Holden Laboratory


Ying Wang studying soybeans grown in nanomaterial-amended agricultural soils.
Dong Li and Jared Ervin (Geosyntec) sampling the surf zone for water quality research.
Sediment corers, in the hands of Laurie Van De Werfhorst, for water quality research.
Dong Li, Naresh Devarajan, and Tania Gomez sampling for coastal water quality research.

McClary-Gutierrez, J.; Mattioli, M.; Marcenac, P.; Silverman, A.; Boehm, A.; Bibby, K.; Balliet, M.; de los Reyes III, F.; Gerrity, D.; Griffith, J.; Holden, P.; Katehis, D.; Kester, G.; LaCross, N.; Lipp, E.; Meiman, J.; Noble, R.; Brossard, D.; McLellan, S. Sars-Cov-2 wastewater surveillance for public health action: connecting perspectives from wastewater researchers and public health officials during a global pandemic. Preprints 2021, 2021040167 (doi: 10.20944/preprints202104.0167.v1).

Pierce, G., Gmoser-Daskalakis, K., Rippy, M.A., Holden, P.A., Grant, Stanley B., Feldman, David L., Ambrose, Richard F. 2021. Environmental attitudes and knowledge: do they matter for support and investment in local stormwater infrastructure? Society & Natural Resources. 2021: 1-21: doi: 10.1080/08941920.2021.1900963.

Wartenberg, A., Holden, P.A., Bodwitch, H., Parker-Shames, P., Novotny, T., Harmon, T., Hart, S., Beutel, M., Gilmore, M., Hoh, E., Butsic, V. 2021. Cannabis and the environment: What science tells us and what we still need to know. Environmental Science & Technology Letters.8, 2, 98–107.

Parker, E. A., Grant, S. B., Cao, Y., Rippy, M. A., McGuire, K. J., Holden, P. A., Feraud, M., Avasarala, S., Liu, H., Hung. W. C., Rugh, M., Jay, J., Peng, J., Shao, S., Li, D. 2021. Predicting solute transport through green stormwater infrastructure with unsteady transit time distribution theory. Water Resources Research.V57(2). February 2021.e2020WR028579. 

Feraud, M., Holden, P.A. 2021. Evaluating the relationships between specific drainage area characteristics and soil metal concentrations in long-established bioswales receiving suburban stormwater. Sci. Tot. Environ. V757, 25 February 2021, 143778. https://doi.org/10.1016/j.scitotenv.2020.143778

Pierce, G,, Gmoser-Daskalakis, K., Jessup, K., Grant, S. B., Mehring, A., Winfrey, B., Rippy, M. A., Feldman, D., Holden, P., Ambrose, R., Levin, L. 2021. University stormwater management within urban environmental regulatory regimes: barriers to progressivity or opportunities to innovate? Environ. Manage. Jan;67(1):12-25. https://doi.org/10.1007/s00267-020-01377-3. 

Mortimer, M., Winchell, A., Holden. P.A. 2020. Evaluation of frameworks proposed as protective of antimicrobial resistance propagation in the environment. Environment International. 144: 106053. open access: https://www.sciencedirect.com/science/article/pii/S0160412020320080
Bivins, A. (plus 60 co-authors). 2020. Wastewater-based epidemiology: global collaborative to maximize contributions in the fight against COVID-19. Environ. Sci. Technol. 54 (13): 7754-7757
Li, D., Van de Werfhorst, L. C., Dunne, T., Devarajan. N., Ayala, T. G., Holden, P.A. 2020. Surf zone microbiological water quality following emergency beach nourishment using sediments from a catastrophic debris flow. Water Res. 176 (June): 115733. DOI: 10.1015/i.watres.2020.115733
Mortimer, M., Li, D., Wang, Y., Holden, P. A. 2020. Physical properties of carbon nanomaterials and nanoceria affect pathways important to the nodulation competitiveness of the symbiotic N2-fixing bacterium Bradyrhizobium diazoefficiens. Small. 1906055: 1-14. DOI: 10.1002/smll.201906055
Wang, Y., Schimel, J. P., Nisbet, R. M., Gardea-Torresdey, J. L., Holden, P. A. 2020. Soybeans grown with carbonaceous nanomaterials maintain nitrogen stoichiometry by assimilating soil nitrogen to offset impaired dinitrogen fixation. ACS Nano. 14(1): 585-594. DOI: 10.1021/acsnano.9b06970
Petersen, E. J., Mortimer, M., Burgess, R. M., Handy, R., Hanna, S., Ho, K. T., Johnson, M., Loureiro, S., Selck, H., Scott-Fordsmand, J. J.. Spurgeon, D.. Unrine, J., van den Brink, N. W., Wang, Y., White, J., Holden, P. 2019. Strategies for robust and accurate experimental approaches to quantify nanomaterial bioaccumulation across a broad range of organisms. Environ Sci: Nano. 6(6):1619-1656. DOI: 10.1039/C8EN01378K
Gao, C-H., Mortimer, M., Zhang, M., Holden, P. A., Cai, P., Wu, S., Xin, Y., Wu, Y., Huang, Q. 2019. Impact of metal oxide nanoparticles on in vitro DNA amplification. PeerJ. 7: e7228. DOI: 0.7717/peerj.7228
Wang, Y., Welch, Z. S., Ramirez, A. R., Bouchard, D. C., Schimel, J. P., Gardea-Torresdey, J. L., Holden, P. A. 2019. Effects of carbonaceous nanomaterials on soil-grown soybeans under combined heat and insect stresses. Environ Chem. 16(6):482-493. https://doi.org/10.1071/EN19047
Holden, P. A., Mortimer, M., Wang, Y. 2019. Engineered nanomaterials and symbiotic dinitrogen fixation in legumes. Curr Opin Environ Sci Health. 6: 54-59. https://doi.org/10.1016/j.coesh.2018.07.012
Ge, Y., Shen, C., Wang, Y., Sun, Y.-Q., Schimel, J. P., Gardea-Torresdey, J. L., Holden, P. A. 2018. Carbonaceous nanomaterials have higher effects on soybean rhizosphere prokaryotic communities during the reproductive growth phase than during vegetative growth. Environ Sci Technol. 52(11): 6636-6646. DOI:10.1021/acs.est.8b00937
Mortimer, M., Devarajan, N., Li, D., Holden, P. A. 2018. Multiwall carbon nanotubes induce more pronounced transcriptomic responses in Pseudomonas aeruginosa PG201 than graphene, exfoliated boron nitride, or carbon black. ACS Nano. 12(3):2728–2740. DOI:10.1021/acsnano.7b08977
Wang, Y., Mortimer, M., Chang, C. H., Holden, P. A. 2018. Alginic acid-aided dispersion of carbon nanotubes, graphene, and boron nitride nanomaterials for microbial toxicity testing. Nanomaterials. 8(76):1-22. DOI:10.3390/nano8020076
Wang, Y., Chang, C. H., Ji, Z., Bouchard, D. C., Nisbet, R. M., Schimel, J. P.. Gardea-Torresdey, J. L.. Holden, P. A. 2017. Agglomeration determines effects of carbonaceous nanomaterials on soybean nodulation, dinitrogen fixation potential, and growth in soil. ACS Nano. 11(6):5753-65.
Klanjšček, T., Muller, E. B., Holden, P. A., Nisbet, R. M. 2017. Host-symbiont interaction model explains non-monotonic response of soybean growth and seed production to nano-CeO2 exposure. Environ. Sci. Technol. 51(9):4944-4950.
Holden, P.A. 2017. DEB modeling for nanotoxicology, microbial ecology, and environmental engineering Comment on: "Physics of metabolic organization" by Marko Jusup et al. Phyics of Life Reviews. 20:49-51.
Zimmer-Faust, A. G., Thulsiraj, V., Marambio-Jones, C., Cao, Y., Griffith, J. F., Holden, P. A., Jay, J. A., 2017. Effect of freshwater sediment characteristics on the persistence of fecal indicator bacteria and genetic markers within a Southern California watershed. Water Res. 119:1-11. http://dx.doi.org/10.1016/j.watres.2017.04.028
Roehrdanz, P. R., Feraud, M., Lee, D. G., Means, J. C., Snyder, S. A., Holden, P. A. 2017.  Spatial models of sewer pipe leakage predict the occurrence of wastewater indicators in shallow urban groundwater. Environ. Sci. Technol..51:1213-23. DOI:  10.1021/acs.est.6b05015
Hjorth, R., Holden, P., Foss Hansen, S., Colman, B., Grieger, K. D., Hendren, C. 2017. The role of alternative testing strategies in environmental risk assessment of engineered nanomaterials. Environ. Sci. Nano. 4(2):292-301. DOI:10.1039/C6EN00443A
Priester, J. H, Moritz, S. C., Espinosa, K., Ge, Y., Wang, Y., Nisbet, R. M., Schimel, J. P., Goggi, A. S., Gardea-Torresdey, J. L., Holden, P. A. 2017.

Damage assessment for soybean cultivated in soil with either CeO2 or ZnO manufactured nanomaterials. Sci. Tot. Environ. 579: 1756-68. DOI:10.1016/j.scitotenv.2016.11.149

Hartline, N. L., Bruce, N. J., Karba, S. N., Ruff, E. O., Sonar, S. U., Holden, P. A. 2016. 

Microfiber masses recovered from conventional machine washing of new or aged garments. Environ. Sci. Technol. 50(21):11532-11538.

Mortimer, M., Petersen, E. J., Bucholz, B. A., Holden, P. A. 2016. Separation of bacteria, protozoa and carbon nanotubes by density gradient centrifugation. Nanomaterials. 6(10):181. 


Shatkin, J. A., Ong, K, J., Beaudrie, C., Clippinger, A. J., Hendren, C. O., Haber, L. T., Hill, M., Holden, P., Kennedy, A. J., Kim, B., MacDonell, M., Powers, C. M., Sharma, M., Sheremeta, L., Stone, V., Sultan, Y., Turley, A., White, R. H. 2016. Advancing risk analysis for nanoscale materials: report from an international workshop on the role of alternative testing strategies for advancement. Risk Analysis. 36(8):1520-1537. DOI: 10.1111/risa.12683
Mortimer, M.,; Petersen, E. J., ; Buchholz, B. A., Orias, E., Holden, P. A. 2016. Bioaccumulation of multiwall carbon nanotubes in Tetrahymena thermophila by direct feeding or trophic transfer. Environmental Science & Technology. 50(16):8876-8885. DOI: 10.1021/acs.est.6b01916
Holden, P.A., Gardea-Torresdey, J., Klaessig, F., Turco, R. F., Mortimer, M., Hund-Rinke, K., Cohen Hubal, E. A., Avery, D., Barceló, D., Behra, R., Cohen, Y., Deydier-Stephan, L., Ferguson, P. L., Fernandes, T. F., Herr Harthorn, B., Henderson, W. M., Hoke, R. A., Hristozov, Johnston, J. M., Kane, A. B., Kapustka, L., Keller, A. A., Lenihan, H. S., Lovell, W., Murphy, C. J., Nisbet, R. M., Petersen, E. J., Salinas, E. R., Scheringer, M., Sharma, M., Speed, D. E., Sultan, Y., Westerhoff, P., White, J. C., Wiesner, M. R., Wong, E. M., Xing, B., Steele Horan, M., Godwin, H. A.,  Nel, A. E. 2016. Considerations of environmentally relevant test conditions for improved evaluation of ecological hazards of engineered nanomaterials. Environmental Science & Technology. 50(12):6124-45. DOI: 10.1021/acs.est.6b00608

Ge, Y., Priester, J. H., Mortimer, M., Chang, C. H.. Ji, Z., Schimel, J. P., Holden, P. A. 2016. Long-term effects of multiwalled carbon nanotubes and graphene on microbial communities in dry soil. Environmental Science & Technology.50(7):3965-74. DOI: 10.1021/acs.est.5b05620

Ge, Y., Horst, A. M., Kim, J., Priester, J. H., Welch, Z. S., Holden, P. A.. 2016. Toxicity of Manufactured Nanomaterials to MIcroorganisms. In Engineered Nanoparticles and the Environment: Biophysicochemical Processes and Biotoxicity, Xing, B.; Vecitis, C. D.; Senesi, N., Eds. Wiley: Vol. 4. pp 320-46.

Lee, D. G., Roehrdanz, P. R., Ferauad, M., Ervin, J., Anumol, T., Jia, A., Park, M., Tamez, C., Morelius, E. W., Gardea-Torresdey, J. L., Izbicki, J., Means, J. C., Snyder, S. A., Holden, P. A. 2015. Wastewater compounds in urban shallow groundwater wells correspond to exfiltration probabilities of nearby sewers. Water Research.85:467-475  http://www.sciencedirect.com/science/article/pii/S0043135415301998

Liu, R., Ge, Y., Holden, P. A., Cohen, Y. 2015. Analysis of soil bacteria susceptibility to manufactured nanoparticles via data visualization. Beilstein Journal of Nanotechnology. 6:1635-1651.

Kaweeteerawat, C., Chang, C. H., Roy, K., Liu, R., Li, R., Toso, D., Fischer, H., Ivask, A.,Ji, Z., Zink, J., Zhou, Z. H., Chanfreau, G., Telesca, D., Cohen, Y., Holden, P., Nel, A., Godwin, H. 2015. Cu nanoparticles have different impacts in Escherichia coli and Lactobacillus brevis than their microsized and ionic analogues. ACS Nano. 9 (7): 7215-7255.

Godwin, H., Nameth, C., Avery, D., Bergeson, L. L., Bernard, D., Beryt, E., Boyes, W., Brown, S., Clippinger, A. J., Cohen, Y., Doa, M., Hendren, C. O., Holden, P., Houck, K., Kane, A. B., Klaessig, F., Kodas, T., Landsiedel, R., Lynch, I., Malloy, T., Miller, M. B., Muller, J., Oberdorster, G., Petersen, E. J., Pleus, R. C., Sayre, P., Stone, V., Sullivan, K. M., Tentschert, J., Wallis, P., Nel, A. E. 2015. Nanomaterial categorization for assessing risk potential to facilitate regulatory decision-making. ACS Nano. 9(7):7215-7255.

Kaweeteerawat, C., Ivask, A., Liu, R., Zhang, H., Chang, C. H., Low-Kam, C., Fischer, H., Ji, Z., Pokhrel, S., Cohen, Y., Telesca, D., Zink, J., Mädler, L., Holden, P. A., Nel, A., Godwin, H. 2015. Toxicity of metal oxide nanoparticles in Escherichia coli correlates with conduction band and hydration energies. Environmental Science & Technology. 49(2):1105-1112.

Priester, J. H., Van De Werfhorst, L. C., Ge, Y., Adeleye, A., Tomar, S., Tom, L. M., Piceno, Y. M., Andersen, G. L., Holden. P. A. 2014. Effects of TiO2 and Ag nanoparticles on polyhydroxybutyrate biosynthesis by activated sludge bacteria. Environmental Science & Technology. 48(24):14712-14720.

Ge, Y., Priester, J. H., Van De Werfhorst, L. C., Walker, S. L., Nisbet, R. M., An, Y-J., Schimel, J. P., Gardea-Torresdey, J. L., Holden, P. A. 2014. Soybean plants modify metal oxide nanoparticle effects on soil bacterial communities. Environmental Science & Technology. 48)22):13489-13496.

Holden, P.A, Klaessig, F., Turco, R. F., Priester, J. H., Rico, C. M., Arias, H. A., Mortimer, M., Pacpaco, K., Gardea-Torresdey, J. L. 2014. Evaluation of exposure concentrations used in assessing manufactured nanomaterial environmental hazards: are they relevant? Environmental Science & Technology. 48:10541-10551.

Ervin, J. S., Van De Werfhorst, L. C., Murray, J. L. S., Holden, P.A. 2014. Microbial source tracking in a coastal California watershed reveals canines as controllable sources of fecal contamination. Environmental Science & Technology. 48:9043-9052.

Ge, Y., Schimel, J. P., Holden, P. A. 2014. Analysis of run-to-run variation of bar-coded pyrosequencing for evaluating bacterial community shifts and individual taxa dynamics. Plos ONE: 9(6):e99414. DOI:10.1371/journal.pone.0099414

Van De Werfhorst, L. C., Murray, J. L. S., Reynolds, S., Reynolds, K., Holden, P.A. 2014. Canine scent detection and microbial source tracking of human waste contamination in storm drains. Water Environment Research. 86:550-558.

Riedel, T. E.; Zimmer-Faust, A. G.; Thulsiraj, V.; Madi, T.; Hanley, K. T.; Ebentier, D. L.; Byappanahalli, M.; Layton, B.; Raith, M.; Boehm, A. B.; Griffith, J. F.; Holden, P. A.; Shanks, O. C.; Weisberg, S. B.; Jay, J. A. 2014. Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters. J. Environ. Management. 136: 112-120.

Priester, J. H.; Singhal, A.; Wu, B.; Stucky, G. D.; Holden, P. A. 2014. Integrated approach to evaluating the toxicity of novel cysteine-capped silver nanoparticles to Escherichia coli and Pseudomonas aeruginosa. Analyst. 139: 954-963.

Peralta-Videa, J. R.; Hernandez-Viezcas, J. A.; Zhao, L.; Diaz, B. C.; Ge, Y.; Priester, J. H. 2014. Holden, P. A.; Gardea-Torresdey, J. L., Cerium dioxide and zinc oxide nanoparticles alter the nutritional value of soil cultivated soybean plants. Plant Physiol. Biochem. 80: 128-135.

Ivask, A.; El Badawy, A.; Kaweeteerawat, C.; Boren, D.; Fischer, H.; Ji, Z. X.; Chang, C. H.; Liu, R.; Tolaymat, T.; Telesca, D.; Zink, J. I.; Cohen, Y.; Holden, P. A.; Godwin, H. A. 2014. Toxicity mechanisms in Escherichia coli vary for silver nanoparticles and differ from ionic silver. ACS Nano. 8: 374-386.

Holden, P. A.; Schimel, J. P.; Godwin, H. A. 2014. Five reasons to use bacteria when assessing manufactured nanomaterial environmental hazards and fates. Curr. Opin. Biotechnol. 27: 73-78.

Yoon, S.-J., Kwak, J. I., Lee, W.-M., Holden, P. A., An, Y. J. 2014. Zinc oxide nanoparticles delay soybean development: a standard soil microcosm study. Ecotoxicology and Environmental Safety. 100:131-137.

Priester, J.H., Ge, Y., Chang, V., Stoimenov, P. K.,  Schimel, J. P, Stucky, G.D., Holden, P. A. 2013. Assessing interactions of hydrophilic nanoscale TiO2 with soil water. Journal of Nanoparticle Research. 15:1-13.

Wang, H. H.; Wu, F. C.; Meng, W.; White, J. C.; Holden, P. A.; Xing, B. S. 2013. Engineered nanoparticles may Induce genotoxicity. Environ. Sci. Technol. 47: 13212-13214.

Ge, Y.; Priester, J. H.; De Werfhorst, L. C. V.; Schimel, J. P.; Holden, P. A. 2013. Potential mechanisms and environmental controls of TiO2 nanoparticle effects on soil bacterial communities. Environ. Sci. Technol. 47: 14411-14417.

Mielke, R. E., Priester, J. H., Werlin, R. A., Gelb, J., Horst, A. M., Orias, E., Holden. P. A. 2013. Differential growth of and nanoscale TiO2 accumulation in Tetrahymena thermophila by direct feeding versus trophic transfer from Pseudomonas aeruginosa. Applied & Environmental Microbiology. 79:5616.

Layton, B. A., Cao, Y., Ebentier, D. L, Hanley, K., Van De Werfhorst, L. C., Wang, D., Tania Madi, T., Whitman, R., Byappanahalli, ; Muruleedhara, Ballesté, E., Meijer, W. G.,, Schriewer, A., Wuertz, S., Converse, R., Noble, R.,  Srinivasan, S., Rose, J. B., Lee, C. S., Lee, J., Gentry-Shields, J., Stewart, J., Reischer, G. H., Farnleitner, A. H., Gidley, M. L., Sinigalliano, C., ; Brandão, J., Rodrigues, R., Lozach, S., Gourmelon, M., Peed, L., Jay, J. A., Holden, P. A., Boehm, A. B., Shanks, O. C., Griffith, J. F. 2013.Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study. Water Research. 47: 6897-6908.

Raith, M.R., Kelty, C. A., Griffith, J. F., Schriewer, A., Wuertz, S., Mieszkin, S., Gourmelon, M., Reischer, G. H., Farnleitner, A. H., Ervin, J. S., Holden, P. A., Ebentier, D. L., Jay, J. A., Wang, D., Boehm, A. B., Aw, T. G., Rose, J. B., Balleste, E., Meijer, W. G., Sivaganesan, M., Shanks, O. 2013. Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources. Water Research. 47:6921-6928

Schriewer, A., Goodwin, K. D., Sinigalliano, C. D., Cox, A., Wanless, D., Bartkowiak, J., Ebentier, D. L., Hanley, K. T., Ervin, J., Deering, L. A., Shanks, O. C., Peed, L. A., Meijer, W. G., Griffith, J. F., SantoDomingo, J., Jay, J. A., Holden, P. A., Wuertz, S. 2013. Performance evaluation of canine-associated Bacteroidales assays in a multi-laboratory comparison study. Water Research. 47:6909-6920.

Cao, Y., Van De Werfhorst, L. C., Scott, E. A., Raith, M. R., Holden, P. A., Griffith, J. F. 2013. Bacteriodales terminal restriction fragment length polymorphism (TRFLP) for fecal source differentiation in comparison to and in combination with universal bacteria TRFLP. Water Research. 47: 6944-6955.

Engeman, C.D., Baumgartner, L., Carr, B.M., Fish, A.M., Meyerhofer, J.D., Satterfield, T.A., Holden, P.A., Harthorn, B.H. 2013. The hierarchy of environmental health and safety practices in the U.S. nanotechnology workplace. Journal of Occupational & Environmental Hygiene. 10:487-495.

Hernandez-Viezcas, J. A., Castillo-Michel, H., Andrews, J. C., Cotte, M., Rico, C., Peralta-Videa, J. R., Ge, Y., Priester, J. H., Holden, P. A., Gardea-Torresdey, J. L. 2013. In situ synchrotron X-ray fluorescence mapping and speciation of CeO2 and ZnO nanoparticles in soil cultivated soybean (Glycine max). ACS Nano. 7(2):1415-1423. DOI:10.1021/nn305196q

Sinigalliano, C. D., Ervin, J., Van De Werfhorst, L. C., Badgley, B., Ballesté, E., Bartkowiak, J., Boehm, A. B., Byappanahalli, M., Goodwin, K. D., Gourmelon, M., Griffith, J., Holden P. A., Jay, J., Layton, B., Lee, C., Lee, J., Meijer, W. G., Noble, R., Raith, M., Ryu, H., Sadowsky, M. J., Schriewer, A., Wang, D., Wanless, D., Whitman, R., Wuertz, S., Santo Domingo, J. W. 2013. Multi-laboratory evaluations of the performance of Catellicoccus marimammalium PCR assays developed to target gull fecal sources. Water Research. 47:6883-6896.

Ervin, J. S., Russell, T. L., Layton, B. A., Yamahara, K. M., Wang, D., Sassoubre, L. M., Cao, Y., Kelty, C. A., Sivaganesan, M., Boehm, A. B., Holden, P. A., Weisberg, S. B., Shanks, O. 2013. Characterization of fecal concentrations in human and other animal sources by physical, culture-based, and quantitative real-time PCR methods. Water Research. 47:6873-6882.

Cao, Y., Van De Werfhorst, L. C., Dubinsky, E. A., Badgley, B. D., Sadowsky, M. J., Andersen, G. L., Griffith, J. G., Holden, P. A. 2013. Evaluation of molecular community analysis methods for discerning fecal sources and human waste. Water Research. 47:6862-6872.

Ebentier, D. L., Hanley, K. T., Cao, Y., Badgley, B. D., Boehm, A. B., Ervin, J. S., Goodwin, K. D., Gourmelon, M., Griffith, J. F., Holden, P. A., Kelty, C. A., Lozach, S., McGee, C., Peed, L. A., Raith, M., Ryu, H., Sadowsky, M. J., Scott, E. A., Domingo, J. S., Schriewer, A., Sinigalliano, C. D., Shanks, O. C., Van De Werfhorst, L. C., Wang, D., Wuertz, S., Jay, J. A. 2013. Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods. Water Research. 47: 6839-6848.

Klanjscek, T., Priester, J.H., Holden, P.A., and Nisbet, R.M. 2013. Dynamic Energy Budget approach to modeling mechanisms of CdSe quantum dot toxicity. Ecotoxicology. 22:319-330. DOI 10.1007/s10646-012-1028-7

Boehm, Alexandria B., Laurie C. Van De Werfhorst, John F. Griffith, Patricia A. Holden, Jenny A. Jay, Orin C. Shanks, Dan Wang, Stephen B. Weisberg. 2013. Performance of forty-three microbial source tracking methods: a twenty-seven lab evaluation study. Water Research. 47: 6812-6828.

Holden, Patricia A., Roger M. Nisbet, Hunter S. Lenihan, Robert J. Miller, Gary N. Cherr, Joshua P. Schimel, Jorge L. Gardea-Torresdey. 2013.  Ecological nanotoxicology: integrating nanomaterial hazard considerations across the subcellular, population, community, and ecosystems levels. Accounts of Chemical Research. 46(3):813-822. DOI:10.1021/ar300069t

Horst, Allison M., Raja Vukanti, John H. Priester, P. A. Holden. 2013. An assessment of fluorescence- and absorbance-based assays to study nanoparticle ROS production and effects on bacterial membranes. Small. 9 (9-10): 1753-1764. DOI: 10.1002/smll.201201455

Xia T, Malasarn D, Lin SJ, Ji ZX, Zhang HY, Miller RJ, Keller AA, Nisbet RM, Harthorn BH, Godwin HA, Lenihan, H. S., Liu, R., Gardea-Torresdey, J., Cohen, Y., Madler, L., Holden, P. A., Zink, J. I., Nel, A. E. 2013. Implementation of a multidisciplinary approach to solve complex nano EHS problems by the UC Center for the Environmental Implications of Nanotechnology. Small 2013, 9:1428-1443.

Sercu, B., A. D.G. Jones, C. H. Wu, M. H. Escobar, C. L. Serlin, T. A. Knapp, G. L. Andersen, P. A. Holden. 2012. The influence of in situ chemical oxidation on microbial community composition in groundwater contaminated with chlorinated solvents. Microbial Ecology. Aug. pp1-11.

Priester, J. H.; Ge, Y.; Mielke, R. E.; Horst, A. M.; Cole-Moritz, S.; Espinosa, K.; Gelb, J.; Walker, S. L.; Nisbet, R. M.; An, Y. J.; Schimel, J. P.; Palmer, R. G.; Hernandez-Viezcas, J.A.; Zhao, L.; Gardea-Torresdey, J. L.; Holden, P. A. 2012. Soybean susceptibility to manufactured nanomaterials with evidence for food quality and soil fertility interruption. Proceedings of the National Academy of Sciences of the United States of America. 109 (37): E2451-E2456.

Ivask, A.; Suarez, E.; Patel, T.; Boren, D.; Ji, Z. X.; Holden, P.; Telesca, D.; Damoiseaux, R.; Bradley, K. A.; Godwin, H. 2012. Genome-wide bacterial toxicity screening uncovers the mechanisms of toxicity of a cationic polystyrene nanomaterial. Environmental Science & Technology. 46: 2398-2405.

Izbicki, John A., Swarzenski, Peter W., Burton, Carmen A., Van De Werfhorst, Laurie C., Holden, Patricia A., Dubinsky, Eric A. 2012. Sources of fecal indicator bacteria to groundwater, Malibu Lagoon and the nearshore ocean, Malibu, California, USA. Annals of Environmental Science. 6: 35-86.

Ge, Y., J. P. Schimel, P. A. Holden. 2012. Identification of soil bacteria susceptible to TiO2 and ZnO nanoparticles. Applied and Environmental Microbiology. 78 (18): 6749-6758.

Horst, Allison M., Ji. Z., Holden, P.A. 2012. Nanoparticle dispersion in environmentally relevant culture media: a TiO2 case study and considerations for a general approach. Journal of Nanoparticle Research 14(8), 1404.

Engeman, C. D., Baumgartner, L., Carr, B. M., Fish, A. M., Meyerhofer, J. D., Satterfield, T. A., Holden, P. A., Harthorn, B. H. 2012. Governance implications of nanomaterials companies' inconsistent risk perceptions and safety practices. Journal of Nanoparticle Research. 14: 749. DOI 10.1007/s11051-012-0749-0

Ivask, A., Suarez, E., Patel, T., Boren, D., Ji, Zhaoxia, Holden, P., Telesca, D., Damoiseaux, R., Bradley, K., Godwin, H. 2012. Genome-wide bacterial toxicity screening uncovers the mechanisms of toxicity of cationic polystyrene nanomaterials. Environmental Science & Technology. 46: 2398-2405

Klanjscek, T., Nisbet, R.M., Priester, J.H. and Holden, P.A. 2012. Modeling physiological processes that relate toxicant exposure and bacterial population dynamics.. PLoS ONE. 7: e26955

Von Der Kammer, F., Ferguson, P. L., Holden, P. A., Masion, A., Rogers, K., Klaine, S. J., Koelmans, A. A., Horne, N., Unrine, J. M. 2012. Analysis of nanomaterials in complex matrices (environment and biota): general considerations and conceptual case studies. Environmental Toxiciology and Chemistry. 31(1): 32-49.

Holden, P.A. 2011. How do the microhabitats framed by soil structure impact soil bacteria and the processes that they regulate? In: (eds.) Ritz, K. and Young, I. “The Architecture and Biology of Soils: Life in Inner Space”, CABI. pp. 118-148.

Schimel, Joshua P., J.Å. Martin Wetterstedt, Patricia A. Holden, and Susan E. Trumbore 2011. Drying/rewetting cycles mobilize old C from deep soils from a California annual grassland. Soil Biology & Biochemistry, 43:1101-1103.

Thomas, C. R., George, S., Horst, A. M., Ji, Z., Miller, R. J., Peralta-Videa, J. R., Xia, T., Pokhrel, S., Mädler, L., Gardea-Torresdey, J. L., Holden, P. A., Keller, A. A., Lenihan, H. S., Nel, A. E., and Zink, J. I. 2011. Nanomaterials in the environment: from materials to high-throughput screening to organisms. ACS Nano. 5(1):13-20.

Cao, Y., Wu, C. H., Andersen, G. L., and Holden, P. A. “Chapter 5. Community Analysis-Based Methods”. 2011. in Hagedorn, C., Blanch, A. and J. Harwood (eds). Microbial Source Tracking: Methods, Applications, and Case Studies. Springer, New York. Pp. 251-282.

Sercu, B., Van De Werfhorst, L. C., Murray, J. L. S., Holden, P.A. 2011. Terrestrial sources homogenize bacterial water quality during rainfall in two urbanized watersheds in Santa Barbara,CA. Microb. Ecol. 62(3):574-583.

Sercu, B., Van De Werfhorst, L. S., Murray, J. L.S., Holden, P.A. 2011. Sewage exfiltration as a source of storm drain contamination during dry weather in urban watersheds. Environ. Sci. Technol. 45(17): 7151-7157.

Cao, Y. P., Van De Werfhorst, L. C., Sercu, B., Murray, J. L. S., Holden, P. A. 2011. Application of an integrated community analysis approach for microbial source tracking in a coastal creek. Environ. Sci. Technol. 45(17): 7195-7201.

Van De Werfhorst, L. S., Sercu, B., P.A. Holden. 2011. Comparison of the host specificities of two Bacteriodales quantitative PCR assays used for tracking human fecal contamination. Appl. Environ. Microbiol. 77(17):6258-60.

Ge, Y., Schimel, J. P., and P. A. Holden. 2011. Evidence for negative effects of TiO2 and ZnO nanoparticles on soil bacterial communities. Environmental Science & Technlogy. 45:1659-64.

Werlin, R., Priester, J. H., Mielke, R. E., Krämer, S., Jackson, S., Stoimenov, P. K., Stucky, G. D., Cherr, G. N., Orias, E., and Holden. P.A. 2011. Biomagnification of cadmium selenide quantum dots in a simple experimental microbial food chain. Nature Nanotechnology. 6:65-71.

Sercu, B., Van De Werfhorst, L. C., Murray, J. L. S., and Holden, P. A. 2011. Cultivation-independent analysis of bacteria in IDEXX quanti-tray/2000 fecal indicator assays. Applied & Environmental Microbiology. 77(2):627-633.

Clarke, S., Mielke, R. E., Neal, A., Holden, P., and Nadeau, J. L. 2010. Bacterial and mineral elements in an Arctic biofilm: a correlative study using fluorescence and electron microscopy. Microscopy and Microanalysis. 16(2):153-165.

Roux-Michollet, D. D., Schimel, J. P., and Holden, P. A. 2010. Pushing the limits for amplifying BrdU-labeled DNA encoding 16S rRNA: Taq DNA polymerase as the determining factor. Journal of Microbiological Methods. 83(3):312-316.

Litton, R. M., Ahn, J. H., Sercu, B., Holden, P. A., Sedlak, D. L., Grant, S. B. 2010. Evaluation of chemical, molecular, and traditional markers of fecal contamination in an effluent dominated urban stream. Environmental Science & Technology. 44: 7369-75.

Horst, A. M., Neal, A. C., Mielke, R. E., Sislian, P. R., Suh, W. H., Mädler, L., Stucky, G. D., and P. A. Holden. 2010. Dispersion of TiO2 nanoparticle agglomerates by Pseudomonas aeruginosa. Applied & Environmental Microbiology. 76(21): 7292-98.

Wu, C. H., Sercu, B., Van De Werfhorst, L. C., Wong, J., DeSantis, T. Z., Brodie, E. L., Hazen, T. C., Holden, P. A., Andersen, G. L. 2010. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS ONE. 5(6).

Zhang, Y., Shi, Y. F., Liou, Y-H., Sawvel, A. M, Sun, X. H., Cai Y., Holden, P.A., and Stucky, G. D. 2010. High performance separation of aerosol sprayed mesoporous TiO2 submicrospheres from aggregates via density gradient centrifugation. Journal of Materials Chemistry. 20(20):4162-4167.

Izbicki, John A., Swarzenski, Peter W., Reich, Christopher D., Rollins, Carole and Holden, Patricia A. 2009. Sources of fecal indicator bacteria in urban streams and ocean beaches, Santa Barbara, California. Annals of Environmental Science. 3: 139-178.

Ehrhardt, C. E., Sievert, S., Haymon, R., P.A. Holden. 2009. An improved method for nanogold labeled in situ hybridization using environmental scanning electron microscopy (ESEM). Journal of Microscopy. 236: 5-10.

Priester, J. P., P. K. Stoimenov, R. E. Mielke, S. M. Webb, C. Ehrhardt, J. P. Zhang, G. D. Stucky, and P. A. Holden.2009. Effects of soluble cadmium salts versus CdSe quantum dots on the growth of planktonic Pseudomonas aeruginosa. Environmental Science & Technology. 43:2589-2594.

Sercu, B., L. C. Van De Werfhorst, J. Murray, and P. A. Holden. 2009. Storm drains are sources of human fecal pollution during dry weather in three urban southern California watersheds. Environmental Science & Technology. 43:293-298.

Cao, Yiping, Green, Peter G., and Patricia A. Holden. 2008. Microbial community composition and denitrifying enzyme activities in salt marsh sediments. Appl. Environ. Microbiol. 74:7585-95.

Xiang, S.R., A. Doyle P. A. Holden, J. P. Schimel. 2008. Drying and rewetting effects on C and N mineralization and microbial activity in surface and subsurface California grassland soils. Soil Biology & Biochemistry. 40(9):2281-2289.

Conti, J.A., K. Killpack, G. Gerritzen, L. Huang, M. Mircheva, M. Delmas, B. Herr Harthorn, R. P. Appelbaum and P. A. Holden. 2008. Health and safety practices in the nanomaterials workplace: results from an international survey. Environmental Science & Technology.

Nadeau, J. L., J. Priester, G. D. Stucky, P. A. Holden. 2008. “Bacterial Interactions with CdSe Quantum Dots and Environmental Implications” In Grassian, V. H. “Nanoscience and Nanotechnology: Environmental and Health Impacts”, Wiley & Sons, NY.

Ehrhardt, C. J., R. M. Haymon, M. G. LaMontagne and P. A Holden. 2007. Evidence for a high temperature subseafloor archaeal biosphere beneath ridge flank abyssal hills. Environmental Microbiology.

Holden, P.A. and A. M. Horst. 2007. Microbes. Encyclopedia of Tidepools and Rocky Shores, Gaines, S. and Denny, M. (eds). U.C. Berkeley Press.

Priester, J.H., Horst, A. M., Van De Werfhorst, L.C., Saleta, J. L., Mertes, L.A. K., and P. A. Holden. 2007. Enhanced visualization of microbial biofilms by staining and environmental scanning electron microscopy. J. Microbiological Methods 68: 577-587.

Cao, Y., G.N. Cherr, A.L. Córdova-Kreylos, T.W.-M. Fan, P.G. Green, R.M. Higashi, M.G. LaMontagne, K.M. Scow, C.A. Vines, J. Yuan and P.A. Holden. 2006. Relationships between sediment microbial communities and pollutants in two California salt marshes. Microbial Ecology, 52:619-633.

Ostomel, T., P. Stoimenov, P.A. Holden, H. Alam and G. Stucky. 2006. Host-guest composites for induced hemostasis and therapeutic healing in traumatic injuries. Journal of Thrombosis and Thrombolysis 22:55-67.

Cordova-Kreylos, A.L., Y Cao, P. G. Green, H. M. Hwang, K. Kuivila, M. G. LaMontagne, L. C. Van De Werfhorst, P. A. Holden and K. M. Scow. 2006. Diversity, composition and geographical distribution of microbial communities in California salt marsh sediments. Applied & Environmental Microbiology 72: 3357-3366.

Priester, J. H., S.G. Olson, S. M.Webb, M. P. Neu, L. E. Hersman, and P. A. Holden. 2006. Enhanced exopolymer production and chromium stabilization in Pseudomonas putida unsaturated biofilms. Applied & Environmental Microbiology 72: 1988-1996.

Steinberger, R.E. and P. A. Holden. 2005. Extracellular DNA in single- and multiple-species unsaturated biofilms. Applied & Environmental Microbiology. 71:5404-5410.

Holden, P. A. and N. Fierer. 2005. Microbial processes in the vadose zone. Vadose Zone Journal. 4:1-21.

Holden, P. A. and N. Fierer. 2004. Vadose zone: microbial ecology. Encyclopedia of Soils in the Environment, Academic Press.

LaMontagne, M.G., I. Leifer, S. Bergmann, L. Van De Werfhorst and P. A. Holden. 2004. Bacterial diversity in marine hydrocarbon seep sediments. Environmental Microbiology. 6:799-808.

Steinberger, R. E. and P.A. Holden. 2004. Macromolecular composition of unsaturated Pseudomonas aeruginosa biofilms with time and carbon source. Biofilms 1:37-47.

Field, K., E. C. Chern, L. K. Dick, J. Fuhrman, J. Griffith, P. A. Holden, M. G. LaMontagne, J. Le, B. Olson and M. T. Simonich. 2003. A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. Journal of Water and Health. 1:181-194.

Fierer, N., A. S. Allen, J. P. Schimel and P.A. Holden. 2003. Controls on microbial CO2 production in surface and subsurface soil horizons. Global Change Biology 9: 1322-1332.

LaMontagne, M.G., J. P. Schimel and P. A. Holden. 2003. Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCR-amplified 16S rDNA. Microbial Ecology 46:216-227.

Steets, B. and P. A. Holden. 2003. A mechanistic model of runoff-associated fecal coliform fate and transport through a coastal lagoon. Water Research 37: 589-608.

Fierer, N., J. P. Schimel and P. A. Holden. 2003. Influence of drying-rewetting frequency on soil bacterial community structure. Microbial Ecology 45: 63-71.

LaMontagne, M. G. and P. A. Holden. 2003. Comparison of free-living and particle-associated bacterial communities in a coastal lagoon. Microbial Ecology 46: 228-237.

Fierer, N., J. P. Schimel and P. A. Holden. 2003. Variations in microbial community composition through two soil depth profiles. Soil Biology & Biochemistry 35: 167-176.

Saleta, J. and P.A. Holden. 2002. Imaging soil bacteria in an environmental scanning electron microscope. Microscopy and Microanalysis 8: (Supplement 2, Proceedings).

Holden, P. A., M.G. LaMontagne, A.K. Bruce, W. G. Miller and S. E. Lindow. 2002. Assessing the role of Pseudomonas aeruginosa surface-active gene expression in hexadecane biodegradation in sand. Applied & Environmental Microbiology 68:2509-18.

Steinberger, R. E., A. R. Allen, H. G. Hansma and P. A. Holden. 2002. Elongation correlates with nutrient deprivation in Pseudomonas aeruginosa unsaturated biofilms. Microbial Ecology 43:416-23.

LaMontagne , M.G., F.C. Michel Jr., P.A. Holden and C.A. Reddy. 2002. Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis. Journal of Microbiological Methods 49:255-64.

Holden, P. A., L. E. Hersman and M.K. Firestone. 2001. Water content mediated microaerophilic toluene biodegradation in arid vadose zone materials. Microbial Ecology 42(3):256-66.

Holden, P. A. and D. Pierce. 2001. New environmental scanning electron microscopic (ESEM) observations of bacteria on simulated soil substrates. Microscopy & Microanalysis, 7 (Suppl 2: Proceedings): 736-7.

Holden, P.A. Biofilms in Unsaturated Environments. 2001. in Doyle, R. Methods of Enzymology, v. 337: 125-143

Auerbach, I. D., C. Sorensen, H. G. Hansma and P.A. Holden. 2000. Physical morphology and surface properties of unsaturated Pseudomonas putida biofilms. Journal of Bacteriology 182:3809-3815.

Hansma, H. G., L. I. Pietrasanta, I. D. Auerbach, C. Sorenson, R. Golan, and P. A. Holden. 2000. Probing biopolymers with the atomic force microscope: a review. Journal of Biomaterials Science, Polymer Edition. 11(7):675-684.

Holden, P. A., J. R. Hunt and M. K. Firestone. 1997. Toluene diffusion and reaction in unsaturated Pseudomonas putida biofilms. Biotechnology & Bioengineering 56:656-670.

Holden, P. A., L. J. Halverson and M. K. Firestone. 1997. Water stress effects on toluene biodegradation by Pseudomonas putida. Biodegradation. 8:143-151.

Holden, P. A. and M. K. Firestone. 1997. Soil microorganisms in soil clean-up: How can we improve our understanding? Journal of Environmental Quality 26 (1): 32-40.

Holden, P. A., M.K. Firestone and J.R. Hunt. 1995. Unsaturated zone gas-phase biodegradation: the importance of water potential. 50th Purdue Industrial Waste Conference Proceedings, Ann Arbor Press, Chelsea, MI. pp. 113-127.

Hunt, J. R., P. A. Holden and M. K. Firestone. 1995. Coupling transport and biodegradation of VOCs in surface and subsurface soils. Environmental Health Perspectives. vol. 103, Supplement 5. pp. 75-78.