Curriculum Vitae

field

William E. Holben
Professor
Cellular, Molecular, and Microbial Biology  & Systems Ecology Programs
Division of Biological Sciences, University of Montana
Missoula, Montana 59812-1002
Phone: (406) 396-9268, Fax: (406) 243-4184

Table of Contents

Education

  • Ph.D., Cell & Molecular Biology, State University of New York at Buffalo, Buffalo, NY, 1985
  • M.S., Biology, State University of New York at Buffalo, Buffalo, NY, 1982
  • B.S., Biology, State University of New York at Fredonia, Fredonia, NY, 1979

Professional Experience

05/01-present

Professor, Cellular, Molecular and Microbial Biology Program and Systems Ecology Program, Division of Biological Sciences, The University of Montana, Missoula, MT

04/15-present

Affiliate Scientist, CENPERM (Center for Permafrost Studies), University of Copenhagen and Geological Survey of Greenland and Denmark

06/06-present

Director, Office of Research and Educational Opportunities for Students (OREOS).

07/15-present

Directory, Microbial Research in Greenland & Denmark (MRGD); a National Science Foundation International Research Experience for Students (NSF-IRES) Project.

04/09-03/16

Director, Integrative Multicultural Summer Undergraduate Research Experience (IM-SURE); a National Science Foundation Research Experience for Students (NSF-REU) Site Project.

09/05-09/13

Director, Montana—Ecology of Infectious Diseases (M-EID) Program; a National Science Foundation Integrative Graduate Education and Research Traineeship (NSF-IGERT) Program.

06/06-09/12

Director, Montana Integrative Learning Experience for Students (MILES) Program; A Howard Hughes Medical Institute Undergraduate Science Education Program.

09/95-04/01

Associate Professor, Microbial Ecology Program, Division of Biological Sciences, University of Montana, Missoula, MT.

08/93-08/95

Research Scientist, Department of Environmental Microbiology, The Agouron Institute, La Jolla, CA.

12/88-08/93

Research Assistant Professor, Center for Microbial Ecology (CME) and Dept. of Crop and Soil Sciences, Michigan State University; and Group Leader for the CME-JRDC (Japanese Research Development Corporation) Joint Research Project on Molecular Evolution of Catabolic Pathways.

11/85-12/88

Post-doctoral fellow, Michigan State University, Dept. of Crop and Soil Sciences and DOE Plant Research Laboratory, East Lansing, MI.

Research Interests

Microbiome structure and function in animals, plants and insects; interactions between microbial communities, natural environments, and human systems; exploring the role of the microbial community in the success of invasive weeds; fate and transport of microbes in the environment; microbial biomarkers for human, plant and animal studies; microbial community roles and responses in climate change scenarios.

Awards, Honors, & Synergistic Activities

Review Panel Member-National Science Foundation Partnerships in International Research and Education Program. January 28-30, 2015, Arlington, VA.

•NIH Study Section-Nutrigenetics and Nutrigenomics Approaches for Nutrition Research (R01) program. October 14-16, 2014, Bethesda, MD

•NIH Study Section-Clinical Research and Field Studies of Infectious Diseases Study Section program. February 26-28, 2014, Bethesda, MD

•Review Panel Member-National Science Foundation—International Research Experience for Students Program. December 8-10, 2013, Arlington, VA.

•Review Panel member-National Institute of Environmental Health Sciences. April 25-27, 2012, Research Triangle Park, NC.

• Local Organizing Committee Member, 13th Int’l Symposium on Microbial Ecology; Aug. 2010, Seattle, WA.

• Instructor for HHMI-SEA Phage Genome Research Initiative course for undergraduates.

• Editorial Board Member, Microbial Ecology Journal, 1997-2006

• Editorial Board Member, Applied and Environmental Microbiology, 2002-2006

• Director—Inland Northwest Research Alliance (DOE) Subsurface Science Graduate Program, 2006; Co-Instructor in full-year Core Course, 2004 -2006.

• Session Chair: 5th Int’l Symposium on Subsurface Micro., Copenhagen, Denmark, 2002

• Review Panel Manager, U.S.D.A. Soils and Soil Biology Program, 2000

• Review Panel Member, DOE Natural and Accelerated Bioremediation Program, 1998

• Review Panel Member, NSF Ecological & Evolutionary Physiology Program, 1997

• Review Panel Member, U.S.D.A. Soils and Soil Biology Program, 1995 & 1996

• AIST Guest Researcher, Nat’l Inst. for Resources and the Environment, Tsukuba, Japan, 1995

• Review Panel Member, EPA-Biological Control Agent Risk Assessment Program, 1994

• Department of Energy Director’s Certificate of Appreciation, 1994

• Co-mentor several Ph.D. students in interdisciplinary projects

• Co-developer of new graduate and undergraduate degree options in Microbial Ecology at UM.

• Chair of Biological Sciences Curriculum Committee, 10 years.

• Instructor in international collaborative workshops for multi-national research training and collaboration: Egypt 1995 & 2001, Spain 2003, Denmark 2010 & 2012.

• Multi-national research collaborations with the Geological Survey of Denmark and Greenland; Chuo University, Japan; and a commercial microbial research company, Alimetrics, in Helsinki, Finland.

Professional Society Memberships

  • International Society for Microbial Ecology
  • American Society for Microbiology
  • American Association for the Advancement of Science

Publications (Last 10 Years)

Morales S.E. and W.E. Holben. 2014. Simulated geologic carbon storage leak reduces bacterial richness and alters bacterial community composition in surface soil. Soil Biology and Biochemistry. DOI: 10.1016/j.soilbio.2014.05.018

Hjelmsø, M.H., L.H. Hansen, J. Bælum, L. Felda, W.E. Holben, and C.S. Jacobsen. 2014. High Resolution Melt analysis for rapid comparison of bacterial community composition.  Appl. Environ. Microbiol. doi: 10.1128/AEM.03923-13

Morales, S.E., and W.E. Holben. 2013. Functional response of a near-surface soil microbial community to a simulated underground CO2 storage leak. PLOS ONE DOI: 10.1371/ journal.pone.0081742

Rout M.E., Chrzanowski T.H., Westlie T.K., Deluca T.H., Callaway R.M., Holben W.E. 2013. Bacterial endophytes enhance competition by invasive plants. Am J Bot. 100:1726–1737; doi: 10.3732/ajb.1200577.

See, W., W.H. Edwards, S. Dauwalter, C. Almendra, M.D. Kardos, J.L. Lowell, R. Wallen, S.L. Cain, W.E. Holben, and G. Luikart. 2012. Yersinia enterocolitica: An unlikely cause of positive Brucellosis tests in Greater Yellowstone Ecosystem bison (Bison bison). J. Wildl. Dis. 48:537-541.

Stibal, M., A. Jensen, J. Bælum, S.R. Sørensen, W.E. Holben, C.S. Jacobsen. 2012. Microbial degradation of 2,4-dichlorophenoxyacetic acid on the Greenland ice sheet. Appl. Environ. Microbiol. 78:5070-5076; doi: 10.1128/AEM.00400-12.

Pollock, J.L., L.A. Kogan, A.S. Thorpe and W.E. Holben. 2011. (±)-Catechin, a root exudate of the invasive Centaurea stoebe Lam. (spotted knapweed) exhibits bacteriostatic activity against multiple soil bacterial populations. J. Chem. Ecol. 37:1044-1053. DOI 10.1007/s10886-011-0005-6.

Holben, W.E. 2011. GC fractionation allows comparative total microbial community analysis, enhances diversity assessment, and facilitates detection of minority populations of bacteria. Chapter 23 in de Bruijn, F.J. (ed.) Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. John Wiley & Sons. ISBN: 978-0-470-64479-9.

Morales, S.E. and W.E. Holben. 2011. Empirical testing of 16S PCR primer pairs reveals variance in target specificity and efficacy not suggested by in silico analysis. Chapter 17 in de Bruijn, F.J. (ed.) Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. John Wiley & Sons. ISBN: 978-0-470-64479-9.

Morales, S.E. and W.E. Holben. 2011. Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters. Chapter 16 in de Bruijn, F.J. (ed.) Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. ISBN: 978-0-470-64719-6.

Morales S.E. and W.E. Holben. 2011. Linking bacterial identities and ecosystem processes: Can ‘omic’ analyses be more than the sum of their parts? FEMS Microbiol. Ecol. 75:2-16.

Ball, P.N., M.D. MacKenzie, T.H. DeLuca, and W.E. Holben. 2010. Wildfire and charcoal enhance nitrification and ammonium-oxidizing bacterial abundance in dry montane forest soils. J. Environ. Qual. 39:1243-1253 doi:10.2134/jeq2009.0082.

Morales, S.E., T. Cosart, and W.E. Holben. 2010. Bacterial gene abundances as indicators of greenhouse gas emission in soils. ISME J. 4, 799–808; doi:10.1038/ismej.2010.8.

Bælum, J; C.S. Jacobsen, and W.E. Holben. 2010. Comparison of 16S rRNA gene phylogeny and functional tfdA gene distribution in thirty-one different 2,4-dichlorophenoxyacetic acid and 4-chloro-2-methylphenoxyacetic acid degraders. System. Appl. Microbiol. 10.1016/j.syapm.2010.01.001.

Lowell, J.L., N. Gordon, D. Engstrom, J.A. Stanford, W.E. Holben and J.E. Gannon. 2009. Habitat heterogeneity and associated microbial community structure in a small-scale floodplain hyporheic flow path. Microb. Ecol. 58:611–620.

Kinnersley MA, W.E. Holben, and F. Rosenzweig 2009. E Unibus Plurum: genomic analysis of an experimentally evolved polymorphism in Escherichia coli. PLoS Genet. 5(11): e1000713. doi:10.1371/journal.pgen.1000713

Pollock, J.L., R.M. Callaway, G.C. Thelen, and W.E. Holben. 2009. Catechin–metal interactions as a mechanism for conditional allelopathy by the invasive plant Centaurea maculosa. J. Ecol. 97:1234–1242. DOI: 9710.1111/j.1365-2745.2009.01553.x

Feris, K.P., P.W. Ramsey, S.M. Gibbons, M.C. Rillig, J.N. Moore, J.E. Gannon, and W.E. Holben. 2009. Hyporheic microbial community development is a sensitive indicator of metal contamination. Environ. Sci. Technol. 43: 6158–6163.

Adams, S.M., A.S. Adams, and W.E. Holben. 2009. Tri-Trophic Linkages in Disease: Pathogen Transmission to Rainbow Trout Through Stonefly Prey. Environ. Entomol. 38:1022-1027.

Gordon, N. S., A. Valenzuela, S.M. Adams, P.W. Ramsey, J.L. Pollock, W.E. Holben, & J.E. Gannon. 2009. Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana floodplain sediment and forest soil. Int J Syst. Evol. Microbiol. 59:1720-1726. 

Morales, S.E., and W.E. Holben. 2009. Empirical testing of 16S PCR primer pairs reveals variance in target specificity and efficacy not suggested by in silico analysis. Appl. Environ. Microbiol. 75:2677-2683.

Morales, S.E., T.F. Cosart, J.V. Johnson and W.E. Holben. 2009. Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters. Appl. Environ. Microbiol. 75: 668-675.

Ramamoorthy S., J.S. Piotrowski, H.W. Langner, W.E. Holben, M.J. Morra, and R.F. Rosenzweig. 2009. Ecology of sulfate-reducing bacteria in an iron-dominated, mining-impacted freshwater sediment. J. Environ. Qual. 38:675-84.

Morales, S.E., T. Cosart, J.V. Johnson, and W.E. Holben. 2008. Supplemental programs for enhanced recovery of data from the DOTUR application. J. Microbiol. Methods 75:572-575.  

Inderjit, J.L. Pollock, R.M. Callaway, and W.E. Holben. 2008. Phytotoxic Effects of (±)-catechin in vitro, in soil, and in the field. PLoS ONE 3(7):e2536. <http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002536>

Adams, A.S., D.L. Six, S.A. Adams, and W.E. Holben. 2008. In vitro interactions between yeasts and bacteria and the fungal symbionts of the mountain pine beetle (Dendroctonus ponderosae). Microb. Ecol. 56:460-466.

Bælum, J. M.H. Nicolaisen, W.E. Holben, B.W. Strobel, J. Sørensen and C.S. Jacobsen. 2008. Direct analysis of tfdA gene expression by indigenous bacteria in phenoxy acid amended agricultural soil. ISME J. 2:677-687.

Jacobsen, C.S., and W.E. Holben. 2007. Quantification of mRNA in Salmonella sp. seeded soil and chicken manure using magnetic capture hybridization RT-PCR. J. Microbiol. Methods. 69:315-321.

Bender. M, W.E. Holben, S.J. Sørensen, and C.S. Jacobsen. 2007. Use of a PNA probe to block DNA-mediated PCR product formation in prokaryotic RT-PCR. BioTechniques 42:609-614.

Mummey, D., W. Holben, J. Six, and P. Stahl. 2006. Spatial stratification of soil bacterial populations in aggregates of diverse soils. Microb. Ecol. 51:404-411.

Ramsey, P.W., K.P. Feris, M.C. Rillig, W.E. Holben, and J.E. Gannon. 2006. Choice of methods for soil microbial community analysis: PLFA maximizes power compared to CLPP and PCR-based approaches. Pedobiologia. 50:275-280.

DeLuca, T.H., M. D. MacKenzie, M. J. Gundale, and W. E. Holben. 2006. Wildfire-produced charcoal directly influences nitrogen cycling in Ponderosa Pine forests. Soil Sci. Soc. Am. J. 70:448–453.

Ramsey, P.W., M.C. Rillig, K.P. Feris, N.S. Gordon, J. N. Moore, W.E. Holben, and J.E. Gannon. 2005. Relationship between communities and processes; New insights from a field study of a contaminated ecosystem. Ecology Letters 8: 1201-1210.

Kovacik, W.P. Jr., K. Takai, M.R. Mormile, J.P. McKinley, F.J. Brockman, J.K. Fredrickson and W.E. Holben. 2006. Molecular analysis of deep subsurface cretaceous rock indicates abundant Fe(III)- and So-reducing bacteria in a sulfate-rich environment. Environ. Microbiol. 1:141-155.

Mummey, D.L., M.C. Rillig and W.E. Holben. 2005. Neighboring plant influences on arbuscular mycorrhiza fungal community composition as assessed by T-RFLP analysis. Plant and Soil: 271:83-90.

Driver J.D., W.E. Holben, M.C. Rillig. 2004. Characterization of glomalin as a hyphal wall component of arbuscular mycorrhizal fungi. Soil Biol. Biochem. 37:101-106.

Holben, W.E., K.P. Feris, A. Kettunen, and J.H.A. Apajalahti. 2004. GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 70:2263-2270.

Feris, K.P., P.W. Ramsey, M. Rillig, J.N. Moore, J.E. Gannon, and W.E. Holben. 2004a. Determining rates of change and evaluating group-level resiliency differences in hyporheic microbial communities in response to fluvial heavy metal deposition. Appl. Environ. Microbiol. 70:4756-4765.

Feris, K. P. Ramsey, C. Frazar, M. Rillig, J.N. Moore, J.E. Gannon, and W.E. Holben. 2004b. Seasonal dynamics of shallow hyporheic zone microbial community structure along a heavy metal contamination gradient. Appl. Environ. Microbiol. 70:2323-2331.

Callaway, R.M., G.C. Thelen, A. Rodriguez, and W.E. Holben. 2004. Soil biota and exotic plant invasion. Nature 427:731-733.

Feris, K. P. Ramsey, C. Frazar, J.N. Moore, J.E. Gannon, and W.E. Holben. 2003a. Differences in hyporheic zone microbial community structure along a heavy metal contamination gradient. Appl Environ. Microbiol. 69:5563-5573.

Apajalahti. J.H.A., A.Kettunen, P.H. Nurminen, H. Jatila, and W.E. Holben. 2003. Selective plating underestimates abundance and shows differential recovery of Bifidobacterial species from human feces. Appl. Envir. Microbiol. 69:5731-5735.

Feris, K.P., P.W. Ramsey, C. Frazar, M.C. Rillig, J.E. Gannon, and W.E. Holben. 2003b. Structure and seasonal dynamics of hyporheic zone microbial communities in free-stone rivers of the western United States. Microb. Ecol. 46:200-215.

Takai, T., M.R. Mormile, J.P. McKinley, F.J. Brockman, W.E. Holben, W.P. Kovacik, and J.K. Fredrickson. 2003. Shifts in archaeal communities associated with lithological and geochemical variations in subsurface Cretaceous rock. Environ. Microbiol. 5:309-320.

Holben W.E., P. Williams, M.A. Gilbert, M. Saarinen, L.K. Sarkilahti, J.H.A. Apajalahti. 2002. Phylogenetic analysis of intestinal microflora indicates a novel Mycoplasma phylotype in farmed and wild salmon. Microb. Ecol. 44:175-85.

Apajalahti, J.H., H. Kettunen, A. Kettunen, W.E. Holben, P.H. Nurminen, N. Rautonen, M. Mutanen. 2002. Culture-independent microbial community analysis reveals that inulin in the diet primarily affects previously unknown bacteria in the mouse cecum. Appl Environ. Microbiol. 68:4986-4995.

Apajalahti, J.H.A., A. Kettunen, M.R. Bedford, and W.E. Holben. 2001. Percent G+C profiling accurately reveals diet-related differences in the gastrointestinal microbial community of broiler chickens. Appl. Environ. Microbiol. 67:5656-5666.

DeFlaun, M, D. Balkwill, J. Chen, M. DeFlaun, F. Dobbs, H. Dong, J. Fredrickson, M. Fuller, M. Green, T. Ginn, T. Griffin, W. Holben, S. Hubbard, W. Johnson, P. Long, B. Mailloux, E. Majer, M. McInerney, C. Murray, T. Onstott, T. Phelps, T. Scheibe, D. Swift, D. White, and F. Wobber. 2001. Breakthroughs in Field-scale Bacterial Transport. Eos. 38:417:425.

DeFlaun, M.F., M.E. Fuller, P. Zhang, W.P. Johnson, B.J. Mailloux, W.E. Holben, W.P. Kovacik, D.L. Balkwill, and T.C. Onstott. 2001. Comparison of methods for monitoring bacterial transport in the subsurface. J. Microbiol. Methods 47:219-231.

Johnson, W. P., P. Zhang, M. E. Fuller, T. D. Scheibe, B. J. Mailloux, T. C. Onstott, M. F. DeFlaun, S. S. Hubbard, J. Radtke, W. P. Kovacik, and W. Holben. 2001. Ferrographic tracking of bacterial transport in the field at the Narrow Channel focus area, Oyster, VA. Environ. Sci. Technol. 35:182-191.

Holben, W.E. and P.H. Ostrom. 2000. Monitoring bacterial transport by stable isotope enrichment of cells. Appl. Environ. Microbiol. 66:4935-4939.

Di Meo, C.A., A.E. Wilbur, W.E. Holben, R.A. Feldman, R.C. Vrijenhoek, and S.C. Cary. 2000. Genetic variation among endosymbionts of widely distributed vestimentiferan tubeworms. Appl. Envir. Microbiol. 66: 651-658.

Apajalahti, J.H.A., L.K. Särkilahti, B.R.E. Mäki, J.P. Heikkinen, P.H. Nurminen, and W.E. Holben. 1998. Effective recovery of bacterial DNA and %G+C based analysis of community structure in the gastrointestinal tract of broiler chickens. Appl. Environ. Microbiol. 64:4084-4088.

Kieft, T.L. E.M. Murphy, D.L. Haldeman, P.S. Amy, B.N. Bjornstad, E.V. McDonald, D. B. Ringelberg, D.C. White, J. Stair, R.P. Griffiths, T.C. Gsell, W.E. Holben, and D.R. Boone. 1998. Microbial transport, survival, and succession in a sequence of buried sediments. Microb. Ecol. 36:336-348

Santo Domingo, J.W., M.G. Kaufman, M.J. Klug, W.E. Holben, D. Harris and J.M. Tiedje. 1998. Influence of diet on the structure and function of the bacterial hindgut community of crickets. Molec. Ecol. 7:761-767.

Holben, W.E., K. Noto, T. Sumino and Y. Suwa. 1998. Molecular analysis of bacterial communities in a three-compartment granular activated sludge system indicates community-level control by incompatible nitrification processes. Appl. Environ. Microbiol. 1998 64: 2528-2532.

Nakatsu, C.H., F. Fukomori, R.R. Fulthorpe, R.P. Hausinger, W.E. Holben, Y. Kamagata, R. Korona, R.E. Lenski, O.V. Maltseva, V.G. Matheson, C. McGowan, Y. Suwa, J.M. Tiedje, N.L. Tonso, E.M. Top, A.D. Wright and L.J. Forney. 1997. Genetic diversity of 2,4-dichlorophenoxyacetic acid (2,4-D) catabolic genes. pp 197-206 in K. Horikoshi, M. Fukuda and T. Kudo (eds.) Microbial Diversity and Genetics of Biodegradation. Japan Scientific Societies Press, Tokyo, Japan.

Gsell, T.C., W.E. Holben and R.M. Ventullo. 1997. Characterization of the sediment bacterial community in groundwater discharge zones of an alkaline fen: a seasonal study. Appl. Environ. Microbiol. 63:3111-3118.

DeFlaun, M.F., C.J. Murray, W. Holben, T. Scheibe, A. Mills, T. Ginn, T. Griffin, E. Majer and J.L. Wilson. 1997. Preliminary observations on bacterial transport in a coastal plain aquifer. FEMS Microbiol. Rev. 20:473-487 .

Schleper, C., W.E. Holben and H.-P. Klenk. 1997. Recovery of crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments. Appl. Environ. Microbiol. 63:321-323

Holben, W.E. 1997. Isolation and purification of bacterial community DNA from environmental samples. pp 431-436 in C.H. Hurst, G.R. Knudsen, M.J. McInerny, L.D. Stetzenbach and M.V. Walter (eds.) Manual of Environmental Microbiology. American Society for Microbiology Press, Washington, D.C.

Matheson, V.G., L.J. Forney, Y. Suwa, C.H. Nakatsu, A.J. Sexstone and W.E. Holben. 1996. Evidence for acquisition in nature of a chromosomal 2,4‑dichlorophenoxyacetic acid /-ketoglutarate dioxygenase gene by different Burkholderia spp. Appl. Environ. Microbiol. 62:2457-2463.

Suwa, Y., A.D. Wright, F. Fukomori, K.A. Nummy, R.P. Hausinger, W.E. Holben, and L.J. Forney. 1996. Characterization of a chromosomally encoded 2,4‑dichlorophenoxyacetic acid/a-ketoglutarate dioxygenase from Burkholderia sp. RASC. Appl. Environ. Microbiol. 62:2464-2469.

Holben, W.E. and D. Harris. 1995. DNA-based monitoring of total bacterial community structure in environmental samples. Molec. Ecol. 4:627-631.

Fulthorpe, R.R., C. McGowan, O.V. Maltseva, W.E. Holben and J.M. Tiedje. 1995. 2,4‑dichlorophenoxyacetic acid-degrading bacteria contain mosaics of catabolic genes. Appl. Environ. Microbiol. 61:3274-3281.

Top, E.M., W.E. Holben and L.J. Forney. 1995. Characterization of diverse 2,4‑D degradative plasmids isolated from soil by plasmid capture. Appl. Environ. Microbiol. 61:1691-1698.

Ka. J.O., P. Burauel, J.A. Bronson, W.E. Holben and J.M. Tiedje. 1995. DNA probe analysis of the microbial community selected in the field by long-term 2,4‑D application. Soil Sci. Soc. Am. J. 59:1581-1587.

Tonso, N.L., V.G. Matheson and W. E. Holben. 1995. Polyphasic characterization of a suite of bacterial isolates capable of degrading 2,4‑D. Microb. Ecol. 30:3-24.

Holben, William E. 1994. Isolation and purification of bacterial DNA from soil, p. 727-751. In R.W. Weaver et al. (ed.) Methods of Soil Analysis, Part 2. Microbiological and Biochemical properties. SSSA Book Series no. 5. Soil Science Society of America, Madison, WI.

Fulthorpe, R., J. Dunbar, B. Holben, L. Forney, O. Maltseva, G. Matheson, C. McGowan, P. Oriel, A. Rhodes, H. Takami, E. Top, J. Tiedje, N. Tonso, T. Vallaeys and A. Wright. 1994. 2,4-Dichlorophenoxyacetate degraders in the real world, do we know who they are? pp 85-99 In Proceedings of the Japanese Research and Development Corporation-Michigan State University Joint Workshop on Microbial Evolution and Biodegradation. Tokyo, Japan

Ka, J.O., W.E. Holben and J.M. Tiedje. 1994. Genetic and phenotypic diversity of 2,4‑D degrading bacteria isolated from 2,4‑D treated field soils. Appl. Environ. Microbiol. 60:1106-1115.

Ka, J.O., W.E. Holben and J.M. Tiedje. 1994. Use of gene probes to aid recovery and identification of functionally dominant 2,4‑D degrading populations in soil. Appl. Environ. Microbiol. 60:1116-1120.

Ka, J.O., W.E. Holben and J.M. Tiedje. 1994. Analysis of competition in soil among 2,4‑D degrading bacteria. Appl. Environ. Microbiol. 60:1121-1128.

Tiedje, J., G.B. Smith, S. Simkins, W.E. Holben, C. Finney and D. Gilichinsky. 1994. Recovery of DNA, denitrifiers, and patterns of antibiotic sensitivity in microorganisms from ancient permafrost soils of Eastern Siberia, p. 83-98. In D. Gilichinsky (ed.) Viable Microorganisms in Permafrost. Russian Academy of Sciences, Pushchino Research Centre, Pushchino, Russia.

Holben, W.E., V.G.M. Calabrese, D. Harris, and J.M. Tiedje. 1993. Analysis of structure and selection in microbial communities by molecular methods. In R. Guererro and C. Pedros-Alio, editors. Trends in Microbial Ecology, p367-370. Spanish Society for Microbiology, Barcelona, Spain.

Holben, W.E., B.M. Schroeter, V.G.M. Calabrese, R.H. Olsen, J.K. Kukor, V.O. Biederbeck, A.E. Smith and J.M. Tiedje. 1992. Gene probe analysis of soil microbial populations selected by amendment with 2,4‑dichlorophenoxyacetic acid. Appl. Environ. Microbiol. 58:3941-3948.

Holben, W.E., J.M. Tiedje and M. Hood. 1992. Survival and transport of genetically engineered microorganisms in the environment. In M. A. Levin, R. J. Seidler and M. Rogul, editors. Microbial Ecology: Principles, Methods and Applications. McGraw-Hill, N. Y., N. Y.

Knight, I.T., W.E. Holben, J.M. Tiedje and R. R. Colwell. 1992. Nucleic acid techniques for detection, identification, and enumeration of microorganisms in the environment. In M. A. Levin, R. J. Seidler and M. Rogul, editors. Microbial Ecology: Principles, Methods and Applications. McGraw-Hill, N. Y., N. Y.

Tiedje, J.M., J.K. Jansson, W.W. Mohn, W.E. Holben and J.F. Quensen III. 1991. Biotechnology for Biodegradation: Reductive dechlorination and nucleic acid probe tracking methods. In L.M. Golovleva, editor. Microbial Degradation of Xenobiotics. USSR Academy of Sciences, Puschino, Moscow Region, USSR.

Hasebe, A., W.E. Holben and J.M. Tiedje. 1990. Effect of percolation on vertical movements of inoculated bacteria in soil. Soil Microorg. 35:31-34.

Jansson, J.K., W.E. Holben and J.M. Tiedje. 1989. Detection in soil of a deletion in an engineered DNA sequence by using DNA probes. Appl. Environ. Microbiol. 55:3022-3025.

Jansson, J.K., W.E. Holben, J.M. Tiedje and B.K. Chelm. 1989. The fate of recombinant Pseudomonads in modified soil-core microcosms (Versacores). In J.K. Fredrickson and R.J. Seidler (eds.) Evaluation of Terrestrial Microcosms for Detection, Fate, and Survival Analysis of Genetically Engineered Microorganisms and Their Recombinant Genetic Material. Environmental Protection Agency, Environmental Research Laboratory/Corvallis.

Holben, W.E. and J.M. Tiedje. 1988. Applications of nucleic acid hybridization in microbial ecology. Ecol. 69:561-568.

Holben, W.E., J.K. Jansson, B.K. Chelm, and J.M Tiedje. 1988. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54:703-711.

Holben, W.E., S. Prasad, and E. Morgan. 1985. Antitermination by both the promoter and leader regions of an Escherichia coli ribosomal RNA operon. Proc. Nat. Acad. Sci. USA, 82:5073-5077.

Holben, W.E. and E. Morgan. 1984. Antitermination of transcription from an Escherichia coli ribosomal RNA promoter. Proc. Nat. Acad. Sci. USA, 81:6789-6792.

Abstracts: (last 10 years only)

Lark, E., E.M. Spaulding, E.J.W. Weber, I.N.A. Ortloff, D.W. Raiford, and W.E. Holben. 2015.  Microbiome composition effects from yogurt consumption are not due to an increased abundance of probiotic bacteria.  American Society for Microbiology 115th General Meeting (2015), New Orleans, LA. 06/2015 (Young Investigator Oral Presentation).

Gilman, F.R., E.M. Spaulding, J. Voriskova, C.S. Jacobsen, D. Raiford, and W.E. Holben. 2015. Implications for climate change predictions: Microbial communities in greenland permafrost respond to seasonal changes and in situ variables. American Society for Microbiology 115th General Meeting (2015), New Orleans, LA. 06/2015.

Pannoni, S., E.M. Spaulding, and W.E. Holben. 2015. Developing non-invasive microbial biomarkers to inform elk (C. canadensis) health in wild Montana populations. 2015. American Society for Microbiology 115th General Meeting (2015), New Orleans, LA. 06/2015.

Lark, E., D.W. Raiford, A.H. Wright, and W.E. Holben. 2014. Evidence for biogeographical distribution of taxa along the mouse gastrointestinal tract. American Society for Microbiology 114th Annual Meeting. 17 – 20 May, 2014. Boston, USA.

Gilman, F.R., K. M. Lund, B. Elberling, C.S. Jacobsen, W.E. Holben. 2013. Microbial Contributions and Responses to Climate Change in Zackenberg Greenland. Polar and Alpine Microbiology Symposium, Big Sky, MT US, September 8 – 12.

Holben, W.E. & S.E. Morales. 2013. Compositional and Functional Response of a Near-Surface Soil Microbial Community to a Simulated Underground CO2 Storage Leak. American Society for Microbiology 114th Annual Meeting, May 18 –21, Denver, CO, USA.

Sergio E. Morales and William E. Holben. 2012. Simulated underground CO2 storage leak reduces bacterial richness and alters community functional and phylogenetic structure in surface soils. 14th International Symposium on Microbial Ecology, Copenhagen, Denmark, August 19-24.

Stibal, M., J. Bælum, W.E. Holben, and C.S. Jacobsen. 2012. Exploring the functional diversity of the supraglacial environment: Microbial degradation of the pesticide 2,4-D on the Greenland Ice Sheet. American Geophysical Union, Fall Meeting 2012, abstract #C13B-0608.

S. Yoo and W.E. Holben. 2012. Investigating Effects of Elevated CO2 on Soil Microbial Communities Using Metagenomic Analysis. 4th OREOS Undergraduate Research Symposium, August 9th, Missoula, MT.

Rout, M.E., T.H. Chrzanowski, R.M. Callaway, and W.E. Holben. 2012. What makes a plant invasive? It might be a matter of microbes. ASM 107th Annual Meeting June 16 – 19, San Francisco.

Lark, E. and W.E. Holben. 2012. Mouse colon luminal microbiome varies by location. Keystone Symposia—The Microbiome, March 4 - 9, Keystone, CO, USA.

Morales, S. & W.E. Holben. 2012. Rapid turnover and high variability of functional gene and transcript abundance in soils. 14th International Symposium on Microbial Ecology, Copenhagen, Denmark, August 19 – 24.

M. Stibal, J. Bælum, W.E. Holben, S.S. Sørensen & C.S. Jacobsen. 2012. Microbial degradation of the pesticide 2,4-D on the Greenland Ice Sheet. 14th International Symposium on Microbial Ecology, Copenhagen, Denmark, August 19 – 24.

Rout, M.E., T.H. Chrzanowski, R.M. Callaway, and W.E. Holben. 2011. What makes a plant invasive? It might be a matter of microbes. BAGECO—11th Conference on Bacterial Genetics and Ecology, May 29 – June 2, Corfu, Greece.

Morales, S.E. and W.E. Holben. 2011. Surface soil microbial community dynamics in response to elevated CO2 exposure from a simulated geological storage leak. BAGECO—11th Conference of Bacterial Genetics and Ecology, May 29 – June 2, Corfu, Greece.

Morales, S.E. and W.E. Holben. 2011. Effect of CO2 seepage on soil microbial communities: Ecosystem effects and suitability of microbes as sentinels for elevated CO2. Keystone Symposium: Microbial Communities as Drivers of Ecosystem Complexity, March 25 - 30, Breckenridge, Colorado.

Jacobsen, C.S., A. Jensen, J. Bælum, A.R. Johnsen, S.R. Sørensen, L. Whyte, E. Willerslev & W.E. Holben. 2010. Arctic POP contamination and microbial activity at and below zero °C. 13th International Symposium on Microbial Ecology, Seattle, Washington, USA, August 22- 26.

Pollock, J & W. Holben. 2010. Catechin, a root exudate of Centaurea maculosa (spotted knapweed) interferes with cell growth, sporulation, and germination in gram-positive bacteria. 13th International Symposium on Microbial Ecology, Seattle, Washington, USA, August, 2010.

Rout, M. T. Chrzanowski, R. Callaway, & W. Holben. 2010. Plant-microbe interactions: synergistic effects of bacterial endophytes promoting plant invasions. 13th International Symposium on Microbial Ecology, Seattle, Washington, USA, August, 2010.

Morales, S.E., T. Cosart, and W.E. Holben. 2009. Bacterial gene abundances as indicators of greenhouse gas emission in soils. BAGECO 10 Bacterial Genetics and Ecology – Coexisting on a Changing Planet 15–19 June 2009, Uppsala, Sweden.

Morales, S., and W. Holben. 2008. qPCR analysis with16S and functional primers shows that cultivation practices and soil successional stage are drivers of microbial community structure. 12th International Symposium on Microbial Ecology, Cairns Australia, August, 2008.

Ramsey, P., K. Feris, W. Holben, M. Rillig, and J. Gannon. 2008.  Ecosystem processes and microbial community structure along a heavy metal contamination gradient in river sediment. 12th International Symposium on Microbial Ecology, Cairns Australia, August, 2008.

Lowell, J., N. Gordon, D. Engstrom, J. Stanford, W. Holben and J. Gannon. 2008. Habitat heterogeneity and associated microbial community structure in a small-scale flood plain hyporheic flow path. 12th International Symposium on Microbial Ecology, Cairns Australia, August, 2008.

Bender, M., Holben, W.E., Sørensen, S.J. & Jacobsen, C.S. 2007: PNA inhibitory probes can replace DNAse in RT-PCR. Cambrigde Healttech Institutes Third Annual Quantitative PCR. 19-21 March, 2007. San Diego, California, U.S.A., Cambridge Healttech Institutes. CD-Rom only, 1 p.

 Bælum, J., Nicolaisen, M.H., Holben, W.E. & Jacobsen, C.S. 2007: Analysing Transcripts of the functional gene tfdA in natural soil microbial populations involved in the degradation of MCPA and 2,4-D through quantitative RT-PCR of directly extracted mRNA. ASM 107th annual meeting. 21-25 May, 2007. Toronto, Canada. American Society of Microbiology. Abstract book (CD-Rom), 1 p.

Calov, G., Holben, W.E., Callaway, R.M. & Jacobsen, C.S. 2007: Microbial communities in autoclaved recolonized and natural soils influenced by Centaurea maculosa and two north american natives. 9th International Conference on the Ecology and Management of Alien Plant Invasions. 17 -21 September, 2007. Perth, Western Australia. Abstract volume, 1 p.

Bælum, J., M. Haubjerg Nicolaisen, W.E. Holben and C.S. Jacobsen. 2007. Studying functional diversity and specific activity of microbial phenoxy acid degraders through tfdA-mRNA extracted from natural soil environment. ASM 107th Annual Meeting.

Morales, S. and W.E. Holben. 2007. A long look at soil microbial community diversity: Combined analysis using GC fractionation and extensive cloning of 16S rRNA gene sequences establishes broad diversity and evenness. Bacterial Genetics and Ecology 9th Symposium (BAGECO-8), Wernigerode, Germany, June 2007

Holben, W.E. 2006. Phylogenetic analysis of intestinal microflora indicates a novel Mycoplasma phylotype in farmed and wild salmon. ASM 106th Annual Meeting.

Adams, S., N. Gordon, A. Valenzuela, J.E. Gannon and W.E. Holben. 2006. Paraperla spp: A novel vector for transmission of the fish pathogen Aeromonas salmonicida. Graduate Student and Faculty Research Conference. The University of Montana, April 2006.

DeLuca, T.H., M.D. MacKenzie, A.Sala, P.N. Ball, and W.E. Holben. 2005. Nitrification and Fire Intervals in Ponderosa Pine Forests. 2005 ASA-CSSA-SSSA International Annual Meetings, Salt Lake City, UT - November 2005

Adams, S., N. Gordon, J.E. Gannon and W.E. Holben. 2005. Plecoptertan nymphs: A potential transmission vector for the fish pathogen Aeromonas salmonicida. Annual Meeting of the Entomological Society of America. Fort Lauderdale, FL, November 2005. Winner of President’s Award for Student Presentations.

Holben, W.E. 2005. Hyporheic Zone Microbial Communities: Examination of Microbial Community Structure and Function in a Pristine Freestone River in the Northwest United States. Bacterial Genetics and Ecology 8th Symposium (BAGECO-8), Lyon, France, June 2005.

Jacobsen, C.S. and Holben, W.E. 2005. Quantification of Salmonella sp. invA mRNA in soil and chicken manure using magnetic capture hybridization RT-PCR Bageco 8 Lyon 26-29 June 2005

Adams, S., N. Gordon, A. Valenzuela, J.E. Gannon and W.E. Holben. 2005. The microbe-stonefly-fish connection—Exploring trophic linkages and fish pathogen transfer through microbial community analysis in the Nyack Floodplain. Clark Fork Symposium, Missoula, MT, April, 2005.

Jacobsen, C.S. and Holben, W.E. 2005. Quantification of Salmonella sp. invA mRNA in soil and chicken manure using magnetic capture hybridization RT-PCR American Society for Microbiology 103 General Meeting, Atlanta 5-9. June 2005

Holben, W.E., E.D. Inkley, and L.S. Mills. 2004. Microbial Tools for Wildlife Studies: Biogeographical Analysis of Snowshoe Hares Based on Fecal Pellet Microflora. ASM 104th Annual Meeting.

Mummey, D.L., W.E. Holben and J. Six. 2004. Small-scale spatial stratification of soil microbial populations: an exploration of the inner-microaggregate. ASA-CSSA-SSSA International Annual Meeting, Seattle, WA

Ramamoorthy, S., L. Winoweicki, H. Langner, W. Holben, M. Morra, and R.F. Rosenzweig. 2004. Influence of Microbial Sulfidogenesis on Trace Element Stability In a Mining-Impacted Freshwater Sediment. ASM 104th Annual Meeting.

Jacobsen, C.S., M. Bender, S.J. Sørensen, and W. E. Holben. 2004. Use of a PNA Probe to Block DNA Mediated PCR Product Formation in RT-PCR. ASM 104th Annual Meeting.

Gsell, T.C., and W.E. Holben. 2004. Characterizing bacterial diversity and ammonia oxidizer phylogeny in aquifer sediments along a northwestern Montana river floodplain. ASM 104th Annual Meeting.

Bender, M.; Holben, W.E.; Sørensen, S.J. and Jacobsen, C.S. 2004. Use of a PNA probe to block DNA mediated PCR product formation in RT-PCR. American Society for Microbiology 102 General Meeting, New Orleans 23-27. May 2004

Ramsey, PW, Feris, KP, Rosier, CL, Rillig, MC, Moore, JN, Holben, WE, Gannon, JE. 2004. Biological and Geochemical Change Along a Steep Functional Gradient in Mine Waste Contaminated Soil. Tenth International Symposium on Microbial Ecology, Cancun, Mexico. August, 2004.

Ramsey, P.W., M.C. Rillig, K. Feris, J.N. Moore, W.E. Holben, and J.E. Gannon. 2004. Long-Term Effects of Toxins on Ecosystems: Microbial Community Structural and Functional Change along an Alluvial Mine Waste Contamination Gradient. ASM 104th Annual Meeting.

Ball, P.N. and W.E. Holben. 2004. Microbial community analysis of the snake river aquifer: Microbial potential for TCE degradation. Tenth International Symposium on Microbial Ecology, Cancun, Mexico. August, 2004.

Bender, M., W.E. Holben, S.J. Sorenson, and C.S. Jacobsen. 2004. PNA inhibitory probes sort the wheat from the chaff in RT-PCR. Tenth International Symposium on Microbial Ecology, Cancun, Mexico. August, 2004

Special Presentations (Since 2000)

Invited participant/presenter for series of three talks: 1) Location, location, location—bacterial biogeography along the intestinal landscape; 2) Sampling & Replicate Handling for Bioinformatic Analyses; 3) Diversity Measurements. Workshop on Amplicon-based analysis of microbial populations. Co-sponsored by mBioinform, Nordic Environmental NUcleotide Network (NENUN), and the Denmark Microbiological Society. February 23 – 27, 2015, Copenhagen, Denmark.

Invited participant/presenter: “GC Fractionation: What is it; What can be learned with it? 2012. Nordic Environmental Nucleotide Network (NENUN) Workshop: Extraction of Microbial DNA & RNA in Environmental Samples; Copenhagen, Denmark, August 22, 2012.

Invited Marsico Speaker at Denver University, April 10, 2012.  Presented unit seminar "Microbial Connections to Environmental Concerns—From Weed Invasion to Greenhouse Gas Emissions" and hosted undergraduate, lower-division, lunch and roundtable discussion.

Invited participant/presenter: "Two decades of molecular analysis of soil communities: What have we learned, where are we going?" Soil Metagenomics—Implications of Next-Generation Sequencing Technologies on Microbial Diversity Research and Soil Ecology; Braunschweig, Germany, Dec. 2010.

Invited participant/presenter: Integrating biological (qPCR) data with physicochemical parameters by multivariate analysis to assess factors controlling bacterial transport in a sandy aquifer. At PATHOS; Pathogens in the Environment Annual Meeting. Copenhagen, Denmark, June 15, 2010.

Invited presentation: Comparing phylogenetic- and functional-based primers for monitoring of microbial populations in soil. BAGECO 10 Bacterial Genetics and Ecology – Coexisting on a Changing Planet 15–19 June 2009, Uppsala, Sweden.

Environmental Nucleotide Workshop, Copenhagen, Denmark, June 8, 2009 : “Comparing and contrasting phylogenetic- and functional-based monitoring of microbial populations in soil”.

Invited speaker; Gastrointestinal Microbial Ecology Workshop, Helsinki, Finland, June 11, 2009: “Comparing and contrasting phylogenetic- and functional-based primers for measuring bacterial diversity and population dynamics in complex communities”.

Invited lecture: Oregon State University Subsurface Biosphere Interdisciplinary Doctoral Program IGERT Seminar Series. “A Tale From the Nyack Floodplain: The Deadly Meal; Pathogen Transmission to Rainbow Trout Via Stonefly Prey”. March 8, 2007.

Invited participant/presenter: NorFA Workshop on Microbial Ecology and Bioremediation in Cold Climate: Molecular Microbial Ecology”. Geological Survey of Denmark, Copenhagen, 11/9/04.

Invited lecture: “Molecular approaches for studying microbial populations and communities in environmental samples: The synergism of combined approaches”. Colorado State University, Department of Horticulture. 10/26/04.

Keynote lecture: American Society for Microbiology Northwest Branch Meeting. August 8, 2003. Vancouver, B.C. “GC fractionation enhances microbial community diversity assessment and facilitates systematic detection of minority populations of bacteria”

Invited lecture: UA Superfund Basic Research Program, Tucson, AZ, Nov 6, 2002. “Integrating biological RT-qPCR data with physicochemical parameters by multivariate analysis to assess factors controlling bacterial transport”

Invited lecture: University of Arizona Dept. of Soil, Water and Environmental Science "Effects of a heavy metal contamination gradient on microbial community structure and function in the Clark Fork River drainage in western Montana". November 2002.

Invited lecture: American Society for Microbiology 102nd Annual Meeting, Salt Lake City, UT, May 2002. “Molecular Methods for Monitoring Microbes in Saturated Porous Media”.

Invited Lecturer/Discussion Leader: US-Egypt Workshop in Microbial Ecology, Cairo Egypt, May 6-11, 2001.

Invited lecture: American Society for Microbiology 101st Annual Meeting, Orlando FL, May 2001. “Tracking microorganisms via stable isotope enrichment and quantitative PCR”.

Invited lecture: Oklahoma State University, Department of Microbiology and Molecular Genetics. April 9, 2001, "Molecular tools for studying microbial community structure and gene transfer in nature".

Grants (Funded proposals, Last 10 Years)

NSF-International Research Experience for Students. International Research Training in Climate Change Microbiology in Greenland and Denmark. (PI Holben). 07/01/2015-06/30/2018. $249,615.

NIH-NIAID-R15: Applying Landscape Ecology, Invasion Ecology and Association Analyses Within the Mouse GI Tract to Understand Clostridium difficile Invasion and Establishment. (PI Holben). 01/01/14 – 12/31/16  $353,750

NSF-REU Site Grant Program Supplement: Developing an undergraduate and Graduate Research Experience in Greenland and Denmark. (PI Holben). 07/14 – 03/16. $30,464

NSF-REU Site Grant Program Continuation: Undergraduate Research in Environmental Biology at The University of Montana. (PI Holben). 09/11 – 08/14. $332,000.

DOE-EPSCoR program. Effects of elevated CO2 on soil microbial structure and function. (PI Cunningham {MSU}; Holben co-PI and leader of UM portion). 09/01/08 – 08/31/11. $505,182 (UM/Holben portion)

NSF-REU Site Grant Program: Undergraduate Research in Environmental Biology at The University of Montana. (PI Holben). 09/08 – 08/11. $234,165

NSF-IGERT Program: Montana Ecology of Infectious Diseases (M-EID): Integrative Graduate Training in Multi-Scalar Computational, Mathematical and Empirical Approaches to Complex Problems. (PI Holben, 8%; co-PIs: Breuner, Graham, Johnson, Luikart. 10/05-09/11, $3,181,000.

Howard Hughes Medical Institute Undergraduate Science Education Program: MILES—Montana Integrative Learning Experience for Students at The University of Montana. Holben PI (30%) with Brewer, Graham, Greene, Johnson co-PIs. 9/06 – 8/11, $1,500,000.

USDA Soils and Soil Biology Program: Towards a comprehensive survey of soil bacterial fractions through analysis of fractionated community DNA. (PI, 8%) 8/04-8/08 $390,900.

NSF Microbial Observatories Program: Nyack Microbial Observatory Project. 5/04-4/09. (Co-PI (8%) with Gannon (PI), Woessner, Stanford). $1,307,312.

NSF Ecosystems Program: Soil charcoal and nitrogen cycling in Pinus ponderosa ecosystems of western Montana.  (Co-PI with DeLuca). 10/03-9/07.  $481,360.

USDA Soils & Soil Biology Program: Centaurea invasion: From molecules and microbes to plant communities.  (Co-PI with Callaway and Vivanco). 6/03-8/05 $220,000.

USDA Soils and Soil Biology Program: Analysis of bacterial communities associated with aggregate size fractions of native vegetation, no-tillage, and conventional tillage systems.  (Co-PI with Mummey) 6/03-1/05 $180,000.

INRA (Inland Northwest Research Alliance): Mapping the Distribution, Abundance, Diversity, and Activity of Methanotrophic Bacteria at the INEEL. (PI) 9/02-3/05 $202,130.