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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”
Indiana Branch Outstanding Microbiology Researcher Award, 2009
2013 AAAS Fellow

Research Description

Research projects in my laboratory are broadly focused on cell-to-cell interactions in prokaryotes. Although a unicellular view of bacteria has dominated microbiology for years, many different bacteria are now known to communicate with and physically contact other bacteria, allowing coordinated behavior and the formation of complex multicellular structures. Such microbial interactions often come into play when microbes colonize a host. Therefore, the study of the interactions of microorganisms may have a significant impact on combating disease and promoting beneficial host-bacterial interactions. We study microbial cellular interactions in several contexts. The first is a process of intercellular signaling called “quorum-sensing” among the plant-associated bacteria Agrobacterium tumefaciens and Rhizobium sp. NGR234, and among the natural microbial consortia of marine sponges. The second area overlaps the first, but more broadly focuses on the mechanisms underlying formation of surface-adherent microbial communities called biofilms. Finally, we study the composition and organization of microbial communities that flourish within the confines of host invertebrates, including several species of hard ticks that are responsible for transmitting human disease in the state of Indiana. Quorum-sensing in host-associated bacteria. Acylated homoserine lactones (acyl HSLs) are a prevalent class of extracellular bacterial signals. Acyl HSLs are produced at low levels and diffuse freely across the bacterial envelope. Although at low population densities they are rapidly diluted, at high population densities their relative concentration increases, eventually reaching a threshold (a bacterial "quorum"), driving association with an intracellular receptor that regulates a constellation of quorum-regulated genes. Acyl HSL quorum sensors exist in a variety of bacteria and regulate diverse functions. In A. tumefaciens and Rhizobium sp. NGR234 quorum-sensing regulates horizontal exchange and replication of large plasmids required for pathogenesis and symbiosis with host plants, respectively. In collaboration with a group at the Center for Marine Biotechnology in Baltimore, MD, we are also investigating quorum-sensing isolates that inhabit marine sponges. The sponge microbes form dense, complex communities that foster the process of quorum sensing. In both the plant-associated and sponge-associated systems, we are combining biochemical and molecular genetic approaches to investigate the mechanisms of (i) acyl HSL synthesis (ii) perception of acyl HSL (iii) control of target gene expression and (iv) integration of the signal with other environmental stimuli. The long-term goal of this work is to develop strategies for deliberate intervention into acyl HSL dependent signaling in order to manipulate the behavior of quorum sensing bacteria. Surface adherence and biofilms. Bacteria rarely ever exist as free-floating, dispersed cells. In the environment (eg. soil, streams, oceans, people, your refrigerator), bacteria usually exist as multicellular biofilms. Biofilms exhibit complex architecture with groups of microcolonies glued together by a bacterially-produced matrix. Biofilms are of great industrial, agricultural, and medical interest due to their prevalence and general resistance to antimicrobial treatment. We are interested in what makes a cell in a biofilm different from a free-floating cell, and what molecular interactions enable bacteria to remain associated with surfaces as well as each other within biofilms. A wide range of surface structures and regulatory mechanisms are employed by bacteria to organize and maintain themselves within biofilms. Special emphasis is placed on potential signaling mechanisms that underlie biofilm development and physiology. We use A. tumefaciens as both a model and a tool for studying microbial biofilms. Tick-associated microorganisms. The most important human disease vectors in the U.S. are the hard (ixodid) ticks, blood-sucking parasites of mammals that transmit a variety of diseases through direct inoculation of the host bloodstream during feeding. At least four different human diseases are vectored through three different species of ticks in the state of Indiana. Although there is a limited understanding of the disease-causing pathogens harbored by ticks, there is almost nothing known about the other microorganisms harbored within ticks, as many of these microbes cannot be cultivated in the laboratory. A multidisciplinary group of ecologists, acarologists, and microbiologists at IU and Ball State University (Muncie, IN) are investigating tick-borne microbial communities. We hypothesize that the microbial constituents within ticks influence the introduction and persistence of infectious agents. Using cultivation-independent molecular approaches we have begun characterizing the structure and composition of the tick-associated microbial communities, and have identified a number of novel microorganisms, some that are endosymbionts (harbored within the cells of the tick) and some that are free-living within the tick. The microbial interactions within ticks, including but not restricted to quorum-sensing and surface interactions, will be an area of emphasis in future studies.

Select Publications
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 (E-Pub Early, Mol. Microbiol.)
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. (E-Pub Early)
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.
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.
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.
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
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., 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. (E-Pub Early, ISME J)
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
White, D., J. Drummond and C. Fuqua. 2012. The Physiology and Biochemistry of Prokaryotes, 4th Edition. Oxford University Press, New York.
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.
Zan, J., C. Fuqua and R.T. Hill. 2011. Diversity and functional analysis of luxS genes in vibrios from marine sponges Mycale laxissima and Ircinia strobilina.  ISME J. 5:1505-1516.
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
Hibbing, M.E., C. Fuqua, M.R. Parsek and S. Brook Peterson. 2010. Surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8:15-25.
Tomlinson, A.D., B. Ramey-Hartung, T.W. Day, P.M. Merritt and C. Fuqua.  2010. Agrobacterium tumefaciens ExoR represses succinoglycan biosynthesis and is required for biofilm formation and motility. Microbiology - SGM 156:2670-81.
Tomlinson, A.D. and C. Fuqua. 2009. Mechanisms and regulation of polar surface attachment in Agrobacterium tumefaciens. Curr. Opin. Microbiol. 12:708-14.

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