Research Emphasis:

I apply evolutionary and ecological genetics approaches and questions to a variety of microbial systems. At the most basic level our overarching goal in my program is to elucidate the genetic basis for adaptation and/or how the patterns of associated phenotypes are distributed in nature or across environmental conditions. My strategy in research is not only to directly test hypotheses central to a specific project, but also, to concomitantly build tools and resources necessary to expand and/or redirect the scope of the project as needed due to opportunity, curiosity or both. Such tools include items like databases, well-characterized libraries of biological materials, and experimental skill-sets among personnel. Currently,  I lead a collaboration among myself, Terry Gentry and Mark Holtzapple to optimize the microbial communities in a carboxylate biofuel platform (CBP) developed at Texas A&M, MixAlco^TM.  We seek to generate a deep understanding of community dynamics within the CBP across time and/or process conditions. Our current research emphasis involves evaluating screens of 501 communities collected over three years from 77 sites distributed throughout the continental United States, Puerto Rico, and Hawaii to determine the degree to which soil environments select for communities pre-adapted to conditions in commonly associated industrial processes with microbes, and 2) characterize the dynamics of many independent microbial communities within the CBP under a variety of process conditions and industrial scales. We are currently resolving a picture of the environmental conditions that prime the most optimal communities for this process, the particular functional categories of taxa that contribute to particular process performance phenotypes, and the role of process conditions in constraining CBP performance phenotypes and community diversity. In combination with other work to create a library of isolates (N>1800) from the top performing communities, we now have both testable hypotheses and well-characterized tools for the next stage where we will conduct directed studies of assembled communities. In addition I expanded into other collaborations associated with screening our isolate library for traits important to additional industries (e.g. bioremediation, hydrocarbon degradation, butanol production, agriculture).

Recent Publications

Recent Publications

Saengkerdsub, S., Lingbeck, J.M., Wilkinson, H.H., O’Bryan, C.A., Crabdall, P.G., Muthaiyan, A., Biswas, D., Ricke, S.C. 2013. Characterization of isolated yeast growth response to methionine analogs. Journal of Environmental Science and Health, Part B Pesticides, Food Contaminants and Agricultural Waste, 48: 1112-1120.

Golub, K.W., Forrest, A.K., Wales, M.E., Hammett, A.J.M., Cope, J.L., Wilkinson, H.H., Holtzapple, M.T. 2013. Comparison of three screening methods to select mixed-microbial inoculum for mixed-acid fermentations. Bioresource Technology, 130, 739-749.

Hou, H., Li, L., Ceylan, C.U., Haynes, A., Cope, J., Wilkinson, H.H., Erbay, C., de Figueiredo, P., Han, A. 2012. A microfluidic microbial fuel cell array that supports long-term multiplexed analyses of electricigens. Lab Chip, 12(20), 4151-9.

Hollister, E.B., Forrest, A.K., Wilkinson, H.H., Ebbole, D.J., Tringe, S.G., Malfatti, S.A., Holtzapple, M.T., Gentry, T.J. 2012. Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PLoS One, 7(6), e39689. 

Forrest, A.K., Hollister, E.B., Gentry, T.J., Wilkinson, H.H., Holtzapple, M.T. 2012. Comparison of mixed-acid fermentations inoculated with six different mixed cultures. Bioresource Technology, 118, 343-9.

Kubicek, C.P., Herrera-Estrella, A., Seidl-Seiboth, V., Martinez, D.A., Druzhinina, I.S., Thon, M., Zeilinger, S., Casas-Flores, S., Horwitz, B.A., Mukherjee, P.K., Mukherjee, M., Kredics, L., Alcaraz, L.D., Aerts, A., Antal, Z., Atanasova, L., Cervantes-Badillo, M.G., Challacombe, J., Chertkov, O., McCluskey, K., Coulpier, F., Deshpande, N., von Dohren, H., Ebbole, D.J., Esquivel-Naranjo, E.U., Fekete, E., Flipphi, M., Glaser, F., Gomez-Rodriguez, E.Y., Gruber, S., Han, C., Henrissat, B., Hermosa, R., Hernandez-Onate, M., Karaffa, L., Kosti, I., Le Crom, S., Lindquist, E., Lucas, S., Lubeck, M., Lubeck, P.S., Margeot, A., Metz, B., Misra, M., Nevalainen, H., Omann, M., Packer, N., Perrone, G., Uresti-Rivera, E.E., Salamov, A., Schmoll, M., Seiboth, B., Shapiro, H., Sukno, S., Tamayo-Ramos, J.A., Tisch, D., Wiest, A., Wilkinson, H.H., Zhang, M., Coutinho, P.M., Kenerley, C.M., Monte, E., Baker, S.E., Grigoriev, I.V. 2011. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol, 12(4), R40. 

Hollister, E. B., A. M. Hammett, M. T. Holtzapple, T. J. Gentry, and H. H. Wilkinson. 2011. Microbial community composition and dynamics in a semi-industrial-scale facility operating under the MixAlco™ bioconversion platform. Journal of Applied Microbiology 110:587-596.

Chung, D.-W., C. Greenwald, S. Upadhyay, S. Ding, H. H. Wilkinson, D. J. Ebbole, and B. D. Shaw. 2011. acon-3, the Neurospora crassa ortholog of the developmental modifier, medA, complements the conidiation defect of the Aspergillus nidulans mutant. Fungal Genetics and Biology.

Hollister, E. B., A. S. Engledow, A. J. M. Hammett, T. L. Provin, H. H. Wilkinson, and T. J. Gentry. 2010a. Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. The ISME Journal 4:829-838.

Hollister, E. B., A. K. Forrest, H. H. Wilkinson, D. J. Ebbole, S. A. Malfatti, S. G. Tringe, M. T. Holtzapple, and T. J. Gentry. 2010b. Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production. Applied Microbiology and Biotechnology 88:389-399.

Greenwald, C. J., T. Kasuga, N. L. Glass, B. D. Shaw, D. J. Ebbole, and H. H. Wilkinson. 2010. Temporal and Spatial Regulation of Gene Expression During Asexual Development of Neurospora crassa. Genetics 186:1217-1230.

Kutil, B., C. Greenwald, G. Liu, M. Spiering, C. Schardl, and H. Wilkinson. 2007. Comparison of loline alkaloid gene clusters across fungal endophytes: Predicting the co-regulatory sequence motifs and the evolutionary history. Fungal Genetics and Biology 44:1002-1010.

Shim, W. B., U. S. Sagaram, Y. E. Choi, J. So, H. H. Wilkinson, and Y. W. Lee. 2006. FSR1 is essential for virulence and female fertility in Fusarium verticillioides and F-graminearum. Molecular Plant-Microbe Interactions 19:725-733.
Saengkerdsub, S., R. C. Anderson, H. H. Wilkinson, W. K. Kim, D. J. Nisbet, and S. C. Ricke. 2006. Identification and Quantification of Methanogenic Archaea in Adult Chicken Ceca. Applied and Environmental Microbiology 73:353-356.

Zhang, J., C. Simmons, N. Yalpani, V. Crane, H. Wilkinson, and M. Kolomiets. 2005. Genomic Analysis of the 12-oxo-phytodienoic Acid Reductase Gene Family of Zea mays. Plant Molecular Biology 59:323-343.

Spiering, M. J., C. D. Moon, H. H. Wilkinson, and C. L. Schardl. 2005. Gene clusters for insecticidal loline alkaloids in the grass-endophytic fungus Neotyphodium uncinatum. Genetics 169:1403-1414.

Li, D., P. Bobrowicz, H. Wilkinson, and D. J. Ebbole. 2005. A Mitogen-Activated Protein Kinase Pathway Essential for Mating and Contributing to Vegetative Growth in Neurospora crassa. Genetics 170:1091-1104.

Xie, X., H. H. Wilkinson, A. Correa, Z. A. Lewis, D. Bell-Pedersen, and D. J. Ebbole. 2004. Transcriptional response to glucose starvation and functional analysis of a glucose transporter of Neurospora crassa. Fungal Genetics and Biology 41:1104-1119.

Wilkinson, H. H., A. Ramaswamy, S. C. Sim, and N. P. Keller. 2004. Increased conidiation associated with progression along the sterigmatocystin biosynthetic pathway. Mycologia 96:1190-1198.

Kutil, B. L., G. Liu, J. Vrebalov, and H. H. Wilkinson. 2004. Contig assembly and microsynteny analysis using a bacterial artificial chromosome library for Epichloë festucae, a mutualistic fungal endophyte of grasses. Fungal Genetics and Biology 41:23-32.

Spiering, M. J., H. H. Wilkinson, J. D. Blankenship, and C. L. Schardl. 2002. Expressed sequence tags and genes associated with loline alkaloid expression by the fungal endophyte Neotyphodium uncinatum. Fungal Genet Biol 36:242-254.

Blankenship, J. D., M. J. Spiering, H. H. Wilkinson, F. F. Fannin, L. P. Bush, and C. L. Schardl. 2001. Production of loline alkaloids by the grass endophyte, Neotyphodium uncinatum, in defined media. Phytochemistry 58:395-401.

Wilkinson, H. H., M. R. Siegel, J. D. Blankenship, A. C. Mallory, L. P. Bush, and C. L. Schardl. 2000. Contribution of fungal loline alkaloids to protection from aphids in a grass-endophyte mutualism. Mol Plant Microbe Interact 13:1027-1033.

Miles, C. O., M. E. di Menna, S. W. Jacobs, I. Garthwaite, G. A. Lane, R. A. Prestidge, S. L. Marshall, H. H. Wilkinson, C. L. Schardl, O. J. Ball, and G. C. Latch. 1998. Endophytic fungi in indigenous Australasian grasses associated with toxicity to livestock. Appl Environ Microbiol 64:601-606.

Parker, M. A. and H. H. Wilkinson. 1997. A locus controlling nodulation specificity in Amphicarpaea bracteata (Leguminosae). Journal of Heredity 88:449-453.

Bush, L. P., H. H. Wilkinson, and C. L. Schardl. 1997. Bioprotective alkaloids of grass-fungal endophyte symbioses. Plant Physiology 114:1-7.

Wilkinson, H. H. and M. A. Parker. 1996. Symbiotic specialization and the potential for genotypic coexistence in a plant-bacterial mutualism. Oecologia 108:361-367.

Wilkinson, H. H., J. M. Spoerke, and M. A. Parker. 1996. Divergence in symbiotic compatibility in a legume-Bradyrhizobium mutualism. Evolution 50:1470-1477.

Spoerke, J. M., H. H. Wilkinson, and M. A. Parker. 1996. Nonrandom genotypic associations in a legume – Bradyrhizobium mutualism. Evolution 50:146-154.