Environmental DNA Metabarcoding for Biodiversity Assessment in Freshwater Ecosystems
DOI:
https://doi.org/10.5281/zenodo.22687807Keywords:
environmental DNA, metabarcoding, freshwater biomonitoring, biodiversity assessment, 12S rRNA, systematic reviewAbstract
Environmental DNA (eDNA) metabarcoding has been promoted for more than a decade as a faster, less invasive
alternative to netting, electrofishing and kick-sampling for characterising freshwater biodiversity, but the published
literature reporting its performance against conventional survey methods is scattered across taxonomic groups,
marker genes and water-body types, making it difficult for a practitioner to judge how reliable the method now is
for routine biomonitoring. We conducted a systematic review and random-effects meta-analysis of studies
published between 2012 and 2024 that directly compared eDNA metabarcoding against a conventional survey
method in a lake, river or pond system, screening 2,418 records identified across four databases and retaining 71
studies that met pre-specified eligibility criteria. Pooled taxon detection sensitivity of eDNA metabarcoding relative
to conventional surveys was 0.86 (95% CI 0.82-0.89) across all taxonomic groups, but sensitivity varied
substantially by marker: studies using 12S rRNA fish-specific primers achieved higher pooled sensitivity (0.91,
95% CI 0.88-0.94) than studies using broad-spectrum COI primers for macroinvertebrate assessment (0.79, 95%
CI 0.73-0.84). Detection sensitivity was significantly higher in lentic systems than in lotic systems
(meta-regression, P=0.003), consistent with reduced eDNA dilution and transport in standing water. False-positive
rates attributable to laboratory contamination or index hopping were inconsistently reported, appearing in only 34
of the 71 included studies, which we flag as a persistent and under-addressed methodological gap. We conclude
that eDNA metabarcoding has reached a level of performance that supports its routine use alongside, though not
yet as a full replacement for, conventional freshwater biomonitoring, with marker choice and water-body hydrology
as the two variables most consistently predictive of performance across the reviewed literature.
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