Elizabeth Dinsdale

Department of Biology
Associate Professor, Biology

Office/Lab: SDSU Main Campus, Life Science North 308
Phone: 619-594-5623 (office)
Email: edinsdale@mail.sdsu.edu

Dinsdale Lab

Dr. Dinsdale’s lab at San Diego State University uses next-generation sequencing to tease apart ecological and evolutionary relationships within marine, coral reef and kelp forest ecosystems. We are a multi-disciplinary team of students and researchers from around the globe.

Dr. Dinsdale helped establish one of the first university-level classes to offer hands-on experience with a pyrosequencing machine. In 2011, students of BIOL596 Ecological Metagenomics at SDSU sequenced the California sea lion genome at 12X coverage. Students applied bioinformatics and statistics techniques to analyze the resulting genomes and metagenomes.

We apply DNA sequencing technology to answer questions in microbial ecology and genetics.

Journals

Meirelles, PM, G.M. Amado-Filho, G.H. Pereira-Filho, H.T. Pinheiro, R.L. de Moura, J. C. Joyeux, E.F. Mazzei, A. C. Bastos, R.A. Edwards, E. Dinsdale, R. Paranhos, E. O. Santos, T. Iida, K. Gotoh, S. Nakamura, T. Sawabe, C. E. Rezende, L. M. R. Gadelha, R. B. Francini-Filho, C. Thompson, F. L. Thompson 2015 Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data. PLOS ONE 10.1371/journal.pone.0130084.

Busch, J.C., Rubem Magalhães, A., J. Ribeiro do Nascimento, E. A. Dinsdale 2015 Copper tolerance of microbes associated with Macrocystis pyrifera across three southern Californian locations. Ecotoxicology 1-10

Matthews, D. R. Schmieder, G. G Silva B. Matlock, D. Green, N. Cassman, J. Busch, B. Heffern, G. Olsen, L. Hanna, D. Schifferli S. Maloy, E. A. Dinsdale R.A. Edwards 2015 Genomic Comparison of the Closely-related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum PLoS ONE 10.1371/journal.pone.0126883. 

Cuevas, D.A., D. Garza, S. E. Sanchez, J. Rostron, C. Henry, V. Vonstein, R. A. Overbeek, F. Rohwer, E.A. Dinsdale, R. A. Edwards 2014 Elucidating Genomic Gaps using Phenotypic Profiles. Foundation 1000

Lim YW, Cuevas DA, Silva GGZ, Aguinaldo K, Dinsdale EA, Haas AF, Hatay M, Sanchez* SE, Wegley-Kelly L, Dutilh BE, Harkins TT, Lee CC, Tom W, Sandin SA, Smith JE, Zgliczynski B, Vermeij MJA, Rohwer F, Edwards RA. 2014 Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition. PeerJ 2:e520.

Dutilh, B.E., N. Cassman, K. McNair, L. Boling, S. Sanchez, M. Wellington-Oguri, J.J. Barr, R.K. Aziz, B. Felts, JL. Mokili, E.A. Dinsdale, RA. Edwards 2014. Ubiquitous phage genome and host identified by depth profiling across metagenomes. Nature Communications. 5: 4498. doi:10.1038/ncomms5498

Dutilh, B., Thompson, C., Vicente, A., Marin, M., Lee, C., Silva, G., Schmieder, R., Andrade, B., Chimetto, L., Cuevas, D., Garza, D., Okeke, I., Aboderin, O., Spangler, J., Ross, T., Dinsdale, E.A., Thompson, F., Harkins, T., and Edwards, R. 2014. Genomic landscape of Vibrio cholerae connects genotype and phenotype across time, space and habitat. BMC genomics 15 (1), 65.

Wegley Kelly, L., G.J. Williams, K.L. Barott, C.A. Carlson, E.A. Dinsdale,R.A. Edwards, A. F. Haas, M. Haynes, Y. W. Lim, T. McDole, C. E. Nelson, E. Sala, S. A. Sadin, J. E. Smith, M. J.A. Vermeij, M. Youlei, and F. Rohwer 2014Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors. Proceedings of the National Academy doi: 10.1073/pnas.1403319111

Mark Eppinger, Katelyn McNair, Xhavit Zogaj, Elizabeth Dinsdale, Robert Edwards, and Karl 2013 Whole Genome Draft Sequence of the fish pathogen Piscirickettsia salmonis” (genomeA00926-13). doi:10.1128/genomeA.00926-13

Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA 2013 Combining de novo and reference-guided assembly with scaffold_builder. Source Code Biol Med. 2013, 8:23. doi: 10.1186/1751-0473-8-23

Edwards, R. A., J.M. Haggerty, N. Cassman, J. C. Busch, K. Aguinaldo$, S. Chinta, R. Morey, M. Houle Vaughn, T.T. Harkins, C. Teiling, K. Fredrikson, and E. A Dinsdale 2013 Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era. BMC Genomics 14:600.

Lipson, D. A., J.M. Haggerty, A. Srinivas, S. Sathe, T. K. Raab, E. A. Dinsdale. 2013 Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile. Plos One 8(5): e64659. doi:10.1371/journal.pone.0064659

Dinsdale, E. A., R. A. Edwards, B. Bailey, I. Tuba, S. Akhter, K. McNair, R. Schmieder, N. Apkarian, M. Creek, E. Guan, M. Hernandez, K. Isaacs, C. Peterson, T. Regh, V. Ponomarenko. 2013 Multivariate analysis of functional metagenomes. Frontiers in Genetics 4:41. doi: 10.3389/fgene.2013.00041

Haggerty, J.M. M.N. Brett, R. B. Francini Filho, E. A. Dinsdale. 2012 Night surveys along the Abrolhos Bank, Brazil, generate first observation of mucous cocoon production in Scarus trispinosus. Bulletin of Marine Science, 88(4):883-88. 

Cassman, N., Prieto-Davó, A. F. Angly, S. Akhter, K Barott, J. Busch, T. McDole, J. M. Haggerty, K. Walsh, G. G. Z. Silva, B, Dutilh, G. Alarcón, O. Ulloa, E. F. DeLong, F. Rohwer, E. A. Dinsdale. 2012 Oxygen minimum zones harbor novel but low diversity viral communities. Environ Microbiol. doi:10.1111/j.1462-2920.2012.02891.

Bruce T, P. M. Meirelles, G. Garcia, R. Paranhos, C. E. Rezende, R. L. de Moura, R. Francini Filho, A. Tereza Vasconcelos, G. Amado Filho, M. Hatay, R. Edwards, R. Schmieder, E.A Dinsdale and F. L. Thompson 2012 Abrolhos Reef Bank health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass. PLoS One. 2012; 7(6):e36687

Hughes T.P, A.H. Baird, E.A. Dinsdale, N.A. Moltschaniwskyji, M.S. Pratchett, J.E. Tanner and B.L. Willis 2012 Assembly rules of reef corals are flexible along a steep climate gradient. Current Biology 22:1-6 Citations – 11 DOI: 10.1016/j.cub.2012.02.068

Hanna, F.L.A, T.D. Matthews, EA Dinsdale, R, Hasty, RA Edwards, 2012 Characterization of the ELPhiS Prophage from Salmonella enterica Serovar Enteritidis strain LK5. Appl Environ Microbiol. 12:1785-1793

Wegley Kelly, L., K. L. Barott, E. A. Dinsdale, B. Nosrat, D. Obura, S. Sandin, J. E. Smith, D. Willner, and F. Rohwer 2011 Black Reefs: Iron induced phase shifts on coral reefs. ISME J. 6: 638–649 Citations – 7 DOI: 10.1038/ismej.2011.114

Jeffries, T.C., J. R. Seymour, E. A. Dinsdale, K. Newton, S. S.C. Leterme, B. Roudnew, R. J. Smith, J. A. Gilbert, L. Seuront, J. G. Mitchell 2011 Substrate type determines metagenomic profiles from diverse chemical habitats. PLoS One. 10.1371

Barott, K.L, J. E. Caselle, E. A. Dinsdale, A. M. Friedlander, J. E. Maragos, D. Obura, F. L. Rohwer, S. A. Sandin, J. E. Smith, and B. Zgliczynski 2010 The Lagoon at Caroline/Millennium Atoll, Republic of Kiribati: Natural history of a nearly pristine ecosystem. PLoS One.2010; 5(6): e10950.

Raina, J.B, E.A. Dinsdale, B. L. Willis and D. G. Bourne 2010 Do organic sulfur compounds DMSP and DMS drive coral microbial associations? Trends Microbiol. 18: 101-108

Rodriguez-Brito, B., L.Li, L. Wegley, M. Furlan, F. Angly, M. Breitbart, J. Buchanan, C. Desnues, E. A. Dinsdale, R. Edwards, B. Felts, D. Willner, M. Haynes, H. Liu, D. Lipson, J Mahaffy, A-B. Martin-Cuadrado, A. Mira-Obrador, J. Nulton, L. Pasic, S. Rayhawk, J. Rodriguez-Mueller, F. Rodriguez-Valera, P. Salamon, S. Srinagesh, T. Frede Thingstad, R. Vega Thurber, T. Tran, F. Rohwer 2010 Kill-the-winner in four aquatic environments. ISME J. 11 doi:10.1038/ismej.2010.

Dinsdale, E.A. 2009 Linking ecological and perceptual assessments for environmental management: a coral reef case study. Ecology and Society 14(2): 28. [online]

Barott K, Smith J, Dinsdale E, Hatay M, Sandin S, et al. 2009 Hyperspectral and physiological analyses of coral-algal interactions. PLoS One. 4(11):e8043. doi:10.1371/journal.pone.0008043

Angly, FE, D. Willner, A. Prieto-Davo, R. A. Edwards, R. Schmieder, R. Vega Thurber, D. A. Antonopoulos, K. Barott, M.T. Cottrell, C. Desnues, EA. Dinsdale M Furlan, M. Haynes 1, M. R. Henn, Y. Hu, D L. Kirchman, T McDole, J. D. McPherson, F. Meyer, R. M. Miller, E. Mundt, R. K. Naviaux, B. Rodriguez-Brito, R Stevens, L. Wegley, L. Zhang and B. Zhu, F. Rohwer 2009 The GAAS Metagenomic Tool and its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes. PLoS Comput Biol. 5: 12 Number: e1000593

Breitbart, M, A. Hoare, A. Nitti, J. Siefert, M. Haynes, E.A. Dinsdale, R.A. Edwards, V. Souza, F. Rohwer, D. Hollander 2009 Microbial communities and stable isotopic analyses of modern microbialites in Cuatro Ciénegas, Mexico. Environ Microbiol. 11:16- 34

Brulc J M., D.A. Antonopoulos, M.E. Berg, M.K. Wilson, A.C. Yannarell, E.A. Dinsdale, R.A. Edwards, E.D. Frank, J.B. Emerson, P. Wacklin, P.M. Coutinho, B. Henrissat, K.E. Nelson, and B.A. White 2009 Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A 106:1948-1953

Vega Thurber R., D. Hall-Willner, B. Rodriguez-Brito, C. Desnues, R.A. Edwards, F. Angly, E.A. Dinsdale, L. Kelly, and F. Rohwer. 2009 Metagenomic Analysis of Stressed Coral Holobionts Environ Microbiol. 11: 2148–2163

Dinsdale, E.A., R.A. Edwards, D. Hall, F. Angly, M. Breitbart, J.M. Brulc, M. Furlan, C. Desnues, M. Haynes; L. Li, L. McDaniel, M.A. Moran, K.E. Nelson, C. Nilsson, R. Olson, J. Paul, B. Rodriguez Brito, Y. Ruan, B.K. Swan, R. Stevens, D. L. Valentine, R. Vega Thurber, L. Wegley, B.A. White, and F. Rohwer 2008 Functional metagenomic profiling of nine biomes. Nature. 452:629-632

Dinsdale, E.A. and F. Rohwer 2008 Dissecting microbial employment. Nat Biotechnol. 26:997-998

Dinsdale, E.A., O. Pantos, S. Smriga, R.A. Edwards, L. Wegley, F. Angly, E. Brown$, M. Haynes, L. Krause, E. Sala, S. Sandin, R. Vega Thurber, B.L. Willis, N. Knowlton, F. Azam, and F. Rohwer. 2008. Microbial ecology of four coral atolls in the Northern Line Islands. PLoS One. 3(2) e1584

Sandin, S., J.E. Smith, E. DeMartini, E.A. Dinsdale, A. Friedlander, J.B.C. Jackson, N. Knowlton, M. Malay, J. Maragos, D. Obura, G. Paulay, M. Richie, S. Walsh, E. Sala. 2008 Degradation and recovery of coral reefs across a gradient of human disturbance. PloS One 3(2) e1548

Qu, A, J.M Brulc, M.K. Wilson, B.F. Law, J.R. Theoret, L.A. Joens, M.E. Konkel, F. Angly, E.A. Dinsdale, R.A. Edwards, K.E. Nelson, and B.A. White 2008. Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One.3(8): e2945

Edwards R.A. and Dinsdale E.A. 2007 Marine environmental genomics: unlocking the oceans secrets. Oceanography 20:56-61

Dinsdale E.A. and D.M. Fenton 2006 Assessing coral reef condition: eliciting community meanings. Society and Natural Resources 19: 239-295

Dinsdale E.A., and Harriott V.J. 2004 Assessing anchor damage on coral reefs: a case study in selection of environmental indicators. Environ Manage. 33: 126-139

Hughes T.P, A.H. Baird, E.A. Dinsdale, V.J. Harriott, N.A. Moltschaniwskyji, M.S. Pratchett, J.E. Tanner and B.L. Willis 2002 Latitudinal patterns in larval recruitment: Detecting regional variation using meta-analysis and large-scale sampling. Ecology 83:436-541

Hughes T.P, A.H. Baird, E.A. Dinsdale, N.A. Moltschaniwskyji, M.S. Pratchett, J.E. Tanner and B.L. Willis 2000 Supply side ecology in reverse: The link between adults, fecundity and larval recruits. Ecology 81:2241-2249

Hughes T.P, A.H. Baird, E.A. Dinsdale, N.A. Moltschaniwskyji, M.S. Pratchett, J.E. Tanner and B.L. Willis 1999 Patterns of recruitment and abundance of corals along the Great Barrier Reef. Nature 397:59-63

In Review

Walsh, K, J.M. Haggerty, J. Spangler, M.B. Turner, C. Lee, G. Amado-Filho, R. Francini-Filho, C.B. Silveira, R. L. Moura, TT. Harkins, R. A. Edwards, F.L. Thompson, and E. A. Dinsdale 2014 Macro-organism Influence on Coral Reef Microbial Communities. Molecular Ecology

Cuevas,D.A., D. Garza, S. E. Sanchez, J. Rostron,C. Henry,V. Vonstein, R. A. Overbeek, F. Rohwer, E.A. Dinsdale, R. A. Edwards 2014 Elucidating Genomic Gaps using Phenotypic Profiles. Foundation 1000

Book Chapters

Minich, J.J. and E. A. Dinsdale 2013 Experimental metagenomics: Experimental metagenomics: Influence of pulses of carbon dioxide on kelp forest microbial ecology. In Nelson, K. (ed) Encyclopedia of metagenomics. Springer

Dinsdale, E.A. and F. Rohwer 2010 Fish or Germs? A microbial perspective on changing trophic structure on coral reefs. Chapter 16, Coral Reef: an ecosystem in transition. In Press (ed) Z. Dubinski, Springer-verlag.

Dinsdale, E. A. 2011 Microbes. Pages 697-698 in D. Hopley (ed) Encyclopedia of Modern Coral Reefs: Structure, Form and Process. Springer-Verlag

Willis, B.L. C. Page, D. Bourne, L. Owens, S. Anthony, H. Boyett, E.A. Dinsdale, D. Harvell, D. Jacobson, C. Lonergan, S. Neale, C. Palmer, L. Raymundo, M. Sussman 2009 Coral disease on the Great Barrier Reef and in the Western Pacific. Pages 234-243 in Galloway, S.B., Bruckner, A.W. and Woodley, C.M. (eds.), 2009. Coral Health and Disease in the Pacific: Vision for Action. NOAA Technical Memorandum NOS NCCOS97 and CRCP 7. National Oceanic and Atmospheric Administration, Silver Spring, MD

Willis B.L., C. Page and E.A. Dinsdale 2004 Coral disease in the Indo-Pacific. Pages 69-104. Loya Y. and R. Rosenberg (eds) Coral health and disease. Springer-verlag.

Micheal Doane (Ph.D.)

B.S. Integrative Biology, University of Illinois, Urbana-Champaign

Research Interests: Microbial community ecology and ecosystem function

Dissertation topic: The shark skin microbiome: Drivers of microbial community structure

Email: mdoane@sdsu.edu

Megan Morris (Ph.D.)

B.S. Biology, San Diego State University (2011)

Research Interests: Microbial ecology, kelp forest ecology, metagenomics

Dissertation topic: Microbial communities associated with Macrocystis pyrifera

Email: mmorris@sdsu.edu