Biodiversity monitoring in marine environments is a complex task. Underwater ecosystems contain a variety of species, each of which is suited to Different monitoring techniques -- from microscopic plankton to large marine mammals. Further complicating matters, these species inhabit many unique habitats, each with their own environmental characteristics such as high turbidity in shallow coastal areas, or low light in deeper waters. This post is a visual guide to some of the main non-invasive approaches available in marine biodiversity monitoring — focusing on methods that can be deployed by small teams with minimal disruption to the environment.
The illustrations and approaches laid out here are summarised from a review paper by English et al. written in 2024, enriched by PEBL’s expertise in biodiversity monitoring for shellfish, seaweed, and finfish aquaculture sites. Since 2020 we have used a combination of our own proprietary devices and third-party equipment to tailor monitoring strategies to the unique sites of our clientele.
Key Methods and Their Applications
eDNA (environmental DNA)
What It Does: Collects and analyzes genetic material shed by organisms into the water.
Best For: Identifying a wide range of species, from microscopic plankton to medium-sized fish.
Strengths & Limitations:
Strengths: Highly sensitive, minimal disturbance.
Limitations: Does not provide exact population counts or behavioral details.
We recommend Applied Genomics for their deep technical expertise in marine eDNA sampling.
Sample Microscopy
What It Does: Examines water or plankton samples under a microscope.
Best For: Small organisms such as plankton, early-life-stage invertebrates.
Strengths & Limitations:
Strengths: Very precise for identifying tiny species.
Limitations: Impractical for larger, more mobile marine life. Human error when identifying species.
We recommend Benthic Solutions for their fast sample turn-around and their highly experienced technical team,
Visual Count Surveys
How It’s Done: Divers, Remotely Operated Vehicles (ROVs), or fixed camera systems equipped with cameras such as the PEBL SUBCAM.
Best For: Observing fish, larger invertebrates, and noticeable behavioral patterns.
Strengths & Limitations:
Strengths: Direct observation of behavior and habitat use.
Limitations: Visibility constraints; can miss cryptic or very small species.
Active Acoustics
How it's done: Sidescan sonar, multibeam sonar, acoustic imaging units.
Best For: Mapping fish schools, detecting marine mammals over larger areas—even in turbid conditions.
Strengths & Limitations:
Strengths: Rapid coverage of large zones; works day or night and very turbid conditions where optical camera have limited use.
Limitations: Not suitable for very small or benthic species; returned acoustic data requires further interpretation.
We recommend: Blueprint Subsea Oculus Series for their high imaging resolution, simple integration and great customer support.
Acoustic Telemetry
What It Does: Tracks the movements of tagged fish or invertebrates.
Best For: Understanding movement patterns, site fidelity, and migration routes.
Strengths & Limitations:
Strengths: Offers long-term, detailed data on habitat use.
Limitations: Requires capturing and tagging; not applicable to plankton or small organisms.
We recommend: Innovasea Fish Tracking Products for their reliability, integration options, and intuitive software.
Passive Acoustic Monitoring (PAM)
What It Does: Uses underwater microphones (hydrophones) to detect and record sounds produced by marine organisms, such as echolocation clicks, whistles, and calls from marine mammals.
Best For: Detecting echolocating marine mammals (e.g., dolphins, porpoises) and some other vocalizing species.
Strengths & Limitations:
Strengths: Continuous, non-intrusive monitoring; effective for vocal animals.
Limitations: Silent or less vocal species may go undetected.
We recommend: Chelonia FPODs for their affordability, user-friendly interface and in-depth analysis software tool.
Bringing It All Together
These methods, with their benefits and limitations, can be successfully used in tandem to understand marine biodiversity at different sites. For example, while human divers or ROVs collect eDNA and water samples for microscopy, they can also perform visual count surveys to identify the larger organisms sometimes missed by these methods. To cut down on human labor, fixed camera systems such as the PEBL SubCam can also provide continuous observation for fish and some invertebrates, while intermittent water samples can be taken from ROV or boat.
Using acoustic methodologies, sonar can scan the water column for schools of fish in murky conditions, while passive acoustic monitoring (PAM) records the presence of dolphins, porpoises and other vocal species around the clock.
If there is a single species of interest, acoustic telemetry can be incorporated into these approaches, following a tagged animal over weeks or months to reveal detailed movement patterns in and around an aquaculture site.
By combining these non-invasive techniques, researchers and aquaculture managers can gain a comprehensive understanding of their local biodiversity — from planktonic life all the way up the food chain to marine mammals. This overview offers a starting point for selecting the right mix of methods, ensuring aquaculture practices remain informed by robust, science-based insights.
Reference: English, G., Lawrence, M. J., McKindsey, C. W., Lacoursière-Roussel, A., Bergeron, H., Gauthier, S., Wringe, B. F., & Trudel, M. (2024). A review of data collection methods used to monitor the associations of wild species with marine aquaculture sites. Reviews in Aquaculture, 16(1), 1160–1185. https://doi.org/10.1111/raq.12890
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