Desulfovibrio brasiliensis sp. nov., a moderate halophilic sulfate-reducing bacterium from Lagoa Vermelha (Brazil) mediating dolomite formation

A novel halotolerant sulfate-reducing bacterium, Desulfovibrio brasiliensis strain LVform1, was isolated from sediments of a dolomite-forming hypersaline coastal lagoon, Lagoa Vermelha, in the state of Rio de Janeiro, Brazil. The cells are vibrio-shaped and 0.30 to 0.45μm by 1.0 to 3.5μm in size. These bacteria mediate the precipitation of dolomite [CaMg(CO3)2] in culture experiments. The strain was identified as a member of the genus Desulfovibrio in the δ-subclass of the Proteobacteria on the basis of its 16S rRNA gene sequence, its physiological and morphological properties. Strain LVform1 is obligate sodium-dependent and grows at NaCl concentrations of up to 15%. The 16S rRNA sequence revealed that this strain is closely related to Desulfovibrio halophilus (96.2% similarity) and to Desulfovibrio oxyclinae (96.8% similarity), which were both isolated from Solar Lake, a hypersaline coastal lake in the Sinai, Egypt. Strain LVform1 is barotolerant, growing under pressures of up to 370bar (37MPa). We propose strain LVform1 to be the type strain of a novel species of the genus Desulfovibrio, Desulfovibrio brasiliensis (type strain LVform1 = DSMZ No. 15816 and JCM No. 12178). The GenBank/EMBL accession number for the 16S rDNA sequence of strain LVform1 is AJ54468

Biomineralization of carbonate and phosphate by moderately halophilic bacteria

We investigated the precipitation of carbonate and phosphate minerals by 19 species of moderately halophilic bacteria using media with variable Mg2+/Ca2+ ratios. The precipitated minerals were calcite, magnesium (Mg) calcite, and struvite (MgNH4PO4·6H2O) in variable proportions depending on the Mg2+/Ca2+ ratio of the medium. The Mg content of the Mg-calcite decreased with increasing Ca2+ concentration in the medium. According to the saturation indices, other minerals could also have precipitated. We observed important differences between the morphology of carbonate and phosphate, which may help us to recognize these minerals in natural systems. We studied the growth and pH curves of four bacteria in media specific for carbonate and struvite precipitation. We consider the biomineralization processes that produce carbonate and phosphate minerals, and propose a hypothesis for the lack of struvite in natural environments and ancient rock

Evolving controls on mineralization in Patagonian microbial mats as inferred by water chemistry, microscopy and DNA signatures

In recent years resulting investigations in living microbialites have provided significant data that have been critical to disentangle the role of the various biotic and abiotic processes contributing to their development. Despite these efforts separating the impact and magnitude of these processes remain a difficult task. At present the Maquinchao Basin in northeastern Patagonia, Argentina, contains both fossil and living microbialites. Thus, the region provides a unique opportunity to investigate the impact of intrinsic and extrinsic parameters in carbonate precipitation. Early investigations (Austral summer 2011) in living microbialites concluded that organomineralization was related to both photosynthetic activity in the more surficial layer (green), and sulfate-reduction in the lower part (beige). Field investigations in the same area four years later showed that the pounds previously containing abundant active mats had dried out, and in general revealed the absence of globular structured clusters of minerals in the microbial mats. Here we present microscale investigations using optical microscopy and SEM along with the 16SrRNA gene sequence diversity, and the physico-chemical parameters of the hosting waters. They were carried out in successive seasonal samplings in November 2015, April-May 2016, August 2016, February 2017, and March 2018. All microbialite samples show regular occurrences of sulfate reducing bacteria (SRB) along with filaments of unknown origin. Carbonates are observed associated with erect filaments in shallow and active running water locations whereas the mineral phase is located below organic matter film in comparatively deeper and calmer water areas. Additionally, seasonal changes in the physico-chemical properties of the hosting waters indicate that extrinsic parameters, especially evaporation, might play a more substantial role in the precipitation of these carbonates than previously proposed. The environmental differences between 2011 and 2015 in meteorological conditions, regional volcanic activity and associated deposits in the basin are analyzed. We concluded that they are likely responsible of the decrease of the mineralization processes, and particularly those associated with photosynthetic activity. These results call for caution when interpreting the degree of biological impact on the formation of microbialites in the geological record. Local extrinsic factors might have a changeable impact over time switching mineral precipitation from biotic to abiotic and viceversa, which can be undistinguishable in fossilized microbialites.Fil: Eymard, Inès. Universidad de Ginebra. Facultad de Ciencias. Sección de Ciencias de la Tierra; SuizaFil: Alvarez, Maria del Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; ArgentinaFil: Bilmes, Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Geología y Paleontología; ArgentinaFil: Vasconcelos, Crisogono. ETH, Geologisches Institut; Suiza. CGA-SGB/CPRM; BrasilFil: Thomas, Camille. Universidad de Ginebra. Facultad de Ciencias. Sección de Ciencias de la Tierra; SuizaFil: Ariztegui, Daniel. Universidad de Ginebra. Facultad de Ciencias. Sección de Ciencias de la Tierra; Suiz

Establishing Sampling Procedures in Lake Cores for Subsurface Biosphere Studies: Assessing In Situ Microbial Activity

Sub-recent sediments in modern lakes are ideal to study early diagenetic processes with a combination of physical, chemical, and biological approaches. Current developments in the rapidly evolving field of geomicrobiology have allowed determining the role of microbes in these processes (Nealson and Stahl, 1997; Frankel and Bazylinski, 2003). Their distribution and diversity in marine sediments have been studied for some years (Parkes et al., 1994; D’Hondt et al., 2004; Teske, 2005). Comparable studies in the lacustrine realm, however, are quite scarce and mainly focused on the water column (Humayoun et al., 2003) and/or very shallow sediments(Spring et al., 2000; Zhao et al., 2007). Thus, there is a need to determine the presence of living microbes in older lacustrine sediments, their growth, and metabolic paths, as well as their phylogenies that seem to differ from already known isolates.During the PASADO (Potrok Aike Maar Lake Sediment Archive Drilling Project) ICDP (International Continental Scientific Drilling Program) drilling, more than 500 meters of sedimentary cores were retrieved from this crater lake (Zolitschka et al., 2009). A 100-m-long core was dedicated to a detailed geomicrobiological study and sampled in order to fill the gap of knowledge in the lacustrine subsurface biosphere. Here we report a complete in situ sampling procedure that aims to recover aseptic samples as well as determining active in situ biological activity. Preliminary results demonstrate that these procedures provide a very useful semi-quantitative index which immediately reveals whether there are biologically active zones within the sediments

Calibration and applications of the dolomite clumped isotope thermometer to high temperatures

Carbonate clumped isotope paleothermometry is based on the temperature-dependent formation of ^(13)C^(18)O^(16)O_2 ^(2-) ion groups within solid carbonate minerals. This thermometer has now been calibrated for various synthetic and natural biogenic and abiogenic minerals (calcite, aragonite and carbonateapatites [e.g., 1, 2]) at temperatures below ~ 50°C. Here we extend the use of the carbonate clumped isotope thermometer to shallow crustal environments by determining the Δ_(47) values of CO_2 extracted from natural and synthetic dolomites grown at know temperatures from 25 to 350ºC. The experimental temperature dependance is not linear in the Δ_(47) vs T^(-2) plot and resembles the predicted theoretical temperature dependence, both in shape and absolute value [3]. These data for synthetic dolomites overlap the previous calibrations for inorganic calcite and some forms of biogenic carbonates between 25 and 50˚C, and are consistent with a single trend that also intersects data for synthetic calcite equilibrated at 1200˚C. These observations suggest that a single temperature dependant relationship reasonably approximates the calibration for both phases. Data from a variety of slowly-cooled (i.e., over geological timescales) natural marbles and rapid (i.e., laboratory timescales) heating experiments provide insights into the kinetics of solid-state ^(13)C-^(18)O bond reordering in carbonates and its closure temperature. More generally, our new calibration and constraints on high-temperature kinetics have implications for the application of this technique to burial and metamorphic processes. These issues will be illustrated through estimates of the thermal history and oxygen isotopic compositions and abundances of pore fluids for several suites of late Neoproterozoic carbonates [e.g., 4]

Microbial mediated formation of Fe-carbonate minerals under extreme acidic conditions

Discovery of Fe-carbonate precipitation in Rio Tinto, a shallow river with very acidic waters, situated in Huelva, South-western Spain, adds a new dimension to our understanding of carbonate formation. Sediment samples from this low-pH system indicate that carbonates are formed in physico-chemical conditions ranging from acid to neutral pH. Evidence for microbial mediation is observed in secondary electron images (Fig. 1), which reveal rod-shaped bacteria embedded in the surface of siderite nanocrystals. The formation of carbonates in Rio Tinto is related to the microbial reduction of ferric iron coupled to the oxidation of organic compounds. Herein, we demonstrate for the first time, that Acidiphilium sp. PM, an iron-reducing bacterium isolated from Rio Tinto, mediates the precipitation of siderite (FeCO3) under acidic conditions and at a low temperature (306C). We describe nucleation of siderite on nanoglobules in intimate association with the bacteria cell surface. This study has major implications for understanding carbonate formation on the ancient Earth or extraterrestrial planetsThis work was supported by the European research project ERC-250350/IPBSL. A.S.-N. acknowledges support from the P11-RNM-7067 (Junta de Andalucía-C.E.I.C.-S.G.U.I.T.) projec

Microbial mediated formation of Fe-carbonate minerals under extreme acidic conditions

Discovery of Fe-carbonate precipitation in Rio Tinto, a shallow river with very acidic waters, situated in Huelva, South-western Spain, adds a new dimension to our understanding of carbonate formation. Sediment samples from this low-pH system indicate that carbonates are formed in physico-chemical conditions ranging from acid to neutral pH. Evidence for microbial mediation is observed in secondary electron images (Fig. 1), which reveal rod-shaped bacteria embedded in the surface of siderite nanocrystals. The formation of carbonates in Rio Tinto is related to the microbial reduction of ferric iron coupled to the oxidation of organic compounds. Herein, we demonstrate for the first time, that Acidiphilium sp. PM, an iron-reducing bacterium isolated from Rio Tinto, mediates the precipitation of siderite (FeCO3) under acidic conditions and at a low temperature (30°C). We describe nucleation of siderite on nanoglobules in intimate association with the bacteria cell surface. This study has major implications for understanding carbonate formation on the ancient Earth or extraterrestrial planets.European research project ERC-250350/IPBSL. A.S.-N.acknowledges support from the P11-RNM-7067 (Junta de Andaluc a-C.E.I.C.-S.G.U.I.T.) projectPeer Reviewe

Calibration of the oxygen and clumped isotope thermometers for (proto-)dolomite based on synthetic and natural carbonates

Dolomite is a very common carbonate mineral in ancient sediments, but is rarely found in modern environments. Because of the difficulties in precipitating dolomite in the laboratory at low temperatures, the controls on its formation are still debated after more than two centuries of research. Two important parameters to constrain the environment of dolomitization are the temperature of formation and the oxygen isotope composition of the fluid from which it precipitated. Carbonate clumped isotopes (expressed with the parameter Δ47) are increasingly becoming the method of choice to obtain this information. However, whereas many clumped isotope studies treated dolomites the same way as calcite, some recent studies observed a different phosphoric acid fractionation for Δ47 during acid digestion of dolomite compared to calcite. This causes additional uncertainties in the Δ47 temperature estimates for dolomites analyzed in different laboratories using different acid digestion temperatures. To tackle this problem we present here a (proto-)dolomite-specific Δ47-temperature calibration from 25 to 1100 °C for an acid reaction temperature of 70 °C and anchored to widely available calcite standards. For the temperature range 25 to 220 °C we obtain a linear Δ47-T relationship based on 289 individual measurements with R2 of 0.864: [Formula presented] Tin Kelvin When including two isotopically scrambled dolomites at 1100 °C, the best fit is obtained with a third order polynomial temperature relationship (R2 = 0.924): [Formula presented]. Applying a calcite Δ47-T relationship produced under identical laboratory conditions results in 3 to 16 °C colder calculated formation temperatures for dolomites (with formation temperature from 0 to 100 °C) than using the (proto-)dolomite specific calibration presented here. For the synthetic samples formed between 70 and 220 °C we also determined the temperature dependence of the oxygen isotope fractionation relative to the water. Based on the similarity between our results and two other recent studies (Vasconcelos et al., 2005 and Horita, 2014) we propose that a combination of the three datasets represents the most robust calibration for (proto-)dolomite formed in a wide temperature range from 25 to 350 °C. 103αCaMg−carbonates−Water=2.9923±0.0557×[Formula presented]−2.3592±0.4116 Because of the uncertainties in the phosphoric acid oxygen and clumped isotope fractionation for (proto-)dolomite, we promote the use of three samples that are available in large amounts as possible inter-laboratory reference material for oxygen and clumped isotope measurements. A sample of the middle Triassic San Salvatore dolomite from southern Switzerland, the NIST SRM 88b dolomite standard already reported in other Δ47 studies and a lacustrine Pliocene dolomite from La Roda (Spain). This study demonstrates the necessity to apply (proto-)dolomite specific Δ47-T relationships for accurate temperature estimates of dolomite formation, ideally done at identical acid digestion temperatures to avoid additional uncertainties introduced by acid digestion temperature corrections. In addition, the simultaneous analyses of dolomite reference material will enable a much better comparison of published dolomite clumped and oxygen isotope data amongst different laboratories

Protection of Possessors in Classical Roman Law -From the Viewpoint of Buyer Protection- (2)

We studied the formation of Mg-rich carbonate in culture experiments using different aerobic bacterial strains and aqueous Mg/Ca ratios (2 to 11.5) at Earth surface conditions. These bacteria promoted the formation of microenvironments that facilitate the precipitation of mineral phases (dolomite, huntite, high Mg-calcite and hydromagnesite) that were undersaturated in the bulk solution or kinetically inhibited. Dolomite, huntite, high Mg-calcite, hydromagnesite and struvite precipitated in different proportions and at different times, depending on the composition of the medium. The Mg content of dolomite and calcite decreased with an increasing Ca concentration in the medium. The stable carbon isotope composition of the Mg-rich carbonate precipitates reflected the isotope composition of the organic compounds present in the media, suggesting that microbial metabolism strongly influenced the carbon isotope composition of biomediated carbonates. We observed that Ca-enriched carbonate precipitates have relatively low carbon isotope composition. These results provide insights into the mechanism(s) of carbonate formation in natural systems, and they are of fundamental importance for understanding modern environments in which carbonate minerals form as a window into the geologic past

Calibration of the dolomite clumped isotope thermometer from 25 to 350°C, and implications for a universal calibration for all (Ca, Mg, Fe)CO_3 carbonates

Carbonate clumped isotope thermometry is based on the temperature-dependent formation of ^(13)C^(18)O^(16)O_2^(2-) ion groups within the lattice of solid carbonate minerals. At low temperatures the bonds between rare, heavy ^(13)C and ^(18)O isotopes are thermodynamically favored, and thus at equilibrium they are present in higher than random abundances. Here we calibrate the use of this temperature proxy in a previously uncalibrated carbonate phase — dolomite [CaMg(CO_3)_2] — over a temperature range that extends to conditions typical of shallow crustal environments, by determining the Δ_(47) values of CO_2 extracted from synthetic or natural (proto)dolomites grown at known temperatures from 25 to 350°C and analyzed in two different laboratories using different procedures for sample analysis, purification and post-measurement data treatment. We found that the Δ_(47) – 1/T^2 dependence for (proto)dolomite is linear between 25 and 350°C, independent of their Mg/Ca compositions or cation order (or the laboratory in which they were analyzed), and offset from, but parallel to, the theoretical predictions of the Δ_(63) dependence to temperature of the abundance of the ^(13)C^(18)O^(16)O_2 isotopologue inside the dolomite and calcite mineral lattices as expected from ab-initio calculations (Schauble et al., 2006). This suggests that neither the equilibrium constant for ^(13)C–^(18)O clumping in (proto)dolomite lattice, nor the experimental fractionation associated with acid digestion to produce CO_2, depend on their formation mechanism, degree of cation order and/or stoichiometry (ie., Mg/Ca ratio) and/or δ^(18)O and δ^(13)C compositions (at least over the range we explored). Thus, we suggest the following single Δ_(47) – 1/T^2 linear regression for describing all dolomite minerals: with T in kelvin and Δ_(47) in the Carbon Dioxide Equilibrium Scale (CDES) of Dennis et al. (2011) and referring to CO_2 extracted by phosphoric acid digestion at 90°C. The listed uncertainties on slope and intercept are 95% confidence intervals. The temperature sensitivity (slope) of this relation is lower than those based on low temperature acid digestion of carbonates, but comparable to most of those based on high temperature acid digestion (with however significantly better constraints on the slope and intercept values, notably due to the large range in temperature investigated and the large number of Δ_(47) measurements performed here, n = 67). We also use this dataset to empirically determine that the acid fractionation factor associated with phosphoric acid digestion of dolomite at 90°C (Δ∗_(dolomite90)) is about + 0.176‰. This is comparable to the Δ∗_(calcite90) experimentally obtained for calcite (Guo et al., 2009), suggesting that the acid fractionation Δ∗ for acid digestion of dolomite and calcite are the same within error of measurement, with apparently no influence of the cation identity. This hypothesis is also supported by the fact that our dolomite calibration data are indistinguishable from published calibration data for calcite, aragonite and siderite generated in similar analytical conditions (ie., carbonate digested at T ⩾ 70°C and directly referenced into CDES), demonstrating excellent consistency among the four (Ca,Mg,Fe)CO_3 mineral phases analyzed in seven different laboratories (this represents a total of 103 mean Δ_(47) values resulting from more than 331 Δ_(47) measurements). These data are used to calculate a composite Δ_(47)–T universal relation for those carbonate minerals of geological interest, for temperatures between -1 and 300°C, that is found to be statistically indistinguishable from the one described by dolomite only: Thus, in order to standardize the temperature estimates out of different laboratories running high temperature digestion of (Ca,Mg,Fe)CO_3 carbonate minerals, we recommend the use of this single Δ_(47)-T calibration to convert Δ_(47CDES) data into accurate and precise temperature estimates. More widely, this study extends the use of the Δ_(47) thermometry to studies of diagenesis and low-grade metamorphism of carbonates with unprecedented precision on temperature estimates based on Δ_(47) measurements — environments where many other thermometers are generally empirical or semi-quantitative