Peer-Reviewed Journal Articles

(*indicates corresponding author, underlined are students or postdoctoral fellows advised by Tao Yan)

Under Review or In Preparation

• Yangyang Zou, Mandy-Tanita Brinkmann, Min Ki Jeon, and Tao Yan* (2025). Monitoring Hazardous Chemicals in Lahaina Beach Systems Immediately After the 2023 Maui Wildfire. In Preparation.
• Bo Li and Tao Yan* (2025). Determining the Role of Primer Dimers in COVID-19 qPCR False Positive Detection. In Preparation.
• Min Ki Jeon and Tao Yan* (2025). Developing A Quantitative Approach for Tracking Influenza Viral Diversity in Wastewater based on Spiked Internal Standards. In Preparation.
• Min Ki Jeon, and Tao Yan* (2025). Fluorescence Damping as Primary Interference Mechanism
  of Humic Acids on qPCR Quantification of SARS-CoV-2 in Wastewater Surveillance. Environmental Science & Technology. Under review.
• Doris Yoong Wen Di, Bo Li, and Tao Yan * (2025). Development of a nested RT-PCR-PCR Assay followed by next generation sequencing to Detect SARS-CoV-2 Spike Protein Mutations in Wastewater, In Preparation.

Published

• Doris Yoong Wen Di, Prakit Saingam, Bo Li, Min Ki Jeon, and Tao Yan * (2024). Enriched Abundance of Diverse Vibrio parahaemolyticus in the Dead-End of the Ala Wai Canal: A Tropical Artificial Urban Estuary. ACS ES&T Water, 4(9), 4091-4098 (https://doi.org/10.1021/acsestwater.4c00368).
• Mandy-Tanita Brinkmann, Catherine Kexin Rong, Yuefeng Xie, and Tao Yan * (2024) Formation Potential of Disinfection Byproducts during Chlorination of Petroleum Hydrocarbon-Contaminated Drinking Water, Chemosphere. 357,142057, (DOI: 10.1016/j.chemosphere.2024.142057).
  This article was the first to report the potential of forming disinfection byproducts when jet fuel is mixed with free chlorine. This was widely reported by the local news media (e.g. KITV, HPR, etc)
• Bo Li, Xingnan Li, Prakit Saingam, and Tao Yan* (2023), Understanding Microbiological Quality of Drinking Water at the Point of Consumption with Citizen Science. ACS ES&T Water, 3(8), 2691–2699 (DOI: 10.1021/acsestwater.3c00184).
• Doris Yoong Wen Di, Bo Li, Min Ki Jeon, and Tao Yan* (2023), Comparing Solid-Based Concentration Methods for Rapid and Efficient Recovery of SARS-CoV-2 for Wastewater Surveillance, Journal of Virological Methods, 320, 114790 (DOI: 10.1016/j.jviromet.2023.114790).
• Min Ki Jeon, Bo Li, Doris Yoong Wen Di, and Tao Yan * (2023). Prewhitening and normalization help detect a strong cross-correlation between daily wastewater SARS-CoV-2 RNA abundance and COVID-19 cases in a community. Environmental Science: Water Research and Technology, 9, 1403-1412 (DOI: 10.1039/D2EW00951J).
• Doris Yoong Wen Di, Guang Xiang Cao, Chuanqing Zhong, and Tao Yan * (2023). Diversity of blaPOM in Carbapenem-resistant Opportunistic Pathogenic Pseudomonas otitidis in Municipal Wastewater. Journal of Water and Health, 21(5) ,560 (DOI: 10.2166/wh.2023.255).
• Bo Li, Min Ki Jeon, Xu Li, and Tao Yan*, (2023) Differential impacts of salinity on antibiotic resistance genes during cattle manure stockpiling are linked to mobility potentials revealed by metagenomic sequencing. Journal of Hazardous Materials. 445, 130590 (DOI: 10.1016/j.jhazmat.2022.130590).
• Sunny C. Jiang, Heather N. Bischel, Ramesh Goel, Diego Rosso, Samendra Sherchan, Katrine L. Whiteson, Tao Yan, Helena M. Solo-Gabriele * (2022) Integrating Virus Monitoring Strategies for Safe Non-potable Water Reuse, Water, 14, 1187 (https://doi.org/10.3390/w14081187).
• Bo Li, Xu Li, Bing Wang, and Tao Yan*, (2022) A Metagenomic Approach for Characterizing Antibiotic Resistance Genes in Specific Bacterial Populations: Demonstration with Escherichia coli in Cattle Manure. Applied and Environmental Microbiology, 2022 88(7) e0255421. doi: 10.1128/aem.02554-21.
• Anndee Huff, Christopher Gordon, Heather Hartmann, Stephen E. Bartell, Emmanuel Ansah, Tao Yan, Bo Li, Nfamara K Dampha, Paul L. Edmiston, Paige J. Novak, Heiko L. Schoenfuss*. (2022) Contaminants of Emerging Concern in the Lower Volta River, Ghana, West Africa: The Agriculture, Aquaculture, and Urban Development Nexus. Environmental Toxicology and Chemistry, 41(2), 369-381 (DOI: 10.1002/etc.5279).
• Prakit Saingam, Doris Y. W. Di, and Tao Yan*, (2021) Diversity and Health Risk Potentials of Enterococcus Population in Tropical Coastal Water Impacted by Hurricane Lane. Journal of Water and Health, 19(6), 990 (DOI: 10.2166/wh.2021.209).
• Lavane Kim*, Tao Yan, Russel Yost, and Guy Porter (2021). Sustainable and Low-Cost Soil Filter Column for Removing Pathogens from Swine Wastewater: The Role of Endogenous Soil Protozoa. Water 13, 2472. (DOI: 10.3390/w13182472
• Bo Li, Xu Li, and Tao Yan* (2021). A Quantitative Metagenomic Sequencing Approach for High Throughput Gene Quantification and Demonstration with Environmental Antibiotic Resistance Genes. Applied and Environmental Microbiology, 87(16), e0087121. (DOI: 10.1128/AEM.00871-21).
• Bo Li, Doris Yoong Wen Di, Prakit Saingam, Min Ki Jeon, and Tao Yan* (2021) Fine-Scale Temporal Dynamics of SARS-CoV-2 RNA Abundance in Wastewater during A COVID-19 Lockdown. Water Research. 197, e117093.
• Bo Li, and Tao Yan* (2021). Next Generation Sequencing Reveals Limitation of qPCR Methods in Quantifying Emerging Antibiotic Resistance Genes (ARGs) in the Environment. Applied Microbiology and Biotechnology, 105(7), 2925-2936 (DOI: 10.1007/s00253-021-11202-4)
• Prakit Saingam, Bo Li, Shihwu Sung, and Tao Yan* (2021). Immediate Impact of Hurricane Lane on Microbiological Coastal Water Quality in Hilo Bay, Hawaii. Environmental Science & Technology. 55(5) 2960-2967 (https://dx.doi.org/10.1021/acs.est.0c07082).
• Lavane Kim*, Tao Yan, and Van Toan Pham (2020). Inactivation of Escherichia coli Enhanced by Anaerobic Microbial Iron Reduction. Environmental Science and Pollution Research, 28(45): 63614–63622. (DOI: 10.1007/s11356-020-11209-w)
• Doan, Viet Sang; Saingam, Prakit; Yan, Tao; Shin, Sangwoo * (2020). A Trace Amount of Surfactants Enables Diffusiophoretic Swimming of Bacteria, ACS Nano, 14(10), 14219–14227 (DOI: 10.1021/acsnano.0c07502).
• Prakit Saingam, Bo Li, and Tao Yan* (2020). Fecal indicator bacteria, direct pathogen detection, and microbial community analysis provide different microbiological water quality assessment of a tropical urban marine estuary. Water Research, 185, e116280.
• Bo Li, Zeng Chen, Fan Zhang, Yongqing Liu, and Tao Yan* (2020). Metagenomic Characterization Reveals Limited Abundance, Diversity, and Mobility Potential of Antibiotic Resistant Genes in Pristine Tibetan Plateau Soil. FEMS Microbiology Ecology, 96(10) fiaa172, (DOI: 10.1093/femsec/fiaa172).
• Sabrina Diemert, and Tao Yan* (2020). Municipal wastewater surveillance reveals high community prevalence of rarely reported Salmonella Derby strain.  Applied and Environmental Microbiology, 86(17) e00814-20 (DOI: 10.1128/AEM.00814-20)
• Linwei Wu, Daning Liang [Qian Zhang and Tao Yan as a member of the Global Water Microbiome Consortium)], and Jizhong Zhou* (2019). Global Diversity and Biogeography of Bacterial Communities in Wastewater Treatment Plants. Nature Microbiology. 4,1183-1195 (DOI: 10.1038/s41564-019-0426-5).
• Sabrina Diemert, and Tao Yan* (2019). Clinically Unreported Salmonellosis Outbreak Detected via Comparative Genomic Analysis of Municipal Wastewater Salmonella Isolates. Applied and Environmental Microbiology. 85 (10) e00139-19. (DOI: 10.1128/AEM.00139-19).
• Bo Li, Prakit Saingam, Satoshi Ishii, and Tao Yan * (2019). Multiplex PCR coupled with Direct Amplicon Sequencing for Simultaneous Detection of Numerous Waterborne Pathogens. Applied Microbiology and Biotechnology. 103 (2), 953-961. (DOI: 10.1007/s00253-018-9498-z).
• Prakit Saingam, Bo Li, and Tao Yan* (2018). Use of Amplicon Sequencing to Improve Sensitivity of PCR-Based Detection of Microbial Pathogens in Environmental Samples. Journal of Microbiological Methods, 149, 73-79. (DOI: 10.1016/j.mimet.2018.05.005).
• Tao Yan*, Pamela O’Brien, Jessica M. Shelton, Andrew C. Whelen, and Eulyn Pagaling (2018). Municipal Wastewater as a Microbial Surveillance Platform for Enteric Diseases: A Case Study for Salmonella and Salmonellosis. Environmental Science & Technology. 52 (8), 4869-4877. (DOI: 10.1021/acs.est.8b00163).
  This article was selected as a research highlight for its May 2018 issue by Nature Sustainability (https://www.nature.com/articles/s41893-018-0074-4).
• Liang Chen, Hang Lang, Fei Liu*, Song Jin, and Tao Yan. (2017) Presence of Antibiotics in Shallow Groundwater in the Northern and Southwestern Regions of China. Groundwater. 56 (3), 451-457. (DOI: 10.1111/gwat.12596).
• Jeonghwan Jang, Hor-Gil Hur, Michael J. Sadowsky, Muruleedhara N. Byappanahalli, Tao Yan, and Satoshi Ishii* (2017). Environmental Escherichia coli: ecology and public health implications—a review. Journal of Applied Microbiology. 123 (3). 570-581. (DOI: 10.1111/jam.13468).
• 35. Chuanqing Zhong, Matthew Nelson, Guangxiang Cao, Michael J. Sadowsky, and Tao Yan* (2017). Complete Genome Sequence of the Triclosan and Multidrug Resistant Pseudomonas aeruginosa strain B10W Isolated from Municipal Wastewater. Genome Announcements, 5 (3) e01489-1416. (DOI: 10.1128/genomeA.01489-16).
• Hanna R Temme, Kipp Sande, Tao Yan, Paige J Novak* (2017). Rapid Enrichment of Dehalococcoides-like Bacteria by Partial Hydrophobic Separation. Applied and Environmental Microbiology, 83 (6) e02946-16. (DOI:10.1128/AEM.02946-16).
• Eulyn Pagaling, Joao Gatica, Kun Yang, Eddie Cytryn, and Tao Yan* (2016). Phylogenetic Diversity of Ceftriaxone Resistance and the Presence of Extended Spectrum Beta-lactamase Genes in the Culturable Soil Resistome. Journal of Global Antimicrobial Resistance. 6, 128-135. (DOI: 10.1016/j.jgar.2016.05.002)
• Xia He and Tao Yan* (2016). Impact of Microbial Activities and Hydraulic Retention Time on the Production and Profile of Long Chain Fatty Acids in Grease Interceptors: A Laboratory Study. Environmental Science: Water Research and Technology. 2, 474-482. (DOI: 10.1039/C6EW00013D).
• Michael Cooney*, Ken Lewis, Keven Harris, Qian Zhang, and Tao Yan* (2016). Start Up Performance of Biochar Packed Bed Anaerobic Digesters. Journal of Water Process Engineering. 9, e7-e13. (DOI: 10.1016/j.jwpe.2014.12.004).
• Joao Gatica#, Kun Yang#, Eulyn Pagaling, Edouard Jurkevitch, Tao Yan, and Eddie Cytryn* (2015). Resistance of undisturbed soil microbiomes to ceftriaxone indicates extended spectrum beta-lactamase activity. Frontiers of Microbiology. 6:1233. (DOI: 10.3389/fmicb.2015.01233)
• Qian Zhang, Xia He and Tao Yan* (2015). Differential Decay of Wastewater Bacteria and Change of Microbial Communities in Beach Sand and Seawater Microcosms. Environmental Science & Technology. 49 (14), 8531–8540. (DOI: 10.1021/acs.est.5b01879)
  This article was reported widely by various public media outlets, including CBS news (http://www.cbsnews.com/news/worst-place-for-bacteria-beach-sand-water/), ABC news (http://abcnews.go.com/Health/contaminated-sand-make-beachgoers-sick-study/story?id=32494886), Daily Mail (http://www.dailymail.co.uk/sciencetech/article-3163494/Beach-goers-beware-sand-sitting-covered-POO-Faecal-matter-common-shore-sea-study-reveals.html), and Science Daily (http://www.sciencedaily.com/releases/2015/07/150715122522.htm).
• Xia He, Qian Zhang, Michael J. Cooney and Tao Yan* (2015). Biodegradation of Fat, Oil and Grease (FOG) Deposits Under Various Redox Conditions Relevant to Sewer Environment. Applied Microbiology and Biotechnology. 99 (14), 6059-6068. (DOI: 10.1007/s00253-015-6457-9)
• Xinru Zhang, Qian Zhang, Tao Yan, Zeyi Jiang, Xinxin Zhang, Yi Y. Zuo* (2015). Quantitatively Predicting Bacterial Adhesion Using Surface Free Energy Determined with a Spectrophotometric Method. Environmental Science & Technology. 49 (10), 6164-6171. (DOI: 10.1021/es5050425).
• Qian Zhang, Xia He, and Tao Yan* (2015). Impact of Indigenous Microbiota of Subtidal Sand on Fecal Indicator Bacteria Decay in Beach Systems: A Microcosm Study. Environmental Science: Water Research & Technology. 1, 306-315.
• Xinru Zhang, Qian Zhang, Tao Yan, Zeyi Jiang, Xinxin Zhang, and Yi Y. Zuo* (2014). Surface Free Energy Activated High-Throughput Cell Sorting. Analytical Chemistry. 86 (18), 9350-9355.
• Eulyn Pagaling, Kun Yang, and Tao Yan* (2014). Pyrosequencing reveals correlations between extremely acidophilic bacterial communities with hydrogen sulphide concentrations, pH and inert polymer coatings at concrete sewer crown surfaces. Journal of Applied Microbiology. 117 (1), 50-64.
• Mark J. Krzmarzick, Hanna R. Miller, Tao Yan, and Paige J. Novak* (2014). Novel Firmicutes group implicated in the dechlorination of two chlorinated xanthones, analogues of natural organochlorines.  Applied and Environmental Microbiology. 80 (3), 1210-1218.
• Ryan J. Lopez, Scott Higgins, Eulyn Pagaling, Tao Yan, and Michael J. Cooney*. (2014). High Rate Anaerobic Digestion of Wastewater Separated From Grease Trap Waste. Renewable Energy. 62, 234-242.
• Lavane Kim, Eulyn Pagaling, Yi Y. Zuo, and Tao Yan* (2014). Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters. Applied and Environmental Microbiology. 80 (1), 177-183.
• Kun Yang, Eulyn Pagaling, and Tao Yan*. (2014). Estimating the Prevalence of Potential Enteropathogenic Escherichia coli and Intimin Gene Diversity in a Human Community by Monitoring Sanitary Sewage. Applied and Environmental Microbiology. 80 (1) 119-127.
• Scott R. Higgins, Ryan J. Lopeza, Eulyn Pagaling, Tao Yan, Michael J. Cooney*. (2013). Towards a hybrid anaerobic digester-microbial fuel cell integrated energy recovery system: An overview of the development of an electrogenic biofilm. Enzyme and Microbial Technology. 52, 344-351.
• Henglin Cui, Kun Yang, Eulyn Pagaling, and Tao Yan* (2013). Spatial and Temporal Variations of Enterococci Abundance and Its Relationship with Microbial Community in Hawai’i Beach Sand and Water. Applied and Environmental Microbiology. 79(12), 3601-3609.
• Qian Zhang, and Tao Yan* (2012). Correlation of Intracellular Trehalose Concentration with Desiccation Resistance of Soil Escherichia coli Populations. Applied and Environmental Microbiology. 78 (20), 7407-7413.
• Muruleedhara N. Byappanahalli, Tao Yan, Matthew J. Hamilton, Satoshi Ishii, Roger S. Fujioka, Richard L. Whitman, and Michael J. Sadowsky* (2012). The Population Structure of Escherichia coli Isolated from Subtropical and Temperate Soils. Science of the Total Environment. 417-418, 273-279
• Jessica Shelton, Lavane Kim, Jiasong Fang, Chittaranjan Ray, and Tao Yan* (2011). Assessing the Severity of Rainfall Derived Infiltration and Inflow and Sewer Deterioration Based on the Flux Stability of Sewage Markers. Environmental Science & Technology. 45 (20), 8683–8690
• Dustin K. Goto and Tao Yan* (2011). Effects of Land Uses on Fecal Indicator Bacteria in the Water and Soil of a Tropical Watershed. Microbes and Environments. 26 (3), 254-260
• Wendi Zheng and Tao Yan* (2011). Impact of different land uses on polycyclic aromatic hydrocarbon contamination in coastal stream sediments. Chemosphere. 84, 376–382
• Dustin K. Goto and Tao Yan* (2011). Genotypic Diversity of Escherichia coli in the Water and Soil of Tropical Watersheds in Hawaii. Applied and Environmental Microbiology. 77 (12) 3988-3997
• Fan Feng, Dustin Goto, and Tao Yan*. (2010) Effects of autochthonous microbial community on the die-off of fecal indicators in tropical beach sand. FEMS Microbiology Ecology. 74 (1), 214-225
• Satoshi Ishii, Tao Yan, Hung Vu, Dennis L. Hansen, Randall E. Hicks, and Michael J. Sadowsky*. (2010) Factors Controlling the Long-term Survival and Growth of Naturalized Escherichia coli Populations in Temperate Field Soil. Microbes and Environments. 25 (1), 8-14
• Ji-Young Ryu, Jiyoung Seo, Tatsuya Unno, Joong-Hoon Ahn, Tao Yan, Michael J. Sadowsky, and Hor-Gil Hur* (2010). Isoeugenol monooxygenase and its putative regulatory gene are located in the eugenol metabolic gene cluster in Pseudomonas nitroreducens Jin1. Archives of Microbiology. 192 (3), 201-209.
• Tao Yan and M. J. Sadowsky*. (2007) Determining sources of fecal bacteria in waterways. Environmental Monitoring and Assessment. 129 (1~3), 97-106
• Tao Yan, M. J. Hamilton, and M. J. Sadowsky*. (2007) High-throughput and quantitative procedure for determining sources of Escherichia coli in waterways using host-specific DNA marker genes. Applied and Environmental Microbiology. 73 (3), 890-896.
• Tao Yan, T. M. LaPara, and P. J. Novak*. (2006) The Impact of Sediment Characteristics on PCB-Dechlorinating Cultures: Implications for Bioaugmentation. Bioremediation Journal. 10 (4), 143-151.
• Ishii, S., Tao Yan, D. A. Shively, M. N. Byappanahalli, R. L. Whitman, and M. J. Sadowsky*. (2006) Cladophora (Chlorophyta) spp. harbor pathogenic bacteria in nearshore water of Lake Michigan. Applied and Environmental Microbiology. 72 (7), 4545-4553.
• Hamilton, M. J., Tao Yan, and M. J. Sadowsky*. (2006) Development of Goose- and Duck-Specific DNA Markers to Determine Sources of Escherichia coli in Waterways. Applied and Environmental Microbiology. 72 (6), 4012-4019.
• Tao Yan., T. M. LaPara, and P. J. Novak*. (2006) The effect of varying levels of sodium bicarbonate on polychlorinated biphenyl dechlorination in Hudson River sediment cultures.  Environmental Microbiology. 8 (7), 1288-1298.
• Tao Yan, T. M. LaPara, and P. J. Novak*.  (2006) The reductive dechlorination of 2,3,4,5-tetrachlorobiphenyl in three different sediment cultures: evidence for the involvement of phylogenetically similar Dehalococcoides-like bacterial populations. FEMS Microbiology Ecology. 55 (2), 248-261.
• Rysavy, J. P., Tao Yan, and P. J. Novak*. (2005) Enhancement of anaerobic polychlorinated biphenyl dechlorinators from sediment with iron as hydrogen source. Water Research, 39 (4), 569-578.
  ory gene are located in the eugenol metabolic gene cluster in Pseudomonas nitroreducens Jin1. Archives of Microbiology. 192 (3), 201-209.

Books and Book Chapters

(*indicates corresponding author, underlined are students or postdoctoral fellows advised by Tao Yan)

• Bo Li and Tao Yan*, (2023) Metagenomic Next Generation Sequencing for Studying Antibiotic Resistance Genes in the Environment, Advances in Applied Microbiology, Published online first (https://doi.org/10.1016/bs.aambs.2023.05.001)