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.

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.

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.

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.

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.

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.

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

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