Marine biomonitoring from environmental DNA

Environmental DNA, usually abbreviated as eDNA, is DNA that organisms leave behind in the surrounding environment. In marine and coastal waters it may originate from shed cells, mucus, faeces, gametes, larvae, decaying tissue or microorganisms. By collecting water, sediment or biofilm samples and analysing the DNA fragments they contain, it is possible to detect organisms that are present, were recently present, or whose DNA has been transported into the sampled water mass.

eDNA analysis has become an important complement to conventional biodiversity monitoring and biomonitoring. It is especially useful for detecting organisms that are rare, small, cryptic, difficult to identify morphologically, or difficult to sample by nets, grabs, visual surveys or diver observations. Examples include invasive species, harmful algal bloom species, microbial communities, fish larvae, benthic organisms with dispersive life stages and species occurring at low abundance.

However, eDNA does not replace conventional biomonitoring. It provides evidence of DNA occurrence, not a direct census of living organisms. The interpretation depends on sampling design, hydrodynamic transport, DNA degradation, reference databases and analytical method. For this reason eDNA is most powerful when used together with ecological knowledge, conventional species observations, environmental measurements and, where relevant, biomarker or chemical monitoring.

Basic principle

The method is based on the fact that a short DNA sequence can often be assigned to a taxonomic group or species if the sequence is sufficiently characteristic and is available in a reference database. The procedure therefore consists of extracting DNA from an environmental sample, selecting or sequencing diagnostic DNA fragments, and comparing the resulting sequences with known reference sequences. eDNA methods include metabarcoding, quantitative polymerase chain reaction (qPCR), digital PCR (ddPCR) and shotgun metagenomics. Polymerase chain reaction (PCR) is a widely used method for amplifying selected DNA fragments, making it possible to detect target organisms or taxonomic groups from very small amounts of DNA. Gene expression requires RNA-based approaches, such as RT-qPCR or metatranscriptomics.

Three approaches are commonly distinguished.

Targeted detection uses qPCR or ddPCR to test for one selected species or a small group of species. This is useful when the monitoring question is specific, for example whether an invasive species, pathogen or harmful algal species is present. These methods quantify copies of a selected DNA marker. Under well-calibrated conditions, marker-copy numbers may give an approximate indication of local abundance or biomass, but they cannot generally be translated directly into numbers of individuals.

Metabarcoding uses primers that amplify a DNA marker shared by a broad group of organisms, for example bacteria, phytoplankton, invertebrates or fish. Sequencing the amplified fragments gives a list of taxa detected in the sample. Metabarcoding is therefore useful for comparing community composition among sites or through time. Read numbers may contain some abundance information, but they are affected by primer bias, gene-copy number, organism size, shedding rate and bioinformatic filtering. They should therefore not be interpreted as direct species abundances unless independently validated.

Shotgun metagenomics sequences a broad mixture of DNA fragments, the metagenome, without first amplifying one selected marker. This avoids primer-specific PCR bias and can provide information on microbial community composition and functional potential. It may therefore be useful for studying ecosystem processes and microbial indicators of environmental change. However, it is still affected by extraction efficiency, sequencing depth and incomplete reference genomes, and is usually more demanding and costly than targeted qPCR or metabarcoding.

Added value for coastal and marine monitoring

eDNA monitoring can add value in several situations.

First, it can increase detection probability. Species that are rare, elusive, nocturnal, microscopic or difficult to identify by morphology may be detected from traces of DNA. This is useful for early detection of non-indigenous species, harmful algae, endangered species or changes in fish and invertebrate communities.

Second, it can broaden taxonomic coverage. A single sample may contain DNA from many groups, including microorganisms, plankton, benthic organisms and vertebrates. This can reveal ecological changes that would be missed if monitoring is restricted to a few indicator groups.

Third, it can make monitoring less invasive. eDNA sampling often requires only water or sediment samples and can reduce the need for destructive sampling, repeated trawling or extensive expert taxonomic sorting.

Fourth, it can support spatial and temporal screening. Because field sampling can be relatively simple, eDNA can be used to compare many sites or to follow rapid seasonal changes. This is useful in estuaries, ports, lagoons, marine protected areas, restoration sites and areas influenced by dredging, aquaculture, wastewater discharge or coastal construction. Recent coastal applications show that eDNA metabarcoding can reveal seasonal and spatial patterns in fish and broader biodiversity communities, but also that sampling frequency strongly influences what is detected.

Finally, eDNA can help target conventional surveys. A positive eDNA signal can indicate where more detailed ecological sampling is needed, while repeated absence of a target signal may help focus monitoring effort elsewhere. In this sense, eDNA is often best used as an early-warning or screening tool rather than as a stand-alone assessment.

Limitations and interpretation

The main limitation is that an eDNA record is not the same as direct observation of a living organism at the sampling location. DNA may persist after an organism has died, may be transported by currents and tides, or may be resuspended from sediments. In coastal waters with strong advection, stratification, tidal exchange or sediment resuspension, a positive signal may represent nearby or upstream presence rather than exact local occurrence.

Absence of a DNA signal is also not definitive proof of absence. The species may have been missed because of low abundance, insufficient sampling volume, degradation of DNA, unsuitable primers, inhibition of the PCR reaction, insufficient sequencing depth or lack of a matching reference sequence.

Reference databases are a major constraint. A sequence can only be assigned reliably if related species have been adequately represented in the database and if the chosen marker has enough taxonomic resolution. For many marine invertebrates, microbes and regional species, reference libraries remain incomplete. In such cases, eDNA may identify organisms only to genus, family or higher taxonomic level.

Quantitative interpretation requires caution. qPCR, ddPCR and metabarcoding can sometimes track changes in relative DNA concentration, but eDNA concentration is influenced by shedding rate, organism size, life stage, activity, water temperature, salinity, microbial degradation, sunlight and transport. Abundance or biomass estimates therefore require calibration and should be checked against independent observations.

Contamination is another important issue. Because eDNA methods are highly sensitive, small amounts of DNA introduced during sampling, filtration, laboratory work or sequencing can produce false positive detections. Reliable studies therefore require field blanks, laboratory blanks, positive controls, replicate samples and transparent reporting of methods.

Relation to pollution biomonitoring

eDNA is mainly a tool for detecting organisms and describing biological community composition. It can show that communities differ between impacted and reference sites, or that sensitive or opportunistic taxa have changed through time. It can also detect microbial indicators, harmful algae or invasive species that are relevant for water quality and ecosystem status.

This differs from biomarker-based pollution monitoring. Biomarkers measure biological responses such as physiological stress, DNA damage, enzyme activity or reproductive effects in organisms exposed to contaminants. eDNA generally does not measure such effects directly. It should therefore be seen as complementary to chemical monitoring and biomarker monitoring, not as a replacement.

For example, eDNA may show a shift in benthic or planktonic community composition near an outfall, harbor or dredging site. Biomarkers and chemical measurements are then needed to determine whether this shift is plausibly related to contaminant exposure, eutrophication, oxygen stress, habitat change or natural variability.

Feasibility for management applications

The feasibility of eDNA monitoring depends on the question being asked. It is relatively mature for targeted detection of well-characterized species and for broad comparison of community composition. It is less mature when exact abundance, biomass, viability or local population size is required.

For management purposes, eDNA is most suitable when the question is one of detection, screening or comparison:

• Is a target invasive or harmful species present?
• Are communities changing through time at a restoration or impact site?
• Do sites differ in biodiversity composition?
• Are conventional surveys missing cryptic or early life stages?
• Where should more detailed field surveys be directed?

It is less suitable as a stand-alone method when the question requires age structure, body size, health status, reproductive condition, exact density or direct evidence of ecological function. Such information still requires conventional sampling, imaging, physiological measurements or other ecological observations.

A well-designed eDNA programme should therefore be judged not only by the analytical method, but also by the monitoring question, spatial and temporal sampling design, quality controls, reference databases, reporting standards and the way results are combined with other evidence.

Quality assurance and reporting

Because eDNA results can be sensitive to methodological choices, transparent reporting is essential. Minimum information should include sample location, date, water depth or sediment type, sampled volume or mass, preservation method, extraction method, marker and primer sequences, controls, sequencing depth, bioinformatic filtering, taxonomic assignment method and reference database used.

Recent guidance for environmental metabarcoding emphasizes that data and metadata should be reported in a way that makes results reproducible, comparable and reusable. For coastal management, this is important because eDNA datasets may otherwise be difficult to compare among years, contractors, laboratories or monitoring programs.

Conclusion

Environmental DNA analysis is a powerful addition to marine biomonitoring. Its main strengths are sensitive detection, broad taxonomic coverage, non-invasive sampling and the possibility of screening many sites or times. Its main limitations are incomplete reference databases, possible contamination, uncertain relation between DNA concentration and abundance, and the influence of transport and degradation in coastal waters.

For coastal professionals, the key point is that eDNA should be interpreted as one line of evidence. It can substantially improve monitoring when used for early detection, biodiversity screening and community comparison, but it should normally be combined with conventional ecological surveys, environmental measurements, chemical monitoring or biomarkers when management decisions require evidence of abundance, organism health, pollutant effects or ecological function.

References

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