Courses » Applied Environmental Microbiology

Applied Environmental Microbiology


This course prepares the student to address pressing environmental challenges by developing a fundamental understanding of the microbial communities and processes in natural and built environments. It lays and builds upon the foundation of basic microbiology, microbial energetics, and diversity, to applying tools provided by microbiology ranging from traditional to state of art for addressing relevant environmental concerns. It provides an indepth exploration of the diverse role microbes and microbial communities and includes topics such as: cell structure and elements, microbial energetics and diversity, ecology and population dynamics, environmental microbial processes including biogeochemical cycling, and microbes involved in biodeterioration and bioremediation.


Water and waste water treatment companies such as VA Tech Wabad GMBH, Thermax India, GE Water, Siemens Water, SFC Environmental Technologies Pvt. Ltd., Voltas Ltd.; Biotechnological companies such as: Bharat Biotech International, Biocon, Biotech Consortium India Ltd;Bioremediation companies such as ONGC Teri Biotech Ltd, Chempure Technologies; CPCB,  Department of Irrigation and Public Health.


Students of Civil Engineering, Chemical Engineering, and related sciences
It is an elective course for UG students.


Week 1: Introduction; cell elements and composition Cell and its composition, cytoplasmic membrane Prokaryotic cell division Microbes and their environmental niches Historical roots of microbiology Nucleic acids and amino acids DNA structure, replication, and manipulation Protein and its structure Regulation Microbial nutrition Microscopy: Light microscopy, 3D Imaging, AFM, Confocal scanning laser microscopy

Week 2: Microbial energetics  and diversity Stoichiometry and bioenergetics Oxidation-reduction NAD, energy-rich compounds and energy storage Mathematics of microbial growth Glycolysis Respiration Citric-acid cycle Catabolic Alternatives Phototrophy, Chemolithotrophy, anaerobic respiration (Nitrate and Sulfate reduction; Acetogenesis; Methanogenesis; Metal, Chlorate, and organic electron acceptors)

Week 3: Microbial metabolism and functional diversity of bacteria Prokaryotic diversity Classical taxonomy  Origin of life Tree of life Major catabolic pathways Catalysis and enzymes Energy conservation Sugars and polysaccharides, amino acids, nucleotides, lipids

Week 4: Microbial ecosystems Population, guilds, and communities Environments and microenvironments Microbial growth on surfaces Environmental effects on microbial growth

Week 5: Environmental genomics and microbial ecology; genetic exchange Environmental genomics Microbial ecology  Horizontal and vertical gene transfer: Replication, Transformation Transduction

Week 6: Microbial symbiosis and virus, Mutation and its rate ,Genetic recombination, Population dynamics ,Virus ,Viroid, Prion ,Application of environmental microbes

Week 7: Investigations in environmental microbiology: sampling, detection, isolation, taxonomic and functional annotation and quantification; Introductory bioinformatics and data analysis Microbial sampling Culture based and culture independent tools Molecular biology tools: Cloning, amplification, sequencing,Case study

Week 8: Bioremediation and wastewater microbiology, Bioremediation and examples, Acid mine drainage, Enhanced metal recovery, Wastewater microbiology

Week 9: Drinking water microbiology, Drinking water microbiome and treatment, Microbial instability ,Water borne microbial diseases

Week 10:
Solid waste microbiology and antimicrobial resistance, Landfills,  Leachate, Anaerobic degradation phases, Antimicrobial resistance

Week  11:
Epidemiology and biosensors ,Public health, Epidemics, Biosensors ,Wearable biosensors

Week 12: Built microbiology, exposomes and bioinformatics, Exposure routes ,Microbes living around us ,Exposomes Basic bioinformatics, Bioinformatics tools available online


Dr. Gargi Singh is currently working at the interface of microbiology and environmental engineering at IIT Roorkee to address environmental challenges of pathogen ingress in water distribution network and environmental proliferation of antibiotic resistance. In her doctoral research, she applied molecular biology tools including quantitative polymerase chain reaction, isolation, selection, high-throughput sequencing on pyrosequencing and Illumina based platforms, and metagenomics to investigate biodegradation of petroleum and nanocellulose, and sequestration of heavy metals. She is also faculty member of Centre of Nanotechnology at IIT Roorkee, where she is currently teaching environmental statistics and environmental implications of nanotechnology.


1. Bruce E. Rittmann, and Perry L. McCarty. Environmental Biotechnology: Principles and Applications. McGraw-Hill, 2001. ISBN: 0071181849. 2017. 

2. Madigan, M., Bender K. S., Buckley D.H., Sattley W. M., and Stahl D.A.. Brock Biology of Microorganisms. 15th ed. New York: Pearson, 2017. ISBN: 0134261925. 2001.


• The exam is optional for a fee.
• Date and Time of Exams: April 28 (Saturday) and April 29 (Sunday) : Afternoon session: 2pm to 5pm
• Registration url: Announcements will be made when the registration form is open for registrations.
• The online registration form has to be filled and the certification exam fee needs to be paid. More details will be made available when the exam registration form is published.


• Final score = 25% assignment score + 75% exam score
• 25% assignment score is calculated as 25% of average of Best 8 out of 12 assignments
• Certificate will have your name, photograph and the score in the final exam with the breakup. It will have the logos of NPTEL and IIT Roorkee. It will be e-verifiable at nptel.ac.in/noc/