Ph.D., The Pennsylvania State University (2000)
B.S., University of Maine (1994)
Biological Concepts And Methods 1 ( Lab )
Biological Concepts And Methods I
Biological Concepts And Methods I I (lab)
Environmental Studies Intro Seminar
Guided Research Penicillin Resistance
Guided Research: Capstone Experience
Microbial Ecology Capstone Lab
Thesis Research Anarobic Microbiology
Thesis Research Metagenomics
Thesis Research Microbial Communities
The study of biology is the quest to understand the fundamental rules that govern the vast diversity of life on planet earth. Although the scope of the science of biology is broad, it impacts our lives in specific ways every single day. As a teacher, it is my objective to pass on knowledge about the ideas and history of the science, to present an in-depth exploration of the subject and its many facets. Course content, while important, is not the only measure for learning in the classroom, however. Biology is not a static science. It is constantly being reviewed and improved as we learn more about the natural world around us. To that end, my purpose as a teacher is to prepare students, not just by teaching the facts as they are understood today, but by providing the training to develop the scientific skills of observation, persistence, critical thinking, and creativity that will serve them in the future.
“Bioremediation” is the use of living organisms (usually plants or bacteria) to clean up environments that have been contaminated with hazardous wastes. My research in the field of heavy metal bioremediation focuses on three major questions:
1.) What kinds of bacteria are capable of bioremediation, and how do these bacteria survive in environments contaminated with hazardous waste?
2.) What are the structural changes that affect the stability, catalytic efficiency, and substrate specificity of the proteins involved in metal resistance?
3.) How has horizontal gene transfer (HGT) played a role in the evolution of metal resistance and other environmentally relevant traits?
J. Coombs. (2011) Impact of cadmium and nickel exposure on microbial populations in sediments from the South Shore Estuary Reserve. Adelphi Faculty Development Grant, Adelphi University.
J. Coombs. (2009) PIB-type ATPases in heavily-impacted vs. minimally impacted sediments of the South Shore Estuary. Adelphi Faculty Development Grant, Adelphi University.
J. Coombs. (2008) Viral Metagenomics. Bettelheim Research Award Grant, Adelphi University
J. Coombs. (2006) Characterization of the structural determinants involved in metal-binding specificity in PIB-type ATPases. Adelphi Faculty Development Grant, Adelphi University
J. Coombs, J. Dooley, and A. Schoenfeld. (2005) Li-Cor Genomics Education Matching Funds Grant Application. Equipment grant for a DNA sequencer. Li-Cor, Inc.
P. A. Sobecky and J. M. Coombs (2009). Horizontal gene transfer in metal and radionuclide contaminated soils. In M. Gogarten and P. Gogarten (Eds.). Horizontal Gene Transfer: Genomes in Flux. Totowa, NJ: Humana Press.
J. M. Coombs (2009). Potential for horizontal gene transfer in subsurface microbial communities. In M. Gogarten and P. Gogarten (Eds.). Horizontal Gene Transfer: Genomes in Flux. (pp. 413-433). Totowa, NJ: Humana Press.
D. R. Nemergut, T. Barkay, and J. Coombs (2007). A review of mobile gene elements and methods to study horizontal gene transfer in environmental microbial communities. In C. J. Hurst, R. L. Crawford, J. L. Garland, D. A. Lipson, A. L. Mills, and L. D. Stetzenbach (Eds.). The Manual of Environmental Microbiology. (pp. 758-768). Washington D.C.: ASM Press.
J. Coombs and T. Barkay (2005). Horizontal gene transfer of metal homeostasis genes and its role in microbial communities of the deep terrestrial subsurface. In G. M. Gadd, K. T. Semple, H. M. Lappin-Scott (Eds.). Microorganisms and Earth Systems--Advances in Geomicrobiology. (pp. 109-130). New York, NY: Cambridge University Press.
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R. J, Martinez, Y. Wang, M. A. Raimondo, J. M. Coombs, T. Barkay, and P. A. Sobecky (2006), Horizontal gene transfer of PIB-type ATPases among bacteria isolated from radionuclide and metal contaminated subsurface soils. Applied and Environmental Microbiology, 72, 3111-3118.
J. Coombs and T. Barkay (2005), New Findings on the Evolution of Metal Homeostasis Genes: Evidence from Comparative Genome Analysis of Bacteria and Archaea. Applied and Environmental Microbiology, 71.
C. Vetriani, Y.S. Chew, S.M. Miller, J. Yagi, J. Coombs, R.A. Lutz, and T. Barkay (2005), Mercury Adaptation among Bacteria from a Deep Sea Hydrothermal Vent. Applied and Environmental Microbiology, 71, 220-226.
J. Coombs and T. Barkay (2004), Molecular Evidence for the Evolution of Metal Homeostasis Genes by Lateral Gene Transfer in Bacteria from the Deep Terrestrial Subsurface. Applied and Environmental Microbiology, 49, 1698-1707.
G. Benyehuda, J. Coombs, P.L. Ward, D. Balkwill, and T. Barkay (2003), Metal Resistance among Aerobic Chemoheterotrophic Bacteria from the Deep Terrestrial Subsurface. Canadian Journal of Microbiology, 49, 151-156.
J. Coombs and J.E. Brenchley (2001), Characterization of Two New Gycosyl Hydrolases from the Lactic Acid Bacterium Carnobacterium piscicola Strain BA. Applied and Environmental Microbiology, 67, 5094-5099.
P.P. Sheridan, N. Panasik, J.M. Coombs, and J.E. Brenchley (2000), Aproaches for Deciphering the Structural Basis of Low Temperature Enzyme Activity. Biochimica et Biophysica Acta, 65, 5443-5450.
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J. Coombs (2008, October). Heavy metals and microbes: examining horizontal gene transfer in the PIB-type ATPase family of metal-transporting proteins. SUNY-ESF, Syracuse NY.
J. Coombs (2008, April). Plasmids, phage, and the spread of metal resistance. Adelphi Biology Department faculty seminar.
J. Coombs (2007, June). Deep impact: subsurface microbes, bioremediation, and microbial evolution. North Eastern Microbiologists: Physiology, Ecology, Taxonomy. Blue Mountain Lake, NY.
J. Coombs (2006, November). Deep impact: subsurface microbes, bioremediation, and microbial evolution. Nassau Community College.
J. Coombs (2006, October). Horizontal gene transfer among bacteria of the deep terrestrial subsurface: mechanisms and implications for the bioremediation of hazardous waste sites. Department of Biology seminar series, Hofstra University, Hempstead NY.
J. Coombs (2005, May). Horizontal gene transfer in the environment. Center for Discrete Mathematics and Theoretical Computer Science (DIMACS) Workshop on Reticulated Evolution, New Brunswick NJ.
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Khemraj, N. and J. Coombs (2011). Isolation and Identification of Bacteriophages found in Estuary Waters off off Long Island Shores. In North Eastern Microbiologists--Physiology, Ecology, and Taxonomy (NEMPET). Blue Mountain Lake, NY.
Shekter, A. and J. Coombs (2011). Analysis of Estuary Soil for the Presence of the zntA Gene. In North Eastern Microbiologists--Physiology, Ecology, and Taxonomy (NEMPET). Blue Mountain Lake, NY.
Sosin, M. and J. Coombs (2011). Comparison of the Microbial Community Ecology of Cadmium Contaminated Estuary Soil Using Quantitative Polymerase Chain Reaction. In Adelphi University Eighth Annual Research Conference. Garden City.
Harrison, E., G. Eduardo and J. Coombs. (2009). Detection and isolation of ds-DNA viruses in estuarine and aquifer waters from Long Island, NY. In American Society for Microbiology General Meeting. Philidelphia PA.
Ziogaite, B., B. Smith, A. Chatziefthimiou, T. Barkay, and J. Coombs. (2009). Isolation and microarray analysis of cryptic plasmids from metal resistant bacteria of the deep terrestrial subsurface. In American Society for Microbiology General Meeting. Philidelphia PA.
Vecchi, A., K. Shah, L. Alexis, and J. Coombs (2009). Random mutagenesis of the zntA gene in the XL1-Red mutator strain and its effect on metal resistance in Escherichia coli. In American Society for Microbiology General Meeting. Philidelphia PA.
Mofunanya, O., B. Ziogaite, B. Smith, and J. Coombs. (2008). Isolation and analysis of cryptic plasmids from metal resistant bacteria of the deep terrestrial subsurface. In Metropolitan Association of College and University Biologists (MACUB). Montclair NJ.
Cuneo, D., and J. Coombs (2007). Potential involvement of phage integrases in the horizontal gene transfer of metal resistance genes. In North Eastern Microbiologists--Physiology, Ecology, and Taxonomy (NEMPET). Blue Mountain Lake NY.
Barkay, T., J. Coombs, and A. Chatziefthimiou (2006). Horizontal gene transfer in microbial communities: Genetic plasticity for coping with environmental change. In The Fourth Okazaki Biology Conference: "Terra Microbiology 2". Okazaki, Japan.
Chatziefthimiou, A., J.M. Coombs, and T. Barkay. (2006). The design, optimization, and testing of a hybridization array for the characterization of broad host range metal resistance plasmids. In International Society for Plasmid Biology and other Mobile Genetic Elements. Fallen Leaf Lake, CA.
J. Coombs, G. Oregaard, I. Torres, P. Sobeckey, and T. Barkay (2006). A horizontal gene transfer microarray for the detection of a genomic linkage between metal resistance and inc/rep genes on broad host range plasmids. In American Society for Microbiology General Meeting. Atlanta GA.
Samantha Kozikott (2009). Microbial biofilms. Adelphi University.
Damiano Cuneo (2007). Evidence for the presence of lysogenic bacteriophages in the genomes of bacteria involved in horizontal gene transfer. Adelphi University.
Honors and Accomplishments
2003--Travel Grant to attend the 11th International Microbial Genomes meeting in Durham, NC.
2002--US-EC fellowship for early career scientists, for a short-term exchange to the University of Copenhagen, Denmark.