Turning sunlight into stone: the oxalate-carbonate pathway in a tropical tree ecosystem.

An African oxalogenic tree, the iroko tree (Milicia excelsa), has the property to enhance carbonate precipitation in tropical oxisols, where such accumulations are not expected due to the acidic conditions in these types of soils. This uncommon process is linked to the oxalate-carbonate pathway, which increases soil pH through oxalate oxidation. In order to investigate the oxalate-carbonate pathway in the iroko system, fluxes of matter have been identified, described, and evaluated from field to microscopic scales. In the first centimeters of the soil profile, decaying of the organic matter allows the release of whewellite crystals, mainly due to the action of termites and saprophytic fungi. In addition, a concomitant flux of carbonate formed in wood tissues contributes to the carbonate flux and is identified as a direct consequence of wood feeding by termites. Nevertheless, calcite biomineralization of the tree is not a consequence of in situ oxalate consumption, but rather related to the oxalate oxidation inside the upper part of the soil. The consequence of this oxidation is the presence of carbonate ions in the soil solution pumped through the roots, leading to preferential mineralization of the roots and the trunk base. An ideal scenario for the iroko biomineralization and soil carbonate accumulation starts with oxalatization: as the iroko tree grows, the organic matter flux to the soil constitutes the litter, and an oxalate pool is formed on the forest ground. Then, wood rotting agents (mainly termites, saprophytic fungi, and bacteria) release significant amounts of oxalate crystals from decaying plant tissues. In addition, some of these agents are themselves producers of oxalate (e.g. fungi). Both processes contribute to a soil pool of "available" oxalate crystals. Oxalate consumption by oxalotrophic bacteria can then start. Carbonate and calcium ions present in the soil solution represent the end products of the oxalate-carbonate pathway. The solution is pumped through the roots, leading to carbonate precipitation. The main pools of carbon are clearly identified as the organic matter (the tree and its organic products), the oxalate crystals, and the various carbonate features. A functional model based on field observations and diagenetic investigations with δ13C signatures of the various compartments involved in the local carbon cycle is proposed. It suggests that the iroko ecosystem can act as a long-term carbon sink, as long as the calcium source is related to non-carbonate rocks. Consequently, this carbon sink, driven by the oxalate carbonate pathway around an iroko tree, constitutes a true carbon trapping ecosystem as defined by ecological theory.

Fungi, bacteria and soil pH: the oxalate-carbonate pathway as a model for metabolic interaction

The oxalatecarbonate pathway involves the oxidation of calcium oxalate to low-magnesium calcite and represents a potential long-term terrestrial sink for atmospheric CO2. In this pathway, bacterial oxalate degradation is associated with a strong local alkalinization and subsequent carbonate precipitation. In order to test whether this process occurs in soil, the role of bacteria, fungi and calcium oxalate amendments was studied using microcosms. In a model system with sterile soil amended with laboratory cultures of oxalotrophic bacteria and fungi, the addition of calcium oxalate induced a distinct pH shift and led to the final precipitation of calcite. However, the simultaneous presence of bacteria and fungi was essential to drive this pH shift. Growth of both oxalotrophic bacteria and fungi was confirmed by qPCR on the frc (oxalotrophic bacteria) and 16S rRNA genes, and the quantification of ergosterol (active fungal biomass) respectively. The experiment was replicated in microcosms with non-sterilized soil. In this case, the bacterial and fungal contribution to oxalate degradation was evaluated by treatments with specific biocides (cycloheximide and bronopol). Results showed that the autochthonous microflora oxidized calcium oxalate and induced a significant soil alkalinization. Moreover, data confirmed the results from the model soil showing that bacteria are essentially responsible for the pH shift, but require the presence of fungi for their oxalotrophic activity. The combined results highlight that the interaction between bacteria and fungi is essential to drive metabolic processes in complex environments such as soil.

Taux sanguins et sériques d'ions métalliques chez les patients porteurs de PHTs à col modulaire - une étude de cohorte prospective comparative

Les évidences s'accumulent concernant des problèmes de corrosion touchant les prothèses à col modulaires. Plusieurs études récentes révèlent des taux d'ions métalliques élevés. Le but de cette étude était de comparer les taux d'ions métalliques (Co, Cr, Mo, Ti), dans le sérum, chez des porteurs de prothèses à col modulaire, à tige monobloc, ainsi que sans implant. Méthodes Nous avons recruté 60 patients, dont 50 porteurs d'une PTH, unilatérale, sans aucun autre implant, non-cimentée, avec tête en céramique, à minimum 1 année postopératoire. Quarante avaient une tige SPS (Symbios) (Ti6Al4 V) modulaire (col en CoCr) et 10 une SPS monobloc (non-modulaire). Les cupules étaient toutes en alliage de Ti (Ti6Al4 V) avec insert céramique ou PE. Nous avons constitué un groupe témoin sans aucun implant. Dans le groupe o modulaires O, le col a été choisi en préopératoire sur la base d'une planification 3D et assemblé à sec avant implantation. Nous avons prélevé un échantillon sérique, un autre sanguin, qui ont été analysés par spectrométrie de masse, permettant une détermination atomique quantitative. Le résultat clinique a été estimé à l'aide du o Oxford Hip Score O. Résultats Nous avons trouvé un Co sérique moyen à 1,54 Ig L dans le groupe O modulaires O et à 0,32 Ig L dans le groupe o monobloc O avec un p < 0,001. Pour le Cr, on a 1,12 Ig L (modulaires) vs 0,60 Ig L (monoblocs) avec un p < 0,001, pour le Ti 31 Ig L (modulaires) vs 22 Ig L (monoblocs) avec p < 0,001 et pour le Mo, 0,96 Ig L (modulaires) vs 0,74 (monoblocs) avec p = 0,254. Deux patients avaient des valeurs de Co supérieures à 7 Ig L et 11 étaient au-dessus de 1 Ig L, valeur considérée comme limite. Les valeurs dans le sang complet étaient similaires. Nous n'avons pas trouvé de différence significative selon les types de col modulaires (longs vs courts et rétro vs normaux). Curieusement, le taux de Cr était significativement plus élevé chez les patients sans aucun implant que chez les porteurs de SPS monobloc, par contre les différences n'étaient pas significatives pour les autres éléments. Conclusion Les taux sériques et sanguins de ions Co, Cr et Ti étaient significativement plus élevés dans le groupe des patients avec col modulaire, avec 2 valeurs 40 extrêmement hautes et plus de la moitié (11 40) anormalement hautes. Bien que ces valeurs soient inférieures à celles d'autres études, nous avons arrêter d'utiliser de tiges à cols modulaires, et avons initié un suivi annuel des patients porteurs, similaire à celui instauré pour les grosses têtes métal-métal.

Urinary oxalate and urate to creatinine ratios in a healthy pediatric population.

The purpose of the study was to determine reference percentiles for the urinary (U) oxalate (Ox) and urate (Ura) to creatinine (Cr) concentration ratios in the second morning urine of healthy infants, children, and adolescents. The urinary oxalate and urate to creatinine ratios were determined in the spontaneously voided second morning urine sample. To test reproducibility, two urine samples were analyzed on 2 consecutive weeks in 63% of the subjects. Three hundred eighty-four healthy children (181 girls, 203 boys), aged 1 month to 17 years, from nurseries, kindergartens, and schools of Lausanne, Switzerland, were studied. The 5th and 95th percentiles were determined from the total number of urine samples (627) after confirmation that there was no order effect between repeated measurements and there were no significant sex differences. A nonlinear regression analysis in terms of age was used to smooth the calculated percentiles. In this manner, curves were obtained from which the reference values can be read at any given age. The 95th percentiles decreased with age: for UOx/Cr from 0.175 mg/mg (0.22 mol/mol) at 1 to 6 months to 0.048 mg/mg (0.06 mol/mol) from 7 years and beyond; and UUra/Cr from 2.378 mg/mg (1.6 mol/mol) at 1 to 6 months to 0.594 mg/mg (0.4 mol/mol) in adolescence. We provide 5th and 95th percentile curves for the UOx/Cr and UUra/Cr ratios determined from the second morning urine samples in a large cohort of healthy infants, children, and adolescents. Values were determined by standard analytical chemical techniques and were analyzed by powerful statistical methods. The calculated 95th percentile for the UOx/Cr values fell rather rapidly and reached normal adult values by the age of 7 years, whereas for UUra/Cr, the 95th percentile decreased slowly and stabilized in adolescence.

Experimental calcium oxalate crystal production and dissolution by selected wood rot fungi.

Twenty-six species of white-rotting Agaricomycotina fungi (Basidiomycota) were screened for their ability to produce calcium-oxalate (CaOx) crystals in vitro. Most were able to produce CaOx crystals in malt agar medium in the absence of additional calcium. In the same medium enriched with Ca2+, all the species produced CaOx crystals (weddellite or whewellite). Hyphae of four species (Ganoderma lucidum, Polyporus ciliatus, Pycnoporus cinnabarinus, and Trametes versicolor) were found coated with crystals (weddellite/whewellite). The production of CaOx crystals during the growth phase was confirmed by an investigation of the production kinetics for six of the species considered in the initial screening (Pleurotus citrinopileatus, Pleurotus eryngii, Pleurotus ostreatus, P. cinnabarinus, Trametes suaveolens, and T. versicolor). However, the crystals produced during the growth phase disappeared from the medium over time in four of the six species (P. citrinopileatus, P. eryngii, P. cinnabarinus, and T. suaveolens). For P. cinnabarinus, the disappearance of the crystals was correlated with a decrease in the total oxalate concentration measured in the medium from 0.65 μg mm−2 (at the maximum accumulation rate) to 0.30 μg mm−2. The decrease in the CaOx concentration was correlated with a change in mycelia morphology. The oxalate dissolution capability of all the species was also tested in a medium containing calcium oxalate as the sole source of carbon (modified Schlegel medium). Three species (Agaricus blazei, Pleurotus tuberregium, and P. ciliatus) presented a dissolution halo around the growth zone. This study shows that CaOx crystal production is a widespread phenomenon in white-rot fungi, and that an excess of Ca2+ can enhance CaOx crystal production. In addition, it shows that some white-rot fungal species are capable of dissolving CaOx crystals after growth has ceased. These results highlight a diversity of responses around the production or dissolution of calcium oxalate in white-rot fungi and reveal an unexpected potential importance of fungi on the oxalate cycle in the environment.

Detection of active oxalate-carbonate pathway ecosystems in the Amazon Basin: Global implications of a natural potential C sink

The oxalate-carbonate pathway (OCP) is a biogeochemical process, which has been described in Milicia excelsa tree ecosystems of Africa. This pathway involves biological and geological parameters at different scales: oxalate, as a by-product of photosynthesis, is oxidized by oxalotrophic bacteria leading to a local pH increase, and eventually to carbonate accumulation through time in previously acidic and carbonate-free tropical soils. Former studies have shown that this pedogenic process can potentially lead to the formation of an atmospheric carbon sink. Considering that 80% of plant species are known to produce oxalate, it is reasonable to assume that M. excelsa is not the only tree that can support OCP ecosystems. The search for similar conditions on another continent led us to South America, in an Amazon forest ecosystem (Alto Beni, Bolivia). This area was chosen because of the absence of local inherited carbonate in the bedrock, as well as its expected acidic soil conditions. Eleven tree species and associated soils were tested positive for the presence of carbonate with a more alkaline soil pH close to the tree than at a distance from it. A detailed study of Pentaplaris davidsmithii and Ceiba speciosa trees showed that oxalotrophy impacted soil pH in a similar way to at African sites (at least with 1 pH unit increasing). African and South American sites display similar characteristics regarding the mineralogical assemblage associated with the OCP, except for the absence of weddellite. The amount of carbonate accumulated is 3 to 4 times lower than the values measured in African sites related to M. excelsa ecosystems. Still, these secondary carbonates remain critical for the continental carbon cycle, as they are unexpected in the acidic context of Amazonian soils. Therefore, the present study demonstrates the existence of an active OCP in South America. The three critical components of an operating OCP are the presence of: i) local alkalinization, ii) carbonate accumulations, and iii) oxalotrophic bacteria, which were identified associated to the oxalogenic tree C. speciosa. If the question of a potential carbon sink related to oxalotrophic-oxalogenic ecosystems in the Amazon Basin is still pending, this study highlights the implication of OCP ecosystems on carbon and calcium biogeochemical coupled cycles. As previously mentioned for M. excelsa tree ecosystems in Africa, carbonate accumulations observed in the Bolivian tropical forest could be extrapolated to part or the whole Amazon Basin and might constitute an important reservoir that must be taken into account in the global carbon balance of the Tropics.

Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil.

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 CO(2) sequestration.

Variability in urinary oxalate measurements between six international laboratories.

BACKGROUND: Hyperoxaluria is a major risk factor for kidney stone formation. Although urinary oxalate measurement is part of all basic stone risk assessment, there is no standardized method for this measurement. METHODS: Urine samples from 24-h urine collection covering a broad range of oxalate concentrations were aliquoted and sent, in duplicates, to six blinded international laboratories for oxalate, sodium and creatinine measurement. In a second set of experiments, ten pairs of native urine and urine spiked with 10 mg/L of oxalate were sent for oxalate measurement. Three laboratories used a commercially available oxalate oxidase kit, two laboratories used a high-performance liquid chromatography (HPLC)-based method and one laboratory used both methods. RESULTS: Intra-laboratory reliability for oxalate measurement expressed as intraclass correlation coefficient (ICC) varied between 0.808 [95% confidence interval (CI): 0.427-0.948] and 0.998 (95% CI: 0.994-1.000), with lower values for HPLC-based methods. Acidification of urine samples prior to analysis led to significantly higher oxalate concentrations. ICC for inter-laboratory reliability varied between 0.745 (95% CI: 0.468-0.890) and 0.986 (95% CI: 0.967-0.995). Recovery of the 10 mg/L oxalate-spiked samples varied between 8.7 ± 2.3 and 10.7 ± 0.5 mg/L. Overall, HPLC-based methods showed more variability compared to the oxalate oxidase kit-based methods. CONCLUSIONS: Significant variability was noted in the quantification of urinary oxalate concentration by different laboratories, which may partially explain the differences of hyperoxaluria prevalence reported in the literature. Our data stress the need for a standardization of the method of oxalate measurement.

Influence of nutrition on urinary oxalate and calcium in preterm and term infants.

Few data for normal urinary oxalate (Ox) and calcium (Ca) excretion related both to gestational age and nutritional factors have been reported in preterm or term infants. We therefore determined the molar Ox and Ca to creatinine (Cr) ratios in spot urines from 64 preterm and 37 term infants aged 1-60 days, either fed formula or human milk (HM). Only vitamin D was supplemented; renal or metabolic diseases were excluded. Urinary Ox/Cr ratio was higher in preterm than in term infants, both when formula fed (1st month 253 vs. 180 mmol/mol and 2nd month 306 vs. 212 mmol/mol; P&lt;0.05) or HM fed (206 vs. 169 mmol/ mol and 283* vs. 232 mmol/mol; *P&lt;0.05). Ox/Cr was also higher in formula- than HM-fed preterm infants. The ratio increased during the first 2 months of life irrespective of nutrition. Urinary Ca/Cr ratio was comparable in all groups during the 1st month of life, except for a lower (P &lt; 0.05) value in term infants fed HM (0.10 mol/mol). It increased in all groups during the 2nd month of life, being highest in HM-fed preterm infants (1.86 mol/mol). In conclusion, urinary Ox and Ca excretion is influenced by both gestational age and nutrient intake in preterm and term infants.

Rôle des champignons dans la voie oxalate-carbonate

La présente thèse met en évidence trois rôles des champignons dans la voie oxalate-carbonate. (i) La dynamique fongique de production des cristaux d'oxalate de calcium montre une diminution du nombre de ces cristaux comparativement à ceux préalablement produits. Afin de confirmer ce résultat, une méthode analytique faisant usage de la chromatographie liquide mesurant l'oxalate total, a été mise en pratique. De plus, des champignons à pourriture blanche ont été cultivés sur un milieu Schlegel couramment utilisé par les bactériologistes pour montrer la dissolution bactérienne des oxalates de calcium. Certains champignons se sont révélés positifs au test. (ii) Une approche en microcosme a été employée pour comprendre le rôle respectif des champignons et des bactéries dans la voie oxalate-carbonate. Champignons et bactéries sont la composante biologique du système oxalate-carbonate et sont donc ajoutés au sol des microcosmes selon les séries : (A) champignons seuls, (B) bactéries seules et (C) champignons et bactéries ensemble. En prenant en considération la variable oxalate et en opérant une approche factorielle en accord avec la théorie de la hiérarchie, les séries additionnelles suivantes ont été étudiées : (D) champignon plus oxalate, (E) bactéries plus oxalate et (F) champignon et bactéries ensemble plus oxalate. En présence d'oxalate de calcium les résultats des quantités de champignon vivant (évaluées par dosage de l'ergostérol) au cours du temps montrent que la rapidité de colonisation des microcosmes est accélérée de trois semaines ; c'est une fertilisation du sol opérée par l'oxalate qui favorise la biomasse vivante du champignon. Les champignons à leur tour survivent sur le long terme (3 mois) seulement en présence des bactéries sinon leur biomasse vivante reste faible. Par conséquent, c'est l'interaction entre champignons et bactéries sous forme de coexistence qui permet leur survie réciproque. Les champignons interagissent en synergie avec les bactéries dans le sol du microcosme mais les bactéries, moteur de l'alcalinisation du sol, survivent plus longtemps et atteignent des populations plus élevées seulement quand le champignon et l'oxalate sont présents. En plus des résultats sur les quantités de champignons et de bactéries, le suivi du pH pour toutes les séries des microcosmes examinées laisse apparaître une propriété émergente. Pour l'unique série (F), il se produit une alcalinisation du milieu de deux unités et demie de pH. L'hypothèse de base selon laquelle l'oxalate est responsable d'une favorisation de la voie oxalate-carbonate a été vérifiée. Le rôle des champignons est de favoriser les populations bactériennes sous l'action fertilisante de l'oxalate. (iii) L'origine du calcium, une des questions à résoudre les plus importantes afin que la voie oxalate-carbonate agisse comme un puits de carbone, a été abordée théoriquement, par une littérature élargie, et expérimentalement en boîte de Pétri, en utilisant la colonisation fongique. Le rôle des champignons est de transloquer et libérer du calcium activement et passivement dans le sol.

Heavy metal ions are potent inhibitors of protein folding.

Environmental and occupational exposure to heavy metals such as cadmium, mercury and lead results in severe health hazards including prenatal and developmental defects. The deleterious effects of heavy metal ions have hitherto been attributed to their interactions with specific, particularly susceptible native proteins. Here, we report an as yet undescribed mode of heavy metal toxicity. Cd2+, Hg2+ and Pb2+ proved to inhibit very efficiently the spontaneous refolding of chemically denatured proteins by forming high-affinity multidentate complexes with thiol and other functional groups (IC(50) in the nanomolar range). With similar efficacy, the heavy metal ions inhibited the chaperone-assisted refolding of chemically denatured and heat-denatured proteins. Thus, the toxic effects of heavy metal ions may result as well from their interaction with the more readily accessible functional groups of proteins in nascent and other non-native form. The toxic scope of heavy metals seems to be substantially larger than assumed so far.

Different concentrations of Mg++ ions affect nuclear matrix protein distribution during thermal stabilization of isolated nuclei.

The nuclear matrix, a proteinaceous network believed to be a scaffolding structure determining higher-order organization of chromatin, is usually prepared from intact nuclei by a series of extraction steps. In most cell types investigated the nuclear matrix does not spontaneously resist these treatments but must be stabilized before the application of extracting agents. Incubation of isolated nuclei at 37C or 42C in buffers containing Mg++ has been widely employed as stabilizing agent. We have previously demonstrated that heat treatment induces changes in the distribution of three nuclear scaffold proteins in nuclei prepared in the absence of Mg++ ions. We studied whether different concentrations of Mg++ (2.0-5 mM) affect the spatial distribution of nuclear matrix proteins in nuclei isolated from K562 erythroleukemia cells and stabilized by heat at either 37C or 42C. Five proteins were studied, two of which were RNA metabolism-related proteins (a 105-kD component of splicing complexes and an RNP component), one a 126-kD constituent of a class of nuclear bodies, and two were components of the inner matrix network. The localization of proteins was determined by immunofluorescent staining and confocal scanning laser microscope. Mg++ induced significant changes of antigen distribution even at the lowest concentration employed, and these modifications were enhanced in parallel with increase in the concentration of the divalent cation. The different sensitivity to heat stabilization and Mg++ of these nuclear proteins might reflect a different degree of association with the nuclear scaffold and can be closely related to their functional or structural role.