New PhD: Mukesh Bhendarkar

On May 20 Mukesh Bhendarkar presented his PhD thesis under the title “Advancing environmental DNA approaches for optimizing aquatic ecosystem monitoring and ecological assessment” at the Plentzia Marine Station (PiE-UPV/EHU). His research has been carried out the supervision of Dr. Naiara Rodríguez-Ezpeleta within the framework of the DIADES, BIOcean5D y OBAMA-NEXT and GENGES projects.

His research critically assessed the use of environmental DNA (eDNA) analysis for monitoring diadromous fish populations in European river systems and evaluating the ecological status of estuarine environments. His work highlighted how methodological choices—ranging from sampling design to analytical frameworks—influence the ecological interpretation and reliability of eDNA data. In parallel, Mukesh conducted a comprehensive review of eDNA applications in tropical fisheries, evaluating the scientific and logistical challenges for implementation in biodiverse but data-limited regions such as India. Supported by the prestigious Netaji Subhas ICAR International Fellowship, he now returns to India to continue his research at the ICAR-National Institute of Abiotic Stress Management (India), equipped with new perspectives and tools for advancing fisheries resource management and ecosystem assessment.

Thesis summary

This work presents a critical and integrative evaluation of environmental DNA (eDNA) analysis for aquatic ecosystem monitoring, with a focus on ecological interpretability, methodological performance, and its incorporation into assessment frameworks. Through applications of targeted (qPCR, dPCR) and community-level (metabarcoding) approaches in European freshwater and estuarine systems, the study shows that eDNA outcomes are shaped by biological complexity as well as technical decisions—such as sampling design, assay sensitivity, capture method, and ecological index calibration.
Results reveal distinct detection dynamics for key diadromous species: while shads were consistently detected by both qPCR and dPCR, sea lamprey required the enhanced sensitivity of dPCR, reflecting species-specific ecology and shedding patterns. Metabarcoding assessments provided broader community insights and, when integrated into ecological indices, yielded classification results aligned with traditional methods—though with a need for recalibrating class boundaries and thresholds.
A systematic review further examined the prospects of transferring these methodologies to tropical ecosystems, highlighting challenges such as reference database gaps, standardization needs, and ecological complexity. The thesis emphasizes that eDNA should not be treated as a standalone tool, but as a methodological approach whose utility depends on strategic choices, ecological context, and robust calibration for accurate and meaningful ecosystem assessment.