Abstract
The smallmouth bass Micropterus dolomieu is a major invasive alien species and has a tremendous negative impact on natural aquatic ecosystems around the world. To prevent its range expansion, early detection and countermeasures are critical. Here, we have developed a primer set that can specifically detect smallmouth bass from environmental DNA (eDNA) using only isothermal reactions by the loop-mediated isothermal amplification (LAMP) method. This primer set was applied to DNA samples from tissues of M. dolomieu, M. nigricans, and Lepomis macrochirus to confirm specificity, and positive reactions indicated by white precipitates were obtained only for samples from smallmouth bass. Furthermore, tests using an eDNA sample obtained from the water of the Kinu River in Japan, where smallmouth bass inhabit, also yielded a positive result, indicating its applicability to eDNA. This primer set will be useful for the early detection of the introduction and range expansion of this species and contribute to stream management.
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References
Diedericks G, Henriques R, von der Heyden S et al (2018) The ghost of introduction past: spatial and temporal variability in the genetic diversity of invasive smallmouth bass. Evol Appl 11:1609–1629. https://doi.org/10.1111/eva.12652
Doi H, Watanabe T, Nishizawa N et al (2021) On-site environmental DNA detection of species using ultrarapid mobile PCR. Mol Ecol Resour 21:2364–2368. https://doi.org/10.1111/1755-0998.13448
Franklin TW, Dysthe JC, Rubenson ES et al (2018) A non-invasive sampling method for detecting non-native smallmouth bass (Micropterus dolomieu). Northwest Sci 92:149–157. https://doi.org/10.3955/046.092.0207
Gifu Prefecture (2023) Comprehensive measures for smallmouth bass extermination in Gifu Prefecture. Gifu Prefecture. https://www.pref.gifu.lg.jp/page/337519.html. (In Japanese)
Havel JE, Kovalenko KE, Thomaz SM et al (2015) Aquatic invasive species: challenges for the future. Hydrobiologia 750:147–170. https://doi.org/10.1007/s10750-014-2166-0
Iguchi K, Matsuura K, McNyset KM et al (2004) Predicting invasions of North American Basses in Japan using native range data and a genetic algorithm. Trans Am Fish Soc 133:845–854. https://doi.org/10.1577/t03-172.1
Jo T, Fukuoka A, Uchida K et al (2020) Multiplex real-time PCR enables the simultaneous detection of environmental DNA from freshwater fishes: a case study of three exotic and three threatened native fishes in Japan. Biol Invasions 22:455–471. https://doi.org/10.1007/s10530-019-02102-w
Jothinarayanan N, Karlsen F, Roseng LE (2023) Comparative evaluation of loop-mediated isothermal amplification and PCR for detection of Esox lucius housekeeping genes for use in on-site environmental monitoring. J Fish Biol 103:897–905. https://doi.org/10.1111/jfb.15476
Kageyama SA, Hoogland MR, Tajjioui T et al (2022) Validation of a portable eDNA detection kit for invasive carps. Fishes 7:363. https://doi.org/10.3390/fishes7060363
Katano O, Aonuma Y (2002) An experimental study of the effects of smallmouth bass on the behavior, growth and survival of prey fish. Fish Sci 68:803–814. https://doi.org/10.1046/j.1444-2906.2002.00496.x
Kim D, Taylor AT, Near TJ (2022) Phylogenomics and species delimitation of the economically important Black Basses (Micropterus). Sci Rep 12:9113. https://doi.org/10.1038/s41598-022-11743-2
Kundapur RR, Nema V (2016) Loop-mediated isothermal amplification: beyond microbial identification. Cogent Biol 2:1137110. https://doi.org/10.1080/23312025.2015.1137110
Loppnow GL, Vascotto K, Venturelli PA (2013) Invasive smallmouth bass (Micropterus dolomieu): history, impacts, and control. Manag Biol Invasions 4:191–206. https://doi.org/10.3391/mbi.2013.4.3.02
Mukai T, Sato C (2009) Complete mitochondrial DNA sequences of two haplotypes of the smallmouth bass, Micropterus dolomieu, collected from nonindigenous populations in Japan. Ichthyol Res 56:204–207. https://doi.org/10.1007/s10228-008-0074-x
Notomi T, Okayama H, Masubuchi H et al (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28:e63. https://doi.org/10.1093/nar/28.12.e63
Peterson MI, Kitano S (2019) Stream drift feeding and microhabitat competition of invasive smallmouth bass Micropterus dolomieu, native Japanese dace Tribolodon hakonensis and pale chub Opsariichthys platypus in the Nogu River, Japan. Environ Biol Fishes 102:69–79. https://doi.org/10.1007/s10641-019-0844-5
Peterson MI, Kitano S (2022) Spawning season and nest guarding behavior of invasive smallmouth bass (Micropterus dolomieu) in a Japanese Lake. Ecol Res 37:598–608. https://doi.org/10.1111/1440-1703.12316
Peterson DL, Pecori F, Luchi N et al (2023) Development of novel LAMP and qPCR assays for rapid and specific identification of Bronze birch borer (Agrilus anxius). Environ DNA 5:1177–1190. https://doi.org/10.1002/edn3.503
Porco D, Hermant S, Purnomo CA et al (2022) eDNA-based detection of the invasive crayfish Pacifastacus leniusculus in streams with a LAMP assay using dependent replicates to gain higher sensitivity. Sci Rep 12:6553. https://doi.org/10.1038/s41598-022-10545-w
Reid AJ, Carlson AK, Creed IF et al (2019) Emerging threats and persistent conservation challenges for freshwater biodiversity. Biol Rev 94:849–873. https://doi.org/10.1111/brv.12480
Schall MK, Bartron ML, Wertz T et al (2017) Evaluation of genetic population structure of smallmouth bass in the Susquehanna River Basin, Pennsylvania. North Am J Fish Manag 37:850–861. https://doi.org/10.1080/02755947.2017.1327902
Sepulveda AJ, Nelson NM, Jerde CL, Luikart G (2020) Are environmental DNA methods ready for aquatic invasive species management? Trends Ecol Evol 35:668–678. https://doi.org/10.1016/j.tree.2020.03.011
Suzuki R, Houki S, Ito K, Shibaike H (2023a) PCR and LAMP detection of environmental DNA of the invasive clam Corbicula fluminea. Plankt Benthos Res 18:206–213. https://doi.org/10.3800/pbr.18.206
Suzuki R, Kawamura K, Mizukami Y (2023b) Simple extraction and analysis of environmental DNA using glass fibers in suspension form. Limnology 24:25–36. https://doi.org/10.1007/s10201-022-00705-2
Yasashimoto T, Sakata KM, Sakita T et al (2021) Environmental DNA detection of an invasive ant species (Linepithema humile) from soil samples. Sci Rep 11:10712. https://doi.org/10.1038/s41598-021-89993-9
Yodo T, Iguchi K (2004) A review on the black bass problem referring to the historical background in Japan. Bull Fish Res Agen 12:10–24 (In Japanese with English Abstract)
Acknowledgements
We are grateful to Kazuhiko Morita and Yuki Matsuzawa for their help in getting the fish individuals. We also thank Yoshie Aishima for her help with the laboratory work.
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S.N. and K.M. conceived and designed the study. S.N., K.M., and K.T. performed the field sampling. S.N. and N.A. performed the laboratory work. S.N. wrote the manuscript, with contributions from N.A., K.M., K.T., and K.S.
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Nakajima, S., Amagai, N., Muraoka, K. et al. Development of LAMP primers for rapid detection of invasive smallmouth bass from environmental DNA. Conservation Genet Resour (2024). https://doi.org/10.1007/s12686-024-01360-8
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DOI: https://doi.org/10.1007/s12686-024-01360-8