Graduation Level 

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1. Bioremediation of Oil-Contaminated Soil Using Indigenous Bacteria
   Collect contaminated soil, isolate hydrocarbon-degrading bacteria, and set up lab-scale microcosms. Monitor TPH reduction by GC-FID and microbial counts over 30–60 days. Optimize nutrient amendment (N:P) and aeration to enhance biodegradation. Demonstrations in Indian coastal spill-prone sites make it locally relevant. Write results as a protocol with sampling schedule and analytical steps.

2. Composting of Agricultural Residues (Rice Straw) Using Microbial Consortia
   Prepare windrow or pit composts mixing rice straw, cow dung, and microbial starters (thermophilic consortia). Measure temperature, pH, C:N and maturity indices weekly. Assess reduction of lignin/cellulose and final nutrient profile (NPK). Practical for India to reduce stubble burning and improve soil health. Protocol includes inoculum prep, turning schedule, and safety steps.

3. Wastewater Treatment by Constructed Wetlands (Small-Scale Model)
   Build a gravel–sand wetland bed planted with Phragmites/Political reeds and vetiver; feed synthetic domestic wastewater. Monitor BOD, COD, TSS, nitrate, and coliform removal over hydraulic retention times. Compare vertical-flow vs horizontal-flow setups for efficiency. Useful for peri-urban Indian communities with decentralized sanitation needs. Provide maintenance protocol and effluent testing timetable.

4. Isolation and Identification of Nitrate-Reducing Bacteria from Paddy Fields
   Collect rhizosphere and flooded soil samples, perform enrichment for denitrifiers using nitrate-containing media. Identify isolates by biochemical tests and 16S rRNA sequencing (basic PCR + Sanger service). Assess denitrification potential in microcosms measuring N2O/NO3 decline. Relevant to minimize nitrate leaching in Indian rice systems. Include sampling, culture, and gas-measurement steps in abstract-style protocol.

5. Biodegradation of Plastic Bags Using Local Fungi
   Screen roadside and landfill soils for ligninolytic and plastic-degrading fungi, isolate strains on minimal media with polyethylene strips. Set up degradation assays and quantify weight loss, surface changes (SEM), and FTIR shifts. Test composting co-treatment to accelerate breakdown. India-relevant due to plastic waste challenges and policy push for biodegradable alternatives. Protocol covers isolation, assay conditions, and analytical checks.

6. Activated Sludge Process — Lab-Scale Aeration and Clarification
   Construct bench-scale aeration tanks with synthetic wastewater and seeded activated sludge from a local STP. Operate SRT and HRT regimes, monitor MLSS, SVI, BOD/COD removal, and nitrification. Study bulking potential and optimize aeration. Practical curricular exercise used in Indian engineering colleges. Provide SOP for sampling and settlability tests.

7. Phytoremediation of Heavy Metals Using Vetiver and Indian Mustards
   Pot experiments with soil spiked at known Cd/Pb concentrations; plant seedlings and harvest at intervals. Analyze root/shoot metal accumulation by AAS and calculate TF and BCF. Evaluate soil health post-harvest and discuss safe disposal or metal recovery. High relevance for mining-affected areas in India. Include planting density, sampling timeline, and digestion protocol.

8. Anaerobic Digestion of Cow Dung for Biogas at Lab Scale
   Set up batch anaerobic digesters (glass bottles) with cow dung and measured TS/VS; monitor biogas volume and methane content by gas chromatography. Study co-digestion with crop residues to improve C:N ratio. Analyze digestate as fertilizer and measure pathogen reduction. Widely applied in Indian households and rural energy programs. Provide inoculum acclimation, temperature control, and gas sampling protocol.

9. Microbial Fuel Cell (MFC) Demonstration Using Domestic Wastewater
   Construct single-chamber MFC with carbon electrodes fed with kitchen wastewater; measure voltage/current and calculate power density. Isolate electrogenic bacteria from anode biofilm and characterize electrochemical performance. Discuss scale-up challenges and potential for rural electrification. Emerging practical experiment for Indian undergraduate labs. Include electrode prep, circuit setup, and data logging steps.

10. Biological Nitrogen Fixation Assays with Azotobacter from Indian Soils
    Sample rhizosphere soils; enrich and isolate free-living nitrogen-fixers using N-free media. Confirm N-fixation by acetylene reduction assay and nifH PCR. Test inoculation impact on seedling growth in pots under controlled conditions. Important for low-input agriculture in India. Protocol contains sampling, assay conditions, and growth evaluation metrics.

11. Rapid Composting Using Earthworms (Vermicomposting) from Kitchen Waste
    Set up small vermicompost bins using Eisenia fetida and kitchen scraps; maintain moisture, temperature and feed schedule. Monitor decomposition rate, pH, electrical conductivity and nutrient content of vermicompost. Compare vermicompost to traditional compost in pot trials for plant growth. Strong applicability for urban organic waste management in India. Provide earthworm stocking density and maturation timeline.

12. Biological Control of Mosquito Larvae Using Bacillus thuringiensis israelensis (Bti)
    Mass-culture Bti in lab flasks, formulate as wettable powder, and perform larval bioassays to determine LC50 against Aedes/Culex larvae. Assess persistence in small artificial ponds and effect on non-target organisms. Relevant for vector control programs in India. Protocol includes cultivation, formulation, and bioassay steps.

13. Enzymatic Treatment of Textile Effluent Using Laccase-Producing Fungi
    Isolate white-rot fungi, produce laccase in submerged culture, and treat simulated dye effluent; monitor color and COD reduction. Optimize mediator concentration, pH, and contact time. Test immobilized enzyme reuse in packed-bed reactors. Indian textile clusters can use this approach to reduce dye pollution. Include enzyme assay, reactor setup, and analytical schedule.

14. Bioaugmentation of Sewage Sludge Composting with Cellulolytic Consortia
    Characterize sewage sludge, inoculate with cellulase-producing bacteria, and monitor temperature profile and pathogen reduction. Assess maturity parameters and nutrient recovery for safe land application. Applicable to municipal solid waste management in India. Provide compost recipe, inoculum prep, and monitoring protocol.

15. Detection of Enteric Pathogens in Surface Waters by qPCR (Introductory)
    Collect river/pond water, concentrate microbes via filtration, extract DNA, and run qPCR for indicator pathogens (E. coli, Salmonella). Correlate microbial load with physicochemical parameters. Include awareness of sample preservation and inhibition controls. Useful for public-health monitoring in Indian water bodies. Provide sampling, concentration, and qPCR control steps.

16. Bioremediation of Chromium-Contaminated Leather Effluent Using Bacterial Consortia
    Enrich for chromate-reducing bacteria from tannery discharge, perform reduction assays under aerobic/anaerobic conditions. Measure Cr(VI) reduction spectrophotometrically and toxicity decrease. Evaluate scaled-up fixed-bed bioreactor options. Highly relevant to Indian leather clusters (e.g., Kanpur, Tamil Nadu). Include enrichment, reduction, and reactor operation SOP.

17. Oil-Degrading Algal-Bacterial Consortia for Marine Pollutant Removal
    Isolate oil-tolerant microalgae and hydrocarbonoclastic bacteria; set up co-culture microcosms with crude oil and monitor degradation products. Analyze biomass valorization (lipid extraction) post-treatment. Relates to coastal cleanup and bioresource recovery in India. Protocol lists isolation, co-culture conditions, and analytical techniques.

18. Evaluation of Biosorbents (Peanut Shell, Rice Husk) for Heavy Metal Removal
    Prepare activated biosorbents via chemical/thermal treatment, run batch adsorption studies for Pb, Cd, and Cr. Determine isotherms (Langmuir/Freundlich) and kinetics. Assess regeneration and reuse cycles. Cost-effective solution for small-scale Indian industries. Include biosorbent prep, adsorption tests, and desorption steps.

19. Assessment of Microplastic Pollution in Urban Rivers (Sampling + Microbial Analysis)
    Collect sediment and water samples, separate microplastics via density separation, characterize by FTIR. Isolate plastic-degrading microbes from particles and test degradation in lab. Correlate microplastic levels with urban inputs and propose mitigation. Important for Indian metro river health studies. Provide sampling grid, separation, and microbial assay protocol.

20. Bioreactor-Based Treatment of Dairy Industry Effluent
    Set up lab-scale UASB or SBR treating high-BOD dairy wastewater and monitor COD removal, methane yield (if UASB), and sludge characteristics. Optimize HRT and organic loading rates. Evaluate post-treatment polishing (constructed wetland). Relevant to dairy hubs in India (e.g., Gujarat). Document reactor startup, monitoring, and performance metrics.

21. Phytodepuration of Greywater Using Floating Treatment Wetlands
    Design small floating mats planted with water hyacinth or vetiver, route greywater through mats and measure BOD, turbidity and nutrient reduction. Study root-associated microbial communities by culturing. Evaluate maintenance needs and plant harvesting for biomass use. Fits decentralized wastewater reuse in Indian urban housing. Include construction, hydraulic loading, and sampling steps.

22. Denitrification Bioreactors Using Agricultural Byproducts as Carbon Source
    Pack column reactors with woodchips or rice husk and pass nitrate-rich water to promote heterotrophic denitrification. Monitor nitrate removal, nitrite accumulation, and DOC consumption. Investigate operation temperature effects and longevity of carbon source. Relevant for agricultural runoff mitigation in India. Protocol spells out packing, flow rates, and monitoring.

23. Biodegradation of Pesticides (e.g., Chlorpyrifos) by Soil Bacteria
    Enrich for organophosphate-degrading bacteria from agricultural fields, identify degradation metabolites via GC-MS, and calculate half-life reduction in microcosms. Test bioaugmentation in field-simulated plots. Important to address pesticide persistence in Indian cropping systems. Provide enrichment, assay, and residue analysis procedure.

24. Molecular Detection and Diversity of PAH-Degrading Genes in Contaminated Sites
    Extract DNA from polluted soils, PCR-amplify ring-hydroxylating dioxygenase genes, clone/sequencing and analyze diversity. Correlate gene abundance with degradation activity in microcosms. Useful in urban/industrial Indian sites contaminated with polyaromatic hydrocarbons. Include sampling, molecular workflow, and data interpretation steps.

25. Algal Biofixation of CO₂ from Flue Gases in Bench-Scale Photobioreactors
    Operate tubular or flat-plate photobioreactors fed with simulated flue gas; measure algal biomass, lipid productivity, and CO₂ uptake. Optimize light intensity, pH, and dilution rates. Evaluate downstream lipid extraction for biodiesel. Potential for Indian power plants’ carbon mitigation pilots. Provide reactor settings, gas composition, and analysis schedule.

26. Biological Monitoring of Air Quality Using Lichen and Moss Biomonitoring
    Collect lichen/moss samples from urban gradients, measure heavy metal accumulation and particulate adsorption. Use simple protocols for sample prep and metal analysis by AAS. Discuss correlation with vehicular and industrial sources in Indian cities. Low-cost environmental monitoring method for campus projects. Include sampling, cleaning, and digestion SOP.

27. Co-Composting of Municipal Solid Waste with Sewage Sludge
    Design pilot compost piles mixing MSW (biodegradable fraction) with stabilized sludge; monitor temperature, pathogen indicators, and maturity. Evaluate contaminants like heavy metals and microplastics in final compost. Suggest safe land-application guidelines relevant for Indian municipalities. Provide feedstock ratios, turning regime, and quality tests.

28. Biological Treatment of Acid Mine Drainage Using Sulfate-Reducing Bacteria
    Set up anaerobic bioreactors inoculated with SRB and organic carbon source; treat simulated AMD and monitor sulfate reduction, metal precipitation, and pH neutralization. Characterize precipitates and sludge handling. Applicable to mining regions in India (e.g., Jharkhand). Protocol details inoculum prep, reactor operation, and metal analysis.

29. Bioremediation of E-Waste Leachate Using Microbial Consortia
    Collect e-waste leachate, enrich metal- and organic-degrading microbial consortia and run bench-scale reactors to reduce metal mobility and organics. Measure metal speciation, COD, and toxicity decline. Explore biosorption by fungal biomass as polishing step. Relevant given India’s e-waste challenges. Include leachate prep, enrichment, and monitoring protocol.

30. Assessment of Soil Microbial Biomass and Respiration in Polluted Sites
    Sample contaminated and reference soils, determine microbial biomass C/N by fumigation-extraction and basal respiration rates. Correlate microbial health with pollutant levels and remediation progress. Simple, informative lab protocol for Indian environmental monitoring. Provide sampling depth, storage, and assay timelines.

31. Biological Degradation of Dyes by Microbial Consortia under Anaerobic–Aerobic Conditions
    Isolate anaerobic and aerobic dye decolorizing microbes; run sequential anaerobic-aerobic reactors to detoxify textile dyes, measure toxicity reduction (e.g., seed germination). Optimize contact times and co-substrates. Highly relevant for Indian textile clusters. Include reactor setup, microbial inocula, and toxicity assays.

32. Bioavailability and Biodegradation Studies of Petroleum Hydrocarbons in Tropical Soils
    Conduct spiked-soil microcosms at ambient Indian temperatures, evaluate bioavailability using cyclodextrin extraction and biodegradation rates by GC-MS. Study effect of surfactants and nutrient amendments. Important for remediation planning in tropical conditions. Provide experimental timelines and analytical methods.

33. Pilot-Scale Vermifiltration for Hostel/Canteen Wastewater Treatment
    Build vermifiltration unit with layered media and earthworms; treat kitchen wastewater and measure BOD, TSS, and pathogen loads in effluent. Monitor worm health and filter clogging. Relevant for institutional waste management in Indian campuses. Provide construction details, flow rates, and maintenance SOP.

34. Biological Denitrification Using Bioelectrochemical Systems (BES)
    Construct small BES with cathodes promoting autotrophic denitrifiers and monitor nitrate removal with simultaneous electricity generation. Analyze microbiome on electrodes by 16S PCR. Investigate system stability under variable loads. Emerging tech with potential for Indian decentralized treatment. Include electrode prep, reactor operation, and molecular sampling.

35. Microbial Ecology of Landfill Bioreactors During Accelerated Decomposition
    Sample landfill bioreactor cells over time, profile microbial succession using culturing and basic molecular markers, and correlate with gas production and leachate quality. Evaluate operational parameters that optimize stabilization. Applicable to municipal solid waste modernization in India. Provide sampling schedule and analysis workflow.

36. Bioremediation of Pulp & Paper Effluent Using White-Rot Fungi
    Culture white-rot fungi, set up treatment reactors for lignin-rich effluent, monitor color, COD, and lignin breakdown by spectroscopy. Explore immobilized fungal beds for continuous operation. Relevant to Indian paper mills seeking eco-friendly treatments. Include inoculum prep, reactor design, and sampling schedule.

37. Evaluation of Indigenous Microalgae for Wastewater Nutrient Removal and Biomass Valorization
    Isolate mixotrophic microalgae from ponds, grow in wastewater for N and P removal, harvest biomass for biofertilizer or biogas feedstock. Measure nutrient uptake rates and biomass composition. Suitable for small-scale Indian aquaculture and farm wastewater reuse. Provide cultivation, harvesting, and utilization steps.

38. Biosensor Development for Rapid Detection of Water Contaminants (Colorimetric/Enzymatic)
    Assemble simple enzyme-based colorimetric strips (e.g., for phenols or nitrate) and validate against standard lab tests. Calibrate sensitivity for Indian groundwater ranges. Assess field robustness and shelf-life. Useful low-cost tool for community water monitoring. Include reagent prep, calibration, and field-use instructions.

39. Evaluation of Microbial Source Tracking (MST) Markers in Indian Rivers
    Collect water samples, apply MST PCR markers (human, bovine, poultry) to identify contamination sources. Correlate land use maps with marker prevalence and recommend management. Important for policy-actionable water quality programs in India. Protocol includes sampling design, DNA extraction and PCR controls.

40. Bioreactor Cultivation of Black Soldier Fly Larvae for Organic Waste Bioconversion
    Set up small-scale BSF rearing units for food waste; monitor larval growth, waste reduction rates and frass quality as biofertilizer. Measure microbial safety and heavy metal uptake. Aligns with circular economy models in Indian urban settings. Include rearing, substrate prep, and processing SOP.

41. Fungal Biosorption of Azo Dye Waste Using Dead Biomass
    Prepare dried fungal biomass, perform batch adsorption of representative azo dyes, analyze kinetics/isotherms and desorption cycles. Test cost-effectiveness with locally available fungal strains. Applicable as polishing step after primary treatment in textile effluents. Provide biomass prep, adsorption protocol, and regeneration steps.

42. Screening of Microbes for Sulfide Oxidation in Sewage and Aquaculture Systems
    Enrich sulfur-oxidizing bacteria, test sulfide removal in aerated microcosms, monitor pH and sulfate formation. Apply isolates in biofilters for shrimp farms and sewage plants. Important to control toxic H₂S in Indian aquaculture. Include enrichment, reactor setup and monitoring guidance.

43. Assessment of Phytoplankton Dynamics as Indicator of Eutrophication in Lakes
    Collect seasonal plankton samples, quantify chlorophyll a, and identify dominant algal groups microscopically. Correlate with nutrient levels and human impacts. Recommend mitigation like floating wetlands or nutrient control. Practical for Indian lake restoration projects. Provide sampling frequency, preservation, and analysis steps.

44. Bioremediation of Pharmaceutical Residues Using Activated Sludge and Bioaugmentation
    Spike lab reactors with common pharmaceuticals, test removal by activated sludge alone vs bioaugmented cultures (e.g., degraders of diclofenac), and measure transformation products. Explore sorption to sludge and implications for sludge disposal. Relevant as India expands pharmaceutical manufacturing. Provide spike dosing, analytical monitoring, and toxicity checks.

45. Characterization and Optimization of Indigenous Anaerobic Consortia for Paddy Straw Digestion
    Isolate consortia, enrich for cellulolytic and methanogenic activity, run co-digestion trials with paddy straw and dung, and monitor methane yield and stability. Aim to valorize straw and reduce burning in India. Provide enrichment, reactor operation, and gas analytics.

46. Biodegradation Kinetics of Synthetic Surfactants in Sewage Treatment Systems
    Set batch reactors with known concentrations of SLES or LAS, monitor biodegradation rates, intermediate metabolites, and influence of microbial community structure. Assess impact on downstream biological processes. Relevant given detergent loads in Indian urban sewage. Include dosing, sampling intervals, and analysis.

47. Microbial Induced Calcite Precipitation (MICP) for Soil Stabilization
    Inoculate ureolytic bacteria into sand columns, supply urea/Ca²⁺, and measure strength improvement and porosity change. Evaluate environmental safety and field applicability for Indian road/embankment repairs. Provide inoculum prep, injection cycles, and mechanical testing steps.

48. Bioremediation Monitoring Using Stable Isotope Probing (SIP) — Introductory
    Set up microcosms with 13C-labeled pollutants (e.g., toluene), extract labeled DNA after incubation, and identify active degraders via PCR/sequencing. Use basic SIP workflow to link function and identity. Powerful method to study in-situ degraders in Indian contaminated sites. Provide labeling, incubation, and molecular handling steps.

49. Study of Biofilms in Water Distribution Systems and Their Role in Pathogen Persistence
    Grow biofilms on coupon materials using pipe-water; characterize microbial composition (culture and microscopy), measure disinfectant penetration and regrowth potential. Recommend flushing and disinfection strategies for Indian municipal systems. Protocol includes coupon setup, sampling schedule, and assays.

50. Evaluation of Low-Cost Decentralized Sewage Treatment Units for Rural India
    Construct small-scale septic + constructed wetland demonstration units, monitor pollutant removal, maintenance needs, and social acceptance. Include cost-benefit and sludge handling strategies in protocol. Valuable for rural sanitation programs in India. Provide construction specs, monitoring schedule, and community engagement steps.

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Post-Graduation Level Topics

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1. Metagenomic-Guided Bioremediation Design for Hydrocarbon-Contaminated Sites
Perform shotgun metagenomics on contaminated soils to identify indigenous degradative pathways and keystone degraders. Use pathway annotation to design bioaugmentation or biostimulation strategies and model predicted degradation rates. Validate in microcosm and pilot plots with temporal metagenomic monitoring. Apply to Indian industrial hotspots for data-driven remediation. Protocol-style abstract includes sampling, sequencing, bioinformatics, and field validation steps.

2. Systems Biology of Microbial Consortia in Anaerobic Digesters
Integrate metagenomics, metatranscriptomics and metabolomics to map functional interactions driving methane yield. Use flux models to predict performance under substrate changes and design targeted feed strategies. Validate via reactor perturbation experiments at pilot scale. Relevant to optimize Indian biogas plants treating mixed agricultural waste. Provide omics workflows, modeling approach, and reactor trial plan.

3. CRISPR-Based Fault Diagnostics and Engineering of Environmental Microbes
Develop CRISPRi/a tools to modulate key catabolic genes in biodegrading bacteria, enabling controlled enhancement of pollutant degradation. Deploy gene-editing in containment for lab-scale performance tests and assess off-target/environmental safety. Use biosensors to monitor engineered strain activity. Cutting-edge methodology for precision bioaugmentation in Indian research labs. Include design, delivery, containment, and monitoring steps.g

4. Stable Isotope-Resolved Metabolomics to Trace Pollutant Fate
Use 13C/15N-labeled contaminants in soil/water microcosms, trace labeled metabolites by LC-MS/MS and link to microbial taxa through SIP-metaproteomics. Model carbon flux through biodegradation pathways and identify bottlenecks. Apply to complex contaminants (e.g., pharmaceuticals) common in Indian effluents. Protocol outlines labeling, sampling, instrumental analysis, and integrative data interpretation.

5. Engineering Synthetic Microbial Consortia for Textile Effluent Detoxification
Design modular consortia combining anaerobic azo-reducer and aerobic oxidizer strains, optimize spatial/temporal reactor arrangement (e.g., sequential reactors) and assess dye decolorization and detoxification in pilot flows. Use genomic tools to ensure stability and absence of toxin formation. Target application in Indian textile clusters with on-site pilot demonstrations. Include consortium design, reactor configuration, and monitoring metrics.

6. Genome-Scale Metabolic Modeling of Algal Strains for High-Value Metabolite Production
Reconstruct algal GEMs using sequencing and annotation, run FBA to predict metabolic engineering targets for omega-3 or carotenoid overproduction. Validate targets via CRISPR knockout/overexpression in lab photobioreactors. Address scale-up parameters for Indian photobioreactor conditions. Protocol includes genome sequencing, model building, in-vivo validation, and scale considerations.

7. Bioelectrochemical Systems for Simultaneous Waste Treatment and Resource Recovery
Develop cathode/anode designs that maximize electron transfer, integrate with nutrient recovery modules (e.g., struvite precipitation), and deploy pilot units treating municipal wastewater. Use community sequencing to identify electrogenic populations. Prove techno-economic viability for Indian decentralized systems. Include BES construction, analytical methods, and recovery workflows.

8. Biotransformation Pathways of Persistent Organic Pollutants (POPs) by Engineered Fungi
Characterize fungal enzymatic routes (P450, peroxidases) transforming POPs; overexpress key enzymes in robust strains for enhanced degradation. Perform bioreactor trials to assess kinetics and byproduct toxicity reduction. Target legacy POP-contaminated soils in Indian industrial regions. Protocol details gene discovery, enzyme engineering, and pilot remediation.

9. High-Resolution Time-Series Metagenomics of Landfill Bioreactor Stabilization
Sequence temporal changes during accelerated landfill bioreactor operation, reconstruct functional dynamics driving methane and leachate quality. Use machine learning to predict optimal operational interventions. Apply to municipal waste modernization projects in India. Provide sampling cadence, sequencing depth, and modeling framework.

10. Synthetic Biology Circuits for Programmable Pollutant Sensing and Remediation
Design genetic circuits in bacteria that detect pollutants and trigger biodegradation enzymes or signal reporters; include kill-switch and biocontainment. Validate circuit robustness under environmental stressors and mixed-community interactions. Applicable to targeted remediation hotspots with strict biosafety oversight in India. Include circuit design, containment testing, and field-tier validations.

11. Advanced Oxidation-Biological Hybrid Systems for Pharmaceutical Removal
Combine UV/H₂O₂ or photo-Fenton pretreatment to transform recalcitrant pharmaceuticals followed by biofiltration to mineralize intermediates. Model kinetics and toxicity reduction; pilot with hospital effluents in Indian cities. Optimize energy and chemical dosing for cost-effectiveness. Protocol includes AOP parameters, sequencing analysis of microbial consortia, and toxicity assays.

12. Integrative Omics to Improve Microalgae Strain Robustness in Flue Gas Environments
Use transcriptomics and proteomics to identify stress pathways activated by flue gas contaminants (SOx/NOx) and engineer tolerance traits. Validate engineered strains in bench photobioreactors with simulated flue gas. Aim to scale for Indian thermal plant CO₂ mitigation. Include omics workflow, engineering targets, and pilot gas exposure experiments.

13. Bioprospecting Extremophiles for Industrial Bioremediation in Hot/Arid Indian Sites
Isolate thermotolerant/halotolerant degraders from geothermal soils or saline deserts, characterize thermostable enzymes for pollutant breakdown, and test in high-temperature bioreactors. Target oil-contaminated hot climates in India. Protocol includes isolation, enzyme characterization, and high-temp reactor testing.

14. Microbial Production and Recovery of Critical Metals from E-Waste Leachates
Apply bioleaching using acidophilic microbes and biosorption with engineered biomass to extract Cu, Au, and rare earth elements. Model kinetics and scale-up to pilot hydrometallurgical integration. Direct relevance to India’s growing e-waste recycling needs. Include leaching conditions, metal recovery assays, and downstream processing steps.

15. Quantitative Microbial Risk Assessment (QMRA) for Reuse of Treated Wastewater in Agriculture
Develop QMRA models incorporating pathogen reduction data from treatment units, crop exposure scenarios, and dose–response curves. Perform sensitivity analyses and propose risk-based guidelines for safe reuse in India. Validate models with field pathogen monitoring. Provide model structure, input data requirements, and risk communication strategy.

16. Directed Evolution of Laccases for Improved Textile Dye Oxidation Under Alkaline Conditions
Perform error-prone PCR and high-throughput screening to evolve laccase variants functional at textile effluent pH. Characterize kinetics, mediator dependency, and stability; implement immobilized enzyme reactors for continuous dye treatment. Target on-site treatment in Indian mills. Protocol includes library construction, screening assay, and reactor tests.

17. Microbial Ecology and Engineering of Methanotroph-Based Bioreactors for Greenhouse Gas Mitigation
Enrich high-activity methanotrophic biofilms, characterize methane oxidation rates under variable temperatures, and design biofilters for fugitive emissions from landfills. Integrate isotope tracing to track carbon flow. Applicable to reduce methane emissions from Indian waste sites. Provide enrichment, biofilter engineering, and monitoring steps.

18. Omics-Guided Enhancement of Biosurfactant Production for Oil Spill Mitigation
Use transcriptomics/proteomics to identify regulatory bottlenecks in biosurfactant-producing strains; engineer regulators or pathways for higher yield and cost-effective production. Test crude oil dispersion/biodegradation in mesocosms. Target scale-up for Indian coastal emergency response teams. Include omics analysis, strain engineering, and mesocosm evaluation.

19. Nanobiotechnology for Filter Media: Antimicrobial and Catalytic Functionalization
Functionalize sand/activated carbon with biogenic nanoparticles (Ag, TiO₂) to impart antimicrobial/photocatalytic properties, evaluate pollutant removal and leaching risks. Test longevity and regeneration for field use in Indian water treatment. Include nanoparticle synthesis, immobilization, and column tests.

20. Eco-Toxicogenomics of Mixed Contaminant Exposure in Aquatic Organisms
Expose model fish/invertebrates to pollutant mixtures and perform transcriptomic analysis to identify stress pathways and biomarkers. Correlate molecular responses with population-level effects to inform remediation endpoints. Useful in Indian river pollution impact assessments. Protocol covers exposure design, omics sampling, and data integration.

21. Bioaugmentation With Genetically Tagged Strains and Environmental Fate Tracking
Introduce marked biodegrading strains into microcosms, track persistence and gene transfer via qPCR/NGS, and evaluate degradation gains vs ecological impacts. Apply rigorous containment and monitoring to inform field deployment in Indian sites. Provide tagging strategy, monitoring, and gene flow assessment steps.

22. Electro-Fenton Coupled Bioreactors for Recalcitrant Organic Removal
Integrate electrochemical Fenton generation upstream of biological reactors to mineralize toxic intermediates and improve biodegradability. Optimize electrode materials, current density, and operating costs. Pilot for pharmaceutical and dye effluents in India. Include electrochemical setup, downstream biological integration, and performance metrics.

23. Machine Learning for Predictive Control of Full-Scale Wastewater Treatment Plants
Train ML models on historical process, weather, and influent data to predict load spikes and optimize aeration, chemical dosing, and sludge handling. Validate prediction accuracy and energy savings in Indian municipal plants. Provide data requirements, modeling pipeline, and deployment plan.

24. Biomining and Biorecovery of Lithium from Geothermal Brines and Spent Batteries
Develop microbial/adsorbent processes for selective lithium recovery, assess economics and integration into battery recycling chains. Pilot with Indian battery waste streams and geothermal sites. Include leaching, adsorption/desorption cycles, and scale-up analysis.

25. Environmental RNA (eRNA) Monitoring for Rapid Biodiversity and Pollution Assessment
Extract eRNA from water/sediment, sequence to detect active organisms and stress-response transcripts, and link signals to pollutant exposures. Use to monitor restoration progress in Indian freshwater ecosystems. Provide sampling preservation, library prep, and bioinformatics steps.

26. Bioprocess Intensification for Waste-to-Product Platforms: Volatile Fatty Acid (VFA) Production
Optimize acidogenic fermentation of organic waste to produce VFAs as chemical precursors, model yields, and downstream fractionation. Assess integration with Indian circular economy initiatives. Protocol includes feedstock prep, reactor control, and product recovery methods.

27. Engineering Photosynthetic Microbial Consortia for CO₂-to-Feedstock Conversion
Design synthetic consortia combining cyanobacteria with heterotrophs that convert CO₂ into polyhydroxyalkanoates or organic acids; optimize light regimes and nutrient cycling. Test in controlled photobioreactors under Indian sunlight regimes. Provide consortium design, reactor ops, and product analysis.

28. Life-Cycle Assessment (LCA) of Emerging Bioremediation Technologies for Indian Context
Perform cradle-to-grave LCA comparing traditional vs biotech remediation (e.g., phyto vs engineered bioaugmentation) using Indian inventory data, identify hotspots and recommend sustainable choices. Use LCA to guide policy and funding decisions. Provide data collection, impact assessment, and interpretation steps.

29. Adaptive Evolution Strategies to Produce Robust Bioremediating Microbes
Apply continuous culture under pollutant stress to evolve strains with enhanced tolerance and degradation; sequence evolved genomes to identify adaptive mutations. Test improved strains in soil microcosms for degradation performance. Potential application for Indian recalcitrant-pollutant hotspots. Include evolution regime, sequencing, and validation steps.

30. Bioprocess Design for Commercial Production of Microbial Biosurfactants
Scale heterologous or native biosurfactant-producing strains in fed-batch/continuous reactors, optimize downstream recovery (foam fractionation), and perform techno-economic analysis targeted to Indian oil-spill response market. Include strain selection, reactor strategy, and product purification steps.

31. CRISPR-Based Biosensors for On-Site Detection of Environmental Contaminants
Develop CRISPR-Cas12/Cas13 collateral-cleavage assays with lateral-flow readouts for rapid detection of toxins or pathogens in water. Validate sensitivity/specificity against lab methods and deploy field kits in Indian testing campaigns. Include assay design, validation and field-deployment checklist.

32. Microbial-Assisted Phytomining for Recovery of Valuable Metals from Polluted Soils
Combine hyperaccumulator plants with rhizosphere microbes enhancing metal uptake, then harvest biomass for metal extraction. Model yields and economic viability for low-grade ore areas in India. Protocol includes plant-microbe selection, field trials, and metal recovery steps.

33. Integration of Remote Sensing and Microbial Data for Large-Scale Algal Bloom Management
Combine satellite-derived chlorophyll/temperature maps with in-situ microbial toxin assays and predictive models to forecast bloom events and optimize mitigation in Indian lakes/coastal zones. Provide data fusion pipeline and early-warning protocol.

34. Directed Microbial Consortia for Plastic Upcycling into Value-Added Products
Engineer consortia that depolymerize PET/PE and funnel monomers into biosynthesis of bioplastics or PHAs; validate at bench and pilot scales. Combine metabolic engineering with enzymatic pretreatment to increase yield. Target plastic circularity efforts in India. Include enzyme prep, consortium balance, and product recovery.

35. Pilot Deployment of Decentralized Living Machine Systems for Urban Wastewater
Design modular ecological treatment systems (plants, microalgae, worms, microbial beds) for apartment complexes; monitor performance, energy use, and social acceptance. Compare to conventional STPs in Indian urban sites. Provide design specs, operation manual, and monitoring schedule.

36. Environmental Genomics of Antimicrobial Resistance (AMR) Dissemination in Wastewater
Sequence resistome in influent, activated sludge and effluent using shotgun metagenomics; analyze ARG abundance, mobile genetic elements, and potential for horizontal gene transfer. Model removal efficiencies and policy implications for antibiotic stewardship in India. Include sampling plan, sequencing depth, and risk assessment.

37. Optimization of Microbial Electrolysis Cells (MEC) for Hydrogen Production from Wastewaters
Engineer electrodes and microbial communities to maximize hydrogen evolution, integrate with real wastewater streams, and assess energy balance. Pilot for decentralized renewable H₂ in Indian industrial parks. Provide MEC design, inoculation strategy, and gas collection/analysis steps.

38. Phytoremediation Assisted by Mycorrhizae for PAH-Contaminated Soils
Inoculate hyperaccumulator plants with arbuscular/mycorrhizal fungi to enhance uptake/ degradation of PAHs; monitor rhizosphere enzyme activities, plant health and pollutant decline. Pilot in contaminated urban plots in India. Include inoculation, planting, and analytical monitoring.

39. Computational Design of Enzymes for Xenobiotic Degradation
Use in-silico protein design and directed evolution simulations to create enzymes with improved affinity for novel pollutants; experimentally validate in microcosms. Apply to pesticides and industrial solvents present in Indian effluents. Provide computational workflow, mutant library strategy, and activity assays.

40. Biochar-Enhanced Bioremediation: Synergy of Adsorption and Microbial Activity
Amend contaminated soils with tailored biochar to adsorb pollutants and support degrading microbial communities; quantify pollutant immobilization vs biodegradation and plant uptake. Develop field protocols for Indian remediation projects. Include biochar production specs, amendment rates, and monitoring.

41.  Advanced Monitoring of Microbial Activity Using Environmental 'Omic' Time Series and AI
Collect high-frequency metagenomic and metabolomic samples from reactors/ sites, apply AI to detect early failure modes or performance drifts. Deploy predictive maintenance and control strategies in Indian bioprocess settings. Provide sampling cadence, AI modeling, and action protocols.

42. Biophysical and Microbial Strategies to Mitigate Soil Salinization
Combine halophytic plantings, salt-tolerant microbial inoculants, and subsurface drainage/bioremediation to reclaim saline agricultural lands. Monitor soil EC, crop yield, and microbial shifts. Applicable to coastal and irrigated Indian regions. Include integrated management steps and measurement plan.

43. Scale-Up and Commercialization Roadmap for Microbial PHA Production from Agro-Wastes
Optimize fermentation with mixed culture and waste feedstocks, design downstream centrifugal/solvent recovery, and model market entry for biodegradable plastics in India. Include life-cycle and regulatory considerations. Provide pilot scale parameters, recovery workflow, and economic analysis.

44. Evaluation of Viral Fate and Inactivation in Wastewater Treatment and Sludge Management
Combine controlled challenge studies, decay modeling, and sludge handling experiments to understand fate of human viruses; propose safety guidelines for Indian biosolids reuse. Use qPCR and infectivity assays where possible. Include experimental conditions, safety and regulatory discussion.

45. Phage-Mediated Control of Biofouling in Water Treatment Systems
Isolate lytic bacteriophages against biofilm-forming taxa, test efficacy in bench membrane modules, and assess phage persistence and resistance development. Evaluate synergy with cleaning regimes for Indian STPs. Provide phage isolation, titration, and pilot testing steps.

46. Environmental Risk Assessment and Containment Strategies for Field Trials of Engineered Microbes
Develop standardized risk-assessment protocols, gene flow monitoring plans, and biocontainment systems (e.g., auxotrophy, kill-switches) for environmental release pilots. Apply to degrade pollutants or recover resources in India with regulatory compliance. Provide assessment framework and monitoring templates.

47. Coupled Physical-Biological Models to Predict Contaminant Transport and Biodegradation in River Systems
Integrate hydrodynamic models with biodegradation kinetics and microbial dynamics to forecast pollutant fate and remediation outcomes in Indian rivers. Calibrate with field monitoring; use for management planning. Include model structure, parameterization, and validation steps.

48. Valorization of Sewage Sludge into Biochar and Its Impact on Soil Microbiome and Crop Performance
Pyrolyze stabilized sludge to produce biochar; assess contaminant stabilization, microbial responses, and agronomic outcomes. Evaluate regulatory and health implications for Indian agricultural reuse. Provide pyrolysis parameters, amendment protocols, and monitoring metrics.

49. Design and Evaluation of Microbial Biorefineries Converting Food Waste into Platform Chemicals
Integrate pre-treatment, mixed-culture fermentation for acids/alcohols, and catalytic upgrading to produce value-added chemicals. Assess mass balances, yields, and techno-economic viability in Indian urban waste contexts. Provide process flow, microbial consortia selection, and downstream steps.

50. Policy-Focused Research: Implementing Evidence-Based Monitoring and Biotech Solutions for India's River Rejuvenation Programs
Develop monitoring frameworks (chemical, microbiological, omic indicators) and pilot demonstrative biotechnologies (constructed wetlands, bioreactors) tailored to river stretches under national cleanup missions. Provide data-driven recommendations for scalable, cost-effective interventions and community engagement strategies. Include monitoring protocol, pilot deployment plan, and policy translation steps.