Manuel
Vieira

Computational Bioacoustics

Soundscape Ecology

Passive Acoustics Monitoring

Machine Learning / AI

Google Scholar ID eXJw6o8AAAAJ&hl
ResearchGate Manuel-Vieira-8

I mostly study bioacoustics and ecoacoustics in estuarine and marine ecosystems, using sound to understand how fish and other aquatic animals communicate, behave, and reproduce. My key work combines field recordings, machine learning and other acoustic analyses to study animal ecological behaviour, assess marine biodiversity, investigate the impacts of human-generated noise, and promote the use of Passive Acoustic Monitoring (PAM) for conservation.

I earned my Biology degree with honors in 2011 and completed an MSc in Bioinformatics and Computational Biology in 2013, developing the first fish call recognition algorithm. In 2022, I received my PhD in Biology, having been awarded Young Scientist of the Year in 2021. I have published widely on marine bio- and ecoacoustics and the effects of noise on aquatic life, serve on the Board of Directors of the Portuguese Ethological Society, and collaborate with NGOs on environmental projects. I'm currently in a visiting fellowship at ENES lab (France) under the supervision of Nicolas Mathevon.

SELECTED RESEARCH PROJECTS

2025/12 – Present | Dynamics of Coral Reef Soundscapes: AI-Based Acoustic Monitoring for Biodiversity Conservation. Postdoctoral Fellow, Université Jean Monnet Saint-Étienne, France (MOPGA 2025, Campus France).
Using AI-based acoustic monitoring to study coral reef soundscapes and their biodiversity, combining computational tools and field recordings to inform marine conservation.
2024 – Present | CoastNet 2030: Monitoring for the Protection of Marine Ecosystems
Investigator, MARE – Marine and Environmental Sciences Centre, Portugal.
Long-term monitoring program of Portuguese coastal ecosystems, integrating acoustic surveys to support management and conservation of marine habitats.
2023 – 2024| BIOMAP-Loulé: Passive Acoustic Monitoring of Biodiversity – Phase 1
Principal Investigator, Centro de Ciências do Mar e do Ambiente, Portugal (Câmara Municipal de Loulé).
Development of a passive acoustic monitoring network to assess local biodiversity and inform municipal conservation strategies.
2018 – 2020 | FISHNOISE: Impact of Anthropogenic Noise on Fish Fitness
Investigator in a FCT project lead by Clara Amorim.
Studied how human-generated noise affects fish behavior and fitness, using passive acoustic monitoring and experimental approaches.
2017 – 2022 | Passive Acoustic Monitoring for Assessment of Natural and Anthropogenic Sound Sources in the Marine Environment.
PhD Fellow, Fundação para a Ciência e a Tecnologia, Portugal.
Assessed human and natural sound sources in marine environments, using automatic recognition to quantify soundscapes and evaluate fish behavior and biodiversity.

SELECTED PUBLICATIONS

Vieira, M., Fonseca, P. J., Amorim, M. C. P., & Teixeira, C. J. C. (2015). Call recognition and individual identification of fish vocalizations based on automatic speech recognition: An example with the Lusitanian toadfish. The Journal of the Acoustical Society of America, 138(6), 3941–3950. https://doi.org/10.1121/1.4936858
Vieira, M., Fonseca, P. J., & Amorim, M. C. P. (2021). Fish sounds and boat noise are prominent soundscape contributors in an urban European estuary. Marine Pollution Bulletin, 172, 112845. https://doi.org/10.1016/j.marpolbul.2021.112845
Vieira, M., Beauchaud, M., Amorim, M. C. P., & Fonseca, P. J. (2021). Boat noise affects meagre (Argyrosomus regius) hearing and vocal behaviour. Marine Pollution Bulletin, 172, 112824. https://doi.org/10.1016/j.marpolbul.2021.112824
Vieira, M., Amorim, M. C. P., & Fonseca, P. J. (2021). Vocal rhythms in nesting Lusitanian toadfish, Halobatrachus didactylus. Ecological Informatics, 63, 101281. https://doi.org/10.1016/j.ecoinf.2021.101281
Turco, T., Vieira, M., Jacquet, S., Guillard, J., Cachera, S., Beauchaud, M., & Médoc, V. (2025). From sky to underwater: Can passive acoustic monitoring replace plane-based aerial photography for quantifying human use of inland waters? Journal of Environmental Management. https://doi.org/10.1016/j.jenvman.2025.127571
Huang, Z., Ochs, D., Amorim, M. C. P., Fonseca, P. J., Goel, M., Nunes, N. J., Vieira, M., & Lopes, M. (2025). Deep learning–based frameworks for the detection and classification of soniferous fish. The Journal of the Acoustical Society of America. https://doi.org/10.1121/10.0038800
Darras, K. F. A., Rountree, R. A., ... Vieira, M., et al. (2025). Worldwide soundscapes: A synthesis of passive acoustic monitoring across realms. Global Ecology and Biogeography, 34(5). https://doi.org/10.1111/geb.70021
Muñoz-Duque, S., Vieira, M., Fonseca, P. J., et al. (2024). First assessment of passive acoustics as a tool to monitor the endangered Mediterranean monk seal in the Madeira Archipelago (Portugal). Aquatic Conservation: Marine and Freshwater Ecosystems, 34(2). https://doi.org/10.1002/aqc.4100
Puebla-Aparicio, M., Vieira, M., Amorim, M. C. P., Fonseca, P. J., et al. (2024). Characterization of the fish acoustic communities in a Mozambican tropical coral reef. Marine Ecology Progress Series. https://doi.org/10.3354/meps14450
Vieira, M., Ríos, N., Muñoz-Duque, S., et al. (2024). Cross-referencing unidentified fish sound data sets to unravel sound sources: A case study from the Temperate Northern Atlantic. Frontiers in Remote Sensing, 5. https://doi.org/10.3389/frsen.2024.1377206
Stratoudakis, Y., Vieira, M., Marques, J. P., Amorim, M. C. P., Fonseca, P. J., & Quintella, B. R. (2023). Long-term passive acoustic monitoring to support adaptive management in a sciaenid fishery (Tagus Estuary, Portugal). Reviews in Fish Biology and Fisheries, 34(1), 491–510. https://doi.org/10.1007/s11160-023-09825-z