David R. Nelson
Professor and Director
URI Genomics and DNA Sequencing Center
Office: 381 CBLS Building
Telephone: (401) 874-5902
- Ph.D. (1979) University of California, Los Angeles
- M.S. (1974) University of Wisconsin, Madison
- A.B. (1972) University of California, Los Angeles
- Post-doctoral fellow (1979-1982) University of California, Berkeley
- MIC413 – Advanced Microbiology Lecture I
- MIC415 – Advanced Microbiology Laboratory I
- MIC414 – Advanced Microbiology Lecture II
- MIC416 – Advanced Microbiology Laboratory II
- MIC561 – Recent Advances in Molecular Cloning
The Nelson lab is investigating the molecular mechanisms of probiotic activity in bacteria that protect marine animals (oysters, shrimp, fish) from infection by various pathogenic marine bacteria. Additionally, in order to understand these mechanisms of probiotic activity, we also are investigating the molecular mechanisms that control virulence in selected pathogenic marine bacteria that cause disease in marine animals. This research is done in collaboration with the laboratories of Prof. Marta Gomez-Chiarri (AVS) and Prof. David Rowley (BPS).
- Probiotic activity of Phaeobacter inhibens S4. This marine bacterium was isolated from the inner shell surface of a healthy adult Eastern oyster (Crassostrea virginica) and found to inhibit the growth of two bacterial pathogens of oysters – Aliiroseovarius crassostreae and Vibrio coralliilyticus. Further, exposure of oyster larvae 24 h prior to challenge by either of the pathogens, protected the larvae from infection and death (Karim et al 2013).
P. inhibens S4 produces a broad-spectrum antibiotic, tropodithietic acid (TDA) and is an avid biofilm former. Examination of mutants unable to produce TDA or mutants deficient in biofilm formation revealed that the loss of TDA production or reduced biofilm formation reduced, but did not eliminate, probiotic activity of these strains of P. inhibens against V. coralliilyticus RE22 (Zhao et al 2016).
Recently, we identified three additional secreted small molecules that contribute to probiotic activity of P. inhibens S4 against V. coralliilyticus RE22. P. inhibens exhibits quorum sensing (QS), which helps to regulate both biofilm formation and TDA biosynthesis. We demonstrated that the three QS compounds (acyl homoserine lactones, AHLs) produced by P. inhibens act to interfere with QS in V. coralliilyticus to prevent induction of protease genes, which are known virulence factors (Zhao et al 2019). The ability of S4-produced AHLs to block QS-mediated induction of RE22 virulence is an example of quorum quenching (QQ)
We are continuing this research to examine the ability of P. inhibens to block the activity of other virulence genes and gene products of V. coralliilyticus. Additionally, we have demonstrated that P. inhibens S4 is able to protect whiteleg shrimp (Litopenaeus vannamei) from acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus strains carrying the toxigenic pirA and pirB genes (Camm, LaPorte et al. manuscript in preparation)
- Pathogenic activity of Vibrio coralliilyticus. This bacterium is a pathogen of larval oysters and of corals. We have sequenced its genome and found that it contains a large number of genes likely to encode proteins that promote virulence (Spinard et al 2015). These genes include proteases, hemolysins, and two different type six secretion systems (T6SS). One T6SS is encoded on Chromosome 1 (T6SS-1) and the second T6SS (T6SS-2) is encoded on Chromosome 2.
We are investigating the role of T6SS in virulence against oyster larvae and have shown that mutants of the hcp1 gene are avirulent against oyster larvae. In contrast, mutants of the hcp2 gene show only a small decline in virulence against oyster larvae, suggesting that T6SS-1 plays a major role in pathogenesis against oyster larvae (Schuttert et al. manuscript in preparation). Further, we have also shown that the T6SSs of V. coralliilyticus RE22 are responsible for killing other bacteria by injecting anti-bacterial effectors into possible competitors of RE22. Our data suggest that T6SS-2 plays a larger role in anti-bacterial activity than T6SS-1 (Schuttert et al. manuscript in preparation).
We are also beginning to investigate the molecular basis of pathogenic activity of V. coralliilyticus against the coral Astrangia poculata. A. poculata is a temperate coral that is facultative with regard to its photosynthetic symbiont (Breviolum sp.).
Selected Publications (since 1993)
- Stevick RJ, Sohn S, Modak TH, Nelson DR, Rowley DC, Tammi K, Smolowitz, Lundgren KM, Post AF, Gomez-Chiarri M. 2019. Bacterial community dynamics in an oyster hatchery in response to probiotic treatment. Microbiol. 10:1060. doi: 10.3389/fmicb.2019.01060
- Ranson H, LaPorte J, Spinard E, Chistoserdov A, Gomez-Chiarri M, Nelson DR, and Rowley D. 2019. Draft genome sequence of the putative marine pathogen Thalassobius I31.1. Microbiol. Resource Announ. 8(6). pii: e01431-18. doi: 10.1128/MRA.01431-18. eCollection 2019 Feb. PMID: 30746516
- Zhao W, Yuan T, Piva C, Spinard EJ, Schuttert C, Rowley DC and Nelson DR. 2019. The probiotic bacterium, Phaeobacter inhibens, down-regulates virulence factor transcription in the shellfish pathogen, Vibrio coralliilyticus, by N-acyl homoserine lactone production. Appl Envir Microbiol 85: e01545-18. https://doi.org/10.1128/AEM.01545-18.
- Ranson HJ, LaPorte J, Spinard E, Gomez-Chiarri M, Nelson DR, Rowley DC. 2018. Draft Genome Sequence of Loktanella maritima Strain YPC211, a Commensal Bacterium of the American Lobster (Homarus americanus).Genome Announc. 6(18). pii: e00314-18. doi: 10.1128/genomeA.00314-18.
- Ranson HJ, LaPorte J, Spinard E, Chistoserdov AY, Gomez-Chiarri M, Nelson DR, Rowley DC. 2018. Draft Genome Sequence of the Putative Marine Pathogen Aquimarina Strain I32.4. Genome Announc. 6(17). pii: e00313-18. doi: 10.1128/genomeA.00313-18.
- LaPorte JP, Spinard EJ, Gomez-Chiarri M, Rowley DC, Mekalanos JJ, Nelson DR. 2018. Draft genome sequence of Bowmanella denitrificans jl63, a bacterium isolated from whiteleg shrimp (Litopenaeus vannamei) that can inhibit the growth of Vibrio parahaemolyticus. Genome Announc. 6(14). pii: e00215-18. doi: 10.1128/genomeA.00215-18.
- Mou X, Spinard EJ, Hillman SL, Nelson DR. Isocitrate dehydrogenase mutation in Vibrio anguillarum results in virulence attenuation and immunoprotection in rainbow trout (Oncorhynchus mykiss). BMC Microbiol. 17(1): 217. doi: 10.1186/s12866-017-1124-1.
- Sohn, S, Lundgren, KM, Tammi, K, Smolowitz, R, Nelson, DR, Rowley, DC, Gómez-Chiarr, M. 2016. Efficacy of Probiotics in Preventing Vibriosis in the Larviculture of Different Species of Bivalve Shellfish. Shellfish Res. 35: 319-328.
- Sohn, S, Lundgren, KM, Tammi, K, Karim, M, Smolowitz, R, Nelson, DR, Rowley, DC, Gómez-Chiarr, M. 2016. Probiotic Strains for Disease Management in Hatchery Larviculture of the Eastern Oyster Crassostrea virginica. Shellfish Res. 35: 307-317.
- Dubert J, Romalde JL, Spinard EJ, Nelson DR, Gomez-Chiarri M, Barja JL. 2016. Reclassification of the larval pathogen for marine bivalves Vibrio tubiashii europaeus as Vibrio europaeus sp. nov. Int J Syst Evol Microbiol. 66: 4791-4796.
- Spinard EJ, Dubert J, Nelson DR, Gomez-Chiarri M, Barja JL. 2016. Draft Genome Sequence of the Emerging Bivalve Pathogen Vibrio tubiashii europaeus. Genome Announc. 4: e00625-16.
- Dubert J, Spinard EJ, Nelson DR, Gomez-Chiarri M, Romalde JL, Barja JL. 2016. Draft Genome Sequence of the New Pathogen for Bivalve Larvae Vibrio bivalvicida. Genome Announc. 4: e00216-16.
- Kessner L, Spinard E, Gomez-Chiarri M, Rowley DC, Nelson DR. 2016. Draft Genome Sequence of Aliiroseovarius crassostreae CV919-312, the Causative Agent of Roseovarius Oyster Disease (Formerly Juvenile Oyster Disease). Genome Announc. 4: e00148-16.
- Zhao, W., Dao, C., Karim, M., Gomez-Chiarri, M., Rowley, D., and Nelson, D.R. Contributions of tropodithietic acid and biofilm formation to the probiotic activity of Phaeobacter inhibens. BMC Microbiol. 16:1 https://doi.org/10.1186/s12866-015-0617-z [URL: https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-015-0617-z]
- Dubert J, Nelson DR, Spinard EJ, Kessner L, Gomez-Chiarri M, da Costa F, Prado S, Barja JL. 2016. Following the infection process of vibriosis in Manila clam (Ruditapes philippinarum) larvae through GFP-tagged pathogenic Vibrio J Invertebr Pathol. 133:27-33.
- Spinard E, Kessner L, Gomez-Chiarri M, Rowley DC, Nelson DR. 2015. Draft Genome Sequence of the Marine Pathogen Vibrio coralliilyticus Genome Announc. 3: e01432-15.
- Hamblin M, Spinard E, Gomez-Chiarri M, Nelson DR, Rowley DC. 2015. Draft Genome Sequence of the Shellfish Larval Probiotic Bacillus pumilus RI06-95. Genome Announc. 3:e00858-15.
- Mou, X., Spinard, E.J., Driscoll, M.V., Zhao, W., and Nelson, D.R. H-NS is a Negative Regulator of the two hemolysin/cytotoxin gene clusters in Vibrio anguillarum. Infect Immun. 81:3566-3576 [URL: http://iai.asm.org/content/81/10/3566.long].
- Atoyan, J., Staroscik, A., Nelson, D., Patenaude, E., Potts, D., and Amador, J. Microbial Community Structure of a Leachfield Soil: Response to Intermittent Aeration and Tetracycline Additions. Water 5:505-524. [URL: http://www.mdpi.com/2073-4441/5/2/505?utm_source=dlvr.it&utm_medium=tumblr].
- Karim, M., Rowley, D., Zhao, W., Nelson, D.R., and Gomez-Chiarri, M. 2013. Probiotic strains for shellfish aquaculture: Protection of Eastern oyster, Crassosteae virginica, larvae and juveniles against experimental bacterial challenge. Shellfish Res. 32:401-408. [URL: http://www.bioone.org/doi/full/10.2983/035.032.0220].
- Li, L., Mou, X., and Nelson, D.R. Characterization of Plp, a phosphatidylcholine-specific phospholipase and hemolysin of Vibrio anguillarum. BMC Microbiology 13:271 (published 27 November 2013; article URL: http://www.biomedcentral.com/1471-2180/13/271) (listed as “Highly Accessed”).
- Li, L., X. Mo, and R. Nelson. 2011. HlyU is a positive regulator of hemolysin expression in Vibrio anguillarum. J. Bacteriol. 193:4779-4789.
- Rhodes, R.G., J.A. Atoyan, and R. Nelson. 2010. The chitobiose transporter, chbC, is required for chitin utilization in Borrelia burgdorferi. BMC Microbiology 10:21.
- Rhodes, R.G., W. Coy, and R. Nelson. 2009. Chitobiose utilization in Borrelia burgdorferi is dually regulated by RpoD and RpoS. BMC Microbiology 9:108.
- Varina, M., S.M. Denkin, A.M. Staroscik, and R. Nelson. 2008. Identification and characterization of Epp, the secreted processing protease for the Vibrio anguillarum EmpA metalloprotease. J. Bacteriol. 190:6589-6597.
- Staroscik, A.M., D.W. Hunnicutt, K.E. Archibald, and R. Nelson. 2008. Development of methods for the genetic manipulation of Flavobacterium columnare. BMC Microbiology 8:115.
- Li, L., J.L. Rock, and R. Nelson. 2008. Identification and characterization of an RTX gene cluster in Vibrio anguillarum. Infect. Immun. 76:2620-2632.
- Staroscik, A.M. and R. Nelson. 2008. The influence of salmon surface mucus on the growth of Flavobacterium columnare. J. Fish Dis. 31:59-69.
- Fallon, B.A., J.G. Keilp, K.M. Corbera, E. Petkova, C.B. Britton, E. Dwyer, I. Slavov, J. Cheng, J. Dobkin, R. Nelson, H.A. Sackeim. 2008. A randomized, placebo-controlled trial of repeated IV antibiotic therapy for Lyme encephalopathy. Neurology 70:992-1003.
- Rock, J.L. and R. Nelson. 2006. Identification and characterization of a hemolysin gene cluster in Vibrio anguillarum. Infect. Immun. 74:2777-2786.
- Staroscik, A.M., S.M. Denkin, and R. Nelson. 2005. Regulation of the Vibrio anguillarum metalloprotease EmpA by post-translational modification. J. Bacteriol. 187:2257-2260.
- Denkin, S.M., P. Sekaric, and R. Nelson. 2004. Gel shift analysis of the empA promoter region in Vibrio anguillarum. BMC Microbiology 4:42.
- Denkin, S.M. and R. Nelson. 2004. Regulation of Vibrio anguillarum empA Metalloprotease Expression and Its Role in Virulence. Appl. Environ. Microbiol. 70:4193-4204.
- Concepcion, M.B. and R. Nelson. 2003. Expression of spoT in Borrelia burgdorferi during serum starvation. J. Bacteriol. 185:444-452.
- Roberts, D.M., M.J. Caimano, J.D. Radolf, R. Nelson, and R.T. Marconi. 2002. Influence of environmental conditions on the expression and cellular partitioning of members of the Bdr protein family in the Lyme disease spirochetes. Infect. Immun. 70:7033-7041.
- Nelson, D.R., Rooney, S., N. Miller, and T.N. Mather. 2000. Complement-mediated killing of Borrelia burgdorferi in deer sera. Parasitol. 86:1232-1238.
- Alban, P.S., P.W. Johnson, and R. Nelson. 2000. Serum starvation-induced changes in protein synthesis and morphology of Borrelia burgdorferi. Microbiology 146:119-127.
- Soffientino, B., T. Gwaltney, R. Nelson, J.L. Specker, M. Mauel, and M. Gomez-Chiarri. 1999. Infectious necrotizing enteritis and mortality caused by Vibrio carchariae in summer flounder (Paralichthys dentatus) during intensive culture. Dis. Aquat. Organ. 38:201-210.
- Denkin, S. M. and R. Nelson. 1999. Induction of protease activity by gastrointestinal mucus in Vibrio anguillarum. Appl. Environ. Microbiol. 65:3555-3560.
- Nelson, D.R., Y. Sadlowski, M. Eguchi, K. Otto, and S. Kjelleberg. The starvation-stress response of Vibrio anguillarum. Microbiology 143:2305-2312.
- Garcia, T., K. Otto, S. Kjelleberg, and R. Nelson. 1997. The growth of Vibrio anguillarum in salmon intestinal mucus. Appl. Environ. Microbiol. 63:1034-1039.