupta
  • Bhawna Tyagi
  • Rashmi Rathour
  • Indu Shekhar ThakurEmail author


Globally, there are concerning trends of waste generation as we progress towards a more developed society. India, the second most populous country, is on the edge of being the fifth largest economy in the world. In the last five decades, its metropolitanization has increased by approximately 10% and would further rise to 20% by 2026. The increasing urbanization and evolving lifestyles, food habits, and standards prompt such exponential expansion of robust waste. It is basically answerable for the introduction of a waste era posing various threats to health and causing ecological deformities. In 1996, the urban number created around 114,576 tonnes of municipal solid waste (MSW) per day, which is predicted to be 440,460 tonnes per day−1 by 2026. A large section of the waste is handled using the concept of 3Rs (reduce, reuse, and recycle), but the biological microbial potential is still underestimated. Less than 1% of the microbial community is culturable due to which the conservative cultural microbiology lags behind in revealing the hidden potential. This limitation is subsided by the introduction of culture-independent techniques. This chapter discusses about the possibilities of waste management using microbes both at culture-dependent and culture-independent levels. Next-generation sequencing is a relatively new and flourishing field and promises to be potent enough to supervise the waste generation. Different techniques and procedures have been discussed. The future challenges for waste management lie in the lack of motivation and public unawareness. Waste management is an immediate need of the hour for a sustainable future tomorrow as covered in the Sustainable Development Goals Agenda 2030.


Solid waste Microbiology Microbial community Culture-dependent approach Culture-independent approach Metagenomics Waste treatment 


  1. Agarwal SK (1998) Advances in environmental biotechnology, 1st edn. APH Publishing Corporation, New Delhi, pp 267–289Google Scholar
  2. Ahsan N (1999) Solid waste management plan for Indian megacities. Indian J Environ Prot 19:90–95Google Scholar
  3. Ali U, Syed JH, Malik RN, Katsoyiannis A, Li J et al (2014) Organochlorine pesticides (OCPs) in South Asian region: a review. Sci Total Environ 476:705–717PubMedCrossRefPubMedCentralGoogle Scholar
  4. Ambulkar AR, Shekdar AV (2004) Prospects of biomethanation technology in the Indian context: a pragmatic approach. Resour Conserv Recycl 40(2):111–128CrossRefGoogle Scholar
  5. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA et al (2006) The marine viromes of four oceanic regions. PLoS Biol 4:e368PubMedPubMedCentralCrossRefGoogle Scholar
  6. Annepu RK (2012) Report on sustainable solid waste management in India. Waste-to-Energy Research and Technology Council (WTERT) 1–189. See Accessed 26 June 2015
  7. Antizar-Ladislao B, Katerina S, Angus JB, Nicholas JR (2008) Microbial community structure changes during bioremediation of PAHs in an aged coal tar contaminated soil by in-vessel composting. Int Biodeterior Biodegradation 61:357–364CrossRefGoogle Scholar
  8. Bank W. O. L. D (2012) What a waste – a global review of solid waste management. New York. No 15Google Scholar
  9. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S et al (2002) ARACHNE: a wholegenome shotgun assembler. Genome Res 12:177–189PubMedPubMedCentralCrossRefGoogle Scholar
  10. Bouchez T, Patureau D, Dabert P, Juretschko S, Doré J et al (2000) Ecological study of a bioaugmentation failure. Environ Microbiol 2:179–190PubMedCrossRefPubMedCentralGoogle Scholar
  11. Bouwer EJ, Zehnder AJ (1993) Bioremediation of organic compounds – putting microbial metabolism to work. Trends Biotechnol 11:360–367PubMedCrossRefPubMedCentralGoogle Scholar
  12. Bredberg K, Persson J, Christiansson M, Stenberg B, Holst O (2001) Anaerobic desulfurization of ground rubber with the thermophilicarchaeon Pyrococcus furiosus – a new method for rubber recycling. Appl Microbiol Biotechnol 55(1):43–48PubMedCrossRefPubMedCentralGoogle Scholar
  13. Central Pollution Control Board (CPCB) (2000a) Management of municipal solid waste Delhi. See Accessed 27 June 2015
  14. Central Pollution Control Board (CPCB) (2000b) Status of municipal solid waste generation, collection, treatment and disposal in class I cities. Series: ADSORBS/31/1999–2000Google Scholar
  15. Central Pollution Control Board (CPCB) (2000c) Status of solid waste generation, collection, treatment and disposal in metrocities. Series: CUPS/46/1999–2000Google Scholar
  16. Central Pollution Control Board (CPCB) (2004) Management of municipal solid waste. Ministry of Environment and Forests, New DelhiGoogle Scholar
  17. Central Pollution Control Board (CPCB) (2012) Status of compliance by CPCB with municipal solid wastes (management and Handling) rules, 2000Google Scholar
  18. Central Pollution Control Board (CPCB) (2013) Status report on municipal solid waste managementGoogle Scholar
  19. Chen WM, Wu CH, James EK, Chang JS (2008) Metal biosorption capability of Cupriavidus taiwanensis and its effects on heavy metal removal by nodulated Mimosa pudica. J Hazard Mater 151(2–3):364–371PubMedCrossRefPubMedCentralGoogle Scholar
  20. Dayal G (1994) Solid wastes: sources, implications and management. Indian J Environ Prot 14(9):669–677Google Scholar
  21. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86–90PubMedCrossRefPubMedCentralGoogle Scholar
  22. Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88(6):1354–1364PubMedCrossRefPubMedCentralGoogle Scholar
  23. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST et al (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci U S A 109(52):21390–21395PubMedPubMedCentralCrossRefGoogle Scholar
  24. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ et al (2008) The Pfam protein families database. Nucleic Acids Res 36:D281–D288PubMedCrossRefPubMedCentralGoogle Scholar
  25. Gandolla M, Aragno M (1992) The importance of microbiology in waste management. Experientia 48:362CrossRefGoogle Scholar
  26. Garg P, Gupta A, Satya S (2006) Vermicomposting of different types of waste using Eisenia foetida: a comparative study. Bioresour Technol 97:391–395PubMedCrossRefPubMedCentralGoogle Scholar
  27. Ghosh P, Swati, Thakur IS (2014) Enhanced removal of COD and color from landfill leachate in a sequential bioreactor. Bioresour Technol 170:10–19PubMedCrossRefPubMedCentralGoogle Scholar
  28. Gielkens MM, Visser J, de Graaff LH (1997) Arabinoxylan degradation by fungi: characterization of the arabinoxylan-arabinofuranohydrolase encoding genes from Aspergillus niger and Aspergillus tubingensis. Curr Genet 31(1):22–29PubMedCrossRefPubMedCentralGoogle Scholar
  29. Goldfarb KC, Karaoz U, Hanson CA, Santee CA, Bradford MA et al (2011) Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol 2:94PubMedPubMedCentralCrossRefGoogle Scholar
  30. Gómez G, Meneses M, Ballinas L, Castells F (2009) Seasonal characterization of municipal solid waste (MSW) in the city of Chihuahua, Mexico. Waste Manag 29:2018–2024PubMedCrossRefPubMedCentralGoogle Scholar
  31. Gordon DC, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202PubMedCrossRefPubMedCentralGoogle Scholar
  32. Gupta R, Mohapatra H (2003) Microbial biomass: an economical alternative for removal of heavy metals from waste water. Indian J Exp Biol 41:945–966PubMedPubMedCentralGoogle Scholar
  33. Gupta A, Thakur IS (2016) Study of optimization of wastewater contaminant removal along with extracellular polymeric substances (EPS) production by a thermotolerant Bacillus sp. ISTVK1 isolated from heat shocked sewage sludge. Bioresour Technol 213:21–30PubMedCrossRefPubMedCentralGoogle Scholar
  34. Gupta J, Rathour R, Kumar M, Thakur IS (2017) Metagenomic analysis of microbial diversity in landfill lysimeter soil of Ghazipur landfill site, New Delhi, India. Genome Announc 5:e01104–e01117PubMedPubMedCentralCrossRefGoogle Scholar
  35. Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y et al (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci U S A 103:18296–18301PubMedPubMedCentralCrossRefGoogle Scholar
  36. Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17:377–386PubMedPubMedCentralCrossRefGoogle Scholar
  37. Indo-UK Seminar Report (2015) Sustainable solid waste management for cities: opportunities in SAARC countries. See Accessed 27 June 2015
  38. Intergovernmental Panel on Climate Change (IPPC) (2007) Climate change 2007: synthesis report. UNEP, WMO: 2007. Accessed 20 Dec 2016
  39. ISWA (International Solid Waste Association) (2012) Globalization and waste management final report from the ISWA task force. See Accessed 27 Apr 2018
  40. Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K et al (2003) Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 13:1–96CrossRefGoogle Scholar
  41. Jayashree R, Nithya SE, Rajesh PP, Krishnaraju M (2012) Biodegradation capability of bacterial species isolated from oil contaminated soil. J Academia Indust Res 1:140–143Google Scholar
  42. Joshi R, Ahmed S (2016) Status and challenges of municipal solid waste management in India: a review. Cogent Environ Sci 2(1):1139434CrossRefGoogle Scholar
  43. Kansal A (2002) Solid waste management strategies for India. Indian J Environ Prot 22(4):444–448Google Scholar
  44. Karigar CS, Rao SS (2011) Role of microbial enzymes in the bioremediation of pollutants: a review. Enzyme Res 2011:1–11CrossRefGoogle Scholar
  45. Kaushal RK, Varghese GK, Chabukdhara M (2012) Municipal solid waste management in India-current state and future challenges: a review. Int J Eng Sci Technol 4(4):1473–1489Google Scholar
  46. Keegan KP, Glass EM, Meyer F (2016) MG-RAST, a metagenomics service for analysis of microbial community structure and function. Methods Mol Biol 1399:207–233PubMedCrossRefPubMedCentralGoogle Scholar
  47. Khan MA, Burney FA (1989) Forecasting solid waste composition – an important consideration in resource recovery and recycling. Resour Conserv Recycl 3(1):1–17CrossRefGoogle Scholar
  48. Khosla K, Rathour R, Maurya R, Maheshwari N, Gnansounou E et al (2017) Biodiesel production from lipid of carbon dioxide sequestrating bacterium and lipase of psychrotolerant Pseudomonas sp. ISTPL3 immobilized on biochar. Bioresour Technol 245:743–750PubMedCrossRefPubMedCentralGoogle Scholar
  49. Kumar JS (2011) Prediction of municipal solid waste with RBF net work – a case study of Eluru, A.P, India. Int J Innov Manag Technol 2:3Google Scholar
  50. Kumar KN, Goel S (2009) Characterization of municipal solid waste (MSW) and a proposed management plan for Kharagpur, West Bengal, India. Resour Conserv Recycl 53(3):166–174CrossRefGoogle Scholar
  51. Kumar A, Samadder SR (2017) A review on technological options of waste to energy for effective management of municipal solid waste. Waste Manag 69:407–422PubMedCrossRefPubMedCentralGoogle Scholar
  52. Kumar S, Bhattacharyya JK, Vaidya AN, Chakrabarti T, Devotta S et al (2009) Assessment of the status of municipal solid waste management in metro cities, state capitals, class I cities, and class II towns in India: An insight. Waste Manag 29(2):883–895PubMedCrossRefPubMedCentralGoogle Scholar
  53. Kumar M, Ghosh P, Khosla K, Thakur IS (2016) Biodiesel production from municipal secondary sludge. Bioresour Technol 216:165–171. CrossRefPubMedPubMedCentralGoogle Scholar
  54. Kumar S, Smith SR, Fowler G, Velis C, Kumar SJ et al (2017) Challenges and opportunities associated with waste management in India. R Soc Open Sci 4(3):160764PubMedPubMedCentralCrossRefGoogle Scholar
  55. Kumari M, Ghosh P, Wanwari S, Thakur IS (2014) Microcosmic study of endosulfan degradation by Paenibacillus sp. ISTP10 and its toxicological evaluation using mammalian cell line. Int Biodeterior Biodegradation 96:33–40CrossRefGoogle Scholar
  56. Kumari M, Ghosh P, Thakur IS (2016) Landfill leachate treatment using bacto-algal co-culture: an integrated approach using chemical analyses and toxicological assessment. Ecotoxicol Environ Saf 128:44–51PubMedCrossRefPubMedCentralGoogle Scholar
  57. Kumari M, Ghosh P, Thakur IS (2017) Application of microbes in remediation of hazardous wastes: a review bioremediation: applications for environmental protection and management. Springer, Singapore, pp 223–241Google Scholar
  58. Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (2008) A bioinformatician’s guide to metagenomics. Microbiol Mol Biol Rev 72(4):557–578PubMedPubMedCentralCrossRefGoogle Scholar
  59. Lombardi L, Carnevale E, Corti A (2015) A review of technologies and performances of thermal treatment systems for energy recovery from waste. Waste Manag 37:26–44PubMedCrossRefPubMedCentralGoogle Scholar
  60. Makan A, Assobhei O, Mountadar M (2013) Effect of initial moisture content on the in-vessel composting under air pressure of organic fraction of municipal solid waste in Morocco. Iran J Environ Health Sci Eng 10(1):3CrossRefGoogle Scholar
  61. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO et al (1999a) Detecting protein function and protein-protein interactions from genome sequences. Science 285:751–753PubMedCrossRefPubMedCentralGoogle Scholar
  62. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D (1999b) A combined algorithm for genome-wide prediction of protein function. Nature 402:83–86PubMedCrossRefPubMedCentralGoogle Scholar
  63. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380PubMedPubMedCentralCrossRefGoogle Scholar
  64. Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F et al (2006) An experimental metagenome data management and analysis system. Bioinformatics 22:e359–e3567PubMedCrossRefPubMedCentralGoogle Scholar
  65. Mathur V (2012) Scope of recycling municipal solid waste in Delhi and NCR- integral review. J Manag 5:27–36Google Scholar
  66. Medhi K, Thakur IS (2018) Bioremoval of nutrients from wastewater by a denitrifier Paracoccus denitrificans ISTOD1. Bioresour Technol Rep 1:56–60CrossRefGoogle Scholar
  67. Medhi K, Mishra A, Thakur IS (2018) Genome sequence of a heterotrophic nitrifier and aerobic denitrifier, Paracoccus denitrificans strain ISTOD1, isolated from wastewater. Microbiol Resour Announc 6:15Google Scholar
  68. Menzel P et al (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun 7:11257PubMedPubMedCentralCrossRefGoogle Scholar
  69. Mishra A, Jha G, Thakur IS (2018a) Draft genome sequence of Zhihengliuella sp. Strain ISTPL4, a psychrotolerant and halotolerant bacterium isolated from Pangong Lake, India. Genome Announc 6(5):e01533–e01517PubMedPubMedCentralCrossRefGoogle Scholar
  70. Mishra A, Medhi K, Maheshwari N, Srivastava S, Thakur IS (2018b) Biofuel production and phycoremediation by Chlorella sp. ISTLA1 isolated from landfill site. Bioresour Technol 253:121–129PubMedCrossRefPubMedCentralGoogle Scholar
  71. Modak P, Jiemian Y, Hongyuan Y, Mohanty CR (2010) Municipal solid waste management: turning waste into resources. In: Shanghai manual: a guide for sustainable urban development in the 21st century. Dong fang chu ban zhong xin, Shanghai Shi, pp 1–36Google Scholar
  72. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP et al (2000) A whole-genome assembly of Drosophila. Science 287:2196–2204PubMedPubMedCentralCrossRefGoogle Scholar
  73. Nandan A, Yadav BP, Baksi S, Bose D (2017) Recent scenario of solid waste management in India. World Sci News 66:56–74Google Scholar
  74. Niu GL, Zhang JJ, Zhao S, Liu H, Boon N et al (2009) Bioaugmentation of a 4-chloronitrobenzene contaminated soil with Pseudomonas putida ZWL73. Environ Pollut 157:763–771PubMedCrossRefPubMedCentralGoogle Scholar
  75. Pappu A, Saxena M, Asolekar SR (2007) Solid wastes generation in India and their recycling potential in building materials. Build Environ 42(6):2311–2320CrossRefGoogle Scholar
  76. Phelps HO, Heinke GW, Jonker JF, Ouano EAR, Vandecasteele C (1995) Management of solid waste. UNESCO, ParisGoogle Scholar
  77. Planning Commission, Government of India (2014) Report of the task force on waste to energy (Volume I) in the context of integrated municipal solid waste management. See Accessed 1 July 2015
  78. Qasim SR, Stinehelfer ML (1982) Effect of a bacterial culture product on biological kinetics. J Water Pollut Control Fed 54(3):255Google Scholar
  79. Rathour R, Gupta J, Kumar M, Hiloidhari M, Mehrotra AK et al (2017) Metagenomic sequencing of microbial communities from brackish water of Pangong Lake of the Northwest Indian Himalayas. Genome Announc 5(40):e01029–e01017PubMedPubMedCentralCrossRefGoogle Scholar
  80. Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14(3):303–310PubMedCrossRefPubMedCentralGoogle Scholar
  81. Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M et al (2007) TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 35:D260–D264PubMedCrossRefPubMedCentralGoogle Scholar
  82. Sethunathan N, Megharaj M, Chen ZL, Williams BD, Lewis G et al (2004) Algal degradation of a known endocrine disrupting insecticide, α-endosulfan, and its metabolite, endosulfansulfate, in liquid medium and soil. J Agric Food Chem 52:3030–3035PubMedCrossRefPubMedCentralGoogle Scholar
  83. Sharholy M, Ahmad K, Mahmood G, Trivedi RC (2005) Analysis of municipal solid waste management systems in Delhi–a review. In: Book of proceedings for the second international congress of chemistry and environment, Indore, India, pp 773–777Google Scholar
  84. Sharholy M, Ahmad K, Vaishya RC, Gupta RD (2007) Municipal solid waste characteristics and management in Allahabad, India. Waste Manag 27(4):490–496PubMedCrossRefPubMedCentralGoogle Scholar
  85. Sharholy M, Ahmad K, Mahmood G, Trivedi RC (2008) Municipal solid waste management in Indian cities–a review. Waste Manag 28(2):459–467PubMedCrossRefPubMedCentralGoogle Scholar
  86. Sharma JK, Gautam RK, Nanekar SV, Weber R, Singh BK et al (2017) Advances and erspective in bioremediation of polychlorinated biphenyl-contaminated soils. Environ Sci Pollut Res 25(17):16355–16375CrossRefGoogle Scholar
  87. Singh SK, Singh RS (1998) A study on municipal solid waste and its management practices in Dhanbad-Jharia coalfield. Indian J Environ Prot 18(11):850–852Google Scholar
  88. Singh SP, Tiwari G (2014) Application of bioremediation on solid waste management: a review. J Bioremed Biodegr 5:06CrossRefGoogle Scholar
  89. Singh R, Singh P, Sharma R (2014) Microorganism as a tool of bioremediation technology for cleaning environment: a review. Proc Int Acad Ecol Environ Sci 4:1–6Google Scholar
  90. Singhal L, Tuli AK, Gautam V (2017) Biomedical waste management guidelines 2016: what’s done and what needs to be done. Indian J Microbol 35(2):194Google Scholar
  91. Sjostrom E (1993) Wood chemistry, fundamentals and applications, 2nd edn. Gulf Professional Publishing Houston, Texas, p 293Google Scholar
  92. Srivastava R, Krishna V, Sonkar I (2014) Characterization and management of municipal solid waste: a case study of Varanasi city. India Int J Curr Res Acad Rev 2:10–16Google Scholar
  93. Stamps BW, Lyles CN, Suflita JM, Masoner JR, Cozzarelli IM et al (2016) Municipal solid waste landfills harbor distinct microbiomes. Front Microbiol 7:534PubMedPubMedCentralCrossRefGoogle Scholar
  94. Stephenson D, Stephenson T (1992) Bioaugmentation for enhancing biological wastewater treatment. Biotechnol Adv 10:549–559PubMedCrossRefPubMedCentralGoogle Scholar
  95. Swati, Thakur IS, Vijay VK, Ghosh P (2018) Scenario of landfilling in India: problems, challenges, and recommendations. In: Hussain C (ed) Handbook of environmental materials management. Springer, Cham, pp 1–16Google Scholar
  96. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631–637PubMedPubMedCentralCrossRefGoogle Scholar
  97. Tchobanoglous G, Eliassen R, Theisen H (1977) Solid wastes; engineering principles and management issues. McGraw-Hill, New YorkGoogle Scholar
  98. Thomas CA Jr (1971) The genetic organization of chromosomes. Annu Rev Genet 5:237–256PubMedCrossRefPubMedCentralGoogle Scholar
  99. Tiwari G, Singh SP (2016) Application of bioremediation on solid waste management: a review. In: Solid waste management: policy and planning for a sustainable society, p 143Google Scholar
  100. Tuomela M, Vikman M, Hatakka A, Itavaara M (2000) Biodegradation of lignin in a compost environment: a review. Bioresour Technol 72:169–183CrossRefGoogle Scholar
  101. UNEP (United Nations Environment Programme) (2005) Solid waste management volume I: Accessed 1 July 2015
  102. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74PubMedPubMedCentralCrossRefGoogle Scholar
  103. Wobus A, Bleul C, Maassen S, Scheerer C, Schuppler M et al (2003) Microbial diversity and functional characterization of sediments from reservoirs of different trophic state. FEMS Microbiol Ecol 46(3):331–347PubMedCrossRefPubMedCentralGoogle Scholar
  104. World Bank (2014) World development indicators 2014. World Development Indicators, Washington, DC. © World Bank. License: CC BY 3.0 IGO
  105. Zhang H, Hu C, Jia X, Xu Y, Wu C et al (2012) Characteristics of c-hexachlorocyclohexane biodegradation by a nitrogen-fixing cyanobacterium Anabaena azotica. J Appl Phycol 24:221–225CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Juhi Gupta
    • 1
  • Bhawna Tyagi
    • 1
  • Rashmi Rathour
    • 1
  • Indu Shekhar Thakur
    • 1
    Email author
  1. 1.School of Environmental SciencesJawaharlal Nehru UniversityNew DelhiIndia

Personalised recommendations