An attempt to semi-quantify potentially toxic diatoms of the genus <i>Pseudo-nitzschia</i> in Tokyo Bay, Japan by using massively parallel sequencing technology

Abstract

Currently, no tool is available that precisely identifies and quantifies all 48 species of Pseudo-nitzschia simultaneously. In the present study, we used massively parallel sequencing-based technology with genus-specific Pseudo-nitzschia primers to investigate the distribution and population dynamics of the genus in Tokyo Bay, Japan. Furthermore, we attempted to quantify the abundance of each species using both relative abundance data detected in the massively parallel sequencing-based survey, and cell count data, obtained by light microscopy. Several species of Pseudo-nitzschia were detected continuously from July 10 to September 9, 2016 in the sampling location. Cell densities ranged from 2-300 cells mL −1 (sample no.=10). Fourteen operational taxonomic units (OTUs) attributable to Pseudonitzschia were detected, and 99.9% of sequences detected by massively parallel sequencing belonged to the genus. Each of the most abundant OTUs comprised a single species, and were identified, in decreasing order of abundance, as P. multistriata (Takano) Takano, P. pungens (Grunow ex Cleve) Hasle, P. fraudulenta (Cleve) Hasle, P. multiseries (Hasle) Hasle, and P. galaxiae Lundholm & Moestrup. Species identification was possible in 9 of the 14 OTUs detected, of which several were detected in Tokyo Bay for the first time. The cell abundance ranges of the five most abundant species were estimated as 1, 976-246,395, 0.03-52,999, 5-42,820, 4-24,617, and 0.03-1,007 cells L −1 , respectively. The detection limit was 0.03 cells L −1.

Monitoring harmful microalgal species and their appearance in Tokyo Bay, Japan, using metabarcoding

“…As both species have been previously reported from Tokyo Bay as HAB causative species (Nomura 1998), the lack of detection by metabarcoding may be explained by the lack of sequences present in the public databases as no 18S rRNA gene sequences were available for D. fragilissimus and only one sequence covering the target region was available for L. minimus. The lack of sequences covering the target region in the database could also explain why Pseudo-nitzschia galaxiae and P. subfraudulenta that have been previously reported from the Bay (Nagai et al 2017) were not detected. In a recent study from the Gulf of Naples, the Mediterranean Sea, P. galaxiae was successfully detected from eDNA samples by targeting the 18S rRNA gene V4 region (Ruggiero et al 2022).…”

“…Furthermore, eDNA metabarcoding has been successfully applied to reveal appearance patterns for several organism groups ranging from bacteria to mammals (Nagai et al 2016;Hirai et al 2017;Sigsgaard et al 2017;Stoeckle et al 2017;Berry et al 2019;Zhang et al 2020;Sildever et al 2021;Alter et al 2022), including the HAB species (Nagai et al 2017(Nagai et al , 2019Sildever et al 2019). As several genes or markers can be amplified from the same sample, co-appearance patterns and associations amongst species and groups can also be investigated (Lima-Mendez et al 2015;Sawaya et al 2019;Djurhuus et al 2020).…”

“…The postbloom accumulation of decaying algal cells in the seabed contributes to the development of hypoxia, resulting in losses in benthic communities (Toba et al 2008;Kodama and Horiguchi 2011). The main HAB causative species in Tokyo Bay are a diatom Skeletonema costatum and a raphidophyte Heterosigma akashiwo (Nomura 1998) with 28 toxin-producing species also recorded from the Bay (Nomura and Yoshida 1997;Nomura 1998;Matsuoka et al 2003;Yap-Dejeto et al 2010;Yuki and Yoshimatsu 2012;Demura et al 2014;Nagai et al 2017).…”

Plankton biodiversity and species co-occurrence based on environmental DNA – a multiple marker study

“…Also, as the approach provides detailed information on the whole community or specific groups targeted (Lima-Mendez et al 2015;Sawaya et al 2019;Djurhuus et al 2020), it can be applied for biodiversity monitoring (Zaiko et al 2015;Nagai et al 2016b;2018;2020a;Valentini et al 2016;Stat et al 2017;Djurhuus et al 2018). The method also allows detection of patterns in the species/groups appearances, providing detailed information on the environmental conditions inhibiting/supporting their presence (Lallias et al 2015;Brannock et al 2016;Nagai et al 2017;Banerji et al 2018;Berry et al 2019;Salonen et al 2018;Sildever et al 2019).…”

Monitoring of the toxic dinoflagellate Alexandrium catenella in Osaka Bay, Japan using a massively parallel sequencing (MPS)-based technique

“…Massively parallel sequencing (MPS) is a powerful method enabling detection of species unidentifiable by LM (e.g. Sogin et al, 2006;Caron et al, 2012;Nagai et al, 2017;Gran-Stadniczeñko et al, 2018) and revealing the hidden diversity of microbial communities in environmental samples (Tanabe et al, 2016;Nagai et al, 2016a;Dzhembekova et al, 2017;Sze et al, 2018).…”