Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique

Nagai, Satoshi; Hida, Kohsuke; Urushizaki, Shingo; Onitsuka, Goh; Yasuike, Motoshige; Nakamura, Yoji; Fujiwara, Atushi; Tajimi, Seisuke; Kimoto, Katsunori; Kobayashi, Takanori; Gojobori, Takashi; Ototake, Mitsuru

doi:10.1016/j.gene.2015.10.025

Cited by 11 publications

(6 citation statements)

References 38 publications

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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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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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“…DNA was extracted shortly after filtration. In preparation for DNA extraction, a 5% Chelex ® suspension (Chelex 100 Molecular Biology Grade Resin; Bio-Rad Laboratories Inc., Richmond, CA, USA) was prepared by dispersing the resin into ultra-pure water (Tanabe et al 2015, Nagai et al 2016a, Nagai et al 2016b. To ensure effective extraction of DNA from planktonic elements trapped on the filters, filters were cut in half and were placed in 1.5-mL tubes (A.150; Assist; Tokyo, Japan) with 150 µL 5% Chelex buffer.…”

Section: Sampling and Dna Extractionmentioning

confidence: 99%

“…Plankton cells were crushed using a motorized pellet pestle (Kontes Glass; Vineland, NJ, USA) for 60 s, and 350 µL buffer was added to achieve a final volume of 500 µL. DNA was extracted by heating the 1.5-mL tubes at 97°C for 20 min (Tanabe et al 2015, Nagai et al 2016a, Nagai et al 2016b. DNA samples extracted from the 8-µm filter and the 1-µm filter were mixed equally (50 µL+50 µL) and were used as template DNA.…”

Section: Sampling and Dna Extractionmentioning

confidence: 99%

“…In other Japanese coastal waters, however, full studies of the distribution, population dynamics, and population genetics of P. multiseries have not yet been carried out. Recently, we conducted time-series monitoring experiments using amplicon sequences of partial 18S-rRNA genes in Japanese coastal waters (Nagai et al 2016a, Nagai et al 2016b, Nagai et al 2016c). Unfortunately, identifying species in the genus Pseudo-nitzschia was rendered difficult by the low resolution of the target gene region (Nagai et al 2016a, Nagai et al 2016b.…”

Section: Introductionmentioning

confidence: 99%

“…Recently, we conducted time-series monitoring experiments using amplicon sequences of partial 18S-rRNA genes in Japanese coastal waters (Nagai et al 2016a, Nagai et al 2016b, Nagai et al 2016c). Unfortunately, identifying species in the genus Pseudo-nitzschia was rendered difficult by the low resolution of the target gene region (Nagai et al 2016a, Nagai et al 2016b. Thus, in the present study, we used primers specific to Pseudo-nitzschia (developed by McDonald et al (2007)) in an MPS-based survey to investigate the distribution and population dynamics of Pseudo-nitzschia species in Tokyo Bay, Japan.…”

Section: Introductionmentioning

confidence: 99%

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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

Nagai¹,

Urusizaki²,

Hongo³

et al. 2017

Plankton Benthos Res

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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.

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From molecules to ecosystem functioning: insight into new approaches to taxonomy to monitor harmful algae diversity in Chile

Mardones

Krock

Marcus

et al. 2022

Advances in Phytoplankton Ecology

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Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique

Cited by 11 publications

References 38 publications

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

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

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

From molecules to ecosystem functioning: insight into new approaches to taxonomy to monitor harmful algae diversity in Chile

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