Environmental DNA (eDNA) is revolutionising biodiversity monitoring by allowing scientists to non-invasively collect and analyse genetic material from various ecosystems, such as soil, water, air, or snow. This technique captures DNA shed by organisms through skin, scales, faeces, and other biological materials, eliminating the need for invasive sampling of individual organisms. eDNA has gained significant traction, particularly in aquatic environments, as it enables the detection of species presence and abundance without causing disturbance to the ecosystem or the organisms themselves. This approach is reshaping how we assess and monitor biodiversity, providing a more efficient, cost-effective, and comprehensive method for understanding and protecting biodiversity on Earth.
The Catfish: A Global Aquatic Citizen
Catfish, belonging to the order Siluriformes, are found on every continent except Australia. They predominantly inhabit freshwater environments, though some marine families exist. Despite their low market value, catfish play a significant role in the global aquaculture industry. One species, the African sharptooth catfish (Clarias gariepinus), is native to Africa but has spread to countries like India, Thailand, and Brazil, where it has become an invasive species. Its hardy nature and rapid growth have led to its introduction beyond its native range, making it a vital aquaculture species and, concomitantly, a potential ecological threat.
In Egypt, the African sharptooth catfish ranks as the third most important species for aquaculture. However, aquaculture practices, such as the continuous use of farm-bred strains, have raised concerns about genetic diversity and stock health. A study was conducted to assess the genetic diversity of African sharptooth catfish in Egypt. This study also aimed to develop an eDNA-based tool for monitoring the abundance and biomass of this species in the Egyptian Nile tributaries, providing a model that could be applied globally.
Harnessing eDNA for Catfish Monitoring
The researchers began by designing species-specific primers targeting the 16srDNA mitochondrial gene of the African sharptooth catfish. These primers were tested on liver samples from various catfish species to ensure specificity. The experiments then moved to the field. Water samples were collected from four canals in Menoufia Governorate, Egypt. Each canal was sampled in areas reported to have catfish abundance and random upstream points. These samples were processed in the laboratory for eDNA extraction. The eDNA was extracted and quantified using qPCR, a method that amplifies DNA and measures its quantity. This process involved creating a standard curve to determine the DNA concentration in each sample accurately. This method allowed researchers to quantify the amount of catfish DNA in the water samples, providing a measure of the species’ abundance in different locations.
Why eDNA Matters for Monitoring Catfish
The study found significant variations in the eDNA concentrations of the Sharptooth catfish across the sampled canals. The highest concentrations were found in the El-Atfy canal, followed by Al-Nenaeia, with lower concentrations in Bahr Seif and Bahr Shebin. These findings indicate that eDNA can effectively reflect the relative abundance of catfish in different habitats. Interestingly, these findings were consistent with reports from local fishermen. Additionally, the study provided insights into the genetic diversity of the species, indicating limited genetic variation within the Egyptian population compared to other African and Asian populations.
Implications and Future Directions
The use of eDNA-based monitoring for economically significant and potentially invasive species, such as the African sharptooth catfish, can have far-reaching implications for conservation strategies and aquaculture practices. The eDNA innovative approach offers several key benefits:
1. Non-Invasive Sampling: By eliminating the need for physical capture and handling of fish, eDNA sampling minimises stress and potential harm to the population, promoting a more ethical and sustainable monitoring practice.
2. Accurate Monitoring: eDNA coupled with qPCR provides a reliable estimate of species presence and abundance, crucial for effectively managing both native and invasive populations. This information can guide targeted conservation efforts and help implement control measures to mitigate ecological impacts.
3. Broad Applicability: The development of specific eDNA primers and qPCR assays for the African sharptooth catfish can be adapted and applied to other regions and species, contributing to enhanced global biodiversity monitoring efforts.
However, it is essential to acknowledge the challenges associated with eDNA analysis. Factors such as water clarity, the presence of PCR inhibitors, and the natural behaviour of the target species can influence the accuracy of eDNA detection. Understanding and accounting for these variables is crucial for the accurate interpretation of eDNA results.
The Egyptian study on the African sharptooth catfish underscores that eDNA will undoubtedly play an increasingly vital role in efforts to understand, manage, and protect aquatic biodiversity. Integrating eDNA into environmental monitoring toolkits will revolutionise how we approach protecting and sustaining our invaluable aquatic ecosystems. Are you considering using eDNA in your projects? Let us talk more in the comments.
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