Environmental DNA (eDNA) involves collecting genetic material from environmental samples, such as water, soil, or air, without needing to directly interact with the organisms. This method detects DNA fragments that organisms leave in their environment, providing real-time data on species distribution, abundance, and habitat preferences. Its non-invasive nature, cost-effectiveness, and the ease of standardising procedures make eDNA an appealing alternative to more disruptive techniques. eDNA is reshaping how scientists monitor marine biodiversity, offering a less intrusive and more comprehensive approach than traditional methods. This article examines a groundbreaking study conducted in Gazi Bay, Kenya, where eDNA methodologies have been applied to assess fish diversity within the region’s seagrass meadows, providing invaluable insights into the ecological dynamics of this critical habitat.
Gazi Bay: An Ecological and Research Overview
Located on Kenya’s South Coast, Gazi Bay covers approximately 10 km². The bay opens into the Indian Ocean through a relatively wide but shallow entrance in the southern part and is flanked by two creeks. The western creek features two freshwater inflows: River Kidogoweni to the north and River Mkurumunji to the west. This area is home to a rich mosaic of habitats, including shallow waters, seagrass meadows, mangrove forests, and coral reefs. The area is surrounded by a dynamic community heavily engaged in fishing activities, which impacts the bay’s biodiversity. Given its ecological importance and the pressures it faces,
Gazi Bay represents an ideal site for deploying innovative monitoring techniques like eDNA. The study delineated three sampling sites within Gazi Bay, each representing different habitat interactions: seagrass-mangrove interfaces, seagrass-only areas, and areas where seagrass meets coral reefs. Researchers collected water samples using sterile techniques to avoid contamination. Samples were then preserved on-site in cooler boxes with ice packs and promptly transported to the laboratory for processing.
At the Kenya Marine and Fisheries Research Institute’s lab, water samples underwent a filtration process using a manifold filtration system with sterile 0.45 µm nitrocellulose filter papers. These filters were immediately stored at -80°C to preserve the DNA. Subsequent steps included DNA extraction using a CTAB-based method, DNA quality and quantity assessment, and preparation for ‘deep sequencing’.
Enhanced Detection with eDNA can benefit from Expanded Reference Sequence Databases
The study’s findings demonstrate the effectiveness of eDNA in assessing marine biodiversity. By identifying 63 different fish species from water samples, eDNA proved to be more comprehensive than traditional methods like net catches and visual surveys, which detected 29 and 43 species, respectively. The researchers employed a rigorous verification process, cross-referencing species identifications with global taxonomic databases such as FishBase, WoRMS, and the NCBI database. This process confirmed the presence of each detected species and incorporated taxonomic updates. Out of the 153 historically recorded species, 109 had corresponding 12S rRNA barcode sequences available in the GenBank database, enhancing the reliability of the identification process.
The study also demonstrated eDNA’s ability to resolve taxonomic discrepancies through detailed genetic analysis. The accuracy of species identification is heavily reliant on the availability of reference sequences in global databases, which can be incomplete or outdated.
When an anomaly arose during the taxonomic assignment phase, with Siganus fuscescens (Mottled spinefoot) initially identified as the species with the highest proportion of reads, contradicting visual and catch survey data, the researchers employed further molecular analysis and comparison with the NCBI database. This investigation confirmed Siganus sutor (African whitespotted rabbitfish) as the correct species, showcasing eDNA’s capacity to rectify identification errors.
Further, the researchers conducted a longitudinal analysis by comparing their findings with historical data to assess changes in biodiversity over time. This comparison is important for understanding the impacts of environmental changes and human activities on Gazi Bay’s marine life. The eDNA results aligned with the historical records of 153 fish species and provided updates and corrections to the species list through high-resolution genetic identification.
Implications of eDNA-based monitoring for Marine Conservation
The application of eDNA in Gazi Bay has demonstrated the potential of this technology to fundamentally change marine biodiversity monitoring. By providing detailed, non-invasive insights into species diversity and distribution, eDNA can significantly enhance marine conservation strategies. Moving forward, improving and expanding genetic reference databases will be crucial to leveraging the full potential of eDNA analysis. Furthermore, integrating eDNA findings with traditional ecological data can offer a more holistic view of marine ecosystems, facilitating better-informed conservation and management decisions.
This study enriches our understanding of the marine biodiversity in Gazi Bay and sets a precedent for applying eDNA in marine ecology globally. The insights gained from such research are invaluable for the scientific community and environmental policy-makers aiming to preserve and sustainably manage marine biodiversity in the face of ongoing environmental challenges.
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