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

Nagai, Satoshi; Chen, Hungyen; Kawakami, Yoko; Yamamoto, Kazuo; Sildever, Sirje; Kanno, Nanako; Yasuike, Motoshige; Nakamura, Yoji; Hongo, Yuki; Fujiwara, Atushi; Kobayashi, Takanori; Gojobori, Takashi

doi:10.1016/j.hal.2019.101660

Cited by 27 publications

(12 citation statements)

References 91 publications

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“…However, it may provide an overall impression of species/classes relative abundances (Eiler et al 2013;Giner et al 2016;Gran-Stadniczeñko et al 2017;Schenk et al 2019). For example, the relative sequence abundances obtained by HTS-approach have been reported to coincide with the yearly total abundance patterns detected by using light microscopy for the toxin-producing dinoflagellate Alexandrium catenella (Nagai et al 2019). Furthermore, in combination with light microscopy-based counts, the relative sequence abundances may provide a semi-quantitative estimate of cell abundances, which has high relevance for morphologically similar species, e.g.…”

Section: Common/dominant/toxin-producing Species Appearance Patternsmentioning

confidence: 99%

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

Sildever¹,

Laas²,

Kolesova³

et al. 2021

MBMG

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Metabarcoding in combination with high-throughput sequencing (HTS) allows simultaneous detection of multiple taxa by targeting single or several taxonomically informative gene regions from environmental DNA samples. In this study, a multiple-marker HTS approach was applied to investigate the plankton diversity and seasonal succession in the Baltic Sea from winter to autumn. Four different markers targeting the 16S, 18S, and 28S ribosomal RNA genes were employed, including a marker for more efficient dinoflagellate detection. Typical seasonal changes were observed in phyto- and bacterioplankton communities. In phytoplankton, the appearance patterns of selected common, dominant, or harmful species followed the patterns also confirmed based on 20 years of phytoplankton monitoring data. In the case of zooplankton, both macro- and microzooplankton species were detected. However, no seasonal patterns were detected in their appearance. In total, 15 and 2 new zoo- and phytoplankton species were detected from the Baltic Sea. HTS approach was especially useful for detecting microzooplankton species as well as for investigating the co-occurrence and potential interactions of different taxa. The results of this study further exemplify the efficiency of metabarcoding for biodiversity monitoring and the advantage of employing multiple markers through the detection of species not identifiable based on a single marker survey and/or by traditional morphology-based methods.

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Section: Common/dominant/toxin-producing Species Appearance Patternsmentioning

confidence: 99%

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

Sildever¹,

Laas²,

Kolesova³

et al. 2021

MBMG

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“…Improved species detection can be achieved by employing high-throughput sequencing (HTS) methods, such as DNA metabarcoding. This approach allows amplifying the gene of interest from a mass collection of organisms or environmental DNA (eDNA) and thus target multiple species simultaneously (Moreno-Pino et al 2018;Nagai 2018;Nagai et al 2019). Metabarcoding has also been applied for investigating the diversity of microalgae, which has uncovered the presence of previously unknown HAB species/genera for the sampling area (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

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

Sildever¹,

Nishi²,

Inaba³

et al. 2022

MBMG

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During the recent decade, high-throughput sequencing (HTS) techniques, in particular, DNA metabarcoding, have facilitated increased detection of biodiversity, including harmful algal bloom (HAB) species. In this study, the presence of HAB species and their appearance patterns were investigated by employing molecular and light microscopy-based monitoring in Tokyo Bay, Japan. The potential co-appearance patterns between the HAB species, as well as with other eukaryotes and prokaryotes were investigated using correlation and association rule-based time-series analysis. In total, 40 unique HAB species were detected, including 12 toxin-producing HAB species previously not reported from the area. More than half of the HAB species were present throughout the sampling season (summer to autumn) and no structuring or succession patterns associated with the environmental conditions could be detected. Statistically significant (p < 0.05, rS ranging from −0.88 to 0.90) associations were found amongst the HAB species and other eukaryotic and prokaryotic species, including genera containing growth-limiting bacteria. However, significant correlations between species differed amongst the years, indicating that variability in environmental conditions between the years may have a stronger influence on the microalgal community structure and interspecies interactions than the variability during the sampling season. The association rule-based time-series analysis allowed the detection of a previously reported negative relationship between Synechococcus sp. and Skeletonema sp. in nature. Overall, the results support the applicability of metabarcoding and HTS-based microalgae monitoring, as it facilitates more precise species identification compared to light microscopy, as well as provides input for investigating potential interactions amongst different species/groups through simultaneous detection of multiple species/genera.

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“…In the same area, Akashiwo sanguinea-dominated algal blooms occurred in mid-June 2016, where the number of copepod species and their abundances in the bloom area were significantly less than those in the nonbloom area, which may be in part due to the fact that the dominant species, such as A. sanguinea and Gonyaulax spinifera, can secrete Ichthyotoxins and Yessotoxins, and similar results about biodiversity also showed that there were no significant differences in the biodiversity indices of zooplankton between the bloom and nonbloom areas [50]. However, it is regrettable that the current research on dinoflagellate blooms is often in the form of cross-sectional voyage surveys (Lin et al [13]) or a longer interval sampling method [12,51], and it is difficult to completely monitor the occurrence and disappearance of a bloom. Therefore, further research is needed to verify the possible impacts of the whole HABs process, including those interactions of diatoms and dinoflagellates on the growth conditions of zooplankton as well as the healthy development of marine ecosystems.…”

Section: Discussionmentioning

confidence: 99%

Zooplankton Population and Community Structure Changes in Response to a Harmful Algal Bloom Caused by Prorocentrum donghaiense in the East China Sea

Shen

Chen

et al. 2022

JMSE

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Blooms of the dinoflagellate Prorocentrum donghaiense have had adverse impacts on marine ecosystems. However, ecological details, particularly the impacts and processes of the P. donghaiense bloom on the zooplankton community structure are poorly known. We investigated the changes of zooplankton communities in situ within the whole process of a P. donghaiense bloom in the coastal waters in southern Zhejiang Province, China, in May 2016. Results showed that ecological changes during the blooms of P. donghaiense could be divided into three major phases, namely the growth, maintenance, and dissipation phases with regard to the cell abundance of P. donghaiense by bottle sampling of plankton. A total of 42 species of zooplankton were identified. The average abundance and species number of zooplankton in the growth phase were significantly higher than those in the maintenance and dissipation phases. It is shown that the top-two highest proportions of zooplankton in the growth phase were small jellyfishes and copepods, while small jellyfishes and chaetognaths, and copepoda larvae and chaetognaths were the top-two highest in the maintenance and dissipation phases respectively. However, the values of biodiversity index have no statistically significant differences between the three phases. The present results suggested that P. donghaiense bloom produced significant negative impacts on the abundance and species composition of zooplankton with particular reference to copepods.

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

Cited by 27 publications

References 91 publications

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

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

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

Zooplankton Population and Community Structure Changes in Response to a Harmful Algal Bloom Caused by Prorocentrum donghaiense in the East China Sea

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

Cited by 27 publications

References 91 publications

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

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

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

Zooplankton Population and Community Structure Changes in Response to a Harmful Algal Bloom Caused by Prorocentrum donghaiense in the East China Sea

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