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Intracellular Ca-carbonate biomineralization is widespread in cyanobacteria
Abstract
Significance
Cyanobacteria are known to promote the precipitation of Ca-carbonate minerals by the photosynthetic uptake of inorganic carbon. This process has resulted in the formation of carbonate deposits and a fossil record of importance for deciphering the evolution of cyanobacteria and their impact on the global carbon cycle. Though the mechanisms of cyanobacterial calcification remain poorly understood, this process is invariably thought of as extracellular and the indirect by-product of metabolic activity. Here, we show that contrary to common belief, several cyanobacterial species perform Ca-carbonate biomineralization intracellularly. We observed at least two phenotypes for intracellular biomineralization, one of which shows an original connection with cell division. These findings open new perspectives on the evolution of cyanobacterial calcification.
... Nonetheless, questions persist regarding whether the mucilaginous EPS serves as the site for nucleation and CaCO 3 crystallization initiation, as well as how the cell wall, EPS, and solidified sheath functionally interact within this process in contrast to intracellular CaCO 3 biomineralization. 35 One of the central inquiries regarding terrestrial cyanobacterial biomineralization pertains to the overarching purpose of this ability, as only speculative hypotheses exist regarding the ecological benefits of ''self-entombment'' with CaCO 3 . 34,36 Despite the uncertainties surrounding the precise cellular mechanisms involved, cyanobacterial calcification abilities are increasingly utilized in the field of applied sciences for biotechnological purposes. ...
... 124 However, this dogma has been challenged by the discovery of several cyanobacterial species forming intracellular amorphous calcium carbonates (ACC). 35,83,125 The simplest explanation for microorganisms serving as "whole-cell biocatalysts" for calcifi-cation would be their ability to influence local Ca 2+ or CO 3 2À saturation states. 126,127 All these processes are related to the evolution of a CCM by cyanobacteria as a strategy to overcome the particularly low affinity of the enzyme RubisCO to bind CO 2 . ...
... 24 The specific hunt for such organisms and the identification of possible model strains that will help to understand the calcification process in terrestrial cyanobacteria will allow an update of previous experiments, 72,188 leading to more sophisticated insights into the calcification process mediated by terrestrial relatives. Here, the advances for intracellular cyanobacterial Ca 2+ accumulation should also be considered, 35 and a combination of experiments will help to uncover the ecological significance of the sheath solidification and therefore tackle the recent theories ( Figure 6). (2) Biochemistry of the calcification process: microbial calcification with the formation of CaCO 3 sheaths around the microbial cells in soils and engineering applications (such as fracture fillings in concrete) does not directly imply an effective cementation of the pore space resulting in an increased water and mechanical stability. ...
Cyanobacteria are the oldest photoautotrophic lineage that release oxygen during photosynthesis, an ability
that possibly evolved as far as 3.5 billion years ago and changed the Earth’s environment—both in water and
on land. Linked to the mechanism of carbon accumulation by cyanobacteria during photosynthesis are their
calcifying properties, a process of biologically mediated mineralization of CO2 by precipitation with calcium
to CaCO3. In recent decades, scientific research has mainly focused on calcifying cyanobacteria from aquatic
habitats, while their terrestrial relatives have been neglected. This review not only presents the ecology of
terrestrial calcifying cyanobacteria in caves and biocrusts but also discusses recent biotechnological applications,
such as the production of living building materials through microbial-induced carbonate precipitation
for structural engineering, which has the potential to open a new and efficient pathway for mitigating
climate change, e.g., as carbon capture and storage technology.
... Phylogenetic analysis of conserved protein markers supported that G. lithophora defined a new cyanobacterial order, the Gloeomargaritales (Moreira et al., 2018). G. lithophora exhibits the unusual ability to synthesize large amounts of intracellular amorphous calcium (Ca) carbonate inclusions, sometimes enriched in barium and strontium (Couradeau et al., 2012;Benzerara et al., 2014). While cyanobacteria have been known for long to induce extracellular Ca carbonate precipitation as a consequence of the environmental pH increase triggered by photosynthesis (Riding, 2006), this intracellular biomineralization process was only recently discovered in several cyanobacterial lineages (Cam et al., 2017;Benzerara et al., 2022). ...
... Up to now, G. lithophora was the only isolated species within the Gloeomargaritales. Nevertheless, environmental surveys identified a large diversity of related 16S rDNA sequences in diverse freshwater environments, mostly microbialites and thermophilic microbial mats (Ragon et al., 2014). Moreover, Gloeomargaritalike cells containing intracellular carbonates have also been observed by electron microscopy in microbial mat samples of the Meskoutine hot spring in Algeria (Amarouche-Yala et al., 2014), although they have never been grown in the laboratory. ...
... 16S rRNA genes were amplified by PCR using the two Gloeomargaritales-specific primers 69 F-Gloeo (AAGTCGAACGGGGKWGCAA) and 1227 R-Gloeo (GATCTGAACTGAGACCAAC), which produced amplicons of ~1200 bp (Ragon et al., 2014). PCR reactions were done in 25 µl of reaction buffer, containing 1 µl of the eluted DNA, 1.5 mM MgCl 2 , dNTPs (10 nmol each), 20 pmol of each primer, and 0.2 U Taq platinum DNA polymerase (Invitrogen). ...
ABSTRACT
A unicellular cyanobacterium, strain VI4D9, was isolated from thermophilic microbial mats thriving in a hot spring of the Ahousaht territory of Vancouver Island, Canada, and characterized using optical and electron microscopy, genome sequencing and cultivation approaches. The cells were elongated rods (5.1 μm in length and 1.2 μm in width, on average). Their UV visible absorption spectra revealed that they contain chlorophyll a, phycocyanin and carotenoids. Transmission electron microscopy showed the presence of thylakoids concentrated on one side of the cells. The strain grew within a temperature range of 37–50°C, with an optimum growth at 45°C. Its genome had a size of 3 049 282 bp and a DNA G + C content of 51.8 mol%. The cells contained numerous intracellular spherical granules easily visible under scanning electron microscopy. Energy dispersive X-ray spectroscopy revealed that these granules were made of Ca-, Ba- and Sr-containing carbonates. A phylogenetic 16S rRNA gene tree robustly placed this strain as sister to several environmental sequences and the described species Gloeomargarita lithophora, also characterized by the possession of intracellular carbonate inclusions. We consider strain VI4D9 to represent a new Gloeomargarita species based on its marked phenotypic differences with G. lithophora, notably, its thermophilic nature and different thylakoid organization, therefore we propose the name Gloeomargarita ahousahtiae sp. nov. The type strain is VI4D9 (Culture Collection of Algae and Protozoa strain 1472/1; Laboratorio de Algas Continentales Mexico strain LAC 140). Gloeomargarita ahousahtiae is the second species described within the recently discovered order Gloeomargaritales.
HIGHLIGHTS
● Gloeomargarita ahousahtiae is a new thermophilic cyanobacterium.
● Growth temperature and thylakoid morphology differentiate G. ahousahtiae and G. lithophora.
● All described Gloeomargaritales synthesize intracellular carbonate inclusions.
... Une précipitation intracellulaire de CaCO 3 a été observée chez certaines cyanobactéries [40][41][42] et chez la protéobactérie Achromatium oxaliferum [43]. La biocalcification extracellulaire reste néanmoins la plus couramment observée au sein des bactéries. ...
... Beaucoup d'espèces bactériennes possèdent une anhydrase carbonique ; celle-ci a en effet été identifiée dans des espèces à la fois d'eau douce et marines, avec différents types trophiques, aussi bien en conditions aérobies que anaérobies [83]. La biocalcification impliquant l'anhydrase carbonique a été essentiellement étudiée chez des bactéries photosynthétiques [41,50,[84][85][86] ou hétérotrophes pour leur capacité à séquestrer CO 2 sous la forme de CaCO 3 [87][88][89]. La contribution des bactéries photosynthétiques, telles que les cyanobactéries, à la précipitation et à la sédimentation de CaCO 3 , via l'anhydrase carbonique, est importante et joue un rôle majeur dans les formations géologiques notamment dans la formation des stromatolites [41,50,90,91]. ...
... La biocalcification impliquant l'anhydrase carbonique a été essentiellement étudiée chez des bactéries photosynthétiques [41,50,[84][85][86] ou hétérotrophes pour leur capacité à séquestrer CO 2 sous la forme de CaCO 3 [87][88][89]. La contribution des bactéries photosynthétiques, telles que les cyanobactéries, à la précipitation et à la sédimentation de CaCO 3 , via l'anhydrase carbonique, est importante et joue un rôle majeur dans les formations géologiques notamment dans la formation des stromatolites [41,50,90,91]. Kamennaya et al. ont répertorié les principales cyanobactéries qui précipitent CaCO 3 , montrant ainsi que le genre Synechococcus est le plus représenté [85]. ...
La précipitation du carbonate de calcium (CaCO 3 ) biologiquement induite en milieu marin joue un rôle important dans le cycle biogéochimique du carbone. Cette biocalcification est gouvernée par quatre facteurs clés : le taux de carbone inorganique dissous dont dépend le taux de carbonates (CO 3 ²⁻ ) dans le système, le taux d’ions calciques (Ca ²⁺ ), le pH et la disponibilité des sites de nucléation c’est-à-dire des zones de cristallisation primaire de la phase solide du minéral. Les bactéries impliquées dans la biocalcification marine vont alors agir sur un ou plusieurs de ces facteurs. Ce processus naturel, qui se produit dans divers contextes géologiques, peut être imité afin de développer un certain nombre de technologies permettant la séquestration des métaux lourds, la protection des métaux contre la corrosion, la restauration et le renforcement de matériaux préexistants et la consolidation de matériaux granulaires. Cette étude passe en revue les différentes activités métaboliques microbiennes menant à la précipitation du CaCO 3 ainsi que leurs applications potentielles en milieu marin.
... Several studies have attempted to identify the physiological function of the intracellular inclusions of ACC in microorganisms and the molecular mechanisms behind their formation and stabilization. It has been suggested that the ACC mineral inclusions in cyanobacteria could (i) have a role in the regulation of intracellular pH and alkalinity (Benzerara et al., 2014;Couradeau et al., 2012;De Wever et al., 2019), (ii) act as ballast by increasing cell density to adapt the position of these microorganisms in the water column (Couradeau et al., 2012;De Wever et al., 2019), (iii) constitute carbon reserves (De Wever et al., 2019), and/or (iv) be involved in cell division (Benzerara et al., 2014). In the green microalgae within the class Chlorodendrophyceae, micropearls have been suggested to constitute Ca deposits that could be linked to the formation of the flagella and theca, as well as to the motility and buoyancy of the cells (Martignier et al., 2020). ...
... Several studies have attempted to identify the physiological function of the intracellular inclusions of ACC in microorganisms and the molecular mechanisms behind their formation and stabilization. It has been suggested that the ACC mineral inclusions in cyanobacteria could (i) have a role in the regulation of intracellular pH and alkalinity (Benzerara et al., 2014;Couradeau et al., 2012;De Wever et al., 2019), (ii) act as ballast by increasing cell density to adapt the position of these microorganisms in the water column (Couradeau et al., 2012;De Wever et al., 2019), (iii) constitute carbon reserves (De Wever et al., 2019), and/or (iv) be involved in cell division (Benzerara et al., 2014). In the green microalgae within the class Chlorodendrophyceae, micropearls have been suggested to constitute Ca deposits that could be linked to the formation of the flagella and theca, as well as to the motility and buoyancy of the cells (Martignier et al., 2020). ...
... In addition, the fact that micropearls are not randomly segregated among the daughter cells during cell division indicates that their location is actively controlled by the cell and can be relocated. In cyanobacteria forming intracellular ACC inclusions, it has been postulated that the spatial organization of the inclusions within the cells may involve cytoskeletal proteins (Benzerara et al., 2014;Li et al., 2016). ...
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 ⁹⁰Sr 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.
... Sample 6 contains the most diverse community including abundant diatoms, the Cyanobacteria Dactylococcopsis, and the unassigned Cyanophyceae ASV3, a possible relative of Oculatella. The phototrophic cyanobacteria Cyanothece is recorded, a biota that commonly mediates calcium carbonate precipitation (Benzerara et al., 2014). Chroococcidiopsis and Coleofasciculus are species recognised to precipitate calcium carbonate from photosynthesis (Benzerara et al., 2014). ...
... The phototrophic cyanobacteria Cyanothece is recorded, a biota that commonly mediates calcium carbonate precipitation (Benzerara et al., 2014). Chroococcidiopsis and Coleofasciculus are species recognised to precipitate calcium carbonate from photosynthesis (Benzerara et al., 2014). The phototrophic biota Chroococcidiopsis found in Samples 1, 2, 4 and 6 is known for association with microbial mat communities (Oren, 2015). ...
A tufa mound developed at La Saline Lake, an oxbow of the Athabasca River in the Athabasca Oil Sands deposit of north‐east Alberta, is characterised by an unusual emplacement of a gypsum caprock. This two‐tiered architecture resulted from the bicarbonate‐saturated groundwater flow along Upper Devonian limestone being redirected deeper and encountering the halite–anhydrite dissolution trend within the underlying Middle Devonian Prairie Evaporite Formation, 175 to 200 m below. Migrations up‐section of sulphate‐saturated brine resulted in the gypsum caprock on the tufa mound and discharge of a sulphate‐saturated brine spring with total dissolved solids of ca 80,000 mg/L. The brine spring is bifurcated with flows to the south‐west and north‐west. Calcite–gypsum thrombolytic bottom sediments along the south‐western branch were covered by a halite deposit and subsequently a gypsum crust with a microbial community dominated by the cyanobacteria Coleofasciculus chthonoplastes. The thrombolite contact zone with the halite–gypsum encrustation has a more diversified community with the cyanobacteria Dactylococcopsis. Cyanobacterial mats that wrap around the bulbous gypsum crust protuberances distributed along the brine pool bottom surfaces have significant eukaryotic diversity, represented by the heterotrophic Ochrophyte Paraphysomonas. In contrast, sediments accumulated along the adjacent spring branch flow to the north‐west were thicker and clogged by abundant decomposed and fermented floral debris, unlike the deposit accumulated along the south‐western branch. This resulted in an oxygen‐depleted anaerobic environment dominated by sulphate‐reducing bacteria resulting in a calcite‐rich and sulphate‐starved anaerobic sediment with ca 20% elemental sulphur and emanation of H2S gas.
... This charge facilitates the adsorption of cations such as calcium, magnesium, and iron, providing essential nucleation sites for the formation of minerals like dolomite, calcite, and ferro-dolomite [61,86,87]. In parallel with extracellular mineralization, intracellular bio-mineralization occurs in certain prokaryotic bacteria, algae, etc. Benzerara et al. found that amorphous calcium carbonate can be formed by some cyanobacterial cells [88]. Yan Huaxiao and other researchers utilized Bacillus subtilis Daniel-1 to study biomineralization and found that intracellular and extracellular mineralization can occur simultaneously and that the two have a synergistic effect under certain conditions [89]. ...
... This charge facilitates the adsorption of cations calcium, magnesium, and iron, providing essential nucleation sites for the form minerals like dolomite, calcite, and ferro-dolomite [61,86,87]. In parallel with extra mineralization, intracellular bio-mineralization occurs in certain prokaryotic bac gae, etc. Benzerara et al. found that amorphous calcium carbonate can be formed cyanobacterial cells [88]. Yan Huaxiao and other researchers utilized Bacillus subt iel-1 to study biomineralization and found that intracellular and extracellular min tion can occur simultaneously and that the two have a synergistic effect under conditions [89]. ...
The goals of carbon neutrality and peak carbon have officially been proposed; consequently, carbon dioxide utilization and sequestration technology are now in the limelight. Injecting carbon dioxide into reservoirs and solidifying and sequestering it in the form of carbonates after a series of geochemical reactions not only reduces carbon emissions but also prevents carbon dioxide from leaking out of the formation. Carbon dioxide mineralization sequestration, which has good stability, has been considered the best choice for large-scale underground CO2 sequestration. To provide a comprehensive exploration of the research and prospective advancements in CO2 mineralization sequestration within Chinese oil and gas reservoirs, this paper undertakes a thorough review of the mechanisms involved in CO2 mineralization and sequestration. Special attention is given to the advancing front of carbon dioxide mineralization, which is driven by microbial metabolic activities and the presence of carbonic anhydrase within oil and gas reservoirs. The paper presents an in-depth analysis of the catalytic mechanisms, site locations, and structural attributes of carbonic anhydrase that are crucial to the mineralization processes of carbon dioxide. Particular emphasis is placed on delineating the pivotal role of this enzyme in the catalysis of carbon dioxide hydration and the promotion of carbonate mineralization and, ultimately, in the facilitation of efficient, stable sequestration.
... An increasing diversity of bacteria forming iACC has been discovered lately, including cyanobacteria [21] and magnetotactic bacteria affiliated to the Proteobacteria phylum [22]. The function of these iACC granules remains uncertain [23]. ...
... The widely-studied cyanobacterium S. elongatus PCC 7942 does not contain ccyA and does not form iACC [21]. In order to test the impact of the expression of the ccyA gene on such a cyanobacterium, we introduced an autonomously replicating expression plasmid (circular DNA), namely the RSF1010-derived pC vector [25,26] or its derivatives overexpressing the ccyA gene from two iACC-forming cyanobacteria, namely Gloeomargarita lithophora and Synechococcus sp. ...
... By contrast, the use of a DIC-CM is poorly captured by δ 13 C POC , although recognition of active DIC uptake has often been based on this signal (by reduced isotopic fractionation with DIC; e.g., Beardall et al., 1982;Erez et al., 1998;Riebesell et al., 2000). Most interestingly, intra-cellular amorphous Ca carbonates (iACC) are formed in some of the cyanobacteria from Alchichica microbialites, possibly due to supersaturated intra-cell media following active DIC uptake through a DIC-CM (Couradeau et al., 2012;Benzerara et al., 2014). While the link between DIC-CM and iACC still needs to be demonstrated (Benzerara et al., 2014), Table 2. Isotopic fractionation between DOC and DIC and between DOC and POC, where 13 C x−y = δ 13 C x − δ 13 C y is the apparent fractionation and ε is computed as the actual metabolic isotopic discrimination between CO 2 and DOC. ...
... Most interestingly, intra-cellular amorphous Ca carbonates (iACC) are formed in some of the cyanobacteria from Alchichica microbialites, possibly due to supersaturated intra-cell media following active DIC uptake through a DIC-CM (Couradeau et al., 2012;Benzerara et al., 2014). While the link between DIC-CM and iACC still needs to be demonstrated (Benzerara et al., 2014), Table 2. Isotopic fractionation between DOC and DIC and between DOC and POC, where 13 C x−y = δ 13 C x − δ 13 C y is the apparent fractionation and ε is computed as the actual metabolic isotopic discrimination between CO 2 and DOC. In Alchichica, δ 13 C DOC was not measured at 5 m, and its value at 10 m was used in this calculation of 13 C DOC-POC . ...
The dissolved organic carbon (DOC) reservoir plays a critical role in the C cycle of marine and freshwater environments because of its size and implication in many biogeochemical reactions. Although it is poorly constrained, its importance in ancient Earth's C cycles is also commonly invoked. Yet DOC is rarely quantified and characterized in modern stratified analogues. In this study, we investigated the DOC reservoirs of four redox-stratified alkaline crater lakes in Mexico. We analyzed the concentrations and isotopic compositions of DOC throughout the four water columns and compared them with existing data on dissolved inorganic and particulate organic C reservoirs (DIC and POC). The four lakes have high DOC concentrations with great variability between and within the lakes (averaging 2 ± 4 mM; 1 SD, n=28; i.e., from ∼ 15 to 160 times the amount of POC). The δ13CDOC signatures also span a broad range of values from -29.3 ‰ to -8.7 ‰ (with as much as 12.5 ‰ variation within a single lake). The prominent DOC peaks (up to 21 mM), together with their associated isotopic variability, are interpreted as reflecting oxygenic and/or anoxygenic primary productivity through the release of excess fixed carbon in three of the lakes (Alberca de los Espinos, La Preciosa, and Atexcac). By contrast, the variability of [DOC] and δ13CDOC in the case of Lake Alchichica is mainly explained by the partial degradation of organic matter and the accumulation of DOC in anoxic waters. The DOC records detailed metabolic functions such as active DIC-uptake and DIC-concentrating mechanisms, which cannot be inferred from DIC and POC analyses alone but which are critical to the understanding of carbon fluxes from the environment to the biomass. Extrapolating our results to the geological record, we suggest that anaerobic oxidation of DOC may have caused the very negative C isotope excursions in the Neoproterozoic. It is, however, unlikely that a large oceanic DOC reservoir could overweigh the entire oceanic DIC reservoir. This study demonstrates how the analysis of DOC in modern systems deepens our understanding of the C cycle in stratified environments and helps to set boundary conditions for the Earth's past oceans.
... But contrary to common belief, several cyanobacterial species perform Ca-carbonate biomineralization intracellularly. Indeed, Benzerara et al. (2014) conducted a study of intracellular CaCO3 biomineralization on 68 different cyanobacterial strains. For each strain, they performed Scanning Electron Microscopy (SEM) observations, Scanning Transmission X-ray Microscopy (STXM) and phylogenetic analyses. ...
... STEM-EDX map is shown in C. Calcium, green; phosphorus, red; carbon, blue. FromBenzerara et al. (2014). ...
... From the literature, many cyanobacterial species encourage the biosorption process, which results in the biomineralization process lately. In general, it is stated that the biomineralization in cyanobacteria is well known (Benzerara et al., 2014). The most studied cyanobacterial species for Ca-carbonate biomineralization is Synechococcus strains (Liang et al., 2013). ...
... The most studied cyanobacterial species for Ca-carbonate biomineralization is Synechococcus strains (Liang et al., 2013). Benzerara et al. (2014) found in a study that three Synechococcus strains were involved in intracellular and extracellular Ca-carbonate biomineralization. ...
The biodesalination potential at different levels of salinity of Phormidium keutzingianum (P. keutzingianum) was investigated. A wide range of salinity from brackish to hypersaline water was explored in this study to ensure the adaptability of P. keutzingianum in extreme stress conditions. Brackish to hypersaline salt solutions were tested at selected NaCl concentrations 10, 30, 50, and 70 g.L⁻¹. Chloride, pH, nitrate, and phosphate were the main parameters measured throughout the duration of the experiment. Biomass growth estimation revealed that the studied strain is adaptable to all the salinities inoculated. During the first growth phase (till day 20), chloride ion was removed up to 43.52% and 45.69% in 10 and 30 g.L⁻¹ of salinity, respectively. Fourier transform infrared spectrometry analysis performed on P. keutzingianum showed the presence of active functional groups at all salinity levels, which resulted in biosorption leading to the bioaccumulation process. Samples for scanning electron microscopy (SEM) analysis supported with electron dispersive X-ray spectroscopy analysis (EDS) showed NaCl on samples already on day 0. This ensures the occurrence of the biosorption process. SEM-EDS results on 10th d showed evidence of additional ions deposited on the outer surface of P. keutzingianum. Calcium, magnesium, potassium, sodium, chloride, phosphorus, and iron were indicated in SEM-EDS analysis proving the occurrence of the biomineralization process. These findings confirmed that P. keutzingianum showed biomass production, biosorption, bioaccumulation, and biomineralization in all salinities; hence, the strain affirms the biodesalination process.
... Cyanothece sp. PCC 7425, which display the inclusions as polyphosphate and ACC granules (Benzerara et al., 2014;Görgen et al., 2021). All physio-biochemical characteristics and antibiotic resistance behaviour of strain MLN22 are shown in Table S1. ...
Groundwater contamination by fluoride (F⁻) poses a notable hazard to the environment, agriculture and human well-being. The present study investigates the potential use of urease-driven microbially induced carbonate precipitation (MICP) for defluoridation from natural groundwater. Previous reports have shown that the urease driven MICP technique can naturally mineralize heavy metal contaminants from the environment, but no such work exists for fluoride ions. For this study, the highly F⁻ resistant ureolytic bacterium Micrococcus yunnanensis MLN22 was isolated and characterized for its urease and CaCO3 production activity. In batch experiments using MICP technique, strain MLN22 showed a maximum F⁻ removal efficacy of 83.4% at optimal conditions (5.0 mg L⁻¹ initial F⁻ concentration, 250 mg L⁻¹ Ca²⁺, 15 g L⁻¹ urea and pH 8.0). The dense and less porous aggregates indicate the morphological features of F⁻ treated bioprecipitates characterized by microscopic analysis using SEM. Moreover, F⁻ is adsorbed and precipitated in two different form of biological crystals (BC) such as CaF2 and Ca5(PO4)3F, which was confirmed by microscopic (SEM and SEM–EDS) and spectroscopic (FTIR and XRD) analysis. Freundlich's isotherm model best described the adsorption mechanism of F⁻ onto BC and showed a multi-layered heterogeneous adsorption pattern. Highlighting its potential for practical applications, the optimized BC extracted from M. yunnanensis MLN22 was used in natural groundwater contaminated with F⁻ (4.95 mg L⁻¹) and reached maximum removal ability of 98.4% at a BC dose of 1.5 g L⁻¹ after 48 h. The final statement of this research is that the urease-driven MICP technique contributes to the production of BC in the defluoridation of F⁻ contaminated groundwater and represents a sustainable and cost-effective solution for fluoride remediation.
Graphical Abstract
... These are hotspots of microbial activity that drive biogeochemical processes sustaining important ecological functions in drylands. Such functions include the alteration of F c (Darrouzet-Nardi et al., 2018), the modification of soil physico-chemical properties such as pH (Büdel et al., 2004;Wu et al., 2013), porosity (Miralles-Mellado et al., 2011), soil water and SOC content (Chamizo et al., 2016), as well as enhanced mineral weathering and biomineralization (Benzerara et al., 2014;Büdel et al., 2004;Chen et al., 2014;Souza-Egipsy et al., 2004). However, considering that the lack of water hinders biological activity and most soil CO 2 consumption processes, it is important to comprehend how these components interact during dry spells. ...
... Bacteria can also actively control the biomineralization process, as evidenced in the case of the Gammaproteobacteria genus Achromatium (e.g., Achromatium oxaliferum; Babenzien, 1991), capable of producing intracellular calcium carbonate precipitates (Gray, 2006;Gray & Head, 2014). Such a trait is also shared by an increasing diversity of cyanobacterial species (Benzerara et al., 2014;Couradeau et al., 2012;Gaëtan et al., 2023) as well as non-phototrophic bacteria (Monteil et al., 2021). While the fate of these precipitates is not clear after cell death, their potential role in micrite formation within sediments should be considered in the future. ...
Micritization is an early diagenetic process that gradually alters primary car-bonate 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 geochemi-cal 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.
... Imaging by SEM revealed the complex structure of the halloysite and latex and the morphological differences of the bacteria. EDX is already widely used in other fields, but only starting to find applications in microbiology, for example, to detect food pathogens (via C, O, and N) or to detect accumulated calcium carbonate in cyanobacteria (27,45,46). This is the first time EDX has been used in the context of biocoatings and is an ingenious method to identify components and the structural complexity of biocoatings not only by shape but by their elemental composition. ...
Biocoatings, in which viable bacteria are immobilized within a waterborne polymer coating for a wide range of potential applications, have garnered greater interest in recent years. In bioreactors, biocoatings can be ready-to-use alternatives for carbon capture or biofuel production that could be reused multiple times. Here, we have immobilized cyanobacteria in mechanically hard biocoatings, which were deposited from polymer colloids in water (i.e ., latex). The biocoatings are formed upon heating to 37°C and fully dried before rehydrating. The viability and oxygen evolution of three cyanobacterial species within the biocoatings were compared. Synechococcus sp. PCC 7002 was non-viable inside the biocoatings immediately after drying, whereas Synechocystis sp. PCC 6803 survived the coating formation, as shown by an adenosine triphosphate (ATP) assay. Synechocystis sp. PCC 6803 consumed oxygen (by cell respiration) for up to 5 days, but was unable to perform photosynthesis, as indicated by a lack of oxygen evolution. However, Chroococcidiopsis cubana PCC 7433, a strain of desiccation-resistant extremophilic cyanobacteria, survived and performed photosynthesis and carbon capture within the biocoating, with specific rates of oxygen evolution up to 0.4 g of oxygen/g of biomass per day. Continuous measurements of dissolved oxygen were carried out over a month and showed no sign of decreasing activity. Extremophilic cyanobacteria are viable in a variety of environments, making them ideal candidates for use in biocoatings and other biotechnology.
IMPORTANCE
As water has become a precious resource, there is a growing need for less water-intensive use of microorganisms, while avoiding desiccation stress. Mechanically robust, ready-to-use biocoatings or “living paints” (a type of artificial biofilm consisting of a synthetic matrix containing functional bacteria) represent a novel way to address these issues. Here, we describe the revolutionary, first-ever use of an extremophilic cyanobacterium ( Chroococcidiopsis cubana PCC 7433) in biocoatings, which were able to produce high levels of oxygen and carbon capture for at least 1 month despite complete desiccation and subsequent rehydration. Beyond culturing viable bacteria with reduced water resources, this pioneering use of extremophiles in biocoatings could be further developed for a variety of applications, including carbon capture, wastewater treatment and biofuel production.
... Filamentous N 2 -fixing cyanobacteria are known to take up excess phosphate and polymerize it in the form of polyphosphate granules for intracellular storage without immediate growth (Allen 1984, Larsson et al. 2001, Benzerara et al. 2014. In general, the availability of excess phosphate did not cause a high growth of the 3 bloom-forming filamentous cyanobacteria genera in our study. ...
Following the spring bloom in the northern Baltic Sea, nitrogen limits phytoplankton growth and there is typically a residual phosphate concentration (>0.2 µmol L-1) remaining that is often assumed to induce the recurring blooms of nitrogen-fixing cyanobacteria. However, these cyanobacterial blooms typically occur 2–3 months later during summer months, when the phosphate concentration has been depleted, and it is unclear what organisms take up the excess phosphate. We studied the removal potential of excess phosphate (0.55 µmol L-1) at different temperatures (10, 13, 16°C) and with or without nitrogen addition in an indoor 20 L tank experiment. In addition, we followed the element pools and plankton community composition. As expected, the phosphate uptake rate was up to 3-fold faster in nitrogen-amended tanks compared to non-amended ones, but complete drawdown of phosphate also occurred under severe nitrogen limitation. The uptake ratio of dissolved inorganic nitrogen to phosphorus was 4.6, which is substantially lower than the Redfield ratio 16, and indicates an excessive phosphate removal potential relative to nitrogen. A large part of the excess phosphate ended up in the particulate pool, which has a higher potential to sink out from the surface. The nitrogen-fixing cyanobacteria, Nodularia spumigena, grew close to summer bloom concentrations only in the highest experimental temperature. However, the combined biovolume of all three major bloom-forming cyanobacteria accounted for only 5.3% of the total autotropic biovolume and their potential phosphate uptake was calculated to be <0.1% of the excess phosphate available at the beginning of the study. Thus, our results demonstrate that the contribution of filamentous cyanobacteria to the removal of excess phosphate is small.
... Biogeochemical cycles in the sea, i.e., the cyclic fluxes of elements and inorganic compounds between the community and the ecotope, in which biogenic and chemogenic processes are coupled, are responsible for both physicochemical phenomena, such as mineralization and sedimentation, and for bioproduction processes [1]. Communities of cyanobacteria and diatoms dominate marine epilithon [2][3][4][5][6] and are actively involved in marine biogeochemical cycles, especially in biomineralization on substrates [7][8][9][10][11][12][13]. Some cyanobacterial species can biomineralize carbonates intracellularly [14]. ...
Rocky seabeds, as an integral part of ecotopes in marine ecosystems, are actively inhabited by diatoms and cyanobacteria. It is currently unknown whether the element contents in the surface layer of seabed rocks affect the epilithon species composition and abundance in microphytobenthos communities in the sea. The results of this study on the rock surface element composition and correlation analysis of the element contents with the abundance of epilithon diatoms and cyanobacteria in three bays in Sevastopol (Black Sea) are presented. Ca, Fe, and Si were the major elements with the largest weight fraction in the rock surface layer. Using cluster analysis, the differentiation of samples in the content and distribution of these three elements was shown. In total, 63 taxa of diatoms and 20 species of cyanobacteria were found, with their abundance ranging from 14,000 to 17,6000 cells/cm 2 and from 12,000 to 1,198,000 cells/cm 2 , respectively. In general, it was found that the elemental composition of the rock surface is not a decisive factor affecting the total abundance of the benthic diatom and cyanobacterial communities as no strong correlations with any element contents were observed. However, when analyzing the abundance of populations of certain largely non-dominant species, the majority of diatoms showed noticeable (r = 0.5-0.7) to very high (r = 0.9-0.99) correlations with Fe. The highest positive correlations were noted for the diatoms Bacil-laria paxillifer and Navicula directa with Fe. For the cyanobacteria Chroococcus minutus, Pseudanabaena minima, and Spirulina subsalsa, strong positive correlations with Ca and negative correlations with Si were observed. The correlations with Fe were very strong and negative for Lyngbya confervoides and strong and positive for Kamptonema laetevirens and Phormidium holdenii.
... This finding revealed that urea metabolism is not the only process involved in the calcium carbonate precipitation by bacteria. Induction of calcium carbonate precipitation by microorganisms can also involve nonureolytic pathway, for example photosynthesis, as found in the Cyanobacteria group 30) .The formation of CaCO3 precipitation through the photosynthesis pathway begins with the capture of CO2 by cells and will concentrate intracellularly. Then the CO2-sequestering process will cause the environment in the bacterial cells to become alkaline, thus encouraging the formation of bicarbonate. ...
The application of calcium carbonate precipitation-inducing bacteria in the past two decades has become an alternative in green technology development, particularly in construction as self healing agent of concrete and in the waste treatment as contaminants remover (e.g., radioactive pollutants and heavy metals). This study aimed to obtain potential bacterial isolates from rock samples that can induce calcium carbonate precipitation and characterize the precipitate produced. This study began with the isolation of bacteria from rock samples taken from an arid area (Malaka, East Nusa Tenggara) using Nutrient Broth-urea-CaCl2 media. Colonies showing the formation of calcium carbonate precipitation were then purified and selected for the ureolytic activity assay using Christensen’s urea agar. Bacterial isolates with high ureolytic activity were selected for further characterization of their ability to produce calcium carbonate precipitation. Five bacterial isolates with the best precipitation ability were obtained. Each isolate had a different ability to induce calcium carbonate precipitation, and the resulting crystal morphology was also different. Isolate M 2.6 was the best bacterial isolate capable of inducing the highest calcium carbonate precipitation, which was 2.6 g/L. This isolate was later identified as Mesobacillus campisalis. The calcium carbonate precipitate produced by the five selected isolates ranged from 1.4 g/L to 2.6 g/L. The Field Emission Scanning Electron Microscopy (FESEM)-Energy Dispersive Spectroscopy (EDS) characterization revealed that the precipitate resulting from the bacterial isolates was calcium carbonate. This was indicated by the mass percent value, which was dominated by three main elements, namely O, Ca, and C, with a mass ratio of approximately matching CaCO3.
... De plus, cette souche possède un set de Glutathion-S-transférase (GST) différent de ceux de Synechocystis PCC 6803 et Synechococcus PCC 7942. Les GST sont impliqués dans la gestion de nombreux stress (Kammerscheit et al., 2019a(Kammerscheit et al., , 2019b (Bandyopadhyay et al., 2013) Récemment, l'équipe de Karim Benzerara avec laquelle le laboratoire collabore s'est intéressée à la capacité de cette souche à réaliser la biominéralisation intracellulaire du carbonate de calcium (Benzerara et al., 2014;Li et al., 2016;Blondeau et al., 2018). Les auteurs ont montré la présence de 2 à 20 inclusions de carbonate de calcium amorphe dans le cytoplasme de la cellule entourées par une monocouche lipidique ou des protéines. ...
Grâce à leur photosynthèse oxygénique, les cyanobactéries peuvent produire des composés d'intérêt à partir de l’énergie solaire, du CO₂ atmosphérique et de l’eau (douce et marine) même polluée. Au laboratoire, on s'intéresse aux terpènes (molécules odorantes et volatiles) qui ont de nombreuses applications pour la cosmétique (parfums), la santé (antimicrobiens) et l'environnement (biocarburants). Peu d’études ont montré la production de terpènes par les cyanobactéries et les rendements obtenus sont faibles et difficilement comparables. L’objectif de mon travail de thèse était de combiner la diversité biologique de 5 cyanobactéries dotées d'atouts différents (Synechocystis PCC 6803, Synechococcus PCC 7942 et PCC 7002, Cyanothece PCC 7425 et PCC 7822), la diversité chimique de 5 terpènes (bisabolène, farnésène, limonène, pinène et santalène) et les outils génétiques polyvalents du laboratoire, pour générer de bons producteurs. Dans ce but j'ai développé la génétique de Cyanothece PCC 7425 (Chenebault et al., 2020). J'ai contribué à montrer que certaines de nos cyanobactéries produisent mieux certains terpènes, validant notre démarche. Ainsi, Synechocystis PCC 6803 produit plus de bisabolène et de farnésène que les autres cyanobactéries et Synechococcus PCC 7002 est le meilleur châssis pour la production du limonène. En outre, j'ai montré que Cyanothece PCC 7425 peut produire des terpènes à partir d'eaux polluées par de l’urée ou du calcium. Enfin, la stabilité des rendements a été analysée sur plusieurs mois.
... 06 biomineralize amorphous calcium carbonate. These calcium carbonate inclusions are located mostly in the cellular poles of the cyanobacterium(Benzerara et al., 2014;De Wever et al., 2019). ...
Cyanobacteria are diverse photosynthetic microorganisms able to produce a myriad of bioactive chemicals. To make possible the rational exploitation of these microorganisms, it is fundamental to know their metabolic capabilities and to have genomic resources. In this context, the main objective of this research was to determine the genome features and the biochemical profile of Synechococcus sp. UCP002. The cyanobacterium was isolated from the Peruvian Amazon Basin region and cultured in BG-11 medium. Growth parameters, genome features, and the biochemical profile of the cyanobacterium were determined using standardized methods. Synechococcus sp. UCP002 had a specific growth rate of 0.086 ± 0.008 μ and a doubling time of 8.08 ± 0.78 h. The complete genome of Synechococcus sp. UCP002 had a size of ∼3.53 Mb with a high coverage (∼200x), and its quality parameters were acceptable (completeness = 99.29%, complete and single-copy genes = 97.5%, and contamination = 0.35%). Additionally, the cyanobacterium had six plasmids ranging from 24 to 200 kbp. The annotated genome revealed ∼3,422 genes, ∼ 3,374 protein-coding genes (with ∼41.31% hypothetical protein-coding genes), two CRISPR Cas systems, and 61 non-coding RNAs. Both the genome and plasmids had the genes for prokaryotic defense systems. Additionally, the genome had genes coding the transcription factors of the metalloregulator ArsR/SmtB family, involved in sensing heavy metal pollution. The biochemical profile showed primary nutrients, essential amino acids, some essential fatty acids, pigments (e.g., all-trans-β-carotene, chlorophyll a, and phycocyanin), and phenolic compounds. In conclusion, Synechococcus sp. UCP002 shows biotechnological potential to produce human and animal nutrients and raw materials for biofuels and could be a new source of genes for synthetic biological applications.
... Microbial activity facilitates the formation of authigenic minerals directly and indirectly through the control and induction of mineralization, respectively . It is found that calcite precipitates can form both within and external to cyanobacteria cells in saturated aqueous solution (Benzerara et al., 2014; (Villalobos et al., 2003;Bargar et al., 2005), implying that the crystallization and aggregation processes of todorokite is related to microbial activity (Biondi et al., 2020). ...
Carbonate-type Mn deposits developed at the top of the Ediacaran Doushantuo Formation (Marinoan glacial aftermath) along the northern margin of the Yangtze Block, South China, provide an exceptional opportunity to study Mn redox cycling in deep time, which remains a controversial topic of Mn biogeochemistry. Here we conduct integrated petrological and geochemical work, which provides constraint on ancient Mn cycling. The results show that Mn oxidizing microorganisms may fix CO2 into organic matter by oxidizing Mn(II). This process provides energy for metabolism of the microorganisms under obligatory oxidation conditions in natural geological environments. At the same time, Mn(II) is oxidized to unstable todorokite, with accompanying Co and Ce oxidation and enrichment. Under suboxic conditions, heterotrophic Mn-reducing bacteria use organic matter as an electron donor and Mn bio-oxide as a terminal electron acceptor to generate Mn(II) and 12C-rich dissolved inorganic carbon (DIC; carbonate and/or bicarbonate). Furthermore, microorganisms and macroalgae also provide nucleation sites for the precipitation of Mn carbonate minerals with structures consistent with microbially precipitated carbonates. Spherical and ellipsoidal Ca-rich rhodochrosite was formed in the syngenetic stage and cemented by Mg-rich kutnohorite in the early diagenetic stage. Microorganisms thus play an important role in Mn redox cycling and precipitation of Mn carbonate minerals, in a possibly universal phenomenon in geological evolution. The bloom of microorganisms and associated formation of mineral deposits may be a general phenomenon in the aftermath of a glaciation.
Nanomaterials have unique properties and play critical roles in the budget, cycling, and chemical processing of elements on Earth. An understanding of the cycling of nanomaterials can be greatly improved if the pathways of their formation are clearly recognized and understood. Here, we show that nanomaterial formation pathways mediated by aqueous fluids can be grouped into four major categories, abiotic and biotic processes coupled and decoupled from weathering processes. These can be subdivided in 18 subcategories relevant to the critical zone, and environments such as ocean hydrothermal vents and the upper mantle. Similarly, pathways in the gas phase such as volcanic fumaroles, wildfires and particle formation in the stratosphere and troposphere can be grouped into two major groups and five subcategories. In the most fundamental sense, both aqueous-fluid and gaseous pathways provide an understanding of the formation of all minerals which are inherently based on nanoscale precursors and reactions.
The acoustic wave produced alongside laser-induced plasmas can be used in conjunction with the recorded atomic spectra of plasma emission to expand the physicochemical information acquired from a single inspection event. Among the most interesting uses of acoustic information is the differentiation of mineral phases with similar optical responses coexisting in geological targets. In addition, laser-induced plasma acoustics (LIPAc) can provide data related to the inspected material's hardness, density, and compactness. In this paper, we present a dual acoustic–optic laser-based strategy for the generation of high-resolution surface images of mineral samples. By combining simultaneous multimodal LIBS (laser-induced breakdown spectroscopy) and LIPAc spectral data from laser-induced plasmas, we explore the mineralogical composition of rocks embedded in resin matrixes to distinguish their chemical composition as well as their crystal phases based on physical changes caused by the different spatial arrangements of the constituent atoms. The multispectral polyhedron created by merging singular optical maps, one per detected elements, and the coincidental acoustic map enhance the distinction between regions present within the matrix of a host rock as compared to the differentiation yielded by each technique when used separately. The chemical information guides the composition of the mineral phases in the host rock. Then, the physical information obtained from acoustics may reinforce the identification of the detected mineral phase, draw the geological history of the inspected section, and showcase possible transformations, mainly of polymorphic nature. To test the combination proposed herein, we also inspected a septarian nodule featuring an ensemble of mineral phases with different origins. Mixed optical and acoustic responses from laser-produced plasmas of this complex sample allowed us to obtain more specific information. This approach constitutes a reliable and high-throughput tool for studying the surface of geological samples, which can substantially supplement well-established techniques for mineralogical analysis such as Raman spectroscopy and X-ray diffraction.
The process of altering the microbial-induced carbonate precipitation (MICP) by adding additives has been extensively studied. The impact of polysaccharides, as an important component of bacteria, still requires deeper exploration on MICP. This work thus focuses on two types of sugars, sodium alginate (SA) and trehalose (Tre), to explore their effects on biomineralization of carbonate induced by Bacillus pumilus Z6. The results show that B. pumilus Z6 can raise the environmental pH and increase the supersaturation of carbonate and bicarbonate ions through carbonic anhydrase. The presence of organic functional groups and the negative carbon isotope signatures in minerals provide evidence of microbial involvement. Tre and SA do not change the mineral phase, which mainly consists of hollow rice-like granular vaterite and irregular calcite. Tre is conducive to the formation of calcite, whereas the carboxyl groups in SA contribute to the stability of vaterite. Both Tre and SA enhance the removal rate of calcium ions; however, SA is more effective for this purpose. Furthermore, mineralization experiments with calcium alginate gel tablets indicate that SA can attract calcium carbonate to nucleate on its surface. This research offers significant insights into biomineralization processes and introduces novel perspectives for advancing MICP technology.
The genesis of sedimentary dolomite has long been a mystery in Earth science. It has been shown that the formation of low-temperature disordered dolomite, a crucial precursor of sedimentary dolomite, can be catalyzed by various heterotrophic microorganisms through organic mineralization. However, the potential role of cyanobacteria, which are common and cosmopolitan photoautotrophs in sedimentary environments, in the precipitation process of disordered dolomite has been largely underestimated. Moreover, recent emphasis on the beneficial influence of dissolved silicon (Si) in directly enhancing the Mg content in Ca–Mg carbonates under oversaturated conditions has emerged. Nevertheless, the effect of dissolved Si on the formation of microbiallyinduced disordered dolomite remains poorly understood. To examine the influence and mechanisms of dissolved Si on the biomineralization of Ca–Mg carbonates by cyanobacteria, biomineralization experiments were conducted using a halophilic cyanobacterium (Synechococcus elongatus FACHB-410) in solutions with varying concentrations of dissolved Si (ranging from 0 to 2 mM). Our findings revealed that the presence of dissolved Si resulted in higher Mg levels in the bio-precipitated Ca–Mg carbonates compared to Si-free systems, with
disordered dolomite formation observed at 2 mM Si. Importantly, an amorphous Mg-silicate phase formed prior to the crystallization of Ca–Mg carbonates during the biomineralization process, intimately associated with the grains of Ca–Mg carbonates. Subsequent abiotic carbonation experiments demonstrated its catalytic role in the nucleation of Ca–Mg carbonates. These observations suggest that, in addition to the direct catalytic effect of dissolved Si, the positive role of Si in the biomineralization of disordered dolomite by cyanobacteria may also be attributed to the templating role of the neoformed amorphous Mg-silicate. These results have important implications for understanding the co-occurrence of Mg-silicate and dolomite observed in geological records.
Microbial communities are important components controlling the fidelity of fossil fish preservation. The Eocene Green River Formation lagerstätten, exceptionally preserved fossil deposits, provides an opportunity to examine the role of microbial communities and their metabolic byproducts, such as chemical precipitated in this spectacularly preserved fish deposit, famous throughout the world. Field emission scanning electron microscope (FESEM) and energy dispersive spectroscopy system (EDS) examination of a well-preserved Knightia eocaena from the Eocene Green River Formation documents the presence of bacteriomorphs. Bacteriomorphs in a sample from the Fossil Butte Member of the Green River Formation consists of spherical structures, coccoid-type bacteria, fibres from two-sized populations of filamentous bacteria, probable filamentous cyanobacteria, capsule-shaped, and bacilliform bacteria, all associated with framboidal iron hydroxide.
Bacteriomorphs consist of external molds composed of nanometer-scale calcium carbonate spheres. Fe-oxide framboids have an amorphous exterior and a sieve-like internal structure. The sieve-like structure consists of nanometer-scale pores, probable sites of bacterial cells with walls composed of 100-nanometer-scale spheres. Fe-oxides are consistent with bacterially mediated precipitation of pyrite followed by an oxidation event. Preserved bacteriomorphs are consistent with degradation of soft tissue, limiting the preservation of soft tissue and leaving bone and scales with no appreciable soft tissue. The microfossils are restricted to the skeleton and are not found in the surrounding rock matrix, suggesting larger microbial mats may not have been present and possibly did not have a significant impact on the preservation of this specimen.
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 (Δ ⁴⁴ Ca) 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 Δ ⁴⁴ Ca 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 Δ ⁴⁴ Ca 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.
Chemosynthetic microorganisms facilitate microbialite development in many caves throughout the world. In Youqin Cave and Tian'e Cave, located in the Carboniferous–Triassic carbonates on the South China Block, five Quaternary speleothems (stalagmite, stalactite and cave pearl) that are 2.3 to 11.0 cm long were examined for their petrographic, geochemical and microbiological features to reveal how chemotrophs contribute to microbialite growth. In the speleothems, millimetre‐sized stromatolites, thrombolites and calcified microbial mats are characterized by alternating light, calcitic microlaminae and dark, clay and organic‐rich calcite microlaminae. Filamentous (reticulate, smooth, nodular and helical), coccoid and bacilliform microbes, originally carried into the caves from surface soils, are more common in the dark microlaminae/clots than in the light microlaminae. 16S rRNA gene sequencing shows that the biotas in the microbialites are dominated by chemoorganotrophic heterotrophic bacteria, including primarily Sphingomonas , Crossiella and Acinetobacter , and rare Archaea. Diverse metabolic pathways of these prokaryotes, including ureolysis, denitrification and nitrite ammonification, contributed to increases in localized pH and/or dissolved inorganic carbon in these microenvironments, prompting carbonate precipitation. Development of the cave microbialites was probably controlled by the evolution of the cave microbial community as environmental conditions changed. Microbialite growth was probably mediated by the microorganisms that flourished on the speleothem surfaces during periods of low drip water rates and slow calcite precipitation. The change from microstromatolites to microthrombolites was probably linked to a decrease in cell populations in the microbial communities. These cave microbialites provide clear insights regarding the biogenicity and growth mechanisms of chemosynthetic microbialites. Given their association with chemolithotrophic activities that can date back to the Meso‐Archean, cave microbialites provide insights into the biogenicity and growth mechanisms of chemosynthesis‐based microbialites throughout geological history.
Field Emission Scanning Electron Microscope (FESEM) and Energy Dispersive Spectroscopy System (EDS) examination of well-preserved Knightia eocaena from the Eocene Green River documents the presence of bacteriomorphs. Bacteriomorphs in samples from the_ Fossil Butte Member consists of fibers with two types and spherical structures, all with associated framboidal Fe-oxides. Fibers and spheres consist of external molds composed of nano-scale calcium carbonate spheres. Fish bone surfaces are corroded by framboids and euhedral rhombohedral molds. Fe-oxide framboids have an amorphous exterior and a sieve-like internal structure. The sieve-like structure consists of nannometer-scale pores with wall composed of 100 nm scale spheres. Fe-oxides are consistent with bacterial-mediated precipitation of pyrite followed by an oxidation event. The presence of the preserved bacteriomorphs is consistent with degradation of soft tissue degradation into adipocere limiting the preservation of soft tissue and leaving refracted bone.
Microbialites provide geological evidence of one of Earth's oldest ecosystems, potentially recording long-standing interactions between coevolving life and the environment. Here, we focus on microbialite accretion and growth and consider how environmental and microbial forces that characterize living ecosystems in Shark Bay and the Bahamas interact to form an initial microbialite architecture, which in turn establishes distinct evolutionary pathways. A conceptual three-dimensional model is developed for microbialite accretion that emphasizes the importance of a dynamic balance between extrinsic and intrinsic factors in determining the initial architecture. We then explore how early taphonomic and diagenetic processes modify the initial architecture, culminating in various styles of preservation in the rock record. The timing of lithification of microbial products is critical in determining growth patterns and preservation potential. Study results have shown that all microbialites are not created equal; the unique evolutionary history of an individual microbialite matters.
Large concentrically laminated carbonate grains (here referred to as pisoids) have been observed sporadically throughout the geological record and in modern environments. Explanations for how these grains form have varied widely in different settings, although microbial effects are often involved. In Ore Lake, a ~1 km2 flow-through lake in southeast Michigan, one to four centimeter oblong calcite pisoids are observed in both lake bottom shallows and mounded as a small spit near the primary outflow. In section mm-scale light and more porous along with and dark and more dense concentric laminations are apparent. Here we use field observations, petrography, water chemistry, and stable isotopes to understand their formation. Measurements of pisoid calcite δ18O and lake water δ18O indicate that precipitation occurs in waters between roughly 19 – 28°C. These warm temperatures imply that pisoid growth happens almost entirely within the summer, contrary to prior work that suggested wintertime precipitation was important. Pisoid δ18O values largely overlap with coexisting lake bivalve values, suggesting that pisoid precipitation is in equilibrium. In contrast, pisoid δ13C is as much as 8‰ more positive than bivalve δ13C due to photosynthetic effects. We propose that the laminations in these pisoids arise from different rates of formation within the warm months, rather than large seasonal differences. A decline in lake alkalinity beginning in late spring likely coincides with more rapid growth, with slower growth mediated by cyanobacteria continuing through the summer. This range of observations enables the use of Ore Lake as a potential model for understanding pisoid formation throughout the geological record.
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.
CaCO3 precipitates occur inside a few cyanobacteria and green algae. More common is precipitation on the surface of cyanobacteria, a range of algae and aquatic plants, and in invaginations of the cell wall in terrestrial plants (cystoliths). In coccolithophores and calcified dinoflagellates, CaCO3 is precipitated with organic matter in intracellular vesicles and the resulting structures are externalised. The precipitation of CaCO3 on the surface of photosynthesising structures is related to the consumption of CO2 in photosynthesis. CO2 production by root respiration can solubilise soil CaCO3. A few cyanobacteria and eukaryotic algae can bore through solid CaCO3 by removing Ca2+ and adding H+ at the site of boring, generating soluble inorganic C that can be used in photosynthesis. Ca(COO)2 is precipitated in the vacuoles of many algae and plants, and the cell walls of some plants.An outcome of precipitation of CaCO3 using CO3= produced from CO2, and Ca2+, is the production of H+; the same is the case for precipitation of Ca(COO)2 from (COOH)2 and Ca2+. The H+ produced by Ca(COO2) can be used to neutralise OH− produced in NO3− assimilation in the shoot without increasing cell osmolarity. There is no evidence of CaCO3 fulfilling this role. Another outcome of CaCO3 and Ca(COO)2 precipitation is Ca2+ immobilisation, though with little evidence of remobilisation of Ca2+ under Ca2+ deficiency. Other consequences of CaCO3 and Ca(COO)2 precipitation are light scattering and increased density, and ‘alarm photosynthesis’. Defence against herbivores and pathogens is better established for Ca(COO)2 than for CaCO3, and pollen release from anthers is a function of Ca(COO)2 but not CaCO3.KeywordsAcid-base regulationAlarm photosynthesisCalciumCarbonateInteractions with photonsOxalate
The increasing environmental and human health concerns about lead in the environment have stimulated scientists to search for microbial processes as innovative bioremediation strategies for a suite of different contaminated media. In this paper, we provide a compressive synthesis of existing research on microbial mediated biogeochemical processes that transform lead into recalcitrant precipitates of phosphate, sulfide, and carbonate, in a genetic, metabolic, and systematics context as they relate to application in both laboratory and field immobilization of environmental lead. Specifically, we focus on microbial functionalities of phosphate solubilization, sulfate reduction, and carbonate synthesis related to their respective mechanisms that immobilize lead through biomineralization and biosorption. The contributions of specific microbes, both single isolates or consortia, to actual or potential applications in environmental remediation are discussed. While many of the approaches are successful under carefully controlled laboratory conditions, field application requires optimization for a host of variables, including microbial competitiveness, soil physical and chemical parameters, metal concentrations, and co-contaminants. This review challenges the reader to consider bioremediation approaches that maximize microbial competitiveness, metabolism, and the associated molecular mechanisms for future engineering applications. Ultimately, we outline important research directions to bridge future scientific research activities with practical applications for bioremediation of lead and other toxic metals in environmental systems.
Microbial-induced carbonate precipitation (MICP) as a novel eco-friendly bioremediation method has been applied tentatively in soil solidification and heavy metal stabilization. In order to deeply study the theoretical knowledge of MICP and its application in environmental engineering, this review summarizes the main mechanisms of MICP, including biosorption and biomineralization. It is proposed innovatively that bacterial cell wall and extracellular polymeric substances (EPS) can provide ions binding sites during the process of biomineral nucleation due to negative charges and functional groups. Engineering properties of soil are regulated, such as increase of unconfined compressive strength (UCS) and shear stress, decrease of permeability and improvement of erosion resistance. Supposing the available CaCO3 content (CCC), UCS can be estimated by two boundary lines with an intersection angle of 2.72°. The great bioremediation capacity of metal cations/anions greatly depends upon carbonate precipitation/coprecipitation. Biotransformation and bioaccumulation of metal poisonousness should be considered as essential mechanisms in bacteria. Finally, according to the authors’ knowledge, current deficiencies and future research directions for the technology were pointed out, which might be beneficial to the optimization, application and generalization of MICP technology.
The success of today’s calcifying organisms in tomorrow’s oceans depends, in part, on the resilience of their skeletons to ocean acidification. To the extent this statement is true there is reason to have hope. Many marine calcifiers demonstrate resilience when exposed to environments that mimic near-term ocean acidification. The fossil record similarly suggests that resilience in skeletons has increased dramatically over geologic time. This “deep resilience” is seen in the long-term stability of skeletal chemistry, as well as a decreasing correlation between skeletal mineralogy and extinction risk over time. Such resilience over geologic timescales is often attributed to genetic canalization—the hardening of genetic pathways due to the evolution of increasingly complex regulatory systems. But paradoxically, our current knowledge on biomineralization genetics suggests an opposing trend, where genes are co-opted and shuffled at an evolutionarily rapid pace. In this paper we consider two possible mechanisms driving deep resilience in skeletons that fall outside of genetic canalization: microbial co-regulation and macroevolutionary trends in skeleton structure. The mechanisms driving deep resilience should be considered when creating risk assessments for marine organisms facing ocean acidification and provide a wealth of research avenues to explore.
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.
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.
Soils are considered as a major reservoir for terrestrial carbon and it can act as a source or sink depending upon the land management activities. In semi-arid areas, the natural recovery of soils degraded by mining activities is complicated. A possible solution to recover soil quality and functionality, plant cover and carbon sequestration capacity could be the application of organic amendments. This work focuses on a restoration carried out in 2018 by applying with different composted organic amendments (stabilized sludge, gardening and greenhouse waste) in a limestone quarry under semi-arid climate (SE Spain). The objective was to evaluate the effects of different organic amendments on net CO2 exchange in two microcosms: soil-Stipa tenacissima and soil-spontaneous vegetation. Soil physical and chemical properties, environmental and ecological variables and their interrelationship were studied in amended and unamended soils. The results obtained under soil-forming factors in the study area showed an increase in soil organic carbon and nitrogen content, improved moisture and plant growth, and plant canopy development in amended soils. Soil moisture, soil temperature and plant cover significantly influenced net CO2 exchange. In general, microcosms with S. tenacissima showed higher carbon sequestration rates than soils with only spontaneous plant cover. Soils treated with a vegetable-only amendments showed higher plant cover and CO2 fixation rates after significant rainfall. On the other hand, the plots treated with sludge compost presented more soil respiration than photosynthesis, especially in the wet seasons. Soils with sludge and greenhouse compost mixed had higher CO2 fixation rates than soils restored with a mixture of sludge and garden compost. Soils with greenhouse waste compost showed CO2 fixation in the microcosm with plants in all campaigns, being the best treatment to promote atmospheric CO2 sequestration in soil restoration.
Microbial-induced calcium carbonate precipitation (MICP) is a technique that uses the metabolic action of microorganisms to produce CO3²⁻ which combines with free Ca²⁺ to form CaCO3 precipitation. It has gained widespread attention in water treatment, aimed with the advantages of simultaneous removal of multiple pollutants, environmental protection, and ecological sustainability. This article reviewed the mechanism of MICP at both intra- and extra-cellular levels. It summarized the parameters affecting the MICP process in terms of bacterial concentration, ambient temperature, etc. The current status of MICP application in practical engineering is discussed. Based on this, the current technical difficulties faced in the use of MICP technology were outlined, and future research directions for MICP technology were highlighted. This review helps to improve the design of existing water treatment facilities for the simultaneous removal of multiple pollutants using the MICP and provides theoretical reference and innovative thinking for related research.
Whiting events-the episodic precipitation of fine-grained suspended calcium car-bonates 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.
The formation of ordered dolomite under Earth’s surface conditions remains a challenge, although many researchers have now shown that microbes can facilitate the precipitation of this common mineral. This study provides the first evidence of dolomite biomineralization by the green alga Spirogyra (Zygnematales, Chlorophyta), a globally dispersed lacustrine genus. Microbial mats formed by Spirogyra occur in the hyperalkaline and ephemeral lake Caballo Alba, located in Central Spain and characterized by water solutions with high Mg/Ca ratios. Microscopic, geochemical, mineralogical and cytochemical studies have shown that accumulations of carbonates occur within different cells and locations of the alga. Biominerals mostly consist of single crystals of magnesian calcite and dolomite with variable proportions of Ca2+ and Mg2+. High‐resolution transmission electron microscopy and selected area electron diffraction patterns of the carbonates confirm the pervasive presence of super‐lattice reflections typical of ordered dolomite in compositions with greater than 32 mol% MgCO3. The curved surfaces of some carbonate crystals and their attachment to the organic surfaces represent imprints of a confined growth in compartments that act as a template for crystal nucleation and shape the crystals. Dyes reveal chemical differences in these compartments which explain the polymineral biomineralization and suggest that the alga do not control strictly the precipitation process. Zygnematales algae related with Spirogyra date back possibly to the Early Paleozoic, thus suggesting that dolomite biomineralization could have been a common process through the Phanerozoic. This discovery provides new insight into the biotic formation of orderly dolomite and aids in the reconstructions of past lacustrine environments of dolomite deposition.
Microbial carbonate mineralization is widespread in nature and among microorganisms, and of vast ecological and geological importance. However, our understanding of the mechanisms that trigger and control processes such as calcification, i.e., mineralization of CO2 to calcium carbonate (CaCO3), is limited and literature on cyanobacterial calcification is oftentimes bewildering and occasionally controversial. In cyanobacteria, calcification may be intimately associated with the carbon dioxide-(CO2) concentrating mechanism (CCM), a biochemical system that allows the cells to raise the concentration of CO2 at the site of the carboxylating enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) up to 1000-fold over that in the surrounding medium. A comprehensive understanding of biologically induced carbonate mineralization is important for our ability to assess its role in past, present, and future carbon cycling, interpret paleontological data, and for evaluating the process as a means for biological carbon capture and storage (CCS). In this review we summarize and discuss the metabolic, physiological and structural features of cyanobacteria that may be involved in the reactions leading to mineral formation and precipitation, present a conceptual model of cyanobacterial calcification, and, finally, suggest practical applications for cyanobacterial carbonate mineralization.
Synechococcus OS-B′, a thermophilic unicellular cyanobacterium, recently isolated from the microbial mats in Octopus Spring (Yellowstone
National Park), induces a suite of genes, including phosphatases and transporters, in response to phosphorus (P) starvation.
Here we describe two different approaches to examine the ability of Synechococcus OS-B′ to synthesize and break down polyphosphate (poly P), a key storage compound in many prokaryotes. First, we developed
a transformation protocol to create mutants in the polyphosphate kinase (ppk), the major enzyme responsible for the synthesis of poly P. The ppk mutant exhibited a pleiotropic phenotype with defects in poly P accumulation, aberrant levels of Pho regulon transcripts,
growth defects, and changes in cell size and exopolysaccharide levels, among others. Second, we measured transcripts of ppk and ppx (encoding the polyphosphatase) directly from mat samples and found that the levels varied dramatically over a diel cycle.
We also used Western blot analysis to quantify levels of PPK and PPX and found that these enzymes differentially accumulated
during the diel cycle. Levels of polyphosphate kinase peaked at night, while polyphosphatase levels were highest during the
early morning hours. We hypothesize that the opposing activities of these two enzymes allow cells to store and utilize poly
P to optimize growth over a diel cycle.
Cyanobacteria are important players in the global carbon cycle, accounting for approximately 25% of global CO2 fixation. Their CO2-concentrating mechanisms (CCMs) are thought to play a key role in cyanobacterial calcification, but the mechanisms are not
completely understood. In Synechocystis sp. strain PCC 6803, a single Ca2+/H+ exchanger (Slr1336) controls the Ca2+/H+ exchange reaction. We knocked out the exchanger and investigated the effects on cyanobacterial calcification and CCMs. Inactivation
of slr1336 significantly increased the calcification rate and decreased the zeta potential, indicating a relatively stronger Ca2+-binding ability. Some genes encoding CCM-related components showed increased expression levels, including the cmpA gene, which encodes the Ca2+-dependent HCO3− transporter BCT1. The transcript level of cmpA in the mutant was 30 times that in wild type. A Western blot analysis further confirmed that protein levels of CmpA were
higher in the mutant than the wild type. Measurements of inorganic carbon fluxes and O2 evolution proved that both the net HCO3− uptake rate and the BCT1 transporter supported photosynthetic rate in the slr1336 mutant were significantly higher than in the wild type. This would cause the mutant cells to liberate more OH− ions out of the cell and stimulate CaCO3 precipitation in the microenvironment. We conclude that the mutation of the Ca2+/H+ exchanger in Synechocystis promoted the cyanobacterial calcification process by upregulating CCMs, especially the BCT1 HCO3− transporter. These results shed new light on the mechanism by which CCM-facilitated photosynthesis promotes cyanobacterial
calcification.
The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of light-harvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.
The timing of the evolution of microbial life has largely remained elusive due to the scarcity of prokaryotic fossil record and the confounding effects of the exchange of genes among possibly distant species. The history of gene transfer events, however, is not a series of individual oddities; it records which lineages were concurrent and thus provides information on the timing of species diversification. Here, we use a probabilistic model of genome evolution that accounts for differences between gene phylogenies and the species tree as series of duplication, transfer, and loss events to reconstruct chronologically ordered species phylogenies. Using simulations we show that we can robustly recover accurate chronologically ordered species phylogenies in the presence of gene tree reconstruction errors and realistic rates of duplication, transfer, and loss. Using genomic data we demonstrate that we can infer rooted species phylogenies using homologous gene families from complete genomes of 10 bacterial and archaeal groups. Focusing on cyanobacteria, distinguished among prokaryotes by a relative abundance of fossils, we infer the maximum likelihood chronologically ordered species phylogeny based on 36 genomes with 8,332 homologous gene families. We find the order of speciation events to be in full agreement with the fossil record and the inferred phylogeny of cyanobacteria to be consistent with the phylogeny recovered from established phylogenomics methods. Our results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record.
Cyanobacteria have affected major geochemical cycles (carbon, nitrogen, and oxygen) on Earth for billions of years. In particular,
they have played a major role in the formation of calcium carbonates (i.e., calcification), which has been considered to be
an extracellular process. We identified a cyanobacterium in modern microbialites in Lake Alchichica (Mexico) that forms intracellular
amorphous calcium-magnesium-strontium-barium carbonate inclusions about 270 nanometers in average diameter, revealing an unexplored
pathway for calcification. Phylogenetic analyses place this cyanobacterium within the deeply divergent order Gloeobacterales.
The chemical composition and structure of the intracellular precipitates suggest some level of cellular control on the biomineralization
process. This discovery expands the diversity of organisms capable of forming amorphous calcium carbonates.
Earth accreted 4567 Myr ago from largely homogeneous material. From this initial capital of matter, differentiation formed the chemical and physical compartments of core, mantle, continents, ocean and atmosphere, that characterize Earth today. Differentiation was, and still is, driven by energy from various sources including radioactive heat and relic heat from accretion. With evolution of photosynthesis, living organisms acquired the ability to harvest Solar energy and channel it into geochemical cycles. On our present Earth, the primary production from life contributes 3 times more energy to these cycles than Earth's internal heat engine. We hypothesize that the emergence of this energy resource modified Earth's geochemical cycles and ultimately stimulated the production of granite during the earliest Archaean, which led to the first stabilization of continents on Earth. Such biological forcing may explain the unique presence of granite on Earth, and why stable continents did not form during the first half billion years of Earth's history.
The main cofactors that determine the photosystem II (PSII) oxygen evolution activity are borne by the D1 and D2 subunits. In the cyanobacterium Thermosynechococcus elongatus, there are three psbA genes coding for D1. Among the 344 residues constituting D1, there are 21 substitutions between PsbA1 and PsbA3, 31 between PsbA1 and PsbA2, and 27 between PsbA2 and PsbA3. Here, we present the first study of PsbA2-PSII. Using EPR and UV-visible time-resolved absorption spectroscopy, we show that: (i) the time-resolved EPR spectrum of Tyr(Z)(•) in the (S(3)Tyr(Z)(•))' is slightly modified; (ii) the split EPR signal arising from Tyr(Z)(•) in the (S(2)Tyr(Z)(•))' state induced by near-infrared illumination at 4.2 K of the S(3)Tyr(Z) state is significantly modified; and (iii) the slow phases of P(680)(+) reduction by Tyr(Z) are slowed down from the hundreds of μs time range to the ms time range, whereas both the S(1)Tyr(Z)(•) → S(2)Tyr(Z) and the S(3)Tyr(Z)(•) → S(0)Tyr(Z) + O(2) transition kinetics remained similar to those in PsbA(1/3)-PSII. These results show that the geometry of the Tyr(Z) phenol and its environment, likely the Tyr-O···H···Nε-His bonding, are modified in PsbA2-PSII when compared with PsbA(1/3)-PSII. They also point to the dynamics of the proton-coupled electron transfer processes associated with the oxidation of Tyr(Z) being affected. From sequence comparison, we propose that the C144P and P173M substitutions in PsbA2-PSII versus PsbA(1/3)-PSII, respectively located upstream of the α-helix bearing Tyr(Z) and between the two α-helices bearing Tyr(Z) and its hydrogen-bonded partner, His-190, are responsible for these changes.
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
Calcium functions as a versatile messenger in a wide variety of eukaryotic and prokaryotic cells. Cyanobacteria are photoautotrophs which have a great ecological impact as primary producers. Our research group has presented solid evidence of a role of calcium in the perception of environmental changes by cyanobacteria and their acclimation to these changes. We constructed a recombinant strain of the freshwater cyanobacterium Anabaena sp. PCC 7120 that constitutively expresses the calcium-binding photoprotein apoaequorin, enabling in-vivo monitoring of any fluctuation in the intracellular free calcium concentration of the cyanobacterium in response to any environmental stimulus. The “Ca2+ signature” is the combination of changes in all Ca2+ signal properties (magnitude, duration, frequency, source of the signal) produced by a specific stimulus. We recorded and analyzed the Ca2+ signatures generated by exposure of the cyanobacterium to different groups of environmental pollutants, for example cations, anions, organic solvents, naphthalene, and pharmaceuticals. We found that, in general, each group of tested chemicals triggered a specific calcium signature in a reproducible and dose-dependent manner. We hypothesize that these Ca2+ signals may be related to the cellular mechanisms of pollutant perception and ultimately to their toxic mode of action. We recorded Ca2+ signals triggered by binary mixtures of pollutants and a signal induced by a real wastewater sample which could be mimicked by mixing its main constituents. Because Ca2+ signatures were induced before toxicity was evident, we propose that intracellular free Ca2+ may serve as an early biomarker of exposure to environmental pollution.
Figure
Cyanobacterial carbon fixation is a major component of the global carbon cycle. This process requires the carboxysome, an
organelle-like proteinaceous microcompartment that sequesters the enzymes of carbon fixation from the cytoplasm. Here, fluorescently
tagged carboxysomes were found to be spatially ordered in a linear fashion. As a consequence, cells undergoing division evenly
segregated carboxysomes in a nonrandom process. Mutation of the cytoskeletal protein ParA specifically disrupted carboxysome
order, promoted random carboxysome segregation during cell division, and impaired carbon fixation after disparate partitioning.
Thus, cyanobacteria use the cytoskeleton to control the spatial arrangement of carboxysomes and to optimize the metabolic
process of carbon fixation.
When cyanobacteria originated and diversified, and what their ancient traits were, remain critical unresolved problems. Here, we used a phylogenomic approach to construct a well-resolved 'core' cyanobacterial tree. The branching positions of four lineages (Thermosynechococcus elongatus, Synechococcus elongatus, Synechococcus PCC 7335 and Acaryochloris marina) were problematic, probably due to long branch attraction artifacts. A consensus genomic tree was used to study trait evolution using ancestral state reconstruction (ASR). The early cyanobacteria were probably unicellular, freshwater, had small cell diameters, and lacked the traits to form thick microbial mats. Relaxed molecular clock analyses suggested that early cyanobacterial lineages were restricted to freshwater ecosystems until at least 2.4 Ga, before diversifying into coastal brackish and marine environments. The resultant increases in niche space and nutrient availability, and consequent sedimentation of organic carbon into the deep oceans, would have generated large pulses of oxygen into the biosphere, possibly explaining why oxygen rose so rapidly. Rapid atmospheric oxidation could have destroyed the methane-driven greenhouse with simultaneous drawdown in pCO(2), precipitating 'Snowball Earth' conditions. The traits associated with the formation of thick, laminated microbial mats (large cell diameters, filamentous growth, sheaths, motility and nitrogen fixation) were not seen until after diversification of the LPP, SPM and PNT clades, after 2.32 Ga. The appearance of these traits overlaps with a global carbon isotopic excursion between 2.2 and 2.1 Ga. Thus, a massive re-ordering of biogeochemical cycles caused by the appearance of complex laminated microbial communities in marine environments may have caused this excursion. Finally, we show that ASR may provide an explanation for why cyanobacterial microfossils have not been observed until after 2.0 Ga, and make suggestions for how future paleobiological searches for early cyanobacteria might proceed. In summary, key evolutionary events in the microbial world may have triggered some of the key geologic upheavals on the Paleoproterozoic Earth.
DNA can be introduced into the thermophilic cyanobacteriumSynechococcus elongatus by electroporation or conjugation. Its genome can be readily manipulated through integrative transformation or by using promiscuous RSF1010-derived plasmids that can be transferred unaltered betweenEscherichia coli andSynechococcus elongatus. These vectors can therefore be used for in vivo studies of cyanobacterial proteins in both mesophilic and thermophilic cyanobacterial backgrounds. As a preliminary step towards the analysis of structure-function relationships of photosystem I (PSI) from this thermophile, the genes encoding the PSI subunits PsaF, PsaL, and PsaK were inactivated and shown to be non-essential inS. elongatus. In addition, PSI reaction centres were extracted from apsaL
− strain exclusively as monomeric complexes.
Three unicellular cyanobacterial strains (PCC 7425, PCC 8303, PCC 9308) assigned to the genus Cyanothece Komárek 1976, which showed an unusually high content of light refractile inclusions when viewed by phase-contrast microscopy, were characterized by confocal laser scanning microscopy and transmission electron microscopy. All strains had concentric cortical thylakoids and a compact central nucleoid. Frequently, the two innermost thylakoid membranes protruded to form circular enclosures containing cytoplasm or electron-transparent granules, or both. The largest granules were partially immersed in the nucleoid region, but they remained attached to the inner cortical thylakoids by a single narrow connection. The pattern of binary cell division in strain PCC 7425 was different than that in strains PCC 8303 and PCC 9308. In the former, all cell wall layers invaginated simultaneously, whereas in the latter the invagination of the outer membrane was delayed compared to that of the cytoplasmic membrane and the peptidoglycan layer. Thus, prior to completion of cell division, the new daughter cells of strains PCC 8303 and PCC 9308 were transiently connected by a thick septum, which was not observed in strain PCC 7425. Nucleoid partitioning coincided with initiation of cell division in all three strains and was unlike that reported in other bacteria and in archaea, in which separation of the nucleoids precedes cell division. Based on the common morphological and ultrastructural features, the three strains of Cyanothece examined constitute a distinct cluster, which might deserve independent generic status.
Photosynthetic activities of a thermophilic blue-green alga, a species of Synechococcus, were studied with special reference to its growth at high temperatures. A rapid algal growth occurred in the temperature range between 50 and 60°C, showing the maximum rate, six doublings per day, at about 57°C. Photosynthetic oxygen evolution and methyl viologen photoreduction in the cells were also active at high temperatures and the optimum temperatures for these activities agreed with that of the algal growth. The growth and photosynthetic activities were very low at room temperature and irreversibly inactivated at temperatures above 60°C.
The thylakoid membranes isolated from the alga were also photochemically active at high temperatures. The membranes mediated ferricyanide photoreduction coupled with a stoichiometric oxygen evolution at a rate comparable to that of photosynthetic oxygen evolution in the cells. The optimum temperature for the reaction was as high as 50°C. The membranes also showed a photosystem I-mediated reaction at high temperatures. These observations indicate that the thylakoid membranes are intrinsically thermophilic in this organism. Thus the growth of the alga at high temperatures can be well correlated to thermophilic properties of the photosynthetic apparatus.
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing
methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform
(FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid
residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy
of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length.
Two different heuristics, the progressive method (FFT‐NS‐2) and the iterative refinement method (FFT‐NS‐i), are implemented
in MAFFT. The performances of FFT‐NS‐2 and FFT‐NS‐i were compared with other methods by computer simulations and benchmark
tests; the CPU time of FFT‐NS‐2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT‐NS‐i is over
100 times faster than T‐COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
Scanning Force Microscopy (SFM) was used to observe near-equilibrium calcite growth processes in solutions of known composition and saturation state. Calcite seeds were reacted in solutions of known saturation state at 25°C and 0.96 atm PCO2 for 1–2 days before transferring to a SFM fluid cell for observations of continued growth in the same solutions.We observed that when solution saturations with respect to calcite were greater than 1–2, precipitation began with the formation of surface nuclei. These nuclei spread, coalesced, and continued growing. Only after nearly two hours was there a transition to a mechanism resembling spiral growth. At these long reaction times, migrating steps assumed individual heights of 1–2 monolayers. We also observed simultaneous growth and dissolution at undersaturated conditions very near equilibrium.The influence of phosphate was also examined and observations suggested two inhibition mechanisms, depending on surface history. Phosphate (6 and 10 μmol PO4) introduced during the nucleation stage results in the formation of nuclei with amorphous shapes. Phosphate introduced during layer growth disrupts the relatively straight steps produced during PO4-free growth to form jagged steps. Both of the phosphate-calcite surface interactions are consistent with mechanisms proposed in previous studies.Our findings suggest that when solution saturations with respect to calcite are greater than two, precipitation always begins with the formation of surface nuclei with a later transition to mononuclear growth mechanisms. These observations have implications for carbonate precipitation in natural systems and suggest that calcite growth in environments with frequent wetting and drying cycles begin each wetting event with precipitation by surface nucleation. Results of this study also suggest that experimental investigations of calcite precipitation kinetics and interpretations of growth mechanisms must account for this early stage contribution by nucleation. Otherwise, such rates of calcite growth may not reflect the overall slower rates that occur in continuously wet environments.
SUMMARY Cyanobacteria are the globally dominant photoautotrophic lineage. Their success is dependent on a set of adaptations collectively termed the CO2-concentrating mechanism (CCM). The purpose of the CCM is to support effective CO2 fixation by enhancing the chemical conditions in the vicinity of the primary CO2-fixing enzyme, d-ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), to promote the carboxylase reaction and suppress the oxygenase reaction. In cyanobacteria and some proteobacteria, this is achieved by encapsulation of RubisCO within carboxysomes, which are examples of a group of proteinaceous bodies called bacterial microcompartments. Carboxysomes encapsulate the CO2-fixing enzyme within the selectively permeable protein shell and simultaneously encapsulate a carbonic anhydrase enzyme for CO2 supply from a cytoplasmic bicarbonate pool. These bodies appear to have arisen twice and undergone a process of convergent evolution. While the gross structures of all known carboxysomes are ostensibly very similar, with shared gross features such as a selectively permeable shell layer, each type of carboxysome encapsulates a phyletically distinct form of RubisCO enzyme. Furthermore, the specific proteins forming structures such as the protein shell or the inner RubisCO matrix are not identical between carboxysome types. Each type has evolutionarily distinct forms of the same proteins, as well as proteins that are entirely unrelated to one another. In light of recent developments in the study of carboxysome structure and function, we present this review to summarize the knowledge of the structure and function of both types of carboxysome. We also endeavor to cast light on differing evolutionary trajectories which may have led to the differences observed in extant carboxysomes.
"Biomineralization links soft organic tissues, which are compositionally akin to the atmosphere and oceans, with the hard materials of the solid Earth. It provides organisms with skeletons and shells while they are alive, and when they die these are deposited as sediment in environments from river plains to the deep ocean floor. It is also these hard, resistant products of life which are mainly responsible for the Earth's fossil record. Consequently, biomineralization involves biologists, chemists, and geologists in interdisciplinary studies at one of the interfaces between Earth and life." (Leadbeater and Riding 1986)
In the present paper, the impact of freshwater (ARC21 and LS0519) and marine (PCC8806) Synechococcus cyanobacteria on calcium carbonate (CaCO3) precipitation has been examined in respect of the formation rates and morphology of crystals. Acid-base potentiometric titrations were employed to study surface functional groups, while CaCO3 experiments have been carried out in presence and absence of cells at low to near-equilibrium conditions in respect to CaCO3. During these experiments, the pH values have been monitored, Ca and alkalinity were measured and precipitates have been investigated by Raman spectroscopy and Atomic Force and Scanning Electron microscopy. Our results showed that the Synechococcus strains exhibited different surface reactivity with total concentration of surface functional groups of 0.342 and 0.350mMg(-1) of dry bact. for freshwater strains, and 0.662mMg(-1) of dry bact. for the marine strain, which are on the same order of magnitude as that reported for bacterial cell surfaces. The marine strain showed the highest CaCO3 formation rate with Ca(2+) removal of 18mMg(-1) dry bact. compared to 6-7mMg(-1) dry bact. for freshwater strains. The morphological diversity in crystals has been linked to presence of specific functional groups. The linking cell surface properties to crystal morphologies and precipitation rates propose that bacterial surfaces may modulate CaCO3 formation. Results of this work should allow better understanding of biominiralization in marine and freshwater systems as they define the precipiatation rates in typical range of pH necessary for estimation of CaCO3 formation by cyanobacterial communities.
The cyanobacterial fossil record is among the oldest for any group of organisms, possibly reaching back to 3500 Ma ago. The molecular phylogeny of cyanobacteria is complementary to the fossil findings, confirming the antiquity of the group, the role of cyanobacteria in the evolution of planetary primary production, and the symbiotic origins of plastids in algae and plants from cyanobacterial ancestors. The study of fossil cyanobacteria followed the discovery of Precambrian microbial fossils by S.A Tyler and E.S. Barghoorn in 1954, and is still developing. Most fossil cyanobacteria are preserved in permineralized conditions in cherts and phosphorites or as organic compressions in shales. The interpretation of fossil cyanobacteria is aided by the study of modern counterparts, preferably within their natural habitats. These comparisons include the post mortem degradation of cellular remains. The fortuitous preservation and fossilization of ancient cyanobacterial communities in growth position, i.e. in the synsedimentary context, allows one to draw conclusions about their palaeoenvironment, including interactions between cyanobacteria and ancient sediments. These relations are based on cyanobacterial ecological requirements, and they compare well with behavioural responses of modern cyanobacteria in microbial mats and modern stromatolites. The general trend in the evolution of cyanobacteria is one of gradually increasing complexity and diversity, but the group shows a conservative maintenance of morphological adaptations to successful ecological niches. Accordingly, a large proportion of ancient morphological types is still represented among modern cyanobacteria. Fossil to Recent counterparts are identified for several coccoid and filamentous cyanobacteria. Evidence for heterocystous cyanobacteria is indirect, through identification of fossil akinetes.
An amorphous or nanocrystalline calcium carbonate (ACC) phase with aragonite-like short-range order was found to be a transient precursor phase of calcite precipitation mediated by cyanobacteria of the strain Synechococcus leopoliensis PCC 7942. Using scanning transmission X-ray microscopy (STXM), different Ca-species such as calcite, aragonite-like CaCO3, and Ca adsorbed on extracellular polymers were discriminated and mapped, together with various organic compounds, at the 30nm-scale. The nucleation of the amorphous aragonite-like CaCO3 was found to take place within the tightly bound extracellular polymeric substances (EPS) produced by the cyanobacteria very close to the cell wall. The aragonite-like CaCO3 is a type of ACC since it did not show either X-ray or electron diffraction peaks. The amount of aragonite-like CaCO3 precipitated in the EPS was dependent on the nutrient supply during bacterial growth. Higher nutrient concentrations (both N and P) during the cultivation of the cyanobacteria resulted in higher amounts of precipitation of the aragonite-like CaCO3, whereas the amount of Ca2+ adsorbed per volume of EPS was almost independent of the nutrient level. After the onset of the precipitation of the thermodynamically stable calcite and loss of supersaturation the aragonite-like CaCO3 dissolved whereas Ca2+ remained sorbed to the EPS albeit at lower concentrations. Based on these observations a model describing the temporal and spatial evolution of calcite nucleation on the surface of S. leopoliensis was developed. In another set of STXM experiments the amount of aragonite-like CaCO3 precipitated on the cell surface was found to depend on the culture growth phase: cells in the exponential growth phase adsorbed large amounts of Ca within the EPS and mediated nucleation of ACC, while cells at the stationary/death phase neither adsorbed large amounts of Ca2+ nor mediated the formation of aragonite-like CaCO3. It is suggested that precipitation of an X-ray amorphous CaCO3 layer by cyanobacteria could serve as a protection mechanism against uncontrolled precipitation of a thermodynamically stable phase calcite on their surface.
On the basis of a comparative study of 178 strains of cyanobacteria, representative of this group of prokaryotes, revised definitions of many genera are proposed. Revisions are designed to permit the generic identification of cultures, often difficult through use of the field-based system of phycological classification. The differential characters proposed are both constant and readily determinable in cultured material. The 22 genera recognized are placed in five sections, each distinguished by a particular pattern of structure and development. Generic descriptions are accompanied by strain histories, brief accounts of strain properties, and illustrations; one or more reference strains are proposed for each genus. The collection on which this analysis was based has been deposited in the American Type Culture Collection, where strains will be listed under the generic designations proposed here.
The entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no plasmid was detected. A total of 2475 potential protein-encoding genes, one set of rRNA genes, 42 tRNA genes representing 42 tRNA species and 4 genes for small structural RNAs were assigned to the chromosome by similarity search and computer prediction. The translated products of 56% of the potential protein-encoding genes showed sequence similarity to experimentally identified and predicted proteins of known function, and the products of 34% of these genes showed sequence similarity to the translated products of hypothetical genes. The remaining 10% lacked significant similarity to genes for predicted proteins in the public DNA databases. Sixty-three percent of the T. elongatus genes showed significant sequence similarity to those of both Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, while 22% of the genes were unique to this species, indicating a high degree of divergence of the gene information among cyanobacterial strains. The lack of genes for typical fatty acid desaturases and the presence of more genes for heat-shock proteins in comparison with other mesophilic cyanobacteria may be genomic features of thermophilic strains. A remarkable feature of the genome is the presence of 28 copies of group II introns, 8 of which contained a presumptive gene for maturase/reverse transcriptase. A trace of genome rearrangement mediated by the group II introns was also observed.
IN the few physiological investigations of thermophilic blue-green algae, species which tolerate temperatures only as high as 55° C have usually been used1,2.
Well preserved filamentous microfossils (Siphonophycus transvaalensis n. sp.) are described here from the carbonate (Campbellrand Subgroup) to iron-formation (Kuruman Iron Formation) transition of the Transvaal Supergroup, South Africa, estimated to be 2.5-2.3 Ga years old. The microfossils occur in petrographic thin-sections of a core sample of carbonate-chert. They are preserved by permineralization in both chert and in sparry ferroan dolomite. Stratigraphically the fossiliferous core sample occurs as part of an upward transition from a stromatolitic dolomite and limestone sequence (Campbellrand) to the overlying iron-rich sediments of the Kuruman-Griquatown Iron Formations. The average δ13C value of the kerogen in the sample is about - 36.9%.
Calcite with laminate structure was successfully prepared by culturing Synechocystis sp. PCC6803 with different concentrations of calcium chloride (CaCl2) in BG11 media. S. PCC6803 was examined by scanning electron microscopy (SEM), transmission electron microscopy (TEM), laser confocal scanning microscope (LCSM) and energy dispersive spectroscopy (EDS). The effects of Ca(2+) concentrations and pH values on calcification were investigated and the micro morphs of the CaCO3 crystals were observed by means of SEM. These results showed that CaCO3 crystals could be more easily formed with increasing the concentration of CaCl2 in S. PCC6803 culture solution. S. PCC6803 could largely bind calcium ions, most of which were present in extracellular polymeric substances and on the cell wall. Inside the cells there were a lot of circular areas rich in calcium ions without the crystallization of calcium. Some cells produced a thicker gelatinous sheath outside of the translucent organic thin layer. And the cells inside also produced major changes that the original chloroplasts were almost transformed into starch grains whose sizes were from 0.5 to 1 μm with relatively uniform in sizes. At the same time the cell sizes significantly reduced to only about 8-9 μm almost changing to half of its original diameters. The calcite crystals with a highly preferred orientation induced by S. PCC6803 were observed with X-ray diffraction (XRD). A critical implication was that S. PCC6803 could induce bio-calcification and then mediate the further growth of CaCO3 crystals in the biological system.
Stromatolites document microbial interactions with sediments and flowing water throughout recorded Earth history and have the potential to illuminate the long term history of life and environments. Modern stromatolites, however, provide analogs to only a small subset of the structures preserved in Archean and Proterozoic carbonates. Thus, interpretations of secular trends in the shapes and textures of ancient columnar stromatolites require non-uniformitarian, scale-dependent models of microbial responses to nutrient availability, seawater chemistry, influx of sediment grains, shear and burial. Models that integrate stromatolite scales, macroscopic organization and shapes could also help test the biogenicity of the oldest stromatolites and other structures whose petrographic fabrics do not preserve direct evidence of microbial activity. An improved understanding of stromatolite morphogenesis in the presence of oxygenic and anoxygenic microbial mats may illuminate the diversity of microbial metabolisms that...
The carbonate sedimentary record contains diverse compositions and textures that reflect the evolution of oceans and atmospheres through geological time. Efforts to reconstruct paleoenvironmental conditions from these deposits continue to be hindered by the need for process-based models that can explain observed shifts in carbonate chemistry and form. Traditional interpretations assume minerals precipitate and grow by classical ion-by-ion addition processes but are unable to reconcile a number of unusual features contained in Proterozoic carbonates. The realization that diverse organisms produce high Mg carbonate skeletal structures by non-classical pathways involving amorphous intermediates raises the question of whether similar processes are also active in sedimentary environments. This study examines the hypothesis that non-classical pathways to mineralization are the physical basis for some of the carbonate morphologies and compositions observed in natural and laboratory settings. We designed exper
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
Microbially mediated calcification can be traced back for at least 2.6 billion years. Although morphological comparison of fossil and recent microbial carbonates suggests that mineralization processes associated with cyanobacteria and their interactions with heterotrophic bacteria have remained similar from the Archaean until today, the metabolic and chemical details remain poorly constrained. Microbial consortia often exhibit an ability to change solution chemistry and control pH at the microscale, passively or actively. This leads to oversaturation of Ca2+ and ions and to the removal of kinetic inhibitors to carbonate precipitation, like sulphate or phosphate. The kinetic barriers of low carbonate ion activity, ion hydration and ion complexing, especially in saline waters, inhibit spontaneous carbonate mineral precipitation from saturated solutions but oxygenic photosynthesis and sulphate reduction by sulphate-reducing bacteria can overcome these natural barriers. Sulphate in seawater tends to form pairs with Ca2+ and Mg2+ ions. The removal of sulphate reduces complexing, raises carbonate alkalinity, and along with pyrite formation, enhances carbonate precipitation. Cyanobacteria can store Ca2+ and Mg2+ ions in organic envelopes and precipitate carbonates within their sheaths and extracellular polymeric substances, thus, triggering sedimentary carbonate production. We propose that this interplay of cyanobacteria and heterotrophic bacteria has been the major contributor to the carbonate factory for the last 3 billion years of Earth history.