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Temporal variation of lagoon-associated and pelagic (open ocean) planktonic 18S rRNA-gene sequences (Mo’orea, French Polynesia).

ABSTRACT: Planktonic 18S rRNA gene sequences (V4 region) from water samples collected inside the northern coral-reef lagoon of Mo’orea (French Polynesia) and 4 km offshore, in the tropical open ocean.

PROVIDER: PRJEB69515 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12265013_1.fastq.gz	Fastqsanger.gz
	ERR12265013_2.fastq.gz	Fastqsanger.gz
	ERR12265014_1.fastq.gz	Fastqsanger.gz
	ERR12265014_2.fastq.gz	Fastqsanger.gz
	ERR12265015_1.fastq.gz	Fastqsanger.gz

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Temporal variation of lagoon-associated and pelagic (open ocean) planktonic 16S rRNA-gene sequences (Mo’orea, French Polynesia).

Project description:Planktonic 16S rRNA gene sequences (V4/V5 region) from water samples collected inside the northern coral-reef lagoon of Mo’orea (French Polynesia) and 4 km offshore, in the tropical open ocean.

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Gene expression profiling of native mussels from Venice lagoon area

Project description:We examined gene expression profiling of native mussels that were sampled in early summer 2003 from sites of the Venice lagoon area known to be differently affected by chemical pollution: Sites 1 and 2 close to the industrial district of Marghera and Site 3 close to the Lido lagoon outlet. Site 4, a current mussel farm located offshore, has been chosen as source of reference targets for microarray hybridizations. We have limited the preliminary assessment to the digestive gland. Digestive gland total RNA of each Site was hybridized in competition with the offshore mussels (Site 4 - Reference) and the relative abundance of each gene was measured by directly comparing fluorescent signals for each probe. We carried out two separate hybridizations for each site of the Venice lagoon area.. Keywords = digestive gland Keywords = Venice lagoon Keywords = chemical pollution Keywords = native mussels Keywords = transcriptional profiling Keywords: ordered

2006-10-10 | GSE2184 | GEO

Coral-associated planktonic 18S rRNA-gene sequences from an Acropora pulchra colony

Project description:Planktonic 18S rRNA gene sequences (V4 region) from water samples collected around an Acropora pulchra colony (Tema’e Beach reef, Mo’orea)

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Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon.

Project description:Diuron is a herbicide commonly used in agricultural areas where excess application causes it to leach into rivers, reach sensitive marine environments like the Great Barrier Reef (GBR) lagoon and pose risks to marine life. To investigate the impact of diuron on whole prokaryotic communities that underpin the marine food web and are integral to coral reef health, GBR lagoon water was incubated with diuron at environmentally-relevant concentration (8 µg/L), and sequenced at specific time points over the following year. 16S rRNA gene amplicon profiling revealed no significant short- or long-term effect of diuron on microbiome structure. The relative abundance of prokaryotic phototrophs was not significantly altered by diuron, which suggests that they were largely tolerant at this concentration. Assembly of a metagenome derived from waters sampled at a similar location in the GBR lagoon did not reveal the presence of mutations in the cyanobacterial photosystem that could explain diuron tolerance. However, resident phages displayed several variants of this gene and could potentially play a role in tolerance acquisition. Slow biodegradation of diuron was reported in the incubation flasks, but no correlation with the relative abundance of heterotrophs was evident. Analysis of metagenomic reads supports the hypothesis that previously uncharacterized hydrolases carried by low-abundance species may mediate herbicide degradation in the GBR lagoon. Overall, this study offers evidence that pelagic phototrophs of the GBR lagoon may be more tolerant of diuron than other tropical organisms, and that heterotrophs in the microbial seed bank may have the potential to degrade diuron and alleviate local anthropogenic stresses to inshore GBR ecosystems.

| S-EPMC4793316 | biostudies-literature

Experimental and Environmental Metabolomics of Coral Reef DOM from Moorea, French Polynesia (2019)

Project description:Non-targeted LC-MS/MS of PPL extracts from experimental and environmental seawater samples from coral reefs from Mo'orea (French Polynesia), collected in May 2019.

2021-08-25 | MSV000088021 | MassIVE

Annotated 18S and 28S rDNA reference sequences of taxa in the planktonic diatom family Chaetocerotaceae.

Project description:The species-rich diatom family Chaetocerotaceae is common in the coastal marine phytoplankton worldwide where it is responsible for a substantial part of the primary production. Despite its relevance for the global cycling of carbon and silica, many species are still described only morphologically, and numerous specimens do not fit any described taxa. Nowadays, studies to assess plankton biodiversity deploy high throughput sequencing metabarcoding of the 18S rDNA V4 region, but to translate the gathered metabarcodes into biologically meaningful taxa, there is a need for reference barcodes. However, 18S reference barcodes for this important family are still relatively scarce. We provide 18S rDNA and partial 28S rDNA reference sequences of 443 morphologically characterized chaetocerotacean strains. We gathered 164 of the 216 18S sequences and 244 of the 413 28S sequences of strains from the Gulf of Naples, Atlantic France, and Chile. Inferred phylogenies showed 84 terminal taxa in seven principal clades. Two of these clades included terminal taxa whose rDNA sequences contained spliceosomal and Group IC1 introns. Regarding the commonly used metabarcode markers in planktonic diversity studies, all terminal taxa can be discriminated with the 18S V4 hypervariable region; its primers fit their targets in all but two species, and the V4-tree topology is similar to that of the 18S. Hence V4-metabarcodes of unknown Chaetocerotaceae are assignable to the family. Regarding the V9 hypervariable region, most terminal taxa can be discriminated, but several contain introns in their primer targets. Moreover, poor phylogenetic resolution of the V9 region affects placement of metabarcodes of putative but unknown chaetocerotacean taxa, and hence, uncertainty in taxonomic assignment, even of higher taxa.

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Octadecabacter arcticus 238

Project description:A psychrophilic marine microorganism collected 350 km offshore Deadhorse, Alaska.

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French Polynesia Sponge Biodiversity

Project description:Poriferans Rift Apart: Molecular sponge biodiversity in Central and French Polynesia and comparison with adjacent marine provinces of the Central Indo-Pacific

| PRJEB54662 | ENA

Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros.

Project description:Concerted evolution is a process of homogenisation of repetitive sequences within a genome through unequal crossing over and gene conversion. This homogenisation is never fully achieved because mutations always create new variants. Classically, concerted evolution has been detected as "noise" in electropherograms and these variants have been characterised through cloning and sequencing of subsamples of amplified products. However, this approach limits the number of detectable variants and provides no information about the abundance of each variant. In this study, we investigated concerted evolution by using environmental time-series metabarcoding data, single strain high-throughput sequencing (HTS) and a collection of Sanger reference barcode sequences. We used six species of the marine planktonic diatom genus Chaetoceros as study system. Abundance plots obtained from environmental metabarcoding and single strain HTS showed the presence of a haplotype far more abundant than all the others (the "dominant" haplotype) and identical to the reference sequences of that species obtained with Sanger sequencing. This distribution fitted best with Zipf's law among the rank abundance/ dominance models tested. Furthermore, in each strain 99% of reads showed a similarity of 99% with the dominant haplotype, confirming the efficiency of the homogenisation mechanism of concerted evolution. We also demonstrated that minor haplotypes found in the environmental samples are not only technical artefacts, but mostly intragenomic variation generated by incomplete homogenisation. Finally, we showed that concerted evolution can be visualised inferring phylogenetic networks from environmental data. In conclusion, our study provides an important contribution to the understanding of concerted evolution and to the interpretation of DNA barcoding and metabarcoding data based on multigene family markers.

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New sponges from French Polynesia

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