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Samir Kumar
KHANAL

PhD in Civil Engineering
Professor
PG Program Coordinator (Civil Engineering)
Room 3566 (Lift 25-26)
2358 8183
0000 0000
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Research Area
Environmental
Research Interests
Anaerobic digestion (Nanaerobic digestion)
Aquaponics
Micro-/macro-algae cultivation
Machine learning and AI applications in bioprocessing
Nanobubble technology
Waste-to-resources
Profile

Ph.D., The Hong Kong University of Science and Technology

Honors and Award

Highly cited Researcher 2024 (Clarivate); Recipient of Board of Regents’ Medal for Excellence in Research (2018); Recipient of Dean's Award for Excellence in Research (2016), University of Hawaii at Manoa

Ph.D. Positions in Environmental Biotechnology

Dr. Samir Kumar Khanal’s research group (https://ce.hkust.edu.hk/people/samir-kumar-khanal) in the Department of Civil and Environmental Engineering at the Hong Kong University of Science and Technology (HKUST) invites applications for multiple fully funded PhD positions starting immediately. HKUST provides highly competitive stipend and other benefits. Selected students will have opportunity to conduct research in state-of-the-art lab. For further information, please browse here or send an informal enquiry to Dr. Samir K. Khanal (cekhanal@ust.hk).

Selected Publications

1.  Campbell, I.R., Shitanaka, T., Egan, H., Kaur, M., Khanal, S.K.* and Roumeli, E.* (2026). The Use of Whole Hawaiian Macroalgae to Engineer Bioplastics and Adhesives for Wood-Particleboards. RSC Sustainability. Accepted 3rd April 2026.

2. Shitanaka, T., Wang, Y., Do, S., Yuson, J., Khanal, S.K., Zienkiewicz, K.* and Du, Z.Y.*(2026). Synthetic Biology and Metabolic Engineering of Microalgae for Sustainable Lipid and Terpenoid Production: An Updated Perspective. Plant Biotechnology Journal. 24 (3): 1359-1376.

3. Marcelino, K.R., Lama, S.L., Wongkiew, S., Surendra, K.C., Hu, Z., Lee, J.W. and Khanal, S.K.* (2026). Chapter 13 - Nutrient removal and recovery in hydroponic, aquaponic, and bioponic systems. In: Nutrients Removal and Recovery in Wastewater Treatment Systems, Elsevier. 269-301.

4. Karki, R., Surendra, K.C., Skerlos, S., Raskin, L.* and Khanal, S.K.* (2026). Anaerobic co-digestion as a strategy for treating coffee Pulp: Insights into process performance. Bioresource Technology. 4442: 133650.

5. Jia, M., Qian, J., Farid, M.U.*, Kharraz, J.A., Hasan, S.W., Khanal, S.K. and An, A.K.* (2026). Nanobubble-enabled wetting control in membrane distillation via interfacial modulation. Chemical Engineering Journal. 527: 172026.

6. Kaur, M., Shitanaka, T., Surendra, K.C. and Khanal, S.K.* (2025). Macroalgae-derived bioactive compounds for functional food and pharmaceutical applications—a critical review. Critical Reviews in Food Science and Nutrition. 65 (21): 4172-4194.

7. Khan, M., Surendra, K.C., Baniya, S., Rhymer, J.H. and Khanal, S.K.* (2025). Biochar-augmented anaerobic digestion system: insights from an interpretable stacking ensemble deep learning. Environmental Science & Technology. 59 (29): 15236-15250.

8. Li, B., Hu, Z.*, Zhao, Q., Heng, J., Wang, S., Khanal, S.K., Guo, Z. and Zhang, J. (2025). Enhanced fluoride removal in a novel magnesium-carbon micro-electrolysis constructed wetland through accelerated electron transport and anodic sacrifice. Journal of Hazardous Materials. 492: 138062.

9. Chuenchart, W., Sawaya, C., Surendra, K.C., Smith, A.L. and Khanal, S.K.* (2025). In-situ intermittent micro-aeration in food waste and sewage sludge anaerobic co-digestion: Performance, stability, and microbial dynamics. Bioresource Technology. 427: 132398.

10. Guo, Y.*, Feng, W., Zhang, Q., Shao, W., Tao, X., Zhao, W., Kim, S.H., Surendra, K.C. and Khanal, S.K. (2025). Efficient Remediation of Cr (VI) in Soil by Polypyrrole Modified Corn-Stover Biochar. Water, Air, & Soil Pollution. 236(7): 403.

11. Wongkiew, S.*, Amnuaychaichana, S., Srithadindang, K., Paisuwan, W., Ajavakom, A., Polprasert, C., Noophan, P.L., Supakata, N., Koottatep, T., Surendra, K.C. and Khanal, S.K. (2025). Enhancing digestate-based bioponics through ceramsite addition with and without biochar: Effects on water quality, nutrient recovery, heavy metal removal, and microbial community composition. ACS ES&T Engineering. 5(10): 2565-2579.

12. Lama, S.L., Marcelino, K.R., Wongkiew, S., Surendra, K.C., Hu, Z., Lee, J.W., and Khanal, S.K*. (2025). Recent advances in aquaponic systems: A critical review. Reviews in Aquaculture. 17 (3): 1-28.

13. Zhou, S., Qiao, L., Jia, Y., Khanal, S.K., Sun, L. and Lu, H.* (2025). Micro-nano bubble ozonation for effective treatment of ibuprofen-laden wastewater and enhanced anaerobic digestion performance. Water Research. 273: 123006.

14. Yang, B., Yan, Y., Jia, Y., Chen, B., Khanal, S.K., Shu, W.S. and Lu, H.* (2025). Optimizing formation of microalgal-bacterial granular sludge for aquaculture wastewater treatment. Chemical Engineering Journal. 504: 158884.

15. Jiang, J., Xiang, X., Zhou, Q., Zhou, L., Bi, X., Khanal, S.K., Wang, Z., Chen, G., and Guo, G. (2024). Optimization of a novel engineered ecosystem integrating carbon, nitrogen, phosphorus, and sulfur biotransformation for saline wastewater treatment using an interpretable machine learning approach. Environmental Science & Technology. 58(29):12989-12999.

16. Jia, Y., Ou, Y., Khanal, S.K*., Sun, L., Shu, W.-S., and Lu, H*. (2024). Biochar-based strategies for antibiotics removal: Mechanisms, factors, and application. ACS ES&T Engineering. 4(6), 1256-1274. (*Co-corresponding authors)

17. Chuenchart, W., Surendra, K.C., and Khanal, S.K*. (2024). Understanding anaerobic co-digestion of organic wastes through meta-analysis. ACS ES&T Engineering. 4 (5): 1177-1192.

18. Shitanaka, T., Fujioka, H., Khan, M., Kaur, M., Du, Z.Y., and Khanal, S.K*. (2024). Recent advances in microalgal production, harvesting, prediction, optimization, and control strategies. Bioresource Technology, 391 Part A: 129924

19. Marcelino, K. R., Wongkiew, S., Shitanaka, T., Surendra, K. C., Song, B., and Khanal, S.K*. (2023). Micronanobubble Aeration Enhances Plant Yield and Nitrification in Aquaponic Systems. ACS ES&T Engineering. 3(11): 2081-2096.

20. Wu, Z., Nguyen, D., Shrestha, S., Raskin, L., Khanal, S. K., and Lee, P. H. (2023). Evaluation of nanaerobic digestion as a mechanism to explain surplus methane production in animal rumina and engineered digesters. Environmental Science & Technology. 57 (33): 12302–12314.

21. Marcelino, K. R., Li, L., Wongkiew, S., Surendra, K.C., Shitanaka, T., Nhan, H.T, Lu, H., and Khanal, S.K*. (2023). Nanobubble Technology Applications in Environmental and Agricultural Systems: Opportunities and Challenges. Critical Reviews in Environmental Science and Technology. 53 (14): 1378-1403.

22. Khan, M., Chuenchart, W., Surendra, K.C., and Khanal, S.K*. (2023). Applications of artificial intelligence in anaerobic co-digestion: Recent advances and prospects. Bioresource Technology. 370: 128501.

23. Zhou, S., Marcelino, K. R., Wongkiew, S., Sun, L., Huang, J., Khanal, S. K., and Lu, H. (2022). Untapped potential: Applying microbubble and nanobubble technology in water and wastewater treatment and ecological restoration. ACS ES&T Engineering. 2 (9): 1558–1573.

24. Oberoi, A.S., Surendra, K.C., Wu, D., Lu, H., Wong, J.W.C., and Khanal, S.K*. (2022). Anaerobic membrane bioreactors for pharmaceutical-laden wastewater treatment: A critical review. Bioresource Technology. 361: 127667.

25. Karki, R., Chuenchart, W., Surendra, K.C., Sung, S., Raskin, L., and Khanal, S.K*. (2022). Anaerobic co-digestion of various organic wastes: Kinetic modeling and synergistic impact evaluation. Bioresource Technology. 343:126063.

26. Cruz, I.A., Chuenchart, W., Long, F., Surendra, K.C., Andrade, R. S. Bilal, M., Liu, H., Figueiredo, R. T., Khanal, S.K*., Ferreira, L.F.R. (2022). Application of machine learning in anaerobic digestion: Perspectives and challenges. Bioresource Technology. 345: 126433.

27. Karki, R., Chuenchart, W., Surendra K.C., Shrestha, S., Raskin, L., Sung, S., Hashimoto, A., and Khanal, S.K*. 2021. Anaerobic co-digestion: Current status and perspectives. Bioresource Technology. 330: 125001.

28. Chuenchart, W., Karki, R., Shitanaka, T., Marcelino, K.R., Lu, H., and Khanal, S.K*. 2021. Nanobubble technology in anaerobic digestion: A review. Bioresource Technology. 329: 124916.

29. Wu, Z, Nguyen, D., Lam, Y.-C, Zhuang, H., Shrestha, S., Raskin, L., Khanal, S.K*. and Lee, P.-H*. 2021. Superior performance of ORP-controlled intermittent microaerobic digestion with of lignocellulosic biomass via synergistic association between cytochrome bd-encoded facultative Proteiniphilum sp. and ROS-scavenging diverse methanogens. Water Research. 190: 116721. (*co-corresponding author)

30. Oliveira, F.R., Surendra, K.C., Jaisi, D.P., Lu, H., and Khanal, S.K*. 2020. Alleviating sulfide toxicity using biochar during anaerobic treatment of sulfate-laden wastewater with simultaneous recovery of sulfur-rich biochar as soil macro-nutrient. Bioresource Technology. 301:122711.

31. Jia, Y*., Yin, L*., Khanal, S.K*., Zhang, H., Oberoi, A., and Lu, H. 2020. Biotransformation of Ibuprofen in biological sludge systems: Investigation of performance and mechanisms. Water Research. 170:115303 (* equal contribution)

32. Nguyen, D., Wu, Z., Shrestha, S., Lee, P.-H., Raskin, L., and Khanal, S.K. 2019. High organic loading rate digestion via bypassing syntrophic acetogenesis though intermittent micro-aeration. Water Research. 166:115080.

33. Zhang, H*., Khanal, S.K*., Jia, Y., Song, S., and Lu, H. 2019. Fundamental insights into ciprofloxacin adsorption by sulfate-reducing bacteria sludge: Mechanisms and thermodynamics. Chemical Engineering Journal. 378:122103. (* equal contribution)

34. Oberoi, A.S., Jia, Y., Zhang, H., Khanal, S.K., Lu, H. 2019. Insights into fate and removal of antibiotics in engineered biological treatment systems: A critical review. Environmental Science & Technology. 53: 7234−7264.

35. Wongkiew, S., Park, M-R., Chandran, K., and Khanal, S.K*. 2018. Aquaponic systems for sustainable resource recovery: Linking nitrogen transformations to microbial communities. Environmental Science & Technology. 52 (21): 12728-12739.

36. Nguyen, D., and Khanal, S.K*. 2018.  A little breath of fresh air into an anaerobic system: How micro-aeration facilitates anaerobic digestion process. Biotechnology Advances. 36 (7): 1971-1983.

37. Zhang, H., Jia, Y., Khanal, S.K., Lu, H., Fang, H., and Zhao, Q. 2018. Understanding the Role of Extracellular Polymeric Substances on Ciprofloxacin Adsorption in Aerobic Sludge, Anaerobic Sludge, and Sulfate-Reducing Bacteria Sludge Systems. Environmental Science & Technology.52: 6476-6486.

38. Sawatdeenarunat, C., Nam, H., Adhikari, S., Sung, S., and Khanal, S.K*. 2018. Innovative decentralized biorefinery for lignocellulosic biomass: Integrating anaerobic digestion with thermochemical conversion. Bioresource Technology. 250: 140-147.

39. Oliveira, F.R., Patel, A.K., Jaisi, D., Liu, H., and Khanal, S.K*. 2017. Environmental applications of biochar: Current status and perspectives. Bioresource Technology. 246: 110-122.

40. Shrestha, S., Fonoll, X., Khanal, S.K*. and Raskin, L*. 2017. Biological strategies for enhanced hydrolysis of lignocellulosic biomass during anaerobic digestion: Current status and future perspectives. Bioresource Technology. 245, Part A: 1245-1257. (*equal contribution).

41. Wongkiew, S., Hu, Z., Chandran, K., Lee, J.W., and Khanal, S.K*. 2017. Nitrogen transformations in aquaponic systems: A review. Aquacultural Engineering. 76: 9-19.

42. Surendra, K.C., Olivier, R., Tomberlin, J.K., Jha, R., and Khanal, S.K*. 2016. Bioconversion of organic wastes into biodiesel and animal feed via insect farming. Renewable Energy. 98: 197-202.

43. Sawatdeenarunat, C. Nguyen, D., Surendra, K.C., Shrestha, S., Rajendran, K., Oechsner, H., Xie, L., and Khanal, S.K*. 2016. Anaerobic biorefinery: current status, challenges, and opportunities. Bioresource Technology. 215: 304-313.

44. Nguyen, D., Gadhamshetty, V., and Khanal, S.K*. 2015. Automatic process control in anaerobic digestion technology: a critical review. Bioresource Technology.193: 513-522.

45. Sawatdeenarunat, C., Surendra, K.C., Takara, D., Oechsner, H., and Khanal, S.K. 2015. Anaerobic digestion of lignocellulosic biomass: Challenges and opportunities. Bioresource Technology. 178: 178-186.

46. Surendra, K.C., Takara, D., Hashimoto, A.G., and Khanal, S.K*. 2014. Biogas as a sustainable energy source for the developing countries: Opportunities and challenges. Renewable and Sustainable Energy Reviews. 31: 846-859.

47. Nitayavardhana, S., Kerati, I., Pavasant, P., and Khanal, S.K*. 2013. Production of protein-rich fungal biomass in an airlift bioreactor using vinasse as substrate. Bioresource Technology.133: 301-306.

48. Hu, Z., Lee, J. W., Chandran, K., Kim, S., and Khanal, S.K*. 2012. Nitrous oxide (N2O) emission from aquaculture system: A review. Environmental Science & Technology. 46 (12): 6470-6480.

49. Nitayavardhana, S., and Khanal, S.K. 2012. Biofuel residues ban or boon? Critical Reviews in Environmental Science and Technology. 42 (1): 1-43.

50. Surendra, K.C., Khanal, S.K*., Shrestha, P., and Lamsal, B. P. 2011. Current Status of Renewable Energy in Nepal: Opportunities and Challenges. Renewable and Sustainable Energy Reviews. 15 (1): 4107-4117.

51. Sindhuja, S., Khanal, S.K., Pometto, A.L., Jin, B., and Van Leeuwen, J. 2010. Use of microfungi for production of high value fungal by-products: A review. Critical Reviews in Environmental Science and Technology. 40 (5): 1-49.

52. Munasinghe, P.C., and Khanal, S.K*. 2010. Syngas fermentation to biofuels: Challenges and opportunities. Bioresource Technology. 101 (13): 5013-5022.

53. Khanal, S.K., Grewell D, Sung, S., and Van Leeuwen, J. 2007. Ultrasound applications in wastewater sludge pretreatment: A review. Critical Reviews in Environmental Science and Technology. 37 (4): 277-313.

54. Khanal, S.K*., Xie, B., Ong, S.K., Thompson, M.L., Sung, S., and Van Leeuwen, J. 2006. Fate, transport and biodegradation of natural estrogens in the environment and engineered systems - A review. Environmental Science and Technology. 40 (21): 6537-6546.

55. Khanal, S.K., and Huang, J.-C. 2003. ORP based oxygenation for sulfide control in anaerobic treatment of high sulfate wastewater. Water Research. 37 (9): 2053-2062.