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RESEARCH INTERESTS
General Research Statement
Bacteria are both agents of environmental restoration and agents of environmental degradation. For the former, bacteria in nature cycle nutrients and transform pollutants; our interest is in developing a predictive understanding of bacterial distribution and function in natural and polluted environments. For the latter, bacteria in human waste are indicative of disease-causing organisms; we want to know the relationships between fecal indicator bacteria and the presence of human waste, the value of culture-independent methods for detecting wastes and pathogens, and the transport and fate of fecal bacteria in the environment.
Current interests and projects include:
- Vadose zone microbial ecology
o Biofilms in unsaturated environments
o Microbial extracellular polymeric substances (EPS)
o Vadose zone saccharides
o Community composition, diversity, function
o Water stress
o Environmental scanning electron microscopy (ESEM) of soils and soil microbes
o Microsite phenomena
o Cell-cell communication in dry systems
o Reaction-diffusion modeling
- Coastal and estuarine bacterial ecology
o Pollutant interactions with bacterial communities in estuarine ecosystems
o Markers of human sewage in aquatic bacterial communities
o Bacterial communities as tracers for other pollutants
o Relationships between urbanization and coastal bacteriological water quality
- Bacterial interactions with nanoparticles
o Bacterial uptake and decomposition of CdSe quantum dots, TiO2 and other nanoparticles
o Toxicity of engineered nanoparticles to environmental bacteria
o Planktonic and biofilm bacterial interactions with nanoparticles
- Petroleum bioremediation in sands, soils, sediments and the sea surface microlayer
o Mechanisms, including roles of biosurfactants and bioemulsifiers
o Mass transfer versus physiological controls on biodegradation rates
Publications
Holden, P.A. 2011 (in press). How do the microhabitats framed by soil structure impact soil bacteria and the processes that they regulate? In: Ritz, K. and Young, I. “The Architecture and Biology of Soils: Life in Inner Space”, Ritz, K. CABI
Cao, Y., Wu, C. H., Andersen, G. L., and Holden, P. A. “Chapter 5. Community Analysis-Based Methods”. 2011 (in press). in Hagedorn, C., Blanch, A. and J. Harwood (eds). Microbial Source Tracking: Methods, Applications, and Case Studies. Springer.
Ge, Y., Schimel, J. P., and P. A. Holden. 2011 (in press). Evidence for negative effects of TiO2 and ZnO nanoparticles on soil bacterial communities. Environmental Science & Technlogy.
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.
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Holden Lab
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Phd Students
Name |
Contact |
Ngoc Hoang |
|
Allison Horst |
|
Randy Mielke |
|
Ning Jiang |