The Challenge of eDNA Extraction in Tropical Aquatic Ecosystems: Implications for Monitoring the Antillean Manatee

Resumen

Background. Monitoring threatened species with low population densities in tropical aquatic ecosystems presents significant methodological challenges, particularly for cryptic organisms such as the Antillean manatee (Trichechus manatus manatus). Environmental DNA (eDNA) has emerged as a promising non-invasive tool; however, its efficiency may be affected by complex matrices such as turbid waters and inhibitor-rich sediments. Goals. To evaluate the effectiveness of eDNA for detecting manatee presence in tropical aquatic systems of the southern Gulf of Mexico and to compare different extraction methods for water and sediment samples. Methods. Water (1000 mL) and sediment samples were collected from four sites in Tabasco, Mexico. Two extraction methods were compared for water samples (phenol–chloroform and QIAGEN DNeasy Blood & Tissue commercial kit) and three for sediments (Chelex, chloroform–isoamyl alcohol, and CTAB). Detection was performed via qPCR using primers specific for T. m. manatus. DNA concentrations and amplification success were statistically analyzed in R. Results. For water samples, both extraction methods yielded quantifiable DNA and amplification success rates above 90%, with no significant differences between them (p > 0.05). In sediments, although Chelex and chloroform methods produced higher DNA concentrations, the CTAB protocol showed a significantly higher proportion of positive amplifications (87.5%, p < 0.001), indicating more effective removal of PCR inhibitors. Conclusions. eDNA analysis confirms its applicability for detecting manatees in tropical environments; however, environmental matrix strongly influences methodological performance. Water samples are more reliable for routine monitoring, while CTAB is recommended for sediment samples due to its superior amplification success.