Research Interests

Climate Change, Biofuels, Clostridia, Microbial Ecology and Evolution, Genomics, Bioinformatics

Our research program is focused on understanding molecular processes involved in the decomposition of plant material, particular the recalcitrant structures in the plant cell wall. This research has important implications for developing climate change research, cellulosic biofuels and animal health and nutrition. A prominent component of our research is using genomic and computational methods to understand variation in molecular processes. Our laboratory is set up for standard molecular biology and microbial physiology research and contains specialized equipment for working with anaerobic bacteria. Below are descriptions of our current funded project areas.

Global warming and forest soil microbiomes

Human activities are having a major impact on the global balance of exchange between carbon reservoirs. Three quarters of the carbon in terrestrial ecosystems is found as organic matter in soils, most of which is derived from plant litter. Accurate models capable of predicting the flux of carbon on a global scale, must be informed by a complete understanding of the complexity of carbon flow in soil, and the mechanisms of carbon transformation through communities of microbes. Our ability to understand carbon cycling by microbial communities is being transformed by rapid advances in DNA sequencing technology. We are developing new bioinformatic approaches for understanding microbial communities and their evolution. We also use microcosms, small experimental ecological systems representing aspects of the natural environment, to conduct replicated, controlled experiments in which system parameters are varied. Microcosms are particularly tractable to metagenomics, metatranscriptomic and other genome-enabled approaches and offer opportunities to apply genomics to analyze the physiological ecology of single cells and microbial consortia. Our research involves laboratory studies and field research at the Harvard Forest.

Renewable biofuels from plant litter using C. phytofermentans and other newly discovered microorganisms

Our primary long-term goal is to contribute to the production of biofuels derived from ecologically and economically sustainable plant feedstocks. Using genome-based technologies we are able to measure changes in the DNA sequences and gene expression levels of all of these parts as they change in response to environmental cues and as they evolve over time. These data are then integrated in genetic and physiological models to improve biofuel production and tested using molecular genetic and biochemical approaches. The questions we are asking include: What are the enzymes used by C. phytofermentans to deconstruct plant cell walls? Why is ethanol the primary product? What is the structure and function of polyhedral microcompartments? How does the cellular energetics constrain engineering for other products?

Representative Publications

Sun, Z., Blanchard, J.L. 2014. Strong genome-wide selection early in the evolution of Prochlorococcus resulted in a reduced genome through the loss of a large number of small effect genes. PLOS ONE. In Press.

Mukherjee, S., Thompson, L.K., Godin, S., Schackwitz, W., Lipzen, A., Martin, J., Blanchard, J.L. 2014. Population level analysis of evolved mutations underlying improvements in plant cellulose and hemicellulose fermentation by Clostridium phytofermentans. PLOS ONE, 9(1): e86731.

Biddle, A.S., Black, S.J., Blanchard, J.L. 2013. An in vitro model of the horse gut microbiome enables identification of lactate-utilizing bacteria that differentially respond to starch induction. PLOS ONE, PLoS ONE 8(10): e77599

Abdul-Rahman, F., Petit, E., Blanchard, J.L. 2013. The Distribution of Polyhedral Bacterial Microcompartments Suggests Frequent Horizontal Transfer and Operon Reassembly. J. Phylogen. Evolution. Biol., 1: e118.

Biddle, A.S., Stewart, L., Blanchard, J.L., Leschine, S.B. 2013. Untangling the Genetic Basis of Fibrolytic Specialization by Lachnospiraceae and Ruminococcaceae in Diverse Gut Communities. Diversity, 5(3), 627-640.

Tolonen, A.C., Petit, E., Blanchard, J.L., Warnick, T., Leschine, S.B. 2013. "Technologies to Study Plant Biomass Fermentation using the Model Bacterium Clostridium phytofermentans." Chapt 7 (pp 114-139) in "Biological Conversion of Biomass for Fuels and Chemicals: Explorations from Natural Utilization Systems". Edited by Jianzhong Sun, Shi-You Ding and Joy Peterson. The Royal Society of Chemistry.

Petit, E., Latouf, W., Coppi, M., Currie, D., Rhomasko, I., Desphande, S., Haas, K., Alvelo-Maurosa, J.G., Wardman, C., Schnell, D., Leschine, L., Blanchard, J. 2013. Involvement of a bacterial microcompartment in the metabolism of fucose and rhamnose by Clostridium phytofermentans. PLoS One, 8(1): e54337.

Damery, D., Hayes, J., Blanchard, J.L. 2010. The potential for production of ethanol from woody biomass by the microbe Clostridium phytofermentans. Wood Structures and Properties '10. Edited by Kúdela and Lagaňa. Arbora Publishers. p21-25.

Hu, J., Blanchard, J.L. 2009. Environmental sequence data from the Sargasso Sea reveal that the characteristics of genome reduction in Prochlorococcus are not a harbinger for an escalation in genetic drift. Molecular Biology and Evolution, Jan;26(1): 5-13.

Lu, S., Becker, K.A., Hagen, M.J., Yan, H., Roberts, A.L., Mathews, L.A., Schneider, S.S., Siegelmann, H.T., Macbeth, K.J., Tirrell, S.M., Blanchard, J.L., Jerry, D.J. 2008. Transcriptional Responses to Estrogen and Progesterone in Mammary Gland Identify Networks Regulating p53 Activity. Endocrinology, Oct;149(10): 4809-20. Epub 2008 Jun 12.

Blanchard, J.L., Chen, W., Conlon, E.M., Pomposiello, P.J. 2007. Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks. PLoS ONE, 2(11): e1186.

Conlon, E.M., Alpargu, G., Blanchard, J.L. 2006. Comparative genomics approaches for identifying genetic regulatory networks. Chance, 19:45-48.

Richards, T.A., Dacks, J.B., Campbell, S.A., Blanchard, J.L., Foster, P.G., McLeod, R., Roberts, C.W. 2006. Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. Eukaryot Cell, 5: 1517-31.

Blanchard, J.L. 2004. Bioinformatics and Systems Biology, rapidly evolving tools for interpreting plant response to global change. Field Crops Research, 90: 117-131.

de Visser, A.J.M., Hermisson, J., Wagner, G.P., Ancel, L.W., Bagheri-Chaichian, H., Blanchard, J.L., Chao, L., Cheverud, J.M., Elena, S.F., Fontana, W., Gibson, G,, Hansen, T.F., Krakauer, D., Lewontin, R.C., Ofria, C., Rice, S.H., von Dassow, G., Wagner, A., Whitlock, M.C. 2003. Evolution and detection of genetic robustness. Evolution, 57: 1959-1972.

Kuffner, R.M., Gonzales, M, Steadman P, Wlodek, D.K., Jankowitz, R.J., Boinoff, J.R., Montoya, A.L., Peterson, T.F., Bulmore, D.L., Blanchard. J.L. 2002. PathDB. Nucleic Acids Research Database Issue.

Brinkman, F.S.L., Blanchard, J.L., Greberg, H., Wan, I., De Koning, A., Av-Gay, Y., Brunham, R.C., Fernandez, R.C., Finlay, B.B., Otto, S.P., Ouellette, B.F., Keeling, P., Hancock, R.E.W., Rose, A.M., S.J.M. Jones. 2002. Plant-like genes in Chlamydia species reflect Chlamydia’s ancestral relationship with cyanobacteria and the chloroplast. Genome Research, 12: 1159-67.

Blanchard, J.L., Lynch, M. 2000. Organelle Genes: why do organellar genes end up in the nucleus? Trends in Genetics, 16: 315-320.

de Visser, A.J.M., Zeyl, C.W., Gerrish, P.J., Blanchard, J.L., Lenski, R.E. 1999. Diminishing returns from mutation supply rate in asexual populations. Science, 283: 404-406.

Lynch, M., Blanchard, J.L., Houle, D., Kibota, T., Schultz, S., Vassileva, L., Willis, J. 1999. Spontaneous deleterious mutation. Evolution, 53: 645-663.

Blanchard, J.L., Hicks, J.S. 1999. The non-photosynthetic plastid in malarial parasites and other apicomplexans is derived from outside the green plastid lineage. Journal of Eukaryotic Microbiology, 46: 367-375.

Lynch, M., Blanchard, J.L. 1998. Deleterious mutation accumulation in organelle genomes. Genetica, 102/103: 29-39.

Bruns, B.U., Blanchard, J.L., Schmidt, G.W. 1998. On the modulation of thylakoid structure and function upon adaptation to prolonged nitrogen-deficiency. Pp. 3081-3086 in Photosynthesis: Mechanisms and Effects (IV), G. Garab (ed), Kluwer Acad. Publ., Dordrecht.

Blanchard, J.L., Schmidt, G.W. 1996. Mitochondrial DNA migration events in yeast and mammals: integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns. Molecular Biology and Evolution, 13: 537-548.

Blanchard, J.L., Schmidt, G.W. 1995. Pervasive migration of organellar DNAto the nucleus in plants. Journal of Molecular Evolution, 41: 397-406.