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Molecular Environmental Science
Dr. Yu Yang




My current research interests and strengths are focused on the organic matter-mineral-bacteria interfacial redox reactions, critical for global cycles of carbon/nitrogen and emergent contaminants. Major on-going projects include: 1) studying the stability of carbon in the redox reactions with long-term goal of accurate understanding and predicting the turnover of carbon in soil; 2) analyzing organic matter-mediated degradation of antimicrobial agents with long-term goal of figuring out an effective way to fight with antibiotic resistance problem; 3) investigating the microbial-mediated plant uptake of carbon nanotube with long-term goal of determining the reaction and plant uptake of nano-materials in agricultural ecosystem. Our studies can provide important information for mitigating the global climate change, curbing the development of antibiotic resistance and preventing human exposure to engineered nano-materials through food chain. .

Lab Research Image 1


diagram showing redox reactions

Funding Source:

US DOE, $650,000, PI, 8/2015-7/2018


  • Eric E. Roden, University of Wisconsin, Madison (Co-Principal Investigator)
  • Daniel Obrist, Desert Research Institute (Co-Principal Investigator)
  • Annie B. Kersting, Lawrence Livermore National Laboratory (Co-Principal Investigator)
  • Baohua Gu, Oak Ridge National Laboratory (Co-Principal Investigator)
  • Shaomei He, University of Wisconsin, Madison (Senior Personnel – Genomics)
  • Yisong Guo, Carnegie Mellon University (Senior Personnel – Spectroscopy)

Major Concept:

A major challenge for Earth system models in predicting the response of the terrestrial ecosystem to climate change is to accurately reflect the biogeochemical processes governing the stability of soil organic matter (SOM). Iron oxide has been suggested as an important mineral phase regulating the SOM stability, with an extensive body of literature exploring SOM-mediated microbial reduction of iron oxide. However, the fate of iron-bound SOM in the redox reactions and its response to warming processes, have not been systematically investigated. This has resulted in a significant knowledge gap for predicting the stability of organic carbon (OC) under global climate change. We therefore propose to identify the critical biogeochemical reactions governing the degradation of iron-bound OC and to link the persistence of OC to redox cycles of iron. The central hypothesis is that the degradation rate of soil organic carbon (SOC) during aerobic-anaerobic redox cycles is governed by the amount of iron-bound OC, and the ability of microbial communities to utilize OC as an energy source and electron shuttle for iron reduction that in turn stimulates reductive release of iron-bound labile dissolved OC.

Atomic Carbon-Degrading Microorganism-Mediated Uptake of Cabron Nanotubes by Tomato Plants

diagram showing degradation process

Funding Source:

USDA, $150,000, Sole-PI, 1/2015-1/2017


  • Baoshan Xing, University of Massachusetts Amherst
  • Hongfei Lin, University of Nevada, Reno

Major Concept:

To explore the microbial-mediated transformation of nanomaterial is important for assessing and managing its environmental fate and impacts. Herein, we would like to investigate the microbial metabolism and degradation of carbon nanotubes, with implication for the uptake by plants. Multiple aromatic carbon-degrading bacteria, e.g. Mycobacterium vanbaalenii PYR-1, will be applied as model microorganisms. These bacteria can potentially degrade or metabolize carbon nanotubes, given their capacity to functionalize and mineralize aromatic carbons. Overall, we hypothesize that: Aromatic carbon-mineralizing bacteria can metabolize and degrade carbon nanotubes. Microbial functionalization of carbon nanotubes will make them more hydrophilic and facilitate their uptake by the plant cells.

Aqueous pyrogenic carbon-stimulated microbial dehalogenation: Natural catalyst for emergent contaminant degradation

diagram showing dehalogenation process

Funding Source:

To be submitted to NSF

Major Concept:

Organohalide constitutes the largest single group of compounds on the list of EPA priority pollutants, and dehalogenation of organohalide is a critical detoxification process. Pyrogenic carbon, carbonaceous materials produced from incomplete combustion of fossil fuel and biomass, has been extensively studied for their sorption and sequestration of hydrophobic organic pollutants. However, little is known about the role of pyrogenic carbon, especially aqueous pyrogenic carbon, in the microbial dehalogenation. Our recent studies have shown that aqueous pyrogenic carbon can facilitate the microbial extracellular electron transport and substantially stimulate the dehalogenation of triclosan, with over 90% of the parent compound degraded within 48 hours.
Leveraging these preliminary results, we hypothesize that: Although solid particles of pyrogenic carbon sorb and sequestrate organic compounds, aqueous pyrogenic carbon can stimulate the microbial reductive dehalogenation for emergent organohalide compounds. The electron shuttling processes mediated by the quinone functional groups in pyrogenic carbon substantially contribute to the reductive dehalogenation reaction.
In this project, I will:
  1. investigate pyrogenic carbon-mediated microbial dehalogenation reaction for organohalides by pure culture
  2. elucidate the pyrogenic carbon-mediated dehalogenation reaction process and mechanism for electron transport
  3. study the impact of physicochemical properties of pyrogenic carbon on the dehalogenation reactions
  4. examine the degradation and mineralization of organohalides by natural microbial community in the presence of aqueous pyrogenic carbon
Integrated outreach and educational activities will target at increasing the public awareness of emergent contaminants and motivating gifted and underrepresented k-12 students to develop environmental science and engineering-related careers.

Lab Members

Dr. Yang's lab provides research opportunties for graduate students and post-doctoral scholars in environmental engineering as well as an introduction to lab research for undergraduate students and high-school interns. Please contact Dr. Yang to learn more about current research opportunities.

Principal Investigator

Yu Yang
Dr. Yu Yang, Assistant Professor of Environmental Engineeering
Ph.D., Peking University
B.S., Peking University
Email: yuy@unr.edu


Yaqi You
Yaqi You, Postdoctoral Associate
Ph.D. Johns Hopkins University
B.S. Nanjing University of Technology, China
Email: you.yaqi@gmail.com
Sarrah Dunham-Cheatham
Sarrah M. Dunham-Cheatham, Postdoctoral Associate, sarrahdc.com
Ph.D. University of Notre Dame
B.S. Purdue University
Email: dr.smdcheatham@gmail.com


Dinesh Akhikari
Dinesh Adhikari, Ph.D. Student
HREL 211 Email: dadhikari05@gmail.com
Kamol Das
Kamol Das, Ph.D. Student
MSc. in Ecological Sciences and Engineering (2015), Purdue University, West Lafayette, Indiana
MSc. in Environmental Studies (2010), Lamar University, Beaumont, Texas
Bachelor of Science in Environmental Sciences (2005), Jahangirnagar University, Bangladesh
Dawit Wordofa
Dawit Wordofa, Ph.D. Student
M.S., Chemical and Environmental Engineering, University of California, Riverside, 2014
B.S., Chemical Engineering, Bahir Dar University, 2008
Qian Zhao
Qian Zhao, Ph.D. Student
M.S. Oklahoma State University
HREL 211
Email: qian.zhao@nevada.unr.edu


Aman Patel


Shengnan Xu, Postdoctoral Scholar, 9/2014 - 10/2015
Hua Zhang, Visiting Scholar, 11/2014 - 9/2015
Lin Wang, Visiting Student, 11/2014 - 1/2016
Riley Murname, Undergraduate Student, 10/2015 - 5/2016
Tayla Travella, High School Intern, 8/2014
Breanna Kjoll, High School Intern, 8/2014
Lindsey Zeising, High School Intern, 8/2014
Kanaha Shoji, Undergraduate, 1/2015 - 9/2015


For a complete list of publications and experience, please download my CV.

20162015201420132012201120102009 2008200720062005

# student/postdoc advised; *, corresponding author


  • You YQ#, Das K#, Guo HY, Chang CW, Navas-Moreno M, Chan JW, Verburg P, Poulson SR, Wang XL, Xing BS, Yang Y. Microbial Transformation of Multi-walled Carbon Nanotubes by Mycobacterium vanbaalenii PYR-1. 2017. Environmental Science & Technology. In press.
  • Zhao Q#, Adhikari D#, Huang RX, Patel A#, Wang XL, Tang YZ, Obrist D, Roden E, Yang Y 2016. Coupled dynamics of iron and iron-bound organic carbon in forest soils during anaerobic reduction. Chemical Geology. In press.
  • Zhang HY, Liu Y, Shen X, Zhang M, Yang Y, Tao S, Wang XL. 2016. Influence of multiwalled carbon nanotubes and sodium dodecyl benzene sulfonate on bioaccumulation and translocation of pyrene and 1-methylpyrene in maize (Zea mays) seedlings. Environmental Pollution. In press
  • Adhikari D#, Poulson S, Sumaila S, Dynes JJ, McBeth JM, Yang Y. 2016. Reductive dissolution kinetics of iron and carbon from hematite-humic substances complexes. Chemical Geology. 430:13-20.
  • Xu SN#, Adhikari D#, Huang RX, Zhang H#, Tang YZ, Roden E, Yang Y. Biochar-mediated iron reduction. 2016. Environmental Science & Technology. In press.
  • Zhao Q#, Poulson S, Obrist D, Sumaila S, Dynes JJ, McBeth JM, Yang Y. 2016. Iron oxide stabilized aliphatic organic carbon in forest soils: Quantification and characterization. Biogeosciences Discussion
  • Gu HP, Lou J, Wang HZ, Yang Y, Wu LS, Wu JJ, Xu JM. 2016. Biodegradation, biosorption of phenanthrene and its trans-membrane transport by Massilia sp. WF1 and Phanerochaete chrysosporium. Frontiers in Microbiology. In Press.


  • Zhang M, Shu L, Guo X, Shen X, Zhang H, Liu Y, Cai F, Chen W, Gao Q, Shen G, Wang B, Yang Y, Tao S, Wang XL. 2015. Impact of Humic Acid Coating on Sorption of Naphthalene by Biochars. Carbon. 94: 946-954.
  • Adhikari D#, Yang Y. 2015. Selective stabilization of aliphatic organic matter by iron oxide. Scientific Reports. 5. Article Number: 11214.
  • Yang Y, Li YQ, Walse S, Mitch WA. 2015. Degradation of Methyl Bromide by Reaction with Thiosulfate and Electrolysis. Environmental Science & Technology. 49: 4515-4521.
  • Wang L, Liang N, Li H, Yang Y, Zhang D, Liao S, Pan B. 2015. Quantifying the dynamic fluorescence quenching of phenanthrene and ofloxacin by dissolved humic acids. Environmental Pollution, 196: 379-385.


  • Yang Y*, Wang S, Albrecht-Schmitt TE. 2014. Bioavailability of crystalline-phase uranium to the microbial reduction by Shewanella oneidensis MR-1. Chemical Geology, 387: 59-65.


  • Yang Y, Wang S, Polinski MJ, Liu Y, Barnett MO, Albrecht-Schmitt TE. 2013. Dissolution of uranyl and plutonyl borates: Influences of crystalline structures and aqueous ligands. Chemical Geology 357: 67-74.
  • Yang Y*, Saiers JE, Barnett MO. 2013. Impact of interactions between colloidal humic acid and metal oxides on the sorption-desorption kinetics of uranium. Environmental Science & Technology 47:2661-2669.


  • Yang Y, Shu L, Wang XL, Xing BS, Tao S. 2012. Mechanisms regulating bioavailability of phenanthrene sorbed on humic substances extracted from a peat soil. Environmental Toxicology & Chemistry 31: 1431-1437.
  • Yang Y*, Saiers JE, Xu N, Minasian SG, Kozimor SA, Tyliszczak T, Shuh DK, Barnett MO. 2012. Impact of natural organic matter on uranium transport through saturated geologic materials: From molecular to column scale. Environmental Science & Technology 46: 5931-5938.


  • Yang Y, Shu L, Wang XL, Xing BS, Tao S. 2011. Impact of de-ashing humic acid and humin on organic matter structural properties and sorption mechanisms of phenanthrene. Environmental Science & Technology 45: 3996-4002.
  • Yang Y, Zhang N, Xue M, Lu ST, Tao S. 2011. Effects of soil organic matter on the development of the microbial polycyclic aromatic hydrocarbons (PAHs) degradation potentials. Environmental Pollution 159: 591-595.
  • Zhang N, Yang Y, Tao S, Liu Y, Shi KL. 2011. Sequestration of organochlorine pesticides in soils of distinct organic carbon content. Environmental Pollution 159: 700-705.
  • Cui XY, Hunter W, Yang Y, Chen YX, Gan J. 2011. Biodegradation of pyrene in sand, silt and clay fractions of sediment. Biodegradation 22: 297-307.
  • Wang XL, Guo XY, Yang Y, Tao S, Xing BS. 2011. Sorption mechanisms of phenanthrene, lindane, and atrazine with various humic acid fractions from a single soil sample. Environmental Science & Technology 45: 2124-2130.
  • Wang B, Xue M, Lv Y, Yang Y, Zhong JJ, Su YH, Wang R, Shen GF, Wang XL, Tao S. 2011. Cell absorption induced desorption of hydrophobic organic contaminants from digested soil residue. Chemosphere 83: 1461-1466.


  • Yang Y, Shu L, Wang XL, Xing BS, Tao S. 2010. Effects of composition and domain arrangement of biopolymer components of soil organic matter on the bioavailability of phenanthrene. Environmental Science & Technology 44: 3339-3344.
  • Yang Y, Zhang N, Xue M, Tao S. 2010. Impact of soil organic matter on the fractionation of polycyclic aromatic hydrocarbons (PAHs) in soils. Environmental Pollution 158: 2170-2174.
  • Yang Y, Tao S, Zhang N, Zhang DY, Li XQ. 2010. The effect of soil organic matter on fate of polycyclic aromatic hydrocarbons in soil: a microcosm study. Environmental Pollution 158: 1768-1774.
  • Cui XY, Hunter W, Yang Y, Chen YX, Gan J. 2010. Bioavailability of sorbed phenanthrene and permethrin in sediments to chironomus tentans. Aquatic Toxicology 98: 83-90.
  • Wang R, Tao S, Wang B, Yang Y, Lang C, Zhang YX, Hu J, Ma JM, Hung H. 2010. Sources and pathways of polycyclic aromatic hydrocarbons transported to Alert, the Canadian high Arctic. Environmental Science & Technology 44: 1017-1022.
  • Tao S, Zhang DY, Lv Y, Li L, Ding JN, Yang Y, Yang YF, Wang XL, Liu WX, Xing BS. 2010. Mobility of polycyclic aromatic hydrocarbons in the gastrointestinal tract assessed using an in vitro digestion model with sorption rectification. Environmental Science & Technology 44: 5608-5612.


  • Yang Y, Hunter W, Tao S, Gan J. 2009. Effect of activated carbon on microbial bioavailability of phenanthrene in soils. Environmental Toxicology & Chemistry 28: 2283-2288.
  • Yang Y, Hunter W, Tao S, Gan J. 2009. Microbial availability of different forms of phenanthrene in soils. Environmental Science & Technology 43: 1852-1857.
  • Yang Y, Hunter W, Tao S, Gan J. 2009. Effects of black carbon on pyrethroid availability in sediment. Journal of Agricultural & Food Chemistry 57: 232-238.
  • Hunter W, Yang Y, Reichenberg F, Mayer P, Gan J. 2009. Measuring pyrethroids in sediment pore water suing matrix-solid phase microextraction. Environmental Toxicology & Chemistry 28: 36-43.
  • Zhang N, Yang Y, Liu Y, Tao S. 2009. Determination of octanol-air partition coefficients and supercooled liquid vapor pressures of organochlorine pesticides. Journal of Environmental Science & Health, Part B 44: 649-656.
  • Tao S, Lu Y, Zhang DY, Yang YF, Yang Y, Lu XX, Sai DJ. 2009. Assessment of oral bioaccessibility of organochlorine pesticides in soil using an in vitro gastrointestinal model. Environmental Science & Technology 43: 4254-4259.


  • Yang Y, Hunter W, Tao S, Gan J. 2008. Relationships between desorption intervals and availability of sediment-associated hydrophobic contaminants. Environmental Science & Technology 42: 8446-8451.
  • Xing GH, Yang Y, Chan JKY, Tao S, Wong MH. 2008. Bioaccessibility of polychlorinated biphenyls in different foods using an in vitro digestion method. Environmental Pollution 156: 1218-1226.
  • Tao S, Liu WX, Li Y, Yang Y, Zuo Q, Li BG, Cao J. 2008. Organochlorine pesticides contaminated surface soil as reemission sources in the Haihe Plain, China. Environmental Science & Technology 42: 8395-8440.


  • Zuo Q, Duan YH, Yang Y, Wang XJ, Tao S. 2007. Source apportionment of polycyclic aromatic hydrocarbons in surface soil in Tianjin, China. Environmental Pollution 147: 303-310.
  • Liu YN, Tao S, Yang YF, Dou H, Yang Y, Coveney RM. 2007. Inhalation exposure of traffic police officers to polycyclic aromatic hydrocarbons during the winter in Beijing, China. Science of the Total Environment 383: 95-105.


  • Yang Y, Shi X, Wong PK, Dawson R, Xu FL, Liu WX, Tao S. 2006. An approach to assess ecological risk for polycyclic aromatic hydrocarbons (PAHs) in surface water from Tianjin. Journal of Environmental Science & Health, Part A 41: 1463-1482.
  • Tao S, Yang Y, Cao HY, Liu WX, Coveney RM, Xu FL, Cao J, Li BG, Wang XJ, Hu JY, Fang JY. 2006. Modeling the dynamic changes in concentrations of gamma-hexachlorocyclohexane (gamma-HCH) in Tianjin region from 1953 to 2020. Environmental Pollution 139: 183-193.
  • Tao S, Li XR, Yang Y, Coveney RM, Lu XX, Chen HT, Shen WR. 2006. Dispersion modeling of polycyclic aromatic hydrocarbons from combustion of biomass and fossil fuels and production of coke in Tianjin, China. Environmental Science & Technology 40: 4586-4591.


  • Yang Y, Tao S, Wong PK, Hu JY, Guo M, Cao HY, Coveney RM, Zuo Q, Li BG, Liu W, Cao J, Xu FL. 2005. Human exposure and health risk of alpha-, beta-, gamma- and delta-hexachlorocyclohexane (HCHs) in Tianjin, China. Chemosphere 60: 753-761.
  • Zhang XL, Tao S, Liu WX, Yang Y, Zuo Q, Liu SZ. 2005. Source diagnostics of polycyclic aromatic hydrocarbons based on species ratios: A multimedia approach. Environmental Science & Technology 39: 9109-9114.


Earth as viewed from space
CEE 418/618 Principles of Water-Quality Modeling
Understanding chemistry for water issues. Development of equations to model reactions, speciation and movement of pollutants in natural waters. Applications of equations to contaminants in streams, lakes, rivers and groundwater.
Download the syllabus for CEE 418/618
Smoke and fire
CEE 756R Environmental Chemical Kinetics
This course provides an overview of environmental chemical kinetics and transformations as they apply to the practice of environmental engineering and science. After completing this course, you will be familiar with the quantitative treatment of organic and metallic pollutants in environmental systems, chemical kinetics, applied redox chemistry in natural and engineered systems, surface reactions, and photochemical transformations.
Download the syllabus for CEE 756



  • In 2016, we got 7 manuscripts published or accepted.
  • Our collaborative proposal (led by Dr. Krishna Pagilla) for U.S. Department of Agriculture was awarded.
  • Frank gave seminars at University of Delaware, Washington University in St. Louis, Oak Ridge University, and Clemson University.
  • Frank has been editing a special volume of Chemical Geology, to be published in 2017 (with Dr. Jeremy Fein at University of Notre Dame).
  • Frank was appointed as an Associate Editor of Journal of Environmental Quality.
  • Dinesh won a travel award from American Chemical Society Geochemistry Division, and gave a 40-min talk in ACS 2016 Spring Meeting.
  • Qian won a travel award from Department of Energy Environmental System Science PI Meeting. Riley and Kamol won poster awards from Nevada Water Environment Association Annual Meeting.


  • Dinesh’s paper was published in Scientific Reports (Nature Publisher). A good kick off for our lab.
  • We received a prestigious grant from U.S. Department of Agriculture, for studying the microbial transformation and plant uptake of carbon nanotube.
  • We received a prestigious grant from U.S. Department of Energy for studying the biogeochemical stability of carbon in soil.
  • Frank gave seminars at U. California, Davis, USGS, ETH (Switzerland), U. Tubingen (Germany), U. Zurich (Switzerland).
  • Frank was appointed as an editorial board member of Chemosphere.