An early-branching microbialite cyanobacterium forms intracellular carbonates

Calcium isotope fractionation by intracellular amorphous calcium carbonate (ACC) forming cyanobacteria

The formation of intracellular amorphous calcium carbonate (ACC) by various cyanobacteria is a widespread biomineralization process, yet its mechanism and importance in past and modern environments remain to be fully comprehended. This study explores whether calcium (Ca) isotope fractionation, linked to ACC-forming cyanobacteria, can serve as a reliable tracer for detecting these microorganisms in modern and ancient settings. Accordingly, we measured stable Ca isotope fractionation during Ca uptake by the intracellular ACC-forming cyanobacterium Cyanothece sp. PCC 7425. Our results show that Cyanothece sp. PCC 7425 cells are enriched in lighter Ca isotopes relative to the solution. This finding is consistent with the kinetic isotope effects observed in the Ca isotope fractionation during biogenic carbonate formation by marine calcifying organisms. The Ca isotope composition of Cyanothece sp. PCC 7425 was accurately modeled using a Rayleigh fractionation model, resulting in a Ca isotope fractionation factor (Δ44Ca) equal to -0.72 ± 0.05‰. Numerical modeling suggests that Ca uptake by these cyanobacteria is primarily unidirectional, with minimal back reaction observed over the duration of the experiment. Finally, we compared our Δ44Ca values with those of other biotic and abiotic carbonates, revealing similarities with organisms that form biogenic calcite. These similarities raise questions about the effectiveness of using the Ca isotope fractionation factor as a univocal tracer of ACC-forming cyanobacteria in the environment. We propose that the use of Δ44Ca in combination with other proposed tracers of ACC-forming cyanobacteria such as Ba and Sr isotope fractionation factors and/or elevated Ba/Ca and Sr/Ca ratios may provide a more reliable approach.

Searching for microbial contribution to micritization of shallow marine sediments

Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.

Remote Laser-Induced Breakdown Spectroscopy of Bacterial Growths in Carbonate Rocks in a Mars-like Atmosphere

Understanding the past habitable environments of Mars increases the requirement to recognize and examine modern analogs and to evaluate the mechanisms that may preserve biosignatures in them. The phenomenon that originates and preserves possible microbial biosignatures in mineral phases is of particular interest in astrobiology. On Earth, the precipitation of carbonate matrices can be mediated by bacteria. Besides microbialites and other sedimentary structures, carbonate formations can be observed in certain karstic caves. The present work is focused on the remote laser-induced breakdown spectroscopy (LIBS) characterization of cyanobacteria, exploring the possibilities for identification and discrimination on carbonate substrates. For this purpose, the extremophile cyanobacterium Chroococcidiopsis sp. (collected from the Nerja Cave, Malaga, Spain) was analyzed under laboratory-simulated martian conditions in terms of chemical composition and gas pressure. LIBS results related to acquired molecular emission features allowed bacterial differentiation from the colonized mineral substrate. In addition, the limits of detection were estimated with a laboratory-grown culture of the cyanobacterium Microcystis aureginosa. Our results reveal LIBS's capability to detect biological traces under simulated martian conditions. Additionally, the time-resolved analysis of the biological samples demonstrates the selection of optimal temporal conditions as a critical parameter for the preferential acquisition of molecular species in organic material.

Will tomorrow's mineral materials be grown?

Biomineralization, the capacity to form minerals, has evolved in a great diversity of bacterial lineages as an adaptation to different environmental conditions and biological functions. Microbial biominerals often display original properties (morphology, composition, structure, association with organics) that significantly differ from those of abiotically formed counterparts, altogether defining the 'mineral phenotype'. In principle, it should be possible to take advantage of microbial biomineralization processes to design and biomanufacture advanced mineral materials for a range of technological applications. In practice, this has rarely been done so far and only for a very limited number of biomineral types. This is mainly due to our poor understanding of the underlying molecular mechanisms controlling microbial biomineralization pathways, preventing us from developing bioengineering strategies aiming at improving biomineral properties for different applications. Another important challenge is the difficulty to upscale microbial biomineralization from the lab to industrial production. Addressing these challenges will require combining expertise from environmental microbiologists and geomicrobiologists, who have historically been working at the forefront of research on microbe-mineral interactions, alongside bioengineers and material scientists. Such interdisciplinary efforts may in the future allow the emergence of a mineral biomanufacturing industry, a critical tool towards the development more sustainable and circular bioeconomies.

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.

High calcium and strontium uptake by the green microalga Tetraselmis chui is related to micropearl formation and cell growth

Strontium-rich micropearls (intracellular inclusions of amorphous calcium carbonate) have been observed in several species of green microalgae within the class Chlorodendrophyceae, suggesting the potential use of these organisms for ⁹⁰ Sr bioremediation purposes. However, very little is known about the micropearl formation process and the Ca and Sr uptake dynamics of these microalgae. To better understand this phenomenon, we investigated, through laboratory cultures, the behaviour of two species within the class Chorodendrophyceae: Tetraselmis chui, forming micropearls, and T. marina, not forming micropearls. We show that T. chui growth and micropearl formation requires available Ca in the culture medium, and that the addition of dissolved Sr can partially replace the function of Ca in cells. On the other hand, T. marina can grow without added Ca and Sr, probably due to its inability to form micropearls. T. chui cells show a high Ca and Sr uptake, significantly decreasing the concentration of both elements in the culture medium. Strontium is incorporated in micropearls in a short period of time, suggesting that micropearl formation is, most likely, a fast process that only takes a few hours. In addition, we show that micropearls equally distribute between daughter cells during cell division.

A New Ecological and Evolutionary Perspective on the Emergence of Oxygenic Photosynthesis

In this hypothesis article, we propose that the timing of the evolution of oxygenic photosynthesis and the diversification of cyanobacteria is firmly tied to the geological evolution of Earth in the Mesoarchean to Neoarchean. Specifically, the diversification of species capable of oxygenic photosynthesis is tied to the growth of subaerial (above sea-level/terrestrial) continental crust, which provided niches for their diversification. Moreover, we suggest that some formerly aerobic bacterial lineages evolved to become anoxygenic photosynthetic as a result of changes in selection following the reintroduction of ferruginous conditions in the oceans at 1.88 GYa. Both conclusions are fully compatible with phylogenetic evidence. The hypothesis carries with it a predictive component-at least for terrestrial organisms-that the development and expansion of photosynthesis species was dependent on the geological evolution of Earth.

The elements of life: A biocentric tour of the periodic table

Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.

Position of Algae on the Tree of Life

Issues related to evolution of algal chloroplasts are considered. The position of algae on the Tree of Life is discussed. Algae are now included in five of the monophyletic eukaryotic supergroups: Archaeplastida (Glaucocystophyta, Rhodophyta, Prasinodermophyta, Chlorophyta, and Charophyta), TSAR (Ochrophyta; Dinophyta; Chlorarachniophyta; and photosynthetic species of the genera Chromera, Vetrella, and Paulinella), Haptista (Prymnesiophyta and Rappemonads), Cryptista (Cryptophyta), and Discoba (Euglenophyta). The algal divisions and the respective supergroups are characterized in brief.

Distribution and Genomic Variation of Thermophilic Cyanobacteria in Diverse Microbial Mats at the Upper Temperature Limits of Photosynthesis

Thermophilic cyanobacteria have been extensively studied in Yellowstone National Park (YNP) hot springs, particularly during decades of work on the thick laminated mats of Octopus and Mushroom springs. However, focused studies of cyanobacteria outside these two hot springs have been lacking, especially regarding how physical and chemical parameters along with community morphology influence the genomic makeup of these organisms. Here, we used a metagenomic approach to examine cyanobacteria existing at the upper temperature limit of photosynthesis. We examined 15 alkaline hot spring samples across six geographic areas of YNP, all with various physical and chemical parameters and community morphology. We recovered 22 metagenome-assembled genomes (MAGs) belonging to thermophilic cyanobacteria, notably an uncultured Synechococcus-like taxon recovered from a setting at the upper temperature limit of photosynthesis, 73°C, in addition to thermophilic Gloeomargarita. Furthermore, we found that three distinct groups of Synechococcus-like MAGs recovered from different temperature ranges vary in their genomic makeup. MAGs from the uncultured very-high-temperature (up to 73°C) Synechococcus-like taxon lack key nitrogen metabolism genes and have genes implicated in cellular stress responses that diverge from other Synechococcus-like MAGs. Across all parameters measured, temperature was the primary determinant of taxonomic makeup of recovered cyanobacterial MAGs. However, total Fe, community morphology, and biogeography played an additional role in the distribution and abundance of upper-temperature-limit-adapted Synechococcus-like MAGs. These findings expand our understanding of cyanobacterial diversity in YNP and provide a basis for interrogation of understudied thermophilic cyanobacteria. IMPORTANCE Oxygenic photosynthesis arose early in microbial evolution-approximately 2.5 to 3.5 billion years ago-and entirely reshaped the biological makeup of Earth. However, despite the span of time in which photosynthesis has been refined, it is strictly limited to temperatures below 73°C, a barrier that many other biological processes have been able to overcome. Furthermore, photosynthesis at temperatures above 56°C is limited to circumneutral and alkaline pH. Hot springs in Yellowstone National Park (YNP), which have a large diversity in temperatures, pH, and geochemistry, provide a natural laboratory to study thermophilic microbial mats and the cyanobacteria within. While cyanobacteria in YNP microbial mats have been studied for decades, a vast majority of the work has focused on two springs within the same geyser basin, both containing similar community morphologies. Thus, the drivers of cyanobacterial adaptations to the upper limits of photosynthesis across a variety of environmental parameters have been understudied. Our findings provide new insights into the influence of these parameters on both taxonomic diversity and genomic content of cyanobacteria across a range of hot spring samples.

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.

Mineralogy of Bioprecipitate Evolution over Induction Times Mediated by Halophilic Bacteria under Various Mg/Ca Molar Ratios

In microbial mineralization experiments, the induction time of mineral precipitation is ambiguous, and this may lead to difficulties in reproducing and confirming the test results. To explore the link between induction time and microbially mediated carbonate precipitation, we report here the mineralogy and morphology of carbonate precipitates induced by the halophilic Halomonas utahensis WMS2 bacterium in media with various Mg/Ca molar ratios over a range of induction times. The results show that the biominerals are formed in an alkaline environment affected by ammonia secreted by H. utahensis WMS2 bacteria. The content of dissolved inorganic carbon increased as a result of carbonic anhydrase catalyzing the hydration of carbon dioxide to release bicarbonate and carbonate ions. The X-ray diffraction (XRD) results show that the phase of mineral precipitated gradually changes from an unstable Mg-rich calcite to metastable monohydrocalcite and then to stable hydromagnesite with an increase in the Mg²⁺ ion concentration and induction time. The scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and Fourier transform infrared spectroscopy (FTIR) results show that minerals mostly change from single particles/crystallites to aggregations under the action of the microorganisms at different Mg²⁺ ion concentrations and induction times. Our experiments demonstrate that the carbonate minerals produced in the presence of microbes change significantly with the induction time, in addition to the influence of the hydrochemical factors; this indicates that the induction time is significant in determining the mineralogy of biominerals.

A critical review of mineral-microbe interaction and coevolution: mechanisms and applications

The mineral-microbe interactions play important roles in environmental change, biogeochemical cycling of elements, and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation, and precipitation of minerals through their activity, resulting in either genetically-controlled or metabolism-induced biomineralization. Through these interactions minerals and microbes coevolve through Earth history. The mineral-microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral-microbe interactions for the benefit of humankind.

Calcium ion biorecovery from industrial wastewater by Bacillus amyloliquefaciens DMS6

Calcium ions in industrial wastewater needs to be removed to prevent the production of limescale, which can have negative consequences. Biomineralization has become the focus due to its lower costs than traditional methods of remediation. In this study, calcium ions were bio-precipitated under the action of free and immobilized Bacillus amyloliquefaciens DMS6 bacteria, and the calcium ion removal efficiency was also compared. The results show that it only needed 3 days to decrease the calcium ion concentration to an ideal level of 76-116 mg/L under the action of DMS6 bacteria immobilized by activated carbon fiber, with calcium ion removal ratios reaching 99%-95% by the 7^th day. DMS6 bacteria immobilized by activated carbon fiber were superior to free bacteria and bacteria immobilized by sodium alginate in calcium ion removal. Calcium ions are biomineralized into calcite, Mg-rich calcite, aragonite and monohydrocalcite with abundant organic functional groups, 4 types of secondary protein structures, amino acids, phospholipids, negative stable carbon isotope δ¹³C_PDB values (-16.68‰ to-17.25‰) and negatively charged biomineral surface. Calcium ions were diffused into cells and took part in the intracellular biomineralization of monohydrocalcite, also facilitating calcium ion removal. The formation of intracellular monohydrocalcite has rarely been reported. This study demonstrates an economic and environmentally friendly method to remove calcium ions from industrial wastewater.

Fungal-induced CaCO3 and SrCO3 precipitation: a potential strategy for bioprotection of concrete

Biomineralization of CaCO₃ by microorganisms is a well-documented process considered applicable to concrete self-healing and metal bioremediation. Urea hydrolysis is the most widely explored and efficient pathway regarding concrete bioprotection. However, the potential of fungi has received relatively little attention compared to bacteria. In this work, we show that Fusarium cerealis, Phoma herbarum and Mucor hiemalis, isolated from concrete, could produce 828.6-941.3 mg L^-1 ammonium‑nitrogen in liquid media through urea hydrolysis indicating significant urease activity, and could grow in moderate (pH 8.3) or even extremely alkaline (pH 10.6) conditions. After culture in media containing 50 mM CaCl₂, at least 48.8% Ca²⁺ was removed from solution by the selected fungi as calcite. The accumulation of Ca by the biomass was around 83.64-114.21 mg g^-1. In addition, all fungi could mediate strontium carbonate formation with F. cerealis processing the highest ability for Sr removal, with ~61% added Sr being removed from solution. Scanning electron microscopy showed carbonate biominerals were encrusted on hyphae or aggregated in fungal pellets. When equivalent concentrations of Ca²⁺ and Sr²⁺ were supplemented to the media, CaCO₃ with incorporated Sr formed with F. cerealis and M. hiemalis, and Sr(Sr, Ca)(CO₃)₂ with P. herbarum. Our results demonstrate the potential of fungi in providing carbonate coatings for concrete surfaces and simultaneous immobilization of Sr. We anticipate our work will promote further practical field research on porous cementitious materials protection by fungi and immobilization of potentially toxic metals from metal-laden ingredients, such as fly ash and granulated ground blast furnace slag.

A New Gene Family Diagnostic for Intracellular Biomineralization of Amorphous Ca Carbonates by Cyanobacteria

Cyanobacteria have massively contributed to carbonate deposition over the geological history. They are traditionally thought to biomineralize CaCO3 extracellularly as an indirect byproduct of photosynthesis. However, the recent discovery of freshwater cyanobacteria-forming intracellular amorphous calcium carbonates (iACC) challenges this view. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and evolutionary history remain elusive. Here, using comparative genomics, we identify a new gene (ccyA) and protein family (calcyanin) possibly associated with cyanobacterial iACC biomineralization. Proteins of the calcyanin family are composed of a conserved C-terminal domain, which likely adopts an original fold, and a variable N-terminal domain whose structure allows differentiating four major types among the 35 known calcyanin homologs. Calcyanin lacks detectable full-length homologs with known function. The overexpression of ccyA in iACC-lacking cyanobacteria resulted in an increased intracellular Ca content. Moreover, ccyA presence was correlated and/or colocalized with genes involved in Ca or HCO3- transport and homeostasis, supporting the hypothesis of a functional role of calcyanin in iACC biomineralization. Whatever its function, ccyA appears as diagnostic of intracellular calcification in cyanobacteria. By searching for ccyA in publicly available genomes, we identified 13 additional cyanobacterial strains forming iACC, as confirmed by microscopy. This extends our knowledge about the phylogenetic and environmental distribution of cyanobacterial iACC biomineralization, especially with the detection of multicellular genera as well as a marine species. Moreover, ccyA was probably present in ancient cyanobacteria, with independent losses in various lineages that resulted in a broad but patchy distribution across modern cyanobacteria.

Successive Modes of Carbonate Precipitation in Microbialites along the Hydrothermal Spring of La Salsa in Laguna Pastos Grandes (Bolivian Altiplano)

Interpreting the paleoecosystems of ancient microbialites relies on our understanding of how modern microbialites form in relation with the bio-physico-chemical conditions of their environment. In this study, we investigated the formation of modern carbonate microbialites in the hydrothermal system of La Salsa in Laguna Pastos Grandes (Bolivia), which spans a wide range of physicochemical conditions and associated microbial communities. By combining dissolved inorganic carbon (DIC) isotope mass balance modeling, analysis of carbonates solubility diagram, and imaging of the microorganisms–mineral assemblages within microbial mats, we found that several modes of carbonate precipitation dominate in distinct portions of the hydrothermal system. (1) In high-[DIC] waters, undersaturated to slightly saturated with respect to calcite, cyanobacterial calcification is promoted by CO2 degassing and photosynthetic activity within the microbial mats. (2) In alkaline waters undergoing sustained evaporation, the precipitation of an amorphous calcium carbonate phase seems to control the water a(Ca2+)/a(CO32−) ratio and to serve as a precursor to micritic calcite formation in microbial mats. (3) In saline ephemeral ponds, where the carbonate precipitation is the highest, calcite precipitation probably occurs through a different pathway, leading to a different calcite texture, i.e., aggregates of rhombohedral crystals.

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.

First Observation of Unicellular Organisms Concentrating Arsenic in ACC Intracellular Inclusions in Lake Waters

In unicellular organisms, intracellular inclusions of amorphous calcium carbonate (ACC) were initially described in cyanobacteria and, later, in unicellular eukaryotes from Lake Geneva (Switzerland/France). Inclusions in unicellular eukaryotes, named micropearls, consist of hydrated ACCs, frequently enriched in Sr or Ba, and displaying internal oscillatory zonations, due to variations in the Ba:Ca or Sr:Ca ratios. An analysis of our database, consisting of 1597 micropearl analyses from Lake Geneva and 34 from Lake Titicaca (Bolivia/Peru), showed that a certain number of Sr- and Ba-enriched micropearls from these lakes contain As in amounts measurable by EDXS. A Q-mode statistical analysis confirmed the existence of five chemically distinct morpho-chemical groups of As-bearing micropearls, among which was a new category identified in Lake Geneva, where As is often associated with Mg. This new type of micropearl is possibly produced in a small (7–12 μm size) bi-flagellated organism. Micropearls from Lake Titicaca, which contain Sr, were found in an organism very similar to Tetraselmis cordiformis, which was observed earlier in Lake Geneva. Lake Titicaca micropearls contain larger As amounts, which can be explained by the high As concentration in the water of this lake. The ubiquity of this observed biomineralization process points to the need for a better understanding of the role of amorphous or crystalline calcium carbonates in As cycling in surface waters.

Superlattice ordering transitions driven by short-range structure in barium calcium carbonates

Balcite (BaxCa1-xCO3) is a synthetic analog of rhombohedral carbonate minerals like calcite and dolomite that is disordered on both the cation and anion sublattices. Here, we show that multiple exotic...

Dense intracellular ion pools in unicellular organisms

Uptake and concentration of inorganic ions are part of the complex cellular processes required for cell homeostasis, as well as for mineral formation by organisms. These ion transport mechanisms include distinct cellular compartments and chemical phases that play various roles in the physiology of organisms. Here, the prominent cases of dense ion pools in unicellular organisms are briefly reviewed. The specific observations that were reported for different organisms are consolidated into a wide perspective that emphasizes general traits. It is suggested that the intracellular ion pools can be divided into three types: a high cytoplasmic concentration, a labile storage compartment that hosts dense ion-rich phases, and a mineral-forming compartment in which a stable long-lived structure is formed. Recently, many labile pools were identified in various organisms using advanced techniques, bringing many new questions about their possible roles in the formation of the stable mineralized structures.

Detection of carbonate, phosphate minerals and cyanobacteria in rock from the Tomtor deposit, Russia, by Raman spectroscopy

Samples of rock from the Tomtor Nb - REE (rare-earth elements) deposit (Russia) have been investigated by Raman micro-spectroscopy using visible 532 nm wavelength excitation. Raman spectra of different samples of this rock confirm their composition as calcites and other carbonates such as rhodochrosite, and mixed solid solution phases (Ca, Mn, Fe, Mg, Ba, Sr, REE)(CO₃). An association between cyanobacteria and the apatite crystals has been noted Cyanobacteria exhibited Raman modes at 1520-1517 cm^-1 located in the double bonds of the central part of the polyene chain of carotenoids. A slight shift of this mode in the apatite-containing samples are dependent upon the compositions of carotenoids, the ratio of the rare earth elements adsorbed by cyanobacteria as well as their interaction with the environment. Laser-induced photoluminescence of REE and Mn⁺², obtained as an analytical artifact in the Raman spectra, has been observed in most cases with significant spectral intensity. The luminescence emission of Mn ²⁺, Sm³⁺, Eu ³⁺, Pr³⁺, Ho³⁺, Er ³⁺ in the spectra of the apatite-containing samples obtained with 532 nm excitation can be attributed both to apatite and to other mineral phases with a low concentration which contain these elemental ions. The results obtained in this study allowed us to confirm that the biogenic presence of the cyanobacterial mat had a significant impact on the formation of the unique Nb-REE Tomtor deposit.

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.

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

Achromatium is a long known uncultured giant gammaproteobacterium forming intracellular CaCO₃ that impacts C and S geochemical cycles functioning in some anoxic sediments and at oxic-anoxic boundaries. While intracellular CaCO₃ granules have first been described as Ca oxalate then colloidal CaCO₃ more than one century ago, they have often been referred to as crystalline solids and more specifically calcite over the last 25 years. Such a crystallographic distinction is important since the respective chemical reactivities of amorphous calcium carbonate (ACC) and calcite, hence their potential physiological role and conditions of formation, are significantly different. Here, we analyzed the intracellular CaCO₃ granules of Achromatium cells from Lake Pavin using a combination of Raman microspectroscopy and scanning electron microscopy. Granules in intact Achromatium cells were unequivocally composed of ACC. Moreover, ACC spontaneously transformed into calcite when irradiated at high laser irradiance during Raman analyses. Few ACC granules also transformed spontaneously into calcite in lysed cells upon cell death and/or sample preparation. Overall, the present study supports the original claims that intracellular Ca-carbonates in Achromatium are amorphous and not crystalline. In that sense, Achromatium is similar to a diverse group of Cyanobacteria and a recently discovered magnetotactic alphaproteobacterium, which all form intracellular ACC. The implications for the physiology and ecology of Achromatium are discussed. Whether the mechanisms responsible for the preservation of such unstable compounds in these bacteria are similar to those involved in numerous ACC-forming eukaryotes remains to be discovered. Last, we recommend to future studies addressing the crystallinity of CaCO₃ granules in Achromatium cells recovered from diverse environments all over the world to take care of the potential pitfalls evidenced by the present study.

Cellular pathways of calcium transport and concentration toward mineral formation in sea urchin larvae

Sea urchin larvae have an endoskeleton consisting of two calcitic spicules. The primary mesenchyme cells (PMCs) are the cells that are responsible for spicule formation. PMCs endocytose sea water from the larval internal body cavity into a network of vacuoles and vesicles, where calcium ions are concentrated until they precipitate in the form of amorphous calcium carbonate (ACC). The mineral is subsequently transferred to the syncytium, where the spicule forms. Using cryo-soft X-ray microscopy we imaged intracellular calcium-containing particles in the PMCs and acquired Ca-L2,3 X-ray absorption near-edge spectra of these Ca-rich particles. Using the prepeak/main peak (L2'/ L2) intensity ratio, which reflects the atomic order in the first Ca coordination shell, we determined the state of the calcium ions in each particle. The concentration of Ca in each of the particles was also determined by the integrated area in the main Ca absorption peak. We observed about 700 Ca-rich particles with order parameters, L2'/ L2, ranging from solution to hydrated and anhydrous ACC, and with concentrations ranging between 1 and 15 M. We conclude that in each cell the calcium ions exist in a continuum of states. This implies that most, but not all, water is expelled from the particles. This cellular process of calcium concentration may represent a widespread pathway in mineralizing organisms.

Biological lipid nanotubes and their potential role in evolution

The membrane of cells and organelles are highly deformable fluid interfaces, and can take on a multitude of shapes. One distinctive and particularly interesting property of biological membranes is their ability to from long and uniform nanotubes. These nanoconduits are surprisingly omnipresent in all domains of life, from archaea, bacteria, to plants and mammals. Some of these tubes have been known for a century, while others were only recently discovered. Their designations are different in different branches of biology, e.g. they are called stromule in plants and tunneling nanotubes in mammals. The mechanical transformation of flat membranes to tubes involves typically a combination of membrane anchoring and external forces, leading to a pulling action that results in very rapid membrane nanotube formation - micrometer long tubes can form in a matter of seconds. Their radius is set by a mechanical balance of tension and bending forces. There also exists a large class of membrane nanotubes that form due to curvature inducing molecules. It seems plausible that nanotube formation and functionality in plants and animals may have been inherited from their bacterial ancestors during endosymbiotic evolution. Here we attempt to connect observations of nanotubes in different branches of biology, and outline their similarities and differences with the aim of providing a perspective on their joint functions and evolutionary origin.

Intracellular amorphous Ca-carbonate and magnetite biomineralization by a magnetotactic bacterium affiliated to the Alphaproteobacteria

Bacteria synthesize a wide range of intracellular submicrometer-sized inorganic precipitates of diverse chemical compositions and structures, called biominerals. Their occurrences, functions and ultrastructures are not yet fully described despite great advances in our knowledge of microbial diversity. Here, we report bacteria inhabiting the sediments and water column of the permanently stratified ferruginous Lake Pavin, that have the peculiarity to biomineralize both intracellular magnetic particles and calcium carbonate granules. Based on an ultrastructural characterization using transmission electron microscopy (TEM) and synchrotron-based scanning transmission X-ray microscopy (STXM), we showed that the calcium carbonate granules are amorphous and contained within membrane-delimited vesicles. Single-cell sorting, correlative fluorescent in situ hybridization (FISH), scanning electron microscopy (SEM) and molecular typing of populations inhabiting sediments affiliated these bacteria to a new genus of the Alphaproteobacteria. The partially assembled genome sequence of a representative isolate revealed an atypical structure of the magnetosome gene cluster while geochemical analyses indicate that calcium carbonate production is an active process that costs energy to the cell to maintain an environment suitable for their formation. This discovery further expands the diversity of organisms capable of intracellular Ca-carbonate biomineralization. If the role of such biomineralization is still unclear, cell behaviour suggests that it may participate to cell motility in aquatic habitats as magnetite biomineralization does.

Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1

Lanthanide elements have been recently recognized as "new life metals" yet much remains unknown regarding lanthanide acquisition and homeostasis. In Methylorubrum extorquens AM1, the periplasmic lanthanide-dependent methanol dehydrogenase XoxF1 produces formaldehyde, which is lethal if allowed to accumulate. This property enabled a transposon mutagenesis study and growth studies to confirm novel gene products required for XoxF1 function. The identified genes encode an MxaD homolog, an ABC-type transporter, an aminopeptidase, a putative homospermidine synthase, and two genes of unknown function annotated as orf6 and orf7. Lanthanide transport and trafficking genes were also identified. Growth and lanthanide uptake were measured using strains lacking individual lanthanide transport cluster genes, and transmission electron microscopy was used to visualize lanthanide localization. We corroborated previous reports that a TonB-ABC transport system is required for lanthanide incorporation to the cytoplasm. However, cells were able to acclimate over time and bypass the requirement for the TonB outer membrane transporter to allow expression of xoxF1 and growth. Transcriptional reporter fusions show that excess lanthanides repress the gene encoding the TonB-receptor. Using growth studies along with energy dispersive X-ray spectroscopy and transmission electron microscopy, we demonstrate that lanthanides are stored as cytoplasmic inclusions that resemble polyphosphate granules.

Benefits at the nanoscale: a review of nanoparticle-enabled processes favouring microbial growth and functionality

Nanoparticles are ubiquitous and co-occur with microbial life in every environment on Earth. Interactions between microbes and nanoparticles impact the biogeochemical cycles via accelerating various reaction rates and enabling biological processes at the smallest scales. Distinct from microbe-mineral interactions at large, microbe-nanoparticle interactions may involve higher levels of active recognition and utilization of the reactive, changeable, and thereby 'moldable' nano-sized inorganic phases by microbes, which has been given minimal attention in previous reviews. Here we have compiled the various cases of microbe-nanoparticle interactions with clear and potential benefits to the microbial cells and communities. Specifically, we discussed (i) the high bioavailabilities of nanoparticles due to increased specific surface areas and size-dependent solubility, with a focus on environmentally-relevant iron(III) (oxyhydr)oxides and pyrite, (ii) microbial utilization of nanoparticles as 'nano-tools' for electron transfer, chemotaxis, and storage units, and (iii) speculated benefits of precipitating 'moldable' nanoparticles in extracellular biomineralization. We further discussed emergent questions concerning cellular level responses to nanoparticle-associated cues, and the factors that affect nanoparticles' bioavailabilities beyond size-dependent effects. We end the review by proposing a framework towards more quantitative approaches and by highlighting promising techniques to guide future research in this exciting field.

Lists of names of prokaryotic Candidatus taxa

We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.

Bio-Precipitation of Carbonate and Phosphate Minerals Induced by the Bacterium Citrobacter freundii ZW123 in an Anaerobic Environment

In this study, a facultative anaerobic strain isolated from marine sediments and identified as Citrobacter freundii, was used to induce the precipitation of carbonate and phosphate minerals in the laboratory under anaerobic conditions. This is the first time that the ability of C. freundii ZW123 to precipitate carbonate and phosphate minerals has been demonstrated. During the experiments, carbonic anhydrase, alkaline phosphatase and ammonium released by the bacteria not only promoted an increase in pH, but also drove the supersaturation and precipitation of carbonate and phosphate minerals. The predominant bio-mediated minerals precipitated at various Mg/Ca molar ratios were calcite, vaterite, Mg-rich calcite, monohydrocalcite and struvite. A preferred orientation towards struvite was observed. Scanning transmission electron microscopy (STEM) and elemental mapping showed the distribution of magnesium and calcium elements within Mg-rich calcite. Many organic functional groups, including C=O, C–O–C and C–O, were detected within the biominerals, and these functional groups were also identified in the associated extracellular polymeric substances (EPS). Fifteen kinds of amino acid were detected in the biotic minerals, almost identical to those of the EPS, indicating a close relationship between EPS and biominerals. Most amino acids are negatively charged and able to adsorb cations, providing an oversaturated microenvironment to facilitate mineral nucleation. The X-ray photoelectron spectroscopy (XPS) spectrum of struvite shows the presence of organic functional groups on the mineral surface, suggesting a role of the microorganism in struvite precipitation. The ZW123 bacteria provided carbon and nitrogen for the formation of the biotic minerals through their metabolism, which further emphasizes the close relationship between biominerals and the microorganisms. Thermal studies showed the enhanced thermal stability of biotic minerals, perhaps due to the participation of the bacteria ZW123. The presence of amino acids such as Asp and Glu may explain the high magnesium content of some calcites. Molecular dynamics simulations demonstrated that the morphological change and preferred orientation were likely caused by selective adsorption of EPS onto the various struvite crystal surfaces. Thus, this study shows the significant role played by C. freundii ZW123 in the bioprecipitation of carbonate and phosphate minerals and provides some insights into the processes involved.

Sequestration of Radionuclides Radium-226 and Strontium-90 by Cyanobacteria Forming Intracellular Calcium Carbonates

²²⁶Ra is a naturally occurring radionuclide with a half-life of 1600 years. In contrast, ⁹⁰Sr is a radionuclide of sole anthropogenic origin, produced by nuclear fission reactions and has a half-life of 29 years; each of these radionuclides poses potential threats to human and ecosystem health. Here, the cyanobacterium Gloeomargarita lithophora, capable of forming intracellular amorphous calcium carbonate inclusions, was investigated for its ability to uptake ²²⁶Ra and ⁹⁰Sr. In BG-11 medium, G. lithophora accumulated 3.9 μg g^-1 of ²²⁶Ra within 144 h and 47.9 ng g^-1 of ⁹⁰Sr within 1 h, corresponding to ∼99% removal of trace radionuclides. The presence of high-concentration Ca²⁺ in the background media solution did not inhibit ⁹⁰Sr and ²²⁶Ra uptake by G. lithophora. In contrast, dead biomass of G. lithophora accumulated 0.8 μg g^-1 of ²²⁶Ra and 8.87 ng g^-1 of ⁹⁰Sr. Moreover, Synechocystis, a nonbiomineralizing cyanobacteria, removed only 14 and 25% of ²²⁶Ra and ⁹⁰Sr, respectively. This suggested that sequestration of ⁹⁰Sr and ²²⁶Ra was not intrinsic to all cyanobacteria but was likely a specific biological trait of G. lithophora related to the formation of intracellular amorphous Ca-carbonates. The unique ability of G. lithophora to uptake ⁹⁰Sr and ²²⁶Ra at high rates makes it an attractive candidate for further studies involving bioremediation of these radionuclides.

Evidence of high Ca uptake by cyanobacteria forming intracellular CaCO3 and impact on their growth

Several species of cyanobacteria biomineralizing intracellular amorphous calcium carbonates (ACC) were recently discovered. However, the mechanisms involved in this biomineralization process and the determinants discriminating species forming intracellular ACC from those not forming intracellular ACC remain unknown. Recently, it was hypothesized that the intensity of Ca uptake (i.e., how much Ca was scavenged from the extracellular solution) might be a major parameter controlling the capability of a cyanobacterium to form intracellular ACC. Here, we tested this hypothesis by systematically measuring the Ca uptake by a set of 52 cyanobacterial strains cultured in the same growth medium. The results evidenced a dichotomy among cyanobacteria regarding Ca sequestration capabilities, with all strains forming intracellular ACC incorporating significantly more calcium than strains not forming ACC. Moreover, Ca provided at a concentration of 50 μM in BG-11 was shown to be limiting for the growth of some of the strains forming intracellular ACC, suggesting an overlooked quantitative role of Ca for these strains. All cyanobacteria forming intracellular ACC contained at least one gene coding for a mechanosensitive channel, which might be involved in Ca influx, as well as at least one gene coding for a Ca²⁺ /H⁺ exchanger and membrane proteins of the UPF0016 family, which might be involved in active Ca transport either from the cytosol to the extracellular solution or the cytosol toward an intracellular compartment. Overall, massive Ca sequestration may have an indirect role by allowing the formation of intracellular ACC. The latter may be beneficial to the growth of the cells as a storage of inorganic C and/or a buffer of intracellular pH. Moreover, high Ca scavenging by cyanobacteria biomineralizing intracellular ACC, a trait shared with endolithic cyanobacteria, suggests that these cyanobacteria should be considered as potentially significant geochemical reservoirs of Ca.

Lake sedimentary biogenic silica from diatoms constitutes a significant global sink for aluminium

Diatoms play an important role in marine biogeochemical cycle of aluminum (Al), as dissolved Al is taken up by diatoms to build their siliceous frustules and is involved in the sedimentation of diatomaceous biogenic silica (BSi). The Al incorporation in BSi facilitates decreasing the dissolution of marine BSi and thus substantially influences the biochemical processes driven by diatoms, such as CO₂ sequestration. However, the role of lake BSi in the terrestrial biochemical Al cycle has not been explored, though lakes represent the second-largest sink for BSi. By identifying the previously unexplored high Al/Si atomic ratios (up to 0.052) in lake BSi, here we show lake BSi is a large terrestrial Al pool due to its high Al content, and lake sedimentary BSi constitutes a significant global sink for Al, which is on the same magnitude as the Al sink in global oceans.

Diatoms drive biogeochemical cycling of aluminum by incorporating this element into their shells, but this process has not been quantified in freshwater systems. Here the authors quantify diatom-mediated aluminum fluxes in lakes and determine that they rival the aluminum sink in the global ocean.

Biomineralization of Monohydrocalcite Induced by the Halophile Halomonas smyrnensis WMS‐3

The halophilic bacterium Halomonas smyrnensis from a modern salt lake used in experiments to induce biomineralization has resulted in the precipitation of monohydrocalcite and other carbonate minerals. In this study, a Halomonas smyrnensis WMS‐3 (GenBank:MH425323) strain was identified based on 16S rDNA homology comparison, and then cultured in mediums with 3% NaCl concentration to induce monohydrocalcite at different Mg/Ca molar ratios of 0, 2, 5, 7, and 9. The growth curve of WMS‐3 bacteria, pH values, NH4+ concentration, HCO3− and CO32− concentration, carbonic anhydrase (CA) activity, and the changes in Ca2+ and Mg2+ ion concentration were determined to further explore the extracellular biomineralization mechanism. Moreover, the nucleation mechanism of monohydrocalcite on extracellular polymeric substances (EPS) was analyzed through studying ultrathin slices of the WMS‐3 strain by High resolution transmission electron microscopy (HRTEM), Selected area election diffraction (SAED), Scanning transmission electron microscopy (STEM), and elemental mapping, besides this, amino acids in the EPS were also analyzed. The results show that pH increased to about 9.0 under the influence of ammonia and CA activity. The precipitation ratio (%, the ratio of the mass/volume concentration) of the Ca2+ ion was 64.32%, 62.20%, 60.22%, 59.57%, and 54.42% at Mg/Ca molar ratios of 0, 2, 5, 7, and 9, respectively, on the 21st day of the experiments, and 6.69%, 7.10%, 7.74%, 8.09% for the Mg2+ ion concentration at Mg/Ca molar ratios 2, 5, 7, and 9, respectively. The obtained minerals were calcite, Mg‐rich calcite, aragonite, and hydromagnesite, in addition to the monohydrocalcite, as identified by X-ray diffraction (XRD) analyses. Monohydrocalcite had higher crystallinity when the Mg/Ca ratio increased from 7 to 9; thus, the stability of monohydrocalcite increased, also proven by the thermogravimetry (TG), derivative thermogravimetry (DTG) and differential scanning calorimetry (DSC) analyses. The C=O and C–O–C organic functional groups present in/on the minerals analyzed by Fourier transform infrared spectroscopy (FTIR), the various morphologies and the existence of P and S determined by scanning electron microscope-energy dispersive spectrometer (SEM‐EDS), the relatively more negative stable carbon isotope values (−16.91‰ to −17.91‰) analyzed by a carbon isotope laser spectrometer, plus the typical surface chemistry by XPS, all support the biogenesis of these mineral precipitates. Moreover, Ca2+ ions were able to enter the bacterial cell to induce intracellular biomineralization. This study is useful to understand the mechanism of biomineralization further and may provide theoretical reference concerning the formation of monohydrocalcite in nature.

Cyanobacteria evolution: Insight from the fossil record

Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 Ga, debatably earlier. They are also major primary producers in past and present oceans, and the ancestors of the chloroplast. Nevertheless, the identification of cyanobacteria in the early fossil record remains ambiguous because the morphological criteria commonly used are not always reliable for microfossil interpretation. Recently, new biosignatures specific to cyanobacteria were proposed. Here, we review the classic and new cyanobacterial biosignatures. We also assess the reliability of the previously described cyanobacteria fossil record and the challenges of molecular approaches on modern cyanobacteria. Finally, we suggest possible new calibration points for molecular clocks, and strategies to improve our understanding of the timing and pattern of the evolution of cyanobacteria and oxygenic photosynthesis.

Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium?

Photosynthetic eukaryotes are the product of an endosymbiotic event between a eukaryotic host and a cyanobacterium that became today's plastid. A new phylogenomic study suggests that the closest relative of plastids among extant cyanobacteria is the recently discovered freshwater-dwelling Gloeomargarita lithophora.

Impact of planktonic low nucleic acid-content bacteria to bacterial community structure and associated ecological functions in a shallow lake

In this study, 0.45 μm filtration, flow cytometric fingerprint, 16S rRNA amplicon sequencing, and bioinformation tools were adopted to analyze the structural diversity and potential functions of planktonic low nucleic acid (LNA)- content bacteria in a shallow lake. Three bacterial groups, namely, "LNA," "high nucleic acid (HNA)-Small," and "HNA-Large," were classified through flow cytometric fingerprint, among which the "HNA-Small" group was possibly in the proliferation stage of the "LNA" group. Total nitrogen and phosphate were the key factors that influence the growth of LNA bacteria. Results of 16S rRNA amplicon sequencing showed that LNA bacteria were phylogenetically less diverse than HNA bacteria, and Actinobacteria and Proteobacteria (especially Gamma-Proteobacteria) were the dominant phyla in LNA bacterial operational taxonomic units (OTUs). Accordingly, hgcI_clade and Pseudomonas were the most abundant bacterial genera in LNA bacterial OTUs. The fraction of low-abundance LNA bacteria was sensitive to several environmental factors, indicating that environmental factors only determined the fraction distribution of low-abundance bacteria. The prediction of metabolic and ecological functions showed that LNA and HNA bacteria had distinct metabolic and ecological functions, which were mainly attributed to the dominant and exclusive bacterial groups.

Solubility investigations in the amorphous calcium magnesium carbonate system

Amorphous precursors are known to occur in the early stages of carbonate mineral formation in both biotic and abiotic environments. Although the Mg content of amorphous calcium magnesium carbonate (ACMC) is a crucial factor for its temporal stabilization, to date little is known about its control on ACMC solubility. Therefore, amorphous Ca x Mg1-x CO3·nH2O solids with 0 ≤ x ≤ 1 and 0.4 ≤ n ≤ 0.8 were synthesized and dispersed in MgCl2-NaHCO3 buffered solutions at 24.5 ± 0.5 °C. The chemical evolution of the solution and the precipitate clearly shows an instantaneous exchange of ions between ACMC and aqueous solution. The obtained ion activity product for ACMC (IAPACMC = "solubility product") increases as a function of its Mg content ([Mg]ACMC = (1 - x) × 100 in mol%) according to the expression: log(IAPACMC) = 0.0174 (±0.0013) × [Mg]ACMC - 6.278 (±0.046) (R 2 = 0.98), where the log(IAPACMC) shift from Ca (-6.28 ± 0.05) to Mg (-4.54 ± 0.16) ACMC endmember, can be explained by the increasing water content and changes in short-range order, as Ca is substituted by Mg in the ACMC structure. The results of this study shed light on the factors controlling ACMC solubility and its temporal stability in aqueous solutions.

Microbial community composition and dolomite formation in the hypersaline microbial mats of the Khor Al-Adaid sabkhas, Qatar

The Khor Al-Adaid sabkha in Qatar is among the rare extreme environments on Earth where it is possible to study the formation of dolomite-a carbonate mineral whose origin remains unclear and has been hypothetically linked to microbial activity. By combining geochemical measurements with microbiological analysis, we have investigated the microbial mats colonizing the intertidal areas of sabhka. The main aim of this study was to identify communities and conditions that are favorable for dolomite formation. We inspected and sampled two locations. The first site was colonized by microbial mats that graded vertically from photo-oxic to anoxic conditions and were dominated by cyanobacteria. The second site, with higher salinity, had mats with an uppermost photo-oxic layer dominated by filamentous anoxygenic photosynthetic bacteria (FAPB), which potentially act as a protective layer against salinity for cyanobacterial species within the deeper layers. Porewater in the uppermost layers of the both investigated microbial mats was supersaturated with respect to dolomite. Corresponding to the variation of the microbial community's vertical structure, a difference in crystallinity and morphology of dolomitic phases was observed: dumbbell-shaped proto-dolomite in the mats dominated by cyanobacteria and rhombohedral ordered-dolomite in the mat dominated by FAPB.

Concurrent biomineralization of silver ions into Ag0 and AgxO by Leptolyngbya strain JSC-1 and the establishment of its axenic culture

Ionic silver is a potential hazard to aquatic life forms because of the increasing usage of silver based materials. The need for developing a sustainable and ecofriendly process to minimize the toxic effects of the free ions burden is now a scientific consensus. Therefore, we report the latest results in cyanobacterium Leptolyngbya JSC-1 investigating the tolerance towards toxic doses of silver, its extracellular biomineralization and silver nano-deposits formation inside the cells, and speculate about potential environmental impacts. In this study, scanning electron microscopy (SEM) and energy dispersive x-ray spectroscopy (EDS) analysis reveal the extracellular biomineralization of soluble silver (1-100 μM) into corresponding nanoparticles (50-100 nm in diameter) by JSC-1, while X-ray photoelectron spectroscopy (XPS) examination divulged the presence of both Ag⁺ and Ag⁰ in extracellularly biomineralized silver, depicting a mixture of both Ag_xO and elemental Ag. The scanning transmission electron microscopy (STEM), EDS and elemental mapping visualized the formation of intracellular silver nanoparticles. Moreover, this feature of silver tolerance in JSC-1 was further exploited and a novel protocol was developed for isolation and maintenance of axenic culture of this filamentous cyanobacterium. Consequently, this capability of silver biomineralization by JSC-1, both extra- and intra-cellularly might be useful for modeling the Ag resistance mechanism in cyanobacteria and also might be a sustainable alternative for heavy metals bioremediation in aquatic environments.

Extracellular and Intracellular Biomineralization Induced by Bacillus licheniformis DB1-9 at Different Mg/Ca Molar Ratios

Biomineralization has become a research hotspot and attracted widespread attention in the field of carbonate sedimentology. In this study, precipitation of carbonate minerals was induced by Bacillus licheniformis DB1-9 bacteria, (identity confirmed with its phylogenetic tree), to further explore the biomineralization mechanisms. During experiments, lasting up to 24 days with varying Mg/Ca molar ratios and regular monitoring of conditions, ammonia and carbonic anhydrase are released by the bacteria, resulting in a pH increase. Carbonic anhydrase could have promoted carbon dioxide hydration to produce bicarbonate and carbonate ions, and so promoted supersaturation to facilitate the precipitation of carbonate minerals. These include rhombohedral, dumbbell-shaped, and elongated calcite crystals; aragonite appears in the form of mineral aggregates. In addition, spheroidal and fusiform minerals are precipitated. FTIR results show there are organic functional groups, such as C–O–C and C=O, as well as the characteristic peaks of calcite and aragonite; these indicate that there is a close relationship between the bacteria and the minerals. Ultrathin slices of the bacteria analyzed by HRTEM, SAED, EDS, and STEM show that precipitate within the extracellular polymeric substances (EPS) has a poor crystal structure, and intracellular granular areas have no crystal structure. Fluorescence intensity and STEM results show that calcium ions can be transported from the outside to the inside of the cells. This study provides further insights to our understanding of biomineralization mechanisms induced by microorganisms.

A microbial role in the construction of Mono Lake carbonate chimneys?

Lacustrine carbonate chimneys are striking, metre-scale constructions. If these were bioinfluenced constructions, they could be priority targets in the search for early and extraterrestrial microbial life. However, there are questions over whether such chimneys are built on a geobiological framework or are solely abiotic geomorphological features produced by mixing of lake and spring waters. Here, we use correlative microscopy to show that microbes were living around Pleistocene Mono Lake carbonate chimneys during their growth. A plausible interpretation, in line with some recent works by others on other lacustrine carbonates, is that benthic cyanobacteria and their associated extracellular organic material (EOM) formed tubular biofilms around rising sublacustrine spring vent waters, binding calcium ions and trapping and binding detrital silicate sediment. Decay of these biofilms would locally have increased calcium and carbonate ion activity, inducing calcite precipitation on and around the biofilms. Early manganese carbonate mineralisation was directly associated with cell walls, potentially related to microbial activity though the precise mechanism remains to be elucidated. Much of the calcite crystal growth was likely abiotic, and no strong evidence for either authigenic silicate growth or a clay mineral precursor framework was observed. Nevertheless, it seems likely that the biofilms provided initial sites for calcite nucleation and encouraged the primary organised crystal growth. We suggest that the nano-, micro- and macroscale fabrics of these Pleistocene Mono Lake chimneys were affected by the presence of centimetre-thick tubular and vertically stacked calcifying microbial mats. Such carbonate chimneys represent a promising macroscale target in the exploration for ancient or extraterrestrial life.

Amorphous Calcium Carbonate Granules Form Within an Intracellular Compartment in Calcifying Cyanobacteria

The recent discovery of cyanobacteria forming intracellular amorphous calcium carbonate (ACC) has challenged the former paradigm suggesting that cyanobacteria-mediated carbonatogenesis was exclusively extracellular. Yet, the mechanisms of intracellular biomineralization in cyanobacteria and in particular whether this takes place within an intracellular microcompartment, remain poorly understood. Here, we analyzed six cyanobacterial strains forming intracellular ACC by transmission electron microscopy. We tested two different approaches to preserve as well as possible the intracellular ACC inclusions: (i) freeze-substitution followed by epoxy embedding and room-temperature ultramicrotomy and (ii) high-pressure freezing followed by cryo-ultramicrotomy, usually referred to as cryo-electron microscopy of vitreous sections (CEMOVIS). We observed that the first method preserved ACC well in 500-nm-thick sections but not in 70-nm-thick sections. However, cell ultrastructures were difficult to clearly observe in the 500-nm-thick sections. In contrast, CEMOVIS provided a high preservation quality of bacterial ultrastructures, including the intracellular ACC inclusions in 50-nm-thick sections. ACC inclusions displayed different textures, suggesting varying brittleness, possibly resulting from different hydration levels. Moreover, an electron dense envelope of ∼2.5 nm was systematically observed around ACC granules in all studied cyanobacterial strains. This envelope may be composed of a protein shell or a lipid monolayer, but not a lipid bilayer as usually observed in other bacteria forming intracellular minerals. Overall, this study evidenced that ACC inclusions formed and were stabilized within a previously unidentified bacterial microcompartment in some species of cyanobacteria.

A synergetic biomineralization strategy for immobilizing strontium during calcification of the coccolithophore Emiliania huxleyi

The coccolithophore species Emiliania huxleyi has one of the most global distributions in the modern oceans. They are characteristically covered with calcite scales called coccoliths. In this study, stable strontium immobilization during the calcification process was investigated to indirectly assess a proposed bioremediation approach for removing Sr²⁺ contamination from marine environments. Results indicate that E. huxleyi has high Sr²⁺ tolerance and removal efficiency in response to Sr²⁺ stress ranging from 5.6 to 105.6 ppm. Sr²⁺ immobilization during E. huxleyi calcification indicates a concentration-dependent synergistic mechanism. At lower concentrations of Sr²⁺ (25.6 ppm), Sr²⁺ is incorporated into coccoliths through competitive supply between Sr²⁺ and Ca²⁺. In addition, calcite productivity decreases with increased Sr²⁺ removal efficiency due to crystallographic transformation of coccoliths from hydrated calcite into aragonite at 55.6 ppm Sr²⁺. Further formation of strontianite at 105.6 ppm Sr²⁺ is due to precipitation of Sr²⁺ on the edge of the rims and radial arrays of the coccoliths. Our study implies that coccolithophores are capable of significant removal of Sr²⁺ from the marine environment.