Marine Ecoacoustics and Informatics Lab

Studying the dynamics of marine ecosystems through informatics

Welcome to the MEIL based in Biodiversity Research Center, Academia Sinica. Led by Dr. Tzu-Hao Lin, the MEIL investigates the applications of ecological informatics in biodiversity monitoring and conservation management.

Ocean sound is one of our primary subjects. We integrate passive acoustics and machine learning to track the spatial-temporal changes of biotic and abiotic sounds. By characterizing soundscapes, we seek to understand the mutual impacts among marine ecosystems, climate change, and anthropogenic activities.

We also interest in other non-acoustic techniques that can visualize the dynamics of marine ecosystems. Our goal is to generate open data and reusable models that can facilitate the retrieval of ecological information and increase the efficiency of decision making.

Topics

Congress of Animal Behavior, Ecology and Environmental Education

This year, we have four presentations at 2021 CABE. Researchers and students from MEIL investigate the applications of machine learning and audio source separation in analyzing the patterns of acoustic diversity in various ecological levels, including species, community, and ecosystem levels.

Open data and codes for exploring coral reef soundscapes off Sesoko Island, Okinawa

In our recent publication of "Exploring coral reef biodiversity via underwater soundscapes", we provided a web portal of the audio data used and Python codes for visualizing soundscapes of shallow-water and upper-mesophotic coral reefs. A Colab notebook was produced to help people understand how to use Soundscape Viewer in the analysis of soundscapes and explore the audio library we created. We hope our data and tools will lead more people to study underwater sounds of coral reef ecosystems!

Building a citizen science platform of marine soundscapes to monitor ecosystem health of coral reefs

Marine soundscapes have been considered as a proxy of marine biodiversity. Is it possible to develop a citizen science project based on marine soundscapes? We compared the quality of audio data collected by an underwater sound recorder commonly applied in academic research and a commercially available underwater video recorder. Despite the distortion of spectral features, an underwater video recorder can still capture sounds of soniferous fish and snapping shrimps. Therefore, we propose:

  1. Deploy underwater video recorders on coral reefs or seagrass beds. Away from the recorders for a short period to reduce noise due to diving regulators and bubbles.

  2. Share your video files via cloud storage and upload the metadata to an open repository.

  3. We will establish an open science computation platform to identify sounds of crustaceans, soniferous fish, and anthropogenic noise.

  4. The analysis result will be uploaded to an open repository so that everyone can explore the acoustic diversity among locations!

This is our preliminary idea. Please let us know if you have any suggestions!

Mini-symposium on cetacean ecology

December 2, 2020 (Wednesday)

Biodiversity Research Center, Academia Sinica

Taiwan features a rich diversity of cetaceans. Studies on cetacean ecology are rapidly growing in recent years. This mini-symposium will review past studies on cetacean ecology in Taiwan and discuss future research directions.

Visualizing coral reef soundscapes using Soundscape Viewer and Plotly

Ever wonder how a coral reef sounds like? Ecoacoustics researchers generally use a long-term spectrogram to investigate the variation of long-duration recordings in spectral, temporal, and spatial domains. If you are interested in this technique, we have created a tutorial of using Soundscape Viewer and Plotly to visualize coral reef soundscapes.

Check our deep-sea soundscape project featured in the New York Times

The Ocean Biodiversity Listening Project is now supported by the Ministry of Science and Technology, Taiwan!

Using Soundscapes to Assess the Interactions between Soniferous Animals and Anthropogenic Activities in Coral Reefs and Seagrass Beds

Conservation of marine biodiversity is crucial for maintaining sustainable marine ecosystem services. To efficiently investigate the potential interference of anthropogenic activities on marine biodiversity, a remote-sensing network that can characterize marine biodiversity's temporal-spatial variability is necessary. The recent development of underwater technology has allowed researchers to evaluate marine ecosystem change by using autonomous audio recorders to detect underwater sounds of marine soniferous animals, geophysical events, and anthropogenic activities. Until now, the analysis of marine soundscapes remains challenging because a comprehensive audio recognition database is not available. Moreover, the analysis reliability may be lowered when an audio clip records multiple sound sources simultaneously. This study will collaborate with scientists from Japan and the Philippines to initiate Ocean Biodiversity Listening Project and collect underwater sounds from coral reefs and seagrass beds via long-term recording stations and transect line surveys. New models of audio source separation and source localization will be developed by integrating domain knowledge from bioacoustics, signal processing, and machine learning. The techniques developed in this study will enable the automatic separation of biological, environmental, and anthropogenic sounds. The acoustic diversity observed in this study will enrich the audio library of coral reefs and seagrass beds, and improve the evaluation of how marine soniferous animals vary among habitats with different levels of anthropogenic activities. This study will also characterize the marine soundscapes during the COVID-19 pandemic in order to understand changes of marine biodiversity in response to the COVID-19 induced lockdown restrictions.

An online GIS of mass stranding events of Taiwan

This interactive map is created via CARTO. We hope such an interactive map can help stakeholders and citizens understand the history of mass stranding events happened in Taiwan and the species-specific stranding hot spots. We also published a short article (in Chinese) to comment on the recent event of a group of pygmy killer whales lost their way in Kaohsiung Harbor.

Recent Outcomes

Tzu-Hao Lin, Chong Chen, Hiromi Kayama Watanabe, Shinsuke Kawagucci, Yung-Che Tseng (2021) Could listening underwater sounds reveal the dynamics of chemosynthetic ecosystems? Japan Geoscience Union Meeting 2021 (online conference) .

Wonder what hydrothermal vents sound like? Most of hydrothermal vents are located in the deepsea or remote areas, where the assessment of biodiversity and ecosystem dynamics is challenging. Underwater sounds have been increasingly used in the monitoring of marine biodiversity and ecosystem health, could this technique facilitate the monitoring of hydrothermal vents?

This video presentation introduces the soundscapes recorded at at Guishan (Turtle) Island, NE Taiwan and Suiyo Seamount, Izu-Bonin Arc. By listening to vent sounds, it is possible to monitor the spatio-temporal changes in vent activities and the interaction with nearby non-vent habitats.

Tzu-Hao Lin, Tomonari Akamatsu, Yu Tsao (2021) Sensing ecosystem dynamics via audio source separation: A case study of marine soundscapes off northeastern Taiwan. PLoS Computational Biology, 17: e1008698.

This work use a computational approach that features the automatic separation of sound sources from a mixture to visualize the diurnal, lunar, and seasonal patterns of marine mammals, soniferous fishes, and shipping activities from 2.5 years of underwater sound recordings. This technique not just helps us evaluate the phenological patterns of each sound source and their potential interactions, it also facilitates the assessment of acoustic diversity. As a result, we identified five types of marine mammal vocalizations (including echolocation clicks and whistles), two types of fish choruses that were not reported in this region before.

By integrating this computational technique in global acoustic observatories, we can investigate the changes in marine biodiversity at various temporal and spatial scales. In addition, we can also use the information specific to anthropogenic noise to monitor human activities and evaluate their impacts on marine biodiversity. We believe that marine soundscapes will be an indispensable component of marine conservation in the future.

Tzu-Hao Lin, Tomonari Akamatsu, Frederic Sinniger, Saki Harii (2021) Exploring coral reef biodiversity via underwater soundscapes. Biological Conservation, 253: 108901.

This work demonstrated the applications of using soundscapes in studying the temporal and spatial changes of coral reef soundscapes. The result revealed amazing dynamics of biological sounds in upper-mesophotic coral reefs. High diversity of biological sounds may be an indicator of coral reef health, long-term monitoring of acoustic diversity will help us know how coral reefs respond to natural and anthropogenic stressors.

Our result also discovered that mesophotic corals are frequently exposed to anthropogenic noise. Considering that soundscapes are an important habitat cue for larvae of corals and reef-associated fish, noise masking may interfere the phonotaxis and reduce the resilience of coral reefs.

We urge to integrate soundscape monitoring in the global research network of coral reefs by characterizing the underwater sounds in healthy and degraded reef habitats, before and after bleaching events and other marine extreme events, in habitats with varying levels of management and regulations. This action will contribute to a data-informed platform for guiding conservation management and strategic investment on regional and global scales.

Joseph Heard, Wei-chen Tung, Yu-de Pei, Tzu-Hao Lin, Chien-Hsiang Lin, Tomonari Akamatsu, Colin KC Wen (2021) Coastal development threatens area supporting greatest fish diversity at Taoyuan Algal Reef, NW Taiwan. Aquatic Conservation: Marine and Freshwater Ecosystems, 3: 590-604.

Taoyuan Algal Reef is a biodiverse coralline algal reef in north‐west Taiwan, that is currently threatened by coastal development and industrial waste runoff. As the reef lies in an exposed area that is frequently disturbed by monsoons, it is difficult to survey using traditional methods. Knowledge of the reef is therefore limited, and has until recently, long been regarded as a barren environment.

We applied soundscapes to assess the quality of algal reef habitats. Our result revealed a positive relationship between the intensity of crustacean sounds and the abundance of tidal pool fishes. The observed soundscapes suggest that there are abundant prey resources for the fish community of algal reef. This study also demonstrated the effectiveness of using soundscapes in the monitoring of marine biodiversity at a challenging environment like algal reefs.

T. Aran Mooney, Lucia Di Iorio, Marc Lammers, Tzu-Hao Lin, Sophie Nedelec, Miles Parsons, Craig Radford, Ed Urban, Jenni Stanley (2020) Listening forward: Approaching marine biodiversity assessments using acoustic methods. Royal Society Open Science, 7: 201287.

Passive acoustics has been widely employed in the monitoring of marine soniferous animals. Here, we provide a summary of the brief history of using passive acoustics to assess marine biodiversity and community structure, a critical assessment of the challenges faced, and outline recommended practices and considerations for acoustic biodiversity measurements.

Important considerations for the acoustical biodiversity assessments should include: (i) replication and site-selection, (ii) recording over sufficient timescales, (iii) evaluation of detectability, (iv) evaluation of propagation-related aspects, (v) making concurrent measurements of complementary variables, (vi) collection of pilot data and making those data available, and (vii) seeking to reduce acoustic noise.

Tzu-Hao Lin, Chong Chen, Hiromi Kayama Watanabe, Shinsuke Kawagucci, Tetsuya Miwa, Hiroyuki Yamamoto, Shinji Tsuchida, Yoshihiro Fujiwara (2020) Characterizing habitat-specific soundscapes in deep-sea benthic ecosystems. eDSBS.

Deep-sea environments are highly dynamic through space and time, but continuous observation over extended periods remains challenging. The monitoring of underwater soundscapes has been proposed as a rapid and cost-effective way to assess the community structure and population dynamics of marine soniferous animals. This passive sensing technology can also produce information associated with the surrounding geophysical environment and anthropogenic activities.

From July 2019 to March 2020, we deployed autonomous sound recorders on baited cameras, the Edokko MARK I, and other seafloor observation platforms of JAMSTEC to collect underwater sounds from multiple deep-sea habitat types with a bathymetric range between 250 m to 5500 m deep.

The spectral characteristics of deep-sea soundscapes significantly varied among habitats. In coastal regions, soundscapes at Tohoku waters (250 – 1011 m) and Sagami Bay (1700 m) were dominated by shipping noise. At the 1385 m deep Suiyo Seamount vent field, soundscapes were characterized by low-frequency sounds (<100 Hz) from venting orifices. Even at 5500 m deep, we could still detect sounds produced from soniferous fish and cetaceans.

Habitat-specific soundscapes are likely important for the dispersal and settlement of deep-sea larvae and should be carefully monitored, especially in habitats attracting mining interests such as vents. To further utilize soundscapes as a tool of deep-sea conservation, we urge for an international collaboration that aims to acquire long-duration recordings from both healthy ecosystems and those disturbed by anthropogenic activities.

Tzu-Hao Lin, Yu Tsao (2020) Source separation in ecoacoustics: A roadmap toward versatile soundscape information retrieval. Remote Sensing in Ecology and Conservation, 6: 236-247.

Interested in using source separation to advance the analysis of acoustic data? In this article, we reviewed techniques of monoaural audio source separation with the fundamental theories and assumptions behind them.