Intracellular amorphous carbonates uncover a new biomineralization process in eukaryotes

Intracellular bioaccumulation of the rare earth element Gadolinium in ciliate cells resulting in biogenic particle formation and excretion

Ciliates are abundant unicellular organisms capable of resisting high concentrations of metal ions in the environment caused by various anthropogenic activities. Understanding the cellular pathways involved in resistance to and detoxification of elements is required to predict the impact of ciliates on environmental element cycles. Here, we investigated the so far unknown process of tolerance, cellular uptake and bioaccumulation of the emerging rare earth element gadolinium (Gd) in the common ciliate Tetrahymena pyriformis. Gd treatment results in the intracellular formation and excretion of biogenic Gd-containing particles. This cellular process effectively removes dissolved Gd from the organic growth medium by 53.37% within 72 h. Based on light and electron microscopic observations, we postulate a detoxification pathway: Cells take up toxic Gd³⁺ ions from the medium by endocytosis, process them into stable Gd-containing particles within food vacuoles, and exocytose them. Stable biogenic particles can be isolated, which are relatively homogeneous and have a diameter of about 3 µm. They consist of the elements Gd, C, O, P, Na, Mg, K, and Ca. These findings broaden the view of metal ion accumulation by protists and are of relevance to understand environmental elemental cycles and may inspire approaches for metal recovery or bioremediation.

Fine-scale dynamics of calcite precipitation in a large hardwater lake

In hardwater lakes, calcite precipitation is an important yet poorly understood process in the lacustrine carbon cycle, in which catchment-derived alkalinity (Alk) is both transformed and translocated. While the physico-chemical conditions supporting the supersaturation of water with respect to calcite are theoretically well described, the magnitude and conditions underlying calcite precipitation at fine temporal and spatial scales are poorly constrained. In this study, we used high frequency, depth-resolved (0-30 m) data collected over 18 months (June 2019 - November 2020) in the deeper basin of Lake Geneva to describe the dynamics of calcite precipitation fluxes at a fine temporal resolution (day to season) and to scale them to carbon fixation by primary production. Calcite precipitation occurred during the warm stratified periods when surface water CO₂ concentrations were below atmospheric equilibrium. Seasonally, the extent of Alk loss due to calcite precipitation (i.e., [30-42] g C m^-2) depended upon the level of Alk in surface waters. Moreover, interannual variability in seasonal calcite precipitation depended on the duration of stratification, which determined the volume of the water layer susceptible to calcite precipitation. At finer timescales, calcite precipitation was characterized by marked daily variability with dynamics strongly related to that of planktonic autotrophic metabolism. Increasing daily calcite precipitation rates (i.e., maximum values 9 mmol C m^-3 d^-1) coincided with increasing net ecosystem production (NEP) during periods of enhanced water column stability. In these conditions, calcite precipitation could remove as much inorganic carbon from the productive layers as NEP. This study provides mechanistic insights into the conditions driving pelagic calcite precipitation, and quantifies its essential contribution to the coupling of organic and inorganic carbon cycling in lakes.

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.

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.

Combined in vitro and in vivo investigation of barite microcrystals in Spirogyra (Zygnematophyceae, Charophyta)

We have investigated the biomineralisation of barite ‒a useful proxy for reconstructing paleoproductivity‒ in a freshwater alga, Spirogyra, by combining in vitro and in vivo approaches to unveil the nature of its barite microcrystals. Scanning electron microscope (SEM) and energy-dispersive X-ray spectroscopy (EDXS) observations on simply dried samples revealed that the number and size of barite crystals were related to the barium concentration in the media. Additionally, their morphology showed a crystallographic face (011), which is not normally observed, suggesting the influence of organic molecules on the growth kinetics. The critical point drying method was used to preserve the internal and external structures of Spirogyra cells for SEM imaging. Crystals were found adjacent to the cytoplasmic membrane, near chloroplasts and fibrillary network. In vivo optical microscopy and Raman tweezer microspectroscopy in living cells showed that barite microcrystals are optically visible and follow cytoplasmic streaming. These results led us to propose that barite formation in Spirogyra occurs in the cytoplasm where barium and sulphate are both available: barium supplied non-selectively through the active transport of the divalent cations needed for actin polymerisation, and sulphate because necessary for amino acid biosynthesis in chloroplasts.

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.

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.

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.

Bio-mineralisation, characterization, and stability of calcium carbonate containing organic matter

The composition of organic matter in biogenic calcium carbonate has long been a mystery, and its role has not received sufficient attention. This study is aimed at elucidating the bio-mineralisation and stability of amorphous calcium carbonate (ACC) and vaterite containing organic matter, as induced by Bacillus subtilis. The results showed that the bacteria could induce various structural forms of CaCO3, such as biogenic ACC (BACC) or biogenic vaterite (BV), using the bacterial cells as their template, and the carbonic anhydrase secreted by the bacteria plays an important role in the mineralisation of CaCO3. The effects of Ca2+ concentration on the crystal structure of CaCO3 were ascertained; when the amount of CaCl2 increased from 0.1% (m/v) to 0.8% (m/v), the ACC was transformed to polycrystalline vaterite. The XRD results demonstrated that the ACC and vaterite have good stability in air or deionised water for one year, or even when heated to 200 °C or 300 °C for 2 h. Moreover, the FTIR results indicated that the BACC or BV is rich in organic matter, and the contents of organic matter in biogenic ACC and vaterite are 39.67 wt% and 28.47 wt%, respectively. The results of bio-mimetic mineralisation experiments suggest that the protein secreted by bacterial metabolism may be inclined to inhibit the formation of calcite, while polysaccharide may be inclined to promote the formation of vaterite. Our findings advance our knowledge of the CaCO3 family and are valuable for future research into organic-CaCO3 complexes.

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.

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.

Linking environmental observations and solid solution thermodynamic modeling: the case of Ba- and Sr-rich micropearls in Lake Geneva

Intracellular inclusions of amorphous Ba- and Sr-rich calcium carbonates – referred to as “micropearls”– have recently been detected in Lake Geneva. These micropearls are formed under conditions of pronounced Ba and Sr undersaturation in the lake waters. Their formation can be explained by the ability of certain microorganisms to preconcentrate these trace elements in tandem with a non-equilibrium solid-solution growing mechanism.