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Verrecchia, Eric
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Verrecchia, Eric
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- PublicationAccès libre
- PublicationAccès libreIdentification of active oxalotrophic bacteria by Bromodeoxyuridine DNA labeling in a microcosm soil experiments(2013)
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- PublicationAccès libreThe impact of oxalogenic plants on soil carbon dynamics: formation of a millennium carbon storage as calcium carbonate(2012)
Les buts de ce travail sont (1) de dresser un bilan de carbone, (2) de modéliser son accumulation et (3) de calculer un temps de résidence du carbone minéral dans le sol sous les arbres. Les échantillons ont été prélevés dans cinq profils à proximité d’arbres oxalogènes et un dans un sol de référence, hors de leur influence. Les teneurs en carbone organique total, en oxalates et en carbonates ont été ensuite mesurées. Les principaux outils utilisés pour quantifier ces trois formes de carbone ont été respectivement la pyrolyse Rock-Eval, la digestion enzymatique (Trinity-Biotech) et la titration en retour après dissolution acide des carbonates.
L’analyse de la matière organique indique que le carbone organique total évolue de manière quantitative et qualitative depuis les feuilles jusqu’aux horizons minéraux. Le stock de carbone organique est intégré dans les bio-molécules dans les horizons de surface (A) et dans les géo-molécules plus stables dans les horizons minéraux (B et C).
Cette étude montre que la quantité en oxalates dans les feuilles (considérées comme un premier réservoir d’oxalate) est de 20 x 10-2 mg/g de matière sèche. A cette source peut être ajoutée celle des champignons excréteurs d’acide oxalique. En effet, par la mise en culture d’échantillons de sol, les espèces oxalogènes suivantes ont été identifiées: Aspergillus sp., Fusarium sp. et Mucor sp..
Malgré ces deux apports d’oxalate (feuilles et champignons), la concentration mesurée dans les sols reste faible, ne dépassant pas 6.5 x 10-3 mg d’oxalate/g de sol à un instant t. Ceci-ci peut être expliqué par l’efficacité de l’oxydation bactérienne des oxalates menant à la précipitation de calcite faiblement magnésienne. En effet cette dernière, non présente dans les feuilles fraîches, a été observée dans la litière et les sols où les concentrations peuvent atteindre 15% de la masse totale.
Ces résultats ont permis de construire un premier modèle proposant que (1) la teneur en carbonates doublerait chaque 30 ans, (2) entre 70 et 170 ans l’accumulation en carbonates serait telle que le sol pourrait être cimenté, et (3) le temps de résidence du carbone pourrait aisément dépasser 4000 ans., South of Burkina Faso, thousands of years of pedogenesis have resulted in “Plinthic Ferralsols (Arenic)” (according to the WRB). However, it is observed that under the influence of oxalogenic trees, such as Milicia excelsa, Afzelia africana, and Bombax costatum, the soil evolves into a “Ferralic Calcisol (Arenic)” in less a millenium. It has been proposed that the driving force of this carbonate accumulation is the bacterial oxalotrophy, which generates a carbon pump between the atmosphere and the soil.
The principal goals of this work are (1) to provide a carbon balance, (2) to propose a model of the carbonate accumulation, and (3) to estimate the residence time of the inorganic carbon in the soil under the trees. Samples were taken from five profiles near the considered oxalogenic trees and a reference soil beyond their respective influence. Contents of total organic carbon, oxalate, and carbonate were measured. The main tools used to quantify these three different forms of carbon were the Rock-Eval pyrolysis, enzymatic digestion (Trinity Biotech), and back titration after acid dissolution of carbonate.
Analysis of organic matter indicates that the total organic carbon evolves both quantitatively and qualitatively from leaves to mineral horizons. The stock of organic carbon is incorporated in the bio-molecules at the surface horizons (A) and in stable geo-molecules in mineral horizons (B and C).
This study shows that the amount of oxalates in leaves (considered as a first oxalate reservoir) is of 20 x 10-2 mg / g of dry matter. Oxalogenic fungi may also have to be added to this source. Indeed, by culturing soil samples, the following oxalogenic strains were identified: Aspergillus sp., Fusarium sp. and Mucor sp..
Despite these contributions (leaves and fungi) of oxalate, the concentration measured in the soil is low, never exceeding 6.5 x 10-3 mg oxalate / g of soil at any time t. This unexpected outcome may be explained by the efficiency of the bacterial oxidation of oxalate, leading to low magnesium calcite precipitation. Indeed, the latter, while not present in fresh leaves, was found in litter and soils, where its concentration can reach values as high as 15% of the soil total mass.
All these results were finally used to propose a preliminary model suggesting that (1) the carbonate content is doubling every 30 years, (2) between 70 and 170 years the accumulation of carbonate is so significant that the soil may even become cemented, and (3) the residence time of carbon may easily exceed 4000 years. - PublicationAccès libreUse of an isothermal microcalorimetry assay to characterize microbial oxalotrophic activity(2011)
; ; Isothermal microcalorimetry (IMC) has been used in the past to monitor metabolic activities in living systems. A few studies have used it on ecological research. In this study, IMC was used to monitor oxalotrophic activity, a widespread bacterial metabolism found in the environment, and particularly in soils. Six model strains were inoculated in solid angle media with K-oxalate as the sole carbon source. Cupriavidus oxalaticus, Cupriavidus necator, and Streptomyces violaceoruber presented the highest activity (91, 40, and 55 μW, respectively) and a maximum growth rate (μmax h−1) of 0.264, 0.185, and 0.199, respectively, among the strains tested. These three strains were selected to test the incidence of different oxalate sources (Ca, Cu, and Fe-oxalate salts) in the metabolic activity. The highest activity was obtained in Ca-oxalate for C. oxalaticus. Similar experiments were carried out with a model soil to test whether this approach can be used to measure oxalotrophic activity in field samples. Although measuring oxalotrophic activity in a soil was challenging, there was a clear effect of the amendment with oxalate on the metabolic activity measured in soil. The correlation between heat flow and growth suggests that IMC analysis is a powerful method to monitor bacterial oxalotrophic activity. - PublicationAccès libreThe transfer of Cadmium from rock to soil and the associated vegetation cover under natural conditions at the Swiss Jura Moutains(2010)
; ; Baize, DenisAs a result of soil-surveying studies conducted in the Swiss and French Jura Mountains during the early 1990's, anomalous cadmium (Cd) concentrations were identified in soils developed mostly on Bajocian and Oxfordian limestone. Measured Cd concentrations exceed in most of the cases the Swiss official tolerance guideline concentration for non-polluted soils established at 0.8 mg⋅kg-1. Several research works have confirmed the geogenic origin of Cd in soils derived mainly from the weathering of a Cd-rich carbonate substrata. Cd is a highly toxic trace element and the pedogenic / physicochemical conditions leading to its transfer from rocks to soils and its potential bioavailability to plants are in need of a detailed geochemical assessment. The aim of the present work is to complete the geochemical database by studying rock-soil-plant interactions with regard to this element under natural conditions in two specific sites. A first study of rock-soil interaction was carried out determining Cd-bearing phases in a soil developed on top of a road-cut section outcropping at the SW-facing slope of the Schleifenberg hill (canton Basel-Land, Switzerland). This section consisting of an oblique succession of Bajocian oolitic carbonate includes several horizons which are anomalously enriched in Cd (0.03–4.90 mg⋅kg-1). Cd contents in this soil are in the 0.3–2.0 mg⋅kg-1 range. Vertical pedogenetic processes (weathering of underlying bedrock) as well as lateral colluvial limestone (weathering of uphill carbonates) are responsible for the origin of Cd in the soil. Half of the Cd still resides in the carbonate fraction, while the Cd released from the weathered carbonates is associated either with organic matter (over 10%) or with Fe and Mn-oxyhydroxides (approximately 30%). Adsorption of a low percentage of Cd on clays is of less importance since Pb, Zn, Cu and Cr ions will compete with Cd to gain adsorbed sites on clays. No exchangeable Cd phase was found and this, together with the buffer capacity of this calcareous soil, suggests that the amount of mobile Cd is quite negligible, which also greatly reduce the amount of bioavailable Cd. Where developed on steep slopes, the soil will hardly accumulate and colluviums will constantly renew it. A second study regarding the transfer and distribution of geogenic Cd in the soil was conducted on six closely spaced soil profiles at the site called Le Gurnigel (canton Neuchâtel, Switzerland). The soils consist mainly of cambisols and cambic-neoluvisols showing an important allochthonous, aeolian fraction. Cd concentrations generally increase down the soil profiles, showing maxima (up to 16.3 mg⋅kg-1) near the soil-bedrock interface. Most Cd resides in the carbonate and organic fractions in topsoils, whereas the amorphous oxyhydroxides fraction becomes the most important Cd-bearing phase in the middle and in subsoils. Cd, Zn and Cr are positively correlated with comparable distributions in the soil profiles suggesting a common bearing phase such as Fe oxyhydroxides for these three elements. A complex transfer pattern of Cd starts with the release of Cd from the underlying bedrock, and then transferred into oxide, hydroxide, carbonate and organic phases. Additionally, the lateral advection of Cd-rich soils formed on steep slopes acts as a local allochthonous input of Cd to these soils, which in turn is transferred from the topsoil towards the deeper horizons by biological and pedogenic processes. The amount of readily exchangeable and therefore potentially bioavailable Cd is low in these soils (on average 0.2 mg⋅kg-1) provided that the pH remains above 5. Under stronger acidic and oxidizing conditions, Cd bound to organic matter may be mobilised and the bioavailability of Cd would range between 3.3–5.4 mg⋅kg-1 in cambisols and reach up to 1.7 mg⋅kg-1 in deeper cambic-neoluvisols. Soil-plant interactions were studied at the Le Gurnigel analyzing six local plants chosen for their ubiquity in the studied soil profiles. Cadmium accumulation was separately determined in roots and shoots. Three herbs, two graminoids and a tree were used for this purpose. They showed that the accumulation of Cd varies from one species to another and even between plants from the same family. Global levels of Cd in the selected vegetation are in the 2–6 mg·kg-1 range, thus exceeding the official limit value of Cd concentration tolerated in vegetal food for animals established at 1 mg·kg-1. The different behaviours were compared as a function of the variability of Cd in soils. A rise in the concentration of Cd in the soil progressively reduces the transport of Cd toward the shoots reducing also the yield production and increasing the accumulation of Cd in roots. Transfer coefficients from soil / rhizosphere to plant are inversely proportional to the total Cd concentration in soils and do not depend on species identity but instead on soil type. Sequential chemical extractions revealed that variations of Cd distribution between distant soil and rhzosperic soil occur mainly in the first three Cdbearing phases due principally to the incorporation of roots exudates that modify pH and redox conditions of the rizhosphere. High levels of Cd (up to 9 mg·kg-1) were found in shoots of three of the studied plants and may represent a mid-term hazard for animals and human health since these plants are used either for grazing of cattle or for medical purposes. The phenomenon of natural enrichment of soils with geogenic Cd and its progressive accumulation in vegetation covers is suspected to have a widespread occurrence elsewhere, as a function of frequent outcrops of Cd-enriched carbonates of Bajocian and Oxfordian age in western and southern Europe principally in France, Spain and Italy. - PublicationMétadonnées seulementUse of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil(2009)
; ; Oxalate catabolism, which can have both medical and environmental implications, is performed by phylogenetically diverse bacteria. The formyl-CoA-transferase gene was chosen as a molecular marker of the oxalotrophic function. Degenerated primers were deduced from an alignment of frc gene sequences available in databases. The specificity of primers was tested on a variety of frc-containing and frc-lacking bacteria. The frc-primers were then used to develop PCR-DGGE and real-time SybrGreen PCR assays in soils containing various amounts of oxalate. Some PCR products from pure cultures and from soil samples were cloned and sequenced. Data were used to generate a phylogenetic tree showing that environmental PCR products belonged to the target physiological group. The extent of diversity visualised on DGGE pattern was higher for soil samples containing carbonate resulting from oxalate catabolism. Moreover, the amount of frc gene copies in the investigated soils was detected in the range of 1.64x10(7) to 1.75x10(8)/g of dry soil under oxalogenic tree (representing 0.5 to 1.2% of total 16S rRNA gene copies), whereas the number of frc gene copies in the reference soil was 6.4x10(6) (or 0.2% of 16S rRNA gene copies). This indicates that oxalotrophic bacteria are numerous and widespread in soils and that a relationship exists between the presence of the oxalogenic trees Milicia excelsa and Afzelia africana and the relative abundance of oxalotrophic guilds in the total bacterial communities. This is obviously related to the accomplishment of the oxalate-carbonate pathway, which explains the alkalinization and calcium carbonate accumulation occurring below these trees in an otherwise acidic soil. The molecular tools developed in this study will allow in-depth understanding of the functional implication of these bacteria on carbonate accumulation as a way of atmospheric CO2 sequestration. (c) 2008 Elsevier B.V. All rights reserved. - PublicationAccès libreUse of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil(2009)
; ; Oxalate catabolism, which can have both medical and environmental implications, is performed by phylogenetically diverse bacteria. The formyl-CoA-transferase gene was chosen as a molecular marker of the oxalotrophic function. Degenerated primers were deduced from an alignment of frc gene sequences available in databases. The specificity of primers was tested on a variety of frc-containing and frc-lacking bacteria. The frc-primers were then used to develop PCR-DGGE and real-time SybrGreen PCR assays in soils containing various amounts of oxalate. Some PCR products from pure cultures and from soil samples were cloned and sequenced. Data were used to generate a phylogenetic tree showing that environmental PCR products belonged to the target physiological group. The extent of diversity visualised on DGGE pattern was higher for soil samples containing carbonate resulting from oxalate catabolism. Moreover, the amount of frc gene copies in the investigated soils was detected in the range of 1.64 × 107 to 1.75 × 108/g of dry soil under oxalogenic tree (representing 0.5 to 1.2% of total 16S rRNA gene copies), whereas the number of frc gene copies in the reference soil was 6.4 × 106 (or 0.2% of 16S rRNA gene copies). This indicates that oxalotrophic bacteria are numerous and widespread in soils and that a relationship exists between the presence of the oxalogenic trees Milicia excelsa and Afzelia africana and the relative abundance of oxalotrophic guilds in the total bacterial communities. This is obviously related to the accomplishment of the oxalate–carbonate pathway, which explains the alkalinization and calcium carbonate accumulation occurring below these trees in an otherwise acidic soil. The molecular tools developed in this study will allow in-depth understanding of the functional implication of these bacteria on carbonate accumulation as a way of atmospheric CO2 sequestration. - PublicationAccès libreDynamique de mise en place des sols en plaine alluviale du Rhône supérieur / Joëlle Farine, Aline Gerber(2007)
; Les zones alluviales sont composées de milieux naturels divers, d’une grande richesse et d’une grande diversité, tant floristique que faunistique. Ces milieux dépendent de l’activité de sédimentation des cours d’eau, qui a pour effet de rajeunir les sols et la végétation. Cette diversité est malheureusement en voie de disparition en Suisse, car 90% des zones alluviales ont déjà disparu, et la dynamique alluviale naturelle a cessé dans 80% des zones restantes. En effet, ces deux cents dernières années ont vu la majorité des rivières être endiguées, et la construction de nombreux ouvrages, comme les barrages hydroélectriques, se faire le long des cours d’eau. Le cours du Rhône supérieur ne fait pas exception. Deux corrections de son cours ont été effectuées depuis 1860. Elles ont eu pour conséquences principales de limiter fortement les crues, et de permettre l’extension des zones agricoles à toute la plaine. Les zones alluviales et les zones de marais ont depuis lors fortement régressé, voire disparu dans la plaine du Rhône. Suite à une rupture des digues en 2000, il a été décidé, au vu de l’état de ces dernières, d’effectuer une troisième correction du fleuve. Elle a pour but, entre autres, de renforcer la sécurité tout en redonnant plus de place au cours d’eau. Cette étude a pour but la description de la mise en place des sols dans la plaine alluviale du Rhône supérieur. Pour ce faire, des sondages à la tarière ont été effectués le long de la plaine sur huit stations, entre Dorénaz (Bas Valais, près de Martigny) et Selkingen (Haut Valais). Leur classification a été effectuée d’après la méthode développée par Bullinger-Weber et Gobat (2006), qui permet de décrire la dynamique de mise en place des sols au niveau d’une station ainsi que la plaine dans son ensemble. Des fosses pédologiques ont ensuite été creusées, afin d’illustrer chaque groupe de sol qui découle de la classification. Des analyses de la matière organique, des analyses granulométriques, ainsi que l’analyse de lames minces ont été effectuées sur les échantillons prélevés dans chaque couche sédimentaire et horizon pédologique des profils. Pour finir, des cartes de la plaine ont été créées à partir d’études cartographiques précédentes (Paulmier, 2004 ; Zanini et al., 2007) ainsi que du plan Napoléon, dessiné en 1802. Les groupes de sols obtenus par classification des sondages y sont représentés. Ces cartes, ainsi que les groupes de sols, permettent de comprendre et de décrire la dynamique de mise en place des sols au niveau des stations, et dans la plaine du Rhône en général. Les résultats des analyses de la matière organique, tout d’abord, ont révélé une grande différence entre les sols des zones où le fleuve est endigué, et les sols des zones alluviales actives encore actuellement ou actives par le passé. Là où le fleuve est endigué, l’activité de la faune du sol est élevée, ce qui se traduit par la maturation, la fragmentation et l’agrégation importante de la matière organique. Elle est clairement encore renforcée lorsque le sol est exploité à des fins agricoles. Ensuite, les résultats de l’analyse granulométrique nous ont permis de décrire la mise en place des sédiments qui forment les sols, et de reconstituer la dynamique alluviale qui est à l’origine de leur dépôt. Il en ressort que la succession des couches sédimentaires, pour certains sols, est le résultat de crues d’intensité moyenne, régulières dans le temps et dans l’espace, et qu’elle est le résultat, pour d’autres sols de la sédimentation forcée effectuée par l’Homme, ou le résultat d’une crue unique de forte intensité. Finalement, l’analyse cartographique ainsi que l’analyse des groupes de sols nous ont permis de proposer une hypothèse de mise en place des sols pour chaque station, ainsi que de vérifier son exactitude. Les zones où le fleuve est endigué, mais dans lesquelles on observe une grande diversité de groupes de sol, s’avèrent être d’anciennes zones alluviales très actives. Il ressort de cette étude que les sols actuels de la plaine du Rhône supérieur sont marqués par les effets de l’endiguement du fleuve et de l’activité agricole encore prépondérante de nos jours. Néanmoins, les sols de la plaine gardent, pour la plupart, la trace de la dynamique alluviale antérieure aux corrections du Rhône. - PublicationMétadonnées seulement
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