Molecular Phylogenetic Evaluation of Classification and Scenarios of Character Evolution in Calcareous Sponges (Porifera, Class Calcarea)

Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a thorough revision, which cannot be achieved by considering morphology alone or relying on a taxon sampling based on the current classification below the subclass level

Sponge Mass Mortalities in a Warming Mediterranean Sea: Are Cyanobacteria-Harboring Species Worse Off?

Mass mortality events are increasing dramatically in all coastal marine environments. Determining the underlying causes of mass mortality events has proven difficult in the past because of the lack of prior quantitative data on populations and environmental variables. Four-year surveys of two shallow-water sponge species, Ircinia fasciculata and Sarcotragus spinosulum, were carried out in the western Mediterranean Sea. These surveys provided evidence of two severe sponge die-offs (total mortality ranging from 80 to 95% of specimens) occurring in the summers of 2008 and 2009. These events primarily affected I. fasciculata, which hosts both phototrophic and heterotrophic microsymbionts, while they did not affect S. spinosulum, which harbors only heterotrophic bacteria. We observed a significant positive correlation between the percentage of injured I. fasciculata specimens and exposure time to elevated temperature conditions in all populations, suggesting a key role of temperature in triggering mortality events. A comparative ultrastructural study of injured and healthy I. fasciculata specimens showed that cyanobacteria disappeared from injured specimens, which suggests that cyanobacterial decay could be involved in I. fasciculata mortality. A laboratory experiment confirmed that the cyanobacteria harbored by I. fasciculata displayed a significant reduction in photosynthetic efficiency in the highest temperature treatment. The sponge disease reported here led to a severe decrease in the abundance of the surveyed populations. It represents one of the most dramatic mass mortality events to date in the Mediterranean Sea

Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida) is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (∼150 Mb). Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi) were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia) and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas) compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST) indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome

Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

Abstract The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits such as nervous systems arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system, which with RNAseq, DNA methylation and bacterial amplicon data spanning its development and range allows exploration of genomic changes both within sponges and in early animal evolution

Thermal and Sedimentation Stress Are Unlikely Causes of Brown Spot Syndrome in the Coral Reef Sponge, Ianthella basta

Background: Marine diseases are being increasingly linked to anthropogenic factors including global and local stressors. On the Great Barrier Reef, up to 66% of the Ianthella basta population was recently found to be afflicted by a syndrome characterized by brown spot lesions and necrotic tissue.\ud \ud Methodology/Principal Findings: Manipulative experiments were undertaken to ascertain the role of environmental stressors in this syndrome. Specifically, the effects of elevated temperature and sedimentation on sponge health and symbiont stability in I. basta were examined. Neither elevated temperature nor increased sedimentation were responsible for the brown spot lesions, but sponges exposed to 32°C developed substantial discoloration and deterioration of their tissues, resulting in death after eight days and a higher microbial diversity in those samples. No shifts in the microbial community of I. basta were observed across a latitudinal gradient or with increased sedimentation, with three previously described symbionts dominating the community of all sponges (Alphaproteobacteria, Gammaproteobacteria and Thaumarchaea).\ud \ud Conclusions/Significance: Results from this study highlight the stable microbial community of I. basta and indicate that thermal and sedimentation stress are not responsible for the brown spot lesions currently affecting this abundant and ecologically important sponge species

Molecular Phylogeny Restores the Supra-Generic Subdivision of Homoscleromorph Sponges (Porifera, Homoscleromorpha)

Homoscleromorpha is the fourth major sponge lineage, recently recognized to be distinct from the Demospongiae. It contains <100 described species of exclusively marine sponges that have been traditionally subdivided into 7 genera based on morphological characters. Because some of the morphological features of the homoscleromorphs are shared with eumetazoans and are absent in other sponges, the phylogenetic position of the group has been investigated in several recent studies. However, the phylogenetic relationships within the group remain unexplored by modern methods.Here we describe the first molecular phylogeny of Homoscleromorpha based on nuclear (18S and 28S rDNA) and complete mitochondrial DNA sequence data that focuses on inter-generic relationships. Our results revealed two robust clades within this group, one containing the spiculate species (genera Plakina, Plakortis, Plakinastrella and Corticium) and the other containing aspiculate species (genera Oscarella and Pseudocorticium), thus rejecting a close relationship between Pseudocorticium and Corticium. Among the spiculate species, we found affinities between the Plakortis and Plakinastrella genera, and between the Plakina and Corticium. The validity of these clades is furthermore supported by specific morphological characters, notably the type of spicules. Furthermore, the monophyly of the Corticium genus is supported while the monophyly of Plakina is not.As the result of our study we propose to restore the pre-1995 subdivision of Homoscleromorpha into two families: Plakinidae Schulze, 1880 for spiculate species and Oscarellidae Lendenfeld, 1887 for aspiculate species that had been rejected after the description of the genus Pseudocorticium. We also note that the two families of homoscleromorphs exhibit evolutionary stable, but have drastically distinct mitochondrial genome organizations that differ in gene content and gene order

Molecular Phylogeny of the Astrophorida (Porifera, Demospongiaep) Reveals an Unexpected High Level of Spicule Homoplasy

Background: The Astrophorida (Porifera, Demospongiae(rho)) is geographically and bathymetrically widely distributed. Systema Porifera currently includes five families in this order: Ancorinidae, Calthropellidae, Geodiidae, Pachastrellidae and Thrombidae. To date, molecular phylogenetic studies including Astrophorida species are scarce and offer limited sampling. Phylogenetic relationships within this order are therefore for the most part unknown and hypotheses based on morphology largely untested. Astrophorida taxa have very diverse spicule sets that make them a model of choice to investigate spicule evolution. Methodology/Principal Findings: With a sampling of 153 specimens (9 families, 29 genera, 89 species) covering the deep- and shallow-waters worldwide, this work presents the first comprehensive molecular phylogeny of the Astrophorida, using a cytochrome c oxidase subunit I (COI) gene partial sequence and the 59 end terminal part of the 28S rDNA gene (C1-D2 domains). The resulting tree suggested that i) the Astrophorida included some lithistid families and some Alectonidae species, ii) the sub-orders Euastrophorida and Streptosclerophorida were both polyphyletic, iii) the Geodiidae, the Ancorinidae and the Pachastrellidae were not monophyletic, iv) the Calthropellidae was part of the Geodiidae clade (Calthropella at least), and finally that v) many genera were polyphyletic (Ecionemia, Erylus, Poecillastra, Penares, Rhabdastrella, Stelletta and Vulcanella). Conclusion: The Astrophorida is a larger order than previously considered, comprising ca. 820 species. Based on these results, we propose new classifications for the Astrophorida using both the classical rank-based nomenclature (i.e., Linnaean classification) and the phylogenetic nomenclature following the PhyloCode, independent of taxonomic rank. A key to the Astrophorida families, sub-families and genera incertae sedis is also included. Incongruences between our molecular tree and the current classification can be explained by the banality of convergent evolution and secondary loss in spicule evolution. These processes have taken place many times, in all the major clades, for megascleres and microscleres

Récupération assistée du pétrole par le C02 : disponibilités et coûts en Europe de l'Ouest

Aux deux périodes de la mise en valeur d'un champ pétrolier par le gaz carbonique : - expérimentation pilote, - puis exploitation industrielle, correspondent des besoins sensiblement différents: de l'ordre de 30 à 100 t/j dans le premier cas, de 300 à 10 000 t/j dans le second, selon l'importance du gisement. Pour satisfaire ces demandes, on peut avoir recours : - soit aux sources actuellement exploitées (essentiellement les unités d'ammoniac), dont il convient alors de répertorier les quantités supplémentaires mobilisables ; - soit aux sources potentielles jusqu'à présent inemployées (fumées d'origines diverses), exigeant des procédés d'extraction complexes et gros consommateurs d'énergie qu'il s'avérerait donc nécessaire d'améliorer. Le prix de revient de la purification du CO2 est fonction de la complexité des traitements de récupération; il est compris entre 150 FF/t et plus de 600 FF/t pour les cas les plus défavorables. Le deuxième élément intervenant dans le coût du CO2 rendu sur site est le transport, variable selon la distance et le moyen d'acheminement choisi (pipeline, citernes routières ou ferroviaires) ; pour les faibles demandes, on utilise les citernes routières, pour les fortes le pipeline et les citernes ferroviaires pour les cas intermédiaires, dans la mesure où la ligne de chemin de fer passe près du gisement. D'autre part, le prix de la tonne de CO2 payée par l'utilisateur dépend de facteurs plus aléatoires tels que l'état du marché et la marge bénéficiaire du fournisseur résultant des négociations entre acheteur et vendeur

Récupération assistée du pétrole par le C02 : disponibilités et coûts en Europe de l'Ouest Enhanced Oil Recovery by C02: Availability and Cost in Western Europe

Aux deux périodes de la mise en valeur d'un champ pétrolier par le gaz carbonique : - expérimentation pilote, - puis exploitation industrielle, correspondent des besoins sensiblement différents: de l'ordre de 30 à 100 t/j dans le premier cas, de 300 à 10 000 t/j dans le second, selon l'importance du gisement. Pour satisfaire ces demandes, on peut avoir recours : - soit aux sources actuellement exploitées (essentiellement les unités d'ammoniac), dont il convient alors de répertorier les quantités supplémentaires mobilisables ; - soit aux sources potentielles jusqu'à présent inemployées (fumées d'origines diverses), exigeant des procédés d'extraction complexes et gros consommateurs d'énergie qu'il s'avérerait donc nécessaire d'améliorer. Le prix de revient de la purification du CO2 est fonction de la complexité des traitements de récupération; il est compris entre 150 FF/t et plus de 600 FF/t pour les cas les plus défavorables. Le deuxième élément intervenant dans le coût du CO2 rendu sur site est le transport, variable selon la distance et le moyen d'acheminement choisi (pipeline, citernes routières ou ferroviaires) ; pour les faibles demandes, on utilise les citernes routières, pour les fortes le pipeline et les citernes ferroviaires pour les cas intermédiaires, dans la mesure où la ligne de chemin de fer passe près du gisement. D'autre part, le prix de la tonne de CO2 payée par l'utilisateur dépend de facteurs plus aléatoires tels que l'état du marché et la marge bénéficiaire du fournisseur résultant des négociations entre acheteur et vendeur. The two periods of production from an oil field by carbon-dioxide injection are: (i) pilot expérimentation and (ii) industrial opération. There are quite différent CO2 requirements for these two periods, i. e. about 30 to 100 t/d for the first case, and 300 to 10000 t/d in the second case, depending on the size of the field. These demands can be fulfilled: (i) either from sources presently exploited (mainly ammonia plants) for which the additional amounts that can be mobilized must be determined, (ü) or potential sources not yet exploited (stock Bases from différent origins) which require complex extraction process demanding high energy consumption installations that will thus have to be improved. The cost of purifying CO2 depends on the complexity of recovery treatments. It is between $25/t and more than$ 1001t for the most unfavorable cases. The second element involved in the cost of C02 delivered to the site is its transportation which varies according to the distance and the method chosen (a) For small demand, road (b) For medium demand, rail (provided that it runs by near the production site) (c) For high demand, pipeline. Furthermore, the price per ton of C02 paid by the user depends on more random factors such as the state of the market and the profit margin of the supplier, resulting from negotiations between buyer and seller

Récupération assistée des hydrocarbures par injection de CO2. Aspects techniques et économiques Enhanced Hydrocarbon Recovery by CO2 Flooding. Technical and Economic Aspects

L'injection de gaz carbonique dans les gisements pétroliers a donné lieu depuis une quinzaine d'années à de très nombreuses études de laboratoire et sur modèles. De multiples pilotes ont été réalisés et quelques projets industriels sont en cours. II est donc intéressant de faire un bilan des connaissances et de l'expérience ainsi acquise, afin de tenter de dégager les perspectives de développement du procédé. La première partie rappelle le comportement du CO2 en présence d'hydrocarbures et les principaux mécanismes d'action dans le processus de récupération. On examine ensuite dans une deuxième partie les principales applications pilotes ou industrielles et les problèmes opérationnels rencontrés. Ce bilan permet de dégager les caractéristiques principales du procédé, les difficultés essentielles rencontrées. Un aperçu est donné sur les recherches en cours en vue de résoudre ces difficultés et améliorer le procédé. La dernière partie s'attache à préciser les perspectives d'application de l'injection de CO2 et pour cela trois aspects essentiels pour le développement du procédé sont discutés : les performances et le domaine d'emploi, la disponibilité et le coût des différentes sources potentielles de CO2 et enfin l'évaluation économique du procédé. The injection of carbon dioxide into oil fields has been the subject of extensive laboratory and modeling research for the last 15 years. Many pilot experiments have been performed, and several industrial projects are under way. Therefore it is interesting to review the state-of-the-art of the know-how and experience thus acquired so as to try to determine the outlook for the development of the process. The first part of this article reviews the behavior of CO2 in the presence of hydrocarbons and the leading action mechanisms in the recovery process. The second part examines the leading pilot or industrial applications and the operational problems encountered. This review brings out the principal characteristics of the process and the main difficulties encountered. A brief survey is made of ongoing research projects aimed at resolving these difficulties and at improving the process. The last part concentrates on the outlook for the application of CO2 flooding, and for this process are discussed, i. e. the performances and the field of application, the avaibility and cost of different potential CO2 sources, and an economic evaluation of the process