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Dong H, Huang L, Zhao L, Zeng Q, Liu X, Sheng Y, Shi L, Wu G, Jiang H, Li F, Zhang L, Guo D, Li G, Hou W, Chen H. A critical review of mineral-microbe interaction and coevolution: mechanisms and applications. Natl Sci Rev 2022; 9:nwac128. [PMID: 36196117 PMCID: PMC9522408 DOI: 10.1093/nsr/nwac128] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
The mineral-microbe interactions play important roles in environmental change, biogeochemical cycling of elements, and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation, and precipitation of minerals through their activity, resulting in either genetically-controlled or metabolism-induced biomineralization. Through these interactions minerals and microbes coevolve through Earth history. The mineral-microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral-microbe interactions for the benefit of humankind.
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Affiliation(s)
- Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Beijing 100083 , China
| | - Liuqin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan 430074 , China
| | - Linduo Zhao
- Illinois Sustainable Technology Center , Illinois State Water Survey, , Champaign , IL 61820 , USA
- University of Illinois at Urbana-Champaign , Illinois State Water Survey, , Champaign , IL 61820 , USA
| | - Qiang Zeng
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Beijing 100083 , China
| | - Xiaolei Liu
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Beijing 100083 , China
| | - Yizhi Sheng
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Beijing 100083 , China
| | - Liang Shi
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan 430074 , China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan 430074 , China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan 430074 , China
| | - Fangru Li
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Beijing 100083 , China
| | - Li Zhang
- Department of Geology and Environmental Earth Science, Miami University , Oxford , OH 45056 , USA
| | - Dongyi Guo
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Beijing 100083 , China
| | - Gaoyuan Li
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Beijing 100083 , China
| | - Weiguo Hou
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Beijing 100083 , China
| | - Hongyu Chen
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Beijing 100083 , China
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Chi ZL, Yu GH, Teng HH, Liu HG, Wang J, Liu CQ, Shen QR, Gadd GM. Molecular Trade-Offs between Lattice Oxygen and Oxygen Vacancy Drive Organic Pollutant Degradation in Fungal Biomineralized Exoskeletons. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:8132-8141. [PMID: 35561278 DOI: 10.1021/acs.est.2c01388] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fungal-mineral interactions can effectively alleviate cellular stress from organic pollutants, the production of which are expected to rapidly increase owing to the Earth moving into an unprecedented geological epoch, the Anthropocene. The underlying mechanisms that may enable fungi to combat organic pollution during fungal-mineral interactions remain unclear. Inspired by the natural fungal sporulation process, we demonstrate for the first time that fungal biomineralization triggers the formation of an ultrathin (hundreds of nanometers thick) exoskeleton, enriched in nanosized iron (oxyhydr)oxides and biomolecules, on the hyphae. Mapped biochemical composition of this coating at a subcellular scale via high spatial resolution (down to 50 nm) synchrotron radiation-based techniques confirmed aromatic C, C-N bonds, amide carbonyl, and iron (oxyhydr)oxides as the major components of the coatings. This nanobiohybrid system appeared to impart a strong (×2) biofunctionality for fungal degradation of bisphenol A through altering molecular-level trade-offs between lattice oxygen and oxygen vacancy. Together, fungal coatings could act as "artificial spores", which enable fungi to combat physical and chemical stresses in natural environments, providing crucial insights into fungal biomineralization and coevolution of the Earth's lithosphere and biosphere.
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Affiliation(s)
- Zhi-Lai Chi
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guang-Hui Yu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - H Henry Teng
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
- Department of Chemistry, George Washington University, Washington, District of Columbia 20006, United States
| | - Hai-Gang Liu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Jian Wang
- Canadian Light Source Inc., University of Saskatchewan, 44 Innovation Boulevard, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Qi-Rong Shen
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, College of Chemical Engineering and Environment, China University of Petroleum, Beijing 102249, China
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Papineau D, She Z, Dodd MS, Iacoviello F, Slack JF, Hauri E, Shearing P, Little CTS. Metabolically diverse primordial microbial communities in Earth's oldest seafloor-hydrothermal jasper. SCIENCE ADVANCES 2022; 8:eabm2296. [PMID: 35417227 PMCID: PMC9007518 DOI: 10.1126/sciadv.abm2296] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The oldest putative fossils occur as hematite filaments and tubes in jasper-carbonate banded iron formations from the 4280- to 3750-Ma Nuvvuagittuq Supracrustal Belt, Québec. If biological in origin, these filaments might have affinities with modern descendants; however, if abiotic, they could indicate complex prebiotic forms on early Earth. Here, we report images of centimeter-size, autochthonous hematite filaments that are pectinate-branching, parallel-aligned, undulated, and containing Fe2+-oxides. These microstructures are considered microfossils because of their mineral associations and resemblance to younger microfossils, modern Fe-bacteria from hydrothermal environments, and the experimental products of heated Fe-oxidizing bacteria. Additional clusters of irregular hematite ellipsoids could reflect abiotic processes of silicification, producing similar structures and thus yielding an uncertain origin. Millimeter-sized chalcopyrite grains within the jasper-carbonate rocks have 34S- and 33S-enrichments consistent with microbial S-disproportionation and an O2-poor atmosphere. Collectively, the observations suggest a diverse microbial ecosystem on the primordial Earth that may be common on other planetary bodies, including Mars.
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Affiliation(s)
- Dominic Papineau
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Sciences, China University of Geosciences, Wuhan, China
- London Centre for Nanotechnology, University College London, London, UK
- Department of Earth Sciences, University College London, London, UK
- Centre for Planetary Sciences, University College London & Birkbeck College London, London, UK
| | - Zhenbing She
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Sciences, China University of Geosciences, Wuhan, China
| | - Matthew S. Dodd
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Sciences, China University of Geosciences, Wuhan, China
| | | | - John F. Slack
- U.S. Geological Survey National Center, Reston, VA, USA
- Department of Earth Sciences, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Erik Hauri
- Department of Terrestrial Magnetism, Carnegie Institution for Science, Washington, DC, USA
| | - Paul Shearing
- Department of Chemical Engineering, University College London, London, UK
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Li X, Graham NJD, Deng W, Liu M, Liu T, Yu W. Structural Variation of Precipitates Formed by Fe(II) Oxidation and Impact on the Retention of Phosphate. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4345-4355. [PMID: 35319869 DOI: 10.1021/acs.est.1c06256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The oxidation-precipitation process of Fe(II) is ubiquitous in the environment and critically affects the fate of contaminants and nutrients in natural systems where Fe(II) is present. Here, we explored the effect of H2O2 concentration on the structure of precipitates formed by Fe(II) oxidation and compared the precipitates to those formed by Fe(III) hydrolysis. Additionally, the phosphate retention under different H2O2 concentrations was evaluated. XRD, TEM, PDA, XPS, and UV-visible absorbance spectroscopy were used to characterize the structure of the formed precipitates; UV-visible absorbance spectroscopy was also used to determine the residual phosphate and Fe(II) in solution. It was found that the predominant precipitates in Fe(II) solution changed from planar-shaped crystalline lepidocrocite (γ-FeOOH) to poor short-range order (poorly crystalline) spherical-shaped hydrous ferric oxide (HFO) with increasing H2O2 concentrations. Although the HFO precipitates formed from Fe(II) resembled those formed from Fe(III) hydrolysis, the former was larger and had clearer lattice fringes. During the formation of γ-FeOOH, both Fe(II)-Fe(III) complexes and ligand-to-metal charge transfer processes were observed, and it was found that Fe(II) was present in the planar-shaped precipitates. Fe(II) might be present in the interior of precipitates as Fe(OH)2, which could serve as a nucleus for the epitaxial growth of γ-FeOOH. In addition, the extent of phosphate retention increased with the H2O2 concentration, indicating the increased reactivity of formed precipitates with H2O2 concentration. More phosphate was retained via coprecipitation with Fe than adsorption on the preformed Fe precipitates due to the incorporation of phosphate within the structure of the formed Fe hydroxyphosphate via coprecipitation.
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Affiliation(s)
- Xian Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Nigel J D Graham
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
| | - Wensheng Deng
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Mengjie Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Ting Liu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Wenzheng Yu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
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5
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Chen R, Liu H, Zhang P, Ma J, Jin M. Co-response of Fe-reducing/oxidizing bacteria and Fe species to the dynamic redox cycles of natural sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152953. [PMID: 34999076 DOI: 10.1016/j.scitotenv.2022.152953] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Fe(III)-reducing bacteria (FRB) and Fe(II)-oxidizing bacteria (FOB) play essential roles in the biogeochemical cycling of iron (Fe). Although the redox transformation of Fe species mediated by FRB/FOB has been extensively studied, the co-responses of FRB and FOB and Fe species transformation in natural sediment under dynamic redox conditions are poorly known. This study explored the variations of potential FRB and FOB abundances and Fe species transformation in natural sediment during successive anoxic-oxic-anoxic-oxic-anoxic cycles. Compared with the pristine sediment sample, the FRB abundance increased 121-793% (initial: (2.6 ± 0.6) × 107 copies/g) in the anoxic stages, while it decreased by 38-64% in the oxic stages. The increase in FRB abundance was ascribed to energy gain of FRB from the reduction of the amorphous Fe(III) (Fe(III)am) and the crystalline Fe(III) (Fe(III)cry) to the aqueous Fe(II) (Fe(II)aq), the adsorbed Fe(II) (Fe(II)ad) and the amorphous Fe(II) (Fe(II)am), while the decrease was attributed to the oxidative stress caused by the reactive oxidant produced from the abiotic oxidation of Fe(II)aq, Fe(II)ad and Fe(II)am to Fe(III)am and Fe(III)cry. The FOB abundance decreased 38-44% (initial: (5 ± 1.8) × 107 copies/g) in the second and third anoxic stages, while slightly fluctuated in the oxic periods. This observation was contrary to the variation of FRB, which might be attributed to the strong resistance to oxidative stress of FOB and its ability to obtain energy under oxic conditions. Although the functions of FRB and FOB were impaired during anoxic-oxic cycles, the transformation of Fe(II)/Fe(III) was not immediately affected, which may be related to the residual reactivity of dead bacteria and the bio-availability of Fe(II)/Fe(III) species. In the anoxic-oxic alternation process, the iron cycle is mainly the mutual transformation between Fe(II)aq, Fe(II)ad, Fe(II)am and Fe(III)am, Fe(III)cry. This finding deepens our understanding of the biogeochemical cycling of Fe in the redox-dynamic environments.
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Affiliation(s)
- Rong Chen
- School of Environmental Studies, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China
| | - Hui Liu
- School of Environmental Studies, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China.
| | - Peng Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China
| | - Jie Ma
- School of Environmental Studies, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China
| | - Menggui Jin
- School of Environmental Studies, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China
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6
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Price A, Macey MC, Pearson VK, Schwenzer SP, Ramkissoon NK, Olsson-Francis K. Oligotrophic Growth of Nitrate-Dependent Fe 2+-Oxidising Microorganisms Under Simulated Early Martian Conditions. Front Microbiol 2022; 13:800219. [PMID: 35418959 PMCID: PMC8997339 DOI: 10.3389/fmicb.2022.800219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/24/2022] [Indexed: 11/30/2022] Open
Abstract
Nitrate-dependent Fe2+ oxidation (NDFO) is a microbially mediated process observed in many anaerobic, low-nutrient (oligotrophic) neutral-alkaline environments on Earth, which describes oxidation of Fe2+ to Fe3+ in tandem with microbial nitrate reduction. Evidence suggests that similar environments existed on Mars during the Noachian epoch (4.1-3.7 Ga) and in periodic, localised environments more recently, indicating that NDFO metabolism could have played a role in a potential early martian biosphere. In this paper, three NDFO microorganisms, Acidovorax sp. strain BoFeN1, Pseudogulbenkiania sp. strain 2002 and Paracoccus sp. strain KS1, were assessed for their ability to grow oligotrophically in simulated martian brines and in a minimal medium with olivine as a solid Fe2+ source. These simulant-derived media were developed from modelled fluids based on the geochemistry of Mars sample locations at Rocknest (contemporary Mars soil), Paso Robles (sulphur-rich soil), Haematite Slope (haematite-rich soil) and a Shergottite meteorite (common basalt). The Shergottite medium was able to support growth of all three organisms, while the contemporary Mars medium supported growth of Acidovorax sp. strain BoFeN1 and Pseudogulbenkiania sp. strain 2002; however, growth was not accompanied by significant Fe2+ oxidation. Each of the strains was also able to grow in oligotrophic minimal media with olivine as the sole Fe2+ source. Biomineralised cells of Pseudogulbenkiania sp. strain 2002 were identified on the surface of the olivine, representing a potential biosignature for NDFO microorganisms in martian samples. The results suggest that NDFO microorganisms could have thrived in early martian groundwaters under oligotrophic conditions, depending on the local lithology. This can guide missions in identifying palaeoenvironments of interest for biosignature detection. Indeed, biomineralised cells identified on the olivine surface provide a previously unexplored mechanism for the preservation of morphological biosignatures in the martian geological record.
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Affiliation(s)
- Alex Price
- School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Michael C. Macey
- School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Victoria K. Pearson
- School of Physical Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Susanne P. Schwenzer
- School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Nisha K. Ramkissoon
- School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Karen Olsson-Francis
- School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
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Goodwin A, Papineau D. Biosignatures Associated with Organic Matter in Late Paleoproterozoic Stromatolitic Dolomite and Implications for Martian Carbonates. ASTROBIOLOGY 2022; 22:49-74. [PMID: 34664990 DOI: 10.1089/ast.2021.0010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The documentation of biosignatures in Precambrian rocks is an important requirement in the search for evidence of life on other ancient planetary surfaces. Three major kinds of biosignatures are crucially important: primary microbial sedimentary textures, diagenetic organomineral assemblages, and stable isotope compositions. This study presents new petrographic, mineralogical, and organic geochemical analyses of biosignatures in dolomitic stromatolites from the Pethei Group (N.W.T., Canada) and the Kasegalik Formation of the Belcher Group (Nunavut, Canada). Both are approximately contemporary late Paleoproterozoic stromatolite-bearing dolomitic units deposited after the Great Oxidation Event. Micro-Raman and optical microscopy are used to identify and characterize possible diagenetic biosignatures, which include close spatial association of diagenetic materials (such as ferric-ferrous oxide and anatase) with disseminated organic matter (OM), dolomitic groundmass textures, and mineralized balls. Many of these petrographic relationships point to the oxidation of OM either biotically or abiotically in association with iron reduction and chemically oscillating reactions. Oxidation of OM in these stromatolites is consistent with the widespread oxidation of biomass during the late Paleoproterozoic Shunga-Francevillian Event. Biosignatures identified in this study are also compared with possible carbonate outcrops on Mars, and thereby contribute a basis for comparison with potential biosignatures in ancient martian terrains. Similarities are drawn between the paleoenvironments of the studied units to the Isidis and Chryse planitia as locations for potential extraterrestrial dolomitic stromatolites.
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Affiliation(s)
- Arthur Goodwin
- Centre for Planetary Sciences, UCL-Birkbeck, London, United Kingdom
| | - Dominic Papineau
- Centre for Planetary Sciences, UCL-Birkbeck, London, United Kingdom
- London Centre for Nanotechnology, University College London, London, United Kingdom
- Department of Earth Sciences, University College London, London, United Kingdom
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8
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Ehrlich H, Bailey E, Wysokowski M, Jesionowski T. Forced Biomineralization: A Review. Biomimetics (Basel) 2021; 6:46. [PMID: 34287234 PMCID: PMC8293141 DOI: 10.3390/biomimetics6030046] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/31/2022] Open
Abstract
Biologically induced and controlled mineralization of metals promotes the development of protective structures to shield cells from thermal, chemical, and ultraviolet stresses. Metal biomineralization is widely considered to have been relevant for the survival of life in the environmental conditions of ancient terrestrial oceans. Similar behavior is seen among extremophilic biomineralizers today, which have evolved to inhabit a variety of industrial aqueous environments with elevated metal concentrations. As an example of extreme biomineralization, we introduce the category of "forced biomineralization", which we use to refer to the biologically mediated sequestration of dissolved metals and metalloids into minerals. We discuss forced mineralization as it is known to be carried out by a variety of organisms, including polyextremophiles in a range of psychrophilic, thermophilic, anaerobic, alkaliphilic, acidophilic, and halophilic conditions, as well as in environments with very high or toxic metal ion concentrations. While much additional work lies ahead to characterize the various pathways by which these biominerals form, forced biomineralization has been shown to provide insights for the progression of extreme biomimetics, allowing for promising new forays into creating the next generation of composites using organic-templating approaches under biologically extreme laboratory conditions relevant to a wide range of industrial conditions.
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Affiliation(s)
- Hermann Ehrlich
- Institute of Electronic and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany
- Center for Advanced Technology, Adam Mickiewicz University, 61614 Poznan, Poland
- Centre for Climate Change Research, Toronto, ON M4P 1J4, Canada
- ICUBE-University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Elizabeth Bailey
- Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064, USA;
| | - Marcin Wysokowski
- Faculty of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, 60-965 Poznan, Poland
| | - Teofil Jesionowski
- Faculty of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, 60-965 Poznan, Poland
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9
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Koeksoy E, Bezuidt OM, Bayer T, Chan CS, Emerson D. Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export. Front Microbiol 2021; 12:679409. [PMID: 34220764 PMCID: PMC8250860 DOI: 10.3389/fmicb.2021.679409] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022] Open
Abstract
Twisted stalks are morphologically unique bacterial extracellular organo-metallic structures containing Fe(III) oxyhydroxides that are produced by microaerophilic Fe(II)-oxidizers belonging to the Betaproteobacteria and Zetaproteobacteria. Understanding the underlying genetic and physiological mechanisms of stalk formation is of great interest based on their potential as novel biogenic nanomaterials and their relevance as putative biomarkers for microbial Fe(II) oxidation on ancient Earth. Despite the recognition of these special biominerals for over 150 years, the genetic foundation for the stalk phenotype has remained unresolved. Here we present a candidate gene cluster for the biosynthesis and secretion of the stalk organic matrix that we identified with a trait-based analyses of a pan-genome comprising 16 Zetaproteobacteria isolate genomes. The “stalk formation in Zetaproteobacteria” (sfz) cluster comprises six genes (sfz1-sfz6), of which sfz1 and sfz2 were predicted with functions in exopolysaccharide synthesis, regulation, and export, sfz4 and sfz6 with functions in cell wall synthesis manipulation and carbohydrate hydrolysis, and sfz3 and sfz5 with unknown functions. The stalk-forming Betaproteobacteria Ferriphaselus R-1 and OYT-1, as well as dread-forming Zetaproteobacteria Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8 contain distant sfz gene homologs, whereas stalk-less Zetaproteobacteria and Betaproteobacteria lack the entire gene cluster. Our pan-genome analysis further revealed a significant enrichment of clusters of orthologous groups (COGs) across all Zetaproteobacteria isolate genomes that are associated with the regulation of a switch between sessile and motile growth controlled by the intracellular signaling molecule c-di-GMP. Potential interactions between stalk-former unique transcription factor genes, sfz genes, and c-di-GMP point toward a c-di-GMP regulated surface attachment function of stalks during sessile growth.
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Affiliation(s)
- Elif Koeksoy
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Leibniz Institute DSMZ (German Collection of Microorganisms and Cell Cultures), Braunschweig, Germany
| | - Oliver M Bezuidt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Timm Bayer
- Geomicrobiology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Clara S Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States.,School of Marine Sciences and Policy, University of Delaware, Newark, DE, United States
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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10
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Little CTS, Johannessen KC, Bengtson S, Chan CS, Ivarsson M, Slack JF, Broman C, Thorseth IH, Grenne T, Rouxel OJ, Bekker A. A late Paleoproterozoic (1.74 Ga) deep-sea, low-temperature, iron-oxidizing microbial hydrothermal vent community from Arizona, USA. GEOBIOLOGY 2021; 19:228-249. [PMID: 33594795 DOI: 10.1111/gbi.12434] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 01/18/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Modern marine hydrothermal vents occur in a wide variety of tectonic settings and are characterized by seafloor emission of fluids rich in dissolved chemicals and rapid mineral precipitation. Some hydrothermal systems vent only low-temperature Fe-rich fluids, which precipitate deposits dominated by iron oxyhydroxides, in places together with Mn-oxyhydroxides and amorphous silica. While a proportion of this mineralization is abiogenic, most is the result of the metabolic activities of benthic, Fe-oxidizing bacteria (FeOB), principally belonging to the Zetaproteobacteria. These micro-organisms secrete micrometer-scale stalks, sheaths, and tubes with a variety of morphologies, composed largely of ferrihydrite that act as sacrificial structures, preventing encrustation of the cells that produce them. Cultivated marine FeOB generally require neutral pH and microaerobic conditions to grow. Here, we describe the morphology and mineralogy of filamentous microstructures from a late Paleoproterozoic (1.74 Ga) jasper (Fe-oxide-silica) deposit from the Jerome area of the Verde mining district in central Arizona, USA, that resemble the branching tubes formed by some modern marine FeOB. On the basis of this comparison, we interpret the Jerome area filaments as having formed by FeOB on the deep seafloor, at the interface of weakly oxygenated seawater and low-temperature Fe-rich hydrothermal fluids. We compare the Jerome area filaments with other purported examples of Precambrian FeOB and discuss the implications of their presence for existing redox models of Paleoproterozoic oceans during the "Boring Billion."
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Affiliation(s)
| | | | - Stefan Bengtson
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Clara S Chan
- Department of Earth Sciences, University of Delaware, Newark, USA
| | - Magnus Ivarsson
- Department of Palaeobiology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Biology, University of Southern Denmark, Odense M, Denmark
| | - John F Slack
- U.S. Geological Survey (Emeritus), National Center, Reston, USA
| | - Curt Broman
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | | | - Tor Grenne
- Geological Survey of Norway, Trondheim, Norway
| | | | - Andrey Bekker
- Department of Earth and Planetary Sciences, University of California, Riverside, USA
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
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11
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Rouillard J, van Zuilen M, Pisapia C, Garcia-Ruiz JM. An Alternative Approach for Assessing Biogenicity. ASTROBIOLOGY 2021; 21:151-164. [PMID: 33544651 PMCID: PMC7876362 DOI: 10.1089/ast.2020.2282] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/07/2020] [Indexed: 05/27/2023]
Abstract
The search for signs of life in the ancient rock record, extreme terrestrial environments, and other planetary bodies requires a well-established, universal, and unambiguous test of biogenicity. This is notably true for cellular remnants of microbial life, since their relatively simple morphologies resemble various abiogenic microstructures that occur in nature. Although lists of qualitative biogenicity criteria have been devised, debates regarding the biogenicity of many ancient microfossils persist to this day. We propose here an alternative quantitative approach for assessing the biogenicity of putative microfossils. In this theoretical approach, different hypotheses-involving biology or not and depending on the geologic setting-are put forward to explain the observed objects. These hypotheses correspond to specific types of microstructures/systems. Using test samples, the morphology and/or chemistry of these systems are then characterized at the scale of populations. Morphologic parameters include, for example, circularity, aspect ratio, and solidity, while chemical parameters could include elementary ratios (e.g., N/C ratio), isotopic enrichments (e.g., δ13C), or chirality (e.g., molar proportion of stereoisomers), among others. Statistic trends distinguishing the different systems are then searched for empirically. The trends found are translated into "decision spaces" where the different systems are quantitatively discriminated and where the potential microfossil population can be located as a single point. This approach, which is formulated here on a theoretical level, will solve several problems associated with the classical qualitative criteria of biogenicity. Most importantly, it could be applied to reveal the existence of cellular life on other planets, for which characteristics of morphology and chemical composition are difficult to predict.
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Affiliation(s)
- Joti Rouillard
- Laboratario de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC—Universidad de Granada, Armilla, Spain
| | - Mark van Zuilen
- Institut de Physique du Globe de Paris, Université de Paris, CNRS UMR 7154, Paris, France
| | - Céline Pisapia
- Institut de Physique du Globe de Paris, Université de Paris, CNRS UMR 7154, Paris, France
| | - Juan-Manuel Garcia-Ruiz
- Laboratario de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC—Universidad de Granada, Armilla, Spain
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12
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Vigliaturo R, Marengo A, Bittarello E, Pérez-Rodríguez I, Dražić G, Gieré R. Micro- and nano-scale mineralogical characterization of Fe(II)-oxidizing bacterial stalks. GEOBIOLOGY 2020; 18:606-618. [PMID: 32459887 PMCID: PMC7442631 DOI: 10.1111/gbi.12398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Neutrophilic, microaerobic Fe(II)-oxidizing bacteria (FeOB) from marine and freshwater environments are known to generate twisted ribbon-like organo-mineral stalks. These structures, which are extracellularly precipitated, are susceptible to chemical influences in the environment once synthesized. In this paper, we characterize the minerals associated with freshwater FeOB stalks in order to evaluate key organo-mineral mechanisms involved in biomineral formation. Micro-Raman spectroscopy and Field Emission Scanning Electron Microscopy revealed that FeOB isolated from drinking water wells in Sweden produced stalks with ferrihydrite, lepidocrocite and goethite as main mineral components. Based on our observations made by micro-Raman Spectroscopy, field emission scanning electron microscopy and scanning transmission electron microscope combined with electron energy-loss spectroscopy, we propose a model that describes the crystal-growth mechanism, the Fe-oxidation state, and the mineralogical state of the stalks, as well as the biogenic contribution to these features. Our study suggests that the main crystal-growth mechanism in stalks includes nanoparticle aggregation and dissolution/re-precipitation reactions, which are dominant near the organic exopolymeric material produced by the microorganism and in the peripheral region of the stalk, respectively.
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Affiliation(s)
- Ruggero Vigliaturo
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Erica Bittarello
- Department of Earth Science, University of Torino, Torino, Italy
| | - Ileana Pérez-Rodríguez
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Goran Dražić
- Department for Materials Chemistry, National Institute of Chemistry, Ljubljana, Slovenia
| | - Reto Gieré
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, USA
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13
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Transformation of siderite to goethite by humic acid in the natural environment. Commun Chem 2020; 3:38. [PMID: 36703449 PMCID: PMC9814924 DOI: 10.1038/s42004-020-0284-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/03/2020] [Indexed: 01/29/2023] Open
Abstract
Humic acid (HA) is particularly important in iron-bearing mineral transformations and erosion at the water-mineral boundary zone of the Earth. In this study, three stages of the possible pathway by which HA causes mineral transformation from siderite to goethite are identified. Firstly, a Fe(II)-HA complex is formed by chelation, which accelerates the dissolution and oxidation of Fe(II) from the surface of siderite. As the Fe(II)-HA complex retains Fe atoms in close proximity of each other, ferrihydrite is formed by the agglomeration and crystallization. Finally, the ferrihydrite structurally rearranges upon attachment to the surface of goethite crystals and merges with its structure. The influence of low concentrations of HA (0-2 mg/L) on phosphate adsorption is found to be beneficial by the inducing of new mineral phases. We believe that these results provide a greater understanding of the impact of HA in the biogeochemical cycle of phosphate, mineral transformation.
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14
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Jacquemot P, Viennet JC, Bernard S, Le Guillou C, Rigaud B, Delbes L, Georgelin T, Jaber M. The degradation of organic compounds impacts the crystallization of clay minerals and vice versa. Sci Rep 2019; 9:20251. [PMID: 31882914 PMCID: PMC6934458 DOI: 10.1038/s41598-019-56756-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 11/28/2019] [Indexed: 12/03/2022] Open
Abstract
Expanding our capabilities to unambiguously identify ancient traces of life in ancient rocks requires laboratory experiments to better constrain the evolution of biomolecules during advanced fossilization processes. Here, we submitted RNA to hydrothermal conditions in the presence of a gel of Al-smectite stoichiometry at 200 °C for 20 days. NMR and STXM-XANES investigations revealed that the organic fraction of the residues is no longer RNA, nor the quite homogeneous aromatic-rich residue obtained in the absence of clays, but rather consists of particles of various chemical composition including amide-rich compounds. Rather than the pure clays obtained in the absence of RNA, electron microscopy (SEM and TEM) and diffraction (XRD) data showed that the mineralogy of the experimental residues includes amorphous silica and aluminosilicates mixed together with nanoscales phosphates and clay minerals. In addition to the influence of clay minerals on the degradation of organic compounds, these results evidence the influence of the presence of organic compounds on the nature of the mineral assemblage, highlighting the importance of fine-scale mineralogical investigations when discussing the nature/origin of organo-mineral microstructures found in ancient rocks.
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Affiliation(s)
- Pierre Jacquemot
- National Museum of Natural History (MNHN), Sorbonne University, CNRS, Institute of Mineralogy, Material Physics and Cosmochemistry (IMPMC - UMR 7590), F-75005, Paris, France
- Sorbonne University, CNRS, Laboratory of Molecular and Structural Archeology (LAMS - UMR 8220), F-75005, Paris, France
| | - Jean-Christophe Viennet
- National Museum of Natural History (MNHN), Sorbonne University, CNRS, Institute of Mineralogy, Material Physics and Cosmochemistry (IMPMC - UMR 7590), F-75005, Paris, France
- Sorbonne University, CNRS, Laboratory of Molecular and Structural Archeology (LAMS - UMR 8220), F-75005, Paris, France
| | - Sylvain Bernard
- National Museum of Natural History (MNHN), Sorbonne University, CNRS, Institute of Mineralogy, Material Physics and Cosmochemistry (IMPMC - UMR 7590), F-75005, Paris, France.
| | | | | | - Ludovic Delbes
- National Museum of Natural History (MNHN), Sorbonne University, CNRS, Institute of Mineralogy, Material Physics and Cosmochemistry (IMPMC - UMR 7590), F-75005, Paris, France
| | | | - Maguy Jaber
- Sorbonne University, CNRS, Laboratory of Molecular and Structural Archeology (LAMS - UMR 8220), F-75005, Paris, France
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15
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Alleon J, Flannery DT, Ferralis N, Williford KH, Zhang Y, Schuessler JA, Summons RE. Organo-mineral associations in chert of the 3.5 Ga Mount Ada Basalt raise questions about the origin of organic matter in Paleoarchean hydrothermally influenced sediments. Sci Rep 2019; 9:16712. [PMID: 31723181 PMCID: PMC6853986 DOI: 10.1038/s41598-019-53272-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/30/2019] [Indexed: 11/27/2022] Open
Abstract
Hydrothermal and metamorphic processes could have abiotically produced organo-mineral associations displaying morphological and isotopic characteristics similar to those of fossilized microorganisms in ancient rocks, thereby leaving false-positive evidence for early life in the geological record. Recent studies revealed that geologically-induced alteration processes do not always completely obliterate all molecular information about the original organic precursors of ancient microfossils. Here, we report the molecular, geochemical, and mineralogical composition of organo-mineral associations in a chert sample from the ca. 3.47 billion-year-old (Ga) Mount Ada Basalt, in the Pilbara Craton, Western Australia. Our observations indicate that the molecular characteristics of carbonaceous matter are consistent with hydrothermally altered biological organics, although significantly distinct from that of organic microfossils discovered in a chert sample from the ca. 3.43 Ga Strelley Pool Formation in the same area. Alternatively, the presence of native metal alloys in the chert, previously believed to be unstable in such hydrothermally influenced environments, indicates strongly reducing conditions that were favorable for the abiotic formation of organic matter. Drawing definitive conclusions about the origin of most Paleoarchean organo-mineral associations therefore requires further characterization of a range of natural samples together with experimental simulations to constrain the molecular composition and geological fate of hydrothermally-generated condensed organics.
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Affiliation(s)
- Julien Alleon
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
- Now at Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland.
| | - David T Flannery
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Nicola Ferralis
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kenneth H Williford
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Yong Zhang
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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16
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Alleon J, Summons RE. Organic geochemical approaches to understanding early life. Free Radic Biol Med 2019; 140:103-112. [PMID: 30858060 DOI: 10.1016/j.freeradbiomed.2019.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/02/2019] [Accepted: 03/05/2019] [Indexed: 11/25/2022]
Abstract
Here we discuss the early geological record of preserved organic carbon and the criteria that must be applied to distinguish biological from non-biological origins. Sedimentary graphite, irrespective of its isotopic composition, does not constitute a reliable biosignature because the rocks in which it is found are generally metamorphosed to the point where convincing signs of life have been erased. Rather, multiple lines of evidence, including sedimentary textures, microfossils, large accumulations of organic matter and isotopic data for co-existing carbon, nitrogen and sulfur are required before biological origin can be convincingly demonstrated.
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Affiliation(s)
- Julien Alleon
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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17
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Igisu M, Yokoyama T, Ueno Y, Nakashima S, Shimojima M, Ohta H, Maruyama S. Changes of aliphatic C-H bonds in cyanobacteria during experimental thermal maturation in the presence or absence of silica as evaluated by FTIR microspectroscopy. GEOBIOLOGY 2018; 16:412-428. [PMID: 29869829 DOI: 10.1111/gbi.12294] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 03/16/2018] [Indexed: 06/08/2023]
Abstract
Aliphatic C-H bonds are one of the major organic signatures detected in Proterozoic organic microfossils, and their origin is a topic of interest. To investigate the influence of the presence of silica on the thermal alteration of aliphatic C-H bonds in prokaryotic cells during diagenesis, cyanobacteria Synechocystis sp. PCC6803 were heated at temperatures of 250-450°C. Changes in the infrared (IR) signals were monitored by micro-Fourier transform infrared (FTIR) spectroscopy. Micro-FTIR shows that absorbances at 2,925 cm-1 band (aliphatic CH2 ) and 2,960 cm-1 band (aliphatic CH3 ) decrease during heating, indicating loss of the C-H bonds, which was delayed by the presence of silica. A theoretical approach using solid-state kinetics indicates that the most probable process for the aliphatic C-H decrease is three-dimensional diffusion of alteration products under both non-embedded and silica-embedded conditions. The extrapolation of the experimental results obtained at 250-450°C to lower temperatures implies that the rate constant for CH3 (kCH3 ) is similar to or lower than that for CH2 (kCH2 ; i.e., CH3 decreases at a similar rate or more slowly than CH2 ). The peak height ratio of 2,960 cm-1 band (CH3 )/2,925 cm-1 band (CH2 ; R3/2 values) either increased or remained constant during the heating. These results reveal that the presence of silica does affect the decreasing rate of the aliphatic C-H bonds in cyanobacteria during thermal maturation, but that it does not significantly decrease the R3/2 values. Meanwhile, studies of microfossils suggest that the R3/2 values of Proterozoic prokaryotic fossils from the Bitter Springs Group and Gunflint Formation have decreased during fossilization, which is inconsistent with the prediction from our experimental results that R3/2 values did not decrease after silicification. Some process other than thermal degradation, possibly preservation of specific classes of biomolecules with low R3/2 values, might have occurred during fossilization.
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Affiliation(s)
- Motoko Igisu
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Tadashi Yokoyama
- Graduate School of Integrated Arts and Sciences, Hiroshima University, Hiroshima, Japan
| | - Yuichiro Ueno
- Department of Subsurface Geobiology Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Tokyo, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Satoru Nakashima
- Department of Earth and Space Science, Osaka University, Osaka, Japan
| | - Mie Shimojima
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Hiroyuki Ohta
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Shigenori Maruyama
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Novosibirsk State University, Novosibirsk, Russia
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18
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Le Guillou C, Bernard S, De la Pena F, Le Brech Y. XANES-Based Quantification of Carbon Functional Group Concentrations. Anal Chem 2018; 90:8379-8386. [DOI: 10.1021/acs.analchem.8b00689] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Corentin Le Guillou
- Unité Matériaux et Transformations (UMET) MR-CNRS 8207, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Sylvain Bernard
- Muséum National d’Histoire Naturelle, Sorbonne Université, CNRS UMR 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, 75005 Paris, France
| | - Francisco De la Pena
- Unité Matériaux et Transformations (UMET) MR-CNRS 8207, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Yann Le Brech
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, UMR 7274, 54001 Nancy, France
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19
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Beam JP, Scott JJ, McAllister SM, Chan CS, McManus J, Meysman FJR, Emerson D. Biological rejuvenation of iron oxides in bioturbated marine sediments. ISME JOURNAL 2018; 12:1389-1394. [PMID: 29343830 DOI: 10.1038/s41396-017-0032-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 11/22/2017] [Accepted: 11/29/2017] [Indexed: 02/04/2023]
Abstract
The biogeochemical cycle of iron is intricately linked to numerous element cycles. Although biological processes that catalyze the reductive side of the iron cycle are established, little is known about microbial oxidative processes on iron cycling in sedimentary environments-resulting in the formation of iron oxides. Here we show that a potential source of sedimentary iron oxides originates from the metabolic activity of iron-oxidizing bacteria from the class Zetaproteobacteria, presumably enhanced by burrowing animals in coastal sediments. Zetaproteobacteria were estimated to be a global total of 1026 cells in coastal, bioturbated sediments, and predicted to annually produce 8 × 1015 g of Fe in sedimentary iron oxides-55 times larger than the annual flux of iron oxides deposited by rivers. These data suggest that iron-oxidizing Zetaproteobacteria are keystone organisms in marine sedimentary environments-despite their low numerical abundance-yet exert a disproportionate impact via the rejuvenation of iron oxides.
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Affiliation(s)
- Jacob P Beam
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA.
| | - Jarrod J Scott
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA.,Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, Republic of Panama
| | - Sean M McAllister
- Department of Geological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Clara S Chan
- Department of Geological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - James McManus
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Filip J R Meysman
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium.,Department of Biotechnology, Technical University of Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
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20
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Kim EM, Oh PS, Jeong HJ, Lim ST, Sohn MH. α v β 3 mediated tumor imaging using 99m Tc labeled NAD/monosaccharide coated ferrihydrite nanoparticles. J Labelled Comp Radiopharm 2017; 61:18-29. [PMID: 28948648 DOI: 10.1002/jlcr.3565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 01/22/2023]
Abstract
This study describes the synthesis of highly water-soluble, non-toxic, and biocompatible nicotinamide adenine dinucleotide (NAD)/glucosamine (=Nga1Fh) and NAD/glucosamine/gluconic acid coated ferrihydrite nanoparticles (=Nga2Fh) and their possible uses to target tumors in living animals via 99m Tc and 125 I radioisotope labeling. The structural properties were investigated using DLS, zeta potential, TEM, FT-IR, XRD, and Raman spectroscopy. The cell toxicity in CT26 cancer cells and in vivo tumor targetability in U87MG and CT26 tumor-bearing mice was further evaluated using cRGDyK-tagged and cRGDfK-tagged ferrihydrite nanoparticles. The average diameters of the resulting Nga1Fh and Nga2Fh nanoparticles were <5 to 7 and <3 nm, respectively. The Nga2Fh nanoparticles did not show cell toxicity until 0.1 mg/mL. Using gamma camera imaging, 99m Tc-cRGDfK-Nga2Fh showed the highest tumor uptake in a U87MG tumor-bearing mouse when compared with that of 99m Tc-cRGDyK-Nga2Fh and 99m Tc-Nga2Fh. The image-based tumor-to-muscle ratio by time for 99m Tc-cRGDfK-Nga2Fh was 3.8 ± 1.7, 4.2 ± 2.0, 7 ± 1.5, 13 ± 2.0, 8 ± 3.7, and 2 ± 1.6 at 5 and 30 minutes, 1, 2, 4, and 24 hours, respectively. Although further studies are needed, the NAD/monosaccharide coated ferrihydrite nanoparticles could be presented as an interesting material for a drug delivery system.
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Affiliation(s)
- Eun-Mi Kim
- Department of Nuclear Medicine, Molecular Imaging and Therapeutic Medicine Research Center, Cyclotron Research Center, Institute for Medical Science, Biomedical Research Institute, Chonbuk National University Medical School and Hospital, Jeonju, Chonbuk, Republic of Korea
| | - Phil-Sun Oh
- Department of Nuclear Medicine, Molecular Imaging and Therapeutic Medicine Research Center, Cyclotron Research Center, Institute for Medical Science, Biomedical Research Institute, Chonbuk National University Medical School and Hospital, Jeonju, Chonbuk, Republic of Korea
| | - Hwan-Jeong Jeong
- Department of Nuclear Medicine, Molecular Imaging and Therapeutic Medicine Research Center, Cyclotron Research Center, Institute for Medical Science, Biomedical Research Institute, Chonbuk National University Medical School and Hospital, Jeonju, Chonbuk, Republic of Korea
| | - Seok Tae Lim
- Department of Nuclear Medicine, Molecular Imaging and Therapeutic Medicine Research Center, Cyclotron Research Center, Institute for Medical Science, Biomedical Research Institute, Chonbuk National University Medical School and Hospital, Jeonju, Chonbuk, Republic of Korea
| | - Myung-Hee Sohn
- Department of Nuclear Medicine, Molecular Imaging and Therapeutic Medicine Research Center, Cyclotron Research Center, Institute for Medical Science, Biomedical Research Institute, Chonbuk National University Medical School and Hospital, Jeonju, Chonbuk, Republic of Korea
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21
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Miot J, Bernard S, Bourreau M, Guyot F, Kish A. Experimental maturation of Archaea encrusted by Fe-phosphates. Sci Rep 2017; 7:16984. [PMID: 29208997 PMCID: PMC5717249 DOI: 10.1038/s41598-017-17111-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/22/2017] [Indexed: 11/15/2022] Open
Abstract
Burial is generally detrimental to the preservation of biological signals. It has often been assumed that (bio)mineral-encrusted microorganisms are more resistant to burial-induced degradation than non-encrusted ones over geological timescales. For the present study, we submitted Sulfolobus acidocaldarius experimentally encrusted by amorphous Fe phosphates to constrained temperature conditions (150 °C) under pressure for 1 to 5 days, thereby simulating burial-induced processes. We document the molecular and mineralogical evolution of these assemblages down to the sub-micrometer scale using X-ray diffraction, scanning and transmission electron microscopies and synchrotron-based X-ray absorption near edge structure spectroscopy at the carbon K-edge. The present results demonstrate that the presence of Fe-phosphates enhances the chemical degradation of microbial organic matter. While Fe-phosphates remained amorphous in abiotic controls, crystalline lipscombite (FeIIxFeIII3-x(PO4)2(OH)3-x) entrapping organic matter formed in the presence of S. acidocaldarius cells. Lipscombite textures (framboidal vs. bipyramidal) appeared only controlled by the initial level of encrustation of the cells, suggesting that the initial organic matter to mineral ratio influences the competition between nucleation and crystal growth. Altogether these results highlight the important interplay between minerals and organic matter during fossilization, which should be taken into account when interpreting the fossil record.
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Affiliation(s)
- J Miot
- IMPMC, Sorbonne Université, MNHN, UPMC, CNRS UMR 7590, 4 pl. Jussieu, 75005, Paris, France.
| | - S Bernard
- IMPMC, Sorbonne Université, MNHN, UPMC, CNRS UMR 7590, 4 pl. Jussieu, 75005, Paris, France
| | - M Bourreau
- MCAM, MNHN, UPMC, CNRS UMR 7245, 63 rue Buffon, 75005, Paris, France
| | - F Guyot
- IMPMC, Sorbonne Université, MNHN, UPMC, CNRS UMR 7590, 4 pl. Jussieu, 75005, Paris, France
| | - A Kish
- MCAM, MNHN, UPMC, CNRS UMR 7245, 63 rue Buffon, 75005, Paris, France
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22
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Delarue F, Robert F, Sugitani K, Tartèse R, Duhamel R, Derenne S. Investigation of the Geochemical Preservation of ca. 3.0 Ga Permineralized and Encapsulated Microfossils by Nanoscale Secondary Ion Mass Spectrometry. ASTROBIOLOGY 2017; 17:1192-1202. [PMID: 29058452 PMCID: PMC5729882 DOI: 10.1089/ast.2016.1531] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 04/14/2017] [Indexed: 05/31/2023]
Abstract
Observations of Archean organic-walled microfossils suggest that their fossilization took place through both encapsulation and permineralization. In this study, we investigated microfossils from the ca. 3.0 Ga Farrel Quartzite (Pilbara, Western Australia) using transmitted light microscopy, scanning electron microscopy, Raman microspectrometry, and nanoscale secondary ion mass spectrometry (NanoSIMS) ion microprobe analyses. In contrast to previous studies, we demonstrated that permineralized microfossils were not characterized by the micrometric spatial relationships between Si and C-N as observed in thin sections. Permineralized microfossils are composed of carbonaceous globules that did not survive the acid treatment, whereas encapsulated microfossils were characterized due to their resistance to the acid maceration procedure. We also investigated the microscale relationship between the 12C14N- and 12C2- ion emission as a proxy of the N/C atomic ratio in both permineralized and encapsulated microfossils. After considering any potential matrix and microtopography effects, we demonstrate that the encapsulated microfossils exhibit the highest level of geochemical preservation. This finding shows that the chemical heterogeneity of the microfossils, observed at a spatial resolution of a few hundreds of micrometers, can be related to fossilization processes. Key Words: Carbonaceous matter-Farrel Quartzite-Fossilization-NanoSIMS-Nitrogen-Permineralization. Astrobiology 17, 1192-1202.
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Affiliation(s)
- Frédéric Delarue
- IMPMC Sorbonne Universités–MNHN, UPMC Univ Paris 06, UMR CNRS 7590, IRD UMR 206, Paris, France
| | - François Robert
- IMPMC Sorbonne Universités–MNHN, UPMC Univ Paris 06, UMR CNRS 7590, IRD UMR 206, Paris, France
| | - Kenichiro Sugitani
- Department of Environmental Engineering and Architecture, Graduate School of Environmental Studies, Nagoya University, Nagoya, Japan
| | - Romain Tartèse
- IMPMC Sorbonne Universités–MNHN, UPMC Univ Paris 06, UMR CNRS 7590, IRD UMR 206, Paris, France
| | - Rémi Duhamel
- IMPMC Sorbonne Universités–MNHN, UPMC Univ Paris 06, UMR CNRS 7590, IRD UMR 206, Paris, France
| | - Sylvie Derenne
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7619 METIS, Paris, France
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23
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Gaboyer F, Le Milbeau C, Bohmeier M, Schwendner P, Vannier P, Beblo-Vranesevic K, Rabbow E, Foucher F, Gautret P, Guégan R, Richard A, Sauldubois A, Richmann P, Perras AK, Moissl-Eichinger C, Cockell CS, Rettberg P, Marteinsson, Monaghan E, Ehrenfreund P, Garcia-Descalzo L, Gomez F, Malki M, Amils R, Cabezas P, Walter N, Westall F. Mineralization and Preservation of an extremotolerant Bacterium Isolated from an Early Mars Analog Environment. Sci Rep 2017; 7:8775. [PMID: 28821776 PMCID: PMC5562696 DOI: 10.1038/s41598-017-08929-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 07/14/2017] [Indexed: 11/09/2022] Open
Abstract
The artificial mineralization of a polyresistant bacterial strain isolated from an acidic, oligotrophic lake was carried out to better understand microbial (i) early mineralization and (ii) potential for further fossilisation. Mineralization was conducted in mineral matrixes commonly found on Mars and Early-Earth, silica and gypsum, for 6 months. Samples were analyzed using microbiological (survival rates), morphological (electron microscopy), biochemical (GC-MS, Microarray immunoassay, Rock-Eval) and spectroscopic (EDX, FTIR, RAMAN spectroscopy) methods. We also investigated the impact of physiological status on mineralization and long-term fossilisation by exposing cells or not to Mars-related stresses (desiccation and radiation). Bacterial populations remained viable after 6 months although the kinetics of mineralization and cell-mineral interactions depended on the nature of minerals. Detection of biosignatures strongly depended on analytical methods, successful with FTIR and EDX but not with RAMAN and immunoassays. Neither influence of stress exposure, nor qualitative and quantitative changes of detected molecules were observed as a function of mineralization time and matrix. Rock-Eval analysis suggests that potential for preservation on geological times may be possible only with moderate diagenetic and metamorphic conditions. The implications of our results for microfossil preservation in the geological record of Earth as well as on Mars are discussed.
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Affiliation(s)
- F Gaboyer
- Centre de Biophysique Moléculaire, CNRS, Orléans, France.
| | - C Le Milbeau
- Institut des Sciences de la Terre d'Orléans, UMR 7327, CNRS-Université d'Orléans, 1A Rue de la Férollerie, 45071, Orléans Cedex 2, France
| | - M Bohmeier
- Institute of Aerospace Medicine, Radiation Biology Department, German Aerospace Center (DLR), Cologne, Germany
| | - P Schwendner
- UK Center for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - P Vannier
- MATIS - Prokaria, Reykjavík, Iceland
| | - K Beblo-Vranesevic
- Institute of Aerospace Medicine, Radiation Biology Department, German Aerospace Center (DLR), Cologne, Germany
| | - E Rabbow
- Institute of Aerospace Medicine, Radiation Biology Department, German Aerospace Center (DLR), Cologne, Germany
| | - F Foucher
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
| | - P Gautret
- Institut des Sciences de la Terre d'Orléans, UMR 7327, CNRS-Université d'Orléans, 1A Rue de la Férollerie, 45071, Orléans Cedex 2, France
| | - R Guégan
- Institut des Sciences de la Terre d'Orléans, UMR 7327, CNRS-Université d'Orléans, 1A Rue de la Férollerie, 45071, Orléans Cedex 2, France
| | - A Richard
- Centre de Microscopie Electronique, Université d'Orléans, Orléans, France
| | - A Sauldubois
- Centre de Microscopie Electronique, Université d'Orléans, Orléans, France
| | - P Richmann
- Institut des Sciences de la Terre d'Orléans, UMR 7327, CNRS-Université d'Orléans, 1A Rue de la Férollerie, 45071, Orléans Cedex 2, France
| | - A K Perras
- University Regensburg, Department of Microbiology, Regensburg, Germany.,Medical University of Graz, Department of Internal Medicine, Graz, Austria
| | | | - C S Cockell
- UK Center for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - P Rettberg
- Institute of Aerospace Medicine, Radiation Biology Department, German Aerospace Center (DLR), Cologne, Germany
| | | | - E Monaghan
- Leiden Observatory, Universiteit Leiden, Leiden, Netherlands
| | - P Ehrenfreund
- Leiden Observatory, Universiteit Leiden, Leiden, Netherlands
| | - L Garcia-Descalzo
- Instituto Nacional de Técnica Aeroespacial - Centro de Astrobiología (INTA-CAB), Madrid, Spain
| | - F Gomez
- Instituto Nacional de Técnica Aeroespacial - Centro de Astrobiología (INTA-CAB), Madrid, Spain
| | - M Malki
- Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - R Amils
- Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - P Cabezas
- European Science Foundation (ESF), Strasbourg, France
| | - N Walter
- European Science Foundation (ESF), Strasbourg, France
| | - F Westall
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
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24
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Freidman BL, Northcott KA, Thiel P, Gras SL, Snape I, Stevens GW, Mumford KA. From urban municipalities to polar bioremediation: the characterisation and contribution of biogenic minerals for water treatment. JOURNAL OF WATER AND HEALTH 2017; 15:385-401. [PMID: 28598343 DOI: 10.2166/wh.2017.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Minerals of biological origin have shown significant potential for the separation of contaminants from water worldwide. This study details the contribution of biologically derived minerals to water treatment operations, with a focus on filtration media from urban municipalities and remote cold regions. The results support biofilm-embedded iron and manganese to be the building blocks of biogenic mineral development on activated carbon and nutrient-amended zeolites. The presence of similar iron and manganese oxidising bacterial species across all filter media supports the analogous morphologies of biogenic minerals between sites and suggests that biological water treatment processes may be feasible across a range of climates. This is the first time the stages of biogenic mineral formation have been aligned with comprehensive imaging of the biofilm community and bacterial identification; especially with respect to cold regions. Where biogenic mineral formation occurs on filter media, the potential exists for enhanced adsorption for a range of organic and inorganic contaminants and improved longevity of filter media beyond the adsorption or exchange capacities of the raw material.
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Affiliation(s)
- Benjamin L Freidman
- Particulate Fluids Processing Centre, Department of Chemical and Biomolecular Engineering, University of Melbourne, Building 165, Parkville 3010, VIC, Australia E-mail: ; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kathy A Northcott
- Veolia Australia and New Zealand, Kangaroo Flat, VIC 3555, Australia
| | - Peta Thiel
- Research Laboratory Services, Eltham, VIC 3095, Australia
| | - Sally L Gras
- Particulate Fluids Processing Centre, Department of Chemical and Biomolecular Engineering, University of Melbourne, Building 165, Parkville 3010, VIC, Australia E-mail: ; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia; The ARC Dairy Innovation Hub, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Ian Snape
- Australian Antarctic Division, Channel Highway, Kingston, Tasmania 7050, Australia
| | - Geoff W Stevens
- Particulate Fluids Processing Centre, Department of Chemical and Biomolecular Engineering, University of Melbourne, Building 165, Parkville 3010, VIC, Australia E-mail:
| | - Kathryn A Mumford
- Particulate Fluids Processing Centre, Department of Chemical and Biomolecular Engineering, University of Melbourne, Building 165, Parkville 3010, VIC, Australia E-mail:
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25
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Alleon J, Bernard S, Le Guillou C, Daval D, Skouri-Panet F, Kuga M, Robert F. Organic molecular heterogeneities can withstand diagenesis. Sci Rep 2017; 7:1508. [PMID: 28473702 PMCID: PMC5431453 DOI: 10.1038/s41598-017-01612-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 03/30/2017] [Indexed: 11/09/2022] Open
Abstract
Reconstructing the original biogeochemistry of organic fossils requires quantifying the extent of the chemical transformations that they underwent during burial-induced maturation processes. Here, we performed laboratory experiments on chemically different organic materials in order to simulate the thermal maturation processes that occur during diagenesis. Starting organic materials were microorganisms and organic aerosols. Scanning transmission X-ray microscopy (STXM) was used to collect X-ray absorption near edge spectroscopy (XANES) data of the organic residues. Results indicate that even after having been submitted to 250 °C and 250 bars for 100 days, the molecular signatures of microorganisms and aerosols remain different in terms of nitrogen-to-carbon atomic ratio and carbon and nitrogen speciation. These observations suggest that burial-induced thermal degradation processes may not completely obliterate the chemical and molecular signatures of organic molecules. In other words, the present study suggests that organic molecular heterogeneities can withstand diagenesis and be recognized in the fossil record.
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Affiliation(s)
- Julien Alleon
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France.,Department of Earth Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sylvain Bernard
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France.
| | | | - Damien Daval
- Laboratoire d'Hydrologie et de Géochimie de Strasbourg, Université de Strasbourg/EOST - CNRS UMR 7517, 1 Rue Blessig, 67084, Strasbourg, France
| | - Feriel Skouri-Panet
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France
| | - Maïa Kuga
- Department of Earth Sciences, ETH Zürich, 8092, Zürich, Switzerland
| | - François Robert
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France
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26
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Microaerophilic Fe(II)-Oxidizing Zetaproteobacteria Isolated from Low-Fe Marine Coastal Sediments: Physiology and Composition of Their Twisted Stalks. Appl Environ Microbiol 2017; 83:AEM.03118-16. [PMID: 28159791 DOI: 10.1128/aem.03118-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/28/2017] [Indexed: 11/20/2022] Open
Abstract
Microaerophilic Fe(II) oxidizers are commonly found in habitats containing elevated Fe(II) and low O2 concentrations and often produce characteristic Fe mineral structures, so-called twisted stalks or tubular sheaths. Isolates originating from freshwater habitats are all members of the Betaproteobacteria, while isolates from marine habitats belong almost exclusively to the Zetaproteobacteria So far, only a few isolates of marine microaerophilic Fe(II) oxidizers have been described, all of which are obligate microaerophilic Fe(II) oxidizers and have been thought to be restricted to Fe-rich systems. Here, we present two new isolates of marine microaerophilic Fe(II)-oxidizing Zetaproteobacteria that originate from typical coastal marine sediments containing only low Fe concentrations (2 to 11 mg of total Fe/g of sediment [dry weight]; 70 to 100 μM dissolved Fe2+ in the porewater). The two novel Zetaproteobacteria share characteristic physiological properties of the Zetaproteobacteria group, even though they come from low-Fe environments: the isolates are obligate microaerophilic Fe(II) oxidizers and, like most isolated Zetaproteobacteria, they produce twisted stalks. We found a low organic carbon content in the stalks (∼0.3 wt%), with mostly polysaccharides and saturated aliphatic chains (most likely lipids). The Fe minerals in the stalks were identified as lepidocrocite and possibly ferrihydrite. Immobilization experiments with Ni2+ showed that the stalks can function as a sink for trace metals. Our findings show that obligate microaerophilic Fe(II) oxidizers belonging to the Zetaproteobacteria group are not restricted to Fe-rich environments but can also be found in low-Fe marine environments, which increases their overall importance for the global biogeochemical Fe cycle.IMPORTANCE So far, only a few isolates of benthic marine microaerophilic Fe(II) oxidizers belonging to the Zetaproteobacteria exist, and most isolates were obtained from habitats containing elevated Fe concentrations. Consequently, it was thought that these microorganisms are important mainly in habitats with high Fe concentrations. The two novel isolates of Zetaproteobacteria that are presented in the present study were isolated from typical coastal marine sediments that do not contain elevated Fe concentrations. This increases the knowledge about possible habitats in which Zetaproteobacteria can exist. Furthermore, we show that the physiology and the typical organo-mineral structures (twisted stalks) that are produced by the isolates do not notably differ from the physiology and the cell-mineral structures of isolates from environments with high Fe concentrations. We also showed that the organo-mineral structures can function as a sink for trace metals.
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27
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Estes ER, Andeer PF, Nordlund D, Wankel SD, Hansel CM. Biogenic manganese oxides as reservoirs of organic carbon and proteins in terrestrial and marine environments. GEOBIOLOGY 2017; 15:158-172. [PMID: 27396696 DOI: 10.1111/gbi.12195] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 05/02/2016] [Indexed: 05/29/2023]
Abstract
Manganese (Mn) oxides participate in a range of interactions with organic carbon (OC) that can lead to either carbon degradation or preservation. Here, we examine the abundance and composition of OC associated with biogenic and environmental Mn oxides to elucidate the role of Mn oxides as a reservoir for carbon and their potential for selective partitioning of particular carbon species. Mn oxides precipitated in natural brackish waters and by Mn(II)-oxidizing marine bacteria and terrestrial fungi harbor considerable levels of organic carbon (4.1-17.0 mol OC per kg mineral) compared to ferromanganese cave deposits which contain 1-2 orders of magnitude lower OC. Spectroscopic analyses indicate that the chemical composition of Mn oxide-associated OC from microbial cultures is homogeneous with bacterial Mn oxides hosting primarily proteinaceous carbon and fungal Mn oxides containing both protein- and lipopolysaccharide-like carbon. The bacterial Mn oxide-hosted proteins are involved in both Mn(II) oxidation and metal binding by these bacterial species and could be involved in the mineral nucleation process as well. By comparison, the composition of OC associated with Mn oxides formed in natural settings (brackish waters and particularly in cave ferromanganese rock coatings) is more spatially and chemically heterogeneous. Cave Mn oxide-associated organic material is enriched in aliphatic C, which together with the lower carbon concentrations, points to more extensive microbial or mineral processing of carbon in this system relative to the other systems examined in this study, and as would be expected in oligotrophic cave environments. This study highlights Mn oxides as a reservoir for carbon in varied environments. The presence and in some cases dominance of proteinaceous carbon within the biogenic and natural Mn oxides may contribute to preferential preservation of proteins in sediments and dominance of protein-dependent metabolisms in the subsurface biosphere.
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Affiliation(s)
- E R Estes
- Department of Marine Chemistry and Geochemistry, MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - P F Andeer
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - D Nordlund
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | - S D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - C M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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28
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Comparative Analysis of Microbial Communities in Iron-Dominated Flocculent Mats in Deep-Sea Hydrothermal Environments. Appl Environ Microbiol 2016; 82:5741-55. [PMID: 27422841 DOI: 10.1128/aem.01151-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/11/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED It has been suggested that iron is one of the most important energy sources for photosynthesis-independent microbial ecosystems in the ocean crust. Iron-metabolizing chemolithoautotrophs play a key role as primary producers, but little is known about their distribution and diversity and their ecological role as submarine iron-metabolizing chemolithotrophs, particularly the iron oxidizers. In this study, we investigated the microbial communities in several iron-dominated flocculent mats found in deep-sea hydrothermal fields in the Mariana Volcanic Arc and Trough and the Okinawa Trough by culture-independent molecular techniques and X-ray mineralogical analyses. The abundance and composition of the 16S rRNA gene phylotypes demonstrated the ubiquity of zetaproteobacterial phylotypes in iron-dominated mat communities affected by hydrothermal fluid input. Electron microscopy with energy-dispersive X-ray microanalysis and X-ray absorption fine structure (XAFS) analysis revealed the chemical and mineralogical signatures of biogenic Fe-(oxy)hydroxide species and the potential contribution of Zetaproteobacteria to the in situ generation. These results suggest that putative iron-oxidizing chemolithoautotrophs play a significant ecological role in producing iron-dominated flocculent mats and that they are important for iron and carbon cycles in deep-sea low-temperature hydrothermal environments. IMPORTANCE We report novel aspects of microbiology from iron-dominated flocculent mats in various deep-sea environments. In this study, we examined the relationship between Zetaproteobacteria and iron oxides across several hydrothermally influenced sites in the deep sea. We analyzed iron-dominated mats using culture-independent molecular techniques and X-ray mineralogical analyses. The scanning electron microscopy-energy-dispersive X-ray spectroscopy SEM-EDS analysis and X-ray absorption fine structure (XAFS) analysis revealed chemical and mineralogical signatures of biogenic Fe-(oxy)hydroxide species as well as the potential contribution of the zetaproteobacterial population to the in situ production. These key findings provide important information for understanding the mechanisms of both geomicrobiological iron cycling and the formation of iron-dominated mats in deep-sea hydrothermal fields.
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29
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Cosmidis J, Templeton AS. Self-assembly of biomorphic carbon/sulfur microstructures in sulfidic environments. Nat Commun 2016; 7:12812. [PMID: 27628108 PMCID: PMC5027620 DOI: 10.1038/ncomms12812] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/01/2016] [Indexed: 01/29/2023] Open
Abstract
In natural and laboratory-based environments experiencing sustained counter fluxes of sulfide and oxidants, elemental sulfur (S0)—a key intermediate in the sulfur cycle—can commonly accumulate. S0 is frequently invoked as a biomineralization product generated by enzymatic oxidation of hydrogen sulfide and polysulfides. Here we show the formation of S0 encapsulated in nanometre to micrometre-scale tubular and spherical organic structures that self-assemble in sulfide gradient environments in the absence of any direct biological activity. The morphology and composition of these carbon/sulfur microstructures so closely resemble microbial cellular and extracellular structures that new caution must be applied to the interpretation of putative microbial biosignatures in the fossil record. These reactions between sulfide and organic matter have important implications for our understanding of S0 mineralization processes and sulfur interactions with organic carbon in the environment. They furthermore provide a new pathway for the synthesis of carbon-sulfur nanocomposites for energy storage technologies. Organic materials mineralized with sulfur are considered to be a product of biological activity in natural environments and the fossil record. Here, Cosmidis and Templeton show that sulfide can abiotically drive the self-assembly of organic carbon microstructures mineralized with elemental sulfur.
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Affiliation(s)
- Julie Cosmidis
- Department of Geological Sciences, University of Colorado, Boulder, Colorado 80309, USA
| | - Alexis S Templeton
- Department of Geological Sciences, University of Colorado, Boulder, Colorado 80309, USA
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30
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Chan CS, Emerson D, Luther GW. The role of microaerophilic Fe-oxidizing micro-organisms in producing banded iron formations. GEOBIOLOGY 2016; 14:509-528. [PMID: 27392195 DOI: 10.1111/gbi.12192] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 04/25/2016] [Indexed: 06/06/2023]
Abstract
Despite the historical and economic significance of banded iron formations (BIFs), we have yet to resolve the formation mechanisms. On modern Earth, neutrophilic microaerophilic Fe-oxidizing micro-organisms (FeOM) produce copious amounts of Fe oxyhydroxides, leading us to wonder whether similar organisms played a role in producing BIFs. To evaluate this, we review the current knowledge of modern microaerophilic FeOM in the context of BIF paleoenvironmental studies. In modern environments wherever Fe(II) and O2 co-exist, microaerophilic FeOM proliferate. These organisms grow in a variety of environments, including the marine water column redoxcline, which is where BIF precursor minerals likely formed. FeOM can grow across a range of O2 concentrations, measured as low as 2 μm to date, although lower concentrations have not been tested. While some extant FeOM can tolerate high O2 concentrations, many FeOM appear to prefer and thrive at low O2 concentrations (~3-25 μm). These are similar to the estimated dissolved O2 concentrations in the few hundred million years prior to the 'Great Oxidation Event' (GOE). We compare biotic and abiotic Fe oxidation kinetics in the presence of varying levels of O2 and show that microaerophilic FeOM contribute substantially to Fe oxidation, at rates fast enough to account for BIF deposition. Based on this synthesis, we propose that microaerophilic FeOM were capable of playing a significant role in depositing the largest, most well-known BIFs associated with the GOE, as well as afterward when global O2 levels increased.
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Affiliation(s)
- C S Chan
- Department of Geological Sciences, University of Delaware, and the Delaware Biotechnology Institute, Newark, DE, USA
- School of Marine Science and Policy, University of Delaware, Newark & Lewes, DE, USA
| | - D Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - G W Luther
- School of Marine Science and Policy, University of Delaware, Newark & Lewes, DE, USA
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31
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Size dependent microbial oxidation and reduction of magnetite nano- and micro-particles. Sci Rep 2016; 6:30969. [PMID: 27492680 PMCID: PMC4974511 DOI: 10.1038/srep30969] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/12/2016] [Indexed: 01/30/2023] Open
Abstract
The ability for magnetite to act as a recyclable electron donor and acceptor for Fe-metabolizing bacteria has recently been shown. However, it remains poorly understood whether microbe-mineral interfacial electron transfer processes are limited by the redox capacity of the magnetite surface or that of whole particles. Here we examine this issue for the phototrophic Fe(II)-oxidizing bacteria Rhodopseudomonas palustris TIE-1 and the Fe(III)-reducing bacteria Geobacter sulfurreducens, comparing magnetite nanoparticles (d ≈ 12 nm) against microparticles (d ≈ 100–200 nm). By integrating surface-sensitive and bulk-sensitive measurement techniques we observed a particle surface that was enriched in Fe(II) with respect to a more oxidized core. This enables microbial Fe(II) oxidation to occur relatively easily at the surface of the mineral suggesting that the electron transfer is dependent upon particle size. However, microbial Fe(III) reduction proceeds via conduction of electrons into the particle interior, i.e. it can be considered as more of a bulk electron transfer process that is independent of particle size. The finding has potential implications on the ability of magnetite to be used for long range electron transport in soils and sediments.
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32
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Alleon J, Bernard S, Le Guillou C, Marin-Carbonne J, Pont S, Beyssac O, McKeegan KD, Robert F. Molecular preservation of 1.88 Ga Gunflint organic microfossils as a function of temperature and mineralogy. Nat Commun 2016; 7:11977. [PMID: 27312070 PMCID: PMC4915024 DOI: 10.1038/ncomms11977] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 05/18/2016] [Indexed: 01/06/2023] Open
Abstract
The significant degradation that fossilized biomolecules may experience during burial makes it challenging to assess the biogenicity of organic microstructures in ancient rocks. Here we investigate the molecular signatures of 1.88 Ga Gunflint organic microfossils as a function of their diagenetic history. Synchrotron-based XANES data collected in situ on individual microfossils, at the submicrometre scale, are compared with data collected on modern microorganisms. Despite diagenetic temperatures of ∼150–170 °C deduced from Raman data, the molecular signatures of some Gunflint organic microfossils have been exceptionally well preserved. Remarkably, amide groups derived from protein compounds can still be detected. We also demonstrate that an additional increase of diagenetic temperature of only 50 °C and the nanoscale association with carbonate minerals have significantly altered the molecular signatures of Gunflint organic microfossils from other localities. Altogether, the present study provides key insights for eventually decoding the earliest fossil record. Thermal diagenesis is generally seen as detrimental to the preservation of organic biosignatures. Using synchrotron-based XANES data, Alleon et al. find preservation of the molecular signatures of organic microfossils from the 1.88 Ga Gunflint cherts.
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Affiliation(s)
- Julien Alleon
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
| | - Sylvain Bernard
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
| | - Corentin Le Guillou
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
| | - Johanna Marin-Carbonne
- Univ Lyon, UJM Saint Etienne, Laboratoire Magma et Volcans, UBP, CNRS, IRD, 23 rue Dr Paul Michelon, 42100 St Etienne, France
| | - Sylvain Pont
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
| | - Olivier Beyssac
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
| | - Kevin D McKeegan
- Department of Earth, Planetary and Space Sciences, University of California-Los Angeles, 595 Charles Young Drive East, Los Angeles, California 90095-1567, USA
| | - François Robert
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ Paris 06, IRD UMR 206, 61 rue Buffon, 75005 Paris, France
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Preservation of Archaeal Surface Layer Structure During Mineralization. Sci Rep 2016; 6:26152. [PMID: 27221593 PMCID: PMC4879539 DOI: 10.1038/srep26152] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/21/2016] [Indexed: 12/18/2022] Open
Abstract
Proteinaceous surface layers (S-layers) are highly ordered, crystalline structures commonly found in prokaryotic cell envelopes that augment their structural stability and modify interactions with metals in the environment. While mineral formation associated with S-layers has previously been noted, the mechanisms were unconstrained. Using Sulfolobus acidocaldarius a hyperthermophilic archaeon native to metal-enriched environments and possessing a cell envelope composed only of a S-layer and a lipid cell membrane, we describe a passive process of iron phosphate nucleation and growth within the S-layer of cells and cell-free S-layer "ghosts" during incubation in a Fe-rich medium, independently of metabolic activity. This process followed five steps: (1) initial formation of mineral patches associated with S-layer; (2) patch expansion; (3) patch connection; (4) formation of a continuous mineral encrusted layer at the cell surface; (5) early stages of S-layer fossilization via growth of the extracellular mineralized layer and the mineralization of cytosolic face of the cell membrane. At more advanced stages of encrustation, encrusted outer membrane vesicles are formed, likely in an attempt to remove damaged S-layer proteins. The S-layer structure remains strikingly well preserved even upon the final step of encrustation, offering potential biosignatures to be looked for in the fossil record.
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Picard A, Obst M, Schmid G, Zeitvogel F, Kappler A. Limited influence of Si on the preservation of Fe mineral-encrusted microbial cells during experimental diagenesis. GEOBIOLOGY 2016; 14:276-292. [PMID: 26695194 DOI: 10.1111/gbi.12171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 11/10/2015] [Indexed: 06/05/2023]
Abstract
The reconstruction of the history of microbial life since its emergence on early Earth is impaired by the difficulty to prove the biogenicity of putative microfossils in the rock record. While most of the oldest rocks on Earth have been exposed to different grades of diagenetic alterations, little is known about how the remains of micro-organisms evolve when exposed to pressure (P) and temperature (T) conditions typical of diagenesis. Using spectroscopy and microscopy, we compared morphological, mineralogical, and chemical biosignatures exhibited by Fe mineral-encrusted cells of the bacterium Acidovorax sp. BoFeN1 after long-term incubation under ambient conditions and after experimental diagenesis. We also evaluated the effects of Si on the preservation of microbial cells during the whole process. At ambient conditions, Si affected the morphology but not the identity (goethite) of Fe minerals that formed around cells. Fe-encrusted cells were morphologically well preserved after 1 week at 250 °C-140 MPa and after 16 weeks at 170 °C-120 MPa in the presence or in the absence of Si. Some goethite transformed to hematite and magnetite at 250 °C-140 MPa, but in the presence of Si more goethite was preserved. Proteins-the most abundant cellular components-were preserved over several months at ambient conditions but disappeared after incubations at high temperature and pressure conditions, both in the presence and in the absence of Si. Other organic compounds, such as lipids and extracellular polysaccharides seemed well preserved after exposure to diagenetic conditions. This study provides insights about the composition and potential preservation of microfossils that could have formed in Fe- and Si-rich Precambrian oceans.
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Affiliation(s)
- A Picard
- Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
| | - M Obst
- Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
| | - G Schmid
- Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
| | - F Zeitvogel
- Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
| | - A Kappler
- Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
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Schmid G, Zeitvogel F, Hao L, Ingino P, Adaktylou I, Eickhoff M, Obst M. Submicron-Scale Heterogeneities in Nickel Sorption of Various Cell-Mineral Aggregates Formed by Fe(II)-Oxidizing Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:114-125. [PMID: 26588096 DOI: 10.1021/acs.est.5b02955] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Fe(II)-oxidizing bacteria form biogenic cell-mineral aggregates (CMAs) composed of microbial cells, extracellular organic compounds, and ferric iron minerals. CMAs are capable of immobilizing large quantities of heavy metals, such as nickel, via sorption processes. CMAs play an important role for the fate of heavy metals in the environment, particularly in systems characterized by elevated concentrations of dissolved metals, such as mine drainage or contaminated sediments. We applied scanning transmission (soft) X-ray microscopy (STXM) spectrotomography for detailed 3D chemical mapping of nickel sorbed to CMAs on the submicron scale. We analyzed different CMAs produced by phototrophic or nitrate-reducing microbial Fe(II) oxidation and, in addition, a twisted stalk structure obtained from an environmental biofilm. Nickel showed a heterogeneous distribution and was found to be preferentially sorbed to biogenically precipitated iron minerals such as Fe(III)-(oxyhydr)oxides and, to a minor extent, associated with organic compounds. Some distinct nickel accumulations were identified on the surfaces of CMAs. Additional information obtained from scatter plots and angular distance maps, showing variations in the nickel-iron and nickel-organic carbon ratios, also revealed a general correlation between nickel and iron. Although a high correlation between nickel and iron was observed in 2D maps, 3D maps revealed this to be partly due to projection artifacts. In summary, by combining different approaches for data analysis, we unambiguously showed the heterogeneous sorption behavior of nickel to CMAs.
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Affiliation(s)
- Gregor Schmid
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Fabian Zeitvogel
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Likai Hao
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Pablo Ingino
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Irini Adaktylou
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Merle Eickhoff
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Martin Obst
- Environmental Analytical Microscopy, Center for Applied Geoscience, University of Tübingen , Hölderlinstrasse 12, 72074 Tübingen, Germany
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Cismasu AC, Williams KH, Nico PS. Iron and Carbon Dynamics during Aging and Reductive Transformation of Biogenic Ferrihydrite. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:25-35. [PMID: 26605981 DOI: 10.1021/acs.est.5b03021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Natural organic matter is often associated with Fe(III) oxyhydroxides, and may be stabilized as a result of coprecipitation or sorption to their surfaces. However, the significance of this association in relation to Fe and C dynamics and biogeochemical cycling, and the mechanisms responsible for organic matter stabilization as a result of interaction with minerals under various environmental conditions (e.g., pH, Eh, etc.) are not entirely understood. The preservation of mineral-bound OM may be affected by OM structure and mineral identity, and bond types between OM and minerals may be central to influencing the stability, transformation and composition of both organic and mineral components under changing environmental conditions. Here we use bulk and submicron-scale spectroscopic synchrotron methods to examine the in situ transformation of OM-bearing, biogenic ferrihydrite stalks (Gallionella ferruginea-like), which formed following injection of oxygenated groundwater into a saturated alluvial aquifer at the Rifle, CO field site. A progression from oxidizing to reducing conditions during an eight-month period triggered the aging and reductive transformation of Gallionella-like ferrihydrite stalks to Fe (hydroxy)carbonates and Fe sulfides, as well as alteration of the composition and amount of OM. Spectromicroscopic measurements showed a gradual decrease in reduced carbon forms (aromatic/alkene, aliphatic C), a relative increase in amide/carboxyl functional groups and a significant increase in carbonate in the stalk structures, and the appearance of organic globules not associated with stalk structures. Biogenic stalks lost ∼30% of their initial organic carbon content. Conversely, a significant increase in bulk organic matter accompanied these transformations. The character of bulk OM changed in parallel with mineralogical transformations, showing an increase in aliphatic, aromatic and amide functional groups. These changes likely occurred as a result of an increase in microbial activity, or biomass production under anoxic conditions. By the end of this experiment, a substantial fraction of organic matter remained in identifiable Fe containing stalks, but carbon was also present in additional pools, for example, organic matter globules and iron carbonate minerals.
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Affiliation(s)
- A Cristina Cismasu
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California, United States
| | - Kenneth H Williams
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California, United States
| | - Peter S Nico
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California, United States
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Bertrand L, Bernard S, Marone F, Thoury M, Reiche I, Gourrier A, Sciau P, Bergmann U. Emerging Approaches in Synchrotron Studies of Materials from Cultural and Natural History Collections. Top Curr Chem (Cham) 2016; 374:7. [DOI: 10.1007/s41061-015-0003-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/24/2015] [Indexed: 12/22/2022]
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Fabisch M, Freyer G, Johnson CA, Büchel G, Akob DM, Neu TR, Küsel K. Dominance of 'Gallionella capsiferriformans' and heavy metal association with Gallionella-like stalks in metal-rich pH 6 mine water discharge. GEOBIOLOGY 2016; 14:68-90. [PMID: 26407813 DOI: 10.1111/gbi.12162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/28/2015] [Indexed: 06/05/2023]
Abstract
Heavy metal-contaminated, pH 6 mine water discharge created new streams and iron-rich terraces at a creek bank in a former uranium-mining area near Ronneburg, Germany. The transition from microoxic groundwater with ~5 mm Fe(II) to oxic surface water may provide a suitable habitat for microaerobic iron-oxidizing bacteria (FeOB). In this study, we investigated the potential contribution of these FeOB to iron oxidation and metal retention in this high-metal environment. We (i) identified and quantified FeOB in water and sediment at the outflow, terraces, and creek, (ii) studied the composition of biogenic iron oxides (Gallionella-like twisted stalks) with scanning and transmission electron microscopy (SEM, TEM) as well as confocal laser scanning microscopy (CLSM), and (iii) examined the metal distribution in sediments. Using quantitative PCR, a very high abundance of FeOB was demonstrated at all sites over a 6-month study period. Gallionella spp. clearly dominated the communities, accounting for up to 88% of Bacteria, with a minor contribution of other FeOB such as Sideroxydans spp. and 'Ferrovum myxofaciens'. Classical 16S rRNA gene cloning showed that 96% of the Gallionella-related sequences had ≥ 97% identity to the putatively metal-tolerant 'Gallionella capsiferriformans ES-2', in addition to known stalk formers such as Gallionella ferruginea and Gallionellaceae strain R-1. Twisted stalks from glass slides incubated in water and sediment were composed of the Fe(III) oxyhydroxide ferrihydrite, as well as polysaccharides. SEM and scanning TEM-energy-dispersive X-ray spectroscopy revealed that stalk material contained Cu and Sn, demonstrating the association of heavy metals with biogenic iron oxides and the potential for metal retention by these stalks. Sequential extraction of sediments suggested that Cu (52-61% of total sediment Cu) and other heavy metals were primarily bound to the iron oxide fractions. These results show the importance of 'G. capsiferriformans' and biogenic iron oxides in slightly acidic but highly metal-contaminated freshwater environments.
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MESH Headings
- Aerobiosis
- Biota
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Ferric Compounds/analysis
- Gallionellaceae/chemistry
- Gallionellaceae/classification
- Gallionellaceae/genetics
- Gallionellaceae/isolation & purification
- Germany
- Hydrogen-Ion Concentration
- Iron/metabolism
- Metals, Heavy/analysis
- Microscopy, Confocal
- Microscopy, Electrochemical, Scanning
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Oxidation-Reduction
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Water/chemistry
- Water Microbiology
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Affiliation(s)
- M Fabisch
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - G Freyer
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - C A Johnson
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
| | - G Büchel
- Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - D M Akob
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- U.S. Geological Survey, Reston, VA, USA
| | - T R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research Leipzig-Halle - UFZ, Magdeburg, Germany
| | - K Küsel
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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Bernard S, Benzerara K, Beyssac O, Balan E, Brown GE. Evolution of the macromolecular structure of sporopollenin during thermal degradation. Heliyon 2015; 1:e00034. [PMID: 27123494 PMCID: PMC4832518 DOI: 10.1016/j.heliyon.2015.e00034] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/28/2015] [Accepted: 09/25/2015] [Indexed: 11/13/2022] Open
Abstract
Reconstructing the original biogeochemistry of organic microfossils requires quantifying the extent of the chemical transformations they experienced during burial and maturation processes. In the present study, fossilization experiments have been performed using modern sporopollenin chosen as an analogue for the resistant biocompounds possibly constituting the wall of many organic microfossils. Sporopollenin powder has been processed thermally under argon atmosphere at different temperatures (up to 1000 °C) for varying durations (up to 900 min). Solid residues of each experiment have been characterized using infrared, Raman and synchrotron-based XANES spectroscopies. Results indicate that significant defunctionalisation and aromatization affect the molecular structure of sporopollenin with increasing temperature. Two distinct stages of evolution with temperature are observed: in a first stage, sporopollenin experiences dehydrogenation and deoxygenation simultaneously (below 500 °C); in a second stage (above 500 °C) an increasing concentration in aromatic groups and a lateral growth of aromatic layers are observed. With increasing heating duration (up to 900 min) at a constant temperature (360 °C), oxygen is progressively lost and conjugated carbon–carbon chains or domains grow progressively, following a log-linear kinetic behavior. Based on the comparison with natural spores fossilized within metasediments which experienced intense metamorphism, we show that the present experimental simulations may not perfectly mimic natural diagenesis and metamorphism. Yet, performing such laboratory experiments provides key insights on the processes transforming biogenic molecules into molecular fossils.
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Affiliation(s)
- S Bernard
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC), Sorbonne Universités - MNHN, UPMC Univ Paris 06, CNRS UMR 7590, IRD UMR 206, 75005 Paris, France
| | - K Benzerara
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC), Sorbonne Universités - MNHN, UPMC Univ Paris 06, CNRS UMR 7590, IRD UMR 206, 75005 Paris, France
| | - O Beyssac
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC), Sorbonne Universités - MNHN, UPMC Univ Paris 06, CNRS UMR 7590, IRD UMR 206, 75005 Paris, France
| | - E Balan
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC), Sorbonne Universités - MNHN, UPMC Univ Paris 06, CNRS UMR 7590, IRD UMR 206, 75005 Paris, France
| | - G E Brown
- Surface & Aqueous Geochemistry Group, Department of Geological and Environmental Sciences, Stanford University, Stanford, CA 94305-2115, USA; Department of Photon Science and Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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