A robust method for collecting and processing PAM data to understand fish and crustacean assemblages associated with extreme shallow structured reefs

Shallow reefs are critical to the economic and ecological functions of coastal regions, specifically oyster production, supporting fishery species, and protection of shorelines. Reefs host a diverse assemblage of organisms; however, understanding the spatiotemporal dynamics of these communities remains challenging. For long-term ecological monitoring, Passive Acoustic Monitoring (PAM) has been emerging as a cost-effective and non-invasive alternative tool to capture sampling methods. Past studies using PAM have been limited to short-term data analysis within a single season and, importantly, have lacked standardized calibration and data processing protocols, without which meaningful comparisons across projects and regions are limited. A custom PAM system was deployed adjacent to an oyster-based living shoreline in Eloi Bay (Louisiana, USA) between September 2022 and July 2023 to record soundscapes of an extreme shallow reef during four sampling periods. Calibrated recordings were analyzed to infer temporal patterns, focusing on diel and seasonal variations in soundscapes. Diel acoustic patterns were captured on the reef and varied seasonally; diel patterns were most distinct during summer months. These seasonal and diel acoustic trends correlated with the presence and diversity of sound-producing species in trawl and net surveys within the region, suggesting that observed sound patterns are biophonically driven. This work leverages best practices in underwater acoustics to advance the use of PAM as a tool to resolve outstanding ecological questions (e.g., examining the diel and seasonal behaviors of species whose catchability varies with light) and enhance PAM feasibility for long-term, non-invasive monitoring of extreme shallow reef species dynamics to inform ecological monitoring, conservation, and restoration efforts. • Long-term acoustic monitoring of an extreme-shallow reef across seasons using broadband PAM. • Acoustic analysis focused on frequency bands of dominant soniferous taxa present on the reef. • Acoustic pattern comparison to net/trawl fish and invertebrate catches. • Diel and seasonal dominant sound intensity shifts suggestive of biophonic soundscape drivers. • Soundscape metrics as scalable indicators for reef restoration monitoring.