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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

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Publications

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

• Holden, P.A. and A. M. Horst. (2007, in press). Microbes. Encyclopedia of the Rocky Intertidal, 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., N. Fierer. 2005. Vadose zone microbial processes, Vadose Zone Journal. 4:1-21.

• Holden, P. A., 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, 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, Katharine, Eunice C. Chern, Linda K. Dick, Jed Fuhrman, John Griffith, Patricia A. Holden, Michael G. LaMontagne, Joann Le, Betty Olson, and Michael 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 a California grassland as assessed by terminal restriction fragment length polymorphisms of PCR-amplified 16S rDNA. Microbial Ecology 46:216-227.

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

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

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

• Fierer, N., J. P. Schimel, P. A. Holden. 2002. Variations in microbial community composition through two soil depth profiles. Soil Biol. Biochem. 35: 167-176.

• Holden, Patricia A., LaMontagne, M.G., Bruce, A.K., Miller, W. G., and S. Lindow. 2002. Assessing the role of Pseudomonas aeruginosa surface-active gene expression in hexadecane biodegradation in sand. Appl. Environ. Microbiol. 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. Microb. Ecol. 43(4; online publication)

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

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

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

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

• Auerbach, I. D., Sorensen, C., Hansma, H. and P.A. Holden. 2000. Physical morphology and surface properties of unsaturated Pseudomonas putida biofilms. J. 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. J. of Biomaterials Sci., Polymer Edition. 11(7):675-684.

• Holden, Patricia A., James R. Hunt and Mary K. Firestone. 1997. Toluene diffusion and reaction in unsaturated Pseudomonas putida biofilms. Biotechnol. & Bioengin. 56:656-670.

• Holden, Patricia A., Larry J. Halverson and Mary K. Firestone. 1997. Water stress effects on toluene biodegradation by Pseudomonas putida. Biodegradation. 8:143-151.

• Holden, Patricia A. and Mary K. Firestone. 1997. Soil microorganisms in soil clean-up: How can we improve our understanding? J. Environ. Qual. 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, James R., Patricia A. Holden, and Mary 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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PhD Students

Name	Home	Research Topic
Daniel Brooks
Rachel Steinberger
Yiping Cao