Unveiling microbial preservation under hyperacidic and oxidizing conditions in the Oligocene Rio Tinto deposit

Fernández-Remolar, David C.; Carrizo, Daniel; Harir, Mourad; Huang, Tur‐Fu; Amils, Ricardo; Schmitt‐Kopplin, Philippe; Sánchez-García, Laura; Gómez-Ortíz, David; Malmberg, Per

doi:10.1038/s41598-021-00730-8

Cited by 5 publications

(13 citation statements)

References 110 publications

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“…Both the reduction and oxidation of Fe could act as different paths to dissolve minerals and further increase the content of soluble metals in the underwater reservoir. Fe 3+ can react with the S 2− of the pyrite (FeS 2 ) oxidizing it to SO 4 2− while Fe 3+ is reduced to Fe 2+ and protons are released as well [93,94]. The Fe 2+ would be oxidized indirectly through the NDFO by Shewanella sp.…”

Section: Iron Oxidation and Reduction Assaysmentioning

confidence: 99%

Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt

Mateos

Bonilla²,

Polanco³

et al. 2022

Microorganisms

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The Iberian Pyrite Belt (IPB) is one of the largest deposits of sulphidic minerals on Earth. Río Tinto raises from its core, presenting low a pH and high metal concentration. Several drilling cores were extracted from the IPB’s subsurface, and strain T2.3D-1.1 was isolated from a core at 121.8 m depth. We aimed to characterize this subterranean microorganism, revealing its phylogenomic affiliation (Average Nucleotide Identity, digital DNA-DNA Hybridization) and inferring its physiology through genome annotation, backed with physiological experiments to explore its relationship with the Fe biogeochemical cycle. Results determined that the isolate belongs to the Shewanella putrefaciens (with ANI 99.25 with S. putrefaciens CN-32). Its genome harbours the necessary genes, including omcA mtrCAB, to perform the Extracellular Electron Transfer (EET) and reduce acceptors such as Fe3+, napAB to reduce NO3− to NO2−, hydAB to produce H2 and genes sirA, phsABC and ttrABC to reduce SO32−, S2O32− and S4O62−, respectively. A full CRISPR-Cas 1F type system was found as well. S. putrefaciens T2.3D-1.1 can reduce Fe3+ and promote the oxidation of Fe2+ in the presence of NO3− under anaerobic conditions. Production of H2 has been observed under anaerobic conditions with lactate or pyruvate as the electron donor and fumarate as the electron acceptor. Besides Fe3+ and NO3−, the isolate also grows with Dimethyl Sulfoxide and Trimethyl N-oxide, S4O62− and S2O32− as electron acceptors. It tolerates different concentrations of heavy metals such as 7.5 mM of Pb, 5 mM of Cr and Cu and 1 mM of Cd, Co, Ni and Zn. This array of traits suggests that S. putrefaciens T2.3D-1.1 could have an important role within the Iberian Pyrite Belt subsurface participating in the iron cycle, through the dissolution of iron minerals and therefore contributing to generate the extreme conditions detected in the Río Tinto basin.

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Section: Iron Oxidation and Reduction Assaysmentioning

confidence: 99%

Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt

Mateos

Bonilla²,

Polanco³

et al. 2022

Microorganisms

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“…The distribution of inorganic and organic ions was performed to understand the association among the inorganic and organic compounds with the different elements of the structure and texture sample. In sample 95E5/3, the ion distribution characterized by the ToF-SIMS mapping capability greatly depends on the arrangement of the rock’s primary components like skeletal/non-skeletal grains and bioclasts, and the mineral matrix or cement [ 34 , 49 ].…”

Section: Resultsmentioning

confidence: 99%

“…Polished sections for sample 95E5/3 were prepared for mineral and textural analysis under a microscope and molecular surface analysis by ToF-SIMS [ 34 ]. The surface sample was extra-polished using a 0.3 mm alumina paste to reduce surface imperfections that produce frequent interferences during the surface analysis.…”

Section: Methodsmentioning

confidence: 99%

“…Furthermore, a multivariate analysis combining the spectral and spatial distribution in the sample was run to find correlations between fragment occurrence and molecular fragmentation patterns. Mass spectral acquisition and image analysis were performed within the ION-TOF Surface Lab software suit (version 7.0), including the overload of Red, Green, and Blue (RGB) images for molecular mapping [ 34 , 37 ]. The analysis of the molecular fragmentation pattern was completed through the Chemical online tool [ 38 ] and the open source mass spectrometry tool mMass [ 39 ].…”

Section: Methodsmentioning

confidence: 99%

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The Molecular Profile of Soil Microbial Communities Inhabiting a Cambrian Host Rock

Huang,

Carrizo,

Sánchez-García

et al. 2024

Microorganisms

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The process of soil genesis unfolds as pioneering microbial communities colonize mineral substrates, enriching them with biomolecules released from bedrock. The resultant intricate surface units emerge from a complex interplay among microbiota and plant communities. Under these conditions, host rocks undergo initial weathering through microbial activity, rendering them far from pristine and challenging the quest for biomarkers in ancient sedimentary rocks. In addressing this challenge, a comprehensive analysis utilizing Gas Chromatography Mass Spectrometry (GC-MS) and Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) was conducted on a 520-Ma-old Cambrian rock. This investigation revealed a diverse molecular assemblage with comprising alkanols, sterols, fatty acids, glycerolipids, wax esters, and nitrogen-bearing compounds. Notably, elevated levels of bacterial C16, C18 and C14 fatty acids, iso and anteiso methyl-branched fatty acids, as well as fungal sterols, long-chained fatty acids, and alcohols, consistently align with a consortium of bacteria and fungi accessing complex organic matter within a soil-type ecosystem. The prominence of bacterial and fungal lipids alongside maturity indicators denotes derivation from heterotrophic activity rather than ancient preservation or marine sources. Moreover, the identification of long-chain (>C22) n-alkanols, even-carbon-numbered long chain (>C20) fatty acids, and campesterol, as well as stigmastanol, provides confirmation of plant residue inputs. Furthermore, findings highlight the ability of contemporary soil microbiota to inhabit rocky substrates actively, requiring strict contamination controls when evaluating ancient molecular biosignatures or extraterrestrial materials collected.

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“…In Rio Tinto, an exhaustive SIMS investigation demonstrated that molecular biosignatures could be well preserved under the acidic oxidative surface of Rio Tinto (Fernández-Remolar et al, 2021). Organic materials as biosignatures in Rio Tinto were isolated from inorganic substances and detected using EA-IRMS (Table 2).…”

Section: Applications Of Instrumentsmentioning

confidence: 99%

Detection of biosignatures in terrestrial Mars analogs: Strategical and technical assessments

Shen¹,

Chen²,

Sun³

et al. 2022

Earth and Planetary Physics

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The search for potential signs of Martian life has been planned and implemented by worldwide countries for decades. Due to the high expenditure on Mars exploration, more easily accessible Marslike regions on Earth are invaluable targets for astrobiology research to understand the detection of potential Martian biosignatures. In order to detect potential life signals beyond Earth, questions on how to define life and biosignatures need to be carefully inspected. This review summarizes scientific instrumental techniques, our "eyes" and "hands", that facilitate identifying and quantifying biosignatures on Mars. Scientific devices that can be applied in astrobiology include electromagnetic spectrum-based spectrometers, mass spectrometers, redox potential indicators, circular dichroism polarimeters, in situ nucleic acid sequencers, life isolation/cultivation systems, and imagers. These techniques should be first tested in Mars analog extreme environments on Earth to validate their practicality on Mars. To better understand the instrumental detectability of biosignatures on Mars through its evolutionary history, terrestrial Mars analogs are divided into four major categories according to their similarities to different geological ages of Mars (the Early-Middle Noachian Period, the Late Noachian-Early Hesperian Period, the Late Hesperian-Early Amazonian Period, and the Middle-Late Amazonian Period). Future missions are suggested to explore more on the early terrains in Mars' Southern Hemisphere once the landing issue is solved engineeringly, since these explorations permit investigating a continuum of the habitability shift through Mars geological history. Moreover, practical applications of scientific instruments listed above are briefly reviewed based on the four categories of Mars analogs, and instruments applied for autonomous robotic rover tests in Mars analogs are further discussed. For engineering efficiency, a Mars rover ought to be equipped with as few assemblable instruments as possible. Therefore, once candidate landing regions 1 Biosignatures in Mars analogson Mars are defined, the portable suites of instruments should be smartly devised on the basis of the geological, geochemical, geomorphological, and chronological characteristics of the landing regions. Laboratory-based experiments without engineering restrictions are further encouraging and appealing if Mars sample-return missions are successfully completed. To exclude false positive and false negative conclusions in life discovery, the combined use and replication studies of multiple analytical techniques must be performed to confirm the observational results.

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Unveiling microbial preservation under hyperacidic and oxidizing conditions in the Oligocene Rio Tinto deposit

Cited by 5 publications

References 110 publications

Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt

Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt

The Molecular Profile of Soil Microbial Communities Inhabiting a Cambrian Host Rock

Detection of biosignatures in terrestrial Mars analogs: Strategical and technical assessments

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