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Pawlowski J.,University of Geneva | Christen R.,University of Nice Sophia Antipolis | Lecroq B.,Japan Agency for Marine - Earth Science and Technology | Bachar D.,University of Nice Sophia Antipolis | And 3 more authors.
PLoS ONE | Year: 2011

Background: The deep sea floor is considered one of the most diverse ecosystems on Earth. Recent environmental DNA surveys based on clone libraries of rRNA genes confirm this observation and reveal a high diversity of eukaryotes present in deep-sea sediment samples. However, environmental clone-library surveys yield only a modest number of sequences with which to evaluate the diversity of abyssal eukaryotes. Methodology/Principal Findings: Here, we examined the richness of eukaryotic DNA in deep Arctic and Southern Ocean samples using massively parallel sequencing of the 18S ribosomal RNA (rRNA) V9 hypervariable region. In very small volumes of sediments, ranging from 0.35 to 0.7 g, we recovered up to 7,499 unique sequences per sample. By clustering sequences having up to 3 differences, we observed from 942 to 1756 Operational Taxonomic Units (OTUs) per sample. Taxonomic analyses of these OTUs showed that DNA of all major groups of eukaryotes is represented at the deep-sea floor. The dinoflagellates, cercozoans, ciliates, and euglenozoans predominate, contributing to 17%, 16%, 10%, and 8% of all assigned OTUs, respectively. Interestingly, many sequences represent photosynthetic taxa or are similar to those reported from the environmental surveys of surface waters. Moreover, each sample contained from 31 to 71 different metazoan OTUs despite the small sample volume collected. This indicates that a significant faction of the eukaryotic DNA sequences likely do not belong to living organisms, but represent either free, extracellular DNA or remains and resting stages of planktonic species. Conclusions/Significance: In view of our study, the deep-sea floor appears as a global DNA repository, which preserves genetic information about organisms living in the sediment, as well as in the water column above it. This information can be used for future monitoring of past and present environmental changes. © 2011 Pawlowski et al.

Pires A.,University of Aveiro | Gentil F.,Station Biologique de Roscoff | Quintino V.,University of Aveiro | Rodrigues A.M.,University of Aveiro
Marine Ecology | Year: 2012

Diopatra neapolitana Delle Chiaje, 1841 (Annelida, Onuphidae) is an important economic natural resource in Ria de Aveiro (northwestern coast of Portugal) and throughout Europe. The species is intensively harvested for use as fresh bait. However, there is only limited knowledge about its life cycle derived from a previous study in Mediterranean Sea. Reproduction and development patterns are known to vary biogeographically, making it important to base management decisions on locally appropriate information. This work examines reproduction patterns for populations from the Eastern Atlantic, which have not previously been assessed, with an eye towards drawing Atlantic-Mediterranean comparisons and informing local management strategies. The study was conducted from May 2007 to April 2009 in Ria de Aveiro. The reproductive biology of D. neapolitana was described from the proportional variation of worms with gametes in the coelom and from the progression of the oocyte diameter. Individuals with gametes inside the coelom were found all year round, but the peak reproductive period occurred between May and August, when almost all individuals had gametes in the coelom and females contained more oocytes than at any other time of the year. The overall male:female ratio was close to 1:1 and the oocyte diameter ranged from 40 to 240μm. In vitro fertilization was performed and the results compared to other studies. Based on the present results, some protection measures are suggested to implement a sustainable exploitation of the species. © 2011 Blackwell Verlag GmbH.

Massana R.,CSIC - Institute of Marine Sciences | Del Campo J.,CSIC - Institute of Marine Sciences | Del Campo J.,University of British Columbia | Sieracki M.E.,Bigelow Laboratory for Ocean Sciences | And 2 more authors.
ISME Journal | Year: 2014

Molecular surveys in planktonic marine systems have unveiled a large novel diversity of small protists. A large part of this diversity belongs to basal heterotrophic stramenopiles and is distributed in a set of polyphyletic ribogroups (described from rDNA sequences) collectively named as MAST (MArine STramenopiles). In the few groups investigated, MAST cells are globally distributed and abundant bacterial grazers, therefore having a putatively large impact on marine ecosystem functioning. The main aim of this study is to reevaluate the MAST ribogroups described so far and to determine whether additional groups can be found. For this purpose, we used traditional and state-of-the-art molecular tools, combining 18S rDNA sequences from publicly available clone libraries, single amplified genomes (SAGs) of planktonic protists, and a pyrosequencing survey from coastal waters and sediments. Our analysis indicated a final set of 18 MAST groups plus 5 new ribogroups within Ochrophyta (named as MOCH). The MAST ribogroups were then analyzed in more detail. Seven were typical of anoxic systems and one of oxic sediments. The rest were clearly members of oxic marine picoplankton. We characterized the genetic diversity within each MAST group and defined subclades for the more diverse (46 subclades in 8 groups). The analyses of sequences within subclades revealed further ecological specializations. Our data provide a renovated framework for phylogenetic classification of the numerous MAST ribogroups and support the notion of a tight link between phylogeny and ecological distribution. These diverse and largely uncultured protists are widespread and ecologically relevant members of marine microbial assemblages. © 2014 International Society for Microbial Ecology All rights reserved.

Oulion S.,University Paris Diderot | Debiais-Thibaud M.,University Paris Diderot | Da Silva C.,French National Center for Scientific Research | Bernard-Samain S.,French National Center for Scientific Research | And 4 more authors.
Molecular Biology and Evolution | Year: 2010

It is now well established that there were four Hox gene clusters in the genome of the last common ancestor of extant gnathostomes. To better understand the evolution of the organization and expression of these genomic regions, we have studied the Hox gene clusters of a shark (Scyliorhinus canicula). We sequenced 225,580 expressed sequence tags from several embryonic cDNA libraries. Blast searches identified corresponding transcripts to almost all the HoxA, HoxB, and HoxD cluster genes. No HoxC transcript was identified, suggesting that this cluster is absent or highly degenerate. Using Hox gene sequences as probes, we selected and sequenced seven clones from a bacterial artificial chromosome library covering the complete region of the three gene clusters. Mapping of cDNAs to these genomic sequences showed extensive alternative splicing and untranslated exon sharing between neighboring Hox genes. Homologous noncoding exons could not be identified in transcripts from other species using sequence similarity. However, by comparing conserved noncoding sequences upstream of these exons in different species, we were able to identify homology between some exons. Some alternative splicing variants are probably very ancient and were already coded for by the ancestral Hox gene cluster. We also identified several transcripts that do not code for Hox proteins, are probably not translated, and all but one are in the reverse orientation to the Hox genes. This survey of the transcriptome of the Hox gene clusters of a shark shows that the high complexity observed in mammals is a gnathostome ancestral feature. © 2010 The Author. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.

Taylor A.G.,University of California at San Diego | Landry M.R.,University of California at San Diego | Freibott A.,University of California at San Diego | Selph K.E.,University of Hawaii at Manoa | Gutierrez-Rodriguez A.,Station Biologique de Roscoff
Journal of Plankton Research | Year: 2015

We investigated biomass, size-structure, composition, depth distributions and spatial variability of the phytoplankton community in the Costa Rica Dome (CRD) in June-July 2010. Euphotic zone profiles were sampled daily during Lagrangian experiments in and out of the dome region, and the community was analyzed using a combination of digital epifluorescence microscopy, flow cytometry and HPLC pigments. The mean depth-integrated biomass of phytoplankton ranged 2-fold, from 1089 to 1858 mg C m-2 (mean ± SE = 1378 ± 112 mg C m-2), among 4 water parcels tracked for 4 days. Corresponding mean (±SE) integrated values for total chlorophyll a (Chl a) and the ratio of autotrophic carbon to Chl a were 24.1 ± 1.5 mg Chl a m-2 and 57.5 ± 3.4, respectively. Absolute and relative contributions of picophytoplankton (∼60%), Synechococcus (>33%) and Prochlorococcus (17%) to phytoplankton community biomass were highest in the central dome region, while >20 μm phytoplankton accounted for ≤10%, and diatoms <2%, of biomass in all areas. Nonetheless, autotrophic flagellates, dominated by dinoflagellates, exceeded biomass contributions of Synechococcus at all locations. Order-of-magnitude discrepancies in the relative contributions of diatoms (overestimated) and dinoflagellates (underestimated) based on diagnostic pigments relative to microscopy highlight potential significant biases associated with making community inferences from pigments. © 2015 The Author 2015. Published by Oxford University Press. All rights reserved.

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