Applicability of massively parallel sequencing on monitoring harmful algae at Varna Bay in the Black Sea

Dzhembekova, Nina; Urusizaki, Shingo; Moncheva, Snejana; Ivanova, Petya; Nagai, Satoshi

doi:10.1016/j.hal.2017.07.004

Cited by 33 publications

(29 citation statements)

References 54 publications

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“…Two-step PCR for the construction of paired-end libraries and HTS on Illumina Miseq 300 PE platform (Illumina, USA) followed the protocols described in Dzhembekova et al (2017) . All the procedures and techniques, applicable to the treatment of the obtained sequences, selection and taxonomic identification of operational taxonomic units (OTUs), were administered according to the workflow described by Dzhembekova et al (2017) . When considering the taxonomic identification, a reference similarity threshold ≥ 98% was found appropriate.…”

Section: Methodsmentioning

confidence: 99%

Comparative analysis of morphological and molecular approaches integrated into the study of the dinoflagellate biodiversity within the recently deposited Black Sea sediments – benefits and drawbacks

Dzhembekova¹,

Rubino²,

Nagai³

et al. 2020

BDJ

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One of the assets, assigned to the phytoplankton resting stages, is that of serving as the “memory” of the aquatic ecosystems and preserved biodiversity in the course of time. However, an accurate cyst identification proves to be a more difficult and extremely challenging process, even today. In order to gain a better taxonomic coverage of cyst assemblages in the Black Sea, an integrated approach of the classical morphological identification with metabarcoding methods (MySeq sequencing of V7-V9 regions of the 18S rDNA) was applied on thirteen surface sediment samples collected from different sites. A total number of 112 dinoflagellate taxa was detected at the species level and ascribed to 51 genera. In general, it is the molecular analysis that yields a higher number of taxa as compared to those obtained through the morphological taxonomy (66 taxa based on the DNA sequences versus 56 morphologically-identified taxa). Besides, it should be pointed out that the integrated dataset includes 14 potentially toxic dinoflagellate species. Discerned, subsequently, was a good dataset consistency for ten species, followed by some discrepancies as to a number of taxa, identified with one of the methods only, due to specific methodological biases. On the whole, it could be concluded that the combination of morphological and molecular methods is likely to increase the potential for a more reliable taxonomic assessment of phytoplankton diversity in marine sediments which, in turn, proves conclusively the utmost importance of the integrated approach.

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Section: Methodsmentioning

confidence: 99%

Comparative analysis of morphological and molecular approaches integrated into the study of the dinoflagellate biodiversity within the recently deposited Black Sea sediments – benefits and drawbacks

Dzhembekova¹,

Rubino²,

Nagai³

et al. 2020

BDJ

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“…Three important aspect concerning the use of 18S rRNA should be highlighted (1) the current sequencing fragment length (∼200 bp) still does not allow a complete coverage of the 18S rRNA gene and thus, taxonomic assignment should be taken with caution; (2) it is well knowing that for certain groups of phytoplankton, not just those that are toxic, the 18S rRNA does not have sufficient resolution for taxonomic discrimination between closely related species; and (3) the high variation of 18S rRNA copy number in marine phytoplankton species, varying from one to hundreds of thousands copies per cell (Zhu et al, 2005). Probably these elements continue limiting the application of this methodology in routine phytoplankton analysis approaches (Dzhembekova et al, 2017).…”

Section: Dinophysis Acuminatamentioning

confidence: 99%

“…This later approach is based on modern analytical techniques, such as liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) (Hess, 2010), which allows the detection of individual compounds, with specific toxicities (Krock et al, 2009a(Krock et al, , 2008. On the other hand, studies utilizing Next Generation Sequencing (NGS) technologies offer an enormous potential for identification of (toxigenic) planktonic organisms due to their high resolution and coverage (Dzhembekova et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Next Generation Sequencing and mass spectrometry reveal high taxonomic diversity and complex phytoplankton-phycotoxins patterns in Southeastern Pacific fjords

Moreno-Pino

Krock

Iglesia

et al. 2018

Toxicon

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In fjord systems, Harmful Algal Blooms (HABs) not only constitute a serious problem when affecting the wildlife and ecosystems, but also human health and economic activities related to the marine environment. This is mostly due to a broad spectrum of toxic compounds produced by several members of the phytoplankton. Nevertheless, a deep coverage of the taxonomic diversity and composition of phytoplankton species and phycotoxin profiles in HAB prone areas are still lacking and little is known about the relationship between these fundamental elements for fjord ecosystems. In this study, a detailed molecular and microscopic characterization of plankton communities was performed, together with an analysis of the occurrence and spatial patterns of lipophilic toxins in a HAB prone area, located in the Southeastern Pacific fjord region. Microscopy and molecular analyses based on the 18S rRNA gene fragment indicated high diversity and taxonomic homogeneity among stations. Four toxigenic genera were identified: Pseudo-nitzschia, Dinophysis, Prorocentrum, and Alexandrium. In agreement with the detected species, liquid chromatography coupled with mass spectrometry revealed the presence of domoic acid (DA), pectenotoxin-2 (PTX-2), dinophysistoxin-2 (DTX-2), and 13-desmethyl spirolide C (SPX-1). Furthermore, a patchy distribution among DA in different net haul size fractions was found. Our results displayed a complex phytoplankton-phycotoxin pattern and for the first time contribute to the characterization of high-resolution phytoplankton community composition and phycotoxin distribution in fjords of the Southeastern Pacific region.

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“…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%

“…Effectiveness of MPS to detect many species simultaneously is especially relevant to reveal the presence of HAB species/genera (e.g. Dzhembekova et al, 2017;Elferink et al, 2017;Moreno-Pino et al, 2018;Nagai, 2018) and gather information on their appearances as some species may be present sporadically or during specific seasons (Sildever et al, 2019). This information is prerequisite for monitoring by other molecular methods, e.g.…”

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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Applicability of massively parallel sequencing on monitoring harmful algae at Varna Bay in the Black Sea

Cited by 33 publications

References 54 publications

Comparative analysis of morphological and molecular approaches integrated into the study of the dinoflagellate biodiversity within the recently deposited Black Sea sediments – benefits and drawbacks

Comparative analysis of morphological and molecular approaches integrated into the study of the dinoflagellate biodiversity within the recently deposited Black Sea sediments – benefits and drawbacks

Next Generation Sequencing and mass spectrometry reveal high taxonomic diversity and complex phytoplankton-phycotoxins patterns in Southeastern Pacific fjords

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

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