Massively parallel sequencing-based survey of eukaryotic community structures in Hiroshima Bay and Ishigaki Island

Nagai, Satoshi; Hida, Kohsuke; Urusizaki, Shingo; Takano, Yoshihito; Hongo, Yuki; Kameda, Takahiko; Abe, Kazuo

doi:10.1016/j.gene.2015.10.026

Cited by 18 publications

(10 citation statements)

References 62 publications

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“…To identify multiple species simultaneously and analyze several samples at once, metabarcoding and high-throughput sequencing (HTS) has been applied to investigate plankton diversity (Sogin et al 2006;de Vargas et al 2015;Massana et al 2015;Sunagawa et al 2015;Chain et al 2016;Nagai et al 2016b;Gran-Stadniczeñko et al 2018;Cui et al 2019;Bucklin et al 2019). Metabarcoding in combination with HTS allows simultaneous detection of multiple taxa by using universal or more specific PCR primers to amplify taxonomically informative gene regions from environmental DNA (eDNA; Taberlet et al 2012;Ji et al 2013).…”

Section: Introductionmentioning

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: Introductionmentioning

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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“…The microscopic observation uses the samples without filtration and fixation to identify Pseudochattonella , one of the notable HAB species in Chile with a small diameter that can be easily filtered out or ruptured with fixatives. The DNA extraction uses the Chelex-buffer method as Nagai et al (2012) previously compared four different DNA extraction methods using A. tamarense and A. catenella and concluded that the 5% Chelex method was superior to others in efficiency, processing time, repeatability of PCR, and successful eukaryotic metabarcoding analysis [ 23 , 24 , 31 , 32 ]. The pigment analysis uses the thirteen most basic pigments because, of more than 70 pigments available, these are required by CHEMTAX, an algorithm program to estimate class abundances from pigment markers using pigment ratio [ 30 ].…”

Section: Resultsmentioning

confidence: 99%

Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile

Yarimizu

Fujiyoshi

Kawai

et al. 2020

IJERPH

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Harmful algae blooms (HABs) cause acute effects on marine ecosystems due to their production of endogenous toxins or their enormous biomass, leading to significant impacts on local economies and public health. Although HAB monitoring has been intensively performed at spatiotemporal scales in coastal areas of the world over the last decades, procedures have not yet been standardized. HAB monitoring procedures are complicated and consist of many methodologies, including physical, chemical, and biological water sample measurements. Each monitoring program currently uses different combinations of methodologies depending on site specific purposes, and many prior programs refer to the procedures in quotations. HAB monitoring programs in Chile have adopted the traditional microscopic and toxin analyses but not molecular biology and bacterial assemblage approaches. Here we select and optimize the HAB monitoring methodologies suitable for Chilean geography, emphasizing on metabarcoding analyses accompanied by the classical tools with considerations including cost, materials and instrument availability, and easiness and efficiency of performance. We present results from a pilot study using the standardized stepwise protocols, demonstrating feasibility and plausibility for sampling and analysis for the HAB monitoring. Such specific instructions in the standardized protocol are critical obtaining quality data under various research environments involving multiple stations, different analysts, various time-points, and long HAB monitoring duration.

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“…MPS technologies deliver high-throughput performance and allow the detection of several hundreds of OTUs (e.g. Tanabe et al, 2016;Nagai et al, 2016a;Hu et al, 2016;Elferink et al, 2017;Piredda et al, 2018). The significant advantage of applying MPS-based technology for monitoring of eukaryotic species is its great potential to identify species by genetic information, in particular, the species that are indistinguishable by morphology-based observation using LM (e.g.…”

Section: Massively Parallel Sequencing Approach For Phytoplankton Monmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

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

Nagai

Chen

Kawakami³

et al. 2019

Harmful Algae

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A B S T R A C TSince 2002, blooms of Alexandrium catenella sensu Fraga et al. (2015) and paralytic shellfish toxicity events have occurred almost yearly in Osaka Bay, Japan. To better understand the triggers for reoccurring A. catenella blooms in Osaka Bay, phytoplankton community was monitored during the spring seasons of 2012-2015. Monitoring was performed using massively parallel sequencing (MPS)-based technique on amplicon sequences of the 18S rRNA gene. Dense blooms of A. catenella occurred every year except in 2012, however, there was no significant correlation with the environmental parameters investigated. Plankton community diversity decreased before and middle of the A. catenella blooms, suggesting that the decline in diversity could be an indicator for the bloom occurrence. The yearly abundance pattern of A. catenella cells obtained by morphology-based counting coincided with the relative sequence abundances, which supports the effectiveness of MPS-based phytoplankton monitoring.

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Massively parallel sequencing-based survey of eukaryotic community structures in Hiroshima Bay and Ishigaki Island

Cited by 18 publications

References 62 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

Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile

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

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