Éditeur(s) : HAL CCSD Wiley-VCH Verlag
Résumé : International audience
Bacterial biofilm development is conditioned by complex processes involving bacterial attachment to surfaces, growth, mobility, and exoproduct production. The marine bacterium Pseudoalteromonas sp. strain D41 is able to attach strongly onto a wide variety of substrates, which promotes subsequent biofilm development. Study of the outer-membrane and total soluble proteomes showed ten spots with significant intensity variations when this bacterium was grown in biofilm compared to planktonic cultures. MS/MS de novo sequencing analysis allowed the identification of four outer-membrane proteins of particular interest since they were strongly induced in biofilms. These proteins are homologous to a TonB-dependent receptor (TBDR), to the OmpW and OmpA porins, and to a type IV pilus biogenesis protein (PilF). Gene expression assays by quantitative RT-PCR showed that the four corresponding genes were upregulated during biofilm development on hydrophobic and hydrophilic surfaces. The Pseudomonas aeruginosa mutants unable to produce any of the OmpW, OmpA, and PilF homologues yielded biofilms with lower biovolumes and altered architectures, confirming the involvement of these proteins in the biofilm formation process. Our results indicate that Pseudoalteromonas sp. D41 shares biofilm formation mechanisms with human pathogenic bacteria, but also relies on TBDR, which might be more specific to the marine environment.
ISSN: 1615-9853

hal-00864093
https://hal.archives-ouvertes.fr/hal-00864093
DOI : 10.1002/pmic.201100644

Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : Deep-sea bivalves found at hydrothermal vents, cold seeps and organic falls are sustained by chemosynthetic bacteria which ensure part or all of their carbon nutrition. These symbioses are of prime importance for the functioning of the ecosystems. Similar symbioses occur in other bivalve species living in shallow and coastal reduced habitats worldwide. In recent years, several deep-sea species have been investigated from continental margins around Europe, West Africa, East America, the Gulf of Mexico, and from hydrothermal vents on the Mid-Atlantic Ridge. In parallel, numerous more easily accessible shallow marine species were studied. We here provide a summary of the current knowledge available on chemosymbiotic bivalves in the area ranging west-to-east from the Gulf of Mexico to Marmara Sea, and north-to-south from the Arctic to the Gulf of Guinea. Characteristics of symbioses in 51 species from the area are summarized for each of the five bivalve families documented to harbor chemosynthetic symbionts (Mytilidae, Vesicomyidae, Solemyidae, Thyasiridae and Lucinidae), and compared among families with special emphasis on ecology, life cycle, and connectivity. Chemosynthetic symbioses are a major adaptation to ecosystems and habitats exposed to reducing conditions, yet relatively little is known regarding their diversity and functioning apart from a few "model species" on which effort has focused over the last 30 yr. In the context of increasing concern about biodiversity and ecosystems, and increasing anthropogenic pressure on Oceans, we advocate for a better assessment of bivalve symbioses diversity in order to evaluate the capacities of these remarkable ecological and evolutionary units to withstand environmental change
Biogeosciences (1726-4170) (Copernicus Gesellschaft Mbh), 2013 , Vol. 10 , N. 5 , P. 3241-3267

Droits : Author(s) 2012. CC Attribution 3.0 License.
http://archimer.ifremer.fr/doc/00133/24417/22431.pdf
DOI:10.5194/bg-10-3241-2013
http://archimer.ifremer.fr/doc/00133/24417/

Résumé : Les biofilms électroactifs (EA) sont des consortia bactériens mono ou pluri-espèces, qui ont la faculté d’échanger des électrons provenant de leur métabolisme avec les surfaces solides conductrices des électrodes. Cette découverte est à l’origine d’un nouveau dispositif énergétique : la pile à combustible microbienne (PACM). Depuis les années 2000, la littérature scientifique sur les biofilms EA et sur les PACM explose, notamment grâce à la découverte de bactéries capables de transférer par voie directe – par des pili ou protéines transmembranaires – des électrons vers les électrodes. Plusieurs sources de bactéries EA ont été à ce jour découvertes, allant de cultures pures à des communautés bactériennes plus complexes. Ces dernières sont issues de milieux aqueux naturels (milieux marins ou d’eau douce), industriels ou urbains (effluents d’industrie, eaux usées domestiques). La plupart de ces sources bactériennes proviennent d’environnements de climat tempéré. Dans ce travail de thèse, plusieurs sols de milieux humides de la Guyane ont été identifiés comme étant de sources de bactéries EA. Les expériences menées sous potentiel d’électrode imposé et constant ont permis d’étudier l’adhésion à la surface d’électrode des biofilms EA issus de la flore endogène des milieux sélectionnés. La formation de bioanodes et de biocathodes a été possible en présence respectivement d’acétate et d’oxygène dans les milieux. Une étude par voltammétrie cyclique a mis en évidence les pics d’oxydo-réduction en lien avec les échanges électroniques du biofilm EA et de l’électrode. En optimisant la procédure de formation des biofilms EA par chronoampérométrie (surface d’électrode plus importante, apport en continu et progressif du substrat), une densité de courant maximale de 12 A/m2 et un rendement faradique de 24 % ont été obtenus. Une autre méthode pour former des biofilms EA à partir d’un milieu choisi, la mangrove, a consisté à utiliser deux prototypes de PACM : une pile à compartiment unique et à cathode à air, et une pile benthique. Dans les deux cas, les biofilms EA ont pu être formés et étudiés, complétant certaines observations faites sous potentiel imposé. La PACM benthique s’est avérée être la plus proche d’une application à grande échelle puisqu’elle a été complètement autonome : anode et cathode utilisant uniquement le milieu pour fonctionner. Elle a pu être étudiée en laboratoire comme sur le terrain.
Electroactive biofilms (EA) are mono or multi-species bacterial consortia, which have the ability to exchange electrons from their metabolism with solid surfaces of conductive electrodes. This discovery is the basis for a device of energy production: microbial fuel cell (MFC). Since the 2000s, the scientific literature on EA biofilms and MFC explodes, thanks to the discovery of bacteria that are able to transfer directly – by pili or trans-membrane proteins – electrons to electrodes. Several sources of EA bacteria were discovered to date, ranging from pure cultures to more complex bacterial communities. Those last are from natural (marine and freshwater), industrial or urban (industrial effluents, domestic wastewater) aqueous environments. However, the vast majority of these are from temperate environments.In this thesis, several wetland soils of French Guiana have been identified as sources of EA bacteria. Experiments under poised and constant electrode potential were used to examine adherence to the electrode surface of EA biofilms from the endogenous flora of selected environments. Formation of bioanodes and biocathodes was possible in the presence respectively of acetate and oxygen in the media. A study by cyclic voltammetry showed the redox peaks related to electronic exchanges between EA biofilm and electrode. By optimizing the process of EA biofilm formation by chronoamperometry (larger electrode surface, providing continuous and progressive substrate), a maximum current density of 12 A/m2 and a coulombic efficiency of 24% were obtained.Another method to form EA biofilms from a chosen medium (mangrove) was to use two MFC prototypes: a single compartment and air cathode one, and a benthic one. In both cases, the EA biofilms have been trained and studied supplementing certain observations made under poised polarization. MFC benthic proved to be the closest to a wide application since it was completely autonomous, anode and cathode only using the medium to function. It has been studied in the laboratory and in the field.

http://www.theses.fr/2012AGUY0560/document

Éditeur(s) : HAL CCSD Station Biologique
Résumé : International audience
Four "morphotypes" of Mytilidae were collected from wood falls in the west Pacific (Vanuatu islands) and in the Bohol sea (Philippines) between 300 and 1800 metre depth. Results from our study demonstrated the existence of extracellular bacteria located between microvilli at the apical surface of the cells all along the lateral zone of the gill filaments in the four mytilid morphotypes analyzed. Based on TEM observations, these Gram-negative bacteria were not methanotrophic due to the lack of concentric stacking of intracellular membranes in their cytoplasm. Based on FISH experiments, these bacteria belong to g-Proteobacteria. These preliminary observations described gill symbiosis-like interactions in metazoan species associated with sunken wood, strengthening the hypothesis that decomposing wood may serve as steps for the introduction of symbiotic Mytilidae to vents and seeps. Phylogenetic analysis of these extracellular bacteria are in progress in our lab in order to compare their 16SrDNA sequences to that of other marine invertebrate symbionts described to date.
ISSN: 0007-9723

hal-00753023
https://hal.univ-antilles.fr/hal-00753023

Résumé : Les mattes de procaryotes constituent une niche écologique diversifiée. peu étudié!<..en mangrove et jamais décrjte dans les Antilles. L'objectif de cette thèse est de décrire les procaryotes filamenteux reposant sur le sédiment marin et de caractériser les interactions entre la matte, milieu et entre les différents micro-organismes. Nous avons d'abord caractérisé les micro-organismes majoritaires de la matte par le séquençage de l'ADNr 16S et des hybridations moléculaires (FISH). Il a ainsi été possible de décrire deux nouvelles espèces de Beggiatoaceae dont la structure a été étudiée par microscopie électronique. De plus, afin de caractériser l'environnement chimique de ces bactéries, des capteurs potentiométriques ont été utilisés. Ils ont permis de démontrer que les Beggiaotaceae oxydaient les sulfures en prélevant l'oxygène du milieu, tandis que des analyses de microscopie couplées à de l'EDX ont mis en évidence des réserves de soufre intracellulaires dans ces bactéries. Le séquençage de l'ADNr 16S des cyanobactéries filamenteuses a mis en évidence quatre nouvelles espèces de l'ord~e des Oscillatoriales. Deux d'entre elles, du genre Planktothricoides ont révélé une toxicité positive sur les Artemia sp:, les deux autres ont été identifiées comme proches d'Oscillatoria spongeliae, une espèce symbiotique d'éponge, bien que les coupes uItrafines d'une de ces souches aient montré une morphologie interne proche des Tychonema. L'analyse des données a permis d'étoffer les connaissances sur les communautés microbiennes de mangrove et constitue une base intéressante de travail sur la contribution des micro-organismes au fonctionnement de l'écosystème mangrove dans son ensemble
Procaryotic mats are ecological niches, occuring in many ecosystems. Those structures are little studied in marine mangrove sediment and have never been described in West Indies. The purpose ofthis thesis is to characterize the interactions between the mat and the environment, and between the different filamentous micro-organisms living into the mat. In a first place, we characterized the mainly micro-organisrns of the mat by sequencing 16S rDNA. We confirmed these sequences by molecular hybridization (FISH) with specific probes designed from sequences obtained. Thus, it was possible to describe two new Beggiatoaceae strains, whose structure has been studied by electronic microscopy. Furthemore, we used potentiometric captors in situ and in laboratory, by creating a mesocosm, in order to define the chemical environment where involved these bacteria. These experiences proved that the Beggiatoaceae of the mat oxidized the sulfur taking the oxygen from the medium, while the microscopic analysis coupled with EDX showed intracellular sulfur granules into the bacteria. The study of the filamentous cyanobacteria of the mat highlighted four new cyanobacteria strains, all studied by electronic rmcroscopy. Two of them belongs to Planktothrlcoides genus and showed positive toxicity on Artemia salina. The others species are close to Oscillatorla spongeliae, a sponge symbiont, nevertheless, one ofthem showed an intemal morphology close to Tychonema. The analysis of the different results adduces sorne knowledge about mangrove microbial communities. Furthermore, this study can be used as an interesting base to study the micro-organisms contribution in functioning mangrove ecosystem

http://www.theses.fr/2013AGUY0614/document

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Archaea may be involved in global energy cycles, and are known for their ability to interact with eukaryotic species (sponges, corals and ascidians) or as archaeal-bacterial consortia. The recently proposed phylum Thaumarchaeota may represent the deepest branching lineage in the archaeal phylogeny emerging before the divergence between Euryarchaeota and Crenarchaeota. Here we report the first characterization of two marine thaumarchaeal species from shallow waters that consist of multiple giant cells. One species is coated with sulfur-oxidizing g-Proteobacteria. These new uncultured thaumarchaeal species are able to live in the sulfide-rich environments of a tropical mangrove swamp, either on living tissues such as roots or on various kinds of materials such as stones, sunken woods, etc. These archaea and archaea/bacteria associations have been studied using light microscopy, transmission electron microscopy and scanning electron microscopy. Species identification of archaeons and the putative bacterial symbiont have been assessed by 16S small subunit ribosomal RNA analysis. The sulfur-oxidizing ability of the bacteria has been assessed by genetic investigation on alpha-subunit of the adenosine-5_- phosphosulfate reductase/oxidase's (AprA). Species identifications have been confirmed by fluorescence in situ hybridization using specific probes designed in this study. In this article, we describe two new giant archaeal species that form the biggest archaeal filaments ever observed. One of these species is covered by a specific biofilm of sulfur-oxidizing g-Proteobacteria. This study highlights an unexpected morphological and genetic diversity of the phylum Thaumarchaeota.
ISSN: 1462-2912

hal-00715219
https://hal.univ-antilles.fr/hal-00715219
DOI : 10.1111/j.1462-2920.2010.02309.x

Éditeur(s) : Society for General Microbiology
Résumé : A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13a(T)) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0.1-50 MPa. Predominant cellular fatty acids were 16:1 omega7c, 15: 0 iso, 16: 0 and 13: 0 iso. The G + C content of the DNA was 44.9 mol%. On the basis of 16S rRNA gene sequences, strain LT13a(T) was shown to belong to the gamma-Proteobacteria, being closely related to Shewanella putrefaciens (98%), Shewanella oneidensis (97%) and Shewanella baltica (96 %). Levels of DNA homology between strain LT13a(T) and S. putrefaciens, S. oneidensis and S. baltica were < 20 %, indicating that strain LT13a(T) represents a novel species. Genetic evidence and phenotypic characteristics showed that isolate LT13a(T) constitutes a novel species of the genus Shewanella, Because of the deep origin of the strain, the name Shewanella profunda sp. nov. is proposed, with LT13a(T) (= DSM 15900(T)-JCM 12080(T)) as the type strain.
International journal of systematic and evolutionary microbiology (1466-5026) (Society for General Microbiology), 2004-11 , Vol. 54 , N. 6 , P. 1943-1949

Droits : 2004 International Union of Microbiological Societies
http://archimer.ifremer.fr/doc/2004/publication-590.pdf
DOI:10.1099/ijs.0.03007-0
http://archimer.ifremer.fr/doc/00000/590/

Éditeur(s) : Elsevier Science Bv
Résumé : In tropical shrimp ponds, the increasing of feed input, concomitantly with the stocking shrimp biomass, induces an eutrophication of the ecosystem. Although difficult to maintain, its stability is required to guarantee the success of the culture. A 110-day period of phytoplankton and bacterioplankton stock and dynamics in an earthen pond (1.2 ha area, 1 m depth) was monitored using flow cytometry to provide baseline information on community characteristics and ecosystem instability. Seven autotrophic cell types were identified over the whole sampling period. Prokaryotic cells included Synechococcus sp., a group named UNK which presented an atypical new flow cytometric signature and picoeukaryotes (PEUK). Nanophytoplankton cells were represented by 4 groups: NAN1, NAN2, NAN3 and Cryptophytes. During the first part of the survey, picophytoplankton dominated the phytoplanktonic assemblage. The mean abundance of total cells (up to 8 x 10(6) cells mL(-1)) was among the highest recorded in marine and brackish waters. Bacterial abundance and production ranged from 0.8 to 5.1 x 10(7) cells mL(-1) and from 30 to 110 mu g C L-1 h(-1). A shift from pico to nanophytoplankton abundance was observed for a few days from d 96. During this period, heterotrophic bacteria production and abundance suddenly dropped, implying a change in the functioning of the microbial loop. This shift was concomitant with a significant shrimp mortality outbreak due to Vibrio penaeicida, the etiological agent of a disease known as Syndrome 93, which affects the shrimp industry in New Caledonia. This survey suggests that flow cytometric analysis could be used for the monitoring of aquaculture systems to improve our understanding of the complex phytoplankton and bacterial dynamics of these systems and its potential influence on disease development. (c) 2010 Elsevier B.V. All rights reserved.
Aquaculture (0044-8486) (Elsevier Science Bv), 2010-12 , Vol. 310 , N. 1-2 , P. 112-121

Droits : 2010 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00029/14068/11312.pdf
DOI:10.1016/j.aquaculture.2010.10.022
http://archimer.ifremer.fr/doc/00029/14068/

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
In marine invertebrates that acquire their symbionts from the environment, these are generally only taken up during early developmental stages. In the symbiosis between lucinid clams and their intracellular sulfur-oxidizing bacteria, it has been shown that the juveniles acquire their symbionts from an environmental stock of free-living symbiont forms, but it is not known if adult clams are still competent to take up symbiotic bacteria from the environment. In this study, we investigated symbiont acquisition in adult specimens of the lucinid clam Codakia orbiculata, using transmission electron microscopy, fluorescence in situ hybridization, immunohistochemistry and PCR. We show here that adults that had no detectable symbionts after starvation in aquaria for 6 months, rapidly reacquired symbionts within days after being returned to their natural environments in the field. Control specimens that were starved and then exposed to seawater aquaria with sulfide did not reacquire symbionts. This indicates that the reacquisition of symbionts in the starved clams returned to the field was not caused by high division rates of a small pool of remaining symbionts that we were not able to detect with the methods used here. Immunohistochemistry with an antibody against actin, a protein involved in the phagocytosis of intracellular bacteria, showed that actin was expressed at the apical ends of the gill cells that took up symbionts, providing further evidence that the symbionts were acquired from the environment. Interestingly, actin expression was also observed in symbiontcontaining cells of untreated lucinids freshly collected from the environment, indicating that symbiont acquisition from the environment occurs continuously in these clams throughout their lifetime.
ISSN: 1462-2912

hal-00743019
https://hal.univ-antilles.fr/hal-00743019
DOI : 10.1111/j.1462-2920.2012.02748.x

Éditeur(s) : Elsevier
Résumé : Vibrio tapetis is the marine bacterium responsible for the brown ring disease (BRD) affecting die manila clam, Ruditapes philippinarum. Identification of V tapelis has been previously performed using biochemical criteria and serological procedures. All of these methods are time consuming and ill-adapted to individual screening. This study describes an oligonucleotidic probe (Vt446) and two PCR primers, deduced from the 16S rDNA sequence, allowing a fast and specific V tapetis identification using dot blot hybridisation and species-specific primed PCR (SSP-PCR). The probe and primers have been tested on 60 strains, including referenced Vibrio sp., Gram negative and positive bacteria, marine bacteria samples and isolated clam bacteria. For all the 19 V tapetis strains, the results of PCR assays consistently corroborated those of the agglutination tests. The detection limit was estimated to be 10(2) CFU ml(-1). The SSP-PCR method has resulted in V tapetis detection in larvae, m diseased clams, and in asymptomatic broodstock clams that later developed BRD. In conclusion, the two SSP-PCR primers were useful for direct and fast identification of V tapetis strains isolated in clams, and are well suited for the screening of individual R. philippilnarum broodstock clams and larvae from the hatchery. (C) 2005 Elsevier B.V. All rights reserved.
Aquaculture (0044-8486) (Elsevier), 2006-03 , Vol. 253 , N. 1-4 , P. 25-38

Droits : 2005 Elsevier B.V. All rights reserved
http://archimer.ifremer.fr/doc/2006/publication-1692.pdf
DOI:10.1016/j.aquaculture.2005.03.047
http://archimer.ifremer.fr/doc/00000/1692/

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Associations between marine invertebrates and chemoautotrophic bacteria constitute a wide field for the study of symbiotic associations. In these interactions, symbiont transmission must represent the cornerstone allowing the persistence of the association throughout generations. Within Bivalvia, in families such as Solemyidae or Vesicomyidae, symbiont transmission is undoubtedly vertical. However, in Lucinidae, symbiont transmission is described in the literature as 'environmental', symbionts being acquired from the environment by the new host generations. Hence, if there is transmission, symbionts should be transmitted from adults to juveniles via the environment. Consequently, we should observe a release of the symbiont by adults. We attempted to detect such a release within two Lucinidae species of the genus Codakia. We sampled 10 Codakia orbicularis and 20 Codakia orbiculata distributed in 10 crystallizing dishes containing filtered seawater. During 1 month of investigation, we analyzed water of the dishes in order to detect any release of a symbiont using catalyzed report deposition-FISH techniques. For 140 observations realized during this period, we did not observe any release of symbionts. This suggests that the idea of host-to-host passage in Lucinidae is inaccurate. We could therefore consider that the transmission mode from generation to generation does not occur within Lucinidae, symbiosis appearing to be advantageous in this case only for the host, and constitutes an evolutionary dead-end for the bacteria.
ISSN: 0168-6496

hal-00751560
https://hal.univ-antilles.fr/hal-00751560
DOI : 10.1111/j.1574-6941.2008.00626.x

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The biogeochemistry of sulfur and carbon during early-diagenetic processes within organic-rich marine mangrove sediments was studied in the “Manche à Eau” lagoon, Guadeloupe, West Indies. These sediments are characterized by a total organic carbon content (TOC) mostly above 11 wt%, δ13CTOC below − 25‰ VPDB and C/Nmolar ratios exceeding 15. Rates of mangrove-derived organic carbon accumulation vary between ~ 200 and 400 gOC·m− 2·yr− 1, with highest rates at the shore of the lagoon. On the lagoon border, where colorless filamentous sulfur-oxidizing bacteria colonize the sediments, active sulfate reduction within the upper 20 cm, with a net removal rate of ~ 0.5 μmol·cm− 3·d− 1, is assumed to be essentially driven by organic carbon oxidation. This is expressed by relatively low apparent sulfur isotope fractionation (34εnet = − 33‰) and a gentle δ18O/δ34Ssulfate apparent slope of 0.36 ± 0.03 (2s). Further inside the lagoon, in the absence of sulfur-oxidizing bacteria, higher apparent sulfur isotope fractionation and a steeper δ18O/δ34Ssulfate slope (0.67 ± 0.20) suggest an overall lower sulfate removal rate that may be coupled to minor sulfur disproportionation. Spatial and vertical variation in sulfur cycling, reflected by oxygen and sulfur isotopic characteristics, seem to be mainly controlled by unsteady to relatively steady organic matter deposition and its reactivity. In all sediments, δ34S values of pyrite are positively correlated with the TOC/TS ratio and negatively correlated with δ13CTOC; suggesting a primary control of the quantity and quality of organic matter on the pyrite isotope records, despite potential iron-limiting conditions for the most active sites. Our results provide insights into the role of organic carbon input on sulfur cycling; stimulating sulfate reduction and in turn the presence of sulfur-oxidizing microbial mats, resulting in an intense cycling of both carbon and sulfur in these marine mangrove sediments.
ISSN: 0009-2541

hal-01507696
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01507696
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01507696/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01507696/file/Cr%C3%A9mi%C3%A8re%20et%20al.%20-%20Sulfur%20diagenesis%20under%20rapid%20accumulation%20of%20orga.pdf
DOI : 10.1016/j.chemgeo.2017.02.017

Éditeur(s) : HAL CCSD SAGE Publications
Résumé : International audience
A multiproxy analysis of lacustrine sediments cored in Grand-Case Pond at Saint-Martin, north of the Lesser Antilles archipelago, reveals three distinct climatic periods for the last 3700 years. From 3700 to ~2500 yr cal. BP and from 1150 yr cal. BP to the present, carbonate mud deposition occurred in connection with pond lowstands. These periods were also punctuated by severe drought events, marked by gypsum laminae, and hurricane landfalls, leading to marine sand inputs into the pond. The intermediate time interval, from 2500 to 1150 yr cal. BP, is typified by black organic mud deposition, suggesting that hypoxic to anoxic conditions prevailed at the pond bottom. These were probably linked with a perennial pond highstand and reflect more uniform and wetter climatic conditions than today. The carbon isotopic composition of the ostracod Perissocytheridea bisulcata shows that the lowest δ13C values are recorded during the hypoxic periods, as a consequence of bacterial recycling of isotopically depleted organic matter. Such a climatic history agrees closely with that documented from other records in the Caribbean area, such as the Cariaco Basin, central coast of Belize or Barbados. By constrast, discrepancies seem to emerge from the comparison between hurricane activity recorded at Saint-Martin on the one hand and Vieques (Puerto Rico) on the other hand. We explain this apparent contradiction by a balance between two distinct storm paths in response to latitudinal shifts of the Intertropical Convergence Zone (ITCZ). Stronger storm activity over the Gulf coast and the inner Caribbean Sea is favoured by a southern position of the ITCZ in connection with dry climatic conditions. Plausible links with the North Atlantic Oscillation (NAO) are also suggested.
ISSN: 0959-6836

halshs-00758748
https://halshs.archives-ouvertes.fr/halshs-00758748
https://halshs.archives-ouvertes.fr/halshs-00758748/document
https://halshs.archives-ouvertes.fr/halshs-00758748/file/Malaize_et_al._2011_cor.pdf
DOI : 10.1177/0959683611400198

Éditeur(s) : Actes de colloques. Ifremer Brest [ACTES COLLOQ. IFREMER.]. 1986
Résumé : A bacteriological monitoring program has been established in order to evaluate the impact of oil activities. The ratio of heterotrophic-hydrocarbonoclastic bacteria was used to follow the evolution in time of both populations. Numerical taxonomic methods were employed in order to define ecotypes of marine oil degraders.
L'impact des activités pétrolières a été mesuré grâce à une étude systématique de la structure des populations hétérotrophes dégradant le pétrole. L'indice bactéries dégradant le pétrole - bactéries hétérotrophes (saprophytes) a été employé pour suivre quantitativement l'évolution dans le temps de ces populations. Des méthodes de taxonomie numérique ont été appliquées afin de constituer des écotypes bactériens des souches capables de dégrader le pétrole en mer.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/1984/acte-1019.pdf
http://archimer.ifremer.fr/doc/00000/1019/

Éditeur(s) : ISTPM
Résumé : Table of Contents The Natural Environment Production centres Oyster farming centres Mussel farming centres Chapter I. - The Physicochemical Environment I. Sea Water a) Transparency, turbidity b) Temperature c) Salinity d) Dissolved gases e) Substances dissolved in the water f) Water movements g) Hydrology of the main shellfish farming centres II. Soils a) Soil properties b) Mechanical amendment of soils, its effects c) Fertilisation of soils in shellfish farming d) Changes in soils due to farming Bibliography Chapter II. - The Natural Environment Phytoplankton Zooplankton Basic biology of phytoplankton Assessment of phytoplankton production, notion of primary productivity Phytoplankton from a few shellfish farming regions Microphytobenthos Factors controlling primary productivity Toxicity of planktonic organisms; red tides Bibliography Chapter III – Alterations in the Natural Environment Pollution I. Chemical Pollution Definitions Influence of turbidity A. Telluric pollution 1o Domestic pollution 2o Agriculture-related pollution 3o Industrial pollution B. Pelagic pollution 1o Pollution through hydrocarbons Conclusion II. Bacterial Pollution Future of micro-organisms in the sea A. Specimen conditions B. Phenomena of dispersion Survival of germs in the marine environment A. Factors influencing the total microbial content B. Resistance of various groups of germs Consequences of bacterial pollutions on shellfish and shellfish farming Shellfish Shellfish farming Conclusion Bibliography
Sommaire : Le milieu naturel Les centres de production Les centres ostréicoles Les centres mytilicoles Chapitre I. - le milieu physico-chimique I. L'eau de mer a) Transparence, turbidité b) Température c) Salinité d ) Les gaz dissous e) Les substances dissoutes dans l'eau f) Les mouvements de l'eau g) Hydrologie des principaux centres conchylicoles IL Les sols a ) Propriétés des sols b) Amendement mécanique des sols, ses effets c) La fertilisation des sols en conchylicutture d) Evolution des sols du fait de la culture Bibliographie Chapitre II. - le milieu biologique Le phytoplancton Le zooplancton Biologie sommaire du phytoplancton Evaluation de la production de phytoplancton, notion de productivité primaire Phytoplancton de quelques régions conchylicoles Le microphytobenthos Facteurs contrôlant la productivité primaire Toxicité d'organismes planctoniques ; les eaux rouges bibliographie Chapitre III - les altérations du milieu naturel. Les pollutions I. Les pollutions chimiques Définitions Influence de la turbidité A. Pollution tellurique 1° Pollution d'origine domestique 2° Pollutions liées aux activités agricoles 3° Pollutions industrielles B. Pollution pélagique 1° Pollution par les hydrocarbures Conclusion II. Les pollutions bactériennes Devenir des microorganismes dans la mer A. Conditions de prélèvements B. Phénomènes de dispersion Survie des germes dans le milieu marin A. Facteurs influant sur la teneur microbienne globale B. Résistance des divers groupes de germes Conséquences des pollutions bactériennes sur les coquillages et sur la conchyliculture Les coquillages La conchyliculture Conclusion Bibliographie
Revue des Travaux de l'Institut des Pêches Maritimes (0035-2276) (ISTPM), 1974-09 , Vol. 38 , N. 3 , P. 217-337

Droits : Ifremer
http://archimer.ifremer.fr/doc/1974/publication-1776.pdf
http://archimer.ifremer.fr/doc/00000/1776/

Résumé : After a period of rapid development of the sites (an increase in both reared surface area and production), tropical shrimp aquaculture is currently being faced with critical problems due to economical and ecological constraints. In many countries with favourable conditions for shrimp aquaculture such as indonesia or Vietnam, sites are often badly selected and/or over-exploited. This conducts to sorne extent to decreases or collapses in the production due to the difficulty in predicting the maximum production capacity of the sites. Furthermore, it appears that production sustainability depends on many factors among which socio-economy and ecolo gy are of prime importance. The STD3 project titled « Assessment of tropical shrimp aquaculture impact on the environment in tropical countries using hydrobiology, ecology and remote sensing as helping tools for diagnosis )) was initiated in 1994, with the aim to study the sustainability of marine shrimp aquaculture in tropical areas, main! y Indonesia and Vietnam, through the following tasks: (i) improve site selection and study the impact of aquaculture on marine environments presenting a variable sensitivity to organic sewage, (ii) analyse the socio-economical aspects and profitability of the aquaculture industry and of common resources (iii) use remote sensing and geographical data bases for diagnosis and monitoring of site degradation (iv) reinforce the capacity of Asian scientists through training. Severa! aquaculture sites have been investigated in the Lampung region (South Sumatra, Indonesia), the Mekong delta (Vietnam) and on the West coast of New-Caledonia, providing a large range of typical ecosystems encountered in Asia and in the Pacifie, from coralline sites to coastal plains with mangrove and deltaic areas. The study concerned the spatial structure and seasonal influence of these ecosystems, the temporal variation during the course of the project (3 years) and the relation between the ecological structure and farm productions. Remote sensing provides a synoptic vision over large land expanses. Severa! scenes were processed for landuse mapping using conventional classification techniques. Concerning water quality assessment, a general relation for the Java sea was found between image and field data in terms of total suspended matter. Applying this relation to a new site in Sumatra has provided an initial approach to water type and, together with land use mapping, a preliminary assessment of the suitability of the area to shrimp aquaculture development. Socio-economic research has been focused on the identification ofneeds for collective action, including public policy, in the perspective of shrimp farming sustainability. The main concern is in the regulation of shrimp farming intensification and extensification at the scale of coastal ecosystemic entities in a common property resource management perspective. The common considered here is coastal water quality. Comparing the local development profiles and the institutional grounds for the design and implementation of collective management rules shows that variables such as land tenure system, farm owner socio-economic profile, social homogeneity or heterogeneity of the farmers are key factors to analyse the potential for sustainability. The defmition of water quality and the possible means to ensure its collective management are discussed. The main conclusion is that the economie incentives to farming development are strong but there is no significant difference among traditional, semi-intensive and intensive systems in terms of economie efficiency or wealth distribution. The description of the functioning of the different kinds of ecosystems make it possible to give an advice concerning the positioning of the activity inside the ecosystem, and furthermore to have a reference state in order to determine the impact of the activity on the coastal environnement. This impact can be summarized as an increase in the concentration of total suspended matt€?r, of particulate organic matter and of sulfate reducing bacterias. This organic ma~.er is either issued from rearing activities or from telluric origine, due to mangrove eradication when building the ponds. An evaluation of the relationship existing between productivity and characteristics of each ecosystem bas been conducted by correlating ecological indicators data (concentration of total suspended matter, particulate organic matter, chlorophyll, percentage of pheopigments in total pigments and cyanobacteria and sulfatereducing bacteria in water and sediments) with the average production of the farms. This comparison lead to the compilation of a scale of observed production integrating the range of these environmental parameters with shrimp production levels, bound to facilitate the positioning of shrimp farming in relation with the confmement leve! of each ecosystem. Lastly, ali geographie data originated from the various compartments of the study have been geo-referenced and loaded into a geographical information system. This allows to display any query made on spatial variables and their related statistical data, including the ir variations over the last few years and to reveal patterns and phenomena otherwise not obvious.
Le programme mis en oeuvre par la DRV (Paris, CREMA-L'Houmeau, DELIAO Brest, COP Tahiti, GIE/RA Nouvelle Calédonie), dans le cadre d'un projet européen STD3 «(Sciences et Technique au Service du Développement», en collaboration avec l'Université de Montpellier II, l'Ecole Nationale d'Agronomie de Rennes, l'ITC (Hollande), l'Institut Océanographique de Nha Trang (Vietnam), le BADC de Jepara et le BPPT de Jakarta (Indonésie), avait pour but la mise au point de méthodes permettant d'améliorer la sélection des sites ainsi que le suivi du développement et de l'impact de l'aquaculture des crevettes Péneides en milieu tropical pour éviter la surexploitation. Quatre axes de recherche ont été défmis : a) identifier la nature et quantifier les rejets de déchets issus de ce type d'aquaculture, b) définir les caractéristiques écologiques des écosystèmes susceptibles d'accueillir l'activité aquacole et suivre leur évolution sous l'influence des rejets, c) déterminer l'influence de la gestion des fermes et des ressources (aspects économiques) sur les performances de productivité, d) déterminer la capacité de la télédétection comme outil de diagnostic d'impact à l'échelle de la région, e) mener un programme de formation d'étudiants et jeunes chercheurs Vietnamiens et Indonésiens.

Droits : 1998 Ifremer
http://archimer.ifremer.fr/doc/00132/24357/22357.pdf
http://archimer.ifremer.fr/doc/00132/24357/

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Until now, the culture of sulphur-oxidizing bacterial symbionts associated with marine invertebrates remains impossible. Therefore, few studies focused on symbiont's physiology under stress conditions. In this study, we carried out a comparative experiment based on two different species of lucinid bivalves (Codakia orbiculata and Lucina pensylvanica) under comparable stress factors. The bivalves were starved for 6months in sulphide-free filtered seawater. For C.orbiculata only, starved individuals were then put back to the field, in natural sediment. We used in situ hybridization, flow cytometry and X-ray fluorescence to characterize the symbiont population hosted in the gills of both species. In L.pensylvanica, no decrease in symbiont abundance was observed throughout the starvation experiment, whereas elemental sulphur slowly decreased to zero after 3months of starvation. Conversely, in C.orbiculata, symbiont abundance within bacteriocytes decreased rapidly and sulphur from symbionts disappeared during the first weeks of the experiment. The modifications of the cellular characteristics (SSC - relative cell size and FL1 - genomic content) of the symbiotic populations along starvation were not comparable between species. Return to the sediment of starved C.orbiculata individuals led to a rapid (2-4weeks) recovery of symbiotic cellular characteristics, comparable with unstressed symbionts. These results suggest that endosymbiotic population regulation is host-species-dependent in lucinids.
ISSN: 0168-6496

hal-01545911
https://hal.archives-ouvertes.fr/hal-01545911
DOI : 10.1111/1574-6941.12366

Éditeur(s) : Wiley-blackwell
Résumé : Aims Exopolysaccharides (EPS) are industrially valuable molecules with numerous useful properties. This study describes the techniques used for the identification of a novel Vibrio bacterium and preliminary characterization of its EPS. Methods and Results Bioprospection in marine intertidal areas of New Caledonia followed by screening for EPS producing brought to selection of the isolate NC470. Phylogenetic analysis (biochemical tests, gene sequencing and DNADNA relatedness) permitted to identify NC470 as a new member of the Vibrio genus. The EPS was produced in batch fermentation, purified using the ultrafiltration process and analysed by colorimetry, Fourier Transform Infrared spectroscopy, gas chromatography, Nuclear Magnetic Resonance and HPLC-size exclusion chromatography. This EPS exhibits a high N-acetyl-hexosamines and uronic acid content with a low amount of neutral sugar. The molecular mass was 672x103Da. These data are relevant for possible technological exploitation. Conclusions We propose the name Vibrio neocaledonicus sp. nov for this isolate NC470, producing an EPS with an unusual sugar composition. Comparison with other known polymers permitted to select applications for this polymer. Significance and Impact of the Study This study contributes to evaluate the marine biodiversity of New Caledonia. It also highlights the biotechnological potential of New Caledonia marine bacteria.
Journal Of Applied Microbiology (1364-5072) (Wiley-blackwell), 2013-06 , Vol. 114 , N. 6 , P. 1702-1712

Droits : 2013 The Society for Applied Microbiology
http://archimer.ifremer.fr/doc/00144/25501/24036.pdf
DOI:10.1111/jam.12184
http://archimer.ifremer.fr/doc/00144/25501/

Résumé : Les aciers inoxydables à haute teneur en molybdène présentent une excellente résistance à la corrosion et ont été récemment utilisés dans des applications marines. L'acier inoxydable de type 254 SMO contient du molybdène (6% Mo) et des quantités plus élevées en éléments d'alliages que les aciers inoxydables plus classiques tels que 304, 316 et 316L. Alors que Anees Uddin Malik et al. montrent que l’acier 254 SMO est moins sensible à la corrosion par piqûre en eau de mer du golfe persique, Abdulsalam et al. démontrent que bien que cet acier présente une bonne résistance à la corrosion, il reste encore sensible à une corrosion caverneuse (surtout en milieu à 16% en masse d’ion chlorure ou à plus de 30°C).La première partie de ce travail traite du comportement électrochimique de l’acier inoxydable 254 SMO immergé dans l’eau de mer naturelle en laboratoire. Ainsi deux sites de la Guyane ont été choisis pour effectuer des prélèvements d’eau. Des analyses physicochimiques de ces eaux sont réalisées et montrent que l’eau du site du Port Larivot contient une quantité en ions chlorures plus importante que celle de l’eau du site du Mahury. Une colonisation par des bactéries et crustacés (balanes) a été mise en évidence, à l’aide du microscope électronique à balayage environnemental. Les mesures électrochimiques, notamment la voltammétrie cyclique a montré l’existence d’une zone de passivation et l’augmentation du courant de passivation par un facteur de 10 en présence d’un biofilm pour l’acier inoxydable immergé en eau du Mahury durant 22 jours. La deuxième partie propose une étude approfondie du comportement de l’interface complexe métal/couche passive/biofilm. Trois différents coupons d’aciers inoxydables (brut, poli et grenaillé) ont été déposés sur site (in-situ) dans un premier temps. Dans une seconde étape, nous avons réalisé des expérimentations mixtes (incubation in-situ et croissance en laboratoire). L’évolution du potentiel d’abandon de ces aciers est très proche pour l’acier brut et l’acier poli. En revanche, celui de l’acier grenaillé, de par la présence des grains d’alumine à sa surface, affiche un comportement différent. Une étude comparative des deux expérimentations montre des différences concernant les paramètres électriques de l’interface complexe métal/couche passive/biofilm.
Stainless steels with high content in molybdenum present an excellent corrosion resistance and were recently used in marine applications. The stainless steel 254 SMO contains molybdenum (6 %) and higher amounts of alloying elements than conventional stainless steels such as 304, 316 and 316L. While Anees Uddin Malik et al. show that 254 SMO steel is less likely to be susceptible to pitting corrosion in Arabian Gulf sea water, Abdulsalam et al. demonstrate that although this steel has good resistance to corrosion, it remains still susceptible to crevice corrosion (especially in environment with 16 chloride percent weight or more than 30 ° C).The first part of this work deals with the electrochemical behaviour of stainless steel 254 SMO immersed in natural seawater at laboratory. Two sites in French Guyane were chosen to take samples of seawater. Physicochemical analyses of these waters are made and show than the in Port Larivot site seawater contains a higher quantity of chloride ion than to Mahury seawater. Colonization by bacteria and crustaceans (barnacles) was highlighted, using the environmental scanning electron microscope. The electrochemical measurements, including cyclic voltammetry showed the existence of a passivation region and increasing the passivation current by a factor of 10 in the presence of biofilm on stainless steel immersed in Mahury seawater during 22 days.The second part offers a detailed study of the behaviour of the interface metal/passive film/biofilm. Three different coupons of stainless steel (crude, polished and blasted) were deposited on the site (in-situ) in the first time. In a second step, we performed experiments mixed (in-situ incubation and growth in the laboratory). The evolution of the free potential of these steels is very close for crude steel and polished steel. Conversely, the blasted steel, by the presence of alumina grains on its surface, shows a different behaviour. A comparative study of those two experiments shows differences in the electrical parameters of the interface metal/passive film/biofilm.

http://www.theses.fr/2013AGUY0598/document

Éditeur(s) : Elsevier Science Bv
Résumé : In New Caledonia, shrimp hatcheries are confronted with mass mortality in the larval stages, a phenomenon poorly understood as no specific causative agent has been identified. This has resulted in an excessive use of prophylactic antibiotics, although their adverse effects in aquaculture are notorious. The present work was thus aimed at selecting potential probiotic strains for penaeid hatcheries. From a pool of more than 400 marine bacterial isolates sampled from the local marine environment seven strains exhibited in vitro antagonistic activity towards Vibrio harveyi. These isolates were characterized both phenotypically and genotypically using a biochemical approach and 16S rDNA sequencing. Six out of these seven strains were found to belong to the genus Pseudoalteromonas, the last one belonging to the Vibrionaceae family and related to the Harveyi clade. Selected probiotic candidates were individually tested for antagonistic activities in vitro using a green fluorescent protein (GFP)-labelled transconjugant of V. harveyi and for inherent pathogenicity towards cultured shrimp larvae at two different developmental stages. This approach enabled rapid processing and selection of candidates to be tested in our experimental hatchery. Four different experiments were conducted to test candidate strains either alone or in combination. Repeated trials showed that postlarval survival was significantly improved by adding the strain NC201 individually to the rearing water compared to unchallenged controls. The analysis of immune-related gene expressions showed that the Litsty PEN3 transcript abundance of larvae was significantly increased after being reared in probiotic-containing water; however no significant difference in lysozyme gene expression was recorded in this study. Together, these results open new insights into the use of these strains as potential substitutes to antibiotherapy in shrimp larval rearing in New Caledonia.
Aquaculture (0044-8486) (Elsevier Science Bv), 2014-08 , Vol. 432 , P. 475-482

Droits : 2014 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00190/30129/28591.pdf
DOI:10.1016/j.aquaculture.2014.04.031
http://archimer.ifremer.fr/doc/00190/30129/