Search

The application of manganese-oxidizing bacteria (MnOB) to produce manganese oxides (MnOx) has been widely studied, but often overlooking the concurrent formation of MnCO 3 . In this study, we found Ca 2+ plays a crucial role in controlling Mn(II) removal in the bacterium Aurantimonas sp. HBX-1. Under conditions with 6.8 mM Ca 2+ and without adding Ca 2+ , 100 μM Mn(II) was removed by 96.96 % and 38.28 % within 8 days, respectively. X-ray photoelectron spectroscopy (XPS) showed that adding Ca 2+ increased the average oxidation state (AOS) of the solid products from 2.05 to 2.37. X-ray absorption fine structure (XAFS) analysis revealed the product proportions as follows: under Ca 2+ -supplemented condition, the ratio of MnOx (1 < x ≤ 2) to MnCO₃ was 52 % to 28.1 %, while under Ca 2+ -free condition, the ratio shifted to 4.6 % for MnOx (1 < x ≤ 2) and 55.2 % for MnCO₃. Urease activity assay and proteomic analysis confirmed the expression of urease and carbonic anhydrase, leading to the formation of MnCO 3 . Additionally, animal heme peroxidase (AHP) in strain HBX-1 was found to be responsible for Mn(II) oxidation through superoxide production, with Ca 2+ addition promoting its expression level. Given the widespread presence of Ca 2+ in wastewater, its potential impact on the biogeochemical Mn(II) cycle driven by bacteria should be reconsidered., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: Glechoma longituba, recognized as a medicinal plant, provides valuable pharmaceutical raw materials for treating various diseases. Saline-alkali stress may effectively enhance the medicinal quality of G. longituba by promoting the synthesis of secondary metabolites. To investigate the changes in the primary medicinal components of G. longituba under saline-alkali stress and improve the quality of medicinal materials, Na 2 CO 3 was applied to induce short-term stress under different conditions and the biomass, physiologically active substances and primary medicinal components of G. longituba were measured in this study., Results: Under alkaline salt stress, the activities of catalase (CAT), superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX) were elevated in G. longituba, accompanied by increased accumulation of proline (Pro) and malondialdehyde (MDA). Furthermore, analysis of the medicinal constituents revealed that G. longituba produced the highest levels of soluble sugars, flavonoids, ursolic acid, and oleanolic acid under 0.6% Na 2 CO 3 stress for 48 h, 0.2% Na 2 CO 3 stress for 72 h, 0.4% Na 2 CO 3 stress for 12 h, and 0.4% Na 2 CO 3 stress for 8 h, respectively., Conclusions: Short-term Na 2 CO 3 stress enhances the synthesis of medicinal components in G. longituba. By manipulating stress conditions, the production of various medicinal substances could be optimized. This approach may serve as a basis for the targeted cultivation of G. longituba, offering potential applications in the treatment of diverse diseases., (© 2024. The Author(s).)

Current evidence suggests that macroalgal-dominated habitats are important contributors to the oceanic carbon cycle, though the role of those formed by calcifiers remains controversial. Globally distributed coralline algal beds, built by pink coloured rhodoliths and maerl, cover extensive coastal shelf areas of the planet, but scarce information on their productivity, net carbon flux dynamics and carbonate deposits hampers assessing their contribution to the overall oceanic carbon cycle. Here, our data, covering large bathymetrical (2-51 m) and geographical ranges (53°N-27°S), show that coralline algal beds are highly productive habitats that can express substantial carbon uptake rates (28-1347 g C m -2  day -1 ), which vary in function of light availability and species composition and exceed reported estimates for other major macroalgal habitats. This high productivity, together with their substantial carbonate deposits (0.4-38 kilotons), renders coralline algal beds as highly relevant contributors to the present and future oceanic carbon cycle., (© 2024. The Author(s).)

Biofuel can be generated by different organisms using various substrates. The green alga Chlorococcum humicola OQ934050 exhibited the capability to photosynthesize carbonate carbon, maybe via the activity of carbonic anhydrase enzymes. The optimum treatment is C:N ratio of 1:1 (0.2 mmoles sodium carbonate and 0.2 mmoles sodium nitrate) as it induced the highest dry mass (more than 0.5 mg.mL -1 ). At this combination, biomass were about 0.2 mg/mL -1 carbohydrates, 0.085 mg/mL -1 proteins, and 0.16 mg/mL -1 oil of this dry weight. The C/N ratios of 1:1 or 10:1 induced up to 30% of the Chlorococcum humicola dry mass as oils. Growth and dry matter content were hindered at 50:1 C/N and oil content was reduced as a result. The fatty acid profile was strongly altered by the applied C.N ratios. The defatted leftovers of the grown alga, after oil extraction, were fermented by a newly isolated heterotrophic bacterium, identified as Bacillus coagulans OQ053202, to evolve hydrogen content as gas. The highest cumulative hydrogen production and reducing sugar (70 ml H 2 /g biomass and 0.128 mg/ml; respectively) were found at the C/N ratio of 10:1 with the highest hydrogen evolution efficiency (HEE) of 22.8 ml H 2 / mg reducing sugar. The optimum treatment applied to the Chlorococcum humicola is C:N ratio of 1:1 for the highest dry mass, up to 30% dry mass as oils. Some fatty acids were induced while others disappeared, depending on the C/N ratios. The highest cumulative hydrogen production and reducing sugar were found at the C/N ratio of 10:1., (© 2024. The Author(s).)

A three-dimensional tubular fabric known as "vermiform microstructure" in Phanerozoic and Neoproterozoic carbonate microbialites has been hypothesized to represent the body fossil of nonspicular keratose demosponges. If correct, this interpretation extends the sponge body fossil record and origin of animals to ~890 Ma. However, the veracity of the keratose sponge interpretation for vermiform microstructure remains in question, and the origin of the tubular fabric is enigmatic. Here we compare exceptionally well-preserved microbialite textures from the Upper Triassic to channel networks created by modern microbial biofilms. We demonstrate that anastomosing channel networks of similar size and geometries are produced by microbial biofilms in the absence of sponges, suggesting the origin for vermiform microstructure in ancient carbonates is not unique to sponges and perhaps best interpreted conservatively as likely microbial in origin. We present a taphonomic model of early biofilm lithification in seawater with anomalously high carbonate saturation necessary to preserve delicate microbial textures. This work has implications for the understanding of three-dimensional biofilm architecture that goes beyond the current micro-scale observations available from living biofilm experiments and suggests that biofilm channel networks have an extensive fossil record., (© 2024 John Wiley & Sons Ltd.)

In recent years, alkaline soda soil has stimulated numerous biological research on plants under carbonate stress. Here, we explored the difference in physiological regulation of rice seedlings between saline (NaCl) and alkaline carbonate (NaHCO3 and Na2 CO3 ) stress. The rice seedlings were treated with 40mM NaCl, 40mM NaHCO3 and 20mM Na2 CO3 for 2h, 12h, 24h and 36h, their physiological characteristics were determined, and organic acid biosynthesis and metabolism and hormone signalling were identified by transcriptome analysis. The results showed that alkaline stress caused greater damage to their photosynthetic and antioxidant systems and led to greater accumulation of organic acid, membrane damage, proline and soluble sugar but a decreased jasmonic acid content compared with NaCl stress. Jasmonate ZIM-Domain (JAZ), the probable indole-3-acetic acid-amido synthetase GH3s, and the protein phosphatase type 2Cs that related to the hormone signalling pathway especially changed under Na2 CO3 stress. Further, the organic acid biosynthesis and metabolism process in rice seedlings were modified by both Na2 CO3 and NaHCO3 stresses through the glycolate/glyoxylate and pyruvate metabolism pathways. Collectively, this study provides valuable evidence on carbonate-responsive genes and insights into the different molecular mechanisms of saline and alkaline stresses.

Sulfide-carbonate-mineralized functional bacterial consortium was constructed for flue gas cadmium biomineralization. A membrane biofilm reactor (MBfR) using the bacterial consortium containing sulfate reducing bacteria (SRB) and denitrifying bacteria (DNB) was investigated for flue gas cadmium (Cd) removal. Cadmium removal efficiency achieved 90%. The bacterial consortium containing Citrobacter, Desulfocurvus and Stappia were dominated for cadmium resistance-nitrate-sulfate reduction. Under flue gas cadmium stress, ten cadmium resistance genes (czcA, czcB, czcC, czcD, cadA, cadB, cadC, cueR, copZ, zntA), and seven genes related to sulfate reduction, increased in abundance; whereas others, nine genes related to denitrification, decreased, indicating that cadmium stress was advantageous to sulfate reduction in the competition with denitrification. A bacterial consortium could capable of simultaneously cadmium resistance, sulfate reduction and denitrification. Microbial induced carbonate precipitation (MICP) and biological adsorption process would gradually yield to sulfide-mineralized process. Flue gas cadmium could transform to Cd-EPS, cadmium carbonate (CdCO 3 ) and cadmium sulfide (CdS) bioprecipitate. The functional bacterial consortium was an efficient and eco-friendly bifunctional bacterial consortium for sulfide-carbonate-mineralized of cadmium. This provides a green and low-carbon advanced treatment technology using sulfide-carbonate-mineralized functional bacterial consortium for the removal of cadmium or other hazardous heavy metal contaminants in flue gas., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Microbially induced carbonate precipitation (MICP) is a common biomineralization method, which is often used for remediation of heavy metal pollution such as hexavalent chromium (Cr(VI)) in recent years. Calcium sources are essential for the MICP process. This study investigated the potential of MICP technology for Cr(VI) remediation under the influence of three calcium sources (CaCl 2 , Ca(CH 3 COO) 2 , Ca(C 6 H 11 O 7 ) 2 ). The results indicated that CaCl 2 was the most efficient in the mineralization of Cr(VI), and Ca(C 6 H 11 O 7 ) 2 could significantly promote Cr(VI) reduction. The addition of different calcium sources all promoted the urease activity of Sporosarcina saromensis W5, in which the CaCl 2 group showed higher urease activity at the same Ca 2+ concentration. Besides, with CaCl 2 , Ca(CH 3 COO) 2 and Ca(C 6 H 11 O 7 ) 2 treatments, the final fraction of Cr species (Cr(VI), reduced Cr(III) and organic Cr(III)-complexes) were mainly converted to the carbonate-bound, cytoplasm and cell membrane state, respectively. Furthermore, the characterization results revealed that three calcium sources could co-precipitate with Cr species to produce Ca 10 Cr 6 O 24 (CO 3 ), and calcite and vaterite were present in the CaCl 2 and Ca(CH 3 COO) 2 groups, while only calcite was present in the Ca(C 6 H 11 O 7 ) 2 group. Overall, this study contributes to the optimization of MICP-mediated remediation of heavy metal contaminated soil. CaCl 2 was the more suitable calcium source than the other two for the application of MICP technology in the Cr(VI) reduction and mineralization., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The geological record of stable carbon isotopes preserved in marine carbonate rocks spans nearly 4 billion years. Numerous perturbations mark this record, but one stands out for its magnitude, the Lomagundi-Jatuli Event, which spanned the transition of the Earth's surface from an anoxic to an oxic state. An Applied and Environmental Microbiology article by D. Y. Sumner (90:e00093-24, 2024, https://doi.org/10.1128/aem.00093-24) provides, for the first time, a biological explanation for its initiation, cessation, environmental specific restriction, and geological singularity., Competing Interests: The author declares no conflict of interest.

Methane is a potent greenhouse gas that enters the marine system in large quantities at seafloor methane seeps. At a newly discovered seep site off the coast of Point Dume, CA, ~ meter-scale carbonate chimneys host microbial communities that exhibit the highest methane-oxidizing potential recorded to date. Here, we provide a detailed assessment of chimney geobiology through correlative mineralogical, geochemical, and microbiological studies of seven chimney samples in order to clarify the longevity and heterogeneity of these highly productive systems. U-Th dating indicated that a methane-driven carbonate precipitating system at Point Dume has existed for ~20 Kyr, while millimeter-scale variations in carbon and calcium isotopic values, elemental abundances, and carbonate polymorphs revealed changes in carbon source, precipitation rates, and diagenetic processes throughout the chimneys' lifespan. Microbial community analyses revealed diverse modern communities with prominent anaerobic methanotrophs, sulfate-reducing bacteria, and Anaerolineaceae; communities were more similar within a given chimney wall transect than in similar horizons of distinct structures. The chimneys represent long-lived repositories of methane-oxidizing communities and provide a window into how carbon can be transformed, sequestered, and altered over millennia at the Point Dume methane seep., (© 2024 John Wiley & Sons Ltd.)

Carbonate bound arsenic act as an important reservoir for arsenic (As) in nature aquifers. Sulfate-reducing bacteria (SRB), one of the dominant bacterial species in reductive groundwater, profoundly affects the biogeochemical cycling of As. However, whether and how SRB act on the migration and transformation of carbonate bound arsenic remains to be elucidated. Batch culture experiment was employed using filed collected arsenic bearing calcite to investigate the release and species transformation of As by SRB. We found that arsenic in the carbonate samples mostly exist as inorganic As(V) (93.92 %) and As(III). The present of SRB significantly facilitated arsenic release from carbonates with a maximum of 22.3 μg/L. The main release mechanisms of As by SRB include 1) calcite dissolution and the liberate of arsenic in calcite lattices, and 2) the break of H-bonds frees arsenic absorbed on carbonate surface. A redistribution of arsenic during culture incubation took place which may due to the precipitation of As 2 S x or secondary FeAl minerals. To our best knowledge, it is the first experimental study focusing on the release of carbonate bound arsenic by SRB. This study provides new insights into the fate and transport of arsenic mediated by microorganism within high arsenic groundwater-sediment system., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Introduction: The level of atmospheric CO 2 has continuously been increasing and the resulting greenhouse effects are receiving attention globally. Carbon removal from the atmosphere occurs naturally in various ecosystems. Among them, saline environments contribute significantly to the global carbon cycle. Carbonate deposits in the sediments of salt lakes are omnipresent, and the biological effects, especially driven by halophilic microalgae and bacteria, on carbonate formation remain to be elucidated., Objectives: The present study aims to characterize the carbonates formed in saline environments and demonstrate the mechanisms underlying biological-driven CO 2 removal via microalgal-bacterial consortium., Methods: The carbonates naturally formed in saline environments were collected and analyzed. Two saline representative organisms, the photosynthetic microalga Dunaliella salina and its mutualistic halophilic bacteria Nesterenkonia sp. were isolated from the inhabiting saline environment and co-cultivated to study their biological effects on carbonates precipitation and isotopic composition. During this process, electrochemical parameters and Ca 2+ flux, and expression of genes related to CaCO 3 formation were analyzed. Genome sequencing and metagenomic analysis were conducted to provide molecular evidence., Results: The results showed that natural saline sediments are enriched with CaCO 3 and enrichment of genes related to photosynthesis and ureolysis. The co-cultivation stimulated 54.54% increase in CaCO 3 precipitation and significantly promoted the absorption of external CO 2 by 49.63%. A pH gradient was formed between the bacteria and algae culture, creating 150.22 mV of electronic potential, which might promote Ca 2+ movement toward D. salina cells. Based on the results of lab-scale induction and 13 C analysis, a theoretical calculation indicates a non-negligible amount of 0.16 and 2.3 Tg C/year carbon sequestration in China and global saline lakes, respectively., Conclusion: The combined effects of these two typical representative species have contributed to the carbon sequestration in saline environments, by promoting Ca 2+ influx and increase of pH via microalgal and bacterial metabolic processes., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Production and hosting by Elsevier B.V.)

Biocrust inoculation and microbially induced carbonate precipitation (MICP) are tools used in restoring degraded arid lands. It remains unclear whether the ecological functions of the two tools persist when these methods are combined and subjected to freeze-thaw (FT) cycles. We hypothesized a synergetic interaction between MICP treatment and biocrust under FT cycles, which would allow both components to retain their ecological functions. We grew cyanobacterial (Nostoc commune) biocrusts on bare soil and on MICP (Sporosarcina pasteurii)-treated soil, subjecting them to repeated FT cycles simulating the Mongolian climate. Generalized linear modeling revealed that FT cycling did not affect physical structure or related functions but could increase the productivity and reduce the nutrient condition of the crust. The results confirm the high tolerance of MICP-treated soil and biocrust to FT cycling. MICP treatment + biocrust maintained higher total carbohydrate content under FT stress. Our study indicates that biocrust on biomineralized soil has a robust enough structure to endure FT cycling during spring and autumn and to promote restoration of degraded lands., (© 2024. The Author(s).)

Transferrin 1 (Tsf1) is an insect-specific iron-binding protein that is abundant in hemolymph and other extracellular fluids. It binds iron tightly at neutral pH and releases iron under acidic conditions. Tsf1 influences the distribution of iron in the body and protects against infection. Elucidating the mechanisms by which Tsf1 achieves these functions will require an understanding of how Tsf1 binds and releases iron. Previously, crystallized Tsf1 from Manduca sexta was shown to have a novel type of iron coordination that involves four iron-binding ligands: two tyrosine residues (Tyr90 and Tyr204), a buried carbonate anion, and a solvent-exposed carbonate anion. The solvent-exposed carbonate anion was bound by a single amino acid residue, a highly conserved asparagine at position 121 (Asn121); thus, we predicted that Asn121 would be essential for high-affinity iron binding. To test this hypothesis, we analyzed the iron-binding and -release properties of five forms of recombinant Tsf1: wild-type, a Y90F/Y204F double mutant (negative control), and three Asn121 mutants (N121A, N121D and N121S). Each of the Asn121 mutants exhibited altered spectral properties, confirming that Asn121 contributes to iron coordination. The N121D and N121S mutations resulted in slightly lower affinity for iron, especially at acidic pH, while iron binding and release by the N121A mutant was indistinguishable from that of the wild-type protein. The surprisingly minor consequences of mutating Asn121, despite its high degree of conservation in diverse insect species, suggest that Asn121 may play a role that is essential in vivo but non-essential for high affinity iron binding in vitro., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Seawater intrusion in coastal aquifers is a significant problem that can be addressed through the construction of subsurface dams or physical cut-off barriers. An alternative method is the use of microbially induced carbonate precipitation (MICP) to reduce the hydraulic conductivity of the porous medium and create a physical barrier. However, the effectiveness of this method depends on various factors, and the scientific literature presents conflicting results, making it challenging to generalise the findings. To overcome this challenge, a statistical and machine learning (ML) approach is employed to infer the causes for the reduction in hydraulic conductivity and identify the optimum MICP parameters for preventing seawater intrusion. The study involves data curation, exploratory analysis, and the development of various models to fit the input data (k-Nearest Neighbours - kNN, Support Vector Regression - SVR, Random Forests - RF, Gradient Boosting - XgBoost, Linear model with interaction terms, Ensemble learning algorithms with weighted averages - EnL-WA and stacking - EnL-Stack). The models performed reasonably well in the region where permeability reduction is sensitive to carbonate increase capturing the permeability reduction profile with respect to cementation level while demonstrating that they can be used in initial assessments of the specific conditions (e.g., soil properties). The best performing algorithms were the EnL-Stack and RF followed by XgBoost and SVR. The MICP method is effective in reducing hydraulic conductivity provided that the various biochemical parameters are optimised. Critical biochemical parameters for successful MICP formulations are the bacterial optical density, the urease activity, calcium chloride concentration and flow rate as well as the interaction terms across the properties of the porous media and the biochemical parameters. The models were used to identify the optimum MICP formulation for various porous media properties and the maximum permeability reduction profiles across cementation levels have been derived., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests. Charalampos Konstantinou reports financial support was provided by Cyprus Research Promotion Foundation. Yuze Wang reports financial support was provided by Science and Technology Innovation Committee of Shenzhen. Yuze Wang reports financial support was provided by Natural Science Foundation of China. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

Restoration is increasingly seen as a necessary tool to reverse ecological decline across terrestrial and marine ecosystems. 1 , 2 Considering the unprecedented loss of coral cover and associated reef ecosystem services, active coral restoration is gaining traction in local management strategies and has recently seen major increases in scale. However, the extent to which coral restoration may restore key reef functions is poorly understood. 3 , 4 Carbonate budgets, defined as the balance between calcium carbonate production and erosion, influence a reef's ability to provide important geo-ecological functions including structural complexity, reef framework production, and vertical accretion. 5 Here we present the first assessment of reef carbonate budget trajectories at restoration sites. The study was conducted at one of the world's largest coral restoration programs, which transplants healthy coral fragments onto hexagonal metal frames to consolidate degraded rubble fields. 6 Within 4 years, fast coral growth supports a rapid recovery of coral cover (from 17% ± 2% to 56% ± 4%), substrate rugosity (from 1.3 ± 0.1 to 1.7 ± 0.1) and carbonate production (from 7.2 ± 1.6 to 20.7 ± 2.2 kg m -2 yr -1 ). Four years after coral transplantation, net carbonate budgets have tripled and are indistinguishable from healthy control sites (19.1 ± 3.1 and 18.7 ± 2.2 kg m -2 yr -1 , respectively). However, taxa-level contributions to carbonate production differ between restored and healthy reefs due to the preferential use of branching corals for transplantation. While longer observation times are necessary to observe any self-organization ability of restored reefs (natural recruitment, resilience to thermal stress), we demonstrate the potential of large-scale, well-managed coral restoration projects to recover important ecosystem functions within only 4 years., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Photosynthesis by marine diatoms contributes significantly to the global carbon cycle. Due to the low concentration of CO 2 in seawater, many diatoms use extracellular carbonic anhydrase (eCA) to enhance the supply of CO 2 to the cell surface. While much research has investigated how the requirement for eCA is influenced by changes in CO 2 availability, little is known about how eCA contributes to CO 2 supply following changes in the demand for carbon. We therefore examined how changes in photosynthetic rate influence the requirement for eCA in three centric diatoms. Modeling of cell surface carbonate chemistry indicated that diffusive CO 2 supply to the cell surface was greatly reduced in large diatoms at higher photosynthetic rates. Laboratory experiments demonstrated a trend of an increasing requirement for eCA with increasing photosynthetic rate that was most pronounced in the larger species, supporting the findings of the cellular modeling. Microelectrode measurements of cell surface pH and O 2 demonstrated that individual cells exhibited an increased contribution of eCA to photosynthesis at higher irradiances. Our data demonstrate that changes in carbon demand strongly influence the requirement for eCA in diatoms. Cell size and photosynthetic rate will therefore be key determinants of the mode of dissolved inorganic carbon uptake., (© 2023 The Authors. Journal of Phycology published by Wiley Periodicals LLC on behalf of Phycological Society of America.)

Carbonate-rich soils limit plant performance and crop production. Previously, local adaptation to carbonated soils was detected in wild Arabidopsis thaliana accessions, allowing the selection of two demes with contrasting phenotypes: A1 (carbonate tolerant, c+) and T6 (carbonate sensitive, c-). Here, A1 (c+) and T6 (c - ) seedlings were grown hydroponically under control (pH 5.9) and bicarbonate conditions (10 mM NaHCO 3 , pH 8.3) to obtain ionomic profiles and conduct transcriptomic analysis. In parallel, A1 (c+) and T6 (c - ) parental lines and their progeny were cultivated on carbonated soil to evaluate fitness and segregation patterns. To understand the genetic architecture beyond the contrasted phenotypes, a bulk segregant analysis sequencing (BSA-Seq) was performed. Transcriptomics revealed 208 root and 2503 leaf differentially expressed genes in A1 (c+) versus T6 (c - ) comparison under bicarbonate stress, mainly involved in iron, nitrogen and carbon metabolism, hormones and glycosylates biosynthesis. Based on A1 (c+) and T6 (c - ) genome contrasts and BSA-Seq analysis, 69 genes were associated with carbonate tolerance. Comparative analysis of genomics and transcriptomics discovered a final set of 18 genes involved in bicarbonate stress responses that may have relevant roles in soil carbonate tolerance., (© 2023 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.)

High carbonate alkalinity is one of the major stress factors for survival of aquatic animals in saline-alkaline water. Exopalaemon carinicauda is a good model for studying the saline-alkaline adaption mechanism in crustacean because of its great adaptive capacity to alkalinity stress. In this study, non-targeted liquid chromatography-mass spectrometry (LC-MS) metabolomics analyses based on high-throughput RNA sequencing (RNA-Seq) were used to study the metabolomic responses of hepatopancreas in E. carinicauda at 12 h and 36 h after acute carbonate alkalinity stress. The results revealed that most of the significantly differential metabolites were related to the lipid metabolism. In particular, the sphingolipid metabolism was observed at 12 h, the glycerophospholipid metabolism was detected at 36 h, and the linoleic acid metabolic pathway was significantly enriched at both 12 h and 36 h. The combined transcriptome and metabolome analysis showed that energy consumption increased at 12 h, resulting in significant enrichment of AMPK signaling pathways, which contributed to maintain energy homeostasis. Subsequently, the hepatopancreas provided sufficient energy supply through cAMP signaling pathway and glycerophosphate metabolism to maintain normal metabolic function at 36 h. These findings might help to understand the molecular mechanisms of the E. carinicauda under carbonate alkalinity stress, thereby promote the research and development of saline-alkaline resistant shrimp., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Low pH conditions, associated with ocean acidification, represent threats to many commercially and ecologically important organisms, including bivalves. However, there are knowledge gaps regarding factors explaining observed differences in biological responses to low pH in laboratory experiments. Specific sources of local adaptation such as upwelling exposure and the role of experimental design, such as carbonate chemistry parameter changes, should be considered. Linking upwelling exposure, as an individual oceanographic phenomenon, to responses measured in laboratory experiments may further our understanding of local adaptation to global change. Here, meta-analysis is used to test the hypotheses that upwelling exposure and experimental design affect outcomes of individual, laboratory-based studies that assess bivalve metabolic (clearance and respiration rate) responses to low pH. Results show that while bivalves generally decrease metabolic activity in response to low pH, upwelling exposure and experimental design can significantly impact outcomes. Bivalves from downwelling or weak upwelling areas decrease metabolic activity in response to low pH, but bivalves from strong upwelling areas increase or do not change metabolic activity in response to low pH. Furthermore, experimental temperature, exposure time and magnitude of the change in carbonate chemistry parameters all significantly affect outcomes. These results suggest that bivalves from strong upwelling areas may be less sensitive to low pH. This furthers our understanding of local adaptation to global change by demonstrating that upwelling alone can explain up to 49 % of the variability associated with bivalve metabolic responses to low pH. Furthermore, when interpreting outcomes of individual, laboratory experiments, scientists should be aware that higher temperatures, shorter exposure times and larger changes in carbonate chemistry parameters may increase the chance of suppressed metabolic activity., Competing Interests: Declaration of competing interest The authors declare no competing interests. Financial support was provided by the New York Ocean Action Plan via New York Sea Grant (grant No. R/FBF-39)., (Copyright © 2023 Elsevier B.V. All rights reserved.)

With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016-2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ω cf ) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ω cf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus., (© 2023. The Author(s).)

Phosphorus is a limiting nutrient that is thought to control oceanic oxygen levels to a large extent 1-3 . A possible increase in marine phosphorus concentrations during the Ediacaran Period (about 635-539 million years ago) has been proposed as a driver for increasing oxygen levels 4-6 . However, little is known about the nature and evolution of phosphorus cycling during this time 4 . Here we use carbonate-associated phosphate (CAP) from six globally distributed sections to reconstruct oceanic phosphorus concentrations during a large negative carbon-isotope excursion-the Shuram excursion (SE)-which co-occurred with global oceanic oxygenation 7-9 . Our data suggest pulsed increases in oceanic phosphorus concentrations during the falling and rising limbs of the SE. Using a quantitative biogeochemical model, we propose that this observation could be explained by carbon dioxide and phosphorus release from marine organic-matter oxidation primarily by sulfate, with further phosphorus release from carbon-dioxide-driven weathering on land. Collectively, this may have resulted in elevated organic-pyrite burial and ocean oxygenation. Our CAP data also seem to suggest equivalent oceanic phosphorus concentrations under maximum and minimum extents of ocean anoxia across the SE. This observation may reflect decoupled phosphorus and ocean anoxia cycles, as opposed to their coupled nature in the modern ocean. Our findings point to external stimuli such as sulfate weathering rather than internal oceanic phosphorus-oxygen cycling alone as a possible control on oceanic oxygenation in the Ediacaran. In turn, this may help explain the prolonged rise of atmospheric oxygen levels., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Calcium carbonate formation is the primary pathway by which carbon is returned from the ocean-atmosphere system to the solid Earth 1,2 . The removal of dissolved inorganic carbon from seawater by precipitation of carbonate minerals-the marine carbonate factory-plays a critical role in shaping marine biogeochemical cycling 1,2 . A paucity of empirical constraints has led to widely divergent views on how the marine carbonate factory has changed over time 3-5 . Here we use geochemical insights from stable strontium isotopes to provide a new perspective on the evolution of the marine carbonate factory and carbonate mineral saturation states. Although the production of carbonates in the surface ocean and in shallow seafloor settings have been widely considered the predominant carbonate sinks for most of the history of the Earth 6 , we propose that alternative processes-such as porewater production of authigenic carbonates-may have represented a major carbonate sink throughout the Precambrian. Our results also suggest that the rise of the skeletal carbonate factory decreased seawater carbonate saturation states., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Serum transferrin (sTf) is a bi-lobal protein. Each lobe of sTf binds one Fe 3+ ion in the presence of a synergistic anion. Physiologically, carbonate is the main synergistic anion but other anions such as oxalate, malonate, glycolate, maleate, glycine, etc. can substitute for carbonate in vitro. The present work provides the possible pathways by which the substitution of carbonate with oxalate affects the structural, kinetic, thermodynamic, and functional properties of blood plasma sTf. Analysis of equilibrium experiments measuring iron release and structural unfolding of carbonate and oxalate bound diferric-sTf (Fe 2 sTf) as a function of pH, urea concentration, and temperature reveal that the structural and iron-centers stability of Fe 2 sTf increase by substitution of carbonate with oxalate. Analysis of isothermal titration calorimetry (ITC) scans showed that the affinity of Fe 3+ with apo-sTf is enhanced by substituting carbonate with oxalate. Analysis of kinetic and thermodynamic parameters measured for the iron release from the carbonate and oxalate bound monoferric-N-lobe of sTf (Fe N sTf) and Fe 2 sTf at pH 7.4 and pH 5.6 reveals that the substitution of carbonate with oxalate inhibits/retards the iron release via increasing the enthalpic barriers., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Coral-reef degradation is driving global-scale reductions in reef-building capacity and the ecological, geological, and socioeconomic functions it supports. The persistence of those essential functions will depend on whether coral-reef management is able to rebalance the competing processes of reef accretion and erosion. Here, we reconstructed census-based carbonate budgets of 46 reefs throughout the Florida Keys from 1996 to 2019. We evaluated the environmental and ecological drivers of changing budget states and compared historical trends in reef-accretion potential to millennial-scale baselines of accretion from reef cores and future projections with coral restoration. We found that historically, most reefs had positive carbonate budgets, and many had reef-accretion potential comparable to the ~3 mm year -1 average accretion rate during the peak of regional reef building ~7000 years ago; however, declines in reef-building Acropora palmata and Orbicella spp. corals following a series of thermal stress events and coral disease outbreaks resulted in a shift from positive to negative budgets for most reefs in the region. By 2019, only ~15% of reefs had positive net carbonate production. Most of those reefs were in inshore, Lower Keys patch-reef habitats with low water clarity, supporting the hypothesis that environments with naturally low irradiance may provide a refugia from thermal stress. We caution that our estimated carbonate budgets are likely overly optimistic; comparison of reef-accretion potential to measured accretion from reef cores suggests that, by not accounting for the role of nonbiological physical and chemical erosion, census-based carbonate budgets may underestimate total erosion by ~1 mm year -1 (-1.15 kg CaCO 3 m -2 year -1 ). Although the present state of Florida's reefs is dire, we demonstrate that the restoration of reef-building corals has the potential to help mitigate declines in reef accretion in some locations, which could allow some key ecosystem functions to be maintained until the threat of global climate change is addressed., (© 2022 The Authors. Global Change Biology published by John Wiley & Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Carbonate alkalinity is a major environmental stress factor affecting aquatic feed configuration, which easily causes oxidative stress and hypoimmunity for fish. Hence, the purpose of the study is to assess the potential effect of phosphorus on growth, intestinal oxidation resistance, physical barrier function, and microflora for Songpu mirror carp ( Cyprinus carpio Songpu) (initial average weight of 2.95 ± 0.21 g) reared at the high-concentration carbonate alkalinity environment. A two-factor, three-level (2 × 3) design was applied, in which diets with three different phosphorus levels (3.6, 7.0, and 10.5 g/kg dry matter) were randomly assigned to 0 and 15 mmol/L carbonate alkalinity groups with three replicate aquariums. After the 8-week trial, we found that weight gain rate (WGR), specific growth rate (SGR), protein efficiency ratio (PER), and lipase and amylase activities in the intestine significantly ( p < 0.05) declined with increasing carbonate alkalinity. Carbonate alkalinity of 15 mmol/L significantly reduced glutathione peroxidase (GSHPx) activities in the intestine ( p < 0.05). The relative expressions of nuclear factor (erythroid-derived 2)-like 2 (Nrf2), glutathione peroxidase 1a (GPX1a), Clautin3, Clautin11, and tumor necrosis factor β (TNF-β) in the intestine were markedly downregulated by increasing carbonate alkalinity levels ( p < 0.05), whilst the relative expressions of interleukin 1β (IL-1β) and tumor necrosis factor α (TNF-α) in the intestine were markedly upregulated ( p < 0.05). At the 15 mmol/L carbonate alkalinity treatment, Songpu mirror carp suffer from hypoimmunity status with failed digestion, antioxidant, inflammation, and immune response, thereby inducing impaired growth. Additionally, significant increments in the abundance of Proteobacteria and a significant decrease in the abundance of Fusobacteria and the Firmicutes/Bacteroidetes ratio were caused due to excessively high carbonate alkalinity (15 mmol/L) and excessively low dietary phosphorus supply (3.6 g/kg). Collectively, 7.0 g/kg dietary phosphorus supplementation was effective in promoting intestinal antioxidant enzyme activities and the corresponding gene expression via the Keap1-Nrf2 signaling pathway and in enhancing intestinal immunity by upregulating anti-inflammatory and downregulating pro-inflammatory genes. Appropriate dietary phosphorus supply could promote the formation of beneficial microflora in freshwater, and it has the potential ability to transfer the adverse effect of carbonate alkalinity stress to the structural composition of intestinal microflora. Hence, consideration should be given to suitable phosphorus supply for fish under the chronic carbonate alkalinity stress., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Fan, Wu, Li, Li, Zheng and Wang.)

Two massive precipitation events of polymetallic ore deposits, encrusted by a mixture of authigenic carbonates, are documented from the Cambrian of the semi-enclosed Baltoscandian Basin. δ 34 S (‒9.33 to ‒2.08‰) and δ 33 S (‒4.75 to ‒1.06‰) values from the basal sulphide breccias, sourced from contemporaneous Pb-Zn-Fe-bearing vein stockworks, reflect sulphide derived from both microbial and abiotic sulphate reduction. Submarine metalliferous deposits were triggered by non-buoyant hydrothermal plumes: plumes of buoyant fluid were trapped by water column stratification because their buoyancy with respect to the environment reversed, fluids became heavier than their surroundings and gravitational forces brought them to a halt, spreading out laterally from originating vents and resulting in the lateral dispersion of effluents and sulphide particle settling. Subsequently, polymetallic exhalites were sealed by carbonate crusts displaying three generations of ikaite-to-aragonite palisade crystals, now recrystallized to calcite and subsidiary vaterite. T h of fluid inclusions in early calcite crystals, ranging from 65 to 78 ºC, provide minimum entrapment temperatures for carbonate precipitation and early recrystallization. δ 13 C carb (‒1.1 to + 1.6‰) and δ 18 O carb (‒7.6 to ‒6.5‰) values are higher than those preserved in contemporaneous glendonite concretions (‒8.5 to ‒4.7‰ and ‒12.4 to ‒9.1‰, respectively) embedded in kerogenous shales, the latter related to thermal degradation of organic matter. Hydrothermal discharges graded from highly reduced, acidic, metalliferous, and hot (~ 150 ºC) to slightly alkaline, calcium-rich and warm (< 100 ºC), controlling the precipitation of authigenic carbonates., (© 2022. The Author(s).)

Cyanobacteria have massively contributed to carbonate deposition over the geological history. They are traditionally thought to biomineralize CaCO3 extracellularly as an indirect byproduct of photosynthesis. However, the recent discovery of freshwater cyanobacteria-forming intracellular amorphous calcium carbonates (iACC) challenges this view. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and evolutionary history remain elusive. Here, using comparative genomics, we identify a new gene (ccyA) and protein family (calcyanin) possibly associated with cyanobacterial iACC biomineralization. Proteins of the calcyanin family are composed of a conserved C-terminal domain, which likely adopts an original fold, and a variable N-terminal domain whose structure allows differentiating four major types among the 35 known calcyanin homologs. Calcyanin lacks detectable full-length homologs with known function. The overexpression of ccyA in iACC-lacking cyanobacteria resulted in an increased intracellular Ca content. Moreover, ccyA presence was correlated and/or colocalized with genes involved in Ca or HCO3- transport and homeostasis, supporting the hypothesis of a functional role of calcyanin in iACC biomineralization. Whatever its function, ccyA appears as diagnostic of intracellular calcification in cyanobacteria. By searching for ccyA in publicly available genomes, we identified 13 additional cyanobacterial strains forming iACC, as confirmed by microscopy. This extends our knowledge about the phylogenetic and environmental distribution of cyanobacterial iACC biomineralization, especially with the detection of multicellular genera as well as a marine species. Moreover, ccyA was probably present in ancient cyanobacteria, with independent losses in various lineages that resulted in a broad but patchy distribution across modern cyanobacteria., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Minerals are formed by organisms in all of the kingdoms of life. Mineral formation pathways all involve uptake of ions from the environment, transport of ions by cells, sometimes temporary storage, and ultimately deposition in or outside of the cells. Even though the details of how all this is achieved vary enormously, all pathways need to respect both the chemical limitations of ion manipulation, as well as the many "housekeeping" roles of ions in cell functioning. Here we provide a chemical perspective on the biological pathways of biomineralization. Our approach is to compare and contrast the ion pathways involving calcium, phosphate, and carbonate in three very different organisms: the enormously abundant unicellular marine coccolithophores, the well investigated sea urchin larval model for single crystal formation, and the complex pathways used by vertebrates to form their bones. The comparison highlights both common and unique processes. Significantly, phosphate is involved in regulating calcium carbonate deposition and carbonate is involved in regulating calcium phosphate deposition. One often overlooked commonality is that, from uptake to deposition, the solutions involved are usually supersaturated. This therefore requires not only avoiding mineral deposition where it is not needed but also exploiting this saturated state to produce unstable mineral precursors that can be conveniently stored, redissolved, and manipulated into diverse shapes and upon deposition transformed into more ordered and hence often functional final deposits.

Biomineralization is a ubiquitous process in organisms to produce biominerals, and a wide range of metallic nanoscale minerals can be produced as a consequence of the interactions of micro-organisms with metals and minerals. Copper-bearing nanoparticles produced by biomineralization mechanisms have a variety of applications due to their remarkable catalytic efficiency, antibacterial properties and low production cost. In this study, we demonstrate the biotechnological potential of copper carbonate nanoparticles (CuNPs) synthesized using a carbonate-enriched biomass-free ureolytic fungal spent culture supernatant. The efficiency of the CuNPs in pollutant remediation was investigated using a dye (methyl red) and a toxic metal oxyanion, chromate Cr(VI). The biogenic CuNPs exhibited excellent catalytic properties in a Fenton-like reaction to degrade methyl red, and efficiently removed Cr(VI) from solution due to both adsorption and reduction of Cr(VI). X-ray photoelectron spectroscopy (XPS) identified the oxidation of reducing Cu species of the CuNPs during the reaction with Cr(VI). This work shows that urease-positive fungi can play an important role not only in the biorecovery of metals through the production of insoluble nanoscale carbonates, but also provides novel and simple strategies for the preparation of sustainable nanomineral products with catalytic properties applicable to the bioremediation of organic and metallic pollutants, solely and in mixtures.

Abstract: Infarct size is a major determinant of outcomes after acute myocardial infarction (AMI). Carbon monoxide-releasing molecules (CORMs), which deliver nanomolar concentrations of carbon monoxide to tissues, have been shown to reduce infarct size in rodents. We evaluated efficacy and safety of CORM-A1 to reduce infarct size in a clinically relevant porcine model of AMI. We induced AMI in Yorkshire White pigs by inflating a coronary angioplasty balloon to completely occlude the left anterior descending artery for 60 minutes, followed by deflation of the balloon to mimic reperfusion. Fifteen minutes after balloon occlusion, animals were given an infusion of 4.27 mM CORM-A1 (n = 7) or sodium borate control (n = 6) over 60 minutes. Infarct size, cardiac biomarkers, ejection fraction, and hepatic and renal function were compared amongst the groups. Immunohistochemical analyses were performed to compare inflammation, cell proliferation, and apoptosis between the groups. CORM-A1-treated animals had significant reduction in absolute infarct area (158 ± 16 vs. 510 ± 91 mm2, P < 0.001) and infarct area corrected for area at risk (24.8% ± 2.6% vs. 45.2% ± 4.0%, P < 0.0001). Biochemical markers of myocardial injury also tended to be lower and left ventricular function tended to recover better in the CORM-A1 treated group. There was no evidence of hepatic or renal toxicity with the doses used. The cardioprotective effects of CORM-A1 were associated with a significant reduction in cell proliferation and inflammation. CORM-A1 reduces infarct size and improves left ventricular remodeling and function in a porcine model of reperfused MI by a reduction in inflammation. These potential cardioprotective effects of CORMs warrant further translational investigations., Competing Interests: The authors report no conflicts of interest., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Background and Aims: Bone turnover is strongly affected by pH of surrounding fluid, and in turn plays a role in maintaining systemic pH, however the quantitative contribution of bone processes to pH regulation is not known. Our goal was to develop a mathematical model describing pH regulation in the interstitial fluid and to examine the contribution of hydroxyapatite dissolution and precipitation to pH regulation., Materials and Methods: We modeled twelve reversible equilibrium reactions of sixteen calcium, phosphate, hydrogen and carbonate species in the interstitial fluid and examined the buffering capacity and range. The effect of hydroxyapatite dissolution and precipitation was modeled by assuming that the calcium, phosphate and hydroxide contained in the bone volume adjacent to the interstitial fluid is instantaneously added to or removed from the interstitial fluid., Results: The carbonate buffer was found to dominate electrochemical buffering system of the bone interstitial fluid. Nevertheless, the phosphate added during dissolution of bone hydroxyapatite significantly improved the interstitial fluid buffering capacity. In contrast, hydroxyapatite precipitation had limited effect on the interstitial fluid pH regulation., Conclusion: This study provides mechanistic insights into the physicochemical processes underlying the known role of bone turnover processes in regulation of body pH homeostasis., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Microbial activities can change the properties of biofilm/metal interfaces to accelerate or decelerate the corrosion of metals in a given environment. Microbiologically influenced corrosion inhibition (MICI) is the inhibition of corrosion that is directly or indirectly induced by microbial action. Compared with conventional methods for protection from corrosion, MICI is environmentally friendly and an emerging approach for the prevention and treatment of (bio)corrosion. However, due to the diversity of microorganisms and the fact that their metabolic processes are greatly complicated by environmental factors, MICI is still facing challenges for practical application. This review provides a comprehensive overview of the mechanisms of MICI under different conditions and their advantages and disadvantages for potential applications in corrosion protection., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Aims: Various applications of microbially induced carbonate precipitation (MICP) has been proposed. However, most studies use cultured pure strains to obtain MICP, ignoring advantages of microbial consortia. The aims of this study were to: (i) test the feasibility of a microbial consortium to produce MICP; (ii) identify functional micro-organisms and their relationship; (iii) explain the MICP mechanism; (iv) propose a way of applying the MICP technique to soil media., Methods and Results: Anaerobic sludge was used as the source of the microbial consortium. A laboratory anaerobic sequencing batch reactor and beaker were used to perform precipitation experiment. The microbial consortium produced MICP with an efficiency of 96·6%. XRD and SEM analysis showed that the precipitation composed of different-size calcite crystals. According to high-throughput 16S rRNA gene sequencing, the functional micro-organisms included acetogenic bacteria, acetate-oxidizing bacteria and archaea Methanosaeta and Methanobacterium beijingense. The methanogenesis acetate degradation provides dissolved inorganic carbon and increases pH for MICP. A series of reactions catalysed by many enzymes and cofactors of methanogens and acetate-oxidizers are involved in the acetate degradation., Conclusion: This work demonstrates the feasibility of using the microbial consortium to achieve MICP from an experimental and theoretical perspective., Significance and Impact of the Study: A method of applying the microbial-consortium MICP to soil media is proposed. It has the advantages of low cost, low environmental impact, treatment uniformity and less limitations from natural soils. This method could be used to improve mechanical properties, plug pores and fix harmful elements of soil media, etc., (© 2020 The Society for Applied Microbiology.)

Photodynamic inactivation (PDI) of pathogenic bacteria is a promising technology in different applications. Thereby, a photosensitizer (PS) absorbs visible light and transfers the energy to oxygen yielding reactive oxygen species (ROS). The produced ROS are then capable of killing microorganisms via oxidative damage of cellular constituents. Among other PS, some flavins are capable of producing ROS and cationic flavins are already successfully applied in PDI. When PDI is used for example on tap water, PS like flavins will encounter various ions and other small organic molecules which might hamper the efficacy of PDI. Thus, the impact of carbonate and phosphate ions on PDI using two different cationic flavins (FLASH-02a, FLASH-06a) was investigated using Staphylococcus aureus and Pseudomonas aeruginosa as model organisms. Both were inactivated in vitro at a low light exposure of 0.72 J cm-2. Upon irradiation, FLASH-02a reacts to single substances in the presence of carbonate or phosphate, whereas the photochemical reaction for FLASH-06a was more unspecific. DPBF-assays indicated that carbonate and phosphate ions decreased the generation of singlet oxygen of both flavins. Both microorganisms could be easily inactivated by at least one PS with up to 6 log10 steps of cell counts in low ion concentrations. Using the constant radiation exposure of 0.72 J cm-2, the inactivation efficacy decreased somewhat at medium ion concentrations but reached almost zero for high ion concentrations. Depending on the application of PDI, the presence of carbonate and phosphate ions is unavoidable. Only upon light irradiation such ions may attack the PS molecule and reduce the efficacy of PDI. Our results indicate concentrations for carbonate and phosphate, in which PDI can still lead to efficient reduction of bacterial cells when using flavin based PS., Competing Interests: Andreas Späth received salaries from the TriOptoTec GmbH. This does not alter our adherence to PLOS ONE policies on sharing data and materials. The other authors have declared that no competing interests exist.

Coral reefs protect islands, coastal areas, and their inhabitants from storm waves and provide essential goods and services to millions of people worldwide. Yet contemporary rates of ocean warming and local disturbances are jeopardizing the reef-building capacity of coral reefs to keep up with rapid rates of sea-level rise. This study compared the reef-building capacity of shallow-water habitats at 142 sites across a potential thermal-stress gradient in the tropical Pacific Ocean. We sought to determine the extent to which habitat differences and environmental variables potentially affect rates of net carbonate production. In general, outer-exposed reefs and lagoonal-patch reefs had higher rates of net carbonate production than nearshore reefs. The study found that thermal anomalies, particularly the intensity of thermal-stress events, play a significant role in reducing net carbonate production-evident as a diminishing trend of net carbonate production from the western to the central tropical Pacific Ocean. The results also showed a latent spatial effect along the same gradient, not explained by thermal stress, suggesting that reefs in the western tropical Pacific Ocean are potentially enhanced by the proximity of reefs in the Coral Triangle-an effect that diminishes with increasing distance and isolation., Competing Interests: The authors declare no competing interests.

Packed red blood cells (pRBCs), the most commonly transfused blood product, are exposed to environmental disruptions during storage in blood banks. In this study, temporal sequence of changes in the ion exchange in pRBCs was analyzed. Standard techniques commonly used in electrolyte measurements were implemented. The relationship between ion exchange and red blood cells (RBCs) morphology was assessed with use of atomic force microscopy with reference to morphological parameters. Variations observed in the Na + , K + , Cl - , H + , HCO 3 - , and lactate ions concentration show a complete picture of singly-charged ion changes in pRBCs during storage. Correlation between the rate of ion changes and blood group type, regarding the limitations of our research, suggested, that group 0 is the most sensitive to the time-dependent ionic changes. Additionally, the impact of irreversible changes in ion exchange on the RBCs membrane was observed in nanoscale. Results demonstrate that the level of ion leakage that leads to destructive alterations in biochemical and morphological properties of pRBCs depend on the storage timepoint.

Biomineralization processes are of key importance in the biogeochemical cycling of metals and other elements by microorganisms, and several studies have highlighted the potential applications of nanoparticle synthesis via biomineralization. The roles played by proteins in the transformation and biologically induced biomineralization of metals by microorganisms is not well understood, despite the interactions of protein and nanoparticles at mineral interfaces attracting much interest in various emerging fields for novel biomaterial synthesis. Here, we have elucidated the association and involvement of fungal proteins in the formation of biogenic copper carbonate nanoparticles (CuNPs) using a carbonate-enriched biomass-free ureolytic fungal culture supernatant. Proteomic analysis was conducted that identified the major proteins present in the culture supernatant. Of the proteins identified, triosephosphate isomerase (TPI) exhibited a strong affinity to the CuNPs, and the impact of purified TPI on CuNP formation was studied in detail. The combined use of scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) confirmed that TPI played an important role in controlling the morphology and structure of the nanomaterials. Fourier transform infrared spectroscopy (FTIR) was applied to examine conformational changes of the proteins to further clarity the interaction mechanisms with CuNPs during biomineralization. Such analyses revealed unfolding of proteins on the mineral surface and an increase in β sheets within the protein structure. These results extend understanding of how microbial systems can influence biomineral formation through protein secretion, the mechanisms involved in formation of complex protein/inorganic systems, and provide useful guidelines for the synthesis of inorganic-protein based nanomaterials., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Speleothems (dominated by cave-hosted carbonate deposits) are valuable archives of paleoclimate conditions. As such, they are potential targets of clumped isotope analyses that may yield quantified data about past temperature variations. Clumped isotope analyses of stalagmites, however, seldom provide useful temperature values due to various isotope fractionation processes. This study focuses on the determination of the microbially induced vital effect, i.e., the isotope fractionation processes related to bacterial carbonate production. A cave site with biologically mediated amorphous calcium carbonate precitation was selected as a natural laboratory. Calcite deposits were farmed under a UV lamp to prevent bacterial activity, as well as under control conditions. Microbiological analyses and morphological investigations using scanning electron microscopy showed that the UV lamp treatment effectively reduced the number of bacterial cells, and that bacterial carbonate production strongly influenced the carbonate's morphology. Stable oxygen isotope analyses of calcite and drip waters, as well as clumped isotope measurements revealed that, although most of the studied carbonates formed close to oxygen isotope equilibrium, clumped isotope Δ47 values varied widely from equilibrium to strongly fractionated data. Site-specific kinetic fractionations played a dominant role in the distribution of Δ47 values, whereas bacterial carbonate production did not result in a detectable clumped isotope effect., Competing Interests: The authors have declared that no competing interests exist.

Microbialites are usually carbonate-rich sedimentary rocks formed by the interplay of phylogenetically and metabolically complex microbial communities with their physicochemical environment. Yet, the biotic and abiotic determinants of microbialite formation remain poorly constrained. Here, we analysed the structure of prokaryotic and eukaryotic communities associated with microbialites occurring in several crater lakes of the Trans-Mexican volcanic belt along an alkalinity gradient. Microbialite size and community structure correlated with lake physicochemical parameters, notably alkalinity. Although microbial community composition varied across lake microbialites, major taxa-associated functions appeared quite stable with both, oxygenic and anoxygenic photosynthesis and, to less extent, sulphate reduction, as major putative carbonatogenic processes. Despite interlake microbialite community differences, we identified a microbial core of 247 operational taxonomic units conserved across lake microbialites, suggesting a prominent ecological role in microbialite formation. This core mostly encompassed Cyanobacteria and their typical associated taxa (Bacteroidetes, Planctomycetes) and diverse anoxygenic photosynthetic bacteria, notably Chloroflexi, Alphaproteobacteria (Rhodobacteriales, Rhodospirilalles), Gammaproteobacteria (Chromatiaceae) and minor proportions of Chlorobi. The conserved core represented up to 40% (relative abundance) of the total community in lakes Alchichica and Atexcac, displaying the highest alkalinities and the most conspicuous microbialites. Core microbialite communities associated with carbonatogenesis might be relevant for inorganic carbon sequestration purposes., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Microbial-induced carbonate precipitation is important in the global carbon cycle, especially in fixing atmospheric CO 2 . Many simulation experiments have shown that microbes can induce carbonate precipitation, although there is no established understanding of the mechanism. In this study, several mineralization experiments were performed using Curvibacter lanceolatus strain HJ-1, including its secreted extracellular polymeric substances (EPS) and carbonic anhydrase (CA). We found that strain HJ-1, EPS, and CA could promote carbonate precipitation if compared with the respective control experiments (CK). Also, both HJ-1 and EPS1 experiments contained calcite and aragonite, whereas CA experiments formed calcite only. Therefore, HJ-1 and EPS is favorable for carbonate precipitation, especially for aragonite. Besides, the formation of calcite in the EPS2 experiments indicated that EPS contains a trace amount of CA, which might promote CO 2 hydration and eventually lead to carbonate precipitation. It was suggested that CA only provide CO 3 2- for the formation of carbonate minerals. In the absence of exogenous HCO 3 -, the optimized calcification rate followed the order: HJ-1(49.5 %) > CA(6.6 %) > EPS2(4.1 %). In addition, MICP mechanisms was studied, an increase in pH and CO 2 hydration by CA play synergetic roles in providing supersaturated alkaline conditions in the system with bacteria. Finally, bacterial cells and EPS promote the formation of calcite and aragonite by acting as nucleation sites., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Rationale: Magnesium is one of the most abundant elements in the earth's crust and in seawater. Fractionation of its stable isotopes has been shown to be a useful indicator of many geological, chemical, and biological processes. For example, biogenic carbonates display an ~5‰ range of δ 26 Mg values, which is attributed to variable degrees of biological control on Mg ions during biomineralisation. Understanding this biological control is essential for developing proxies based on biogenic carbonates., Methods: In this work, we present a new approach of measuring Mg isotopes in biogenic carbonates using Laser Ablation Multi-Collector Inductively Coupled Plasma Mass Spectrometry (LA-MC-ICPMS)., Results: Our results show that this microanalytical approach provides relatively fast, high spatial resolution (<0.2 μm) measurements with high precision and accuracy down to 0.2‰ (2SE). To achieve high levels of precision and accuracy, baseline interferences need to be monitored and a carbonate standard with a relatively low trace metal composition similar to biogenic carbonates should be used. We also demonstrate that the matrix effect on Mg isotopes in carbonates with low Fe and Mn is limited to less than 0.2‰ fractionation under different laser parameters and low oxide condition (<0.3% ThO/Th)., Conclusions: Our newly developed LA-MC-ICPMS method and its applications to biogenic carbonates show significant advantages provided by the microanalytical approach in understanding complex processes of biomineralisation in marine calcifiers., (© 2020 John Wiley & Sons, Ltd.)

Using a sample from a terrestrial hot spring (pH 6.8, 60 °C), we enriched a thermophilic microbial consortium performing anaerobic autotrophic oxidation of hydrothermal siderite (FeCO 3 ), with CO 2 /bicarbonate as the electron acceptor and the only carbon source, producing green rust and acetate. In order to reproduce Proterozoic environmental conditions during the deposition of banded iron formation (BIF), we incubated the microbial consortium in a bioreactor that contained an unmixed anoxic layer of siderite, perfectly mixed N 2 /CO 2 -saturated liquid medium and microoxic (2% O 2 ) headspace. Long-term incubation (56 days) led to the formation of magnetite (Fe 3 O 4 ) instead of green rust as the main product of Fe(II) oxidation, the precipitation of newly formed metabolically induced siderite in the anoxic zone, and the deposition of hematite (Fe 2 O 3 ) on bioreactor walls over the oxycline boundary. Acetate was the only metabolic product of CO 2 /bicarbonate reduction. Thus, we have demonstrated the ability of autotrophic thermophilic microbial consortium to perform a short cycle of iron minerals transformation: siderite-magnetite-siderite, accompanied by magnetite and hematite accumulation. This cycle is believed to have driven the evolution of the early biosphere, leading to primary biomass production and deposition of the main iron mineral association of BIF.

The aim of the current study was to investigate the effect of an acidity regulator (SPORIX®), lactose, and vitamin D 3 as excipient ingredients on digestive solubility and intestinal transport of calcium from four different calcium materials (tricalcium phosphate (TCP), fish bone (FB), nano-fish bone (NFB), and algae calcium (AC)) through an in vitro digestion model system combined with Caco-2 cells. The concentration of ionized calcium (Ca 2+ ) in an aqueous fraction after in vitro digestion increased with the addition of SPORIX®, and it was further enhanced by adding SPORIX® + lactose + vitamin D 3 into TCP, FB, NFB, and AC, respectively. In particular, FB with SPORIX® + lactose + vitamin D 3 enhanced calcium ionization to 33.89 ± 0.69 mg g -1 , which was about 11.76 times higher than that of FB only. In the case of intestinal cellular uptake of calcium, there was no significant difference in all the tested calcium materials with SPORIX® + lactose + vitamin D 3 . However, the absolute amount of intestinal transport of calcium in FB (43.95 ± 3.29 μg) was significantly higher than other calcium materials with the addition of SPORIX® + lactose + vitamin D 3 (p < 0.05). This study suggests that the co-consumption of SPORIX®, lactose, and vitamin D 3 with FB could enhance the calcium bioavailability by lowering pH as well as improving calcium intestinal transport by modulating the paracellular and transcellular uptake mechanism.

Cancer cells tend to increase intracellular pH and, at the same time, are known to intensively produce and uptake polyamines such as spermine. Here, we show that various amines, including biogenic polyamines, boost the activity of proteasomes in a dose-dependent manner. Proteasome activity in the classical amine-containing buffers, such as 2-(N-morpholino)ethanesulfonic acid (MES), Tris, (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), glycylglycine, bis-Tris propane, and bicine, has a skewed distribution with a maximum at pH of 7.0-8.0. The activity of proteasomes in buffers containing imidazole and bis-Tris is maintained almost on the same level, in the pH range of 6.5-8.5. The third type of activation is observed in buffers based on the amino acids arginine and ornithine, as well as the natural polyamines spermine and spermidine. Proteasome activity in these buffers is dramatically increased at pH values greater than 7.5. Anionic buffers such as phosphate or carbonate, in contrast, inhibit proteasome activity during alkalization. Importantly, supplementation of a carbonate-phosphate buffer with spermine counteracts carbonate-driven proteasome stalling in alkaline conditions, predicting an additional physiological role of polyamines in maintaining the metabolism and survival of cancer cells.

Globally, many saline-alkali soils are rich in NaHCO 3 and Na 2 CO 3 , which are characterized by a high pH Carbonate stress caused by this kind of soil severely damages plant cells and inhibits plant growth. Biotin and HCO 3 - participate in the first and rate-limiting reaction of the fatty acid biosynthesis pathway, but whether biotin contributes to plant responses to carbonate stress is unclear. In this study, we revealed that high carbonate and biotin concentrations inhibited Arabidopsis (Arabidopsis thaliana) seedling growth. However, specific concentrations of carbonate and biotin decreased the inhibitory effects of the other compound at the germination and seedling stages. Additionally, a carbonate treatment increased the endogenous biotin content and expression of AtBIO2, which encodes a biotin synthase. Moreover, phenotypic analyses indicated that the overexpression of AtBIO2 in Arabidopsis enhanced the tolerance to carbonate stress, whereas mutations to AtBIO2 had the opposite effect. Furthermore, the carbonate stress-induced accumulation of reactive oxygen species was lower in plants overexpressing AtBIO2 than in the wild-type and bio2 mutants. Accordingly, biotin, which is an essential vitamin for plants, can enhance the resistance to carbonate stress., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Carbon monoxide (CO) is an endogenously synthesized gaseous mediator and is involved in the regulation of numerous physiological processes. Mitochondria, in which hemoproteins are abundant, are among the targets for CO action. Large-conductance calcium-activated (mitoBK Ca ) channels in the inner mitochondrial membrane share multiple biophysical similarities with the BK Ca channels of the plasma membrane and could be a potential target for CO. To test this hypothesis, the activity of the mitoBK Ca channels in human astrocytoma U-87 MG cell mitochondria was assessed with the patch-clamp technique. The effects of CO-releasing molecules (CORMs), such as CORM-2, CORM-401, and CORM-A1, were compared to the application of a CO-saturated solution to the mitoBK Ca channels in membrane patches. The applied CORMs showed pleiotropic effects including channel inhibition, while the CO-containing solution did not significantly modulate channel activity. Interestingly, CO applied to the mitoBK Ca channels, which were inhibited by exogenously added heme, stimulated the channel. To summarize, our findings indicate a requirement of heme binding to the mitoBK Ca channel for channel modulation by CO and suggest that CORMs might have complex unspecific effects on mitoBK Ca channels., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Ocean acidification (OA) represents a serious challenge to marine ecosystems. Laboratory studies addressing OA indicate broadly negative effects for marine organisms, particularly those relying on calcification processes. Growing evidence also suggests OA combined with other environmental stressors may be even more deleterious. Scaling these laboratory studies to ecological performance in the field, where environmental heterogeneity may mediate responses, is a critical next step toward understanding OA impacts on natural communities. We leveraged an upwelling-driven pH mosaic along the California Current System to deconstruct the relative influences of pH, ocean temperature, and food availability on seasonal growth, condition and shell thickness of the ecologically dominant intertidal mussel Mytilus californianus. In 2011 and 2012, ecological performance of adult mussels from local and commonly sourced populations was measured at 8 rocky intertidal sites between central Oregon and southern California. Sites coincided with a large-scale network of intertidal pH sensors, allowing comparisons among pH and other environmental stressors. Adult California mussel growth and size varied latitudinally among sites and inter-annually, and mean shell thickness index and shell weight growth were reduced with low pH. Surprisingly, shell length growth and the ratio of tissue to shell weight were enhanced, not diminished as expected, by low pH. In contrast, and as expected, shell weight growth and shell thickness were both diminished by low pH, consistent with the idea that OA exposure can compromise shell-dependent defenses against predators or wave forces. We also found that adult mussel shell weight growth and relative tissue mass were negatively associated with increased pH variability. Including local pH conditions with previously documented influences of ocean temperature, food availability, aerial exposure, and origin site enhanced the explanatory power of models describing observed performance differences. Responses of local mussel populations differed from those of a common source population suggesting mussel performance partially depended on genetic or persistent phenotypic differences. In light of prior research showing deleterious effects of low pH on larval mussels, our results suggest a life history transition leading to greater resilience in at least some performance metrics to ocean acidification by adult California mussels. Our data also demonstrate "hot" (more extreme) and "cold" (less extreme) spots in both mussel responses and environmental conditions, a pattern that may enable mitigation approaches in response to future changes in climate., Competing Interests: The authors have declared that no competing interests exist.

Reversible oxidation of thiol proteins is an important cell signalling mechanism. In many cases, this involves generation or exposure of the cells to H2O2, and oxidation of proteins that are not particularly H2O2-reactive. There is a conundrum as to how these proteins are oxidised when other highly reactive proteins such as peroxiredoxins are present. This article discusses potential mechanisms, focussing on recent evidence for oxidation being localised within the cell, redox relays involving peroxiredoxins operating in some signalling pathways, and mechanisms for facilitated or directed oxidation of specific targets. These findings help define conditions that enable redox signalling but there is still much to learn regarding mechanisms., (© 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.)

Clostridium tetani produces a potent neurotoxin, the tetanus toxin (TeNT), which is responsible for an often-fatal neurological disease (tetanus) characterized by spastic paralysis. Prevention is efficiently acquired by vaccination with the TeNT toxoid, which is obtained by C. tetani fermentation and subsequent purification and chemical inactivation. C. tetani synthesizes TeNT in a regulated manner. Indeed, the TeNT gene ( tent ) is mainly expressed in the late exponential and early stationary growth phases. The gene tetR ( tetanus regulatory gene ), located immediately upstream of tent , encodes an alternative sigma factor which was previously identified as a positive regulator of tent . In addition, the genome of C. tetani encodes more than 127 putative regulators, including 30 two-component systems (TCSs). Here, we investigated the impact of 12 regulators on TeNT synthesis which were selected based on their homology with related regulatory elements involved in toxin production in other clostridial species. Among nine TCSs tested, three of them impact TeNT production, including two positive regulators that indirectly stimulate tent and tetR transcription. One negative regulator was identified that interacts with both tent and tetR promoters. Two other TCSs showed a moderate effect: one binds to the tent promoter and weakly increases the extracellular TeNT level, and another one has a weak inverse effect. In addition, CodY (control of dciA (decoyinine induced operon) Y) but not Spo0A (sporulation stage 0) or the DNA repair protein Mfd (mutation frequency decline) positively controls TeNT synthesis by interacting with the tent promoter. Moreover, we found that inorganic phosphate and carbonate are among the environmental factors that control TeNT production. Our data show that TeNT synthesis is under the control of a complex network of regulators that are largely distinct from those involved in the control of toxin production in Clostridium botulinum or Clostridium difficile .