Verrecchia, Eric

2009, Khammar, Nadia, Martin, Gaëtan, Ferro, Katia, Job, Daniel, Aragno, Michel, Verrecchia, Eric

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.

2005, Cailleau, Guillaume, Verrecchia, Eric

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.

2006, Verrecchia, Eric, Braissant, Olivier, Cailleau, Guillaume

2004, Dupraz, Christophe, Pattisina, Ronny, Verrecchia, Eric

Stromatolites are examples of ail iterative system involving radiate accretive growth of microbial mats, biofilm and/or minerals that result from interaction between intrinsic and extrinsic factors, which progressively shape the final morphology. These interactions call neither be easily described by simple mathematical equations, nor by simple physical laws or chemical reactions. Therefore, a holistic approach that will reduce the system to a set of variables (which are combinations of natural variables) is proposed in order to create virtual morphologies which will be compared with their natural counterparts. The combination of both Diffusion Limited Aggregation (DLA) and cellular automata (CA) allows the exploration of the stromatolite morphological space and a representation of the intrinsic and extrinsic factors responsible for natural stromatolite morphogenesis. The holistic approach provides a translation in simple parameters of (I) the way that energy, nutrients and sedimentary particles reach the active surface of a future build-up, (2) flow these elements are distributed and used in order to create morphology, and (3) how simple environmental parameters, such as sedimentation, can disturb morphogenesis. In addition, most Precambrian stromatolite morphologies that are impossible to produce with numerical modeling such as the Kardar-Parisi-Zhan (KPZ) equation can be simulated with the DLA-CA model and this, with a minimum set of variables. (c) 2005 Elsevier B.V. All rights reserved.

2005, Braissant, Olivier, Verrecchia, Eric

L'influence des micro-organismes sur la précipitation et la dissolution des minéraux est connue depuis longtemps. Dans ce contexte, le cas particulier de l'oxalate de calcium est particulièrement intéressant car l'oxalate est présent dans de nombreux systèmes biologiques tels que chez les plantes et chez les champignons. L'oxalate joue aussi un rôle important dans certains cycles biogéochimiques ainsi que dans certaines pathologies humaines telles que les calculs rénaux. Malgré la faible solubilité des complexes métaux-oxalates et le degré d'oxydation élevé de l'anion oxalate, un nombre limité de bactéries sont capables d'utiliser l'acide oxalique et l'oxalate de calcium comme sources de carbone et d'énergie. La dégradation de l'oxalate par des bactéries aérobies mène à une augmentation du pH qui permet la précipitation de minéraux carbonatés. L'étude de ce processus dans les sols autour de l'iroko (Milicia excelsa), de cactus, et de plants de vigne montre que les pools d'oxalates sont très variables et que leur dégradation dans le sol et la rhizosphère est assurée principalement par les streptomycètes et les protéobacteries, respectivement. Dans tous les cas, on observe une alcalinisation des sols et une précipitation de carbonate de calcium. De plus les carbonates observés dans les différents sols peuvent être reproduits en laboratoire en utilisant les bactéries oxalotrophes isolées. L'étude de la morphologie et de la minéralogie des carbonates produits en laboratoire montre que les exopolysaccharides et les polymères pariétaux ont une grande influence sur la nature des carbonates produits. De même la cristallisation abiotique de différents polymorphes du carbonate de calcium dans un EPS commercial souligne l'importance de celui-ci dans la formation de phases métastables et des morphologies particulières du carbonate de calcium. Considérant ces éléments, cette étude propose le modèle suivant pour résumer le fonctionnement du cycle oxalate-carbonate dans les sols. Les plantes produisent un premier reservoir d'oxalate. Lors de la dégradation des tissus ligneux et de la litière, les champignons saprophytes produisent un second pool d'oxalate. De plus ils favorisent la libération des cristaux d'oxalate de calcium enchâssés dans les tissus végétaux. Ces deux pools d'oxalate sont ensuite consommés par les bactéries oxalotrophes. Il en résulte une augmentation du pH et une précipitation concomitante de carbonate de calcium., The influence of microbes on the precipitation and dissolution of minerals is known for a long time. In this context the case of calcium oxalate is particularly interesting because calcium oxalate is present in many biological systems such as plant and fungi. Oxalate also plays an important role in biogeochemical cycles and human diseases such as kidney stones. Despite the poor solubility of metal oxalate complexes and the high oxidation state of oxalate, a limited number of bacteria are able to use oxalate and calcium oxalate as carbon and energy sources. Bacterial aerobic degradation of oxalates leads to a pH increase that allows the precipitation of carbonate minerals. The investigation of such processes in soils around an African tree (iroko, Milicia excelsa), cacti, and grape plants shows that oxalate pools are highly variable. In the soil and the rhizosphere, oxalic acid and oxalate crystals are mainly degraded by streptomycetes and proteobacteria respectively. In each case, an alcalinization of soil solution is observed and precipitation of calcium carbonate can occur. Moreover, calcium carbonate crystals observed in soils can be reproduced in the laboratory using isolated oxalotrophic bacteria. The study of the different morphologies and mineralogies produced by oxalotrophic bacteria in the laboratory shows that exopolysaccharides (EPS) and parietal polymers have a great influence on the nature of calcium carbonate crystal produced. In addition, abiotic crystallization of different polymorphs of calcium carbonate in an industrial EPS emphasizes EPS role in the formation of metastable phases and specific morphologies of calcium carbonate. Considering these points, this study proposes the following model for the oxalate-carbonate cycle in soils. Plants produce a first pool of oxalate. During wood and litter degradation, saprophytic fungi produces a second pool of oxalate, increasing the release of oxalate crystals encased in plant tissues. These two pools of oxalates are consumed by oxalotrophic bacteria resulting in a pH increase and a concomitant calcium carbonate precipitation

2003, Braissant, Olivier, Cailleau, Guillaume, Dupraz, Christophe, Verrecchia, Eric