Scientific Insights: a brief guide to how marine biologists measure biodiversity in inshore reef environments

Environment | Oceans

By Julia Riopelle, Co-Editor in Chief

Published December 26th, 2021

Inshore reef environments (IREs) are the first affected by plastic and chemical pollutants, which enter oceans via industrial development, shipping waste, and river runoff. Thus, the monitoring of biodiversity along coastlines is vital to measure and understand the health of these keystone ecosystems.

Coral reefs are biodiversity hotspots, as despite only taking up 0.5% of the Earth’s surface, they house 25% of all marine species (USGS, 2021). For this reason, biodiversity hotspots are considered areas of priority when allocating conservation efforts and policy decisions, as due to their high concentration of endemic flora and fauna, their loss would be unsalvageable.

Turtle swimming through the corals of the Great Barrier Reef, Australia. | Jordan Robins / Ocean Image Bank

Measuring the success of marine programmes, which work to mitigate plastic and chemical pollutants in inshore reef environments (IREs), requires seasonal and annual monitoring and often combines data collected from in-situ assays, remote sensing and databases. Ever wonder how scientists come up with numbers describing the biodiversity and ecosystem health of our coastal environments? Here are some of the methods they use to do it.

Measuring inshore reef environment primary productivity

Due to their autotrophic ecophysiology, phytoplankton, coralline algae and seaweeds are key to transferring energy to higher trophic levels. This means these primary producers are indispensable in supporting all ocean ecosystems.

According to Tetu (2020), microplastics can ‘leach organic compounds and metals’ that hinder the growth of algae. Plastics were also found to increase coral disease occurrence from 4% to 89%, by either harbouring bacteria or causing surface tears that provide entry points for pathogens.

Multiple studies established that ‘active ingestion of microplastics and passive surface adhesion can affect coral energetics, growth and health’. Due to their critical role in supporting IRE biomass, marine biologists often monitor IRE net primary productivity to collect data on ecosystem health.

A small-scale, non-invasive method of evaluating coral growth rates is using underwater photogrammetry—taking multiple pictures from multiple angles of an environment—in order to create 3D reef models.

Whilst traditional methods also include repeated measurements of tagged branches, coring—which may impair growth—and morphometrics; traditional methods are time-consuming, whereas photogrammetry is an accurate technique that allows one to overlap digital photographs, in order to monitor colony-scale growth patterns over time.

Coral in Bacong, Central Visayas, Philippines. | Elias Levy / Flickr

A mid-scale in-situ (meaning in the ocean) technique employs bathyphotometers, a device that detects bioluminescence as a proxy for measuring coastal plankton density, biomass and productivity.

However, most bathyphotometres were designed with high-flow rates, in order to ensure optimal capture efficiency of widely distributed plankton across the open ocean. This may prove a limitation when applying it to spatially closed IREs. Therefore, using smaller bathyphotometres with moderate flow rates for coastal research.

Satellite remote sensing is a cost-effective, large-scale method of measuring trends in coral seafloor cover and plankton distribution. Different satellites are able to measure different things in the ocean, depending on their orbit speed, altitude and electromagnetic bands.

In order to measure primary productivity, one would opt for a visible electromagnetic band, in order to measure average colour changes associated with phytoplankton net primary productivity, at a geo-synchronous orbit.

This specific orbit allows monitoring of a fixed location, and despite its lower resolution, has been used to assess the chlorophyll content of IREs. In recent years, high-resolution satellite systems with 1.8 metre to 4 metre pixels (i.e. Ikonos, Geobird, Quickeye) have been employed to monitor reefs up to 600 kilometres-squared in size.

Some cases have been able to distinguish live from dead coral at three-metre depth—however, ‘spectral confusion’ was a limiting factor and thus may not be applicable to heterogeneous reef environments.

Phytoplankton bloom in the Bay of Biscay. | NASA Goddard Space Flight Center / Flickr

Measuring the levels of microplastics and chemicals in inshore reef environments

Microplastics act as vectors in absorbing pollutants and contributing to bioaccumulation across food webs. Additionally, plastic waste often includes UV stabilizers, dyes and metals, which can dissolve into the ocean. This affects metabolic and reproductive processes in marine organisms.

Mesh nets (20 to 5000 micrometres) are the most common microplastic sampling method in seawater, occurring in 76% of studies. Mesh can additionally be equipped with flow meters, which measures the amount of water filtered, and discrete sampling devices, which can specifically evaluate small fractions of microplastics.

A limitation of these nets is that mesh sizes can either get clogged if too small, or underestimate microplastic levels if too large. As an alternative, Anderson (2018) found that microplastic concentrations from dipped-glass-plate sampling (where water is sampled by adhering to the plate) were higher than in other sampling methods.

In order to monitor Polychlorinated biphenyls (PCB)—highly toxic industrial chlorine waste compounds—and heavy metal bioaccumulation in fish, most studies use dissections to analyse tissues. However this requires killing marine organisms in order to evaluate the health of their population.

The alternative non-lethal method, muscle tissue biopsies, has been successful in detecting similar mercury levels as those measured via lethal dissections. Therefore, more and more marine biologists are using passive sampling devices (which mimic bioaccumulation rates) attached to adipose fins or scale-epithelial tissues, as a non-invasive method to measure plastic and chemical contamination in marine organisms—a method first successfully employed by Heltsley and her team in 2005.

Additionally, the effects of chemical pollution can be detected by measuring and comparing concentrations of target pollutants, changes in ocean pH and coral bioerosion rates.

Blacktip sharks patrolling the reef, French Polynesia. | Hannes Klostermann / Ocean Image Bank

Measuring in inshore reef environment biodiversity

Measuring species abundance is another indicator of ecosystem health. In order to get an accurate picture, marine biologists opt for a combination of methods, such as both in-situ data collection through eDNA metabarcoding, as well as remote sensing via photo-quadrat/video recordings and passive acoustics.

Environmental DNA (eDNA) is a cost-effective sampling method for identifying species presence—from microorganisms to macrofauna. eDNA is DNA which has essentially shed from the organism and is floating around in the ocean—taking the form of feces, mucus, gametes, shed skin, carcasses and hair.

eDNA sampling filters DNA from water samples and species identified via Illumina sequencing, nanopore technology or 16S/18S metabarcoding—all methods of identifying DNA sequences and genes, which allows one to identify the organisms present in the water column.

A study comparing tropical reef eDNA analysis via shotgun sequencing versus metabarcoding, found metabarcoding to be more promising for assessing eukaryotic biodiversity. When using eDNA sampling, one must ensure to cover a wide range of reef sites, in order to gain an accurate representation of species diversity.

Fish on coral reef, Bali. | David P. Robinson / Ocean Image Bank

However, a limitation of eDNA analysis is that despite detecting species presence, ‘a reliable link between the abundance of organisms and the quantity of DNA remains elusive’ (Nichols, 2019). To remedy this, pairing eDNA with photo-quadrat/video recordings offers a non-disruptive way of assaying species abundance.

The Australian Institute for Marine Science, for example, monitors three sites per reef, with five transects per site; where 40 photographs are taken of each transect. However, this only covers 150 kilometres-squared per reef, which represents a challenge when needing to assess large areas of high biodiversity.

Therefore, another monitoring method is passive acoustics, which uses sound in order to identify population densities and species that are difficult to detect through imaging techniques. The soundscapes of healthy coral reefs are much louder than degraded ones, and reef noise is known to help orientate species towards them.

Additionally, acoustic tags can be attached to a target animal in order to detect species abundance. Unlike GPS, this would identify whether the presence of a tagged individual in IREs is a solo anomaly, or whether they are migrating with a pod. Tracking migration trends reveals whether their presence is part of the species’ seasonal cycle or whether there is an actual increase or decrease of their numbers.

Great Southern Reef, Australia. | Stefan Andrews / Ocean Image Bank

Due to the benefits and drawbacks of data methodologies, it is important for scientists to use an array of complementary, cost-effective and minimally invasive methods in order to monitor inshore reef biodiversity and ecosystem health. Particularly as our inshore reef environments are often the first marine ecosystems to be affected by plastic and chemical pollution.

Featured Image: Jake Stone / Unsplash

Australian Institute of Marine Science (2021) Monitoring inshore reefs. Australian Government. Available at: [Accessed May 21st, 2021].

Anderson Z., Cundy A., Croudace I., Warwick P., Celis-Hernandez O. and Stead J. (2018) A rapid method for assessing the accumulation of microplastics in the sea surface microlayer (SML) of estuarine systems. Scientific Reports. Volume 8, issue 1, page 9428.

Antich A., Palacín C., Cebrian E., Golo R., Wangensteen O. and Turon X. (2020) Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities? Special Issue Molecular Ecology. Volume 30, issue 13 pages 1-14.

Conservation International (2021) Biodiversity Hotspots. Conservation International. Available at: [Accessed May 21st, 2021]

Cutroneo L., Reboa A., Besio G. et al. (2020) Microplastics in seawater: sampling strategies, laboratory methodologies, and identification techniques applied to port environments. Environmental Science and Pollution Research. Volume 27, pages 8938-8952.

Genner M., Hastings R., Freer J., Collins R. and Simpsons S. (2020) Climate Change Drives Poleward Increases and Equatorward Declines in Marine Species. Current Biology. Volume 30, issue 8, pages 1572-1577.

Hedley J., Roelfsema C., Chollett I. et al. (2016) Remote Sensing of Coral Reefs for Monitoring and Management: A Review. Remote Sensing. Volume 8, issue 118.

Heltsley R., Cope G., Shea D., Bringolf R., Kwak T. and Malindzak E. (2005) Assessing organic contaminants in fish: comparison of a nonlethal tissue sampling technique to mobile and stationary passive sampling devices. Environmental Science Technology. Volume 39, issue 19, pages 7601-7608.

Herren C., Haddock S., Johnson C., Orrico C., Moline M. and Case J. (2005) A multi-platform bathyphotometer for fine-scale, coastal bioluminescence research. Limnology and Oceanography: Methods. Volume 3, pages 247-262.

Huang W., Chen M., Song B. et al. (2021) Microplastics in the coral reefs and their potential impacts on corals: A mini-review. Science of the Total Environment. Volume 762.

Jones G., McCormick M., Srinivasan M. and Eagle J. (2004) Coral decline threatens fish biodiversity in marine reserves. PNAS. Volume 101, No. 21, pages 8251-8253.

Lange I. and Perry C. (2020) A quick, easy and non-invasive method to quantify coral growth rates using photogrammetry and 3D model comparisons. Methods in Ecology and Evolution. Volume 11, Issue 6, pages 714-726.

Lechene M., Haberstroh A., Byrne M., Figueira W. and Ferrari R. (2006) Optimising Sampling Strategies in Coral Reefs Using Large-Area Mosaics. Remote Sensing. Volume 11, Issue 24.

Lennox R., Aarestrup K., Cooke S. et al. (2017) Envisioning the Future of Aquatic Animal Tracking: Technology, Science, and Application. BioScience. Volume 67, Issue 10, pages 884-896.

Nichols P. and Marko P. (2019) New eDNA technology used to quickly assess coral reefs. The University of Hawaii at Manoa.

NOAA (2019) Coral reefs in the Pacific. NOAA Fisheries. Available at: [Accessed May 21st, 2021]

Odgen (2018) Sounds Good? The Acoustic Monitoring of Coral-Reef Health. BioScience. Volume 68, Issue 1, page 48.

Pacific Islands Fisheries Science Center (2021) Calcification rates of crustose coralline algae (CCA) derived from Calcification Accretion Units (CAUs) deployed at coral reef sites in Batangas, Philippines from 2012 to 2015. NOAA Fisheries. Available at: [Accessed May 21st, 2021]

Radford A., Duarte C., Chapuis L., Collin S. et al. (2021) The soundscape of the Anthropocene ocean. Science. Volume 371, issue 6529.

Tan Suet May A., Khalik W., Ong M. et al. (2021) Marine microplastics as vectors of major ocean pollutants and its hazards to the marine ecosystem and humans. Progress in Earth and Planetary Science. Volume 8, No. 12.

Tetu S., Sarker I. and Moore L. (2020) How will marine plastic pollution affect bacterial primary producers? Communications Biology. Volume 3, No. 55.

USGS (2021) Pacific Coral Reefs. USGS—Coastal and Marine Hazards and Resources Program. Available at: [Accessed May 21st, 2021].

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