An advanced tool, droplet digital PCR (ddPCR), for absolute quantification of the red-tide dinoflagellate, Cochlodinium polykrikoides Margalef (Dinophyceae)

Lee, Hyun-Gwan; Kim, Hye Mi; Min, Juhee; Kim, Keunyong; Park, Myung Gil; Jeong, Hae Jin; Kim, Kwang Young

doi:10.4490/algae.2017.32.9.10

Cited by 20 publications

(20 citation statements)

References 29 publications

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“…For instance, the AOA abundances in the Bay of Gdańsk and Öre Estuary were markedly lower than the up to about 10 8 copies l −1 found in the Gulf of California (Beman et al ., ), the Atlantic Ocean (Wuchter et al ., ) or the Southeastern US Coast (Hollibaugh et al ., ), but similar to the range reported from the Yangtze River estuary (Zhang et al ., ). We applied the ddPCR technique for gene quantification because it is relatively insensitive to the existence of PCR inhibitors, has been shown to produce correct quantification of cells in marine samples (Lee et al ., ), a verified protocol for amoA gene quantification was available (Dong et al ., ), and our specific hardware has earlier been used successfully for gene quantification (e.g., Nygaard et al ., ). Hence, we find a systematic methodological underestimation of amoA genes in our study unlikely, and therefore speculate whether these low abundances could be due to competitive exclusion imposed by the special Baltic Sea environment; for example, by the sharp salinity gradients (Herlemann et al ., ) or the massive outlet of terrigenous carbon in the Öre Estuary (Sandberg et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea

Happel

Bartl

Voß

et al. 2018

Environmental Microbiology

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Nitrification is important in nitrogen (N) cycling of aquatic environments, but knowledge about its regulation and importance is sparse. Here we examined nitrification and ammonia oxidizers in the Baltic Sea. We investigated two sites with different catchment characteristics (agricultural and forest), the Bay of Gdánsk (south) and the Öre Estuary (north), and measured pelagic nitrification rates and abundance, composition and expression of ammonia monooxygenase (amoA) genes. Highest nitrification rates were found in the nutrient rich Bay of Gdańsk. Interestingly, abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were orders of magnitude lower than reported from other sites. Although AOA were most abundant at both sites, the highest expression levels were from AOB. Interestingly, few AOA and AOB taxa dominated amoA gene expression, with a Nitrosomarinus related phylotype showing widespread expression. AOA and AOB communities differed between sites and depths, respectively, with the composition in rivers being distinct. A storm event, causing an even depth distribution of nitrification and particles in the Bay of Gdańsk, indicated that the presence of particles stimulate nitrification. The study highlights coastal regions as dynamic sites of extensive pelagic nitrification, which may affect local food web dynamics and loss of N mediated by denitrification.

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Section: Discussionmentioning

confidence: 99%

Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea

Happel

Bartl

Voß

et al. 2018

Environmental Microbiology

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“…Many of these programs continue to innovate as new technologies become available. In Korea, for example, monitoring programs are evaluating the use of acoustics (Kang et al, 2016), molecular methods such as digital PCR (Lee et al, 2017), unmanned aerial vehicles (Oh et al, 2016), and new satellite platforms such as the Geostationary Ocean Color Imager (GOCI) coupled to numerical models to provide real-time decision-support tools for managers (Kim et al, 2017).…”

Section: Asiamentioning

confidence: 99%

Scaling Up From Regional Case Studies to a Global Harmful Algal Bloom Observing System

Anderson¹,

Berdalet²,

Kudela³

et al. 2019

Front. Mar. Sci.

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Anderson et al. Harmful Algal Bloom Observing System automated, near real-time information from nearshore and offshore sites situated in HAB transport pathways to provide improved, advanced HAB warnings; (4) merge ecological knowledge and models with existing Earth System Modeling Frameworks to enhance end-to-end capabilities in forecasting and scenario-building; (5) provide seasonal to decadal forecasts to allow governments to plan, adapt to a changing marine environment, and ensure coastal industries are supported and sustained in the years ahead; and (6) support implementation of the recent calls for action by the United Nations Decade 2010 Sustainable Development Goals (SDGs) to develop indicators that are relevant to an effective and global HAB early warning system.

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“…For example, metagenome skimming, first coined by Straub et al (2012), is the low-coverage shotgun metagenomics sequencing of bulk DNA from environmental samples. De novo assembly analyses are performed through lowcoverage genomic sequencing to provide a high-copy of metabarcoding markers that have been used as phylo-sity is identifying the distribution and abundance of species across space and time (Losos 2010, Lee et al 2017. Over the past few decades, identification and mapping of biodiversity based on morphological and microscopic approaches has been developed and is being widely used in a variety of studies (Roy andFoote 1997, McManus andKatz 2009).…”

Section: Introductionmentioning

confidence: 99%

SoEM: a novel PCR-free biodiversity assessment method based on small-organelles enriched metagenomics

Jo¹,

Lee²,

Kim³

et al. 2019

ALGAE

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DNA metabarcoding is currently used for large-scale taxonomic identification to understand the community composition in various marine ecosystems. However, before being widely used in this emerging field, this experimental and analytic approach still has several technical challenges to overcome, such as polymerase chain reaction (PCR) bias, and lack of well-established metabarcoding markers, a task which is difficult but not impossible to achieve. In this study, we present an adapted PCR-free small-organelles enriched metagenomics (SoEM) method for marine biodiversity assessment. To avoid PCR bias and random artefacts, we extracted target DNA sequences without PCR amplification from marine environmental samples enriched with small organelles including mitochondria and plastids because their genome sequences provide a valuable source of molecular markers for phylogenetic analysis. To experimentally enrich small organelles, we performed subcellular fractionation using modified differential centrifugation for marine environmental DNA samples. To validate our SoEM method, two marine environmental samples from the coastal waters were tested the taxonomic capturing capacity against that of traditional DNA metabarcoding method. Results showed that, regardless of taxonomic levels, at least 3-fold greater numbers of taxa were identified in our SoEM method, compared to those identified by the conventional multi-locus DNA metabarcoding method. The SoEM method is thus effective and accurate for identifying taxonomic diversity and presents a useful alternative approach for evaluating biodiversity in the marine environment.

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An advanced tool, droplet digital PCR (ddPCR), for absolute quantification of the red-tide dinoflagellate, Cochlodinium polykrikoides Margalef (Dinophyceae)

Cited by 20 publications

References 29 publications

Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea

Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea

Scaling Up From Regional Case Studies to a Global Harmful Algal Bloom Observing System

SoEM: a novel PCR-free biodiversity assessment method based on small-organelles enriched metagenomics

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