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

Cite this dataset

Brandl, Simon et al. (2023). Using standardized fish-specific autonomous reef monitoring structures (FARMS) to quantify cryptobenthic fish communities [Dataset]. Dryad.


1. Biodiversity inventories and monitoring techniques for marine fishes often overlook small (<5cm), 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.

2. 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).

3. 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 species representative of those present on local coral and oyster reefs. While FARMS yield fewer individuals per sample and are restricted to cryptobenthic species, they are efficient sampling devices relative to the sampled area.

4. 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 anesthetics 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.


This dataset contains the raw data obtained from Fish-specific Autonomous Reef Monitoring Structures (FARMS), which were deployed to sample communities of cryptobenthic fishes in a standardized, quantitative fashion. The units were deployed in five locations (Brazil, Panama, Hawaii, Saudi Arabia, and Texas) for which data were formally analyzed, as well as in Curaçao, for which no formal raw data was collected (kjust anecdotal observations). FARMS consist of several stacked levels of horizpontally mounted PVC pipes to provide shelter for small, bottom-dwelling fishes. As such, they offer a useful avenue for sampling cryptobenthic fishes in habitats or locations where other sampling methods are not possible. The abstract of the paper that these data underpin is pasted below. 


Smithsonian Institution, Award: TMON MarineGEO Postdoctoral Fellowship