Diverse harmful microalgal community assemblages in the Johor Strait and the environmental effects on its community dynamics

A comparative analysis of real-time quantitative PCR and metabarcoding methods for eDNA-based detection of the toxic dinophyte Alexandrium tamiyavanichii (Dinophyceae)

The marine dinophyte Alexandrium tamiyavanichii is a toxigenic species that produces a group of neurotoxins that is responsible for paralytic shellfish poisoning in humans. Early detection of the species is essential for efficient monitoring. Harmful microalgal monitoring systems have evolved over the years with the advent of environmental DNA (eDNA)-based species detection techniques. In this study, eDNA samples were collected from a large-scale sampling covering the southern South China Sea. The sensitivity and specificity of metabarcoding of the V4 and V9 18S ribosomal DNA barcodes by high-throughput sequencing (HTS) were compared to the species-specific real-time qPCR targeting the A. tamiyavanichii ITS2 region. Environmental samples were screened for A. tamiyavanichii by qPCR (n = 43) and analyzed with metabarcoding (n = 30). Our results revealed a high occupancy profile across samples for both methods; 88% by qPCR, and 80-83% by HTS. When comparing the consistency between the two approaches, only two samples out of 30 were discordant. The V4 and V9 molecular units detected in each sample were positively correlated with the qPCR ITS2 gene copies (V4, rs = 0.67, p < 0.0001; V9, rs = 0.65, p < 0.0001), indicating that metabarcoding could be used as a useful tool for early detection of the species. Our results also revealed that the estimation of A. tamiyavanichii cell abundances based on the HTS read abundances was comparable to that of the qPCR quantification. For long-term monitoring, metabarcoding could serve as a cost-effective screening of detecting not only single HAB species but also simultaneously detecting a multitude of potentially harmful species, which is valuable in informing the subsequent implementation of species-specific monitoring strategies.

Mapping harmful microalgal species by eDNA monitoring: A large-scale survey across the southwestern South China Sea

A large-scale sampling was undertaken during a research cruise across the South China Sea in August 2016, covering an area of about 100,000 km2 to investigate the molecular diversity and distributions of micro-eukaryotic protists, with a focus on the potentially harmful microalgal (HAB) species along the east coast of Peninsular Malaysia. Environmental DNAs from 30 stations were extracted and DNA metabarcoding targeting the V4 and V9 markers in the 18S rDNA was performed. Many protistan molecular units, including previously unreported HAB taxa, were discovered for the first time in the water. Our findings also revealed interesting spatial distribution patterns, with a marked signal of compositional turnover between latitudinal regimes of water masses, where dinophytes and diatom compositions were among the most strongly enhanced at the fronts, leading to distinct niches. Our results further confirmed the widespread distribution of HAB species, such as the toxigenic Alexandrium tamiyavaichii and Pseudo-nitzschia species, and the fish-killing Margalefidinium polykrikoides and Karlodinium veneficum. The molecular information obtained from this study provides an updated HAB species inventory and a toolset that could facilitate existing HAB monitoring schemes in the region to better inform management decisions.

A combined approach detected novel species diversity and distribution of dinoflagellate cysts in the Yellow Sea, China

Resting cysts of dinoflagellates seed harmful algal blooms (HABs) and their geographic expansion, which makes it fundamentally important to obtain comprehensive inventories of dinoflagellate resting cysts in HABs-prone regions. The Yellow Sea (YS) of China has observed numerous outbreaks of dinoflagellate HABs with some novel species recorded recently indicating an underestimated HABs-causing species diversity. We report our investigation of dinoflagellate cysts of YS via an approach combining metabarcoding sequencing and single-cyst morpho-molecular identification, which identified many novel cyst species and a significant controlling effect of the Yellow Sea Cold Water Mass on cyst composition. The metabarcoding and single cyst-based sequencing detected 11 cyst species never being unambiguously reported in China, 10 never reported as cyst producers, and 3 HABs-causing species never reported from YS. Our detections of many potentially toxic or HABs-causative, particularly novel, cysts and distribution pattern provide important insights into the risks and ecology of dinoflagellate HABs.

Description of two new species Chattonella tenuiplastida sp. nov. and Chattonella malayana sp. nov. (Raphidophyceae) from South China Sea, with a report of wild fish mortality

Fisheries damage caused by Chattonella red tide has been recorded in Southeast Asia. Molecular studies have clarified the presence of two species, Chattonella marina complex and Chattonella subsalsa in the region, unlike East Asia that had only C. marina complex. To elucidate the phylogeography of Chattonella in Asia, further phylogenetic and morphological examinations were carried out with 33 additional culture strains, including the strains isolated during a bloom of Chattonella sp. (up to 142 cells mL^-1) that was associated with a wild fish mortality along the northeastern coast of Peninsular Malaysia in 2016, and those from Yellow Sea, where the Chattonella genotypes have not been determined. LSU rDNA and ITS2 trees showed five intrageneric clades in the genus Chattonella, which were clades I and II (C. subsalsa), clade III (C. marina complex) and two new clades, namely clade IV from Thailand and Malaysia, and clade V from Peninsular Malaysia. The positions of the two new clades were different in LSU rDNA and ITS2 trees. LSU rDNA divergences of clades IV and V from the other clades were ≥ 4.01% and ≥ 5.70%, while their ITS2 divergences were ≥ 7.44% and ≥ 16.43%, respectively. Three and five compensatory base changes (CBCs) were observed in the clades IV and V, respectively, when compared to each of their closest clade. Cells from clades IV and V showed similar morphology to C. marina complex and C. subsalsa clade II, including the presence of button-like granules on cell surface and oboe-shaped mucocysts. However, cell size, the number and shape of chloroplasts in Chattonella clades IV and V, and the non-stacked thylakoids penetrated the pyrenoid in C. subsalsa clade II, were distinctive. Based on the diagnostic chloroplast shape, we proposed the designation of clades IV and V to two new species, Chattonella tenuiplastida sp. nov. and Chattonella malayana sp. nov.

Spatial-temporal variability of microphytoplankton assemblages including harmful microalgae in a tropical semi-enclosed strait (Johor Strait, Malaysia)

Harmful algal blooms (HABs) were not new to the tropical semi-enclosed Johor Strait, with incident records that could trace back to the 1980s. HAB monitoring in the area, often, is reactive, focusing only on HAB taxa previously causing problems but neglecting potential emerging HABs. To develop datasets on HABs that can better inform and improve management practices, monitoring should expand to sample whole microphytoplankton communities. In this study, microphytoplankton community structure across the Strait was investigated. Abundances of microphytoplankton and a suite of in situ water parameters of temperatures, salinity, pH, dissolved oxygen levels, macronutrients, and chlorophyll-a contents were collected at ten sites across the Strait at monthly intervals from January 2017 to December 2018. A total of 48 genera (51 taxa) microphytoplankton were identified microscopically. Diatom was the most diverse group (32 genera), followed by dinophyte (15 genera). Bloom-forming species included diatoms Chaetoceros, Coscinodiscus, Eucampia, Pseudo-nitzschia, Rhizosolenia, Skeletonema, Thalassiosira, and dinophytes Blixaea quinquecornis and Scrippsiella. Diatom taxa that exhibit high in situ growth rates were predominant in the low-nutrient marine-influenced environment. Bloom-forming taxa including HAB taxa were found dominant in the environment with high nutrient levels and mesohaline, salinity-stratified conditions. This study provides valuable baseline data that could assist in monitoring and prediction of HABs in the Johor Strait and could be of reference to other similar tropical coastal systems.