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Hoffmann F.G.,Mississippi State University | Opazo J.C.,Austral University of Chile | Hoogewijs D.,University of Zürich | Hankeln T.,Johannes Gutenberg University Mainz | And 4 more authors.
Molecular Biology and Evolution | Year: 2012

In the Metazoa, globin proteins display an underlying unity in tertiary structure that belies an extraordinary diversity in primary structures, biochemical properties, and physiological functions. Phylogenetic reconstructions can reveal which of these functions represent novel, lineage-specific innovations, and which represent ancestral functions that are shared with homologous globin proteins in other eukaryotes and even prokaryotes. To date, our understanding of globin diversity in deuterostomes has been hindered by a dearth of genomic sequence data from the Ambulacraria (echinoderms + hemichordates), the sister group of chordates, and the phylum Xenacoelomorpha, which includes xenoturbellids, acoelomorphs, and nemertodermatids. Here, we report the results of a phylogenetic and comparative genomic analysis of the globin gene repertoire of deuterostomes. We first characterized the globin genes of the acorn worm, Saccoglossus kowalevskii, a representative of the phylum Hemichordata. We then integrated genomic sequence data from the acorn worm into a comprehensive analysis of conserved synteny and phylogenetic relationships among globin genes from representatives of the eight lineages that comprise the superphylum Deuterostomia. The primary aims were 1) to unravel the evolutionary history of the globin gene superfamily in deuterostomes and 2) to use the estimated phylogeny to gain insights into the functional evolution of deuterostome globins. Results of our analyses indicate that the deuterostome common ancestor possessed a repertoire of at least four distinct globin paralogs and that different subsets of these ancestral genes have been retained in each of the descendant organismal lineages. In each major deuterostome group, a different subset of ancestral precursor genes underwent lineage-specific expansions of functional diversity through repeated rounds of gene duplication and divergence. By integrating results of the phylogenetic analysis with available functional data, we discovered that circulating oxygen-transport hemoglobins evolved independently in several deuterostome lineages and that intracellular nerve globins evolved independently in chordates and acoelomorph worms. The Author 2012. All rights reserved. © The Author(s) 2012.


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.


Guegan C.,University of Southern Brittany | Garderes J.,University of Southern Brittany | Le Pennec G.,University of Southern Brittany | Gaillard F.,Station biologique de Roscoff | And 5 more authors.
Colloids and Surfaces B: Biointerfaces | Year: 2014

The aim of this paper is to study the impact of the substrate stiffness on the bacterial adhesion. For this purpose, agarose hydrogels are used as substrates with controlled mechanical properties. Indeed, the elastic modulus of these hydrogels, more precisely the shear storage moduli G', evolves with the agarose concentration (in this study from 0.75% to 3%). Other physico-chemical characteristics of the surface, known to be involved in bacterial adhesion, as hydrophobicity, were confirmed to remain constant. Two marine bacterial strains, a positive Gram Bacillus sp. 4J6 and a negative Gram Pseudoalteromonas sp. D41 were selected. Their retention on the substrates was analysed by confocal laser scanning microscopy and by counting of viable adhered bacteria. It was demonstrated that surface elastic modulus correlated with bacterial retention. Bacteria D41 adhered in higher numbers to rigid surfaces. For 4J6, bacterial adhesion patterns were changed: clusterings were observed on surfaces with lower elastic modulus. Furthermore, a proteomic study, based on the total soluble proteome of D41 strain, highlights an impact of elastic modulus on proteins synthesis. These data demonstrated an adapted response of adhering bacteria on hydrogels of varying mechanical properties. © 2013 Elsevier B.V.


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.


Teixeira S.,French Research Institute for Exploitation of the Sea | Teixeira S.,University of Algarve | Olu K.,French Research Institute for Exploitation of the Sea | Decker C.,French Research Institute for Exploitation of the Sea | And 5 more authors.
Molecular Ecology | Year: 2013

Chemosynthetic ecosystems are distributed worldwide in fragmented habitats harbouring seemingly highly specialized communities. Yet, shared taxa have been reported from highly distant chemosynthetic communities. These habitats are distributed in distinct biogeographical regions, one of these being the so-called Atlantic Equatorial Belt (AEB). Here, we combined genetic data (COI) from several taxa to assess the possible existence of cryptic or synonymous species and to detect the possible occurrence of contemporary gene flow among populations of chemosynthetic species located on both sides of the Atlantic. Several Evolutionary Significant Units (ESUs) of Alvinocarididae shrimp and Vesicomyidae bivalves were found to be shared across seeps of the AEB. Some were also common to hydrothermal vent communities of the Mid-Atlantic Ridge (MAR), encompassing taxa morphologically described as distinct species or even genera. The hypothesis of current or very recent large-scale gene flow among seeps and vents was supported by microsatellite analysis of the shrimp species Alvinocaris muricola/Alvinocaris markensis across the AEB and MAR. Two nonmutually exclusive hypotheses may explain these findings. The dispersion of larvae or adults following strong deep-sea currents, possibly combined with biochemical cues influencing the duration of larval development and timing of metamorphosis, may result in large-scale effective migration among distant spots scattered on the oceanic seafloor. Alternatively, these results may arise from the prevailing lack of knowledge on the ocean seabed, apart from emblematic ecosystems (chemosynthetic ecosystems, coral reefs or seamounts), where the widespread classification of endemism associated with many chemosynthetic taxa might hide wider distributions in overlooked parts of the deep sea. © 2013 John Wiley & Sons Ltd.


Eichinger I.,University of Vienna | Hourdez S.,Station Biologique de Roscoff | Bright M.,University of Vienna
Organisms Diversity and Evolution | Year: 2013

Sclerolinum is a small genus of Siboglinidae (Annelida) living in an obligate mutualistic association with thiotrophic bacteria as adults. Its taxonomic position, based on morphology, has been controversial; however, molecular data point to a sister taxa relationship with vestimentiferans. 16S rRNA gene sequencing and comparative morphology revealed that the studied population from deep-sea hydrocarbon seeps of the Gulf of Mexico belongs to Sclerolinum contortum known from the Arctic Sea. Since no anatomical and microanatomical studies have been published yet, we conducted such a study on S. contortum using serial sectioning and light and transmission electron microscopy. We show that the Sclerolinum body, divided into a head, trunk, and opisthosoma, is very similar to that of the vestimentiferans, and therefore we propose that the body regions are homologous in both taxa. © 2013 The Author(s).


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.


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.


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.


Herve C.,Station Biologique de Roscoff
Methods in molecular biology (Clifton, N.J.) | Year: 2011

Plant cell walls are diverse composites of complex polysaccharides. Molecular probes such as monoclonal antibodies (MABs) and carbohydrate-binding modules (CBMs) are important tools to detect and dissect cell wall structures in plant materials. We provide an account of methods that can be used to detect cell wall polysaccharide structures (epitopes) in plant materials and also describe treatments that can provide information on the masking of sets of polysaccharides that may prevent detection. These masking -phenomena may indicate potential interactions between sets of cell wall polysaccharides, and methods to uncover them are an important aspect of cell wall immunocytochemistry.

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