Résumé : The MEDECO Leg 2 cruise followed the MEDECO Leg 1 cruise that had crossed the Mediterranean Sea from the west to the east to study benthic communities of the Var canyon, deep corals found on the Calabrian Margin and cold seep ecosystems of the Mediterranean Ridge. The main objective of the MEDECO Leg 2 cruise was to study and compare, using a multidisciplinary approach, the structure and dynamics of deep-sea ecosystems at various active cold seep sites from the Nile deep sea fan and the Calabrian Arc, in the Eastern Mediterranean sea. During MEDECO Legs 1 & 2, a multiscale strategy was promoted to integrate (1) a high resolution cartography of geological structures (km2 scale), (2) a detailed mapping, including video imagery, of smaller-scale areas (scale 100 to 300 m2), (3) the physical, chemical and sedimentary characteristics of the habitat (multiscale), (4) the structure and functioning of faunal communities, including microbes, in terms of composition, diversity and biomass (multiscale), (5) small scale studies of interactions between organisms and their environment (scale < m2), (6) detailed ecophysiological studies at the organism scale on invertebrates. The use of the ROV “Victor 6000” and of various equipments for in situ and ex situ observations and measurements has helped reaching our objectives. The MEDECO cruise represented the key-Mediterranean cruise of the HERMES project “Hotspot Ecosystem Research on the Margins of European Seas” (P.I. P. Weaver, NOC-Southampton). The cruise was organized to follow the objectives of the HERMES program to better understand the functioning of deep ecosystems of the continental margins aiming at obtaining: (1) the description and quantification of the natural drivers (geological, hydrological, chemical factors) that control the distribution of ecosystems on margins; (2) the characterization and quantification of biodiversity, from bacteria to megafauna, as well as the knowledge of ecosystem functioning; (3) the study of ecosystems dynamics including the biology/physiology of key-species. Specific objectives. Colonization experiments conducted in the frame of two European programs, Diwoo and Chemeco, have given the opportunity to recover the fauna installed in the devices deployed during the Bionil cruise (2006) and to deploy new ones at the same site located in the pockmark area of the central province of Nile deep sea fan.

Droits : 2008 Insu, Cnrs, Locean
http://archimer.ifremer.fr/doc/00134/24550/22583.pdf
http://archimer.ifremer.fr/doc/00134/24550/

Éditeur(s) : Wiley-blackwell
Résumé : Marine bacteria are a rich source of bioactive metabolites. However, the microbial diversity of marine ecosystem still needs to be explored. The aim of this study was to isolate and characterize bacteria with antimicrobial activities from various marine coastal environment of New Caledonia. We obtained 493 marine isolates from various environments and samples of which 63 (12.8%) presented an antibacterial activity against a panel of reference pathogenic strains (Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli and Enterococcus faecalis). Ten out of the most promising strains were cultured, fractionated and screened for antibacterial activity. Four of them (NC282, NC412, NC272 and NC120) showed at least an activity against reference and multidrug-resistant pathogenic strains and were found to belong to the genus Pseudoalteromonas, according to the 16S phylogenetic analysis. The NC282 strain does not belong to any described Pseudoalteromonas species and might be of interest for further chemical and biological characterization. These findings suggest that the identified strains may contribute to the discovery for new sources of antimicrobial substances to develop new therapies to treat infections caused by multidrug-resistant bacteria.
Letters In Applied Microbiology (0266-8254) (Wiley-blackwell), 2014-02 , Vol. 58 , N. 2 , P. 102-108

Droits : 2013 The Society for Applied Microbiology
http://archimer.ifremer.fr/doc/00174/28552/26994.pdf
DOI:10.1111/lam.12162
http://archimer.ifremer.fr/doc/00174/28552/

Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : Metazooplankton abundance, biomass (<80 mu m, 200-500 mu m and >500 mu m) and community structure in the Ahe atoll were studied together with their relationships with environmental factors (temperature, salinity, wind) and trophic factors (phytoplankton, bacteria, heterotrophic nanoflagellates (HNF) and ciliates) during three periods in 2008-2009. Meroplankton, mainly bivalve and gastropod larvae, was dominant. Holoplankton was dominated by copepods, the main species being Oithona spp., Paracalanus parvus, Clausocalanus spp., Corycaeus spp., Acartia fossae and Undinula vulgaris. The results suggest a clear wind influence on the structure and horizontal distribution of the zooplankton communities. The metazooplankton appeared to be controlled mainly by food resources, suggesting a bottom-up control. The low nanophytoplankton biomass in contrast to the high abundance of picophytoplankton, HNF and nano-particle grazers (mainly Oithona spp., Paracalanus and bivalve larvae) highlighted the importance of the microbial loop in the food web. (C) 2012 Elsevier Ltd. All rights reserved.
Marine Pollution Bulletin (0025-326X) (Pergamon-elsevier Science Ltd), 2012 , Vol. 65 , N. 10-12 , P. 538-548

Droits : 2012 Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00101/21207/19419.pdf
DOI:10.1016/j.marpolbul.2012.01.025
http://archimer.ifremer.fr/doc/00101/21207/

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : International audience
Portable microbial samplers are useful for detecting microorganisms in the air. However, limited data are available on their performance when sampling airborne biological agents in a routine practice. We compared bacterial and fungal concentrations obtained in field conditions using three impactor samplers with different designs (AES Chemunex Sampl'Air, bioMérieux Air Ideal, and Sartorius AirPort MD8/BACTair). The linearity of mold collection was tested in the range of 100 L to 1000 L, and all the devices had a correlation coefficient higher than 0.95. For optimal comparison of the samplers, we performed experiments in different hospital rooms with varying levels of air biocontamination. Each sampling procedure was repeated to assess reproducibility. No significant difference between the samplers was observed for the mold concentrations on Sabouraud agar, whereas Sampl'Air collected significantly more bacteria on tryptic soy agar than Air Ideal or BACTair at one of the sites. Impactor location in the room was nevertheless associated with the variability observed with the three samplers at the highest microbial concentration levels. On the basis of their performance, autonomy and simplicity of use, these three impactors are suitable for routine indoor evaluation of microbial air contamination.
ISSN: 1545-9624

hal-00874614
https://hal.archives-ouvertes.fr/hal-00874614
DOI : 10.1080/15459624.2013.800955
PUBMED : 23799861

Éditeur(s) : Springer
Résumé : Batch culture experiments using viral enrichment were conducted to test the response of a coastal bacterial community to autochthonous (i.e., co-existing) or allochthonous riverine viruses. The effects of viral infections on bacterial dynamics and activity were assessed by epifluorescence microscopy and thymidine incorporation, respectively, whereas the effect of viral infection on bacterial community composition was examined by polymerase chain reaction-single strand conformation polymorphism 16S ribosomal RNA fingerprinting. The percentages of high nucleic acid-containing cells, evaluated by flow cytometry, were significantly correlated (r (2) = 0.91, n = 12, p < 0.0001) to bacterial production, making this value a good predictor of active cell dynamics along the study. While confinement and temperature were the two principal experimental factors affecting bacterial community composition and dynamics, respectively, additions of freshwater viruses had significant effects on coastal bacterial communities. Thus, foreign viruses significantly reduced net bacterial population increase as compared to the enrichment treated with inactivated virus. Moreover, freshwater viruses recurrently and specifically affected bacterial community composition, as compared to addition of autochthonous viruses. In most cases, the combined treatment viruses and freshwater dissolved organic matter helped to maintain or even enhance species richness in coastal bacterial communities in agreement to the 'killing the winner' hypothesis. Thus, riverine virus input could potentially influence bacterial community composition of the coastal bay albeit with modest modification of bulk bacterial growth.
Microbial Ecology (0095-3628) (Springer), 2009-02 , Vol. 57 , N. 2 , P. 295-306

Droits : 2009 Springer
http://archimer.ifremer.fr/doc/2009/publication-6636.pdf
DOI:10.1007/s00248-008-9428-1
http://archimer.ifremer.fr/doc/00000/6636/

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : International audience
Adult lymphatic filariae (Wuchereria bancrofti, Brugia malayi) can cause blocking of lymphatics producing obliterating endolymphitis lesions. The subsequent extravasation of lymph (or chyle when the obstruction is canal) is at the origin of the formation of lymphedema or elephantiasis, in which the main histological finding is great hypertrophy of collagen elements. This theory involving filaria only is not the full picture, and bacterial infection, mainly by streptococci, is an important factor. The association of filaria with microbes is particularly dangerous because the presence of the latter, or its toxins, causes death of local microfilariae and even adult worms, which are known to be more harmful dead than alive. The progression of the disease, especially in cases with lymphedema, which mainly affects the limbs and the genital organs, depends on three factors: the species of filaria, the degree of transmission, and the receptivity of the patient to the parasite. Large differences are found according to the region involved, and in the same endemic zone, according to the individuals affected. However, they almost always occur progressively in areas where there have been recurrent attacks of acute lymphangitis.
ISSN: 0398-0499

hal-00715440
https://hal.univ-antilles.fr/hal-00715440
PUBMED : 7007545

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Although ants may induce community-wide effects via changes in physical habitats in terrestrial environments, their influence on aquatic communities living in plant-held waters remains largely underexplored. The neotropical tank-bromeliad Aechmea mertensii (Bromeliaceae) occurs along forest edges in ant-gardens initiated by Camponotus femoratus or by Pachycondyla goeldii. Its leaves form wells that hold rainwater and provide suitable habitats for many aquatic organisms. We postulated that these ant-plant mutualisms indirectly affect the microbial community structure via changes in the environmental conditions experienced by the plants. To test this hypothesis, we analyzed the protist communities from 63 tank-bromeliads associated with either C. femoratus or P. goeldii (hereafter Cf-Aechmea and Pg-Aechmea) along a forest edge in French Guiana. For each plant, a large number of environmental variables (including habitat structure, food resources, incident radiation and the presence of aquatic invertebrates) were quantified to determine their relative importance in driving any observed differences across ant-associated plants. Pg-Aechmea are located in sun-exposed areas and hold low volumes of water and low amounts of detritus, whereas Cf-Aechmea are located in partially shaded areas and accumulate higher amounts of water and detritus. Protists (i.e., protozoa and algae) inhabiting Cf-Aechmea exhibit greater richness and abundances than those in Pg-Aechmea. Variations in detritus content, number of leaves, incident radiation, and the epiphyte richness of the ant-garden were the main factors explaining the variation in protist richness. A shift in the functional group composition of protists between bromeliads tended by different ant species suggested that mutualistic ants indirectly mediate changes in the microbial food web.
Basic and Applied Ecology

hal-00913126
https://hal.archives-ouvertes.fr/hal-00913126
https://hal.archives-ouvertes.fr/hal-00913126/document
DOI : 10.1016/j.baae.2012.10.002
OATAO : 10190

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Much research is being carried out into indoor exposure to harmful agents. This review focused on the impact on children's health, taking a broad approach to the indoor environment and including chemical, microbial, physical and social aspects. Papers published from 2006 onwards were reviewed, with regards to scientific context. Most of publications dealt with chemical exposure. Apart from the ongoing issue of combustion by-products, most of these papers concerned semi volatile organic compounds (such as phthalates). These may be associated with neurotoxic, reprotoxic or respiratory effects and may, therefore, be of particular interest so far as children are concerned. In a lesser extent, volatile organic compounds (such as aldehydes) that have mainly respiratory effects are still studied. Assessing exposure to metals is still of concern, with increasing interest in bioaccessibility. Most of the papers on microbial exposure focused on respiratory tract infections, especially asthma linked to allergens and bio-aerosols. Physical exposure includes noise and electromagnetic fields, and articles dealt with the auditory and non auditory effects of noise. Articles on radiofrequency electromagnetic fields mainly concerned questions about non-thermal effects and papers on extremely low-frequency magnetic fields focused on the characterization of exposure. The impact of the indoor environment on children's health cannot be assessed merely by considering the effect of these different types of exposure: this review highlights new findings and also discusses the interactions between agents in indoor environments and also with social aspects.
ISSN: 1438-4639

hal-00687403
https://hal.archives-ouvertes.fr/hal-00687403
DOI : 10.1016/j.ijheh.2011.07.008
PUBMED : 21889403

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
The Anopheles midgut hosts diverse bacterial communities and represents a complex ecosystem. Several evidences indicate that mosquito midgut microbiota interferes with malaria parasite transmission. However, the bacterial composition of salivary glands and ovaries, two other biologically important tissues, has not been described so far. In this study, we investigated the dynamics of the bacterial communities in the mosquito tissues from emerging mosquitoes until 8 days after a blood meal containing Plasmodium falciparum gametocytes and described the temporal colonization of the mosquito epithelia. Bacterial communities were identified in the midgut, ovaries, and salivary glands of individual mosquitoes using pyrosequencing of the 16S rRNA gene. We found that the mosquito epithelia share a core microbiota, but some bacteria taxa were more associated with one or another tissue at a particular time point. The bacterial composition in the tissues of emerging mosquitoes varied according to the breeding site, indicating that some bacteria are acquired from the environment. Our results revealed temporal variations in the bacterial community structure, possibly as a result of the mosquito physiological changes. The abundance of Serratia significantly correlated with P. falciparum infection both in the midgut and salivary glands of malaria challenged mosquitoes, which suggests that interactions occur between microbes and parasites. These bacteria may represent promising targets for vector control strategies. Overall, this study points out the importance of characterizing bacterial communities in malaria mosquito vectors.
ISSN: 1664-302X

hal-01546162
https://hal.archives-ouvertes.fr/hal-01546162
DOI : 10.3389/fmicb.2015.01500

Éditeur(s) : HAL CCSD
Résumé : International audience
BACKGROUND: Dairy working increases the prevalence of lower airway respiratory diseases, especially COPD and asthma. Epidemiological studies have reported that chronic inhalation of organic dusts released during specific daily tasks could represent a major risk factor for development of these pathologies in dairy workers. Knowledge on size, nature and biological activity of such organic dusts remain however limited. OBJECTIVE: To compare size distribution, microbial composition and cellular effects of dusts liberated by the spreading of straw bedding in five French dairy farms located in Brittany. RESULTS: Mechanized distribution of straw bedding generated a cloud of inhalable dusts in the five dairy farms' barns. Thoracic particles having a 3-7.5µm size constituted 58.9-68.3% of these dusts. Analyses of thoracic dusts by next generation sequencing showed that the microbial dust composition differed between the five French farms, although Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria represent more than 97.5% of the bacterial phyla detected in each sample. Several bacteria genera comprising of human pathogenic species, such as Pseudomonas, Staphylococcus, Thermoactinomyces or Saccharopolyspora were identified. Cladosporium and Alternaria fungal genera, which are potent environmental determinants of respiratory symptoms, were detected in dusts collected in the five farms and their levels reached 15.5-51.1% and 9-24.7% of assignable fungal sequences in each sample, respectively. Finally, all dust samples significantly and strongly increased the expression of the pro-inflammatory TNF-α, IL-1β, IL-6 and IL-8 cytokines at both mRNA and protein levels in human monocyte-derived macrophages. Their effects were dose-dependent and detectable from 1µg/ml. The intensity of the macrophage responses however differed according to the samples. CONCLUSIONS: Our results strengthen the hypothesis that organic dusts released during the distribution of straw bedding are mainly constituted of thoracic particles which are small enough to deposit on lower bronchial epithelium of dairy farmers and induce inflammation.
Environmental Research

hal-01579610
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01579610
DOI : 10.1016/j.envres.2017.07.025
PUBMED : 28735230

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
Résumé : Diffusion du document : INRA Documentation de Centre, Domaine de Duclos, 97170 Petitt-Bourg (Guadeloupe, France) Diplôme : DEA
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
Because soil respiration representes 80% of ecosystem respiration, it is a major flux between biosphere and atmosphere. We examined the effects of root and litter exclusion on soil CO! efflux (Rsu1) using trenching and litter exclusion in a tropical plantation constituted of trees seedlings installed in 16 mono-specific stands 20 years ago near Kourou, French Guyana. Soil CO2 efflux was measured using an infra red gas analyser (PP System,EGM4 ) at 16 randomly distributed plot in each treatment: control, root exclusion, litter exclusion and both root and litter exclusion. in the plantation. We measured R'1l1during four periods, and we have collected soil samples, litter biomass and measured moisture at 5 cm depth in the soil. Soil CO, efflux varied significantly among species from 2,8±O,7f1mo l. m''. s' (mean ± standard deviation) to 7.4± 1.7fLmol. n'-' . s ' for Qualea rosea and Vochys ia tomentosa, respectively. 1'0 significant correlation was found between RSIlI variability and soil moisture, which is mostly related to soil texture in the experimental site. Soil CO2 efflux was significantly reduced in litter exclusion treatment and root exclusion plots (6 months litter and/or root exclusion) during ail measurements period and for ail species, compared to control plots. The reduction of soil CO, efflux was higher in plot without root than in plot without litter of control plot (42% and 25%, respectively). There was an import ant specific diversity in these reductions . We estimated the contribution of roof respiration (Rr) to total Rso1 by calculating the difference between Rso1 control and Rsn l root exclusion plot corrected for the decomposition of root that were killed following t re n e h in ~. Thus the heterotrophic component of soil carbon efflux accounts for 46% of total carbon efflux (1,9f1 mol. rn" . s•') while root respiration accounts for 54% of soil carbon release (2,3 ~t mo l. m-2 S-I) . Because there was a negative and significant correlation between microbial respiration (Rrn) and C/N of mature leaves it seemed to be possible to predict Rm if we known the mature leaves quality. In addition a good estimate theorical R ~, values from R~, measured in different treatments.
La respiration du sol en représentant une part de 80% de la respiration de l'écosystème apparaît être un flux majeur entre la biosphère et l'atmosphère. Nous avons étudié les effets de l'exclusion racinaire et de la litière sur le flux de CO, du sol (R ~ , ) en utilisant la méthode de " Trench-plots" et de suppression de litière dans une plantation d'arbres tropicaux. Ces arbres, âgés de 20 ans ont été plantés sur un sol uniforme, près de Kourou en Guyane française, en 16 placeaux mono-spécifiques. Pour mesurer les flux de CO2 provenant du sol, nous avons utilisé un analyseur différentiel de gaz infrarouge portable muni d'une chambre. Les mesures ont été faites sur 4 traitements différents tels que : le contrôle, l'exclusion racinaire, l'exclusion de litière et l'exclusion de litière et de racine et ce, répétés sur chacune des 16 placettes mono-spécifiques. Cette étude comporte 4 campagnes de mesures. Nous avons également effectué des prélèvements de sol de litière et nous avons fait des mesures d’humidité de sol à une profondeur de 5 cm. Les flux de C01 du sol varient fortement entre espèces de 2.8±O.7 ~t m o 1. m-2. sol à 7 A± 1. 7 ~t m o l. m•1 sol pour Qua/ev rosea ct Vochysto tomentasa, respectivement. Il n'existe pas de corrélation significative entre les variations de Rw l ct celles de l'humidité du sol (indication sur la texture du sol de la plantation ). Nous avons observé que Rso1 était significativement plus faible dans les placeaux sans racines et/ou sans litière (6 mois après la mise en place de l'expérimentation) pour toutes les campagnes de mesures et pour toutes les espèces que dans les placeaux contrôlés. Cette réduction du flux de CO2 du sol est plus forte dans les "trench-plots " que dans les traitement s d'exclusion de litière avec 42 et 25% respectivement. Un effet "traitement " et un effet "espèce" important expliquent 3 1"/.. ct 13% de la variabilité totale de R~. Nous avons cherché à connaître la contribution des racines dans les valeurs de R""I. en comparant le flux de CO2 provenant du sol sur des "trench -plot s'' au flux de COl provenant du sol dans les placeaux contrôlés . Cette estimation a été corrigée pour prendre en compte la décomposition des racines tuées par les tranchées. Ainsi, la composante appartenant aux micro -organismes représente 46% du flux total de carbone provenant du sol (1.9Jlmo l. m-2 S•I ) alors que la respiration des racines représente 54% du dégagement de carbone (2 ,3~lmol. m ol . 5-La respiration des micro-organismes pourrait être estimée en mesurant le C/N des feuilles matures puisqu'il existe une corrélation significative et négative entre les deux. Enfin les résultats obtenus sur les différents traitements permettent d'obtenir une bonne estimation de la respiration du sol avec un RSIlI théorique corrélé à 66% avec les valeurs réelles mesurées.
https://hal.archives-ouvertes.fr/hal-01189239

hal-01189239
https://hal.archives-ouvertes.fr/hal-01189239
PRODINRA : 18212

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The susceptibility of Anopheles mosquitoes to Plasmodium infections relies on complex interactions between the insect vector and the malaria parasite. A number of studies have shown that the mosquito innate immune responses play an important role in controlling the malaria infection and that the strength of parasite clearance is under genetic control, but little is known about the influence of environmental factors on the transmission success. We present here evidence that the composition of the vector gut microbiota is one of the major components that determine the outcome of mosquito infections. A. gambiae mosquitoes collected in natural breeding sites from Cameroon were experimentally challenged with a wild P. falciparum isolate, and their gut bacterial content was submitted for pyrosequencing analysis. The meta-taxogenomic approach revealed a broader richness of the midgut bacterial flora than previously described. Unexpectedly, the majority of bacterial species were found in only a small proportion of mosquitoes, and only 20 genera were shared by 80% of individuals. We show that observed differences in gut bacterial flora of adult mosquitoes is a result of breeding in distinct sites, suggesting that the native aquatic source where larvae were grown determines the composition of the midgut microbiota. Importantly, the abundance of Enterobacteriaceae in the mosquito midgut correlates significantly with the Plasmodium infection status. This striking relationship highlights the role of natural gut environment in parasite transmission. Deciphering microbe-pathogen interactions offers new perspectives to control disease transmission.
ISSN: 1553-7366

hal-01546176
https://hal.archives-ouvertes.fr/hal-01546176
DOI : 10.1371/journal.ppat.1002742

Éditeur(s) : HAL CCSD Inter-Research
Résumé : International audience
Sphaeroma serratum is a marine isopod species that inhabits seashores from Europe to West Africa. The individuals live under stones in direct contact with reduced sediments and harbour a diverse bacterial community on the cuticle of their pleopods. We investigated the diversity of these epibiotic bacteria on male (pubescent and senescent) and female specimens with electron microscopic obser vations and molecular tools. The microbial community of S. serratum was shown to be composed of at least 5 bacterial morphotypes observed on the pleopodal cuticle in all male specimens. Using fluorescence in situ hybridization, we identified 5 major phylogenetic groups (α-, β-, γ- and δ-Proteobacteria and Archaea) whereas denaturing gradient gel electro - phoresis (DGGE) of PCR-amplified 16S rRNA gene fragments of epibiotic bacteria revealed 50 bands. The bacterial community associated with S. serratum seems more diverse than in other marine crustaceans, such as Rimicaris. The relative diversity of this bacterial community was also studied in relation to the molt cycle. The comparison of DGGE band patterns of several individuals from female, pubescent male and senescent male groups revealed that the bacterial community diversity was dependent on the sex and the age of the individuals and more generally on the molt status.
Marine Ecology Progress Series

hal-00743743
https://hal.univ-antilles.fr/hal-00743743
DOI : 10.3354/meps09711

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) : 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/

Éditeur(s) : HAL CCSD
Résumé :   Diplôme : Master Recherche
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
Notre étude porte sur la caractérisation à l'échelle de l'hectare de la variabilité spatiale (1) du fonctionnement microbien du sol et (2) de sa stabilité (i.e. de sa réponse à un stress). Elle a été menée sur une forêt tropicale humide (forêt primaire) proche de Kourou en Guyane (site de Paracou). Les indicateurs fonctionnels utilisés sont les potentiels d'activités respiratoires (RP) et dénitrifiantes (OP). La variabilité spatiale du fonctionnement microbien du sol a fait l'objet d'un nombre important d'études mais très peu d'entre elles ont concerné ce type d'écosystème. Un autre aspect novateur réside dans la recherche de la variabilité spatiale de la stabilité du fonctionnement. A notre connaissance, il s'agit de la première étude de ce type en milieu tropical comme en milieu tempéré. Les principales conclusions sont les suivantes : (1) à l'échelle 10m (grille principale) les coefficients de variation (CV) des potentiels de fonction sont similaires pour les 2 processus et élevés (RP : 53% ; OP : 54%) au regard des valeurs de la littérature sur des milieux tempérés, mais RP et OP présentent des variabilités spatiales différentes à des échelles inférieures ; (2) l'utilisation d'un indice de densité locale (ID) des arbres n'a pas permis de mettre en évidence une corrélation entre les répartitions spatiales de la végétation et du fonctionnement microbien du sol. De même, aucun déterminisme clair de l'intensitè des potentiels microbiens n'a pu être dégagé par la prise en compte de la variabilité des caractéristiques physico-chimiques du sol; (3) un stress thermique génère à très court terme (résistance) un accroissement de la spatialisation du potentiel de respiration. A plus long terme, la variabilité inter-échantillons s'atténue pour retrouver ses valeurs initiales et, (4) l'activité originelle (avant stress) n'est pas corrélée avec la résistance et est négativement corrélée aux valeurs observées 15 et 30 jours après le stress. Outre son intérêt intrinsèque, cette étude vise à se doter de données de « cadrage » sur la forêt primaire (non perturbée) qui nous permettront d'accéder à de meilleures évaluations et compréhensions des mécanismes impliqués dans la réponse des écosystèmes tropicaux à l'anthropisation lors de projets en cours. Un exemple de ce type d'application est brièvement décrit.
https://hal.archives-ouvertes.fr/hal-01189259

hal-01189259
https://hal.archives-ouvertes.fr/hal-01189259
PRODINRA : 20250

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
1. A substantial fraction of the freshwater available in neotropical forests is impounded within the rosettes of bromeliads that form aquatic islands in a terrestrial matrix. The ecosystem functioning of bromeliads is known to be influenced by the composition of the contained community but it is not clear whether bromeliad food webs remain functionally similar against a background of variation in the understorey environment. 2. We considered a broad range of environmental conditions, including incident light and incoming litter, and quantified the distribution of a very wide range of freshwater organisms (from viruses to macroinvertebrates) to determine the factors that influence the functional structure of bromeliad food webs in samples taken from 171 tank-bromeliads. 3. We observed a gradient of detritus-based to algal-based food webs from the understorey to the overstorey. Algae, rotifers and collector and predatory invertebrates dominated bromeliad food webs in exposed areas, whereas filter-feeding insects had their highest densities in shaded forest areas. Viruses, bacteria and fungi showed no clear density patterns. Detritus decomposition is mainly due to microbial activity in understorey bromeliads where filter feeders are the main consumers of microbial and particulate organic matter (POM). Algal biomass may exceed bacterial biomass in sun-exposed bromeliads where amounts of detritus were lower but functional diversity was highest. 4. Our results provide evidence that tank-bromeliads, which grow in a broad range of ecological conditions, promote aquatic food web diversity in neotropical forests. Moreover, although bromeliad ecosystems have been categorised as detritus-based systems in the literature, we show that algal production can support a non-detrital food web in these systems.
ISSN: 0046-5070

hal-00819103
https://hal.archives-ouvertes.fr/hal-00819103

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Losses of corals worldwide emphasize the need to understand what drives reef decline. Stressors such as overfishing and nutrient pollution may reduce resilience of coral reefs by increasing coral–algal competition and reducing coral recruitment, growth and survivorship. Such effects may themselves develop via several mechanisms, including disruption of coral microbiomes. Here we report the results of a 3-year field experiment simulating overfishing and nutrient pollution. These stressors increase turf and macroalgal cover, destabilizing microbiomes, elevating putative pathogen loads, increasing disease more than twofold and increasing mortality up to eightfold. Above-average temperatures exacerbate these effects, further disrupting microbiomes of unhealthy corals and concentrating 80% of mortality in the warmest seasons. Surprisingly, nutrients also increase bacterial opportunism and mortality in corals bitten by parrotfish, turning normal trophic interactions deadly for corals. Thus, overfishing and nutrient pollution impact reefs down to microbial scales, killing corals by sensitizing them to predation, above-average temperatures and bacterial opportunism.
ISSN: 2041-1723

Droits : http://creativecommons.org/licenses/by/
hal-01340547
https://hal-univ-perp.archives-ouvertes.fr/hal-01340547
https://hal-univ-perp.archives-ouvertes.fr/hal-01340547/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01340547/file/ncomms11833.pdf
DOI : 10.1038/ncomms11833

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Although ants may induce community-wide effects via changes in physical habitats in terrestrial environments, their influence on aquatic communities living in plant-held waters remains largely underexplored. The neotropical tank-bromeliad Aechmea mertensii (Bromeliaceae) occurs along forest edges in ant-gardens initiated by Camponotus femoratus or by Pachycondyla goeldii. Its leaves form wells that hold rainwater and provide suitable habitats for many aquatic organisms. We postulated that these ant-plant mutualisms indirectly affect the microbial community structure via changes in the environmental conditions experienced by the plants. To test this hypothesis, we analyzed the protist communities from 63 tank-bromeliads associated with either C. femoratus or P. goeldii (hereafter Cf-Aechmea and Pg-Aechmea) along a forest edge in French Guiana. For each plant, a large number of environmental variables (including habitat structure, food resources, incident radiation and the presence of aquatic invertebrates) were quantified to determine their relative importance in driving any observed differences across ant-associated plants. Pg-Aechmea are located in sun-exposed areas and hold low volumes of water and low amounts of detritus, whereas Cf-Aechmea are located in partially shaded areas and accumulate higher amounts of water and detritus. Protists (i.e., protozoa and algae) inhabiting Cf-Aechmea exhibit greater richness and abundances than those in Pg-Aechmea. Variations in detritus content, number of leaves, incident radiation, and the epiphyte richness of the ant-garden were the main factors explaining the variation in protist richness. A shift in the functional group composition of protists between bromeliads tended by different ant species suggested that mutualistic ants indirectly mediate changes in the microbial food web.
ISSN: 1439-1791

hal-00817519
https://hal.archives-ouvertes.fr/hal-00817519