Paper-Based Chip Platform: PCR-SERS-LFA Integration for On-Site Coastal Harmful Microorganism Detection

Harmful algal blooms (HABs) and pathogenic microorganisms threaten coastal ecosystems and public health, requiring rapid field-deployable detection. Herein, we present an integrated paper-based platform combining polymerase chain reaction (PCR), surface-enhanced Raman scattering (SERS), and lateral flow assay (LFA) for on-site nucleic acid detection. The platform integrates a miniature thermal cycler, lyophilized paper-based reaction chambers, and a capillary-driven detection pen for contamination-free transfer and dual-mode readout. The platform achieved limits of detection of 10 1 –10 2 copies μL –1 by SERS and 10 3 –10 4 copies μL –1 by visualization for Enterococcus spp., Escherichia coli, Alexandrium tamarense, and Noctiluca scintillans, with complete amplification and detection within 30 min. Field validation at a coastal bathing beach showed agreement with laboratory-based quantitative PCR (qPCR), with only one discordant result out of 36 environmental samples, demonstrating comparable performance to the current gold-standard method while offering portability and rapid on-site response. Furthermore, the platform identified Ulva prolifera (a key driver of green tide) micropropagules as small as 600 μm and enabled large-scale mapping of overwintering zones across the Yellow-Bohai Sea. This platform supports rapid environmental monitoring and public health surveillance.