Invasive Caulerpa prolifera detection with eDNA
Our team developed and tested a new eDNA method to better detect the invasive algae Caulerpa prolifera, aiming to improve early detection and support marine ecosystem management.
This project evaluates a new eDNA assay targeting the tufA gene to improve early detection of the invasive algae Caulerpa prolifera, which poses a major threat to California’s marine ecosystems.
The invasive green algae genus, Caulerpa prolifera, threatens California’s marine ecosystems and benthic environments due to its rapid spreading and infestation rate, low DNA shedding rate and high capacity for ecological disruption which includes outcompeting native species and releasing toxins. Identifying and eradicating Caulerpa Prolifera outbreaks can be challenging due to its rapid spreading rate and difficulties in early detection (Waters et al., 2023). Traditional monitoring methods, such as diver surveys, are limited in turbid environments and only detect established colonies. Environmental DNA (eDNA) monitoring offers a more sensitive, early-detection alternative, but C. prolifera‘s unique unicellular biology and low shedding rates make detection challenging, even using eDNA. A previous study by Tanner Waters assessed the efficacy of the nuclear ITS gene as an assay target for the detection of C. Prolifera eDNA in the water column, but had limited results (Waters et al., 2023).
To address this, SCCWRP developed a new assay targeting the chloroplast-encoded tufA gene, hypothesizing that it could improve detection due to higher gene copy numbers and different shedding properties. This project evaluates the efficacy of the tufA assay by reanalyzing samples from Newport Bay Caulerpa prolifera outbreaks and tank-based shedding experiments originally examined with the ITS assay.
By comparing detection rates between the two assays, we aim to determine whether improved sensitivity stems from gene target selection, outbreak differences, or assay specificity. Ultimately, our research will support better eDNA-based monitoring of C. prolifera, enhancing early detection and informing future management efforts. Outreach materials will be created to share findings beyond SCCWRP.
See figures A and B for location of field samples and tank experiment workflow.