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Verrecchia, Eric
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Verrecchia, Eric
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- PublicationAccès libre
- PublicationAccès libre
- PublicationAccès libreIdentification of active oxalotrophic bacteria by Bromodeoxyuridine DNA labeling in a microcosm soil experiments(2013)
; ; ; - 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. - 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
- PublicationMétadonnées seulementCycle du carbone et biominéralisation carbonatée en milieu continental: la diagénèse des phases oxalate-carbonate(2005)
; In terrestrial environments, the carbon sequestration pool in the global carbon cycle is almost entirely attributed to soil and plant organic carbon storage while soil mineral carbon is generally neglected. Nevertheless, significant biologically induced accumulations of carbonate have been observed in soils under the tropical tree "iroko" (Milicia excelsa). Without an input of calcium from carbonate sources in the system, these accumulations constitute a carbon sink by definition. Approximately 1.2. 10-4 to 2.3.10-3 PgC are not sequestered each year due to deforestation of irokos. This calculation is based on an average of 5.76 kg/yr of carbon sequestration by one tree and extrapolated for to the iroko population in Africa. This proposed quantification suggests that the iroko carbon sink is about one or two orders of magnitude less than some environments such as coral reefs or continental shelfes. Furthermore, this carbon sink is highly significant because the residence time of mineral carbon in carbonate-enriched soils associated with the irokos is 102 - 106 years, i.e. 100,000 times longer than soil organic matter residence time. These accumulations of carbonate are the result of the oxalate-carbonate transformation by oxalotrophic bacteria. The iroko tree provides a large amount of oxalate (a photosynthetic by-product), which once released in the soil, can be consumed by soil oxalotrophic bacteria. There are two consequences of this consumption: (i) carbonate ions are produced and available in the soil solution, (ii) and soil pH increases leading to favorable conditions for carbonate precipitation (in a primary acid soil with a pH around 5, the induced pH can reach 9). In the iroko ecosystem, biological agents are present and active at various scales. Termites and saprophytic fungi are involved in the release of oxalate crystals in the soil. Soil oxalotrophic bacteria are able to consume oxalate leading to CO32- production. Carbonate ions can be pumped by iroko roots, circulating into wood vessels in which they can form calcium carbonate crystals in the presence of calcium, when conditions are favorable. They can also precipitate as calcium carbonate in soil pores, depending on local conditions. Soil bacteria and fungi obviously influence precipitation of carbonate inside the soil. Moreover, regarding carbon isotopic signatures and crystallographic properties of needle fiber calcite (NFC) observed in surficial environments, including African soils, they result from a direct biogenic influence. The nomenclature of the various types of NFC has been reinterpreted regarding diagenesis and geochemical fingerprints. The possible biogenic origin of nanorods usually found in the presence of NFC is also discussed from new observations and experiments. In conclusion, this study has demonstrated the potential importance of the oxalate-carbonate pathway in the global carbon cycle, emphasizing the crucial interrelations between geological and biological processes. - PublicationAccès libreBiomineralization in plants as a long-term carbon sink(2004)
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