Retrospective eDNA assessment of potentially harmful algae in historical ship ballast tank and marine port sediments

Abstract

Microalgal bloom events can cause major ecosystem disturbances, devastate local marine economies, and endanger public health. Therefore, detecting and monitoring harmful microalgal taxa is essential to ensure effective risk management in waterways used for fisheries, aquaculture, recreational activity, and shipping. To fully understand the current status and future direction of algal bloom distributions, we need to know how populations and ecosystems have changed over time. This baseline knowledge is critical for predicting ecosystem responses to future anthropogenic change and will assist in the future management of coastal ecosystems. We explore a NGS metabarcoding approach to rapidly identify potentially harmful microalgal taxa in 63 historic and modern Australian marine port and ballast tank sediment samples. The results provide a record of past microalgal distribution and important baseline data that can be used to assess the efficacy of shipping guidelines, nutrient pollution mitigation, and predict the impact of climate change. Critically, eDNA surveys of archived sediments were able to detect harmful algal taxa that do not produce microscopic fossils, such as Chattonella, Heterosigma, Karlodinium, and Noctiluca. Our data suggest a potential increase in Australian harmful microalgal taxa over the past 30 years, and confirm ship ballast tanks as key dispersal vectors. These molecular mapping tools will assist in the creation of policies aimed at reducing the global increase and spread of harmful algal taxa and help prevent economic and public‐health problems caused by harmful algal blooms.

Improving detection capabilities of a critically endangered freshwater invertebrate with environmental DNA using digital droplet PCR

“…All aquatic organisms shed DNA traces in their environment 17 , and it is now possible to detect a specific species (barcoding) or assess an entire community (metabarcoding) by sampling an aquatic system and amplifying the existing DNA traces using PCR (Polymerase Chain Reaction) based techniques 17 . Since the implementation of eDNA techniques in environmental studies last decade, it has been proven to be successful for the monitoring of invasive 18–22 , endangered 23,24 and/or economically important species from a wide range of taxa 25–27 . However, few studies have used eDNA for monitoring rare or indicator macroinvertebrate species 28–30 .…”

A global perspective for biodiversity history with ancient environmental DNA

“…Together, the body of published studies on aeDNA from sediments, and the papers published here (Gomez Cabrera et al, ; Shaw et al, ), show that the information gained on different temporal scales and from different environments can offer a novel, integrated view on temporal biodiversity change (Balint et al, ), and on a global scale. In fact, for many issues that are of immediate relevance for conservation, historic records spanning the last decades or centuries are most important, and these can be obtained from many localities in the world, including tropical environments (Figure ).…”

“…Studying such dynamics is particularly pertinent in light of 20th century ecosystem modifications all over the world, where, for example, neobiota and increased nutrient loads have drastically altered diversity and functionality (Figure ). As demonstrated by the aeDNA analysis of sediments from ship ballast tanks (Shaw, Weyrich, Hallegraeff, & Cooper, ), historical collections of sediments can furthermore elucidate past global species' distributions and migration routes and provide an efficient tool for monitoring and tracking migrations.…”

“…This also seems to hold true for aeDNA of coral reefs (Gomez Cabrera et al, ). In addition, and as exemplified by the study of Shaw et al () focussing on taxa involved in harmful algal blooms (HAB), meaningful biological interpretation can best be accomplished with optimal taxonomic assignments of target taxa ‐ calling for the further development of high quality sequence reference databases.…”

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

“…Compared to water, the collection of sediments to survey eukaryotic organisms has received much less attention, and to our knowledge has been attempted only in 6 studies (Table S2, Fig. 1B, Koziol et al 2018, Holman et al 2019, Leduc et al 2019, Shang et al 2019, Shaw et al 2019, Rey et al 2020. Metabarcoding of eDNA extracted from sediments can provide a rapid screen for a wide range of taxa in ballast tanks and marine port sediments (Holman et al 2019, Shang et al 2019, Shaw et al 2019.…”