James Oliver

 

Academic Degrees and Honors

  • B.S. Microbiology, University of Arizona (1968)
  • Ph.D. Microbiology, Georgetown University (1973)
  • Postdoctoral Fellow, University of Ottawa, Canada (1973-1974)
  • Academy of Sciences Exchange Scientist, Romania (1982)
  • First Citizens Bank Scholar Award for Excellence in Research (1988)
  • Fellow, American Academy of Microbiology (1990-)
  • Member, Phi Kappa Phi (Academic Excellence), Phi Beta Delta (Honor Society for   International Scholars)
  • Visiting Professor, University of Göteborg, Sweden (1990)
  • Visiting Professor, Duke University Marine Laboratory (1991, 1992)
  • Member, Editorial Board, Applied and Environmental Microbiology (1988-1993)
  • Visiting Professor, North Carolina State University (1994,1995,1996)
  • Bonnie E. Cone Distinguished Professor for Teaching (1998)
  • Visiting Professor, Royal Veterinary and Agricultural University, Copenhagen, Denmark (1998)
  • Burroughs Welcome Fund Visiting Professor in the Microbiological Sciences (1999)
  • Member, Standard Methods Committee, Standard Council, American Water Works Association (2000-2012)
  • Member, Working Party on Culture Media, International Committee on Food Microbiology and Hygiene, International  Union of Microbiological Sciences (2000-)
  • Harshini V. de Silva Graduate Student Mentoring Award (2002)
  • Senior Faculty Fellow, Global Institute for Energy and Environmental Systems (2001-)
  • Member, Editorial Board, FEMS Microbiology Ecology (2005-2010, 2012-2016)
  • Visiting Professor National University of Ireland, Galway (2006)
  • First “Jay and Beverly Grimes Distinguished Lecturer”, Gulf Coast Research Lab, Univ. Southern Mississippi, 2007
  • Visiting Professor (Sabbatical) University of Aberdeen, Scotland (2008)
  • Member, Editorial Board, Advanced Studies in Biology (2009-2015)
  • Member, Working Group on Vibrio Taxonomy, Subcommittee on the Taxonomy of Aeromonadaceae, Vibrionaceae and related organisms, International Committee on Systematics of Prokaryotes (2009-)
  • Member, Editorial Board, Pathogens (2011-)
  • Mary Derrickson McCurdy Visiting Scholar, Duke Univ. Marine Lab  (2012)
  • Member, Editorial Board, International Journal of Microbiology (2012-2013)
  • Adjunct Professor, Marine Sciences and Conservation division,Nicholas School of the Environment,                             Duke University (2012-)
  • Member, Scientific Board, “How Dead is Dead III – Life Cycles” Conference, Berlin (2013)
  • Member, International Organizing Committee, Vibrio2014, Edinburgh (2013-14)

 

Courses Taught

  • BIOL 4250 Microbiology
  • BIOL 4257 Microbial Physiology and Metabolism

 

Areas of Research

The major areas of study in my laboratory are Vibrio vulnificus and other pathogenic marine Vibrio spp., the “viable but nonculturable” state, and bacterial stress responses and their relationship to environmental survival and human virulence.

Vibrio vulnificus

First described in 1976, Vibrio vulnificus is a halophilic bacterial species that causes primary septicemia and wound infections (Fig. 1). Disease in humans results from contamination of a skin lesion or ingestion of contaminated seafood. A striking feature is that many victims die with a few hours of symptom development) and the high mortality rate (>50% and 25%, respectively). The infectious dose of V. vulnificus is believed to be low and fatal infections have been reported after the ingestion of a single oyster (the primary source in 93% of all cases). Fatal wound infections acquired by contamination of ant bite lesions have also been reported. Between 1989 and 2008, 520 ingestion cases with 263 deaths (51%) were reported. Most cases (>85%) occur in males over the age of 40 (Fig. 2), as estrogen appears to block the endotoxin produced by this species. This is an opportunistic pathogen, with infections largely restricted (>95% of cases) to those having underlying liver diseases (such as liver cirrhosis or hepatitis). Three biotypes of V. vulnificus exist, and among biotype 1, the primary type in human infections, several very distinct genotypes are known to occur. One area of our study involves these genotypes. The “C-genotype” correlates strongly with a clinical origin, and these strains appear to be highly virulent. In contrast, the “E-genotype” correlates with isolation from the environment, and appears to be of lower virulence. At the DNA level, the two genotypes differ significantly from each other (some genes differ in >30% of their sequence), yet the two genotypes are highly similar within the genotype (Fig. 3). One enigma we are investigating is a result of our observation that, while the distribution of the two genotypes in estuarine waters appears to be approximately equal (Fig. 4), the oysters that inhabit those waters carry a high proportion (ca 85:15) of the E-genotype.

Some Recent Papers on this Topic:

     Vibrio vulnificus integration into marine aggregates and subsequent uptake by the oyster, Crassostrea virginica. Froelich, B., M. Ayrapetyan, and J.D. Oliver. 2013. Appl. Environ. Microbiol. 79:1454-1458

     Vibrio vulnificus: Death on the half shell. A personal journey with the pathogen and its ecology. 2013. Oliver, J.D. Microb. Ecol. 65:793-799.

A new culture-based method for the improved identification of Vibrio vulnificus from environmental samples, reducing the need for molecular confirmation. Williams,T., B. Froelich, and J.D. Oliver. 2013. J. Microbiol. Meth. 93:277-283.

The interactions of Vibrio vulnificus and the oyster Crassostrea virginica. Froelich, B. and J.D. Oliver. 2013. Microb. Ecol. 65:807-816.

Survival of Vibrio vulnificus genotypes in male and female serum, and production of siderophores in human serum and seawater. 2014. Kim, Hye-young, M. Ayrapetyan, and J.D. Oliver. Foodborne Path. Dis. 11:119-125.

Serum survival of Vibrio vulnificus: role of genotype, capsule, complement, clinical origin, and in situ incubation. 2014. Williams, T.C., M. Ayrapetyan, H. Ryan, and J.D. Oliver. Pathogens 3:822-832.

Non-native macroalga may increase concentrations of Vibrio bacteria on intertidal mudflats. Gonzalez, D.J., R.A. Gonzalez, B.A. Froelich, J.D. Oliver, R.T. Noble, and K.J. McGlathery. 2014. Mar. Ecol. Progr Ser. 505:29-36.

Implications of chitin attachment on the environmental persistence and clinical nature of the human pathogen, Vibrio vulnificus. 2014. Williams, T.C., M. Ayrapetyan and J.D. Oliver. Appl. Environ. Microbiol. 80:1580-1587.

Impact of analytic provenance in genome analysis. 2014. Morrison, S.S., R. Pyzh, J.S. Jeon, C. Amaro, C. Baker-Austin, J.D. Oliver, and C. Gibas. BMC Genomics 15(Suppl. 8):S1. doi:10.1186/1471-2164-15-S8-S1

The development of a decision matrix tool for the prediction of potentially pathogenic Vibrio species in oysters harvested from North Carolina. 2015. B. Froelich, M. Ayrapetyan, P. Fowler, J.D. Oliver, and R. Noble. Appl. Environ. Microbiol. 81:1111-1119.

Transcriptome-based analysis of clinical strains of the opportunistic human pathogen, Vibrio vulnificus, exposed to human serum. 2014. Williams, T.C., E. Blackman, S.S. Morrison, C.J. Gibas, and J.D. Oliver. PLoS One 10.1371/journal.pone.0114376

Role of anaerobiosis on capsule production and biofilm formation in Vibrio vulnificus. 2014. Phippen, B. and J.D. Oliver. Infect. Immun. doi:10.1128/IAI.02559-14

The Biology of Vibrio vulnificus. Oliver, J.D. 2015. Microbiol. Spectrum 3:1-10.doi:10.1128/microbiolspec.VE-0001-2014

Molecular and physical factors that influence attachment of Vibrio vulnificus to chitin. 2015. TC Williams, M. Ayrapetyan, and JD Oliver. Appl. Environ. Microbiol. 81:6158-6165.

Clinical and environmental genotypes of Vibrio vulnificus display distinct, quorum sensing mediated, chitin detachment dynamics. 2015. Phippen, B.L. and J.D. Oliver. Path. Dis. Doi:10.1093/femspd/ftv072

 

Bacterial Stress Responses

Many of the so-called heat shock proteins, such as chaperone proteins (e.g. DnaK and GroEL) and proteases (e.g. Clp, Lon), are also induced by other environmental changes, such as high osmolarity, nutrient starvation, exposure to low temperature, the presence of heavy metals, oxidative agents or pollutants, and interaction with eukaryotic hosts.Therefore, the heat shock response can more accurately be considered a general stress response.Through a process termed cross protection, this response improves tolerance to otherwise lethal temperatures, high or low salt levels, heavy metals, UV exposure, and starvation, and plays a critical role in bacterial pathogenesis.Such stress responses are critical forbacterial adaptation to the constant changes in the environment experienced by estuarine bacteria, such as most Vibrio spp., and are therefore a major link between microbial ecology, physiology, and microbial pathogenesis.One example is the htrA system, the product of which is essential for bacterial growth only at elevated (e.g. human body) temperatures. This system is activated by the alternate sigma factor, sE, encoded by the rpoE gene.This gene has been shown to control mucoidy in cystic fibrosis isolates of Pseudomonas aeruginosa.In E. coli, transcriptional activation of the heat shock genes is induced by the alternate sigma factor, s32 (product of the rpoH gene). Our lab is interested in the bacterial response to a variety of environmental stresses, especially starvation, low temperature, high salinity (osmotic stress), and oxidative (e.g. peroxide) stress.The bacterium under greatest investigation I this lab is V. vulnificus. We study the mechanisms by which this pathogen survives in the estuarine environment, the molecular regulatory mechanisms which occur during these survival responses. Of special interest in this regard is the use of membrane diffusion chambers to examine in situ gene expression by cells in their natural aquatic environment.

Some Recent Papers on this Topic:

RpoS involvement in osmotically-induced cross protection in Vibrio vulnificus. 2005. Rosche, T.M., T.C. Bates, D.J. Smith, E.E. Parker, and J.D. Oliver. FEMS. Microbiol. Ecol. 53:455-462.

Survival and in situ gene expression of Vibrio vulnificus at varying salinities in estuarine environments. 2008. Jones, M.K., E. Warner, and J.D. Oliver. Appl. Environ. Microbiol. 74:182-187.

Adaptation of Vibrio vulnificus and an rpoS mutant to bile salts. 2010. W.-L. Chen, J. D. Oliver, and H.-c. Wong. Intern. J. Food Microbiol. 140:232–238.

Role of RpoS in the susceptibility of low salinity-adapted Vibrio vulnificus to environmental stresses. 2010. Tan, H.-J., S.-H. Liu, J.D. Oliver, and H.-c. Wong. Intern. J. Food Microbiol. 137:137-142.

Interactive effects of cadmium and hypoxia on metabolic responses and bacterial loads of Eastern oysters Crassostrea virginica Gmelin. 2011. Ivanina, A.V., B. Froelich, T. Williams, E.P. Sokolov, J.D. Oliver, and I.M. Sokolova. Chemosphere 82:377–389

Santander, R.D., J.D. Oliver, and E.G. Biosca. 2012. Expression analysis of oxidative stress katA, katG, and oxyR genes in Erwinia amylovora in the viable but nonculturable state. Indus. Microbes Appl. Res. pp. 624-628.

Apparent loss of Vibrio vulnificus from North Carolina oysters coincides with a drought-induced increase in salinity. 2012. Froelich, B., T. Williams, R. Nobel, and J.D. Oliver. Appl. Environ. Microbiol. 78:3885-3889.

 

The Viable but Nonculturable State

Microbial ecologists have long recognized that large proportions of the microbial populations inhabiting natural habitats appear to be nonculturable. Indeed, plate counts of bacteria in soil, rivers and oceans typically indicate that far less than 1% of the total bacteria observed by direct microscopic examination can be grown on culture media. Further, it has also long been known that certain portions of bacterial populations in natural environments seem to disappear during certain seasons, only to reappear at other times. We now understand that at least part of the explanation for these observations is not due to seasonal die-off of the cells, but to their entry into a physiological state most commonly called the “viable but nonculturable” state.

A bacterial cell in the viable but nonculturable (VBNC) state may be defined as one which fails to grow on the routine bacteriological media on which it would normally grow and develop into a colony, but which is in fact alive and metabolically active.Bacteria enter into this dormant state in response to one or more environmental stresses which might otherwise be lethal to the cell.Thus, the VBNC state should be considered a means of cell survival.Eventually, when the inducing stress is removed, these cells are able to emerge from the VBNC state and again become culturable on routine media.

The typical VBNC response is seen in this figure, which shows the response of Vibrio vulnificus to exposure to low temperature (5oC). Such a temperature is below that at which this aquatic bacterium can grow and, if it were not for the VBNC response, is a temperature which would eventually lead to death of the population.

VBNC cells lose their ability to be cultured  in a rather linear manner, eventually reaching a point where plate counts suggest a total lack of any living cells.However, whereas death of a bacterial population generally leads to lysis of the cells and loss of cell structure, direct examination of cells entering the VBNC state indicates that the cells remain intact. Such cells could, of course, have died, but simply not undergone lysis.The primary evidence that such cells are alive, even if nonculturable, is from data obtained when a “direct viability” assay is applied to such cultures, or continued production of mRNA is detected.Such assays allow direct determination of individual cell viability, without the need for culture.  Such assays generally indicate that a large portion of the apparently dead population is, in fact, alive.

Cells entering the VBNC state generally undergo a reduction in size, and during this time, significant changes in membrane structure, protein composition, ribosomal content, and possibly even DNA arrangement are experienced.However, decreases macromolecular synthesis do not mean that all synthesis has ceased. Indeed, protein synthesis appears to be essential for entry into this state, and under these conditions V. vulnificus produces some 40 new proteins not seen during growth at “normal” temperatures.At the same time, dramatic decreases in membrane fatty acid composition, and in nutrient transport and respiration rates, have generally been reported to occur as cells enter this dormant state. Cell wall synthesis, or at least metabolism of the constituents of these structures, also apparently continues.

Some of our most recent studies indicate that quorum sensing plays a significant role in resuscitation of cells from the VBNC state, signaling to dormant cells that conditions are good, and growth is now permissive.

 

Some Recent Papers on this Topic:

The viable but nonculturable state in bacteria. 2005. Oliver, J.D. J. Microbiol. 43:93-100.

Recent findings on the viable but nonculturable state in pathogenic bacteria. 2009. Oliver, J.D. FEMS Microbiology Rev. 34:415-425.

      Survival of spinach-associated Helicobacter pylori in the viable but nonculturable state. 2010. Buck, A. and J.D. Oliver. Food Control 21:1150-1154.

Apparent loss of Vibrio vulnificus from North Carolina oysters coincides with a drought-induced increase in salinity. 2012. Froelich, B., T. Williams, R. Nobel, and J.D. Oliver. Appl. Environ. Microbiol. 78:3885-3889.

Resistance to environmental stresses by Vibrio vulnificus in the viable but nonculturable state. Nowakowska, J. and J.D. Oliver. 2013. FEMS Microbiol. Ecol. 84:213–222.

Increases in the amounts of Vibrio spp. in oysters upon addition of exogenous bacteria. Froelich, B. and J.D. Oliver. 2013. Appl. Environ. Microbiol. 79:5208-5213.

Cellular, physiological and molecular adaptive responses of Erwinia amylovora to starvation. 2014. Santander, R.D., J.D. Oliver, and E.G. Biosca. FEMS Microb. Ecol. 88:258-271.

Interspecific quorum sensing mediates the resuscitation of viable but nonculturable vibrios. 2014. Ayrapetyan, M., T.C. Williams, and J.D. Oliver. Appl. Environ. Microbiol. 80:2478-2483.

The importance of the viable but non-culturable state in human pathogens. Li, L., N. Mendis, H. Trigui, J.D. Oliver and S.P. Faucher. 2014. Front. Microbiol. 5:72-100

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria. 2014. Ayrapetyan, M., T.C. Williams, and James D. Oliver. Trends in Microbiology 23:7-13.

Viable but nonculturable and persister cells coexist stochastically and are induced by human serum. 2015. Ayrapetyan, M., T. Williams and J.D. Oliver. Infect. Immun. 83:4194-4203.

 

Current Lab Members

Tiffany Williams (Postdoctoral Fellow)

Ms. Brittney Phippen (PhD)

Leigh Robertson (MS)

Allison Dews, Christopher Carpen (UG)

 

Recent Graduate Students

  • Buck, Alan. 2008. Survival of, and gene expression by, Helicobacter pylori on plant surfaces.
  • Kim, Erica. 2008. Expression of Vibrio vulnificus catecholate and hydroxamate siderophores in natural and human environments.
  • Casey Taylor. 2012. Role of motility in V. vulnificus genotypes as a determinant in survival in Crassostrea virginica and human hosts.
  • Joanna Nowakowska. 2012. Induction of cross-protection against environmental stresses by the VBNC state of Vibrio vulnificus.
  • Eric Binder. 2012. The effects of salinity on the production of autoinducer-2 by Vibrio vulnificus.
  • Leslie McKee. 2015. The relationship of reproductive hormones and host susceptibility to the opportunistic pathogen, Vibrio vulnificus.