Metabarcoding as a tool to enhance marine surveillance of nonindigenous species in tropical harbors: A case study in Tahiti

Abstract

Globalization has increased connectivity between countries enhancing the spread of marine nonindigenous species (NIS). The establishment of marine NIS shows substantial negative effects on the structure and functioning of the natural ecosystems by competing for habitats and resources. Ports are often hubs for the spread of NIS via commercial and recreational vessels. Prevention, detection, and mitigation efforts are required to avoid and manage the establishment of NIS in new ecosystems. In this study, metabarcoding approaches targeting the nuclear small‐subunit ribosomal RNA (18S rRNA) gene and mitochondrial cytochrome c oxidase I (COI) gene were used to investigate planktonic and sessile (i.e., biofouling) communities and NIS at four locations in Tahiti, including two marinas and one port with varying anthropogenic impacts, and a relatively pristine site (Manava) used as a control. ASV richness values showed significant differences (18S rRNA gene: p = .023; COI: p < .001) between locations in the plankton samples, with the control site (low impact) having the highest diversity for both genes. ASV richness was also significantly different among locations for the biofouling samples in the COI dataset (p = .002). Community composition differed between locations with spatial patterns appearing stronger for the plankton samples compared with the biofouling samples. Detection of NIS based on selected lists of globally invasive species revealed a wide diversity of potentially invasive taxa especially in the more anthropogenically impacted regions. The use of a multigene approach improved the detection of NIS. This study demonstrates the utility of using a metabarcoding approach to routinely monitor areas most at risk from NIS establishment in Tahiti and other coastal nations. These coastal nations are vulnerable to shipping‐mediated incursions, and baseline information is required for both native diversity and nonindigenous diversity.

Towards reproducible metabarcoding data: Lessons from an international cross‐laboratory experiment

“…This suggests that neither marker is more susceptible to differences in laboratory processing protocols and associated data biases. The 18S rRNA marker is more conserved than the COI , which typically results in comparatively lower species resolution and underestimation of species richness (von Ammon et al, 2018; Leray & Knowlton, 2016; Pearman et al, 2021). This may explain our observation of slightly stronger clustering of 18S rRNA data points according to the sample origin and substantial improvement of classification of 18S rRNA data sets following the removal of low‐quality samples (i.e., those with only a small number of resulting sequence reads).…”

Monitoring Non-indigenous Species in Port Habitats: First Application of a Standardized North American Protocol in the Mediterranean Sea

“…Lastly, the broadest investigation of non-indigenous invertebrates in Mediterranean marinas was conducted by Ulman et al (2017) with both modified RAS and scrapes by hand-held rigid net. During the last few years, the metabarcoding approach has also started to be employed in NIS surveys with satisfying results (see also Borrell et al, 2017;Miralles et al, 2021;Pearman et al, 2021). Metabarcoding can be considered as an efficient tool to detect cryptic species or early life stages, but one of the main disadvantages is the incompleteness of genetic sequence reference libraries (Zaiko et al, 2018;Duarte et al, 2021).…”

Eco-Plastics in the Sea: Succession of Micro- and Macro-Fouling on a Biodegradable Polymer Augmented With Oyster Shell

“…Although members of the family Bougainvilliidae are found worldwide (Vannucci and Rees, 1961), the genus has been described as colonizing artificial surfaces in coastal waters (mostly ports and marinas) from the South Pacific Ocean, particularly in Australia (Wyatt et al, 2005;Grey et al, 2018), and New-Zealand (Schuchert, 1998;Cairns et al, 2009). A recent metabarcoding study of biofouling from submerged surfaces (buoys, ropes, tires, and pontoon structures) in Tahiti revealed the highest relative abundance of Bougainvillia among detected NIS (Pearman et al, 2021). Comparison of the seasonal recruitment of fouling hydroids on settlement panels between cold and warm months in Brazil, Migotto et al (2001) revealed that Bougainvillia spp.…”