Special Issue "Biomineralization: Towards a Unification of Concepts in Chemistry, Physics, Earth Sciences and Biology"

A special issue of Minerals (ISSN 2075-163X).

Deadline for manuscript submissions: closed (29 February 2016).

Special Issue Editors

Dr. Karim Benzerara
E-Mail Website
Guest Editor
Université Pierre et Marie Curie, Museum National d'Histoire Naturelle et CNRS, 75252 Paris cedex 05, France
Dr. Jennyfer Miot
E-Mail Website
Guest Editor
Université Pierre et Marie Curie, Museum National d'Histoire Naturelle et CNRS, 75252 Paris cedex 05, France
Dr. Thibaud Coradin
E-Mail Website
Guest Editor
CNRS, UPMC,Collège de France, UMR 7574
Interests: biochemistry of solids; sol-gel technology; biomimetic processes; cell encapsulation; biomaterials; green materials
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Keywords

  • biomineralization
  • evolution
  • controlled
  • induced
  • biomimetism
  • magnetotactic
  • mesocrystal
  • apatite
  • paleoenvironments
  • cyanobacteria
  • silica
  • fossilization
  • prokaryotes
  • Fe biomineralization

Published Papers (11 papers)

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Research

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Open AccessArticle
Raman Investigations to Identify Corallium rubrum in Iron Age Jewelry and Ornaments
Minerals 2016, 6(2), 56; https://doi.org/10.3390/min6020056 - 15 Jun 2016
Cited by 1
Abstract
During the Central European Iron Age, more specifically between 600 and 100 BC, red precious corals (Corallium rubrum) became very popular in many regions, often associated with the so-called (early) Celts. Red corals are ideally suited to investigate several key questions [...] Read more.
During the Central European Iron Age, more specifically between 600 and 100 BC, red precious corals (Corallium rubrum) became very popular in many regions, often associated with the so-called (early) Celts. Red corals are ideally suited to investigate several key questions of Iron Age research, like trade patterns or social and economic structures. While it is fairly easy to distinguish modern C. rubrum from bone, ivory or shells, archaeologists are confronted with ancient, hence altered, artifacts. Due to ageing processes, archaeological corals lose their intensive red color and shiny surface and can easily be confused with these other light colored materials. We propose a non-destructive multi-stage approach to identify archaeological corals amongst other biominerals used as ornament during the central European Iron Age with emphasis on optical examination and mobile Raman spectroscopy. Our investigations suggest that the noticeably high amount of misidentifications or at least uncertain material declarations existing in museums or even in the literature (around 15%) could be overcome by the proposed approach. Furthermore, the range of different materials is higher than previously expected in archaeological research. This finding has implications for contemporary concepts of social structures and distribution networks during the Iron Age. Full article
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Open AccessArticle
Fungal Iron Biomineralization in Río Tinto
Minerals 2016, 6(2), 37; https://doi.org/10.3390/min6020037 - 18 Apr 2016
Cited by 7
Abstract
Although there are many studies on biomineralization processes, most of them focus on the role of prokaryotes. As fungi play an important role in different geological and biogeochemical processes, it was considered of interest to evaluate their role in a natural extreme acidic [...] Read more.
Although there are many studies on biomineralization processes, most of them focus on the role of prokaryotes. As fungi play an important role in different geological and biogeochemical processes, it was considered of interest to evaluate their role in a natural extreme acidic environment, Río Tinto, which has a high level of fungal diversity and a high concentration of metals. In this work we report, for the first time, the generation of iron oxyhydroxide minerals by the fungal community in a specific location of the Tinto basin. Using Transmission Electron Microscopy (TEM) and High Angle Angular Dark Field coupled with Scanning Transmission Electron Microscopy (HAADF-STEM) and Energy-Dispersive X-ray Spectroscopy (EDX), we observed fungal structures involved in the formation of iron oxyhydroxide minerals in mineralized sediment samples from the Río Tinto basin. Although Río Tinto waters are supersaturated in these minerals, they do not precipitate due to their slow precipitation kinetics. The presence of fungi, which simply provide charged surfaces for metal binding, favors the precipitation of Fe oxyhydroxides by overcoming these kinetic barriers. These results prove that the fungal community of Río Tinto participates very actively in the geochemical processes that take place there. Full article
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Open AccessArticle
Mineralogical Diversity in Lake Pavin: Connections with Water Column Chemistry and Biomineralization Processes
Minerals 2016, 6(2), 24; https://doi.org/10.3390/min6020024 - 23 Mar 2016
Cited by 11
Abstract
As biominerals are good tracers of microbial interactions with the environment, they may provide signatures of microbial evolution and paleoenvironmental conditions. Since modern analogues of past environments help with defining proxies and biosignatures, we explored microbe mineral interactions in the water column of [...] Read more.
As biominerals are good tracers of microbial interactions with the environment, they may provide signatures of microbial evolution and paleoenvironmental conditions. Since modern analogues of past environments help with defining proxies and biosignatures, we explored microbe mineral interactions in the water column of a maar lake, located in France: Lake Pavin. This lake is considered as a potential Precambrian ocean analogue, as it is ferruginous and meromictic, i.e., stratified with a superficial O2-rich layer (mixolimnion) and a deeper permanently anoxic layer (monimolimnion). We combined bulk chemical analyses of dissolved and particulate matter in combination with electron microscopy analyses of the particulate matter at different depths along the water column. The mineralogy changed along with water chemistry, and most of the minerals were intimately associated with microorganisms. Evolution of the redox conditions with depth leads to the successive precipitation of silica and carbonates, Mn-bearing, Fe-bearing and S-containing phases, with a predominance of phosphates in the monimolimnion. This scheme parallels the currently-assessed changes of microbial diversity with depth. The present results corroborate previous studies that suggested a strong influence of microbial activity on mineralogical diversity through extracellular and intracellular biomineralization. This paper reports detailed data on mineralogical profiles of the water column and encourages extended investigation of these processes. Full article
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Open AccessArticle
A Solid State NMR Investigation of Recent Marine Siliceous Sponge Spicules
Minerals 2016, 6(1), 21; https://doi.org/10.3390/min6010021 - 10 Mar 2016
Cited by 4
Abstract
The composition of four recent siliceous marine sponge spicules was studied and compared. In particular, multinuclear (29Si, 13C, 31P) solid state nuclear magnetic resonance (NMR) allowed the characterization of both the mineral and organic constituents in a non-destructive manner. [...] Read more.
The composition of four recent siliceous marine sponge spicules was studied and compared. In particular, multinuclear (29Si, 13C, 31P) solid state nuclear magnetic resonance (NMR) allowed the characterization of both the mineral and organic constituents in a non-destructive manner. The silica network condensation was similar for all samples. The organic matter showed a similar pattern but varied in abundance as a function of the sponge group (Hexactinellida or Demospongiae) and sampling conditions (living or dead organisms). This indicates that the striking morphological differences observed at the macroscale for the various samples do not lead to significant fingerprints in the spectroscopic signatures of the mineral and organic constituents. Full article
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Open AccessArticle
Biomineralization Patterns of Intracellular Carbonatogenesis in Cyanobacteria: Molecular Hypotheses
Minerals 2016, 6(1), 10; https://doi.org/10.3390/min6010010 - 03 Feb 2016
Cited by 16
Abstract
The recent discovery of intracellular carbonatogenesis in several cyanobacteria species has challenged the traditional view that this process was extracellular and not controlled. However, a detailed analysis of the size distribution, chemical composition and 3-D-arrangement of carbonates in these cyanobacteria is lacking. Here, [...] Read more.
The recent discovery of intracellular carbonatogenesis in several cyanobacteria species has challenged the traditional view that this process was extracellular and not controlled. However, a detailed analysis of the size distribution, chemical composition and 3-D-arrangement of carbonates in these cyanobacteria is lacking. Here, we characterized these features in Candidatus Gloeomargarita lithophora C7 and Candidatus Synechococcus calcipolaris G9 by conventional transmission electron microscopy, tomography, ultramicrotomy, and scanning transmission X-ray microscopy (STXM). Both Ca. G. lithophora C7 and Ca. S. calcipolaris G9 formed numerous polyphosphate granules adjacent or engulfing Ca-carbonate inclusions when grown in phosphate-rich solutions. Ca-carbonates were scattered within Ca. G. lithophora C7 cells under these conditions, but sometimes arranged in one or several chains. In contrast, Ca-carbonates formed at cell septa in Ca. S. calcipolaris G9 and were segregated equally between daughter cells after cell division, arranging as distorted disks at cell poles. The size distribution of carbonates evolved from a positively to a negatively skewed distribution as particles grew. Conventional ultramicrotomy did not preserve Ca-carbonates explaining partly why intracellular calcification has been overlooked in the past. All these new observations allow discussing with unprecedented insight some nucleation and growth processes occurring in intracellularly calcifying cyanobacteria with a particular emphasis on the possible involvement of intracellular compartments and cytoskeleton. Full article
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Open AccessArticle
New Insights in the Ontogeny and Taphonomy of the Devonian Acanthodian Triazeugacanthus affinis From the Miguasha Fossil-Lagerstätte, Eastern Canada
Minerals 2016, 6(1), 1; https://doi.org/10.3390/min6010001 - 23 Dec 2015
Cited by 6
Abstract
Progressive biomineralization of a skeleton occurs during ontogeny in most animals. In fishes, larvae are poorly mineralized, whereas juveniles and adults display a progressively more biomineralized skeleton. Fossil remains primarily consist of adult specimens because the fossilization of poorly-mineralized larvae and juveniles necessitates [...] Read more.
Progressive biomineralization of a skeleton occurs during ontogeny in most animals. In fishes, larvae are poorly mineralized, whereas juveniles and adults display a progressively more biomineralized skeleton. Fossil remains primarily consist of adult specimens because the fossilization of poorly-mineralized larvae and juveniles necessitates exceptional conditions. The Miguasha Fossil-Lagerstätte is renowned for its Late Devonian vertebrate fauna, revealing the exceptional preservation of fossilized ontogenies for 14 of the 20 fish species from this locality. The mineralization of anatomical structures of the acanthodian Triazeugacanthus affinis from Miguasha are compared among larval, juvenile and adult specimens using Energy Dispersive X-ray Spectrometry. Chemical composition of anatomical structures of Triazeugacanthus reveals differences between cartilage and bone. Although the histology and anatomy is well-preserved, Fourier transform infrared spectrometry shows that the original chemical composition of bone is altered by diagenesis; the mineral phase of the bone (i.e., hydroxyapatite) is modified chemically to form more stable carbonate-fluorapatite. Fluorination occurring in mineralized skeletal structures of adult Triazeugacanthus is indicative of exchanges between groundwater and skeleton at burial, whereas the preservation of larval soft tissues is likely owing to a rapid burial under anoxic conditions. The exceptional state of preservation of a fossilized ontogeny allowed us to characterize chemically the progressive mineralization of the skeleton in a Devonian early vertebrate. Full article
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Open AccessArticle
Formation of Microbial Mats and Salt in Radioactive Paddy Soils in Fukushima, Japan
Minerals 2015, 5(4), 849-862; https://doi.org/10.3390/min5040529 - 01 Dec 2015
Cited by 5
Abstract
Coastal areas in Minami-soma City, Fukushima, Japan, were seriously damaged by radioactive contamination from the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident that caused multiple pollution by tsunami and radionuclide exposure, after the Great East Japan Earthquake, on 11 March 2011. Some areas [...] Read more.
Coastal areas in Minami-soma City, Fukushima, Japan, were seriously damaged by radioactive contamination from the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident that caused multiple pollution by tsunami and radionuclide exposure, after the Great East Japan Earthquake, on 11 March 2011. Some areas will remain no-go zones because radiation levels remain high. In Minami-soma, only 26 percent of decontamination work had been finished by the end of July in 2015. Here, we report the characterization of microbial mats and salt found on flooded paddy fields at Karasuzaki, Minami-soma City, Fukushima Prefecture, Japan which have been heavily contaminated by radionuclides, especially by Cs (134Cs, 137Cs), 40K, Sr (89Sr, 90Sr), and 91 or 95Zr even though it is more than 30 km north of the FDNPP. We document the mineralogy, the chemistry, and the micro-morphology, using a combination of micro techniques. The microbial mats were found to consist of diatoms with mineralized halite and gypsum by using X-ray diffraction (XRD). Particular elements concentrated in microbial mats were detected using scanning electron microscopy equipped with energy dispersive spectroscopy (SEM-EDS) and X-ray fluorescence (XRF). The objective of this contribution is to illustrate the ability of various diatoms associated with minerals and microorganisms which are capable of absorbing both radionuclides and stable isotopes from polluted paddy soils in extreme conditions. Ge semiconductor analysis of the microbial mats detected 134Cs, 137Cs, and 40K without 131I in 2012 and in 2013. Quantitative analysis associated with the elemental content maps by SEM-EDS indicated the possibility of absorption of radionuclide and stable isotope elements from polluted paddy soils in Fukushima Prefecture. In addition, radionuclides were detected in solar salts made of contaminated sea water collected from the Karasuzaki ocean bath, Minami-soma, Fukushima in 2015, showing high Zr content associated with 137Cs and 40K without 131I. The results obtained here provide evidence of the ability of microorganisms to grow in this salty contaminated environment and to immobilize radionuclides. It is possible that the capability of radioactive immobilization can be used to counteract the disastrous effects of radionuclide-polluted paddy soils. Full article
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Open AccessArticle
The Role of Chloride Ions during the Formation of Akaganéite Revisited
Minerals 2015, 5(4), 778-787; https://doi.org/10.3390/min5040524 - 23 Nov 2015
Cited by 12
Abstract
Iron(III) hydrolysis in the presence of chloride ions yields akaganéite, an iron oxyhydroxide mineral with a tunnel structure stabilized by the inclusion of chloride. Yet, the interactions of this anion with the iron oxyhydroxide precursors occurring during the hydrolysis process, as well as [...] Read more.
Iron(III) hydrolysis in the presence of chloride ions yields akaganéite, an iron oxyhydroxide mineral with a tunnel structure stabilized by the inclusion of chloride. Yet, the interactions of this anion with the iron oxyhydroxide precursors occurring during the hydrolysis process, as well as its mechanistic role during the formation of a solid phase are debated. Using a potentiometric titration assay in combination with a chloride ion-selective electrode, we have monitored the binding of chloride ions to nascent iron oxyhydroxides. Our results are consistent with earlier studies reporting that chloride ions bind to early occurring iron complexes. In addition, the data suggests that they are displaced with the onset of oxolation. Chloride ions in the akaganéite structure must be considered as remnants from the early stages of precipitation, as they do not influence the basic mechanism, or the kinetics of the hydrolysis reactions. The structure-directing role of chloride is based upon the early stages of the reaction. The presence of chloride in the tunnel-structure of akagenéite is due to a relatively strong binding to the earliest iron oxyhydroxide precursors, whereas it plays a rather passive role during the later stages of precipitation. Full article
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Open AccessArticle
Calcification and Diagenesis of Bacterial Colonies
Minerals 2015, 5(3), 488-506; https://doi.org/10.3390/min5030488 - 22 Jul 2015
Cited by 12
Abstract
Evidencing ancient interspecific associations in the fossil record may be challenging, particularly when bacterial organisms have most likely been degraded during diagenesis. Yet, documenting ancient interspecific associations may provide valuable insights into paleoenvironmental conditions and paleocommunities. Here, we report the multiscale characterization of [...] Read more.
Evidencing ancient interspecific associations in the fossil record may be challenging, particularly when bacterial organisms have most likely been degraded during diagenesis. Yet, documenting ancient interspecific associations may provide valuable insights into paleoenvironmental conditions and paleocommunities. Here, we report the multiscale characterization of contemporary and fossilized calcifying bacterial colonies found on contemporary shrimps from Mexico (La Paz Bay) and on 160-Ma old fossilized decapods (shrimps) from the Lagerstätte of La Voulte-sur-Rhône (France), respectively. We document the fine scale morphology, the inorganic composition and the organic signatures of both the contemporary and fossilized structures formed by these bacterial colonies using a combination of electron microscopies and synchrotron-based scanning transmission X-ray microscopy. In addition to discussing the mechanisms of carbonate precipitation by such bacterial colonies, the present study illustrates the degradation of bacterial remains occurring during diagenesis. Full article
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Review

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Open AccessReview
Role of Fungi in the Biomineralization of Calcite
Minerals 2016, 6(2), 41; https://doi.org/10.3390/min6020041 - 05 May 2016
Cited by 25
Abstract
In the field of microbial biomineralization, much of the scientific attention is focused on processes carried out by prokaryotes, in particular bacteria, even though fungi are also known to be involved in biogeochemical cycles in numerous ways. They are traditionally recognized as key [...] Read more.
In the field of microbial biomineralization, much of the scientific attention is focused on processes carried out by prokaryotes, in particular bacteria, even though fungi are also known to be involved in biogeochemical cycles in numerous ways. They are traditionally recognized as key players in organic matter recycling, as nutrient suppliers via mineral weathering, as well as large producers of organic acids such as oxalic acid for instance, an activity leading to the genesis of various metal complexes such as metal-oxalate. Their implications in the transformation of various mineral and metallic compounds has been widely acknowledged during the last decade, however, currently, their contribution to the genesis of a common biomineral, calcite, needs to be more thoroughly documented. Calcite is observed in many ecosystems and plays an essential role in the biogeochemical cycles of both carbon (C) and calcium (Ca). It may be physicochemical or biogenic in origin and numerous organisms have been recognized to control or induce its biomineralization. While fungi have often been suspected of being involved in this process in terrestrial environments, only scarce information supports this hypothesis in natural settings. As a result, calcite biomineralization by microbes is still largely attributed to bacteria at present. However, in some terrestrial environments there are particular calcitic habits that have been described as being fungal in origin. In addition to this, several studies dealing with axenic cultures of fungi have demonstrated the ability of fungi to produce calcite. Examples of fungal biomineralization range from induced to organomineralization processes. More examples of calcite biomineralization related to direct fungal activity, or at least to their presence, have been described within the last decade. However, the peculiar mechanisms leading to calcite biomineralization by fungi remain incompletely understood and more research is necessary, posing new exciting questions linked to microbial biomineralization processes. Full article
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Open AccessReview
Apatite Biominerals
Minerals 2016, 6(2), 34; https://doi.org/10.3390/min6020034 - 05 Apr 2016
Cited by 34
Abstract
Calcium phosphate apatites offer outstanding biological adaptability that can be attributed to their specific physico-chemical and structural properties. The aim of this review is to summarize and discuss the specific characteristics of calcium phosphate apatite biominerals in vertebrate hard tissues (bone, dentine and [...] Read more.
Calcium phosphate apatites offer outstanding biological adaptability that can be attributed to their specific physico-chemical and structural properties. The aim of this review is to summarize and discuss the specific characteristics of calcium phosphate apatite biominerals in vertebrate hard tissues (bone, dentine and enamel). Firstly, the structural, elemental and chemical compositions of apatite biominerals will be summarized, followed by the presentation of the actual conception of the fine structure of synthetic and biological apatites, which is essentially based on the existence of a hydrated layer at the surface of the nanocrystals. The conditions of the formation of these biominerals and the hypothesis of the existence of apatite precursors will be discussed. Then, we will examine the evolution of apatite biominerals, especially during bone and enamel aging and also focus on the adaptability of apatite biominerals to the biological function of their related hard tissues. Finally, the diagenetic evolution of apatite fossils will be analyzed. Full article
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