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Indiana University Bloomington

Department of Biology

Faculty & Research

Faculty Profile

Clay Fuqua

Photo of Clay Fuqua
Research Images
Research photo by Clay Fuqua


Professor and Chair of Biology

IU Affiliations
Center for Genomics & Bioinformatics
Indiana Molecular Biology Institute

Contact Information
By telephone: 812-856-6005/6-5186(lab)
By fax: 812-855-6705
JH 425E /JH 425 (lab)


Research Areas
  • Microbial Cell Biology and Environmental Responses
  • Microbial Interactions and Pathogenesis

Ph.D., University of Maryland, 1991 Postdoctoral Fellow, Cornell University, 1991-95


Indiana University Outstanding Junior Faculty Award
2003 American Society for Microbiology “Waksman Foundation Lecturer”
2009 Indiana Branch Outstanding Microbiology Researcher Award
2013 AAAS Fellow
2014 American Academy of Microbiology

Research Description

Research projects in the Fuqua laboratory utilize the model Alphaproteobacterium, Agrobacterium tumefaciens, a well-studied bacterial pathogen of plants that causes the disease crown gall.  A. tumefaciens is best known for its ability to transfer DNA to plants during pathogenesis, via an interkingdom genetic transfer mechanism  that has been extensively utilized to genetically engineer plants. We have discovered that this rod-shaped bacterium exhibits profound asymmetries at the subcellular level that are intimately tied to its cell biology, physiology, genetics and host interactions.  One of these asymmetric activities is the production of an adhesive glue at one end of the cell, a structure we call the unipolar polysaccharide (UPP).  The UPP is required to cement A. tumefaciens to biotic and abiotic surfaces during formation of the multicellular structures known as biofilms.  A. tumefaciens forms robust biofilms on a variety of surfaces, and production of the UPP is a crucial first step in this process.  The UPP adhesive is only produced once the cell contacts the surface, and as such is very tightly regulated.  We are studying the mechanism of UPP production, its spatial and temporal regulation, and the complex control networks that coordinate attachment with other aspects of cellular physiology and the bacterial cell cycle.  Other surface structures such as flagella and pili are also asymmetrically distributed on the cell surface, reflecting a discrete underlying cellular architecture.  Recent work demonstrates that A. tumefaciens cells divide asymmetrically via a budding mechanism, in contrast to the standard paradigm of binary fission.  We are interested in how the extensive asymmetric organization of the A. tumefaciens cell, its division, and all the activities that it contains, are coordinated. These basic properties are also shared with a growing range of different bacteria, including pathogens and commensals, and thus our fundamental work is broadly relevant.

            We also utilize A. tumefaciens as an ecological and evolutionary model for facultative pathogens; bacteria with complex ecologies, that engage in disease under certain conditions, but also have an extensive host-independent existence.  Many of the A. tumefaciens populations in the natural environment live as heterotrophic saprophytes, not engaged in plant disease.  How do the environmental reservoirs for A. tumefaciens impact the dynamics of disease, and the propensity of this pathogen for virulence?  A. tumefaciens has a complex genome, with multiple chromosomes, and megaplasmids.  Virulence functions are carried on the tumor-inducing (Ti) plasmid, a 200 kb, self-transmissible plasmid that is required for pathogenesis.  A second large, self-transmissible plasmid, called the At plasmid, ranging from 300-800 kb, encodes many functions that enhance A. tumefaciens survival in the rhizosphere (the soil environment influenced by plants) but is not directly involved in pathogenesis.  We are interested in how these plasmids shape and are shaped by the ecology and dynamics of disease for A. tumefaciens, how they interact with each other, and how they impact the fitness and virulence of this facultative pathogen in its diverse environments. 

Select Publications
Mohari, B. N.A. Licata, D.T. Kysela, P.M. Merritt, S. Mukhopadhyay, Y.V. Brun, S. Setayeshgar and C. Fuqua. 2015.  Novel pseudotaxis mechanisms improve migration of straight swimming bacterial mutants through a porous environment. mBio 6:e00005-15
Rynkiewicz, E.C., C. Hemmerich, C. Fuqua and K. Clay. 2015. Concordance of bacterial communities of two tick species and blood of their shared rodent host. Mol. Ecol. 24:2566-79.
Feirer, N., J. Xu, K.D. Allen, B.J. Koestler, E. Bruger, C.M. Waters, RH. White and C. Fuqua. 2015. A pterin-dependent signaling pathway regulates a dual function diguanylate cyclase-phosphodiesterase controlling surface attachment in Agrobacterium tumefaciens. mBio 6:e00156-15.
Wang, Y, C.H. Haitjema and C. Fuqua. 2014. The Ctp Type IVb pilus locus of Agrobacterium tumefaciens directs formation of the common pili and contributes to reversible surface attachment. J. Bacteriol. 196:2979-88.
Heindl, J.E., Y. Wang, B.C. Heckel, B. Mohari, N. Feirer and C. Fuqua. 2014. Mechanisms and regulation of surface interactions and biofilm formation in Agrobacterium. Frontiers. Plant Sci. 5:176.
Morton, E.R., T.G. Platt, C. Fuqua and J.D. Bever. 2014. Non-additive costs and interactions alter the competitive dynamics of co-occurring ecologically distinct plasmids. Proc. R. Soc. B 281:20132173
Heckel, B.C., A.D. Tomlinson, E.R. Morton, J.-H. Choi and C. Fuqua. 2014. Agrobacterium tumefaciens ExoR controls acid response genes and impacts exopolysaccharide synthesis, horizontal gene transfer and virulence gene expression. J. Bacteriol. 196:3221-33.
Xu, J., J. Kim, B.J. Koestler, C.M. Waters and C. Fuqua. 2013. Genetic analysis of Agrobacterium tumefaciens unipolar polysaccharide production reveals complex integrated control of the motile-to-sessile switch. Mol. Microbiol. 89:929-948.
Zan, J., J.E. Heindl, Y. Liu, C. Fuqua and R.T. Hill. 2013. The cckA-chpT-ctrA phosphorelay system is regulated by quorum sensing and controls flagellar motility in the marine sponge symbiont Ruegeria sp. KLH11. PLOS ONE 8:e66346.
Morton, E.R., P.M. Merritt, J.D. Bever and C. Fuqua. 2013. Large deletions in the pAtC58 megaplasmid of Agrobacterium tumefaciens can confer reduced carriage cost and increased virulence. Genome Biol. Evol. 5:1353-1364
Kim, J., J.E. Heindl and C. Fuqua. 2013. Coordination of division and development influences complex multicellular behavior in Agrobacterium tumefaciens PLOS ONE 8: e56682.
White, D., J. Drummond and C. Fuqua. 2012. The Physiology and Biochemistry of Prokaryotes, 4th Edition. Oxford University Press, New York.
Platt, T.G., J.D. Bever and C. Fuqua. 2012. Fitness costs of the Agrobacterium tumefaciens cooperative virulence plasmid depends on environmental conditions. Proc. R. Soc. Lond. Ser. B: Biol. Sci., 279:1691-9
Hawlena, H., E. Rynkiewicz, E. Toh, A. Alfred, L.A. Durden, M.W Hastriter, D.E. Nelson, R. Rong, Q. Dong, C. Fuqua and K. Clay. 2012. Arthropod traits dictate bacterial community composition of fleas and ticks. 7:211-213.
Zan, J., Cicirelli, E.M., N.M. Mohamed, H. Sibhatu, S. Kroll, O Choi, C.L. Uhlson, C. L. Wysoczinski, R.C. Murphy, M.E.A. Churchill, R.T. Hill and C. Fuqua. 2012. A complex LuxR-LuxI type quorum sensing network in a roseobacterial marine sponge symbiont activates flagellar motility and inhibits biofilm formation. Mol. Microbiol. 85:916-933.
Platt, T.G., C. Fuqua and J.D. Bever. 2012.  Resource and competitive dynamics shape the benefits of public goods cooperation in a plant pathogen. Evolution 66:1953-65
Hibbing, M.E. and C. Fuqua. 2012. Inhibition and dispersal of Agrobacterium tumefaciens biofilms by a small diffusible Pseudomonas aeruginosa exoproduct(s). Arch. Microbiol. 194:391-403.
Brown, P.J.B., M.A. De Pedro, D.T. Kysela, C. Van Der Henst, J. Kim, X. De Bolle, C. Fuqua and Y.V. Brun. 2012.  Polar growth in the Alphaproteobacterial order Rhizobiales. Proc. Natl. Acad. Sci, USA. 109:1697-701
Xu, J., J. Kim, T. Danhorn, P.M. Merritt and C. Fuqua.  2012.  Phosphorus limitation increases attachment in Agrobacterium tumefaciens and reveals a conditional functional redundancy in adhesin biosynthesis. Res. Microbiol. 163:674-684.
Li, G., P.J.B. Brown, J.X. Tang, J. Xu, E.M. Quardokus, C. Fuqua and Y.V. Brun. 2012. Surface contact stimulates the just-in-time deployment of bacterial adhesins. Mol. Microbiol., 83:41-51.
Hibbing, M.E. and C. Fuqua. 2011. Anti-parallel and interlinked control of cellular iron levels by the Irr and RirA regulators of Agrobacterium tumefaciens. J. Bacteriol. 193:3461-72

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