The gammaproteobacterium Achromatium forms intracellular amorphous calcium carbonate and not (crystalline) calcite

Physicochemical understanding of biomineralization by molecular vibrational spectroscopy: From mechanism to nature

The process and mechanism of biomineralization and relevant physicochemical properties of mineral crystals are remarkably sophisticated multidisciplinary fields that include biology, chemistry, physics, and materials science. The components of the organic matter, structural construction of minerals, and related mechanical interaction, etc., could help to reveal the unique nature of the special mineralization process. Herein, the paper provides an overview of the biomineralization process from the perspective of molecular vibrational spectroscopy, including the physicochemical properties of biomineralized tissues, from physiological to applied mineralization. These physicochemical characteristics closely to the hierarchical mineralization process include biological crystal defects, chemical bonding, atomic doping, structural changes, and content changes in organic matter, along with the interface between biocrystals and organic matter as well as the specific mechanical effects for hardness and toughness. Based on those observations, the special physiological properties of mineralization for enamel and bone, as well as the possible mechanism of pathological mineralization and calcification such as atherosclerosis, tumor micro mineralization, and urolithiasis are also reviewed and discussed. Indeed, the clearly defined physicochemical properties of mineral crystals could pave the way for studies on the mechanisms and applications.

Microbial biosignatures in ancient deep-sea hydrothermal sulfides

Deep-sea hydrothermal systems provide ideal conditions for prebiotic reactions and ancient metabolic pathways and, therefore, might have played a pivotal role in the emergence of life. To understand this role better, it is paramount to examine fundamental interactions between hydrothermal processes, non-living matter, and microbial life in deep time. However, the distribution and diversity of microbial communities in ancient deep-sea hydrothermal systems are still poorly constrained, so evolutionary, and ecological relationships remain unclear. One important reason is an insufficient understanding of the formation of diagnostic microbial biosignatures in such settings and their preservation through geological time. This contribution centers around microbial biosignatures in Precambrian deep-sea hydrothermal sulfide deposits. Intending to provide a valuable resource for scientists from across the natural sciences whose research is concerned with the origins of life, we first introduce different types of biosignatures that can be preserved over geological timescales (rock fabrics and textures, microfossils, mineral precipitates, carbonaceous matter, trace metal, and isotope geochemical signatures). We then review selected reports of biosignatures from Precambrian deep-sea hydrothermal sulfide deposits and discuss their geobiological significance. Our survey highlights that Precambrian hydrothermal sulfide deposits potentially encode valuable information on environmental conditions, the presence and nature of microbial life, and the complex interactions between fluids, micro-organisms, and minerals. It further emphasizes that the geobiological interpretation of these records is challenging and requires the concerted application of analytical and experimental methods from various fields, including geology, mineralogy, geochemistry, and microbiology. Well-orchestrated multidisciplinary studies allow us to understand the formation and preservation of microbial biosignatures in deep-sea hydrothermal sulfide systems and thus help unravel the fundamental geobiology of ancient settings. This, in turn, is critical for reconstructing life's emergence and early evolution on Earth and the search for life elsewhere in the universe.

Widespread formation of intracellular calcium carbonates by the bloom-forming cyanobacterium Microcystis

The formation of intracellular amorphous calcium carbonates (iACC) has been recently observed in a few cultured strains of Microcystis, a potentially toxic bloom-forming cyanobacterium found worldwide in freshwater ecosystems. If iACC-forming Microcystis are abundant within blooms, they may represent a significant amount of particulate Ca. Here, we investigate the significance of iACC biomineralization by Microcystis. First, the presence of iACC-forming Microcystis cells has been detected in several eutrophic lakes, indicating that this phenomenon occurs under environmental conditions. Second, some genotypic (presence/absence of ccyA, a marker gene of iACC biomineralization) and phenotypic (presence/absence of iACC) diversity have been detected within a collection of strains isolated from one single lake. This illustrates that this trait is frequent but also variable within Microcystis even at a single locality. Finally, one-third of publicly available genomes of Microcystis were shown to contain the ccyA gene, revealing a wide geographic and phylogenetic distribution within the genus. Overall, the present work shows that the formation of iACC by Microcystis is common under environmental conditions. While its biological function remains undetermined, this process should be further considered regarding the biology of Microcystis and implications on the Ca geochemical cycle in freshwater environments.

Earthworm granules: A model of non-classical biogenic calcium carbonate phase transformations

Different non-classical crystallization mechanisms have been invoked to explain structural and compositional properties of biocrystals. The identification of precursor amorphous nanoparticle aggregation as an onset process in the formation of numerous biominerals (crystallization via particle attachment) constituted a most important breakthrough for understanding biologically mediated mineralization. A comprehensive understanding about how the attached amorphous particles transform into more stable, crystalline grains has yet to be elucidated. Here, we document structural, biogeochemical, and crystallographic aspects of the formation as well as the further phase transformations of the amorphous calcium carbonate particles formed by cultured specimens of earthworm Lumbricus terrestris. In-situ observations evidence the formation of proto-vaterite after dehydration of earthworm-produced ACC, which is subsequently followed by proto-vaterite transformation into calcite through nanoparticle attachment within the organic framework. In culture medium spiked with trace amounts of Mn²⁺, the cauliflower-like proto-vaterite structures become longer-lived than in the absence of Mn²⁺. We propose that the formation of calcite crystals takes place through a non-classical recrystallization path that involves migration of proto-vaterite nanoparticles to the crystallization site, and then, their transformation into calcite via a dissolution-recrystallization reaction. The latter is complemented by ion-by-ion crystal growth and associated with impurity release. These observations are integrated into a new model of the biocrystallization of earthworm-produced carbonate granules which highlights the sensibility of this process to environmental chemical changes, its potential impact on the bioavailability of contaminants as well as the threat that chemical pollution poses to the normal development of its early stages. STATEMENT OF SIGNIFICANCE: Understanding the mechanisms of nucleation, stabilization and aggregation of amorphous calcium carbonate (ACC) and factors controlling its further transformation into crystalline phases is fundamental for elucidation of biogenic mineralization. Some species of earthworms are natural workbench to understand the biogenic ACC, stabilization and the transformation mechanisms, because they create millimeter-sized calcareous granules from amorphous calcium carbonate, which crystallize to a more stable mineral phase (mostly calcite). This study undergoes into the mechanisms of ACC stabilization by the incorporation of trace elements, as manganese, and the ulterior precipitation of calcareous granules by a coupled process of amorphous particle attachment and ion-by-ion growth. The study points to sensibility of this process to environmental chemical changes.

A re-examination of the mechanism of whiting events: A new role for diatoms in Fayetteville Green Lake (New York, USA)

Whiting events-the episodic precipitation of fine-grained suspended calcium carbonates in the water column-have been documented across a variety of marine and lacustrine environments. Whitings likely are a major source of carbonate muds, a constituent of limestones, and important archives for geochemical proxies of Earth history. While several biological and physical mechanisms have been proposed to explain the onset of these precipitation events, no consensus has been reached thus far. Fayetteville Green Lake (New York, USA) is a meromictic lake that experiences annual whitings. Materials suspended in the water column collected through the whiting season were characterized using scanning electron microscopy and scanning transmission X-ray microscopy. Whitings in Fayetteville Green Lake are initiated in the spring within the top few meters of the water column, by precipitation of fine amorphous calcium carbonate (ACC) phases nucleating on microbial cells, as well as on abundant extracellular polymeric substances (EPS) frequently associated with centric diatoms. Whiting particles found in the summer consist of 5-7 μm calcite grains forming aggregates with diatoms and EPS. Simple calculations demonstrate that calcite particles continuously grow over several days, then sink quickly through the water column. In the late summer, partial calcium carbonate dissolution is observed deeper in the water column. Settling whiting particles, however, reach the bottom of the lake, where they form a major constituent of the sediment, along with diatom frustules. The role of diatoms and associated EPS acting as nucleation surfaces for calcium carbonates is described for the first time here as a potential mechanism participating in whitings at Fayetteville Green Lake. This mechanism may have been largely overlooked in other whiting events in modern and ancient environments.

Detection of biogenic amorphous calcium carbonate (ACC) formed by bacteria using FTIR spectroscopy

While the formation of intracellular amorphous calcium carbonate (ACC) by living organisms is widespread, its detection in prokaryotes remains difficult owing to its susceptibility to transform or dissolve upon sample preparation. Because of these challenges, a large number of ACC-forming prokaryotes may have been undetected and their abundance in the natural environment is possibly underestimated. This study identifies diagnostic spectral markers of ACC-forming prokaryotes that facilitate their detection in the environment. Accordingly, ACC formed by cyanobacteria was characterized using Fourier transform infrared (FTIR) spectroscopy in near-IR, mid-IR, and far-IR spectral regions. Two characteristic FTIR vibrations of ACC, at ∼ 860 cm^-1and ∼ 306 cm^-1, were identified as reliable spectral probes to rapidly detect prokaryotic ACC. Using these spectral probes, several Microcystis strains whose ACC-forming capability was unknown, were tested. Four out of eight Microcystis strains were identified as possessing ACC-forming capability and these findings were confirmed by scanning electron microscopy (SEM) observations. Overall, our findings provide a systematic characterization of prokaryotic ACC that facilitate rapid detection of ACC forming prokaryotes in the environment, a prerequisite to shed light on the role of ACC-forming prokaryotes in the geochemical cycle of Ca in the environment.

Bacterial Carbonate Precipitation Using Active Metabolic Pathway to Repair Mortar Cracks

A study was conducted to check the efficacy of microbial pathways for calcite precipitation to heal pre-existing cracks in mortar. In this experiment, realistic cracks of varying widths were induced on a mortar sample. Different repair methods were applied to a total of 22 mortar samples. Twelve cracked mortar samples with average crack widths ranging from 0.29 to 1.08 mm were subjected to biodeposition treatment using calcium lactate as a food source. The remaining ten samples were split into two groups: five cracked mortar samples were exclusively exposed to the bacterial solution, while the remaining five samples were immersed in distilled water. Digital image processing was used to extract the crack characteristics before and after the repair application. During several repair cycles, image processing was used to track healing. Further, these repaired mortar samples underwent examination for water permeability, ultra-sonic examination, and examination for recovered compressive strength. A forensic examination of the healing product in terms of morphology and elemental composition was conducted using RAMAN, XRD, SEM-EDS, and TGA. The water permeability of the repaired mortar sample using biodeposition with Ca-lactate was dramatically reduced, but samples treated with bacterial solution and distilled water did not exhibit any significant reduction. Complete crack healing was observed when using Ca-lactate as a food source for microbial repair. The forensic analysis confirmed the presence of calcite in healing precipitates.

In situ carbon dioxide capture to co-produce 1,3-propanediol, biohydrogen and micro-nano calcium carbonate from crude glycerol by Clostridium butyricum

Background

Climate change caused by greenhouse gas emission has become a global hot topic. Although biotechnology is considered as an environmentally friendly method to produce chemicals, almost all biochemicals face carbon dioxide emission from inevitable respiration and energy metabolism of most microorganisms. To cater for the broad prospect of biochemicals, bioprocess optimization of diverse valuable products is becoming increasingly important for environmental sustainability and cleaner production. Based on Ca(OH)₂ as a CO₂ capture agent and pH regulator, a bioprocess was proposed for co-production of 1,3-propanediol (1,3-PDO), biohydrogen and micro-nano CaCO₃ by Clostridium butyricum DL07.

Results

In fed-batch fermentation, the maximum concentration of 1,3-PDO reached up to 88.6 g/L with an overall productivity of 5.54 g/L/h. This productivity is 31.9% higher than the highest value previously reports (4.20 g/L/h). In addition, the ratio of H₂ to CO₂ in exhaust gas showed a remarkable 152-fold increase in the 5 M Ca(OH)₂ group compared to 5 M NaOH as the CO₂ capture agent. Green hydrogen in exhaust gas ranged between 17.2% and 20.2%, with the remainder being N₂ with negligible CO₂ emissions. During CO₂ capture in situ, micro-nano calcite particles of CaCO₃ with sizes in the range of 300 nm to 20 µm were formed simultaneously. Moreover, when compared with 5M NaOH group, the concentrations of soluble salts and proteins in the fermentation broth of 5 M Ca(OH)₂ group were notably reduced by 53.6% and 44.1%, respectively. The remarkable reduction of soluble salts and proteins would contribute to the separation of 1,3-PDO.

Conclusions

Ca(OH)₂ was used as a CO₂ capture agent and pH regulator in this study to promote the production of 1,3-PDO. Meanwhile, micro-nano CaCO₃ and green H₂ were co-produced. In addition, the soluble salts and proteins in the fermentation broth were significantly reduced.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02190-2.

An exceptionally stable and widespread hydrated amorphous calcium carbonate precipitated by the dog vomit slime mold Fuligo septica (Myxogastria)

Biogenic amorphous calcium carbonate (ACC) is typically metastable and can rapidly transform through aging, dehydration, and/or heating to crystalline calcium carbonate. Gaining insight into its structure and properties is typically hampered by its tendency to crystallize over short time periods once isolated from the host organism, and also by the small quantities that are usually available for study. Here we describe an exceptionally stable hydrated ACC (HACC) precipitated by the cosmopolitan slime mold Fuligo septica (L.) F.H. Wigg. (1780). A single slime mold can precipitate up to a gram of HACC over the course of one night. Powder x-ray diffraction (XRD) patterns, transmission electron microscopy images, infrared absorption spectra, together with the lack of optical birefringence are consistent with an amorphous material. XRD simulations, supported by thermogravimetric and evolved gas analysis data, are consistent with an intimate association of organic matter with ~ 1-nm-sized ACC units that have monohydrocalcite- and calcite-like nano-structural properties. It is postulated that this association imparts the extreme stability of the slime mold HACC by inhibiting loss of H₂O and subsequent crystallization. The composition, structure, and thermal behavior of the HACC precipitated by F. septica collected over 8000 km apart and in markedly different environments, suggests a common structure, as well as similar biochemical and biomineralization mechanisms.

Biogeochemical Niche of Magnetotactic Cocci Capable of Sequestering Large Polyphosphate Inclusions in the Anoxic Layer of the Lake Pavin Water Column

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.

A Novel Magnetotactic Alphaproteobacterium Producing Intracellular Magnetite and Calcium-Bearing Minerals

Magnetotactic bacteria (MTB) are prokaryotes that form intracellular magnetite (Fe₃O₄) or greigite (Fe₃S₄) nanocrystals with tailored sizes, often in chain configurations. Such magnetic particles are each surrounded by a lipid bilayer membrane, called a magnetosome, and provide a model system for studying the formation and function of specialized internal structures in prokaryotes. Using fluorescence-coupled scanning electron microscopy, we identified a novel magnetotactic spirillum, XQGS-1, from freshwater Xingqinggong Lake, Xi'an City, Shaanxi Province, China. Phylogenetic analyses based on 16S rRNA gene sequences indicate that strain XQGS-1 represents a novel genus of the Alphaproteobacteria class in the Proteobacteria phylum. Transmission electron microscopy analyses reveal that strain XQGS-1 forms on average 17 ± 3 magnetite magnetosome particles with an ideal truncated octahedral morphology, with an average length and width of 88.3 ± 11.7 nm and 83.3 ± 11.0 nm, respectively. They are tightly organized into a single chain along the cell long axis close to the concave side of the cell. Intrachain magnetic interactions likely result in these large equidimensional magnetite crystals behaving as magnetically stable single-domain particles that enable bacterial magnetotaxis. Combined structural and chemical analyses demonstrate that XQGS-1 cells also biomineralize intracellular amorphous calcium phosphate (2 to 3 granules per cell; 90.5- ± 19.3-nm average size) and weakly crystalline calcium carbonate (2 to 3 granules per cell; 100.4- ± 21.4-nm average size) in addition to magnetite. Our results expand the taxonomic diversity of MTB and provide evidence for intracellular calcium phosphate biomineralization in MTB. IMPORTANCE Biomineralization is a widespread process in eukaryotes that form shells, teeth, or bones. It also occurs commonly in prokaryotes, resulting in more than 60 known minerals formed by different bacteria under wide-ranging conditions. Among them, magnetotactic bacteria (MTB) are remarkable because they might represent the earliest organisms that biomineralize intracellular magnetic iron minerals (i.e., magnetite [Fe₃O₄] or greigite [Fe₃S₄]). Here, we report a novel magnetotactic spirillum (XQGS-1) that is phylogenetically affiliated with the Alphaproteobacteria class. In addition to magnetite crystals, XQGS-1 cells form intracellular submicrometer calcium carbonate and calcium phosphate granules. This finding supports the view that MTB are also an important microbial group for intracellular calcium carbonate and calcium phosphate biomineralization.

Micropearls and other intracellular inclusions of amorphous calcium carbonate: an unsuspected biomineralization capacity shared by diverse microorganisms

An unsuspected biomineralization process, which produces intracellular inclusions of amorphous calcium carbonate (ACC), was recently discovered in unicellular eukaryotes. These mineral inclusions, called micropearls, can be highly enriched with other alkaline‐earth metals (AEM) such as Sr and Ba. Similar intracellular inclusions of ACC have also been observed in prokaryotic organisms. These comparable biomineralization processes involving phylogenetically distant microorganisms are not entirely understood yet. This review gives a broad vision of the topic in order to establish a basis for discussion on the possible molecular processes behind the formation of the inclusions, their physiological role, the impact of these microorganisms on the geochemical cycles of AEM and their evolutionary relationship. Finally, some insights are provided to guide future research.