Work

A digital PCR assay for the dabA gene involved in domoic acid biosynthesis by Pseudo-nitzschia spp

Year: 2025

Type: article

Abstract: • A new dPCR assay detects dabA genes from four Pseudo-nitzschia species and in the environment. • Pseudo-nitzschia dabA was detected in samples collected during a toxic HAB event. • Results indicate sequence variation among Pseudo-nitzschia dabA genes • The dabA assay is a potential predictive tool for a toxic Pseudo-nitzschia event Successful harmful algal bloom (HAB) prediction and monitoring employs a variety of observational and research strategies. We add to the existing suite of tools for detecting toxigenic Pseudo-nitzschia diatoms by developing a novel digital PCR (dPCR) assay targeting a key gene of the domoic acid biosynthetic pathway, dabA. Sequence alignments and synthetic gene fragments of dabA genes from Pseudo-nitzschia australis, P. multiseries, P. multistriata , and P. seriata , along with the closely-related red-algal genes kabA and radA, were used to design a dPCR assay and assess its specificity. This dPCR assay was demonstrated to be specific for dabA and can quantify concentrations >1 copy µL -1 in a reaction. The biogeography of published dabA genes suggests that the assay may be useful globally for target species. When screening a culture collection of Pseudo-nitzschia isolated from coastal California, the dPCR assay detected dabA genes from three of the eleven species tested . In samples collected during field campaigns in 2022 off Santa Barbara, CA and in 2023 in Monterey Bay, CA during toxic HAB events, Pseudo-nitzschia dabA genes were only detected in Monterey Bay samples. While the dPCR assay does not capture all dabA diversity, it is specific and provides a targeted means to assess the genetic potential of a toxic HAB event by dominant and potent toxin-producing Pseudo-nitzschia species in coastal California. Because dabA expression is a key indicator of DA production, using the assay to quantify gene transcription could speed the acquisition of data needed to forecast HABs before toxin is detected.

Source: Harmful Algae

DOI: 10.1016/j.hal.2025.103024