Using qPCR and high-resolution sensor data to model a multi-species Pseudo-nitzschia (Bacillariophyceae) bloom in southeastern Australia

An On-Farm Workflow for Predictive Management of Paralytic Shellfish Toxin-Producing Harmful Algal Blooms for the Aquaculture Industry

Paralytic shellfish toxins (PSTs) produced by marine dinoflagellates significantly impact shellfish industries worldwide. Early detection on-farm and with minimal training would allow additional time for management decisions to minimize economic losses. Here, we describe and test a standardized workflow based on the detection of sxtA4, an initial gene in the biosynthesis of PSTs. The workflow is simple and inexpensive and does not require a specialized laboratory. It consists of (1) water collection and filtration using a custom gravity sampler, (2) buffer selection for sample preservation and cell lysis for DNA, and (3) an assay based on a region of sxtA, DinoDtec lyophilized quantitative polymerase chain reaction (qPCR) assay. Water samples spiked with Alexandrium catenella showed a cell recovery of >90% when compared to light microscopy counts. The performance of the lysis method (90.3% efficient), Longmire's buffer, and the DinoDtec qPCR assay (tested across a range of Alexandrium species (90.7-106.9% efficiency; r2 > 0.99)) was found to be specific, sensitive, and efficient. We tested the application of this workflow weekly from May 2016 to 30th October 2017 to compare the relationship between sxtA4 copies L-1 in seawater and PSTs in mussel tissue (Mytilus galloprovincialis) on-farm and spatially (across multiple sites), effectively demonstrating an ∼2 week early warning of two A. catenella HABs (r = 0.95). Our tool provides an early, accurate, and efficient method for the identification of PST risk in shellfish aquaculture.

Pseudo-nitzschia species, toxicity, and dynamics in the southern Indian River Lagoon, FL

The Indian River Lagoon (IRL) spans approximately one-third of the east coast of Florida and, in recent years, has faced frequent harmful algal blooms (HABs). Blooms of the potentially toxic diatom, Pseudo-nitzschia, occur throughout the lagoon and were reported primarily from the northern IRL. The goal of this study was to identify species of Pseudo-nitzschia and characterize their bloom dynamics in the southern IRL system where monitoring has been less frequent. Surface water samples collected from five locations between October 2018 and May 2020 had Pseudo-nitzschia spp. present in 87% of samples at cell concentrations up to 1.9×10³ cells mL^-1. Concurrent environmental data showed Pseudo-nitzschia spp. were associated with relatively high salinity waters and cool temperatures. Six species of Pseudo-nitzschia were isolated, cultured, and characterized through 18S Sanger sequencing and scanning electron microscopy. All isolates demonstrated toxicity and domoic acid (DA) was present in 47% of surface water samples. We report the first known occurrence of P. micropora and P. fraudulenta in the IRL, and the first known DA production from P. micropora.

Mapping the development of a Dinophysis bloom in a shellfish aquaculture area using a novel molecular qPCR assay

Diarrhetic shellfish toxins produced by certain species of the marine dinoflagellate Dinophysis can accumulate in shellfish in high concentrations, representing a significant food safety issue worldwide. This risk is routinely managed by monitoring programs in shellfish producing areas, however the methods used to detect these harmful marine microbes are not usually automated nor conducted onsite, and are often expensive and require specialized expertise. Here we designed a quantitative real-time polymerase chain reaction (qPCR) assay based on the ITS-5.8S ribosomal region of Dinophysis spp. and evaluated its specificity, efficiency, and sensitivity to detect species belonging to this genus. We designed and tested twenty sets of primers pairs using three species of Dinophysis - D. caudata, D. fortii and D. acuminata. We optimized a qPCR assay using the primer pair that sufficiently amplified each of the target species (Dacu_11F/Dacu_11R), and tested this assay for cross-reactivity with other dinoflagellates and diatoms in the laboratory (11 species) and in silico 8 species (15 strains) of Dinophysis, 3 species of Ornithocercus and 2 species of Phalacroma. The qPCR assay returned efficiencies of 92.4% for D. caudata, 91.3% for D fortii, and 91.5% for D. acuminata, while showing no cross-reactivity with other phytoplankton taxa. Finally, we applied this assay to a D. acuminata bloom which occurred in an oyster producing estuary in south eastern Australia, and compared cell numbers inferred by qPCR to those determined by microscopy counts (max abund. ∼6.3 × 10³ and 5.3 × 10³ cells L^-1 respectively). Novel molecular tools such as qPCR have the potential to be used on-farm, be automated, and provide an early warning for the management of harmful algal blooms.

Real-Time Environmental Monitoring for Aquaculture Using a LoRaWAN-Based IoT Sensor Network

IoT-enabled devices are making it easier and cheaper than ever to capture in situ environmental data and deliver these data-in the form of graphical visualisations-to farmers in a matter of seconds. In this work we describe an aquaculture focused environmental monitoring network consisting of LoRaWAN-enabled atmospheric and marine sensors attached to buoys on Clyde River, located on the South Coast of New South Wales, Australia. This sensor network provides oyster farmers operating on the river with the capacity to make informed, accurate and rapid decisions that enhance their ability to respond to adverse environmental events-typically flooding and heat waves. The system represents an end-to-end approach that involves deploying a sensor network, analysing the data, creating visualisations in collaboration with farmers and delivering them to them in real-time via a website known as FarmDecisionTECH®. We compared this network with previously available infrastructure, the results of which demonstrate that an in situ weather station was ∼5 ∘C hotter than the closest available real-time weather station (∼20 km away from Clyde River) during a summertime heat wave. Heat waves can result in oysters dying due to exposure if temperatures rise above 30 ∘C for extended periods of time (such as heat waves), which will mean a loss in income for the farmers; thus, this work stresses the need for accurate in situ monitoring to prevent the loss of oysters through informed farm management practices. Finally, an approach is proposed to present high-dimensional datasets captured from the sensor network to oyster farmers in a clear and informative manner.

Update of the Planktonic Diatom Genus Pseudo-nitzschia in Aotearoa New Zealand Coastal Waters: Genetic Diversity and Toxin Production

Domoic acid (DA) is produced by almost half of the species belonging to the diatom genus Pseudo-nitzschia and causes amnesic shellfish poisoning (ASP). It is, therefore, important to investigate the diversity and toxin production of Pseudo-nitzschia species for ASP risk assessments. Between 2018 and 2020, seawater samples were collected from various sites around Aotearoa New Zealand, and 130 clonal isolates of Pseudo-nitzschia were established. Molecular phylogenetic analysis of partial large subunit ribosomal DNA and/or internal transcribed spacer regions revealed that the isolates were divided into 14 species (Pseudo-nitzschia americana, Pseudo-nitzschia arenysensis, Pseudo-nitzschia australis, Pseudo-nitzschia calliantha, Pseudo-nitzschia cuspidata, Pseudo-nitzschia delicatissima, Pseudo-nitzschia fraudulenta, Pseudo-nitzschia galaxiae, Pseudo-nitzschia hasleana, Pseudo-nitzschia multiseries, Pseudo-nitzschia multistriata, Pseudo-nitzschia plurisecta, Pseudo-nitzschia pungens, and Pseudo-nitzschia cf. subpacifica). The P. delicatissima and P. hasleana strains were further divided into two clades/subclades (I and II). Liquid chromatography-tandem mass spectrometry was used to assess the production of DA and DA isomers by 73 representative strains. The analyses revealed that two (P. australis and P. multiseries) of the 14 species produced DA as a primary analogue, along with several DA isomers. This study is the first geographical distribution record of P. arenysensis, P.cuspidata, P. galaxiae, and P. hasleana in New Zealand coastal waters.