Metabarcoding of harmful algal bloom species in sediments from four coastal areas of the southeast China

Abstract

In the past three decades, harmful algal blooms (HAB) have become more frequent and widespread in southeast Chinese sea areas. Resting stages are regarded as the “seed bank” of algal blooms, and play an important role in initiating HABs. The distribution of resting stages in sediments especially those of HAB species can make good predictions about the potential risk of future blooms, however with limited reports. In this study, surface sediment samples were collected in the four sea areas along the southeast Chinese coasts, including Dafeng Port (DF) in the southern Yellow Sea, Xiangshan Bay (XS), Funing Bay (FN), and Dongshan Bay (DS) in the East China Sea. Diversity and community structure of eukaryotic microalgae in surface sediments were assessed by metabarcoding V4 region of the 18S rDNA, focusing on the distribution of HAB species. Biogenic elements including total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP), biogenic silicon (BSi), and moisture content (MC) were analyzed. A total of 454 eukaryotic algal OTUs were detected, which belonged to 31 classes of 9 phyla. Altogether 149 algal species were detected in this study, and 59 taxa have been reported to form resting stages. Eukaryotic algal community was similar in XS, FN and DS of the East China Sea, which were predominated by dinoflagellates. However, algal community was different in DF of the Yellow Sea, and characterized by the dominance of chrysophytes and low OTU richness. The distribution of most abundant HAB species showed positive correlations with TN, BSi, and TOC, suggesting that eutrophication and consequent increase in diatom productivity may have a significant influence on the distribution of HAB species and facilitate the occurrence of HABs. Furthermore, HAB species occurred more abundantly and widely in FN. Our results suggest high potential risks of HABs in the southeast Chinese coast especially in Funing Bay.

DNA and RNA Stability of Marine Microalgae in Cold-Stored Sediments and Its Implications in Metabarcoding Analyses

“…These results and those of other previous studies allow us to conclude that the higher the sequencing depth, the more taxa will be detected, especially for those with low abundance and low biomass and those strongly affected by primer bias [61][62][63][64]. The sequencing depth of our study with five species was about 50,000 reads, which is equal to or higher than that of other studies targeting natural sediment samples with much higher richness values and abundances of intact or live cells (resting cysts) [46][47][48][49][50], which means that the positive detection of the relic DNA of microalgal vegetative cells via metabarcoding in our study largely resulted from the high sequencing depth, and the relic DNA of microalgal vegetative cells, especially those after 45 days of storage, would be more likely to be undetectable if a lower sequencing depth was applied. As we discussed above, the relic DNA of microalgal vegetative cells in natural sediments will degrade much faster than that in the facsimile sediments in our study due to higher temperatures, oxygen, and degrading microorganisms in the field.…”

“…Therefore, identification based on morphology only has numerous limitations for species of tiny sizes which have not been taxonomically described, lack reference micrographs, or lack distinct diagnostic features [46]. With advancements in molecular techniques in recent decades, metabarcoding analyses have been increasingly applied to the identification and quantification of dinoflagellates [46][47][48][49][50][69][70][71]. While the metabarcoding approach is advantageous in detecting large numbers of samples efficiently and in detecting the assemblages of all known and unknown species present in the samples, a possible drawback is that when the method is applied to cyst detection from sediment samples, a crucial question may be raised regarding whether the retrieved DNA sequences are factually from cysts or otherwise from vegetative cells and/or cell fragments [48].…”

“…However, morphological identification has numerous limitations for species of tiny sizes that were not taxonomically described, lack reference micrographs, or lack distinctive taxonomic characters [45]. Metabarcoding analysis thus provides a powerful tool for determining resting cyst diversity [46][47][48][49][50]. However, these investigations face challenging questions regarding the possible interferences of relic DNA with the data interpretations of metabarcoding.…”