Passive Acoustic Monitoring of Noisy Coral Reefs

TL;DR

This study demonstrates that passive acoustic monitoring of coral reefs in Singapore is feasible over extended periods despite pervasive ship- and tide-induced noise. By developing a Conv-TasNet reef denoiser, the authors recover biologically meaningful low-frequency soundscapes and reveal morning and evening choruses suppressed by noise in raw data. They systematically evaluate acoustic indices—snapping shrimp snap rate, low-frequency SPL, and Acoustic Complexity Index—and show strong temporal and spatial correlations with diver-measured reef health metrics, with the snap rate emerging as a particularly robust proxy for live coral richness, size, and cover. The work further introduces composite acoustic indices that integrate multiple metrics to monitor reef health, offering a scalable, non-invasive approach to long-term monitoring in noisy marine environments.

Abstract

Passive acoustic monitoring offers the potential to enable long-term, spatially extensive assessments of coral reefs. To explore this approach, we deployed underwater acoustic recorders at ten coral reef sites around Singapore waters over two years. To mitigate the persistent biological noise masking the low-frequency reef soundscape, we trained a convolutional neural network denoiser. Analysis of the acoustic data reveals distinct morning and evening choruses. Though the correlation with environmental variates was obscured in the low-frequency part of the noisy recordings, the denoised data showed correlations of acoustic activity indices such as sound pressure level and acoustic complexity index with diver-based assessments of reef health such as live coral richness and cover, and algal cover. Furthermore, the shrimp snap rate, computed from the high-frequency acoustic band, is robustly correlated with the reef parameters, both temporally and spatially. This study demonstrates that passive acoustics holds valuable information that can help with reef monitoring, provided the data is effectively denoised and interpreted. This methodology can be extended to other marine environments where acoustic monitoring is hindered by persistent noise.

Figures (17)

• Figure 1: Passive recorder and anchoring bracket for deployment. The blue bar is a mounting structure for the PVC pipe to slot in.
• Figure 2: Locations in Singapore strait near reefs where passive acoustic recorders were deployed (blue markers), and (inset) zoomed out map of the region around Singapore showing the area studied marked by a red box.
• Figure 3: Photos taken during the deployments.
• Figure 4: Spectrograms depicting 1 minute of acoustic data in two different bands, revealing the presence of (a) shrimp snaps in the 1-20 kHz band, and (b) fish chorus in the 0.1-1 kHz band.
• Figure 5: The average SPL over a 24-hour period (a) in the high-frequency 1-20 kHz band, (b) in the low-frequency 0.1-1 kHz band without denoising, and (c) in the low-frequency band after denoising using the Conv-TasNet reef denoiser. While the choruses are visible in (a) in the form of peaks around 4-7 AM and 6-9 PM, they are not apparent for many of the sites in (b). Also, (b) shows a much larger vertical spread between SPL at different sites due to the impact of additional noise sources. Applying the denoiser reveals the choruses in the low-frequency band in (c), indicating that the noise from shipping and flow effects is effectively suppressed, allowing better observation of biologically relevant acoustic activity.