petre dish with pink organism

Recent Publications


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, & G. Luikart. 2012. Yersinia enterocolitica: An unlikely cause of positive Brucellosis tests in Greater Yellowstone Ecosystem bison (Bison bison). Journal of Wildlife Diseases, 48(3):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. Applied and Environmental Microbiology, 78:5070-5076; DOI: 10.1128/AEM.00400-12.


Pollock, J.L., L.A. Kogan, A.S. Thorpe, & W.E. Holben. 2011. (±)-Catechin, a root exudate of the invasive Centaurea stoebe Lam. (spotted knapweed) exhibits bacteriostatic activity against multiple soil bacterial populations. Journal of Chemical Ecology, 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. & 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. & 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. John Wiley & Sons ISBN: 978-0-470-64719-6.

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


Ball, P.N., M.D. MacKenzie, T.H. DeLuca, & W.E. Holben. 2010. Wildfire and charcoal enhance nitrification and ammonium-oxidizing bacterial abundance in dry montane forest soils. Journal of Environmental Quality, 39:1243–1253; DOI:10.2134/jeq2009.0082.

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

Bælum, J., C.S. Jacobsen, & 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. Systematic and Applied Microbiology, 33:67-70; DOI: 10.1016/j.syapm.2010.01.001.



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

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

Pollock, J.L, R.M. Callaway, G.C. Thelen, & W.E. Holben. 2009. Catechin–metal interactions as a mechanism for conditional allelopathy by the invasive plant Centaurea maculosa. Journal of Ecology, 97:1234–1242; DOI: 10.1111/j.1365-2745.2009.01553.x

Feris, K.P., P.W. Ramsey, S.M. Gibbons, M.C. Rillig, J.N. Moore, J.E. Gannon, & W.E. Holben. 2009. Hyporheic microbial community development is a sensitive indicator of metal contamination. Environmental Science and Techchnology, 43:6158–6163; DOI: 10.1021/es9005465.

Adams, S.M., A.S. Adams, & W.E. Holben. 2009. Tri-Trophic Linkages in Disease: Pathogen Transmission to Rainbow Trout Through Stonefly Prey. Environmental Entomology, 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. International Journal of Systematic and Evolutionary Microbiology, 59:1720-1726.

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

Morales, S.E., T.F. Cosart, J.V. Johnson, & 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. Applied and Environmental Microbiology, 75: 668-675.

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


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

Inderjit, J.L. Pollock, R.M. Callaway, & W.E. Holben. 2008. Phytotoxic Effects of (±)-catechin in vitro, in soil, and in the field. PLoS ONE, 3(7):e2536.

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

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


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

Bender. M, W.E. Holben, S.J. Sørensen, & 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, & P. Stahl. 2006. Spatial stratification of soil bacterial populations in aggregates of diverse soils. Microbial Ecology, 51:404-411.

Ramsey, P.W., K.P. Feris, M.C. Rillig, W.E. Holben, & 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, & W.E. Holben. 2006. Wildfire-produced charcoal directly influences nitrogen cycling in Ponderosa Pine forests. Soil Science Society of America Journal, 70:448–453.

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


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

Mummey, D.L., M.C. Rillig, & 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 Biology and Biochemistry, 37:101-106.

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

Feris, K.P., P.W. Ramsey, M. Rillig, J.N. Moore, J.E. Gannon, & 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. Applied and Environmental Microbiol, 70:4756-4765.

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

Callaway, R.M., G.C. Thelen, A. Rodriguez, & 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, & W.E. Holben. 2003a. Differences in hyporheic zone microbial community structure along a heavy metal contamination gradient. Applied and Environmental Microbiology, 69:5563-5573.

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

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

Takai, T., M.R. Mormile, J.P. McKinley, F.J. Brockman, W.E. Holben, W.P. Kovacik, & J.K. Fredrickson. 2003. Shifts in archaeal communities associated with lithological and geochemical variations in subsurface Cretaceous rock. Environmental Microbiology, 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. Microbial Ecology, 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. Applied and Environmental Microbiology, 68:4986-4995.


Apajalahti, J.H.A., A. Kettunen, M.R. Bedford, & W.E. Holben. 2001. Percent G+C profiling accurately reveals diet-related differences in the gastrointestinal microbial community of broiler chickens. Applied and Environmetnal Microbiology, 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, & 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, & T.C. Onstott. 2001. Comparison of methods for monitoring bacterial transport in the subsurface. Journal of Microbiological 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, & W. Holben. 2001. Ferrographic tracking of bacterial transport in the field at the Narrow Channel focus area, Oyster, VA. Environmental Science and Technology, 35:182-191.


Holben, W.E. & 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, & S.C. Cary. 2000. Genetic variation among endosymbionts of widely distributed vestimentiferan tubeworms. Applied and Environmental Microbiology, 66: 651-658.



Apajalahti, J.H.A., L.K. Särkilahti, B.R.E. Mäki, J.P. Heikkinen, P.H. Nurminen, & W.E. Holben. 1998. Effective recovery of bacterial DNA and %G+C based analysis of community structure in the gastrointestinal tract of broiler chickens. Applied and Environmental Microbiology, 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, & D.R. Boone. 1998. Microbial transport, survival, and succession in a sequence of buried sediments. Microbial Ecology, 36:336-348.

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

Holben, W.E., K. Noto, T. Sumino , & Y. Suwa. 1998. Molecular analysis of bacterial communities in a three-compartment granular activated sludge system indicates community-level control by incompatible nitrification processes. Applied and Environmental Microbiology, 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, & 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, & R.M. Ventullo. 1997. Characterization of the sediment bacterial community in groundwater discharge zones of an alkaline fen: a seasonal study. Applied and Environmental Microbiology, 63:3111-3118.

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

Schleper, C., W.E. Holben, & H.-P. Klenk. 1997. Recovery of crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments. Applied and Environmental Microbiology, 63:321-323.

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


Matheson, V.G., L.J. Forney, Y. Suwa, C.H. Nakatsu, A.J. Sexstone, & W.E. Holben. 1996. Evidence for acquisition in nature of a chromosomal 2,4-dichlorophenoxyacetic acid /(alpha)-ketoglutarate dioxygenase gene by different Burkholderia spp. Applied and Environmental Microbiology, 62:2457-2463.

Suwa, Y., A.D. Wright, F. Fukomori, K.A. Nummy, R.P. Hausinger, W.E. Holben, & L.J. Forney. 1996. Characterization of a chromosomally encoded 2,4-dichlorophenoxyacetic acid/(alpha)-ketoglutarate dioxygenase from Burkholderia sp. RASC. Applied and Environmental Microbiology, 62:2464-2469.


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

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

Top, E.M., W.E. Holben, & L.J. Forney. 1995. Characterization of diverse 2,4-D degradative plasmids isolated from soil by plasmid capture. Applied and Environmental Microbiology, 61:1691-1698.

Ka, J.O., P. Burauel, J.A. Bronson, W.E. Holben, & J.M. Tiedje. 1995. DNA probe analysis of the microbial community selected in the field by long-term 2,4-D application. Soil Science Society of America Journal, 59:1581-1587.

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


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

Ka, J.O., W.E. Holben, & J.M. Tiedje. 1994. Genetic and phenotypic diversity of 2,4-D degrading bacteria isolated from 2,4-D treated field soils. Applied and Environmental Microbiology, 60:1106-1115.

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

Ka, J.O., W.E. Holben, & J.M. Tiedje. 1994. Analysis of competition in soil among 2,4-D degrading bacteria. Applied and Environmental Microbiology, 60:1121-1128.

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


Holben, W.E., V.G.M. Calabrese, D. Harris, & J.M. Tiedje. 1993. Analysis of structure and selection in microbial communities by molecular methods. In R. Guererro and C. Pedros-Alio (eds.) 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, & J.M. Tiedje. 1992. Gene probe analysis of soil microbial populations selected by amendment with 2,4-dichlorophenoxyacetic acid. Applied and Environmental Microbiology, 58:3941-3948.

Holben, W.E., J.M. Tiedje, & M. Hood. 1992. Survival and transport of genetically engineered microorganisms in the environment. In M. A. Levin, R. J. Seidler and M. Rogul (eds.) Microbial Ecology: Principles, Methods and Applications. McGraw-Hill, New York, NY.

Knight, I.T., W.E. Holben, J.M. Tiedje. & 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 (eds.) Microbial Ecology: Principles, Methods and Applications. McGraw-Hill, New York, NY.


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


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



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

Jansson, J.K., W.E. Holben, J.M. Tiedje, & 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. & 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, & J.M Tiedje. 1988. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Applied and Environmental Microbiology, 54:703-711.

Holben, W.E., S. Prasad, & E. Morgan. 1985. Antitermination by both the promoter and leader regions of an Escherichia coli ribosomal RNA operon. Proceedings of the National Academy of Sciences, 82:5073-5077.

Holben, W.E. & E. Morgan. 1984. Antitermination of transcription from an Escherichia coli ribosomal RNA promoter. Proceedings of the National Academy of Sciences, 81:6789-6792.