Environmental DNA (eDNA) techniques are a suite of molecular detection tools, which are becoming increasingly prominent in aquatic sciences, with exciting possibilities in aquatic animal health. Environmental DNA sampling is most concisely defined as the collection of genetic material from the environment where individuals, or pieces of individuals, are not isolated from the abiotic components of the ecosystem (soil, water, etc.) at the time of collection. This definition is adapted from Díaz-Ferguson and Moyer (2014) and Thomsen and Willerslev (2015).
The purpose of this site is to aggregate references focusing on aquatic microbial eDNA, with an emphasis on applications in aquatic animal health. I have chosen this narrow focus because of the nascent character of this sub-discipline, my professional interests, and because eDNA use in microbial ecology and diversity is a well-established discipline with a separate and extensive body of literature.
For clarity, (and following the example of Taylor Wilcox) I use the terminology of Turner et al., (2014) where microbial eDNA refers to sampling of small, whole individuals (such as bacterial cells and other microbes) and macrobial eDNA refers to sampling of genetic material that has been separated from the body of a relatively large organism (such as shed fish fish epithelial cells).
For an extensive bibliography of macrobial eDNA references please visit the list curated by Taylor Wilcox.
This is a dynamic bibliography which will be updated periodically as I have time to review the published literature. Suggestions, additions, and corrections are welcomed and can be sent to mae (DOT) giddings (AT) (g) mail (DOT) com.
References:
Díaz-Ferguson, E., & Moyer, G. (2014). History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments. RBT Revista De Biología Tropical, 62(4), 1273-1284.
Thomsen, P. F., & Willerslev, E. (2015). Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation, 183, 4-18. doi:10.1016/j.biocon.2014.11.019
Turner, C. R., Barnes, M. A., Xu, C. C., Jones, S. E., Jerde, C. L., & Lodge, D. M. (2014). Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods in Ecology and Evolution, 5(7), 676-684. doi:10.1111/2041-210x.12206
Aquatic Microbial eDNA Bibliography
Aygen, T., Ünal E.M., Kaynar S., Genç, E.,& Keskin, E. (2016) Using biological filters as a source for environmental DNA in recirculating aquaculture systems. FABA International Symposium Fisheries and Aquatic Science. Antalya, Turkey 2016
Cardona, E., Gueguen, Y., Magré, K., Lorgeoux, B., Piquemal, D., Pierrat, F., . . . Saulnier, D. (2016). Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system. BMC Microbiology,16(1).
Dittami, S. M., Riisberg, I., & Edvardsen, B. (2013). Molecular probes for the detection and identification of ichthyotoxic marine microalgae of the genus Pseudochattonella (Dictyochophyceae, Ochrophyta). Environmental Science and Pollution Research, 20(10), 6824-6837. doi:10.1007/s11356-012-1402-2
Eckford-Soper, L. K., & Daugbjerg, N. (2015). Development of a multiplex real-time qPCR assay for simultaneous enumeration of up to four marine toxic bloom-forming microalgal species. Harmful Algae,48, 37-43.
Fong, J., Cho, H., Park, M., & Lim, Y. (2016). Evaluating seasonality and pathogenicity of Aeromonas in Korea using environmental DNA. Asian Jr. of Microbiol. Biotech. Env. Sc, 18(3), 605-613.
Gomes, G. B., Hutson, K. S., Domingos, J. A., Chung, C., Hayward, S., Miller, T. L., & Jerry, D. R. (2017). Use of environmental DNA (eDNA) and water quality data to predict protozoan parasites outbreaks in fish farms. Aquaculture, 479, 467-473. doi:10.1016/j.aquaculture.2017.06.021
Hartikainen, H., Bass, D., Briscoe, A. G., Knipe, H., Green, A. J., & Okamura, B. (2016). Assessing myxozoan presence and diversity using environmental DNA. International Journal for Parasitology,46(12), 781-792. doi:10.1016/j.ijpara.2016.07.006
Hashizume, H., Sato, M., Sato, M. O., Ikeda, S., Yoonuan, T., Sanguankiat, S., . . . Minamoto, T. (2017). Application of environmental DNA analysis for the detection of Opisthorchis viverrini DNA in water samples. Acta Tropica, 169, 1-7. doi:10.1016/j.actatropica.2017.01.008
Honjo, M. N., Minamoto, T., & Kawabata, Z. I. (2012). Reservoirs of Cyprinid herpesvirus 3 (CyHV-3) DNA in sediments of natural lakes and ponds. Veterinary microbiology, 155(2), 183-190.
Huver, J. R., Koprivnikar, J., Johnson, P. T., & Whyard, S. (2015). Development and application of an eDNA method to detect and quantify a pathogenic parasite in aquatic ecosystems. Ecological Applications, 25(4), 991-1002. doi:10.1890/14-1530.1
Kim, Y., Bonn, W. V., Aw, T. G., & Rose, J. B. (2017). Aquarium Viromes: Viromes of Human-Managed Aquatic Systems. Frontiers in Microbiology, 8.
Lyons, M., Smolowitz, R., Dungan, C., & Roberts, S. (2006). Development of a real time quantitative PCR assay for the hard clam pathogen Quahog Parasite Unknown (QPX). Diseases of Aquatic Organisms, 72, 45-52.
Minamoto, T., Honjo, M. N., Uchii, K., Yamanaka, H., Suzuki, A. A., Kohmatsu, Y., . . . Kawabata, Z. (2009). Detection of cyprinid herpesvirus 3 DNA in river water during and after an outbreak. Veterinary Microbiology,135(3-4), 261-266.
Minamoto, T., Honjo, M. N., Yamanaka, H., Uchii, K., & Kawabata, Z. (2012). Nationwide Cyprinid herpesvirus 3 contamination in natural rivers of Japan. Research in Veterinary Science,93(1), 508-514.
Picón-Camacho, S. M., Thompson, W. P., Blaylock, R. B., & Lotz, J. M. (2013). Development of a rapid assay to detect the dinoflagellate Amyloodinium ocellatum using loop-mediated isothermal amplification (LAMP). Veterinary Parasitology, 196(3-4), 265-271. doi:10.1016/j.vetpar.2013.04.010
Schmidt, B. R., Kéry, M., Ursenbacher, S., Hyman, O. J., & Collins, J. P. (2013). Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen. Methods in Ecology and Evolution, 4(7), 646-653.
Strand, D., Jussila, J., Johnsen, S., Viljamaa-Dirks, S., Edsman, L., Wiik-Nielsen, J., . . . Vrålstad, T. (2014). Detection of crayfish plague spores in large freshwater systems. Journal of Applied Ecology J Appl Ecol, 544-553.
Verhoeven, J. T. P., Salvo, F., Hamoutene, D., & Dufour, S. C. (2016). Bacterial community composition of flocculent matter under a salmonid aquaculture site in Newfoundland, Canada Aquaculture and Environmental Interactions, 8, 637-646.
Aygen, T., Ünal E.M., Kaynar S., Genç, E.,& Keskin, E. (2016) Using biological filters as a source for environmental DNA in recirculating aquaculture systems. FABA International Symposium Fisheries and Aquatic Science. Antalya, Turkey 2016
Cardona, E., Gueguen, Y., Magré, K., Lorgeoux, B., Piquemal, D., Pierrat, F., . . . Saulnier, D. (2016). Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system. BMC Microbiology,16(1).
Dittami, S. M., Riisberg, I., & Edvardsen, B. (2013). Molecular probes for the detection and identification of ichthyotoxic marine microalgae of the genus Pseudochattonella (Dictyochophyceae, Ochrophyta). Environmental Science and Pollution Research, 20(10), 6824-6837. doi:10.1007/s11356-012-1402-2
Eckford-Soper, L. K., & Daugbjerg, N. (2015). Development of a multiplex real-time qPCR assay for simultaneous enumeration of up to four marine toxic bloom-forming microalgal species. Harmful Algae,48, 37-43.
Fong, J., Cho, H., Park, M., & Lim, Y. (2016). Evaluating seasonality and pathogenicity of Aeromonas in Korea using environmental DNA. Asian Jr. of Microbiol. Biotech. Env. Sc, 18(3), 605-613.
Gomes, G. B., Hutson, K. S., Domingos, J. A., Chung, C., Hayward, S., Miller, T. L., & Jerry, D. R. (2017). Use of environmental DNA (eDNA) and water quality data to predict protozoan parasites outbreaks in fish farms. Aquaculture, 479, 467-473. doi:10.1016/j.aquaculture.2017.06.021
Hartikainen, H., Bass, D., Briscoe, A. G., Knipe, H., Green, A. J., & Okamura, B. (2016). Assessing myxozoan presence and diversity using environmental DNA. International Journal for Parasitology,46(12), 781-792. doi:10.1016/j.ijpara.2016.07.006
Hashizume, H., Sato, M., Sato, M. O., Ikeda, S., Yoonuan, T., Sanguankiat, S., . . . Minamoto, T. (2017). Application of environmental DNA analysis for the detection of Opisthorchis viverrini DNA in water samples. Acta Tropica, 169, 1-7. doi:10.1016/j.actatropica.2017.01.008
Honjo, M. N., Minamoto, T., & Kawabata, Z. I. (2012). Reservoirs of Cyprinid herpesvirus 3 (CyHV-3) DNA in sediments of natural lakes and ponds. Veterinary microbiology, 155(2), 183-190.
Huver, J. R., Koprivnikar, J., Johnson, P. T., & Whyard, S. (2015). Development and application of an eDNA method to detect and quantify a pathogenic parasite in aquatic ecosystems. Ecological Applications, 25(4), 991-1002. doi:10.1890/14-1530.1
Kim, Y., Bonn, W. V., Aw, T. G., & Rose, J. B. (2017). Aquarium Viromes: Viromes of Human-Managed Aquatic Systems. Frontiers in Microbiology, 8.
Lyons, M., Smolowitz, R., Dungan, C., & Roberts, S. (2006). Development of a real time quantitative PCR assay for the hard clam pathogen Quahog Parasite Unknown (QPX). Diseases of Aquatic Organisms, 72, 45-52.
Minamoto, T., Honjo, M. N., Uchii, K., Yamanaka, H., Suzuki, A. A., Kohmatsu, Y., . . . Kawabata, Z. (2009). Detection of cyprinid herpesvirus 3 DNA in river water during and after an outbreak. Veterinary Microbiology,135(3-4), 261-266.
Minamoto, T., Honjo, M. N., Yamanaka, H., Uchii, K., & Kawabata, Z. (2012). Nationwide Cyprinid herpesvirus 3 contamination in natural rivers of Japan. Research in Veterinary Science,93(1), 508-514.
Picón-Camacho, S. M., Thompson, W. P., Blaylock, R. B., & Lotz, J. M. (2013). Development of a rapid assay to detect the dinoflagellate Amyloodinium ocellatum using loop-mediated isothermal amplification (LAMP). Veterinary Parasitology, 196(3-4), 265-271. doi:10.1016/j.vetpar.2013.04.010
Schmidt, B. R., Kéry, M., Ursenbacher, S., Hyman, O. J., & Collins, J. P. (2013). Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen. Methods in Ecology and Evolution, 4(7), 646-653.
Strand, D., Jussila, J., Johnsen, S., Viljamaa-Dirks, S., Edsman, L., Wiik-Nielsen, J., . . . Vrålstad, T. (2014). Detection of crayfish plague spores in large freshwater systems. Journal of Applied Ecology J Appl Ecol, 544-553.
Verhoeven, J. T. P., Salvo, F., Hamoutene, D., & Dufour, S. C. (2016). Bacterial community composition of flocculent matter under a salmonid aquaculture site in Newfoundland, Canada Aquaculture and Environmental Interactions, 8, 637-646.
About Mae Giddings: I am a laboratory manager by trade and a fish health specialist by training. I use my background in aquatic sciences to manage laboratories in a safe and efficient manner. I really enjoy identifying methods and procedures to continually improve lab outcomes. My professional interests include include laboratory management, data management and stewardship, and technical writing. My interest in information stewardship lead me to create this site. I had a pretty extensive aquatic eDNA reference list and I found that Taylor Wilcox did too. Rather than reinvent the wheel, I turned my general aquatic eDNA reference list over to Taylor's very capable hands and I'm now focusing on an aquatic animal-health sub-list. Based on my extensive study of the published literature I think that eDNA techniques will soon be extensively adapted for use in aquatic animal health diagnostics and management. I hope that this bibliography can help disseminate information about eDNA in aquatic sciences.