A Thorough Analysis of the Assessment of Fish Biodiversity in Estuaries Using Environmental DNA Metabarcoding

Zereth Kaelthorn^*
*Correspondence: Zereth Kaelthorn, Department of Marine Biodiversity, Charles Darwin University, Casuarina, Australia, Email:

Introduction

The biodiversity of estuarine ecosystems holds immense ecological, economic, and scientific value. Estuaries, where freshwater meets seawater, are critical habitats for numerous fish species, offering breeding, feeding, and nursery grounds. However, the pressures of human activities, pollution, climate change, and habitat degradation have significantly threatened the biodiversity in these regions. Accurate and efficient methods for assessing biodiversity are essential for monitoring and conservation efforts. Among the modern techniques, environmental DNA (eDNA) metabarcoding has emerged as a transformative tool for studying fish biodiversity in estuaries, offering a non-invasive, comprehensive, and efficient alternative to traditional survey methods [1].

eDNA metabarcoding involves the collection and analysis of genetic material shed by organisms into their environment, such as scales, mucus, or waste, which can be detected in water samples. By using high-throughput sequencing techniques, scientists can identify the species present in an area based on the unique genetic sequences found in the DNA fragments. This method has gained popularity due to its potential to provide high-resolution biodiversity data without the need for direct observation or physical capture of organisms. The application of eDNA metabarcoding to estuaries is particularly promising, given the challenges associated with traditional fish biodiversity surveys in such environments. Estuaries are often dynamic and complex systems characterized by fluctuating salinity levels, turbidity, and tides [2].

Description

eDNA metabarcoding addresses many of these limitations. Water samples can be collected with minimal disruption to the environment and at various points across an estuary to account for spatial variability. The DNA extracted from these samples is then amplified using primers that target specific regions of the genome, such as mitochondrial genes commonly used for species identification. High-throughput sequencing generates large volumes of data, which are then matched to reference databases to determine the species composition of the sample. One of the significant advantages of eDNA metabarcoding is its ability to detect cryptic or rare species that might be overlooked by traditional methods. In estuarine environments, this is particularly important for identifying migratory species or those that utilize the estuary as a transient habitat [3].

For instance, studies have shown that eDNA metabarcoding can reveal the presence of commercially valuable species, such as certain flatfish and salmonids, during critical life stages, offering insights into their ecology and population dynamics. Despite its advantages, the use of eDNA metabarcoding in estuaries is not without challenges. One of the primary issues is the degradation of DNA in aquatic environments, which can occur rapidly due to factors such as UV radiation, microbial activity, and chemical conditions. This degradation can lead to underestimation of species richness if not properly accounted for. Furthermore, estuaries present a unique challenge due to their mixing of freshwater and saltwater, which can affect DNA preservation and the efficiency of amplification [4].

Another consideration is the potential for contamination and the risk of false positives. Because eDNA is extremely sensitive, it can detect DNA from upstream or adjacent areas, leading to species being recorded in locations where they are not physically present. Additionally, cross-contamination during sample collection, processing, or analysis can compromise the accuracy of results. To mitigate these issues, stringent protocols for sample handling and robust bioinformatics pipelines for data analysis are essential. The success of eDNA metabarcoding in estuarine biodiversity assessments also depends on the availability and quality of reference databases. Accurate species identification requires comprehensive databases containing the genetic sequences of all potential species in the study area. However, these databases are often incomplete, particularly for less-studied regions or taxa. Efforts to expand and validate these reference libraries are critical to enhancing the reliability of eDNA-based studies [5].

Conclusion

Looking forward, the future of eDNA metabarcoding in estuarine biodiversity assessment will likely involve the integration of complementary technologies and interdisciplinary approaches. For example, coupling eDNA data with remote sensing and hydrodynamic modeling could provide a more comprehensive understanding of species distributions and habitat preferences. Advances in sequencing technologies and bioinformatics will also continue to improve the efficiency and accuracy of eDNA analyses.

In conclusion, the assessment of fish biodiversity in estuaries using eDNA metabarcoding represents a significant advancement in ecological monitoring. By overcoming many of the limitations of traditional survey methods, eDNA offers a powerful tool for capturing the complexity and richness of estuarine ecosystems. However, realizing its full potential will require addressing challenges related to DNA degradation, contamination, and database completeness, as well as fostering collaboration among scientists, policymakers, and the public. As these efforts progress, eDNA metabarcoding is poised to play a central role in ensuring the sustainable management and conservation of estuarine biodiversity for generations to come.

Acknowledgement

None.

Conflict of Interest

None.

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