Using standardized fish-specific autonomous reef monitoring structures ( FARMS ) to quantify cryptobenthic fish communities

Biodiversity inventories and monitoring techniques for marine fishes often overlook small (<5 cm), bottom-associated (‘cryptobenthic’) fishes, and few standardized, comparative assessments of cryptobenthic fish communities exist. We sought to develop a standardized, quantitative survey method for cryptobenthic fishes that permits their sampling across a variety of habitats and conditions. Fish-specific autonomous reef monitoring structures (FARMS) are designed to sample cryptobenthic fishes using a suite of accessible and affordable materials. To generate a variety of microhabitats, FARMS consist of three layers of stacked PVC pipes in three different sizes, as well as a bottom and top level of loose PVC-pipe fragments in a mesh basket. We deployed FARMS across a variety of habitats, including coral reefs, seagrass beds, oyster reefs, mangroves, and soft-bottom habitats across six locations (Hawai'i, Texas, Panama, Saudi Arabia, Brazil, and Curaçao). From shallow estuaries to coral reefs beyond 100 m depth, FARMS attracted distinct communities of native cryptobenthic fishes with strong site or habitat specificity. Comparing the FARMS to communities sampled with alternative methods (enclosed clove-oil stations on coral reefs in Panama and oyster sampling units on oyster reefs in Texas) suggests that FARMS yield a subset of cryptobenthic fish species that are representative of those present on local coral and oyster reefs. While FARMS yield fewer individuals per sample, they are efficient sampling devices relative to the sampled area. We demonstrate that FARMS represent a useful tool for standardized collections of cryptobenthic fishes. While natural substrata are bound to yield more mature communities with a larger number of individuals and wider range of specialist species, the potential to deploy and retrieve FARMS in turbid environments, beyond regular SCUBA depth, and where fish collections using anaesthetics or ichthyocides are forbidden suggests that they are a valuable complementary technique to survey fishes in aquatic ecosystems. Deploying FARMS in locations and habitats where cryptobenthic fish communities have not been studied in detail may yield many valuable specimens of unknown or poorly known species.

Brandl, S. J., Weigt, L. A., Pitassy, D. E., Coker, D. J., Patrick, C. J., Luchese, M. H., Berumen, M. L., Buskey, E. J., Casey, J. M., Di Domenico, M., Soeth, M., Topor, Z. M., Duffy, J. E., Baldwin, C. C., Hagedorn, M., & Parenti, L. R. (2023). Using standardized fish-specific autonomous reef monitoring structures ( FARMS ) to quantify cryptobenthic fish communities. Methods in Ecology and Evolution. Portico.

National Academy of Science Engineering and Medicine Early Career Gulf Research Fellowship; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; Herbert R. and Evelyn Axelrod Endowment in Systematic Ichthyology; King Abdullah University of Science and Technology; Leonard P. Schultz Fund; Mission-Aransas National Estuarine Research Reserve, Grant/Award Number: EJB; Tennenbaum Marine Observatories Network. The authors thank STRI Research Station in Bocas del Toro, Substation Curaçao, the KAUST Coastal and Marine Resources Core Lab, the Laboratory of Fish Ecology of the Center for Marine Studies; and the Hagedorn Laboratory and Hawai'i Institute of Marine Biology, especially Jason Jones, the Marine Safety Officer. The authors also thank Claire Lager, Nikolas Zuchowicz, E. Michael Henley, Leon Weaver, Tina Ramoy, Division Aquatics Resources of Alien Invasive Species Team Hawai'I; Alexander Kattan, Lucia Pombo Ayora, Barbara Maichak de Carvalho, Lilyane de Oliveira Santos Fontoura, Victoria Jenkins, Seanahlisa Crenshaw; and the students of TAMUCC's BIOL4409. This research was supported by a MarineGEO postdoctoral research fellowship (SJB), the Herbert R. and Evelyn Axelrod Endowment in Systematic Ichthyology and the Leonard P. Schultz Fund in the Division of Fishes, National Museum of Natural History (CCB and LRP), KAUST baseline funding (MLB), a National Academy of Science Engineering and Medicine Early Career Gulf Research Fellowship (CJP), the Mission-Aransas National Estuarine Research Reserve (EJB), a Master's scholarship from the Coordination for the Improvement of Higher Education (CAPES) (MHL). This is contribution 126 from the Smithsonian Institution's MarineGEO and Tennenbaum Marine Observatories Network.


Methods in Ecology and Evolution


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  • [Dataset]
    Brandl, S., Weigt, L., Pitassy, D., Coker, D., Patrick, C., Luchese, M., Berumen, M., Buskey, E., Casey, J., Di Domenico, M., Soeth, M., Topor, Z., Duffy, E., Baldwin, C., Hagedorn, M., & Parenti, L. (2023). Using standardized fish-specific autonomous reef monitoring structures (FARMS) to quantify cryptobenthic fish communities (Version 4) [Data set]. Dryad. DOI: 10.5061/dryad.cjsxksnb0 Handle: 10754/692448

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