Identifying active foraminifera in the Sea of Japan using metatranscriptomic approach

Lejzerowicz, Franck; Voltsky, Ivan; Pawłowski, Jan

doi:10.1016/j.dsr2.2012.08.008

Cited by 39 publications

(33 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previous studies reported overall similar communities of coastal marine protists recovered from DNA and RNA templates, with some revealing exceptions in particular groups (Logares et al, 2014; Massana et al, 2015; Lejzerowicz, Volstky & Pawlowski, 2013). Our results showed that eDNA and eRNA capture different community composition, affording useful information in particular for groups showing discordances for both templates.…”

Section: Discussionmentioning

confidence: 81%

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Guardiola

Wangensteen

Taberlet

et al. 2016

PeerJ

107

View full text Add to dashboard Cite

We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda, Arthropoda and Annelida were the most diverse. We found a marked heterogeneity at all scales, with important differences between layers of sediment and significant changes in community composition with zone (canyon vs slope), depth, and season. We compared the information obtained from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs per sample with DNA (ca. 20% and 40% increase, respectively). Both datasets showed overall similar spatial trends, but most groups had higher MOTU richness with the DNA template, while others, such as nematodes, were more diverse in the RNA dataset. We provide metabarcoding protocols and guidelines for biomonitoring of these key communities in order to generate information applicable to management efforts.

show abstract

Section: Discussionmentioning

confidence: 81%

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Guardiola

Wangensteen

Taberlet

et al. 2016

PeerJ

107

View full text Add to dashboard Cite

show abstract

“…However, we cannot exclude that some of these sequences originated from the extracellular DNA known to be extremely abundant in deep-sea sediments (Dell'Anno and Danovaro, 2005). It is only by targeting RNA instead of DNA that their living state could be confirmed (Lejzerowicz et al, 2013b). Using RNA-based sequencing, surprisingly similar microbial communities were found active in the sediments of the investigated stations, exposed to contrasting levels of particulate organic matter (Ruff et al, 2014), suggesting comparable particulate organic matter qualities.…”

Section: Replicate Heterogeneity and Common Sequencesmentioning

confidence: 90%

Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing

Lejzerowicz

Esling

Pawłowski

2014

Deep Sea Research Part II: Topical Studies in Oceanography

Self Cite

View full text Add to dashboard Cite

“…Additional PCR amplifications were conducted using primer sets targeting foraminiferal SSU rDNA fragments of approximately 400 and approximately 1000 bp (see the electronic supplementary material, table S2). Sanger sequences were assigned as previously (foraminiferans, [8]; radiolarians, [9]) and clustered into operational taxonomic units (OTUs) as in Lejzerowicz et al [8] at 3 per cent divergence. Illumina sequences were treated separately and clustered to Sanger OTUs at 5 per cent divergence.…”

Section: Methodsmentioning

confidence: 99%

“…Controlled PCR amplifications realized in dedicated hoods (blank ratio 1 : 2 to 1 : 3) and using specific primers targeting the small subunit of the ribosomal RNA gene (SSU rDNA) of radiolarians (approx. 270 bp) or foraminiferans (68-196 bp) were prepared, cloned and Sanger sequenced as in Lejzerowicz et al [8] or using the next-generation sequencing (NGS) technology Illumina (MiSeq instrument). Additional PCR amplifications were conducted using primer sets targeting foraminiferal SSU rDNA fragments of approximately 400 and approximately 1000 bp (see the electronic supplementary material, table S2).…”

Section: Methodsmentioning

confidence: 99%

Ancient DNA complements microfossil record in deep-sea subsurface sediments

et al. 2013

Self Cite

View full text Add to dashboard Cite

Deep-sea subsurface sediments are the most important archives of marine biodiversity. Until now, these archives were studied mainly using the microfossil record, disregarding large amounts of DNA accumulated on the deep-sea floor. Accessing ancient DNA (aDNA) molecules preserved down-core would offer unique insights into the history of marine biodiversity, including both fossilized and non-fossilized taxa. Here, we recover aDNA of eukaryotic origin across four cores collected at abyssal depths in the South Atlantic, in up to 32.5 thousand-year-old sediment layers. Our study focuses on Foraminifera and Radiolaria, two major groups of marine microfossils also comprising diverse non-fossilized taxa. We describe their assemblages in down-core sediment layers applying both micropalaeontological and environmental DNA sequencing approaches. Short fragments of the foraminiferal and radiolarian small subunit rRNA gene recovered from sedimentary DNA extracts provide evidence that eukaryotic aDNA is preserved in deep-sea sediments encompassing the last glacial maximum. Most aDNA were assigned to non-fossilized taxa that also dominate in molecular studies of modern environments. Our study reveals the potential of aDNA to better document the evolution of past marine ecosystems and opens new horizons for the development of deep-sea palaeogenomics.

show abstract

Identifying active foraminifera in the Sea of Japan using metatranscriptomic approach

Cited by 39 publications

References 34 publications

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing

Ancient DNA complements microfossil record in deep-sea subsurface sediments

Contact Info

Product

Resources

About