Message in a Bottle
Observing Marine Ecosystems Through eDNA

Environmental DNA or eDNA is a powerful conservation genetics tool for monitoring ecosystems. Just like we shed skin and hair in the shower, organisms shed their DNA into the environment. We can capture and sequence this DNA by collecting water, soil, or air and reconstruct the species living there. My research goals are to develop and implement rapid, reliable, and repeatable eDNA methods to to provide both scientists, resource managers, and policymakers better tools to assess marine biodiversity and the impacts of human stressors on marine ecosystems. All of my research projects have a strong conservation focus whether it is to survey endangered and threatened species, monitor or marine protected areas, or characterize zooplankton assemblage responses to warming, ocean acidification, and hypoxia. eDNA has the potential to transform the way that marine ecosystems are monitored, giving resource managers the ability to monitor biodiversity, in a simple, cost effective manner.

Projects

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Foraging Ecology of Cook Inlet Beluga Whales
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Monitoring Southern California Marine Protected Areas Using eDNA
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Endangered Fairy Shrimp and Vernal Pools
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Indonesia Biodiversity Monitoring
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Unlocking ethanol-preserved CalCOFI samples with eDNA
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A manager’s guide to using eDNA metabarcoding in marine ecosystems
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Monitoring Surf Zone Ecosystems
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Heat Tolerant Corals
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Bioinformatics and Data Analysis Tools

Publications

  • Gold, Z., Kelly, R.P., Shelton, A.O., Thompson, A.R., Goodwin, K.D., Gallego, R., Parsons, K.M., Thompson, L.R., Kacev, D. and Barber, P.H., 2023. Message in a bottle: Archived DNA reveals marine heatwave‐associated shifts in fish assemblages. Environmental DNA.
  • Gold, Z., Shelton, A.O., Casendino, H.R., Duprey, J., Gallego, R., Van Cise, A., Fisher, M., Jensen, A.J., D’Agnese, E., Andruszkiewicz Allan, E. and Ramón-Laca, A., 2023. Signal and noise in metabarcoding data. Plos one, 18(5), p.e0285674.
  • Gold, Zachary, McKenzie Q. Koch, Nicholas K. Schooler, Kyle A. Emery, Jenifer E. Dugan, Robert J. Miller, Henry M. Page et al. A comparison of biomonitoring methodologies for surf zone fish communities. Plos one 18, no. 6 (2023): e0260903.
  • Kelly, Ryan P., David M. Lodge, Kai N. Lee, Susanna Theroux, Adam J. Sepulveda, Christopher A. Scholin, Joseph M. Craine et al. Toward a national eDNA strategy for the United States. Environmental DNA (2023).
  • Satterthwaite, E.V., A.E. Allen, R.H. Lampe, Z. Gold, A.R. Thompson, N. Bowlin, R. Swalethorp, K.D. Goodwin, E.L. Hazen, S.J. Bograd, S.A. Matthews, and B.X. Semmens. (2023). Toward Identifying the Critical Ecological Habitat of Larval Fishes: An Environmental DNA Window into Fisheries Management In Frontiers in Ocean Observing: Emerging Technologies for Understanding and Managing a Changing Ocean. Oceanography 36(Supplement 1), https://doi.org/10.5670/oceanog.2023.s1.29.
  • Gold, Zachary, Adam R. Wall, Teia M. Schweizer, N. Dean Pentcheff, Emily E. Curd, Paul H. Barber, Rachel S. Meyer et al. "A manager’s guide to using eDNA metabarcoding in marine ecosystems." PeerJ 10 (2022): e14071. https://peerj.com/articles/14071/
  • Shelton, A.O., Gold, Z.J., Jensen, A.J., D′ Agnese, E., Andruszkiewicz Allan, E., Van Cise, A., Gallego, R., Ramón‐Laca, A., Garber‐Yonts, M., Parsons, K. and Kelly, R.P. (2022). Toward quantitative metabarcoding. Ecology, e3906. https://doi.org/10.1002/ecy.3906
  • Marwayana, O. N., Gold, Z., Meyer, C. P., & Barber, P. H. (2022). Environmental DNA in a global biodiversity hotspot: Lessons from coral reef fish diversity across the Indonesian archipelago. Environmental DNA, 4(1), 222-238.  
    https://doi.org/10.1002/edn3.257
  • Min, M. A., Barber, P. H., & Gold, Z. (2021). MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes). Conservation Genetics Resources, 13(4), 447-456. min2021_article_misebastesanednametabarcodingp.pdf
  • Monuki, K., Barber, P. H., & Gold, Z. (2021). eDNA captures depth partitioning in a kelp forest ecosystem. PloS one, 16(11), e0253104. https://doi.org/10.1371/journal.pone.0253104
  • Gold, Z., Curd, E. E., Goodwin, K. D., Choi, E. S., Frable, B. W., Thompson, A. R., ... & Barber, P. H. (2021). Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem. Molecular Ecology Resources, 21(7), 2546-2564. gold2021_mer_bioinformatic_benchmarking.pdf
  • Ely, T., Barber, P. H., Man, L., & Gold, Z. (2021). Short-lived detection of an introduced vertebrate eDNA signal in a nearshore rocky reef environment. Plos one, 16(6), e0245314. https://doi.org/10.1371/journal.pone.0245314
  • Willette, D. A., Navarrete-Forero, G., Gold, Z., Lizano, A. M. D., Gonzalez-Smith, L., & Sotil, G. (2021). Characterizing Industrial and Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data. Foods, 10(6), 1425. https://doi.org/10.3390/foods10061425
  • Gold Z, Sprague J, Kushner DJ, Zerecero Marin E, Barber PH (2021) eDNA metabarcoding as a biomonitoring tool for marine protected areas. PLOS ONE 16(2): e0238557. https://doi.org/10.1371/journal.pone.0238557
  • Meyer R, Ramos M, Lin M, Schweizer T, Gold Z, Ramos D, Shirazi S, Kandlikar G, Kwan W, Curd E, Freise A, Parker J, Sexton J, Wetzer R, Pentcheff N, Wall A, Pipes L, Garcia-Vedrenne A, Mejia M, Moore T, Orland C, Ballare K, Worth A, Beraut E, Aronson E, Nielsen R, Lewin H, Barber P, Wall J, Kraft N, Shapiro B, Wayne R. 2021. The CALeDNA program: Citizen scientists and researchers inventory California's biodiversity. Calif Agr 75(1):20-32. https://doi.org/10.3733/ca.2021a0001.
  • ​Lin M, Simons AL, Harrigan RJ, Curd EE, Schneider FD, Ruiz-Ramos DV, Gold Z, Osborne MG, Shirazi S, Schweizer TM, Moore TN, Fox EA, Turba R, Garcia-Vedrenne AE, Helman SK, Rutledge K, Palacios Mejia M, Marwayana O, Munguia Ramos MN, Wetzer R, Pentcheff ND, McTavish EJ, Dawson MN, Shapiro B, Wayne RK, Meyer RS. Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California. Ecol Appl. 2021 May 20:e2379.  
    https://doi.org/10.1002/eap.2379
  • Gold, Z., Wall., A.R., Curd, E.E., Ripma, L., Pentcheff, D.N., Kelly, R., Barber, P.H., Wetzer, R. (2020). eDNA metabarcoding bioassessment of endangered fairy shrimp (Branchinecta spp.). Conservation Genetics Resources, 1-6. https://doi.org/10.1007/s12686-020-01161-9
  • Gold, Z. J. (2020). Design and Implementation of Environmental DNA Metabarcoding Methods for Monitoring the Southern California Marine Protected Area Network. UCLA. Retrieved from https://escholarship.org/uc/item/7zf5g0cb
  • Emily Curd, Zachary Gold, Gaurav Kandlikar, Jesse Gomer, Max Ogden, TaylorO'Connell, Lenore Pipes, Teia Schweizer, Laura Rabichow, Meixi Lin, Baochen Shi, PaulBarber, Nathan Kraft, Robert Wayne, Rachel S. Meyer. "Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets. Methods in Ecology and Evolution. doi: https://doi.org/10.1111/2041-210X.13214
  • Kandlikar, Gaurav S., Zachary Gold, Madeline C. Cowen, Rachel S. Meyer, Amanda C. Freise, Nathan JB Kraft, Jordan Moberg-Parker, Joshua Sprague, David J. Kushner, and Emily E. Curd. "ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations." F1000Research 7 (2018). doi: 10.12688/f1000research.16680.1​
  • Gold, Zachary, and Stephen R. Palumbi. "Long-term growth rates and effects of bleaching in Acropora hyacinthus." Coral Reefs 37, no. 1 (2018): 267-277. https://doi.org/10.1007/s00338-018-1656-3 ​​​