scispace - formally typeset
Search or ask a question
Author

Tomaso R. R. Bontognali

Bio: Tomaso R. R. Bontognali is an academic researcher from University of Basel. The author has contributed to research in topics: Dolomite & Sabkha. The author has an hindex of 20, co-authored 45 publications receiving 1392 citations. Previous affiliations of Tomaso R. R. Bontognali include ETH Zurich & California Institute of Technology.
Topics: Dolomite, Sabkha, Carbonate, Authigenic, Cave

Papers
More filters
Journal ArticleDOI
TL;DR: In this article, a geochemical and petrographic investigation of three sites located on the coastal sabkha of Abu Dhabi, along a transect from the intertidal to the supratidal zone, revealed a close association between microbial mats and dolomite.
Abstract: Microbial mediation is the only demonstrated mechanism to precipitate dolomite under Earth surface conditions. A link between microbial activity and dolomite formation in the sabkha of Abu Dhabi has, until now, not been evaluated, even though this environment is cited frequently as the type analogue for many ancient evaporitic sequences. Such an evaluation is the purpose of this study, which is based on a geochemical and petrographic investigation of three sites located on the coastal sabkha of Abu Dhabi, along a transect from the intertidal to the supratidal zone. This investigation revealed a close association between microbial mats and dolomite, suggesting that microbes are involved in the mineralization process. Observations using scanning electron microscopy equipped with a cryotransfer system indicate that authigenic dolomite precipitates within the exopolymeric substances constituting the microbial mats. In current models, microbial dolomite precipitation is linked to an active microbial activity that sustains high pH and alkalinity and decreased sulphate concentrations in pore waters. Such models can be applied to the sabkha environment to explain dolomite formation within microbial mats present at the surface of the intertidal zone. By contrast, these models cannot be applied to the supratidal zone, where abundant dolomite is present within buried mats that no longer show signs of intensive microbial activity. As no abiotic mechanism is known to form dolomite at Earth surface conditions, two different hypotheses can reconcile this result. In a first scenario, all of the dolomite present in the supratidal zone formed in the past, when the mats were active at the surface. In a second scenario, dolomite formation continues within the buried and inactive mats. In order to explain dolomite formation in the absence of active microbial metabolisms, a revised microbial model is proposed in which the mineral-template properties of exopolymeric substances play a crucial role.

267 citations

Journal ArticleDOI
TL;DR: A review of the direct and indirect mechanisms by which microbes facilitate the nucleation and shallow burial diagenetic stabilization of dolomite in marine sediments is presented in this paper.

187 citations

Journal ArticleDOI
01 Aug 2008-Geology
TL;DR: In this paper, microbe-mineral interactions in experimentally produced carbonate globules were investigated under anoxic conditions at 30 °C with Desulfovibrio brasiliensis, a sulfate-reducing bacteria (SRB) known to mediate dolomite formation.
Abstract: Microsedimentary structures referred to as nanobacteria-like particles were described from modern carbonate environments, where they form in close spatial association with sulfate-reducing bacteria (SRB). However, the exact mechanism of their formation, as well as their paleontological significance, remains controversial. Here we report on an investigation of microbe-mineral interactions in experimentally produced carbonate globules. The experiments were carried out under anoxic conditions at 30 °C with Desulfovibrio brasiliensis, a SRB known to mediate dolomite formation. We observed that extracellular polymeric substances (EPS) secreted by the microbial community play a key role in the mineralization process. Nanobacteria-like particles represent the early stage of carbonate nucleation within the EPS, which progressively evolve to larger globules displaying a grainy texture. We excluded the possibilities that these structures are fossils of nanobacteria, dissolution surfaces, or artifacts created during sample preparation. D. brasiliensis cells are predominantly located outside of the EPS aggregates where mineral growth takes place. As a result, they remain mobile and are rarely entombed within the mineral. This self-preservation behavior may not be limited to D. brasiliensis. Other microbes may produce, or may have produced during the geological past, biogenic minerals through a similar process. Mineralization within EPS explains why microbial relics are not necessarily present in biogenic carbonates.

165 citations

Journal ArticleDOI
TL;DR: Positive Δ33S anomalies suggest that disproportionation of elemental sulfur would have been a prominent microbial process in these communities, and are interpreted as recording the process of sulfurization of organic matter by H2S in heterogeneous mat pore-waters influenced by respiratory S metabolism.
Abstract: The 3.45-billion-year-old Strelley Pool Formation of Western Australia preserves stromatolites that are considered among the oldest evidence for life on Earth. In places of exceptional preservation, these stromatolites contain laminae rich in organic carbon, interpreted as the fossil remains of ancient microbial mats. To better understand the biogeochemistry of these rocks, we performed microscale in situ sulfur isotope measurements of the preserved organic sulfur, including both Δ^(33)S and δ^(34)S_(CDT). This approach allows us to tie physiological inference from isotope ratios directly to fossil biomass, providing a means to understand sulfur metabolism that is complimentary to, and independent from, inorganic proxies (e.g., pyrite). Δ^(33)S values of the kerogen reveal mass-anomalous fractionations expected of the Archean sulfur cycle, whereas δ^(34)S_(CDT) values show large fractionations at very small spatial scales, including values below −15‰. We interpret these isotopic patterns as recording the process of sulfurization of organic matter by H_2S in heterogeneous mat pore-waters influenced by respiratory S metabolism. Positive Δ^(33)S anomalies suggest that disproportionation of elemental sulfur would have been a prominent microbial process in these communities.

130 citations

Journal ArticleDOI
TL;DR: In this paper, the formation of carbonate minerals by sulphate-reducing bacteria (SRB) can occur in the absence of living cells, through passive mineralization of their exopolymeric substances (EPS).
Abstract: Some species of sulphate-reducing bacteria (SRB) are known to mediate the formation of dolomite and Mg-calcite. However, their exact role in the mineralization process remains elusive. Here, we present the result of a laboratory experiment that was designed to test whether formation of carbonate minerals by SRB can occur in the absence of living cells, through passive mineralization of their exopolymeric substances (EPS). SRB capable of mediating dolomite were cultivated in the laboratory, allowing them to secrete EPS. Microbial activity within the cultures was subsequently inhibited with antibiotics. Only after this step, Ca2+ and Mg2+ were added to the solution and carbonate minerals could form. Mg-calcite and disordered Ca-dolomite precipitated in association with EPS. The mol.% of Mg2+ in the crystals increased with longer incubation times. This result demonstrates that organic compounds produced by SRB can mediate the formation of Ca-Mg carbonates in the absence of an active metabolism.

126 citations


Cited by
More filters
Journal ArticleDOI
TL;DR: It is proposed that, due to limited mass transfer, high photosynthetic activity in Fe2-rich environments forms a protective zone where Fe2+ precipitates abiotically at a non-lethal distance from the cyanobacteria.
Abstract: If O2 is available at circumneutral pH, Fe2+ is rapidly oxidized to Fe3+, which precipitates as FeO(OH). Neutrophilic iron oxidizing bacteria have evolved mechanisms to prevent self-encrustation in iron. Hitherto, no mechanism has been proposed for cyanobacteria from Fe2+-rich environments; these produce O2 but are seldom found encrusted in iron. We used two sets of illuminated reactors connected to two groundwater aquifers with different Fe2+ concentrations (0.9 μM vs. 26 μM) in the Aspo Hard Rock Laboratory (HRL), Sweden. Cyanobacterial biofilms developed in all reactors and were phylogenetically different between the reactors. Unexpectedly, cyanobacteria growing in the Fe2+-poor reactors were encrusted in iron, whereas those in the Fe2+-rich reactors were not. In-situ microsensor measurements showed that O2 concentrations and pH near the surface of the cyanobacterial biofilms from the Fe2+-rich reactors were much higher than in the overlying water. This was not the case for the biofilms growing at low Fe2+ concentrations. Measurements with enrichment cultures showed that cyanobacteria from the Fe2+-rich environment increased their photosynthesis with increasing Fe2+ concentrations, whereas those from the low Fe2+ environment were inhibited at Fe2+ > 5 μM. Modeling based on in-situ O2 and pH profiles showed that cyanobacteria from the Fe2+-rich reactor were not exposed to significant Fe2+ concentrations. We propose that, due to limited mass transfer, high photosynthetic activity in Fe2+-rich environments forms a protective zone where Fe2+ precipitates abiotically at a non-lethal distance from the cyanobacteria. This mechanism sheds new light on the possible role of cyanobacteria in precipitation of banded iron formations.

968 citations

Journal ArticleDOI
TL;DR: It is proposed that biofilms drive all biogeochemical processes and represent the main way of active bacterial and archaeal life and are the most prominent and influential type of microbial life.
Abstract: Biofilms are a form of collective life with emergent properties that confer many advantages on their inhabitants, and they represent a much higher level of organization than single cells do. However, to date, no global analysis on biofilm abundance exists. We offer a critical discussion of the definition of biofilms and compile current estimates of global cell numbers in major microbial habitats, mindful of the associated uncertainty. Most bacteria and archaea on Earth (1.2 × 1030 cells) exist in the ‘big five’ habitats: deep oceanic subsurface (4 × 1029), upper oceanic sediment (5 × 1028), deep continental subsurface (3 × 1029), soil (3 × 1029) and oceans (1 × 1029). The remaining habitats, including groundwater, the atmosphere, the ocean surface microlayer, humans, animals and the phyllosphere, account for fewer cells by orders of magnitude. Biofilms dominate in all habitats on the surface of the Earth, except in the oceans, accounting for ~80% of bacterial and archaeal cells. In the deep subsurface, however, they cannot always be distinguished from single sessile cells; we estimate that 20–80% of cells in the subsurface exist as biofilms. Hence, overall, 40–80% of cells on Earth reside in biofilms. We conclude that biofilms drive all biogeochemical processes and represent the main way of active bacterial and archaeal life. In this Analysis article, Flemming and Wuertz calculate the total number of bacteria and archaea on Earth and estimate the fraction that lives in biofilms. They propose that biofilms are the most prominent and influential type of microbial life.

808 citations

Journal ArticleDOI
TL;DR: For example, in this article, the authors present a method for interpreting carbonate diagenesis of carbonate rocks by analyzing the δ18O value of any fluid inclusions or by measuring the temperature using a method such as the clumped isotope technique.
Abstract: Stable carbon and oxygen isotopes (δ18O and δ13C values) and trace elements have been applied to the study of diagenesis of carbonate rocks for over 50 years. As valuable as these insights have been, many problems regarding the interpretation of geochemical signals within mature rocks remain. For example, while the δ18O values of carbonate rocks are dependent both upon the temperature and the δ18O value of the fluid, and additional information including trace element composition aids in interpreting such signals, direct evidence of either the temperature or the composition of the fluids is required. Such information can be obtained by analysing the δ18O value of any fluid inclusions or by measuring the temperature using a method such as the ‘clumped’ isotope technique. Such data speak directly to a large number of problems in interpreting the oxygen isotope record including the well-known tendency for δ18O values of carbonate rocks to decrease with increasing age. Unlike the δ18O, δ13C values of carbonates are considered to be less influenced by diagenesis and more a reflection of primary changes in the global carbon cycle through time. However, many studies have not sufficiently emphasized the effects of diagenesis and other post-depositional influences on the eventual carbon isotopic composition of the rock with the classic paradigm that the present is the key to the past being frequently ignored. Finally, many additional proxies are poised to contribute to the interpretation of carbonate diagenesis. Although the study of carbonate diagenesis is at an exciting point with an explosion of new proxies and methods, care should be taken to understand both old and new proxies before applying them to the ancient record.

415 citations

Journal ArticleDOI
TL;DR: The second ExoMars mission will be launched in 2020 to target an ancient location interpreted to have strong potential for past habitability and for preserving physical and chemical biosignatures (as well as abiotic/prebiotic organics).
Abstract: The second ExoMars mission will be launched in 2020 to target an ancient location interpreted to have strong potential for past habitability and for preserving physical and chemical biosignatures (as well as abiotic/prebiotic organics). The mission will deliver a lander with instruments for atmospheric and geophysical investigations and a rover tasked with searching for signs of extinct life. The ExoMars rover will be equipped with a drill to collect material from outcrops and at depth down to 2 m. This subsurface sampling capability will provide the best chance yet to gain access to chemical biosignatures. Using the powerful Pasteur payload instruments, the ExoMars science team will conduct a holistic search for traces of life and seek corroborating geological context information. Key Words: Biosignatures-ExoMars-Landing sites-Mars rover-Search for life. Astrobiology 17, 471-510.

349 citations