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Guido A, Calcagnile M, Talà A, Tredici SM, Belmonte G, Alifano P. Microbial consortium involved in ferromanganese and francolite biomineralization in an anchialine environment (Zinzulùsa Cave, Castro, Italy). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 936:173423. [PMID: 38797412 DOI: 10.1016/j.scitotenv.2024.173423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/03/2024] [Accepted: 05/19/2024] [Indexed: 05/29/2024]
Abstract
Tidally-influenced subterranean settings represent natural geomicrobiological laboratories, relatively unexplored, that facilitate the investigation of new biomineralization processes. The unusual water chemistry of Zinzulùsa Cave and its oligotrophic and aphotic conditions have allowed the development of a unique ecosystem in which complex bacterial activities induce rare biomineralization processes. A diversified microbial community develops on centimeter-thick crusts that form in the submerged part of the cave. The crusts are formed of Ca-phosphate minerals, mostly carbonate-fluoroapatite (francolite), covered by a black crust, few microns in thickness, composed of ferromanganiferous oxides (hematite and vernadite). Diffuse coccoidal and filamentous bacteria and amorphous organic matter are mixed with the minerals. The micromorphologies and comparative 16S rRNA gene-based metabarcoding analyses identify a "core microbiota" also common to other natural environments characterized by FeMn and Ca-phosphate mineralization. The microbiota is characterized by nitrifying, sulfide/sulfur/thiosulfate-oxidizing and sulfate/thiosulfate/sulfur-reducing bacteria. In addition, manganese-oxidizing bacteria include the recently described "Ca. Manganitrophus noduliformans" and an abundance of bacteria belonging to the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum, as well as Haliangiales (fruiting body-forming bacteria) and Hyphomicrobiales (stalked and budding bacteria) that are known to produce extracellular polymers that trap iron and manganese oxides. 16S rRNA gene metabarcoding analysis showed the presence of bacteria able to utilize many organic P substrates, including Ramlibacter, and SEM images revealed traces of fossilized microorganisms resembling "cable bacteria", which may play a role in Ca-phosphate biomineralization. Overall, the data indicate biomineralization processes induced by microbial metabolic activities for both ferromanganiferous oxide and francolite components of these crusts.
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Affiliation(s)
- Adriano Guido
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Cosenza, Italy.
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy.
| | - Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy.
| | | | - Genuario Belmonte
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy.
| | - Pietro Alifano
- Department of Experimental Medicine, University of Salento, Lecce, Italy.
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2
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Environmental Factors Affecting Feather Taphonomy. BIOLOGY 2022; 11:biology11050703. [PMID: 35625431 PMCID: PMC9138376 DOI: 10.3390/biology11050703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022]
Abstract
The exceptional preservation of feathers in the fossil record has led to a better understanding of both phylogeny and evolution. Here we address factors that may have contributed to the preservation of feathers in ancient organisms using experimental taphonomy. We show that the atmospheres of the Mesozoic, known to be elevated in both CO2 and with temperatures above present levels, may have contributed to the preservation of these soft tissues by facilitating rapid precipitation of hydroxy- or carbonate hydroxyapatite, thus outpacing natural degradative processes. Data also support that that microbial degradation was enhanced in elevated CO2, but mineral deposition was also enhanced, contributing to preservation by stabilizing the organic components of feathers.
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3
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Łukawska-Matuszewska K, Brocławik O, Brodecka-Goluch A, Rzepa G, Manecki M, Bolałek J. Biogeochemical and mineralogical effects of Fe-P-S dynamics in sediments of continental shelf sea: Impact of salinity, oxygen conditions, and catchment area characteristics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151035. [PMID: 34666081 DOI: 10.1016/j.scitotenv.2021.151035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
In this study, we investigate how salinity, oxygen concentration and catchment area characteristics impact the dynamics of Fe-P-S cycling in the continental shelf sea sediments. Samples were collected from three sites representing different environmental conditions: Gdańsk Deep (southern Baltic Sea), Gotland Deep (central Baltic Sea) and Bothnian Sea (northern Baltic Sea). Sediments were analysed for their mineral composition and speciation of iron and phosphorus. The main groups of Prokaryota involved in Fe-P-S cycling in sediments were indicated. Concentrations of sulphate, hydrogen sulphide, alkalinity, chloride, calcium, phosphate and iron were measured in pore waters. We demonstrated that in the eutrophicated southern region with moderate salinity and oxygen deficit in bottom water, sediments had high potential for retaining Fe and releasing P as indicated by high concentrations of pyrite and labile forms of phosphorus, respectively. Strong salinity stratification and intermittent pelagic redoxcline in the central Baltic Sea resulted in a clearly higher rate of pyrite deposition. Sediment was enriched with Mn due to the formation of Ca-Mn carbonates driven by intensive Mn redox cycling and sulphate reduction. Because of high availability of Mn oxides connected with episodic inflows of oxic seawater from the North Sea, sulphate was present in the entire profile of the studied sediments in the Gotland Deep. Sediments in the well-oxygenated, virtually fresh and rich in land-derived iron northern Baltic Sea retained significant amounts of P in authigenic minerals. Organic matter mineralisation in the surface sediment of this area was dominated by iron reduction. The variability of environmental conditions and consequent availability of electron acceptors were the cause of regional differences in the composition of Prokaryota communities - the number of sulphate reducers in the Gdańsk and Gotland Deeps was greater than in the Bothnian Sea, where there were more Fe reducers and bacteria that oxidise Fe and S.
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Affiliation(s)
- Katarzyna Łukawska-Matuszewska
- Faculty of Oceanography and Geography, Institute of Oceanography, University of Gdańsk, Al. Marszałka Piłsudskiego 46, 81-378 Gdynia, Poland.
| | - Olga Brocławik
- Faculty of Oceanography and Geography, Institute of Oceanography, University of Gdańsk, Al. Marszałka Piłsudskiego 46, 81-378 Gdynia, Poland
| | - Aleksandra Brodecka-Goluch
- Faculty of Oceanography and Geography, Institute of Oceanography, University of Gdańsk, Al. Marszałka Piłsudskiego 46, 81-378 Gdynia, Poland
| | - Grzegorz Rzepa
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Kraków, Poland
| | - Maciej Manecki
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Kraków, Poland
| | - Jerzy Bolałek
- Faculty of Oceanography and Geography, Institute of Oceanography, University of Gdańsk, Al. Marszałka Piłsudskiego 46, 81-378 Gdynia, Poland
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4
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Bidaud CC, Monteil CL, Menguy N, Busigny V, Jézéquel D, Viollier É, Travert C, Skouri-Panet F, Benzerara K, Lefevre CT, Duprat É. Biogeochemical Niche of Magnetotactic Cocci Capable of Sequestering Large Polyphosphate Inclusions in the Anoxic Layer of the Lake Pavin Water Column. Front Microbiol 2022; 12:789134. [PMID: 35082768 PMCID: PMC8786505 DOI: 10.3389/fmicb.2021.789134] [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: 10/04/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Magnetotactic bacteria (MTB) are microorganisms thriving mostly at oxic–anoxic boundaries of aquatic habitats. MTB are efficient in biomineralising or sequestering diverse elements intracellularly, which makes them potentially important actors in biogeochemical cycles. Lake Pavin is a unique aqueous system populated by a wide diversity of MTB with two communities harbouring the capability to sequester not only iron under the form of magnetosomes but also phosphorus and magnesium under the form of polyphosphates, or calcium carbonates, respectively. MTB thrive in the water column of Lake Pavin over a few metres along strong redox and chemical gradients representing a series of different microenvironments. In this study, we investigate the relative abundance and the vertical stratification of the diverse populations of MTB in relation to environmental parameters, by using a new method coupling a precise sampling for geochemical analyses, MTB morphotype description, and in situ measurement of the physicochemical parameters. We assess the ultrastructure of MTB as a function of depth using light and electron microscopy. We evidence the biogeochemical niche of magnetotactic cocci, capable of sequestering large PolyP inclusions below the oxic–anoxic transition zone. Our results suggest a tight link between the S and P metabolisms of these bacteria and pave the way to better understand the implication of MTB for the P cycle in stratified environmental conditions.
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Affiliation(s)
- Cécile C Bidaud
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France.,Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France.,Université de Paris, Centre de Recherches Interdisciplinaires (CRI), Paris, France
| | - Caroline L Monteil
- Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France
| | - Nicolas Menguy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Vincent Busigny
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, France
| | - Didier Jézéquel
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, France.,INRAE & Université Savoie Mont Blanc, UMR CARRTEL, Thonon-les-Bains, France
| | - Éric Viollier
- LSCE, CEA/CNRS/UVSQ/IPSL, Université Paris Saclay & Université de Paris France, Gif-sur-Yvette Cedex, France
| | - Cynthia Travert
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Fériel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Christopher T Lefevre
- Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France
| | - Élodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
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5
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Hoffmann TD, Reeksting BJ, Gebhard S. Bacteria-induced mineral precipitation: a mechanistic review. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001049. [PMID: 33881981 PMCID: PMC8289221 DOI: 10.1099/mic.0.001049] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/15/2021] [Indexed: 11/18/2022]
Abstract
Micro-organisms contribute to Earth's mineral deposits through a process known as bacteria-induced mineral precipitation (BIMP). It is a complex phenomenon that can occur as a result of a variety of physiological activities that influence the supersaturation state and nucleation catalysis of mineral precipitation in the environment. There is a good understanding of BIMP induced by bacterial metabolism through the control of metal redox states and enzyme-mediated reactions such as ureolysis. However, other forms of BIMP often cannot be attributed to a single pathway but rather appear to be a passive result of bacterial activity, where minerals form as a result of metabolic by-products and surface interactions within the surrounding environment. BIMP from such processes has formed the basis of many new innovative biotechnologies, such as soil consolidation, heavy metal remediation, restoration of historic buildings and even self-healing concrete. However, these applications to date have primarily incorporated BIMP-capable bacteria sampled from the environment, while detailed investigations of the underpinning mechanisms have been lagging behind. This review covers our current mechanistic understanding of bacterial activities that indirectly influence BIMP and highlights the complexity and connectivity between the different cellular and metabolic processes involved. Ultimately, detailed insights will facilitate the rational design of application-specific BIMP technologies and deepen our understanding of how bacteria are shaping our world.
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Affiliation(s)
- Timothy D. Hoffmann
- Department of Biology and Biochemistry, Milner Centre for Evolution, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Bianca J. Reeksting
- Department of Biology and Biochemistry, Milner Centre for Evolution, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Susanne Gebhard
- Department of Biology and Biochemistry, Milner Centre for Evolution, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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Büttner SH, Isemonger EW, Isaacs M, van Niekerk D, Sipler RE, Dorrington RA. Living phosphatic stromatolites in a low-phosphorus environment: Implications for the use of phosphorus as a proxy for phosphate levels in paleo-systems. GEOBIOLOGY 2021; 19:35-47. [PMID: 33067916 DOI: 10.1111/gbi.12415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 08/01/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
In the geological record, fossil phosphatic stromatolites date back to the Great Oxidation Event in the Paleoproterozoic, but living phosphatic stromatolites have not been described previously. Here, we report on cyanobacterial stromatolites in a supratidal freshwater environment at Cape Recife, South African southern coast, precipitating Ca carbonate alternating with episodes of Ca phosphate deposition. In their structure and composition, the living stromatolites from Cape Recife closely resemble their fossilized analogues, showing phosphatic zonation, microbial casts, tunnel structures and phosphatic crusts of biogenic origin. The microbial communities appear to be also similar to those proposed to have formed fossil phosphatic stromatolites. Phosphatic domains in the material from Cape Recife are spatially and texturally associated with carbonate precipitates, but form distinct entities separated by sharp boundaries. Electron Probe Micro-Analysis shows that Ca/P ratios and the overall chemical compositions of phosphatic precipitates are in the range of octacalcium phosphate, amorphous tricalcium phosphate and apatite. The coincidence in time of the emergence of phosphatic stromatolites in the fossil record with a major episode of atmospheric oxidation led to the assumption that at times of increased oxygen release the underlying increased biological production may have been linked to elevated phosphorus availability. The stromatolites at Cape Recife, however, form in an environment where ambient phosphorus concentrations do not exceed 0.28 μM, one to two orders of magnitude below the previously predicted minimum threshold of >5 μM for biogenic phosphate precipitation in paleo-systems. Accordingly, we contest the previously proposed suitability of phosphatic stromatolites as a proxy for high ambient phosphate concentrations in supratidal to shallow ocean settings in earth history.
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Affiliation(s)
- Steffen H Büttner
- Department of Geology, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Eric W Isemonger
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Michelle Isaacs
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Deon van Niekerk
- Department of Geology, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Rachel E Sipler
- Department of Ocean Sciences, Memorial University of Newfoundland, St John's, NL, Canada
| | - Rosemary A Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda (Grahamstown), South Africa
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7
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Precipitation of Inorganic Salts in Mitochondrial Matrix. MEMBRANES 2020; 10:membranes10050081. [PMID: 32349446 PMCID: PMC7281443 DOI: 10.3390/membranes10050081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 11/17/2022]
Abstract
In the mitochondrial matrix, there are insoluble, osmotically inactive complexes that maintain a constant pH and calcium concentration. In the present paper, we examine the properties of insoluble calcium and magnesium salts, such as phosphates, carbonates and polyphosphates, which might play this role. We find that non-stoichiometric, magnesium-rich carbonated apatite, with very low crystallinity, precipitates in the matrix under physiological conditions. Precipitated salt acts as pH buffer, and, hence, can contribute in maintaining ATP production in ischemic conditions, which delays irreversible damage to heart and brain cells after stroke.
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8
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Larina E, Bottjer DJ, Corsetti FA, Zonneveld JP, Celestian AJ, Bailey JV. Uppermost Triassic phosphorites from Williston Lake, Canada: link to fluctuating euxinic-anoxic conditions in northeastern Panthalassa before the end-Triassic mass extinction. Sci Rep 2019; 9:18790. [PMID: 31827166 PMCID: PMC6906467 DOI: 10.1038/s41598-019-55162-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/19/2019] [Indexed: 12/02/2022] Open
Abstract
The end-Triassic mass extinction (ETE) is associated with a rise in CO2 due to eruptions of the Central Atlantic Magmatic Province (CAMP), and had a particularly dramatic effect on the Modern Fauna, so an understanding of the conditions that led to the ETE has relevance to current rising CO2 levels. Here, we report multiple phosphorite deposits in strata that immediately precede the ETE at Williston Lake, Canada, which allow the paleoenvironmental conditions leading up to the mass extinction to be investigated. The predominance of phosphatic coated grains within phoshorites indicates reworking in shallow water environments. Raman spectroscopy reveals that the phosphorites contain organic carbon, and petrographic and scanning electron microscopic analyses reveal that the phosphorites contain putative microfossils, potentially suggesting microbial involvement in a direct or indirect way. Thus, we favor a mechanism of phosphogenesis that involves microbial polyphosphate metabolism in which phosphatic deposits typically form at the interface of euxinic/anoxic and oxic conditions. When combined with data from deeper water deposits (Kennecott Point) far to the southwest, it would appear a very broad area of northeastern Panthalassa experienced anoxic to euxinic bottom water conditions in the direct lead up to the end-Triassic mass extinction. Such a scenario implies expansion and shallowing of the oxygen minimum zone across a very broad area of northeastern Panthalassa, which potentially created a stressful environment for benthic metazoan communities. Studies of the pre-extinction interval from different sites across the globe are required to resolve the chronology and spatial distribution of processes that governed before the major environmental collapse that caused the ETE. Results from this study demonstrate that fluctuating anoxic and euxinic conditions could have been potentially responsible for reduced ecosystem stability before the onset of CAMP volcanism, at least at the regional scale.
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Affiliation(s)
- Ekaterina Larina
- Earth Sciences, University of Southern California, Los Angeles, USA.
| | - David J Bottjer
- Earth Sciences, University of Southern California, Los Angeles, USA
| | - Frank A Corsetti
- Earth Sciences, University of Southern California, Los Angeles, USA
| | | | | | - Jake V Bailey
- Earth Sciences, University of Minnesota, Minneapolis, USA
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9
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Fossilized Endolithic Microorganisms in Pillow Lavas from the Troodos Ophiolite, Cyprus. GEOSCIENCES 2019. [DOI: 10.3390/geosciences9110456] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The last decade has revealed the igneous oceanic crust to host a more abundant and diverse biota than previously expected. These underexplored rock-hosted deep ecosystems dominated Earth’s biosphere prior to plants colonized land in the Ordovician, thus the fossil record of deep endoliths holds invaluable clues to early life and the work to decrypt them needs to be intensified. Here, we present fossilized microorganisms found in open and sealed pore spaces in pillow lavas from the Troodos Ophiolite (91 Ma) on Cyprus. A fungal interpretation is inferred upon the microorganisms based on characteristic morphological features. Geochemical conditions are reconstructed using data from mineralogy, fluid inclusions and the fossils themselves. Mineralogy indicates at least three hydrothermal events and a continuous increase of temperature and pH. Precipitation of 1) celadonite and saponite together with the microbial introduction was followed by 2) Na and Ca zeolites resulting in clay adherence on the microorganisms as protection, and finally 3) Ca carbonates resulted in final fossilization and preservation of the organisms in-situ. Deciphering the fossil record of the deep subseafloor biosphere is a challenging task, but when successful, can unlock doors to life’s cryptic past.
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D'Hondt S, Pockalny R, Fulfer VM, Spivack AJ. Subseafloor life and its biogeochemical impacts. Nat Commun 2019; 10:3519. [PMID: 31388058 PMCID: PMC6684631 DOI: 10.1038/s41467-019-11450-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 07/10/2019] [Indexed: 11/08/2022] Open
Abstract
Subseafloor microbial activities are central to Earth's biogeochemical cycles. They control Earth's surface oxidation and major aspects of ocean chemistry. They affect climate on long timescales and play major roles in forming and destroying economic resources. In this review, we evaluate present understanding of subseafloor microbes and their activities, identify research gaps, and recommend approaches to filling those gaps. Our synthesis suggests that chemical diffusion rates and reaction affinities play a primary role in controlling rates of subseafloor activities. Fundamental aspects of subseafloor communities, including features that enable their persistence at low catabolic rates for millions of years, remain unknown.
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Affiliation(s)
- Steven D'Hondt
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA.
| | - Robert Pockalny
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA
| | - Victoria M Fulfer
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA
| | - Arthur J Spivack
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA
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11
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Zoss R, Medina Ferrer F, Flood BE, Jones DS, Louw DC, Bailey J. Microbial communities associated with phosphogenic sediments and phosphoclast-associated DNA of the Benguela upwelling system. GEOBIOLOGY 2019; 17:76-90. [PMID: 30369004 DOI: 10.1111/gbi.12318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/20/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
The processes that lead to the precipitation of authigenic calcium phosphate minerals in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating bacteria. These bacteria are believed to concentrate phosphate in sediment pore waters, creating supersaturated conditions with respect to apatite precursors. However, the relationship between microbes and phosphorite formation is not fully resolved. To further study this association, we examined microbial community data generated from two sources: sediment cores recovered from the shelf of the Benguela upwelling region where phosphorites are currently forming, and DNA preserved within phosphoclasts recovered from a phosphorite deposit along the Benguela shelf. iTag and clone library sequencing of the 16S rRNA gene showed that many of our sediment-hosted communities shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfate-reducing bacteria and sulfur-oxidizing bacteria were particularly abundant in our datasets, as were phylotypes that are known to carry out nitrification and the anaerobic oxidation of ammonium. The DNA extracted from phosphoclasts contained the signature of a distinct microbial community from those observed in the modern sediments. While some aspects of the modern and phosphoclast communities were similar, we observed both an enrichment of certain common microbial classes found in the modern phosphogenic sediments and a relative depletion of others. The phosphoclast-associated DNA could represent a relict signature of one or more microbial assemblages that were present when the apatite or its precursors precipitated. While these taxa may or may not have contributed to the precipitation of the apatite that now hosts their genetic remains, several groups represented in the phosphoclast extract dataset have the genetic potential to metabolize polyphosphate, and perhaps modulate phosphate concentrations in pore waters where carbonate fluorapatite (or its precursors) are known to be precipitating.
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Affiliation(s)
- Roman Zoss
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
| | | | - Beverly E Flood
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
| | - Daniel S Jones
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
- BioTechnology Institute, University of Minnesota, St. Paul, Minneapolis
| | - Deon C Louw
- Ministry of Fisheries and Marine Resources, National Marine Information and Research Centre, Swakopmund, Namibia
| | - Jake Bailey
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
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12
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Mänd K, Kirsimäe K, Lepland A, Crosby CH, Bailey JV, Konhauser KO, Wirth R, Schreiber A, Lumiste K. Authigenesis of biomorphic apatite particles from Benguela upwelling zone sediments off Namibia: The role of organic matter in sedimentary apatite nucleation and growth. GEOBIOLOGY 2018; 16:640-658. [PMID: 30062734 DOI: 10.1111/gbi.12309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 05/09/2018] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
Sedimentary phosphorites comprise a major phosphorus (P) ore, yet their formation remains poorly understood. Extant polyphosphate-metabolizing bacterial communities are known to act as bacterial phosphate-pumps, leading to episodically high dissolved phosphate concentrations in pore waters of organic-rich sediment. These conditions can promote the precipitation of amorphous precursor phases that are quickly converted to apatite-usually in carbonate fluorapatite form [Ca10 (PO4 ,CO3 )6 F2-3 ]. To assess the mechanisms underpinning the nucleation and growth of sedimentary apatite, we sampled P-rich sediments from the Namibian shelf, a modern environment where phosphogenesis presently occurs. The P-rich fraction of the topmost centimetres of sediment mainly consists of pellets about 50-400 μm in size, which in turn are comprised of micron-sized apatite particles that are often arranged into radial structures with diameters ranging from 2 to 4 μm, and morphologies that range from rod-shapes to dumbbells to spheres that resemble laboratory-grown fluorapatite-gelatin nanocomposites known from double-diffusion experiments in organic matrices. The nucleation and growth of authigenic apatite on the Namibian shelf is likely analogous to these laboratory-produced precipitates, where organic macromolecules play a central role in apatite nucleation and growth. The high density of apatite nucleation sites within the pellets (>109 particles per cm3 ) suggests precipitation at high pore water phosphate concentrations that have been reported from the Namibian shelf and may be attributed to microbial phosphate pumping. The intimate association of organic material with the apatite could suggest a possible role of biological substrata, such as exopolymeric substances (EPS), in the nucleation of apatite precursors. Importantly, we do not observe any evidence that the apatite particles are actual phosphatized microbes, contradicting some earlier studies. Nevertheless, these results further evidence the potential importance of microbially derived (extracellular) organic matter as a template for phosphatic mineral nucleation in both recent and ancient phosphorites.
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Affiliation(s)
- Kaarel Mänd
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Geology, University of Tartu, Tartu, Estonia
| | - Kalle Kirsimäe
- Department of Geology, University of Tartu, Tartu, Estonia
| | - Aivo Lepland
- Department of Geology, University of Tartu, Tartu, Estonia
- Department of Geosciences, CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, UiT The Arctic University of Norway, Tromsø, Norway
- Geological Survey of Norway, Trondheim, Norway
- Institute of Geology, Tallinn University of Technology, Tallinn, Estonia
| | - Chris H Crosby
- Department of Earth Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Jake V Bailey
- Department of Earth Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Richard Wirth
- GFZ German Research Centre for Geosciences, Section 4.3: Chemistry and Physics of Earth Materials, Potsdam, Germany
| | - Anja Schreiber
- GFZ German Research Centre for Geosciences, Section 4.3: Chemistry and Physics of Earth Materials, Potsdam, Germany
| | - Kaarel Lumiste
- Department of Geology, University of Tartu, Tartu, Estonia
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13
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The effects of marine eukaryote evolution on phosphorus, carbon and oxygen cycling across the Proterozoic-Phanerozoic transition. Emerg Top Life Sci 2018; 2:267-278. [PMID: 32412617 PMCID: PMC7289021 DOI: 10.1042/etls20170156] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/27/2018] [Accepted: 05/01/2018] [Indexed: 12/03/2022]
Abstract
A ‘Neoproterozoic oxygenation event’ is widely invoked as a causal factor in animal evolution, and often attributed to abiotic causes such as post-glacial pulses of phosphorus weathering. However, recent evidence suggests a series of transient ocean oxygenation events ∼660–520 Ma, which do not fit the simple model of a monotonic rise in atmospheric oxygen (pO2). Hence, we consider mechanisms by which the evolution of marine eukaryotes, coupled with biogeochemical and ecological feedbacks, potentially between alternate stable states, could have caused changes in ocean carbon cycling and redox state, phosphorus cycling and atmospheric pO2. We argue that the late Tonian ocean ∼750 Ma was dominated by rapid microbial cycling of dissolved organic matter (DOM) with elevated nutrient (P) levels due to inefficient removal of organic matter to sediments. We suggest the abrupt onset of the eukaryotic algal biomarker record ∼660–640 Ma was linked to an escalation of protozoan predation, which created a ‘biological pump’ of sinking particulate organic matter (POM). The resultant transfer of organic carbon (Corg) and phosphorus to sediments was strengthened by subsequent eukaryotic innovations, including the advent of sessile benthic animals and mobile burrowing animals. Thus, each phase of eukaryote evolution tended to lower P levels and oxygenate the ocean on ∼104 year timescales, but by decreasing Corg/P burial ratios, tended to lower atmospheric pO2 and deoxygenate the ocean again on ∼106 year timescales. This can help explain the transient nature and ∼106 year duration of oceanic oxygenation events through the Cryogenian–Ediacaran–Cambrian.
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14
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Polyphosphate-Accumulating Bacteria: Potential Contributors to Mineral Dissolution in the Oral Cavity. Appl Environ Microbiol 2018; 84:AEM.02440-17. [PMID: 29352083 PMCID: PMC5861820 DOI: 10.1128/aem.02440-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023] Open
Abstract
Bacteria that accumulate polyphosphates have previously been shown to dynamically influence the solubility of phosphatic minerals in marine settings and wastewater. Here, we show that dental plaque, saliva, and carious lesions all contain abundant polyphosphate-accumulating bacteria. Saturation state modeling results, informed by phosphate uptake experiments using the model organism Lactobacillus rhamnosus, which is known to inhabit advanced carious lesions, suggest that polyphosphate accumulation can lead to undersaturated conditions with respect to hydroxyapatite under some oral cavity conditions. The cell densities of polyphosphate-accumulating bacteria we observed in some regions of oral biofilms are comparable to those that produce undersaturated conditions (i.e., those that thermodynamically favor mineral dissolution) in our phosphate uptake experiments with L. rhamnosus These results suggest that the localized generation of undersaturated conditions by polyphosphate-accumulating bacteria constitutes a new potential mechanism of tooth dissolution that may augment the effects of metabolic acid production.IMPORTANCE Dental caries is a serious public health issue that can have negative impacts on overall quality of life and oral health. The role of oral bacteria in the dissolution of dental enamel and dentin that can result in carious lesions has long been solely ascribed to metabolic acid production. Here, we show that certain oral bacteria may act as a dynamic shunt for phosphate in dental biofilms via the accumulation of a polymer known as polyphosphate-potentially mediating phosphate-dependent conditions such as caries (dental decay).
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15
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Siahi M, Hofmann A, Master S, Mueller CW, Gerdes A. Carbonate ooids of the Mesoarchaean Pongola Supergroup, South Africa. GEOBIOLOGY 2017; 15:750-766. [PMID: 28737010 DOI: 10.1111/gbi.12249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
Ooids from the Mesoarchaean Chobeni Formation, Pongola Supergroup, KwaZulu-Natal, South Africa are older than any ooids reported to date. They are made of dolomite and ankerite and show concentric, radial-concentric, micritic, and radial fabrics. Radial ooids are interpreted to have originated from high-Mg-calcite and probably formed by microbial activity in a low-energy regime, while concentric ooids had an aragonite precursor and formed biotically under agitated/high-energy environmental conditions. Micritic ooids formed via the recrystallization of concentric ooids. Ooids and other allochems, such as intraclasts and peloids, contain carbonaceous matter. The close association of carbonaceous matter within ooid cortices with metabolically important elements, such as N, S and P, as identified by nano-scale secondary ion mass spectrometry analysis, allows us to propose a biologically induced origin for some ooids. By analogy with modern examples, a variety of microbial communities probably played a role in carbonate precipitation and ooid formation. Shale-normalized rare earth element (REE) distribution patterns of ooids and other allochems show positive LaSN , GdSN and YSN anomalies, superchondritic Y/Ho ratios and depleted light rare earth elements (LREEs) relative to the heavy rare earth elements (HREEs), which resemble those of seawater. These anomalies are less pronounced than expected for an open marine setting, which is interpreted as evidence for deposition in restricted shallow marine environments. Non-seawater REE patterns in recrystallized matrix and pore- and vein-filling carbonate likely reflect redistribution of rare earth elements during post-depositional alteration and/or reflect differences in the elemental and REE compositions of diagenetic fluids.
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Affiliation(s)
- M Siahi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-University, Munich, Germany
- Economic Geology Research Institute, School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A Hofmann
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
| | - S Master
- Economic Geology Research Institute, School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - C W Mueller
- Department of Ecology and Ecosystem Management, Soil Science, Technical University, Munich, Germany
| | - A Gerdes
- Institute of Geosciences, Goethe-University Frankfurt, Frankfurt, Germany
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16
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The Bruneau Woodpile: A Miocene Phosphatized Fossil Wood Locality in Southwestern Idaho, USA. GEOSCIENCES 2017. [DOI: 10.3390/geosciences7030082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Abstract
This paper addresses the taphonomic processes responsible for fossil preservation in calcium phosphate, or phosphatization. Aside from silicification and rarer examples of carbonaceous compression, phosphatization is the only taphonomic mode claimed to preserve putative subcellular structures. Because this fossilization window can record such valuable information, a comprehensive understanding of its patterns of occurrence and the geochemical processes involved in the replication of soft tissues are critical endeavors. Fossil phosphatization was most abundant during the latest Neoproterozoic through the early Paleozoic, coinciding with the decline of non-pelletal phosphorite deposits. Its temporal abundance during this timeframe makes it a particularly valuable window for the study of early animal evolution. Several occurrences of phosphatization from the Ediacaran through the Permian Period, including Doushantuo-type preservation of embryo-like fossils and acritarchs, phosphatized gut tracts within Burgess Shale-type carbonaceous compressions, Orsten-type preservation of meiofaunas, and other cases from the later Paleozoic are reviewed. In addition, a comprehensive description of the geochemical controls of calcium phosphate precipitation from seawater is provided, with a focus on the rates of phosphate nucleation and growth, favorable nucleation substrates, and properties of substrate tissue and pore-fluid chemistry. It is hoped that the paleontological and geochemical summaries provided here offer a practical and valuable guide to the Neoproterozoic–Paleozoic phosphatization window.
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18
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Flood BE, Fliss P, Jones DS, Dick GJ, Jain S, Kaster AK, Winkel M, Mußmann M, Bailey J. Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity. Front Microbiol 2016; 7:603. [PMID: 27199933 PMCID: PMC4853749 DOI: 10.3389/fmicb.2016.00603] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/11/2016] [Indexed: 11/23/2022] Open
Abstract
The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group I intron also carried a MITE sequence that, like the hupL MITE family, occurs broadly across the genome. The presence of a high degree of mobile elements in genes central to Thiomargarita's core metabolism has not been previously reported in free-living bacteria and suggests a highly mutable genome.
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Affiliation(s)
- Beverly E Flood
- Department of Earth Sciences, University of Minnesota Minneapolis, MN, USA
| | - Palmer Fliss
- Department of Earth Sciences, University of Minnesota Minneapolis, MN, USA
| | - Daniel S Jones
- Department of Earth Sciences, University of MinnesotaMinneapolis, MN, USA; Biotechnology Institute, University of MinnesotaSt. Paul, MN, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA
| | - Sunit Jain
- Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA
| | - Anne-Kristin Kaster
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ Braunschweig, Germany
| | - Matthias Winkel
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences Potsdam, Germany
| | - Marc Mußmann
- Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Jake Bailey
- Department of Earth Sciences, University of Minnesota Minneapolis, MN, USA
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19
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Auer G, Hauzenberger CA, Reuter M, Piller WE. Orbitally paced phosphogenesis in Mediterranean shallow marine carbonates during the middle Miocene Monterey event. GEOCHEMISTRY, GEOPHYSICS, GEOSYSTEMS : G(3) 2016; 17:1492-1510. [PMID: 27570497 PMCID: PMC4984836 DOI: 10.1002/2016gc006299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/29/2016] [Indexed: 06/06/2023]
Abstract
During the Oligo-Miocene, major phases of phosphogenesis occurred in the Earth's oceans. However, most phosphate deposits represent condensed or allochthonous hemipelagic deposits, formed by complex physical and chemical enrichment processes, limiting their applicability for the study regarding the temporal pacing of Miocene phosphogenesis. The Oligo-Miocene Decontra section located on the Maiella Platform (central Apennines, Italy) is a widely continuous carbonate succession deposited in a mostly middle to outer neritic setting. Of particular interest are the well-winnowed grain to packstones of the middle Miocene Bryozoan Limestone, where occurrences of authigenic phosphate grains coincide with the prominent carbon isotope excursion of the Monterey event. This unique setting allows the analysis of orbital forcing on phosphogenesis, within a bio, chemo, and cyclostratigraphically constrained age-model. LA-ICP-MS analyses revealed a significant enrichment of uranium in the studied authigenic phosphates compared to the surrounding carbonates, allowing natural gamma-radiation (GR) to be used as a qualitative proxy for autochthonous phosphate content. Time series analyses indicate a strong 405 kyr eccentricity forcing of GR in the Bryozoan Limestone. These results link maxima in the GR record and thus phosphate content to orbitally paced increases in the burial of organic carbon, particularly during the carbon isotope maxima of the Monterey event. Thus, phosphogenesis during the middle Miocene in the Mediterranean was controlled by the 405 kyr eccentricity and its influence on large-scale paleoproductivity patterns. Rare earth element data were used as a tool to reconstruct the formation conditions of the investigated phosphates, indicating generally oxic formation conditions, which are consistent with microbially mediated phosphogenesis.
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Affiliation(s)
- Gerald Auer
- Institute of Earth Sciences, University of Graz, NAWI Graz Geocenter Graz Austria
| | | | - Markus Reuter
- Institute of Earth Sciences, University of Graz, NAWI Graz Geocenter Graz Austria
| | - Werner E Piller
- Institute of Earth Sciences, University of Graz, NAWI Graz Geocenter Graz Austria
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20
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Dorozhkin SV. Calcium orthophosphates (CaPO 4): occurrence and properties. Prog Biomater 2015; 5:9-70. [PMID: 27471662 PMCID: PMC4943586 DOI: 10.1007/s40204-015-0045-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/05/2015] [Indexed: 01/02/2023] Open
Abstract
The present overview is intended to point the readers' attention to the important subject of calcium orthophosphates (CaPO4). This type of materials is of the special significance for the human beings because they represent the inorganic part of major normal (bones, teeth and antlers) and pathological (i.e., those appearing due to various diseases) calcified tissues of mammals. For example, atherosclerosis results in blood vessel blockage caused by a solid composite of cholesterol with CaPO4, while dental caries and osteoporosis mean a partial decalcification of teeth and bones, respectively, that results in replacement of a less soluble and harder biological apatite by more soluble and softer calcium hydrogenorthophosphates. Therefore, the processes of both normal and pathological calcifications are just an in vivo crystallization of CaPO4. Similarly, dental caries and osteoporosis might be considered as in vivo dissolution of CaPO4. In addition, natural CaPO4 are the major source of phosphorus, which is used to produce agricultural fertilizers, detergents and various phosphorus-containing chemicals. Thus, there is a great significance of CaPO4 for the humankind and, in this paper, an overview on the current knowledge on this subject is provided.
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21
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Sánchez-Román M, Puente-Sánchez F, Parro V, Amils R. Nucleation of Fe-rich phosphates and carbonates on microbial cells and exopolymeric substances. Front Microbiol 2015; 6:1024. [PMID: 26441946 PMCID: PMC4585095 DOI: 10.3389/fmicb.2015.01024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/26/2015] [Indexed: 11/28/2022] Open
Abstract
Although phosphate and carbonate are important constituents in ancient and modern environments, it is not yet clear their biogeochemical relationships and their mechanisms of formation. Microbially mediated carbonate formation has been widely studied whereas little is known about the formation of phosphate minerals. Here we report that a new bacterial strain, Tessarococcus lapidicaptus, isolated from the subsurface of Rio Tinto basin (Huelva, SW Spain), is capable of precipitating Fe-rich phosphate and carbonate minerals. We observed morphological differences between phosphate and carbonate, which may help us to recognize these minerals in terrestrial and extraterrestrial environments. Finally, considering the scarcity and the unequal distribution and preservation patterns of phosphate and carbonates, respectively, in the geological record and the biomineralization process that produces those minerals, we propose a hypothesis for the lack of Fe-phosphates in natural environments and ancient rocks.
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Affiliation(s)
- Mónica Sánchez-Román
- Department of Planetology and Habitability, Centro de Astrobiología (INTA-CSIC) Madrid, Spain
| | | | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC) Madrid, Spain
| | - Ricardo Amils
- Department of Planetology and Habitability, Centro de Astrobiología (INTA-CSIC) Madrid, Spain ; Department of Virology and Microbiology, Centro de Biología Molecular Severo Ochoa Madrid, Spain
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22
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Marlow J, Peckmann J, Orphan V. Autoendoliths: a distinct type of rock-hosted microbial life. GEOBIOLOGY 2015; 13:303-307. [PMID: 25879487 DOI: 10.1111/gbi.12131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 02/21/2015] [Indexed: 06/04/2023]
Affiliation(s)
- J Marlow
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - J Peckmann
- Department of Geodynamics and Sedimentology, University of Vienna, Vienna, Austria
| | - V Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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23
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Cosmidis J, Benzerara K, Nassif N, Tyliszczak T, Bourdelle F. Characterization of Ca-phosphate biological materials by scanning transmission X-ray microscopy (STXM) at the Ca L2,3-, P L2,3- and C K-edges. Acta Biomater 2015; 12:260-269. [PMID: 25305511 DOI: 10.1016/j.actbio.2014.10.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 08/19/2014] [Accepted: 10/02/2014] [Indexed: 02/05/2023]
Abstract
Several naturally occurring biological materials, including bones and teeth, pathological calcifications, microbial mineral deposits formed in marine phosphogenesis areas, as well as bio-inspired cements used for bone and tooth repair are composed of Ca-phosphates. These materials are usually identified and characterized using bulk-scale analytical tools such as X-ray diffraction, Fourier transform infrared spectroscopy or nuclear magnetic resonance. However, there is a need for imaging techniques that provide information on the spatial distribution and chemical composition of the Ca-phosphate phases at the micrometer- and nanometer scales. Such analyses provide insightful indications on how the materials may have formed, e.g. through transient precursor phases that eventually remain spatially separated from the mature phase. Here, we present scanning transmission X-ray microscopy (STXM) analyses of Ca-phosphate reference compounds, showing the feasibility of fingerprinting Ca-phosphate-based materials. We calibrate methods to determine important parameters of Ca-phosphate phases, such as their Ca/P ratio and carbonate content at the ∼25nm scale, using X-ray absorption near-edge spectra at the C K-, Ca L2,3- and P L2,3-edges. As an illustrative case study, we also perform STXM analyses on hydroxyapatite precipitates formed in a dense fibrillar collagen matrix. This study paves the way for future research on Ca-phosphate biomineralization processes down to the scale of a few tens of nanometers.
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Affiliation(s)
- Julie Cosmidis
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC), Sorbonne Universités, Univ Paris 06, CNRS UMR 7590, MNHN, IRD UMR 206, F-75252 Paris 05, France
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux, et de Cosmochimie (IMPMC), Sorbonne Universités, Univ Paris 06, CNRS UMR 7590, MNHN, IRD UMR 206, F-75252 Paris 05, France.
| | - Nadine Nassif
- Lab Chim Matière Condensée (LMCM), Univ Paris 06, Coll France, CNRS UMR 7574, F-75231 Paris 05, France
| | - Tolek Tyliszczak
- Lawrence Berkeley National Laboratory, Advanced Light Source, Berkeley, CA 94720 USA
| | - Franck Bourdelle
- Lab Génie Civil et géo-Environnement (LGCgE), Univ Lille 1, SN5, 59655 Villeneuve-d'Ascq, France
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24
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Omelon S, Ariganello M, Bonucci E, Grynpas M, Nanci A. A review of phosphate mineral nucleation in biology and geobiology. Calcif Tissue Int 2013; 93:382-96. [PMID: 24077874 PMCID: PMC3824353 DOI: 10.1007/s00223-013-9784-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 08/06/2013] [Indexed: 11/26/2022]
Abstract
Relationships between geological phosphorite deposition and biological apatite nucleation have often been overlooked. However, similarities in biological apatite and phosphorite mineralogy suggest that their chemical formation mechanisms may be similar. This review serves to draw parallels between two newly described phosphorite mineralization processes, and proposes a similar novel mechanism for biologically controlled apatite mineral nucleation. This mechanism integrates polyphosphate biochemistry with crystal nucleation theory. Recently, the roles of polyphosphates in the nucleation of marine phosphorites were discovered. Marine bacteria and diatoms have been shown to store and concentrate inorganic phosphate (Pi) as amorphous, polyphosphate granules. Subsequent release of these P reserves into the local marine environment as Pi results in biologically induced phosphorite nucleation. Pi storage and release through an intracellular polyphosphate intermediate may also occur in mineralizing oral bacteria. Polyphosphates may be associated with biologically controlled apatite nucleation within vertebrates and invertebrates. Historically, biological apatite nucleation has been attributed to either a biochemical increase in local Pi concentration or matrix-mediated apatite nucleation control. This review proposes a mechanism that integrates both theories. Intracellular and extracellular amorphous granules, rich in both calcium and phosphorus, have been observed in apatite-biomineralizing vertebrates, protists, and atremate brachiopods. These granules may represent stores of calcium-polyphosphate. Not unlike phosphorite nucleation by bacteria and diatoms, polyphosphate depolymerization to Pi would be controlled by phosphatase activity. Enzymatic polyphosphate depolymerization would increase apatite saturation to the level required for mineral nucleation, while matrix proteins would simultaneously control the progression of new biological apatite formation.
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Affiliation(s)
- Sidney Omelon
- Chemical and Biological Engineering, University of Ottawa, Ottawa, Canada
| | | | - Ermanno Bonucci
- Department of Experimental Medicine, La Sapienza University of Rome, Rome, Italy
| | - Marc Grynpas
- Laboratory Medicine and Pathobiology, Samuel Lunenfeld Research Institute of Mt. Sinai Hospital, Toronto, Canada
| | - Antonio Nanci
- Faculty of Dentistry, Université de Montréal, Montreal, Canada
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25
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Bailey JV, Corsetti FA, Greene SE, Crosby CH, Liu P, Orphan VJ. Filamentous sulfur bacteria preserved in modern and ancient phosphatic sediments: implications for the role of oxygen and bacteria in phosphogenesis. GEOBIOLOGY 2013; 11:397-405. [PMID: 23786451 DOI: 10.1111/gbi.12046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 05/24/2013] [Indexed: 06/02/2023]
Abstract
Marine phosphate-rich sedimentary deposits (phosphorites) are important geological reservoirs for the biologically essential nutrient phosphorous. Phosphorites first appear in abundance approximately 600 million years ago, but their proliferation at that time is poorly understood. Recent marine phosphorites spatially correlate with the habitats of vacuolated sulfide-oxidizing bacteria that store polyphosphates under oxic conditions to be utilized under sulfidic conditions. Hydrolysis of the stored polyphosphate results in the rapid precipitation of the phosphate-rich mineral apatite-providing a mechanism to explain the association between modern phosphorites and these bacteria. Whether sulfur bacteria were important to the formation of ancient phosphorites has been unresolved. Here, we present the remains of modern sulfide-oxidizing bacteria that are partially encrusted in apatite, providing evidence that bacterially mediated phosphogenesis can rapidly permineralize sulfide-oxidizing bacteria and perhaps other types of organic remains. We also describe filamentous microfossils that resemble modern sulfide-oxidizing bacteria from two major phosphogenic episodes in the geologic record. These microfossils contain sulfur-rich inclusions that may represent relict sulfur globules, a diagnostic feature of modern sulfide-oxidizing bacteria. These findings suggest that sulfur bacteria, which are known to mediate the precipitation of apatite in modern sediments, were also present in certain phosphogenic settings for at least the last 600 million years. If polyphosphate-utilizing sulfide-oxidizing bacteria also played a role in the formation of ancient phosphorites, their requirements for oxygen, or oxygen-requiring metabolites such as nitrate, might explain the temporal correlation between the first appearance of globally distributed marine phosphorites and increasing oxygenation of Neoproterozoic oceans.
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Affiliation(s)
- J V Bailey
- Department of Earth Sciences, University of Minnesota- Twin Cities, Minneapolis, MN, USA.
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26
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White A, Dyhrman S. The marine phosphorus cycle. Front Microbiol 2013; 4:105. [PMID: 23734145 PMCID: PMC3659303 DOI: 10.3389/fmicb.2013.00105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 04/12/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Angelicque White
- College of Oceanography and Atmospheric Sciences, Oregon State University Corvallis, OR, USA
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