From Water to DNA: The Evaluation of Environmental DNA (eDNA) Sampling Volume in a Tropical Blackwater Peat Swamp in Dungun, Terengganu
DOI:
https://doi.org/10.11113/mjfas.v21n5.4246Keywords:
Environmental DNA, Blackwater Peat Swamps, Water Filtration, DNA Extraction, Biodiversity MonitoringAbstract
Blackwater peat swamps in Peninsular Malaysia support diverse aquatic species including cryptic and elusive taxa. However, extreme environmental conditions such as high acidity, turbidity and organic content hinder biodiversity monitoring, leaving these ecosystems largely understudied. Environmental DNA (eDNA) offers a non-invasive approach for species detection, thus providing a promising tool for biodiversity assessment. This study investigates the influence of water filtration volume and hydrological factors on DNA concentration in a blackwater peat in Dungun, Terengganu. Water sampling was conducted between November and December 2023 at three substations—designated as upper (A), middle (B) and lower (C) which spaced at 50-meter intervals with five replicate samples filtered from each substation. A total of 2L blackwater per station was filtered using a 0.45 µm mixed cellulose ester (MCE) membrane and an oil-free vacuum pump. eDNA was extracted using a modified DNeasy® Blood & Tissue Kit, quantified with a NanoDrop spectrophotometer and assessed through gel electrophoresis. Results showed that eDNA concentration varied significantly across stations and was influenced by the filtered water volume. The highest eDNA concentrations were recorded at the middle stretch (B1: 480 mL, 32.00 ng/μL; B2: 480 mL, 38.22 ng/μL), followed by the lower stretch (C1: 460 mL, 14.00 ng/μL; C3: 400 mL, 11.00 ng/μL). Sample replicates with filtration volumes below 400 mL (A5, B4, B5, C4, C5) failed to yield detectable DNA, likely due to insufficient water filtration. Despite optimal filtration volumes (>400 mL), A1 (420 mL, 7.66 ng/μL) and C2 (450 mL, 9.10 ng/μL) exhibited low DNA concentrations, suggesting hydrological influences that resulted in localized accumulation or dilution of genetic material. Replicate B3 from Station B (400 mL, 19.50 ng/μL) recorded higher DNA compared to replicate C1 and C3 as this area has a moderate and consistent water flow which likely enhanced the dispersal of eDNA throughout the water column. Gel electrophoresis confirmed high molecular weight DNA in samples exceeding 400 mL, particularly in B1 and B2 which displayed the brightest bands. Statistical analysis (Spearman's ρ = 0.809, p = 0.005) revealed a strong positive correlation between filtration volume and eDNA yield. In conclusion, optimizing filtration volume and accounting for hydrological conditions are crucial for effective eDNA sampling, emphasizing the need for standardized protocols to improve biodiversity monitoring in blackwater peat swamp ecosystems.
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