The frequency of growth increments in the tube wall of the Mesozoic and Cenozoic serpulids is in the range of modern species (i.e. 7–37 growth lines per 50 μm). The growth increments of serpulids do not show correlation with the water temperature and presumably cold water and warm water serpulid species are growing on average with similar speed in terms of number of growth lines per 50 μm. The large serpulid species have usually significantly larger growth increments than smaller species and presumably also grew faster than smaller species. The species with denser skeletons have lower growth rates than species with more porous skeletons. It is possible that serpulids do not have to calcify faster to produce thicker growth increments with lower density.

Microbial structures in the form of banded zebra patterns have been found as periodic iron-manganese layers in living biomats on the coast of Satsuma-Iwo Jima, a small volcanic island near southern Kyushu, Japan. Electron microscopic observation shows that coccus, fibrous, and bacillus-type bacterial communities construct zebra architecture Fe-Mn layers through biomineralization on and within cells. A living microbial fumarolic ferro-manganese precipitation growing in seawater around an active volcanic island explains one mechanism of banded formation. Biological processes form the elemental zebra pattern, with periodic distribution of bacterial cells with Fe-Mn in each layer of the architecture. Fibrous bacteria are sometimes mineralized with goethite, ferrihydrite, and buserite microcrystals, coated with granular mucoid substances. The biomineralization may then mature to form a recent stratified banded-iron formation. The Satsuma-Iwo Jima zebra architecture is unusual in that it forms under aerobic conditions in a warm shallow-water environment, in contrast to the intermittent oxidizing and reducing conditions in which deep-sea analogues develop.

Nontronite and microbes were detected in the surface layers of deep-sea sediments from Iheya Basin, Okinawa Trough, Japan. Nontronite, an Fe-rich smectite mineral, was embedded in acidic polysaccharides that were exuded by microbial cells and electron microscopy showed that the nontronite layers were apparently oriented in the polysaccharide materials. We propose that the formation of nontronite was induced by the accumulation of Si and Fe ions from the ambient seawater and that extracellular polymeric substances (EPS) served as a template for layer-silicate synthesis. Experimental evidence for this hypothesis was obtained by mixing a solution of polysaccharides (dextrin and pectin) with ferrosiliceous groundwater. After stirring the mixture in a sealed vessel for two days, and centrifuging, Fe-rich layer silicates were identified within the precipitate of both the dextrin and pectin aggregates, whereas rod-shaped or spheroidal Si-bearing iron hydroxides were found in the external solution. Microbial polysaccharides would appear to have affected layer-silicate formation.

The formation of siderite and magnetite by Fe(III)-reducing bacteria may play an important role in C and Fe geochemistry in subsurface and ocean sediments. The objective of this study was to identify environmental factors that control the formation of siderite (FeCO3) and magnetite (Fe3O4) by Fe(III)-reducing bacteria. Psychrotolerant (<20°C), mesophilic (20–35°C) and thermophilic (>45°C) Fe(III)-reducing bacteria were used to examine the reduction of a poorly crystalline iron oxide, akaganeite (β-FeOOH), without a soluble electron shuttle, anthraquinone disulfuonate (AQDS), in the presence of N2, N2-CO2(80:20, V:V), H2 and H2-CO2 (80:20, V:V) headspace gases as well as in -buffered medium (30–210 mM) under a N2 atmosphere. Iron biomineralization was also examined under different growth conditions such as salinity, pH, incubation time, incubation temperature and electron donors. Magnetite formation was dominant under a N2 and a H2 atmosphere. Siderite formation was dominant under a H2-CO2 atmosphere. A mixture of magnetite and siderite was formed in the presence of a N2-CO2 headspace. Akaganeite was reduced and transformed to siderite and magnetite in a -buffered medium (>120 mM) with lactate as an electron donor in the presence of a N2 atmosphere. Biogeochemical and environmental factors controlling the phases of the secondary mineral suite include medium pH, salinity, electron donors, atmospheric composition and incubation time. These results indicate that microbial Fe(III) reduction may play an important role in Fe and C biogeochemistry as well as C sequestration in natural environments.

The built environment contributes to global carbon dioxide emissions with carbon-emitting building materials and construction processes. While achieving carbon-neutral construction is not feasible with conventional construction methods, microbial-based construction processes were suggested over three decades ago to reduce carbon dioxide emissions. With time, questions regarding scaling, predictability, and the applicability of microbial growth and biomass production emerged and still needed to be resolved to allow manufacturing. Within this opinion, we will discuss what can be achieved not to ‘grow a building’ per se but to ‘grow environmentally friendly biocement’. Elaborate pathways leading to the formation of cementitious materials by genetically manipulatable microorganisms have been described so far, providing options to enhance the suitability of these pathways for construction with synthetic biology and bioconvergence. These processes can also be combined with additional beneficial properties of cement-producing organisms, such as antimicrobial properties and carbon fixation by photosynthesis. Therefore, while we cannot yet ‘grow a building’, we can grow and design biocement for the construction industry.

Investigations into the existence of life in other parts of the cosmos find strong parallels with studies of the origin and evolution of life on our own planet. In this way, astrobiology and paleobiology are married by their common interest in disentangling the interconnections between life and the surrounding environment. In this way, a cross-point of both sciences is paleometry, which involves a myriad of imaging and geochemical techniques, usually non-destructive, applied to the investigation of the fossil record. In the last decades, paleometry has benefited from an unprecedented technological improvement, thus solving old questions and raising new ones. This advance has been paralleled by conceptual approaches and discoveries fuelled by technological evolution in astrobiological research. In this context, we present some new data and review recent advances on the employment of paleometry to investigations on paleobiology and astrobiology in Brazil in areas such biosignatures in Ediacaran microbial mats, biogenicity tests on enigmatic Ediacaran structures, research on Ediacaran metazoan biomineralization, fossil preservation in Cretaceous insects and fish, and finally the experimental study on the decay of fish to test the effect of distinct types of sediment on soft-tissue preservation, as well as the effects of early diagenesis on fish bone preservation.

Elemental behaviour, during the process of weathering of glazed sekishu roof-tiles affected by Lecidea s.lat. sp. (a crustose lichen), was investigated using optical and fluorescence microscopy, field emission scanning electron microscopy (FE-SEM) and transmission electron microscopy. Sekishu roof tiles have an opaque reddish brown glaze on their surfaces which consist of an alkali feldspar-type X-ray amorphous glass recrystallized at 1200°C. Optical and fluorescence microscopy revealed the presence of corrosion pits (at a depth of ∼50 μm) at the lichen-glaze interface. Elemental mapping by FE-SEM identified the concentrations of Ti and Fe in the section of the glazed tile analysed. The behaviour of C was correlated with those elements, suggesting the possibility of biomineralization.

The mineralogy of the glazed surfaces of Japanese sekishu roof tiles covered by a crustose lichen – Lecidella asema (Nyl.) Knoph & Hertel – was investigated using transmission electron microscopy (TEM). The study sought to identify the Ti-Fe mineral observed as a low concentration of Ti and Fe in a previous study of the glazed surfaces of the same roof tile. The TEM analysis revealed that: (1) a thin layer of the Ti-Fe mineral pseudobrookite exists on the glaze surface; (2) the pseudobrookite consists of well-ordered single crystals, continuously and widely distributed on the glaze surface.

This paper highlights new research on the biomineralization of otoliths and uses a mineralogical approach to understand mechanisms of crystal growth and metal incorporation into otoliths. Petrographic observations of the nucleation of otolith growth in the core for several fish species reveals that sagittal otoliths appear to nucleate around a few or many nucleation sites (primordia) and that these sites vary in size (ranging in diameter from 1 to 20 μm), depending on the species. Spectroscopic data show a large Mn-enrichment in the primordia within the core but the reasons for this enrichment are still unclear (e.g. organic matter or possibly another material other than CaCO3). This study also provides the first multi trace-element data for endolymph fluid and the growing otolith; we found large enrichments (Ca and Sr) and depletions (Na, K, Zn and Rb) of elements in the otolith relative to the endolymph. The last part of this paper examines the effect of crystal structure on the microchemistry ofotoliths. Our investigation helps understand how the chemical characteristics of the metal ions (i.e. ionic radii) and the crystalline structure interact to cause differential trace-metal uptake between the CaCO3 polymorphs, aragonite and vaterite.

Brachiopods are a phylum of shell-forming sessile marine invertebrates which have existed since the early Cambrian. Two very different biomaterial design strategies for their shells evolved early in their history. Both strategies use hybrid fibre composites, however, one is based on mineral fibres embedded in ~2 wt.% of organic biopolymer sheaths and the inorganic fibres are calcite single crystals. In the second strategy the fibres are biopolymers and are reinforced with Ca-phosphate nanoparticles to form a fibrous nanocomposite. Here the organic component (chitin) dominates. The Ca-phosphate nanoparticle-reinforcement strategy is not unlike that in vertebrate bone, however, the microscale structure is laminated with alternating laminae which have a different degree of mineralization.

The calcitic shells feature an outer compact layer of calcite micro- and nanoparticles protecting the inner fibrous layer from the outside. Transmission electron microscopy of the fibrous layer reveals intercrystalline and intracrystalline biopolymers. The calcitic shell material is stiff with nano-indentation E-moduli of 63±8 GPa and relatively hard (Vickers microhardness up to 400 HV 0.0005/10 and nanohardness 4±0.5 GPa). Compared to inorganic calcite the microhardness is doubled and the nanohardness increases by 60%. We attribute this increased hardness to intracrystalline biopolymers. The nano-indentation E-moduli of the chitinophosphatic shells range from 3 to 55 GPa as a result of the varying degree of mineralization between their laminae, and similarly their nanohardness varies between 0.1 and 3 GPa. For brachiopods burrowing inside the sediment, the alternation of non-mineralized laminae with thin, more strongly mineralized laminae provides abrasion-resistance, hardness and longitudinal stiffness while it preserves the flexibility provided by the organic component for bending movements.

Atomic force microscopy (AFM) and transmission electron microscopy (TEM) were used to investigate the fine structure of the calcite prisms from the pearl-oyster shell Pinctada margaritifera. The AFM analysis shows that the prisms are made of densely packed circular micro-domains (in the 0.1 μm range) surrounded by a dense cortex. The TEM images and diffraction patterns allow the internal structure of the micro-domains to be described. Each of them is enriched in Ca-carbonate. Hosted in distinct regions of each prism, some are fully amorphous, and some others fully crystallized as subunits of a large calcite single crystal. At the border separating the two regions, micro-domains display a crystallized core and an amorphous rim. Such a border probably marks out an arrested crystallization front having propagated through a previously bio-controlled architecture of the piling of amorphous micro-domains. Compared to recent data concerning the stepping mode of growth of the calcite prisms and the resulting layered organization at the μm-scale, these results give unexpected views regarding the modalities of biocrystallization.

Biominerals are a subset of the mineral kingdom, those created by living creatures. In spite of usually fine grain size and intimate association with organic materials, biominerals are readily identified as common mineral species. Iron hydroxides and oxyhydroxides, calcium carbonates and calcium phosphates from uni- and multi-cellular species are presented as examples of biominerals, and biomineralization processes. Their special morphological, and crystal chemical, characteristics provide unique structural contributions to the life forms that create them. Investigations of novel habitats should present opportunities to expand the number of biominerals and their potential for industrial applications.

In this reconnaissance study, skeletal materials from people, dating from ∼1500 B.P., who lived by or worked at the ancient copper mines and furnaces of the Wadi Faynan in southern Jordan, were analysed using atomic absorption spectrophotometry (AAS) to determine the intensities of accumulation of copper and lead in their bones. Many of the bones analysed contained concentrations of these metals which are comparable to those of modern individuals who are heavily exposed to metals through contemporary industrial processes.

Patterns of partitioning throughout the skeleton of a number of individuals were also studied. These AAS data suggest that within the human organism there may be some ability to influence the patterns of accumulation of copper within the skeleton. The humerus was frequently found to contain more copper than other bones studied. Within the humerus itself, the medial epicondyle frequently contained the highest concentrations, which may indicate a significant degree of organization or control of the process. These metal concentration data together with their toxicological consequences suggest that the health of the ancient human populations must have been adversely affected by exposure during life to copper in the environment. They also point to the need for further detailed studies of metal partitioning within the bones of the human skeleton.

Vaterite and aragonite polymorphs in freshwater cultured pearls from mussels of the genus Hyriopsis (Unionidae) were structurally and compositionally characterized by Raman spectroscopy, Micro computer tomography, high resolution field emission scanning electron microscopy, electron microprobe analysis and laser ablation inductively coupled plasma mass spectrometry. The appearance of vaterite in pearls is related to the initial stages of biomineralization, although we demonstrate that vaterite can not be a precursor to aragonite. It is not related to a particular crystal habit and therefore does not have a structural functionality in the pearls. Larger contents of elements typically bound to organic molecules, such as P and S in vaterite, as well as larger total organic contents in vaterite as opposed to aragonite in conjunction with larger concentrations of Mn2+ and Mg2+, imply a stabilizing role of organic macromolecules and X2+ ions for biological vaterite. Distribution coefficients between aragonite and vaterite for provenance-independent elements, such as Mn and Mg (0.27 and 0.04, respectively) agree very well with those observed in fish otoliths.

Neptunium-237 will be present in radioactive wastes over extended time periods due to its long half-life (2.13 × 106 years). Understanding its behaviour under conditions relevant to radioactive waste disposal is therefore of particular importance. Here, microcosm experiments were established using sediments from a legacy lime workings with high-pH conditions as an analogue of cementitious intermediate-level radioactive waste disposal. To probe the influence of Fe biogeochemistry on Np(V) in these systems, additional Fe(III) (as ferrihydrite) was added to select experiments. Biogeochemical changes were tracked in experiments with low levels of Np(V) (20 Bq ml–1; 3.3 μM), whilst parallel higher concentration systems (2.5 KBq ml–1; 414 μM) allowed X-ray absorption spectroscopy. As expected, microbial reduction processes developed in microbially-active systems with an initial pH of 10; however, during microbial incubations the pH dropped from 10 to ∼7, reflecting the high levels of microbial metabolism occurring in these systems. In microbially-active systems without added Fe(III), 90% sorption of Np(V) occurred within one hour with essentially complete removal by one day. In the ferrihydrite-amended systems, complete sorption of Np(V) to ferrihydrite occurred within one hour. For higher-activity sediments, X-ray absorption spectroscopy (XAS) at end points where Fe(II) ingrowth was observed confirmed that complete reductive precipitation of Np(V) to Np(IV) had occurred under similar conditions to low-level Np experiments. Finally, pre-reduced, Fe(III)-reducing sediments, with and without added Fe(III) and held at pH 10, were spiked with Np(V). These alkaline pre-reduced sediments showed significant removal of Np to sediments, and XAS confirmed partial reduction to Np(IV) with the no Fe system, and essentially complete reduction to Np(IV) in the Fe(III)-enriched systems. This suggested an indirect, Fe(II)-mediated pathway for Np(V) reduction under alkaline conditions. Microbial analyses using 16S rRNA gene pyrosequencing suggested a role for alkali-tolerant, Gram-positive Firmicutes in coupled Fe(III) reduction and Np immobilization in these experiments.

The crayfish Cherax quadricarinatus stores calcium ions, easily mobilizable after molting, for calcifying parts of the new exoskeleton. They are chiefly stored as amorphous calcium carbonate (ACC) during each premolt in a pair of gastroliths synthesized in the stomach wall. How calcium carbonate is stabilized in the amorphous state in such a biocomposite remains speculative. The knowledge of the microstructure at the nanometer level obtained by field emission scanning electron microscopy and atomic force microscopy combined with scanning electron microscopy energy-dispersive X-ray spectroscopy, micro-Raman and X-ray absorption near edge structure spectroscopy gave relevant information on the elaboration of such an ACC-stabilized biomineral. We observed nanogranules distributed along chitin-protein fibers and the aggregation of granules in thin layers. AFM confirmed the nanolevel structure, showing granules probably surrounded by an organic layer and also revealing a second level of aggregation as described for other crystalline biominerals. Raman analyses showed the presence of ACC, amorphous calcium phosphate, and calcite. Elemental analyses confirmed the presence of elements like Fe, Na, Mg, P, and S. P and S are heterogeneously distributed. P is present in both the mineral and organic phases of gastroliths. S seems present as sulfate (probably as sulfated sugars), sulfonate, sulfite, and sulfoxide groups and, in a lesser extent, as sulfur-containing amino acids.

The ability to discriminate biogenic from abiogenic calcium carbonate (CaCO3) would be useful in the search for extant or extinct life, since CaCO3 can be produced by both biotic and abiotic processes on Earth. Bioprecipitated CaCO3 material was produced during the growth of heterotrophic microbial isolates on medium enriched with calcium acetate or calcium citrate. These biologically produced CaCO3, along with natural and synthetic non-biologically produced CaCO3 samples, were analysed by reflectance spectroscopy (0.35–2.5 μm), Raman spectroscopy (532 and 785 nm), and laser-induced fluorescence spectroscopy (365 and 405 nm excitation). Optimal instruments for the discrimination of biogenic from abiogenic CaCO3 were determined to be reflectance spectroscopy, and laser-induced fluorescence spectroscopy. Multiple absorption features in the visible light region occurred in reflectance spectra for most biogenic CaCO3 samples, which are likely due to organic pigments. Multiple fluorescence peaks occurred in emission spectra (405 nm excitation) of biogenic CaCO3 samples, which also are best attributed to the presence of organic compounds; however, further analyses must be performed in order to better determine the cause of these features to establish criteria for confirming the origin of a given CaCO3 sample. Raman spectroscopy was not useful for discrimination since any potential Raman peaks in spectra of biogenic carbonates collected by both the 532 and 785 nm lasers were overwhelmed by fluorescence. However, this also suggests that biogenic carbonates may be identified by the presence of this organic-associated fluorescence. No reliable spectroscopic differences in terms of parameters such as positions or widths of carbonate-associated absorption bands were found between the biogenic and abiogenic carbonate samples. These results indicate that the presence or absence of organic matter intimately associated with carbonate minerals is the only potentially useful spectral discriminator for the techniques that were examined, and that multiple spectroscopic techniques are capable of detecting the presence of associated organic materials. However, the presence or absence of intimately associated organic matter is not, in itself, an indicator of biogenicity.

Biosynthetic calcite samples were investigated using combined synchrotron X-ray microspectroscopy mapping. These samples were prepared with bacteria isolated from the Large cave of Arcy-sur-Cure in which prehistoric figures are masked by an opaque calcite layer. The biotic or abiotic origin of this layer is the issue of the present work. As previously known, a large community of bacteria may be involved in the CaCO3 formation in caves. A mixture of calcite/vaterite was obtained from bacteria isolated from the cave. Therefore, we can offer conclusions on their calcifying capability. The rare presence of vaterite in cave environments may be treated as a marker of biotic carbonate formations. Moreover, an amorphous calcium phosphate phase was present in the form of a calcite/vaterite mixture in the biotic model samples. This mixture of phases could be used as a tracer of the biotic process of CaCO3 formation. These biotic tracer phases were not identified using the applied analytical methods in the natural samples taken from the opaque calcite layers that covered the prehistoric figures of the Large cave. In this case, based on the obtained results, the biotic calcite formation process is likely to be considered as an undetectable effect at minimum.