Dr Dayi Zhang



My main research area focuses on the environmental monitoring and assessment of contaminated sites, as well as their ecological impacts on microbial communities.

  • Application of whole cell bioreporter in environmental monitoring

Whole cell bioreporters are biological sensing devices with living microorganisms, which have been demonstrated as a useful and complementary tool to conventional chemical and physical analytical method for environmental monitoring. With engineered sensing element, usually regulatory proteins, the whole cell bioreporter can specifically recognize the environmental chemicals and promote reporter genes to express detectable signals in the presence of contaminants.

  • Bioavailability and ecotoxicity estimation for environmental assessment

Of all types of pollutants in the environment, their bioavailable proportion has significant ecotoxic impacts on ecological system and microbial communities. The frequent environmental accidents require a rapid detection of toxicity and bioavailability of contaminated water and sediments for effective risk assessments and support management decisions. Traditional chemistry and toxicity analyses for such complex organic mixtures could be laborious, time-consuming and costly, which face a challenge to achieving a fast and in situ assessment. Whole cell bioreporters can therefore be an effective tool in this respect as a complementary tool to traditional chemical analysis and ecotoxicological assessment of mixed compounds in environmental samples.

  • Environmental microbiology

Though microorganisms are ubiquitous and account for nearly half of the total biomass on earth, more than 99% of microorganisms were unculturable or at least as-yet-uncultured. Those uncultivable microorganisms play important roles in ecological system but their functions are hard to be identified and characterized due to the uncultivable challenges. Conventional tools of stable isotope probing (SIP) and metagenomic can reveal the potential functional species and genes related to specific biochemical process. However, they suffered from distinguishing respective roles between identified species or link them with their functional genes at single cell level. A novel toolbox of magnetic nanoparticles (MNPs) and Raman micro-spectroscopy can initiate a marker free, low cost and culture-independent approach to provide detailed insights into the uncultivable microorganisms and characterize their ecological roles.

  • Biotechnology and synthetic biology

As a systematic approach, synthetic biology aims to design and rewire existing and new biological parts, devices, and systems for useful purposes. The current main challenges of synthetic biology include developing reliable and robust chassis, standardisation of bio-parts and logic gate assembly. With the novel and directed evolutionary tools, Acinetobacter baylyi performs as a perfect candidate for all the challenges when addressed on environmental issues, such as contamination assessment and bioremediation.

  • Gene regulation mechanisms

Quantitative gene regulation behavior, especially real-time dynamics, is important for synthetic biological prediction, design and approach for the metabolite pathway and energy flow. Gene expression is such a complex stochastic event that random timing and discrete nature of bioprocess associated with synthesis/decay rate of mRNA and protein, where stochastic effects cannot be ignored. Here we describe a real-time quantum gene expression model to reveal on-or-off gene status of DNA, demonstrating that stochastic cellular phenotypic variation, which is usually considered as the result of gene expression (intrinsic noise) and cellular components fluctuation (extrinsic noise). Finite gene states are switched by collision frequency and bonding strength of regulator, causing discontiguous gene burst in single copy chromosome system. Such quantum DNA status causes principle gene expression stochastic, while the DNA bonding probability and strength for both activator and repressor depend on the energy gap between regulator monomer and regulator-DNA holoenzyme. With the quantum mechanisms, the stochastic gene expression behavior at real time and single cell level can be revealed with the Markov processed dynamics. The amplitude of noise at protein level is controlled by both distributed quantum gene states. Genetically identical cells exposed to the same environmental conditions are predicted and observed to show significant variation in molecular content and marked differences in phenotypic characteristics due to DNA quantum pattern.

Combined electro-catazone/electro-peroxone process for rapid and effective Rhodamine B degradation
Li, X., Sun, S., Zhang, X., Liu, G., Renjun Zheng, C., Zheng, J., Zhang, D., Yao, H. 7/05/2017 In: Separation and Purification Technology. 178, p. 189-192. 4 p.
Journal article

Fingerprinting microbiomes towards screening for microbial antibiotic resistance
Jin, N., Zhang, D., Martin, F.L. 27/04/2017 In: Integrative Biology. 12 p.
Journal article

Quantification of chemotaxis-related alkane accumulation in Acinetobacter baylyi using Raman microspectroscopy
Li, H., Martin, F.L.L., Zhang, D. 4/04/2017 In: Analytical Chemistry. 89, 7, p. 3909-3918. 10 p.
Journal article

Biodegradation of Phenanthrene in Polycyclic Aromatic Hydrocarbon-Contaminated Wastewater Revealed by Coupling Cultivation-Dependent and -Independent Approaches
Li, J., Luo, C., Song, M., Dai, Q., Jiang, L., Zhang, D., Zhang, G. 21/03/2017 In: Environmental Science and Technology. 51, 6, p. 3391-3401. 11 p.
Journal article

Cost-effectiveness Analysis on Magnetic Harvesting of Algal Cells
Xu, Y., Fu, Y., Zhang, D. 19/03/2017 In: Materials Today: Proceedings. 4, 1, p. 50-56. 7 p.
Journal article

Diagnose Pathogens in Drinking Water via Magnetic Surface-Enhanced Raman Scattering (SERS) Assay
Li, H., Li, C., Martin, F.L., Zhang, D. 19/03/2017 In: Materials Today: Proceedings. 4, 1, p. 25-31. 7 p.
Journal article

Di(2-ethylhexyl) phthalate induces apoptosis through mitochondrial pathway in GC-2spd cells
Fu, G., Dai, J., Zhang, D., Zhu, L., Tang, X., Zhang, L., Zhou, T., Duan, P., Quan, C., Zhang, Z., Song, S., Shi, Y. 03/2017 In: Environmental Toxicology. 32, 3, p. 1055-1064. 10 p.
Journal article

The dynamic change of microbial communities in crude oil contaminated soils from oilfields in China
Jia, J., Zong, S., Hu, L., Shi, S., Zhai, X., Wang, B., Li, G., Zhang, D. 02/2017 In: Soil and Sediment Contamination: An International Journal. 26, 2, p. 171-183. 13 p.
Journal article

Characterisation of the phenanthrene degradation-related genes and degrading ability of a newly isolated copper-tolerant bacterium
Song, M., Yang, Y., Jiang, L., Hong, Q., Zhang, D., Shen, Z., Yin, H., Luo, C. 01/2017 In: Environmental Pollution. 220, Part B, p. 1059-1067. 9 p.
Journal article

Assessing the impacts of phosphorus inactive clay on phosphorus release control and phytoplankton community structure in eutrophic lakes
Su, Y., Zhang, C., Liu, J., Weng, Y., Li, H., Zhang, D. 12/2016 In: Environmental Pollution. 219, p. 620-630. 11 p.
Journal article

Separating and characterizing functional alkane degraders from crude-oil-contaminated sites via magnetic nanoparticle-mediated isolation
Wang, X., Zhao, X., Li, H., Jia, J., Liu, Y., Ejenavi, O., Ding, A., Sun, Y., Zhang, D. 11/2016 In: Research in Microbiology. 167, 9-10, p. 731-744. 14 p.
Journal article

Exploring the Influence of Environmental Factors on Bacterial Communities within the Rhizosphere of the Cu-tolerant plant, Elsholtzia splendens
Jiang, L., Song, M., Yang, L., Zhang, D., Sun, Y., Shen, Z., Luo, C., Zhang, G. 26/10/2016 In: Scientific Reports. 6, 10 p.
Journal article

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil
Song, M., Jiang, L., Zhang, D., Luo, C., Wang, Y., Yu, Z., Yin, H., Zhang, G. 5/05/2016 In: Journal of Hazardous Materials. 308, p. 50-57. 8 p.
Journal article

Moisture content-affected electrokinetic remediation of Cr(VI)-contaminated clay by a hydrocalumite barrier
Xu, Y., Xu, X., Hou, H., Zhang, J., Zhang, D., Qian, G. 04/2016 In: Environmental Science and Pollution Research. 23, p. 6517-6523. 7 p.
Journal article

Recruitment of cyanobacteria from the sediments in the eutrophic Shanzi Reservoir
Su, Y., You, X., Lin, H., Zhuang, H., Weng, Y., Zhang, D. 03/2016 In: Environmental Technology. 37, 6, p. 641-651. 11 p.
Journal article

Enhancing pentachlorophenol degradation by vermicomposting associated bioremediation
Lin, Z., Bai, J., Zhen, Z., Lao, S., Li, W., Wu, Z., Li, Y., Spiro, B., Zhang, D. 02/2016 In: Ecological Engineering. 87, p. 288-294. 7 p.
Journal article

Could uptake and acropetal translocation of PBDEs by corn be enhanced following Cu exposure?: evidence from a root damage experiment
Wang, S., Wang, Y., Luo, C., Jiang, L., Song, M., Zhang, D., Wang, Y., Zhang, G. 19/01/2016 In: Environmental Science and Technology. 50, 2, p. 856-863. 8 p.
Journal article

Preparing and characterizing Fe3O4@cellulose nanocomposites for effective isolation of cellulose-decomposing microorganisms
Zhao, X., Li, H., Ding, A., Zhou, G., Sun, Y., Zhang, D. 15/01/2016 In: Materials Letters. 163, p. 154-157. 4 p.
Journal article

The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils
Lin, Z., Zhen, Z., Wu, Z., Yang, J., Zhong, L., Hu, H., Luo, C., Bai, J., Li, Y., Zhang, D. 15/01/2016 In: Journal of Hazardous Materials. 301, p. 35-45. 11 p.
Journal article

Magnet bioreporter device for ecological toxicity assessment on heavy metal contamination of coal cinder sites
Jia, J., Li, H., Zong, S., Jiang, B., Li, G., Ejenavi, O., Zhu, J., Zhang, D. 01/2016 In: Sensors and Actuators B: Chemical. 222, p. 290-299. 10 p.
Journal article

Interrogating chemical variation via layer-by-layer SERS during biofouling and cleaning of nanofiltration membranes with further investigations into cleaning efficiency
Cui, L., Chen, P., Zhang, B., Zhang, D., Li, J., Martin, F.L., Zhang, K. 15/12/2015 In: Water Research. 87, p. 282-291. 10 p.
Journal article

Electrosorption for organic pollutants removal and desalination by graphite and activated carbon fiber composite electrodes
Zhou, G., Li, W., Wang, Z., Wang, X., Li, S., Zhang, D. 1/12/2015 In: International Journal of Environmental Science and Technology. 12, 12, p. 3735-3744. 10 p.
Journal article

Identification of Benzo[a]pyrene-metabolizing bacteria in forest soils by using DNA-based stable-isotope probing
Song, M., Luo, C., Jiang, L., Zhang, D., Wang, Y., Zhang, G. 11/2015 In: Applied and Environmental Microbiology. 81, 21, p. 7368-7376. 9 p.
Journal article

Application and reactivation of magnetic nanoparticles in Microcystis aeruginosa harvesting
Lin, Z., Xu, Y., Zhen, Z., Fu, Y., Liu, Y., Li, W., Luo, C., Ding, A., Zhang, D. 08/2015 In: Bioresource Technology. 190, p. 82-88. 7 p.
Journal article

Method to predict key factors affecting lake eutrophication: a new approach based on Support Vector Regression model
Xu, Y., Ma, C., Liu, Q., Xi, B., Qian, G., Zhang, D., Huo, S. 08/2015 In: International Biodeterioration and Biodegradation. 102, p. 308-315. 8 p.
Journal article

Novel phenanthrene-degrading bacteria identified by DNA-stable isotope probing
Jiang, L., Song, M., Luo, C., Zhang, D., Zhang, G. 22/06/2015 In: PLoS ONE. 10, 6, 14 p.
Journal article

Graphene-oxide modified polyvinyl-alcohol as microbial carrier to improve high salt wastewater treatment
Zhou, G., Wang, Z., Li, W., Yao, Q., Zhang, D. 10/06/2015 In: Materials Letters. 156, p. 205-208. 4 p.
Journal article

The influence of carbon sources on the expression of the recA gene and genotoxicity detection by an Acinetobacter bioreporter
Jiang, B., Song, Y., Zhang, D., Huang, W.E., Zhang, X., Li, G. 8/04/2015 In: Environmental Science: Processes and Impacts. 17, 4, p. 835-843. 9 p.
Journal article

Innovative slow-release organic carbon-source material for groundwater in situ denitrification
Zhang, D., Zhang, X., Wang, Y., Zhou, G., Li, G. 1/04/2015 In: Environmental Technology. 36, 7, p. 909-919. 11 p.
Journal article

Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community
Zhang, D., Berry, J.P., Zhu, D., Wang, Y., Chen, Y., Jiang, B., Huang, S., Langford, H., Li, G., Davison, P.A., Xu, J., Aries, E., Huang, W.E. 1/03/2015 In: ISME Journal. 9, 3, p. 603-614. 12 p.
Journal article

Biodegradation of Dichlorodiphenyltrichloroethanes (DDTs) and Hexachlorocyclohexanes (HCHs) with plant and nutrients and their effects on the microbial ecological kinetics
Sun, G., Zhang, X., Hu, Q., Zhang, H., Zhang, D., Li, G. 1/02/2015 In: Microbial Ecology. 69, 2, p. 281-292. 12 p.
Journal article

Use of a whole-cell bioreporter, Acinetobacter baylyi, to estimate the genotoxicity and bioavailability of chromium(VI)-contaminated soils
Jiang, B., Zhu, D., Song, Y., Zhang, D., Liu, Z., Zhang, X., Huang, W.E., Li, G. 1/02/2015 In: Biotechnology Letters. 37, 2, p. 343-348. 6 p.
Journal article

Structure and mass transportation model of slow-release organic carbon-source material for groundwater in situ denitrification
Zhang, D., Zhou, G., Zhang, X., Wang, Y., Li, G. 02/2015 In: Environmental Technology. 36, 3, p. 395-403. 9 p.
Journal article

Anaerobic degradation of Polychlorinated Biphenyls (PCBs) and Polychlorinated Biphenyls Ethers (PBDEs), and microbial community dynamics of electronic waste-contaminated soil
Song, M., Luo, C., Li, F., Jiang, L., Wang, Y., Zhang, D., Zhang, G. 1/01/2015 In: Science of the Total Environment. 502, 1, p. 426-433. 8 p.
Journal article

Establishing reference conditions for lake water quality: a novel extrapolation approach
Xu, Y., Ma, C., Huo, S., Zhang, D., Xu, Z., Qian, G., Xi, B. 1/06/2014 In: Water Resources Management. 28, 8, p. 2161-2178. 11 p.
Journal article

Toxicity assessment and modeling of Moringa oleifera seeds in water purification by whole cell bioreporter
Al-Anizi, A.A., Hellyer, M.T., Zhang, D. 1/06/2014 In: Water Research. 56, p. 77-87. 11 p.
Journal article

Application of magnetic nanoparticles in drinking water purification
Xu, Y., Zhang, D. 2014 In: Environmental Engineering and Management Journal. 13, 8
Journal article

Bacterial whole-cell biosensors for the detection of contaminants in water and soils
Zhang, D. 2014 In: Environmental microbiology. Humana Press p. 155-168. 14 p.
Chapter (peer-reviewed)

Functionalization and immobilization of whole cell bioreporters for the detection of environmental contamination
Chen, C., Zhang, D., Thornton, S.F., Duan, M., Luo, Y., Ding, A., Huang, W.E. 1/07/2013 In: Environmental Engineering and Management Journal. 12, 7, p. 1417-1422. 6 p.
Journal article

Whole cell bioreporter for the estimation of oil contamination
Li, C., Zhang, D., Song, Y., Jiang, B., Li, G., Huang, W.E. 07/2013 In: Environmental Engineering and Management Journal. 12, 7, p. 1353-1358. 6 p.
Journal article

Whole cell bioreporter application for rapid detection and evaluation of crude oil spill in seawater caused by Dalian oil tank explosion
Zhang, D., Ding, A., Cui, S., Hu, C., Thornton, S.F., Dou, J., Sun, Y., Huang, W.E. 1/03/2013 In: Water Research. 47, 3, p. 1191-1200. 10 p.
Journal article

Characterization and modeling of transcriptional cross-regulation in Acinetobacter baylyi ADP1
Zhang, D., Zhao, Y., He, Y., Wang, Y., Zhao, Y., Zheng, Y., Wei, X., Zhang, L., Li, Y., Jin, T., Wu, L., Wang, H., Davison, P.A., Xu, J., Huang, W.E. 07/2012 In: ACS Synthetic Biology. 1, 7, p. 274-283. 10 p.
Journal article

Whole-cell bacterial bioreporter for actively searching and sensing of alkanes and oil spills
Zhang, D., He, Y., Wang, Y., Wang, H., Wu, L., Aries, E., Huang, W.E. 01/2012 In: Microbial Biotechnology. 5, 1, p. 87-97. 11 p.
Journal article

Bacterial whole cell bioreporters in environmental health
Song, Y., Zhang, D., Polizzi, K., Zhang, E., Li, G., Huang, W. 2012 In: Biosensors and environmental health. Boca Raton, Fl. : Science Publishers Inc.
Chapter (peer-reviewed)

Functionalization of whole-cell bacterial reporters with magnetic nanoparticles
Zhang, D., Fakhrullin, R.F., Ozmen, M., Wang, H., Wang, J., Paunov, V.N., Li, G., Huang, W.E. 01/2011 In: Microbial Biotechnology. 4, 1, p. 89-97. 9 p.
Journal article

Synthetic biology approach for mining new enzymes from unculturable microorganisms
Wang, Y., Zhang, D., Huang, W.E. 04/2010
Meeting abstract

Bio-geological processes of nitrogen transport and transformation in the aeration zone and aquifer
Zhang, D., Li, G., Yang, Y.S., Zhang, X., Guo, H. 04/2009 In: Hydrological Sciences Journal. 54, 2, p. 316-326. 11 p.
Journal article

Effects of water table and fertilization management on nitrogen loading to groundwater
Guo, H., Li, G., Zhang, D., Zhang, X., Lu, C. 10/04/2006 In: Agricultural Water Management. 82, 1-2, p. 86-98. 13 p.
Journal article

Structure and function of slow release organic carbon source in groundwater in-situ denitrification
Zhang, D.Y., Li, G.H., Wang, Y., Zhou, G.Z. 2006 In: 5th World Water Congress. London : I W A PUBLISHING p. 105-113. 9 p.

A spatial research of denitrification and nitrification potential of agricultural soils in relation to fertilization practice
Guo, H., Li, G., Zhang, X., Yan, F., Zhang, D., Lu, C. 2003 In: Proceedings of the International Symposium on Water Resources and the Urban Environment . Beijing : CHINA ENVIRONMENTAL SCIENCE PRESS p. 179-185. 7 p.