Éditeur(s) : University of West Indies, Trinidad &Tobago Université des Antilles. Service commun de la documentation
Extrait de : 52e congrès annuel de la Société caribéenne des plantes alimentaires / 52nd annual meeting of the Caribbean food crops society (CFCS), du 10 au 16 juillet 2016. INRA, CFCS
Description : Carbon dioxide (CO2) accounts for the largest proportion (74%) of total greenhouse gas (GHG) emissions globally, with agricultural activities contributing approximately 25% of this gas. Opportunities to reduce the emissions in the sector can therefore contribute significantly to mitigating global climate change. Ag-lime is used extensively to alleviate problems of soil acidity and the potential for this material to contribute to C sequestration in soils is gaining interest among researchers. A laboratory experiment using C-13 isotopic labelling techniques was therefore established to answer the following questions: 1) Is there a potential for sequestering C using ag-lime in Trinidad acid soils? 2) Does enhancing soil microbial respiration by applying labile organic amendments enhance the C sequestration potential of ag-lime? 3) Are lime-derived C (LDC) estimates from non-isotopic difference technique comparable to that from the C- 13 isotopic labelling technique? The results ascertained for the study showed significant (P<0.05) differences between the LDC estimates from the two techniques with the non-isotopic techniques yielding higher estimates. Over the 32- day experiment, between 16.4 to 85.4% of the ag-lime C was released as CO2 with values being lower for the Piarco soil. The LDC in the CO2 was also significantly (P<0.05) lower for the poultry litter treatments comparison to the other organic amendments for the Piarco soil but not the Nariva soil. This effect may not have been as a result of an enhancement of the carbon sequestration potential of the ag-lime due to an elevation in soil microbial respiration since the LDC in the glucose-amended soils did not differ significantly from the no-amendment control soils.
Siècle(s) traité(s) : 21
Droits : CC-BY-NC-ND - Attribution - Pas d'utilisation commerciale - Pas de modification
Permalien : http://www.manioc.org/fichiers/V16308
V16308

Résumé : The slides were taken on collecting trips sponsored by the William L. Bryant Foundation, where books, music and art indigenous to the regions were gathered. The are organized by geographical location.
Many citizens throughout the street. Also venders on horseback. Commercial buildings include a notary office and a Coca-Cola building.
Cuba -- Caribbean region -- Trinidad

Droits : All rights to images are held by the respective holding institution. This image is posted publicly for non-profit educational uses, excluding printed publication. For permission to reproduce images and/or for copyright information contact Special Collections & University Archives, University of Central Florida Libraries, Orlando, FL 32816 phone (407) 823-2576, email: speccoll@mail.ucf.edu
CFM1972_01a
Sheet 24: 13
http://ufdc.ufl.edu/CA01200372/00001

Éditeur(s) : Elsevier
Résumé : A study of organic carbon mineralization from the Congo continental shelf to the abyssal plain through the Congo submarine channel and Angola Margin was undertaken using in situ measurements of sediment oxygen demand as a tracer of benthic carbon recycling. Two measurement techniques were coupled on a single autonomous platform: in situ benthic chambers and microelectrodes, which provided total and diffusive oxygen uptake as well as oxygen microdistributions in porewaters. In addition, sediment trap fluxes, sediment composition (Org-C, Tot-N, CaCO3, porosity) and radionuclide profiles provided measurements of, respectively input fluxes and burial rate of organic and inorganic compounds. The in situ results show that the oxygen consumption on this margin close to the Congo River is high with values of total oxygen uptake (TOU) of 4 +/- 0.6, 3.6 +/- 0.5 mmol m(-2) d(-1) at 1300 and 3100m depth, respectively, and between 1.9 +/- 0.3 and 2.4 +/- 0.2 mmol m(-2) d(-1) at 4000 m depth. Diffusive oxygen uptakes (DOU) were 2.8 +/- 1.1, 2.3 +/- 0.8, 0.8 +/- 0.3 and 1.2 +/- 0.1 mmol m(-2) d(-1), respectively at the same depths. The magnitude of the oxygen demands on the slope is correlated with water depth but is not correlated with the proximity of the submarine channel-levee system, which indicates that cross-slope transport processes are active over the entire margin. Comparison of the vertical flux of organic carbon with its mineralization and burial reveal that this lateral input is very important since the sum of recycling and burial in the sediments is 5-8 times larger than the vertical flux recorded in traps. Transfer of material from the Congo River occurs through turbidity currents channelled in the Congo valley, which are subsequently deposited in the Lobe zone in the Congo fan below 4800 m. Ship board measurements of oxygen profiles indicate large mineralization rates of organic carbon in this zone, which agrees with the high organic carbon content (3%) and the large sedimentation rate (19 mm y(-1)) found on this site. The Lobe region could receive as high as 19 mol C m(-2) y(-1), 1/3 being mineralized and 2/3 being buried and could constitute the largest depocenter of organic carbon in the South Atlantic.
Deep Sea Research Part II: Topical Studies in Oceanography (0967-0645) (Elsevier), 2009-11 , Vol. 56 , N. 23 , P. 2223-2238

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-7316.pdf
DOI:10.1016/j.dsr2.2009.04.005
http://archimer.ifremer.fr/doc/00000/7316/

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : Fire-free forest conversion with organic inputs as an alternative to slash-and-burn could improve agro-ecosystem sustainability. We assessed soil carbon mass changes in a sandy-clayey and well-drained soil in French Guiana after forest clearing by the chop-and-mulch method and crop establishment. At the experimental site of Combi, native forest was cut down in October 2008; woody biomass was chopped and incorporated into the top 20 cm of soil. After about one year of legume and grass cover, three forms of land management were compared: grassland (Urochloa ruziziensis), maize/soybean crop rotation with disk tillage and in direct seeding without tillage. There were four replicates. We measured 14.16 kg m(-2) of carbon in 2 mm-sieved soil down to 2 m depth for the initial forest. Forest clearing did not induce significant soil compaction; neither did any specific agricultural practice. In converted soils, C stocks were measured in the 0-30 cm layer after each crop for three years. Carbon mass changes for soil fractions <2 mm (soil C stock) and >2 mm (soil C pool) in the 0-5, 5-10, 10-20 and 20-30 cm soil layers were assessed on an equivalent soil mass basis. One year and 1.5 years after deforestation, higher C stocks (+0.64 to 1.16 kg C m(-2) yr(-1)) and C pools (+0.52 to 0.90 kg C m(-2) yr(-1)) were measured in converted soils, compared to those of the forest into the top 30 cm of soil. However, the masses of carbon in these converted soils declined later. The highest rates of carbon decrease were measured between 1.5 and 2 years after forest conversion in the <2 mm soil fraction, from 0.46 kg Cm-2 yr(-1) (in grassland soils) to 0.71 kg C m(-2) yr(-1) (in cropland under no tillage). The carbon pool declined during the third year at rates of 0.41 kg C m(-2) yr(-1) (cropland under disk tillage) to 0.76 kg C m(-2) yr(-1) (grassland soils). Three years after forest conversion, C masses in the top 30 cm of soils for grassland showed similar values than for forest. In comparison, the carbon stock in cropped soils managed under no tillage in direct seeding (without mulch) was significantly 17% and 16% lower than in forest and grassland soils, respectively. None of the studied agricultural practices succeeded in accumulating carbon from the chopped forest biomass.
ISSN: 0167-8809

hal-01032438
https://hal.archives-ouvertes.fr/hal-01032438
DOI : 10.1016/j.agee.2013.11.009

Éditeur(s) : HAL CCSD
Résumé : The Franceville Basin (2.1 Ga) in southeastern Gabon, hosts a black shale series well preserved (FB Formation) which represents an exceptional example of unmetamorphised Paleoproterozoic sediment strata. This basin includes the protore of one of the largest Mn-oxide laterite ore worldwide, mined by Eramet-Comilog. The aim of this this work is to determine formation conditions of this protore and to characterize the global sedimentary evolution of the FB Formation which include the protore. This 75 m thick protore is constituted of Mn carbonate-rich black shales which represent a potential ore deposit for the future. It was drilled, on the Bangombé plateau, during a recent campaign of 24 boreholes with an average depth of 125 m.Through multidisciplinary study on these cores and key outcrops of the basin, this work focuses on : i) the depositional environment of the Mn-protore and FB Formation ; ii) the processes of formation of the Mn-carbonates at 2.1 Ga and iii) the architecture and distribution of Mn-rich levels of the protore on the Bangombé Plateau.A detailed sedimentological and petrological study allowed us to redefine the division of the FB into nine units, named U1 to U9 from the base to the top. These units show a fine upward cycle up to U5 and a reverse coarse loop until U9. This division leads to a new interpretation to propose an evolution from a shoreface depositional environment controlled by deltaic currents (U1) to an offshore depositional environment with anoxic conditions (U2). In this basin, a system of submarine fan is developed, feeding a network of sand injections (injectites) covering the Bangombé plateau (70 km²) and with a thickness of 150 m affecting U4 to U7, including the Mn-protore. The protore depositional environment formed below the wave base limit (U4, U5 and U6) in a starved basin, controlled by biochemical sedimentation allowed the formation of Mn-carbonates. The end of starved basin, would allow the re-opening of the detrital input into the offshore basin (U7). This basin is then filled by storm bar deposits intersected by deltaic sub-aquatic channels (U8). The U9 unit corresponds to a quiet lagoon environment, allowing the multicellular organism development for the first time on the planet.A geochemical study allowed the characterization of the depositional environment of Mn-carbonates as an anoxic to sub-oxic and alkaline environment. For the first time, we showed that the manganese carbonates, present as bacteriomorph forms, are precipitated from the seawater by the mediated photosynthetic cyanobacterial activity, which allows CO2 / HCO3 depression of the environment and a local increase of pH. The cyanobacterial activity is controlled by the absence of bottom currents, which increase the detrital input. This would stop the activity of the cyanobacteria and thus would lead to the decrease of the Mn-concentration along the protore.Finally, well-log and a sequential correlation analyses allowed us to detail spatial and timing repartition of FB Formation deposit, controlled by a tectono-sedimentary model. We propose two- tectono-sedimentary phases. A first syn-tectonic phase (U1 to U3) controls the depocentres and sedimentation gaps. Turbidite coarse deposits are located in the most subsident part, clay deposits rather on the slope and carbonates on shoals. A second post-tectonic phase (U4 to U7) allows isopach deposits. The Mn-protore formed during the post-tectonic phase. However, it shows a variable thickness due to subsidence to the north of the Bangombé plateau. So, on the Bangombé plateau, Mn-contents increase towards the south, whereas the protore thickness increases towards the NNE. Moreover sand injectites decrease Mn-content in the eastern part of the Bangombé plateau and impact on the economic evaluation of the Mn-carbonates. Currently, the protore is structured by post-sedimentary faults, which lead to a non-continuity of the high Mn levels on the Bangombé plateau.
Le Bassin de Franceville situé au SE du Gabon présente une série de black shales (Formation FB) d'âge Paléoprotérozoïque (2,1 Ga) surmontant les grès de la Formation FA. Ce bassin peu déformé et non métamorphique représente une archive exceptionnelle des processus de dépôt de cette période de l’histoire de la Terre où la vie commence à se développer. En particulier, la Formation FB contient le protore d'un gisement mondial d'oxydes de manganèse exploité par la société Eramet-Comilog. L’objectif de ce travail est de préciser les conditions de formation de ce protore et de le replacer dans l’histoire du remplissage du bassin. Ce protore d'une épaisseur moyenne de 75 m est constitué de carbonates de manganèse ; il a fait l'objet d'une récente campagne de 24 forages carottés d'une profondeur moyenne de 125 m sur le plateau de Bangombé.A travers une approche pluridisciplinaire comprenant l'étude de ces forages et des affleurements clefs du bassin, ce travail porte sur la caractérisation i) de l'environnement de dépôt du protore et des séries qui l'encadrent (du toit du FA au toit du FB) ; ii) du mode de formation des carbonates de Mn à 2,1 Ga et iii) de l'architecture et de la répartition des hautes teneurs en Mn du protore qui représente un gisement potentiel du futur.L’étude pétro-sédimentaire détaillée a permis de distinguer neuf unités (U1 à U9) au sein de la Formation FB organisées suivant un cycle rétrogradant jusqu’à U5 puis progradant jusqu’à U9. Ce découpage montre une évolution du milieu de dépôt depuis un domaine de shoreface contrôlé par des courants deltaïques (U1) évoluant vers des dépôts d’offshore restreint (U2). Ce bassin enregistre ensuite un système de chenaux-levées turbiditiques (U3) qui alimentent un réseau d'injectites reconnu sur l’ensemble du Pl. de Bangombé et qui traverse 150 m de série (U4 à U7) en affectant le protore et ainsi les teneurs en Mn. L'environnement de dépôt du protore (U5 et U6) marque l’isolement du bassin qui devient affamé et contrôlé par une sédimentation biochimique à l’origine du dépôt des carbonates de Mn. L'Unité 7 correspond à la réouverture des apports détritiques en domaine d'offshore supérieur puis en domaine de shoreface dominé par des dépôts de tempêtes et de chenaux sous-aquatiques deltaïques (U8), et enfin lagunaire (U9) dans lequel apparaissent les premiers métazoaires de l’histoire de la planète, suivant une séquence régressive.Une étude géochimique a permis de préciser les conditions de dépôt du protore qui se forme en milieu alcalin anoxique à sub-oxique. Dans ce milieu, nous montrons pour la première fois une précipitation directe des carbonates de Mn sous forme bactériomorphe induite par l'activité photosynthétique des cyanobactéries qui consomment le CO2/HCO3 et conduisent à une augmentation du pH favorable à la formation des carbonates de Mn. L'activité cyanobactérienne est conditionnée par l’absence de courants de fond qui augmentent la turbidité du milieu et stoppent cette dernière.Les corrélations diagraphiques et séquentielles permettent de préciser la répartition spatiale et temporelle du FB permettant ainsi de replacer le protore dans l’histoire tectono-sédimentaire du bassin. Une première phase syn-tectonique (U1 à U3) contrôle l’épaisseur et la mise en place de dépôts turbiditiques dans les parties subsidentes, de dépôts argileux sur les pentes et de dépôt de carbonates sur les hauts-fonds. La seconde phase post tectonique (U4 à U7) permet la mise en place de dépôts relativement isopaques, bien que le protore enregistre une subsidence plus importante au nord du Pl. de Bangombé. On observe ainsi, sur le Plateau de Bangombé, des teneurs en Mn qui augmentent vers le sud alors que l’épaisseur du protore augmente vers le NNE. Postérieurement au dépôt du FB, le protore est structuré par des failles qui le compartimentent en touches de piano limitant ainsi sa continuité sur le Plateau de Bangombé.
https://hal.archives-ouvertes.fr/tel-01621460

tel-01621460
https://hal.archives-ouvertes.fr/tel-01621460
https://hal.archives-ouvertes.fr/tel-01621460/document
https://hal.archives-ouvertes.fr/tel-01621460/file/these_Dubois2017-MnGabon.pdf

Éditeur(s) : HAL CCSD
Résumé : The present study addresses the question of increasing need in water supply. One line of research consists in investigating karst aquifers that represent significant water supplies for the areas around the Mediterranean. This work aims at developing a methodology of predictive evaluation of karst distribution and karst thickness within the carbonate massifs. It is based on the study of the Tethysian carbonate platform from the area of Montpellier, South of France. This area underwent a polyphased, complex, tectonic evolution, involving successive karst forming events. The approach is based on the relationships between eustacy and geodynamics, on one hand, and base-level variation recorded within palaeokarsts, on the other hand. Sedimentary fill of palaeokarsts allows to identify distinct karstification phases and sometimes to date them. It is a marker of base-level variations, which we attempt to quantify, that is responsible for karst formation and karst filling and sealing. For three palaeokarsts of regional extent, we analyze : karst sedimentary-fill, the distribution along upstream-downstream profile, the vertical extension of palaeokarsts, indicative of the base-level lowering. - The " Bauxite palaeokarst " results from the two-stage evolution of the " Isthme Durancien " : i) Bauxitic weathering of the Neocomian cover over the southern Massif Central , related to an inversion during Barremian ; ii) ≥1600 m uplift and exhumation during Aptian-Albian, inducing erosion of alterites, upstream, and deposition of detrital bauxites, downstream. - The " Early Paleocene palaeokarsts with marine sedimentary-fill " indicate base level variations of more than 350m in the upstream area. It is suggested here that such base-level variations, exceeding eustacy and recorded in tabular undeformed series, result from desiccation-flooding events in an endoreic silled basin. - The " Miocene palaeokarst with Cevennes-sourced sediment-fill " records a Serravalian-Tortonian base-level drop, depicted by canyon incision in the hinterland of the Gulf of Lion Margin. Uplift values of ≥ 400m upstream, about 250m in an intermediate area and 10's of m downstream, are measured. The present 3D geometry and distribution of carbonate massifs (exposed and covered) are modeled in the study area, from the Cevennes to the Mediterranean. The 3D geological model integrates seismic reflection, borehole and gravimetric data. Tectonic restoration of a N-S section, extracted from the 3D model, allows to reconstruct paleo-base-levels with respect with the carbonate massifs, at different stages of deformation and successive phases of karstification. The 3D paleo-flows through carbonates across the study area, are thus constrained, especially during the Messinian desiccation stage. Application of the results to hydrogeology leads to the following : - Uplift of upstream hinterland (Cretaceous, Miocene) produces large amplitude karsts, but they do not make significant reservoirs. - Karstification responsible for the development of important and deep karst reservoirs is related to desiccation of endoreic basins (early Paleocene and Messinian). - Theses two events have produced two main deep karst reservoirs, with a gravimetric signature : (1) Upstream of Montpellier Thrust, between Pic St Loup, Les Matelles Fault and Hérault Basin, a deep karsts developed over 900m thickness in the Malm limestone, during Paleocene. (2) Downstream (south) of Montpellier Thrust, the coastal karsts extend offshore over more than 10km, they are sealed by a thick Miocene to Quaternary cover, and they result from the Messinian event.
Cette étude s'inscrit dans un contexte de demande croissante en ressources en eau, conduisant à mieux contraindre et estimer la distribution des aquifères karstifiés qui représentent une ressource importante, notamment sur le pourtour méditerranéen. Le but de ce travail est d'élaborer une méthode prédictive de la distribution de la karstification et de l'épaisseur de massifs carbonatés karstifiés, notamment pour les karsts profonds. La méthodologie est développée à partir de l'étude des karsts de la plateforme carbonatée téthysienne du Languedoc montpelliérain; région qui a subi une histoire tectonique complexe et polyphasée, entrainant des phases de karstification successives. Elle est basée sur la compréhension des relations entre eustatisme, géodynamique et niveau de base, enregistrées par les paléokarsts de la région. Le remplissage sédimentaire des paléokarsts permet d'identifier les épisodes de karstification et de les dater ; c'est un marqueur des variations -que l'on cherche à quantifier- du niveau de base local responsable de la formation et du comblement des karsts. On analyse 3 paléokarsts d'extension régionale dont on peut étudier : le remplissage karstique, la distribution le long de profils amont-aval et l'extension verticale indicatrice de l'amplitude de l'abaissement du niveau de base dont il est issu. On en déduit les causes géodynamiques à l'origine de leur formation: - Le " paléokarst des bauxites " à remplissage caractéristique, résulte de l'évolution en 2 phases de " l'Isthme Durancien " : altération bauxitique de la couverture néocomienne sur le sud du Massif Central, liée à une inversion au Barrémien, suivi d'une surrection ≥ 1600m à l'Aptien-Albien, causant l'érosion des altérites en amont et le dépôt des bauxites détritiques en aval. - Le " paléokarst à remplissage marin paléocène inférieur " indique des variations du niveau de base local ≥350m dans la zone amont sud-cévenole. On propose que ces variations de niveau de base d'amplitude très supérieures aux variations eustatiques et dans une zone faiblement déformée, résultent d'assèchements et d'ennoiements d'un bassin endoréique à seuil. - Le " paléokarst à remplissage détritique d'origine cévenole ", enregistre la chute du niveau de base au Serravalien-Tortonien, qui se traduit par l'incision de canyons dans l'arrière-pays de la marge du Golfe du Lion. On détermine une surrection de plus de 400 mètres à l'amont, près de 250m dans les blocs faillés intermédiaires et quelques dizaines de mètres dans la zone avale. En parallèle, on établit la géométrie et la distribution actuelles des massifs carbonatés dans la zone d'étude (y compris sous couverture), en construisant un modèle géologique 3D, des Cévennes à la Méditerranée. On intègre les données de sismique réflexion, de forages et les données gravimétriques. La restauration tectonique séquentielle d'une coupe Nord-Sud extraite du modèle géologique permet d'appréhender la position des paléo-niveaux de base par rapport aux massifs carbonatés, pour chaque époque de karstification. On déduit l'organisation 3D des paléo-écoulements à travers la géométrie complexe des massifs carbonatés languedociens, notamment pendant l'évènement messinien. En terme d'évaluation de la ressource en eau, on déduit que: - Les surrections de l'arrière-pays (Crétacé " moyen ", Miocène) produisent des karsts de grande amplitude, mais ne constituent pas de réservoirs significatifs. - La karstification à l'origine de réservoirs exploitables importants et profonds est créée par l'assèchement de bassins endoréiques, qui ont affecté la région au Paléocène inférieur et au Messinien . - Ces deux évènements sont à l'origine de deux principaux réservoirs karstiques profonds qui ont une signature gravimétrique : (1) En amont du chevauchement de Montpellier, entre le Pic Saint Loup, la faille des Matelles et le bassin de l'Hérault, le karst profond se développe sur une épaisseur atteignant 900m, et est attribuée à l'événement du Paléocène. (2) Au Sud du chevauchement de Montpellier les karsts côtiers s'étendent jusqu'à plus de 10 km au large, scellés par une épaisse couverture Miocène et Plio-Quaternaire, et résultent de l'événement Messinien.
https://tel.archives-ouvertes.fr/tel-00936257

tel-00936257
https://tel.archives-ouvertes.fr/tel-00936257
https://tel.archives-ouvertes.fr/tel-00936257/document
https://tel.archives-ouvertes.fr/tel-00936257/file/thA_se_husson_couleurs.pdf

Résumé : Les stocks des éléments dans les sols, et en particulier ceux du carbone, sont en constante évolution sous l’effet de facteurs naturels (climat, végétation, teneurs en argiles, etc.) et anthropiques (usages des sols, etc.). Notre objectif est donc, (i) de mieux comprendre les relations entre type de sol, système de culture et quantité de carbone stockée, (ii) d’étudier les conséquences des changements d’usage et de gestion des terres sur les formes de matière organique dans les sols et (iii) de préciser le rôle de la matière organique sur les propriétés physiques des sols.Des situations agro-pédologiques représentatives des trois grands modèles minéralogiques des sols tropicaux (Sols à allophanes (argiles non cristallisées), Sols à argiles 1/1 et Sols à argiles 2/1) et présentant des systèmes culturaux de différents niveaux d’intensification (monocultures intensives destinées à l’exportation, systèmes paysans faiblement intensifiés, etc.) ont ainsi été sélectionnées sur les sols de Martinique. Par ailleurs, afin de limiter les effets des usages antérieurs des parcelles, nous avons généralement choisi des situations culturales âgées au minimum de 3 ans.L’analyse des stocks de carbone des différentes parcelles fait apparaître des comportements différents : dans les sols à allophanes, il y a un effet de la minéralogie sur la stabilisation des matières organiques ; dans les sols à argiles cristallisées, il existe une corrélation entre la teneur en carbone (ou le stock organique) et la texture (ou teneur en éléments fins), aussi bien pour les situations non cultivées que pour les situations sous cultures. L’amplitude des variations (diminution) des stocks en carbone observées sous l’effet de différents modes de gestion des sols, dépend elle aussi de la texture : dans les sols sableux, la potentialité de séquestration du carbone est faible ou nulle, en revanche, les potentialités de stockage du carbone sont plus fortes dans les sols argileux.L’estimation des stocks totaux de carbone à l’échelle de la Martinique, pour un mètre de profondeur et pour une situation moyenne entre les cartes d’usage des terres de 1969/1970 et 1979/1980, s’élèvent à 11,859 Mt de C calculés pour 95,8% de la surface.La distribution de la matière organique du sol varie avec la texture du sol : dans les sols sableux, à faibles teneurs en matière organique, les matières organiques sont principalement associées aux fractions sableuses ; dans les sols argileux, plus riches en matières organiques, 50 à 60 % de la matière organique sont associées à la fraction argileuse. De même, la dynamique de la matière organique dépend également de la texture du sol : dans les sols sableux, les variations des stocks organiques sont essentiellement dues à la perte ou à l’accumulation en carbone de la fraction sableuse ; dans les sols argileux, la fraction argileuse participe de manière prépondérante aux variations des stocks organiques de ces sols lors de leur mise en culture ou en prairie ; les sols sablo-argileux ont un comportement intermédiaire entre ces deux pôles.La stabilité structurale varie avec la minéralogie. Les andosols (ou ALL) présentent un haut degré d’agrégation et de stabilité, du à la présence d’allophanes et à leur association particulière avec les composés organiques. Dans les sols à argiles cristallisées, la stabilité de l’agrégation est plus élevée dans les sols à argiles 1/1 (ou LAC) ; les valeurs les plus faibles sont généralement observées dans les parcelles sur sols à argiles 2/1 (ou HAC). En outre, la mise en culture se traduit généralement par une diminution de la stabilité de l’agrégation.L’intensification des cultures (labours fréquents, faibles restitutions de matière organique au sol, etc.) accentue la perte de la stabilité de l’agrégation provoquée par la mise en culture, en particulier dans les parcelles sur sols à argiles 2/1 (ou HAC).
Soils elements stocks, and particularly those of carbon, are in constant evolution under natural factors effect (climate, vegetation, clays content, etc) and anthropic factors effect (soils uses, etc). Our objective is thus, (i) to better understand the relations between soil, farming system and stored carbon quantity, (ii) to study the consequences of soils uses changes and of soils managements changes on organic matter shapes in soil and (iii) to specify organic matter role on soil properties physics.Representative agri-pedological situations of the three great mineralogical models of tropical soils (allophonic soils (not crystallized clays), 1:1 clay soils and 2:1 clay soils) and presenting agricultural systems of various levels of intensification (intensive monocultures intended for export, slightly intensified farming systems, etc) were thus selected in the soils of Martinique. In addition, to limit the effects of their former uses, we generally chose to the minimum 3 years old farming situations.The analysis of the various lands carbon stocks reveals different behaviors: in allophonic soils, a correlation exists between carbon content (or organic stock) and texture (or fine elements content), as well for not cultivated as for cultivated situations. Variations ranges (reduction) of carbon stocks observed under various management soils systems effect, also depends on texture: in sandy soils, carbon sequestration potentiality is low or null, on the other hand, carbon storage potentialities are higher in clay soils.The estimation of total carbon stocks on the scale of Martinique, for one meter of depth and for and average situation between the use soils charts of 1969/70 and 1979/80, rises to 11,859 Mt of C calculated for 95,8% of the surface.Soil organic matter distribution varies with soil texture: in sandy soils, with low contents of organic matter, organics matters are mainly associated with the sandy fractions; in clay soils, richer in organic matters, 50 to 60% of the organic matters are associated with the argillaceous fraction. In the same way, the organic matter dynamics also depends on soil texture: in sandy soils, organic stocks variations are primarily due to carbon loss or accumulation of the sandy fraction; in clay soils, the argillaceous fraction takes part in a dominating way in organic stocks variations of these soils at the time of their setting in culture or meadow; the sand-clay soils have an intermediate behavior between these two poles.Structural stability varies with mineralogy. Andosols (or ALL) present a high degree of aggregation and stability, due to the presence of allophones and their particular association with the organics compounds. In crystallized clay soils, aggregation stability is higher in 1:1 clay soils (or LAC); the lowest values are generally observed in the lands on 2:1 clay soils (or HAC). Moreover, culture setting generally results in aggregation stability reduction.Cultures intensification (frequent ploughings, low organic matter restitutions to the soil, etc) accentuates aggregation stability loss caused by culture setting, particularly in lands on 2:1 clay soils (or HAC).

http://www.theses.fr/2012AGUY0513/document

Éditeur(s) : Public Library Science
Résumé : Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.
Plos One (1932-6203) (Public Library Science), 2014-08 , Vol. 9 , N. 8 , P. e104427

Droits : This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
http://archimer.ifremer.fr/doc/00203/31408/29801.pdf
DOI:10.1371/journal.pone.0104427
http://archimer.ifremer.fr/doc/00203/31408/

Éditeur(s) : HAL CCSD
Résumé : During the course of their life cycle organisms are exposed to natural environment variations capable of inducing physiological, morphological and behaviour changes, thus a phenotypic plasticity. Phenotypic plasticity is the ability of a genotype to generate a new phenotype following exogeneous or endogeneous stress. Here, we investigated the phenotypic plasticity of the non-calcifying symbiotic cnidarian Anemonia viridis at multiple levels of structural complexity, in vivo and in vitro. In vivo, we determined the mechanisms behind the phenotypic plasticity under expected future climate change (i.e. ocean acidification and ocean warming). Our results show physiological changes in the inorganic carbon use of the sea anemone A. viridis exposed to high pCO2 during a long-term stress in natura or a short-term stress in controlled conditions. We then observed an equivalent decrease in carbonic anhydrase activity, a key enzyme of cnidarian carbon concentrating mechanisms. Also, we demonstrated that an increase in seawater temperature modified the response observed during a high pCO2 scenario. In vitro, we established a viable primary cell culture from regenerating tentacles of A. viridis. We determined the gastrodermal tissue origin of the cultivated cells and validated the use of this new tool to the in vitro study of stress response at the cellular level. The set-up of this powerful in vitro tool will open a multitude of perspectives for the study of cellular responses to exogeneous stress (as global change perturbations) and to endogeneous stress (as the symbiosis constraints experienced by symbiotic cnidarians)
Durant leur cycle de vie, les organismes sont exposés à des variations environnementales capables d'induire des changements physiologiques, morphologiques et comportementaux, résultant d’une plasticité phénotypique. La plasticité phénotypique est la capacité d'un génotype à générer un nouveau phénotype suite à un stress. Ici, nous avons étudié la plasticité phénotypique d’un Cnidaire symbiotique et non-calcifiant, l’anémone de mer Anemonia viridis, à de multiples niveaux de complexité structurale, in vivo et in vitro. In vivo, nous avons identifié les mécanismes sous-jacents de la plasticité phénotypique potentiellement induits par les futurs changements climatiques (acidification et réchauffement des océans). Nos résultats montrent des modifications dans l'utilisation du carbone inorganique par A. viridis exposée à une forte pCO2 lors d’un stress chronique in natura ou lors d’un stress court en conditions contrôlées. Nous avons ainsi observé une diminution des activités anhydrase carbonique, une enzyme clé des mécanismes de concentration du carbone chez les Cnidaires. Nous avons aussi démontré que l'augmentation concomittante de la température modifie la réponse observée lors d'une élévation seule de la pCO2. In vitro, nous avons établi une culture de cellules primaires viables issue de tentacules d’A. viridis en régénération. Nous avons déterminé l'origine gastrodermale des cellules cultivées et validé l'utilisation de ce nouvel outil pour l'étude de la réponse au stress au niveau cellulaire. Ce nouvel outil ouvre une multitude de perspectives pour l'étude des réponses cellulaires aux stress exogènes (changement climatique) et endogènes (contraintes dues à la symbiose)
https://tel.archives-ouvertes.fr/tel-01674220

Droits : info:eu-repo/semantics/OpenAccess
NNT : 2016AZUR4136
tel-01674220
https://tel.archives-ouvertes.fr/tel-01674220
https://tel.archives-ouvertes.fr/tel-01674220/document
https://tel.archives-ouvertes.fr/tel-01674220/file/2016AZUR4136.pdf

Éditeur(s) : HAL CCSD IWA Publishing
Résumé : International audience
UV spectrophotometry is largely used for water and wastewater quality monitoring. The measurement/estimation of specific and aggregate parameters such as nitrate and dissolved organic carbon (DOC) is possible with UV spectra exploitation, from 2 to multi wavelengths calibration. However, if nitrate determination from UV absorbance is known, major optical interferences linked to the presence of suspended solids, colloids or dissolved organic matter limit the relevance of UV measurement for DOC assessment. A new method based on UV spectrophotometric measurement of raw samples (without filtration) coupling a dual pathlength for spectra acquisition and the second derivative exploitation of the signal is proposed in this work. The determination of nitrate concentration is carried out from the second derivative of the absorbance at 226 nm corresponding at the inflexion point of nitrate signal decrease. A short optical pathlength can be used considering the strong absorption of nitrate ion around 210 nm. For DOC concentration determination the second derivative absorbance at 295 nm is proposed after nitrate correction. Organic matter absorbing slightly in the 270-330 nm window, a long optical pathlength must be selected in order to increase the sensitivity. The method was tested on several hundred of samples from small rivers of two agricultural watersheds located in Brittany, France, taken during dry and wet periods. The comparison between the proposed method and the standardised procedures for nitrate and DOC measurement gave a good adjustment for both parameters for ranges of 2-100 mg/L NO3 and 1 30 mg/L DOC. (C) 2016 Elsevier Ltd. All rights reserved.
ISSN: 0043-1354

hal-01460742
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01460742
DOI : 10.1016/j.watres.2016.11.010
PUBMED : 27838025

Éditeur(s) : HAL CCSD European Geosciences Union (EGU)
Résumé :  
The production of aboveground soft tissue represents an important share of total net primary production in tropical rain forests. Here we draw from a large number of published and unpublished datasets (n = 81 sites) to assess the determinants of litterfall variation across South American tropical forests. We show that across old-growth tropical rainforests, litterfall averages 8.61±1.91Mgha−1 yr−1 (mean±standard deviation, in dry mass units). Secondary forests have a lower annual litterfall than old-growth tropical forests with a mean of 8.01±3.41Mgha−1 yr−1. Annual litterfall shows no significant variation with total annual rainfall, either globally or within forest types. It does not vary consistently with soil type, except in the poorest soils (white sand soils), where litterfall is significantly lower than in other soil types (5.42±1.91Mgha−1 yr−1). We also study the determinants of litterfall seasonality, and find that it does not depend on annual rainfall or on soil type. However, litterfall seasonality is significantly positively correlated with rainfall seasonality. Finally, we assess how much carbon is stored in reproductive organs relative to photosynthetic organs. Mean leaf fall is 5.74±1.83Mgha−1 yr−1 (71% of total litterfall). Mean allocation into reproductive organs is 0.69±0.40Mgha−1 yr−1 (9% of total litterfall). The investment into reproductive organs divided by leaf litterfall increases with soil fertility, suggesting that on poor soils, the allocation to photosynthetic organs is prioritized over that to reproduction. Finally, we discuss the ecological and biogeochemical implications of these results.
Biogeosciences

hal-01032140
https://hal.archives-ouvertes.fr/hal-01032140
DOI : 10.5194/bg-7-43-2010

Éditeur(s) : Inter-research
Résumé : Environmental conditions experienced by aquatic organisms are archived in biogenic carbonates such as fish otoliths, bivalve shells and coral skeletons. These calcified structures present an accretionary growth and variations in optical properties - color or opacity - that are used to reconstruct time. Full and reliable exploitation of the information extracted from these structures is, however, often limited as the metabolic processes that control their growth and their optical properties are poorly understood. Here, we propose a new modeling framework that couples both the growth of a biogenic carbonate and its optical properties with the metabolism of the organism. The model relies on well-tested properties of Dynamic Energy Budget (DEB) theory. It is applied to otoliths of the Bay of Biscay anchovy (Engraulis encrasicolus) for which a DEB model has been previously developed. The model reproduces well-known otolith patterns and thus provides us with mechanisms for the metabolic control of otolith size and opacity at the scale of an individual lifespan. Two original contributions using this framework are demonstrated. First, the model can be used to reconstruct the temporal variations in the food assimilated by an individual fish. Reconstructing food conditions of past and present aquatic species in their natural environment is key ecological information to better understand population dynamics. Second, we show that non-seasonal checks can be discriminated from seasonal checks, which is a well-recognized problem when interpreting fish otoliths. We discuss further developments of the model and the experimental settings required to test this new promising framework.
Marine Ecology-progress Series (0171-8630) (Inter-research), 2012 , Vol. 447 , P. 151-164

Droits : 2012 Inter-Research
http://archimer.ifremer.fr/doc/00060/17082/14593.pdf
DOI:10.3354/meps09492
http://archimer.ifremer.fr/doc/00060/17082/

Éditeur(s) : HAL CCSD
Résumé : Eight drill cores cutting through the Mn-carbonate bearing black shales from the Bangombé Plateau were studied. Mn-carbonates (up to 80 m thick) are underlain by laminated pyrite rich shales with organic carbon contents of about 4 wt. % and MnO contents of about 6 wt. %. Mn and Fe, S poor shales are intercalated. Mn-carbonate rich shales (20-29 wt. % MnO) have low contents of phyllosilicates, but are rich in organic carbon (about 7 wt. %) with moderate S contents (about 2 wt. %). All shale facies were deposited in a closed basin through suspension settling and precipitations under anoxic conditions. The Mn-carbonates, towards the top, were formed most likely under suboxic conditions. Pyrite and Mn-carbonates are characterized by bacteriomorphous structures. The latter are composed of micrometric carbonates finely intergrown with clays, quartz and organic matter. They formed around and corroded the dolomite and/or organic matter. Mn-carbonates and pyrite both form also several tenths of micrometer large agglomerates and sub-automorphous grains. The agglomerates can be attributed to evolving diagenesis. Carbonate chemistry varies mainly from rhodochrosite to dolomite. The present results point to primary microbial Mn-carbonate formation. No signs for a Mn-oxide precursor were detected. Slumping and shearing structures, distortion and disruption of thin pyrite beds indicate synsedimentary deformations.
13th Biennial SGA Meeting
Nancy, France

hal-01356155
https://hal.archives-ouvertes.fr/hal-01356155

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 Springer Verlag
Résumé : International audience
The New Jersey continental shelf extends 150 km off the shoreline. During IODP Expedition 313, siliciclastic deposits of late Eocene to late Pleistocene age were drilled down to 631, 669 and 755 m below seafloor at sites 27A, 28A and 29A respectively in very shallow waters (33.5 to 36 m depth). Pore water salinities display multilayered brackish-salty-brine units 10 to 170 m thick, where low-salinity water is preferentially stored in fine-grained sediments. The sharp boundaries of these buried aquifers are often marked by cemented layers a few centimetres thick. The mineralogy and scanning electron microscope observations of these layers show two phases of cementation by authigenic minerals: (1) the early carbonate cement is frequently associated with pyrite, and (2) the late silicate cement infills the residual porosity. The isotopic compositions of the carbonate cements vary widely: −2.4 < δ¹⁸O ‰ VPDB < +2.8; −15.1 < δ¹³C ‰ VPDB < +15.6. The δ¹⁸O values indicate that the carbonate cements precipitated with pore waters comprising variable mixtures of seawater and ¹⁸O-depleted fresh water originating from submarine groundwater discharge. The δ¹³C values of the carbonate cements are related to organic matter diagenesis, providing ¹³C-depleted dissolved inorganic carbon during bacterial sulphate reduction and anaerobic oxidation of methane, and ¹³C-rich dissolved inorganic carbon during methanogenesis. The diagenetic cementation processes included chemical weathering of reactive silicate minerals by the CO²-rich pore waters issued from organic matter diagenesis that released bicarbonate, cations and dissolved silica, which were further precipitated as carbonate and silicate cements. The estimated range of temperature (18±4 °C) during carbonate precipitation is consistent with carbonate cementation at moderate burial depths; however, silicate cementation occurred later during diagenesis at deeper burial depths.
ISSN: 0276-0460

hal-01559985
https://hal.archives-ouvertes.fr/hal-01559985
DOI : 10.1007/s00367-017-0506-6

Éditeur(s) : Gauthier-Villars
Résumé : Samples of recent sediments and marine organisms from seven coastal lagoons along the Mexican coast of the Gulf of Mexico were analyzed by gas chromatography and GC-MS coupled system to determine the present levels of fossil hydrocarbons. Results show that the highest concentrations of fossil hydrocarbons are present in organisms and sediments located near petrochemical plants and oil refineries, indicating that petroleum hydrocarbons are being released into the coastal lagoons. Stable carbon isotope ratios (12C/13C) of sedimentary organic carbon in sediment and organism samples were also determined. For most of the lagoons, the delta 13C ratios for sediments ranged from -19.0 to -23.9%, anomalous ratios ranging from -26.8 to -29.3% were shown for sediments and organisms (oysters) of two of the studied areas, probably because of the presence of organic carbon from anthropogenic terrestrial sources.
Oceanologica Acta, Special issue (0399-1784) (Gauthier-Villars), 1982

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00246/35713/34222.pdf
http://archimer.ifremer.fr/doc/00246/35713/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
PurposeMarine mangrove sediments in the Manche-à-Eau lagoon (Guadeloupe, Caribbean Sea) harbor locally extensive, white microbial mats. These mats cover the surface of reduced sediments near the roots of red mangrove trees, Rhizophora mangle, and are mainly composed of sulfur-oxidizing bacteria belonging to the Beggiatoaceae family, with some filamentous cyanobacteria. The goal of this study was to investigate the possible influence of sediment characteristics on the presence of these microbial mats.Materials and methodsFour push cores were collected in April 2013, two from zones with microbial mats and two from zones without mats. Sediment characteristics (grain-size distribution, mineralogy, total organic carbon (TOC) and total nitrogen (TN) contents, atomic TOC/TN ratios, and organic matter (OM) δ13C values) were compared for all four cores.Results and discussionSignificant differences were observed between sediments below microbial mats and those without mats. Sediments with microbial mats contained greater amounts of clay, and higher TOC, TN, and TOC/TN ratios, with lower total carbonate content and δ13C values. The higher clay content most likely results from lower fluid flow velocity near to mangrove roots, while higher TOC/TN ratios and lower δ13C values indicate higher inputs of OM from mangrove trees. These results are consistent with the fact that microbial mats were observed near the roots of mangrove trees, which trap OM from terrestrial vegetation and fine sediments.ConclusionsThe grain-size distribution of sediment particles, the total carbonate content, and the δ13C values are the main parameters discriminating between zones with microbial mats and those without mats. Variations in total carbonate content, which is mainly of biogenic origin, result from conditions that are more favorable for benthic organisms in zones without microbial mats. Variations of the TOC/TN ratios are controlled by the presence of a non-negligible amount of inorganic nitrogen bound to surface clay mineral particles and/or by microbial processes.
ISSN: 1439-0108

hal-01545903
https://hal.archives-ouvertes.fr/hal-01545903
DOI : 10.1007/s11368-016-1555-6

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
We assessed the occurrence of algae in five species of tank-bromeliads found in contrasting environmental sites in a Neotropical, primary rainforest around the Nouragues Research Station, French Guiana. The distributions of both algal abundance and biomass were examined based on physical parameters, the morphological characteristics of bromeliad species and with regard to the structure of other aquatic microbial communities held in the tanks. Algae were retrieved in all of the bromeliad species with mean densities ranging from ∼10(2) to 10(4) cells/mL. Their biomass was positively correlated to light exposure and bacterial biomass. Algae represented a tiny component of the detrital food web in shaded bromeliads but accounted for up to 30 percent of the living microbial carbon in the tanks of Catopsis berteroniana, located in a highly exposed area. Thus, while nutrient supplies are believed to originate from wind-borne particles and trapped insects (i.e., allochtonous organic matter), our results indicate that primary producers (i.e., autochtonous organic matter) are present in this insectivorous bromeliad. Using a 24-h incubation of size-fractionated and manipulated samples from this plant, we evaluated the impact of mosquito foraging on algae, other microorganisms and rotifers. The prey assemblages were greatly altered by the predation of mosquito larvae. Grazing losses indicated that the dominant algal taxon, Bumilleriopsis sp., like protozoa and rotifers, is a significant part of the diet of mosquito larvae. We conclude that algae are a relevant functional community of the aquatic food web in C. berteroniana and might form the basis of a complementary non-detrital food web.
ISSN: 1932-6203

hal-00819161
https://hal.archives-ouvertes.fr/hal-00819161
https://hal.archives-ouvertes.fr/hal-00819161/document
https://hal.archives-ouvertes.fr/hal-00819161/file/Brouard2011_AreAlgae.pdf
DOI : 10.1371/journal.pone.0020129

Éditeur(s) : HAL CCSD
Résumé : International audience
Symbiosis is a widespread phenomenon in the biosphere. In marine benthic environments breakdown of symbiosis is responsible for coral bleaching and dramatically affects coral reef ecosystems functioning [1]. In the water column, planktonic organisms are key component of pelagic ecosystems and a number of species form mutualistic association with microalgae forming a photosymbiosis [2]. Here we intended to investigate the genetic basis of photosymbiosis, through a transcriptomic approach on marine plankton organisms. We focused more specifically on associations occurring between radiolarian host (protist, zooplankton) and dinoflagellates symbiont (protist, phytoplankton) living inside the host cell. It has recently been highlighted that these holobionts are widespread in oligotrophic open oceans and there are also evidences of their fundamental implication in biogeochemical carbon, silica and strontium cycles [3, 4, 5, 6]. RNA-seq technologies allow obtaining an unprecedented amount of data for unicellular organisms isolated from the environment [7]. The study of such non-model holobionts datasets requires de novo assembly, which implies considerable computational resources and the potential production of chimeric sequences [8, 9].We therefore developed an original strategy aiming at accelerating and improving de novo assembly for holobiont datasets. We chose SIMKA [10] a fast kmer-based method initially developed to estimate the similarity between numerous metagenomic datasets, and which has been recently adapted to extract their common sequences. As our symbionts are identified, we used SIMKA to compare our holobionts transcriptomes to publicly available dinoflagellates transcriptomes [11] generating two datasets, one composed of reads from the symbionts and another with reads from the host (for which no reference data are currently available). Independent assemblies were then performed in parallel, accelerating the study process, and minimizing the proportion of resulting chimeric sequences. Our strategy produced a unique and comprehensive genomic dataset for Radiolaria [12, 13], and offers a pragmatic, large scale, comparison strategy to assemble and study holobionts [9]. Our new sequences obtained from holobionts study will be used for phylogenomics investigation, as reference for environmental metagenomic studies and ultimately to understand and characterize the molecular basis of symbiotic relationships in the plankton.Bibliografic references :[1] Simon K. Davy, Denis Allemand, and Virginia M. Weis. “Cell Biology of Cnidarian-Dinoflagellate Symbiosis”. In: Microbiology and Molecular Biology Reviews 76.2 (June 1, 2012), pp. 229–261. issn: 1092-2172, 1098- 5557. doi: 10.1128/MMBR.05014-11.[2] Janouškovec, J. et al. “Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics”. in: PNAS 201614842 (2016). doi:10.1073/pnas.1614842114[3] Tristan Biard et al. “In situ imaging reveals the biomass of giant protists in the global ocean”. In: Nature advance online publication (Apr. 20, 2016). issn: 0028-0836. doi: 10.1038/nature17652.[4] Lionel Guidi et al. “Plankton networks driving carbon export in the olig- otrophic ocean”. In: Nature 532.7600 (Apr. 28, 2016), pp. 465–470. issn: 0028-0836. doi: 10.1038/nature16942.[5] Diane K. Stoecker et al. “Acquired phototrophy in aquatic protists”. In: Aquatic Microbial Ecology 57.3 (Nov. 24, 2009), pp. 279–310. doi: 10.3354/ame01340.[6] Johan Decelle et al. “An original mode of symbiosis in open ocean plankton”. In: Proceedings of the National Academy of Sciences 109.44 (Oct. 30, 2012), pp. 18000–18005. issn: 0027-8424, 1091-6490. doi: 10. 1073/pnas.1212303109.[7] Sergio Balzano et al. “Transcriptome analyses to investigate symbiotic relationships between marine protists”. In: Frontiers in Microbiology 6 (Mar. 17, 2015). issn: 1664-302X. doi: 10.3389/fmicb.2015.00098.[8] Li, B. et al. “Evaluation of de novo transcriptome assemblies from RNA-Seq data”. In: Genome Biology 15, 553 (2014).[9] Sangwan, N., Xia, F. & Gilbert, J. A. “Recovering complete and draft population genomes from metagenome datasets”. In: Microbiome 4, 8 (2016).[10] Gaëtan Benoit et al. “Multiple comparative metagenomics using mul- tiset k -mer counting”. In: PeerJ Computer Science 2 (Nov. 14, 2016). doi: 10.7717/peerj-cs.94.[11] Patrick J. Keeling et al. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing”. In: PLOS Biol 12.6 (June 2014), e1001889. issn: 1545-7885. doi: 10.1371/journal.pbio.1001889.[12] Burki, F. et al. “Evolution of Rhizaria: new insights from phylogenomic analysis of uncultured protists”. In BMC Evolutionary Biology 10, 377 (2010).
International Conference on Holobionts
Paris, France

hal-01575069
https://hal.inria.fr/hal-01575069

Éditeur(s) : Gauthier-Villars
Résumé : Five particle traps were deployed at depths of 4 400 to 4 900 rn at two stations on the Demerara abyssal plain and one station on the Cape Verde abyssal plain (tropical Atlantic). At the same time, an intensive sampling of superficial sediments was carried out using a 0,25 m2 box corer. The total particle flux varied from 372 to 87,7 mg dry weightfm2/day. The average concentration of organic carbon was 40 mg/g of material collected. ln the surface sediment this was only 4 mg/g. A direct relationship existed between the intensity of the flux of organic matter and the richness of the organic matter of the deposited sediment. According to our calculations, more than 90% of the organic matter arriving at the bottom is consumed by the abyssal benthos and only 1% is lost to permanent sediment deposits. For 100 calories consumed by the benthos, 99 are utilized by the infauna and flora, 0, 7 by the holothurian egafauna and 0,3 by near-bottom fisches. The biochemical composition of the particles is characterized at ali stations by a predominance of "humic" material in the total organic matter (more than 55%). The part of the molecules unaltered form living material varied from on station to another: for the most oceanic station the protein dominated, composing 20% of the total energy. At the station onder the influence of the continent the lipid fraction grew and was almost equal to that of the protein. ln this case, the carbohydrate fraction was very weak (7% of the organic matter). Finally the preference of the animais which feed on the particles is principally for the most energetic (lipid) and the most easily hydrolysable (labile protein) molecules: the other molecules, such as the humic matter, are less preferred, although they still contribute to about half of the energy consumed by the abyssal benthic animais.
Cinq pièges à particules ont été déployés à des profondeurs comprises entre 4400 et 4 900 rn sur deux stations dans la plaine abyssale de Demerara et une station dans la plaine abyssale du Cap Vert (Atlantique tropical). Dans le même temps, un échantillonnage intensif du sédiment superficiel a été réalisé à l'aide d'un carottier de 0,25 m2 d'ouverture. Le flux particulaire total mesuré varie de 372 mg de matière sèche/m2/jour à 87,7 mg/m2/g de matériel récolté. Dans les sédiments superficiels, elle n'est plus que d'environ 4 mg/g. Il existe une relation directe entre l'intensité du flux organique et la richesse en composés organiques du sédiment. D'après nos estimations, plus de 90% du matériel organique arrivant sur le fond sont consommés par les organismes benthiques abyssaux et seulement 1% est perdu dans la sédimentation permanente. Pour 100 calories consommées par le benthos, 99 le sont par la petite faune et la flore vivant dans le sédiment, 0, 7 calories sont utilisées par les holothuries (mégafaune) et 0,3 calories par les poissons. La composition biochimique des particules se caractérise, à toutes les stations, par la prédominance des composés organiques transformées néobiogéniques ( « humus ») dans la matière organique totale (plus de 55%). La part des molécules de la matière vivante varie d'une station à l'autre: à la station la plus océanique, les protéines dominent et composent 200/o de l'énergie totale des apports. Dans la station plus soumise aux influences continentales, la concentration en lipides augmente et peut égaler celle des protéines. Dans ce cas, le taux de glucides des particules est très faible (7% des apports organiques). Enfin, les préférences nutritionnelles des animaux qui s'alimentent sur ces particules se portent principalement sur les molécules les plus énergétiques (lipides) et les plus facilement hydrolysables (protéines labiles) : les autres molécules, comme les composés néobiogéniques sont moins recherchés bien qu'ils contribuent pour moitié à l'énergie consommée par les animaux benthiques abyssaux
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1985 , Vol. 8 , N. 3 , P. 293-301

Droits : Gauthier-Villars
http://archimer.ifremer.fr/doc/00112/22318/19991.pdf
http://archimer.ifremer.fr/doc/00112/22318/