A comprehensive review of recent advancements in microbial-induced mineralization: biosynthesis and mechanism, with potential implementation in various environmental, engineering, and medical sectors

Biomineralization has garnered profuse attention in multidisciplinary fields. Using this strategy, living things, including eukaryotes or prokaryotes, mediate the uptake of ions from the surrounding environment, followed by assembling and depositing them as greatly configured structures inside the organic matrix. The generated biominerals, including nanomaterials, possess outstanding hierarchical structures that exceed their chemically synthesized counterparts. Despite the significant progress achieved in microbial-mediated mineralization, several key knowledge gaps remain, including mechanisms controlling biomineralization pathways and the impact of environmental factors on mineral morphology, crystallinity, and stability. This review provides a comprehensive description of this biomineralization, which can be categorized into controlled, influenced, and induced biomineralization. Interestingly, we highlighted biologically-induced mineralization approaches, such as photosynthesis, methane oxidation, and nitrogen-based metabolic pathways, and identified various chemical interactions during mineral production following analytical chemistry. This review also extensively delineates updates on application of biominerals across all fields, commencing with the remediation of deleterious pollutants and biominerals exploited in industrial sectors, moving on to using them to reinforce soil, generate biocement for construction, and delving into their utilization in pharmaceutical applications to deliver drugs, repair teeth and bones, and combat cancer and pathogenic microorganisms. Moreover, the review outlines the drawbacks and adequate solutions for biomineralization, particularly CaCO₃-mediated processes, such as the generation of ammonium and nitrate during the CaCO₃ precipitation process and the relatively slow rate of microbial-mediated mineralization. Biomineralization inspired the fabrication of smart biomaterials, which combine biological advantages. Overall, this comprehensive review discusses updated research and highlights potential approaches to future studies.

Microbial Community Shifts and Nitrogen Utilization in Peritidal Microbialites: The Role of Salinity and pH in Microbially Induced Carbonate Precipitation

Microbialites have the potential to record environmental changes and act as biosignatures of past geochemical conditions. As such, they could be used as indicators to decipher ancient rock records. Modern microbialites are primarily found in environments where competitors and destructors are absent or where biogeochemical conditions favor their continuous formation. Many previous studies have essentially focused on the role of photosynthetic microbes in controlling pH and carbonate speciation and potentially overlooked alternative non-photosynthetic pathways of carbonate precipitation. Given that microbial activity induces subtle geochemical changes, microbially induced carbonate precipitation (MICP) can involve several mechanisms, from extracellular polymeric substances (EPS), sulfate reduction, anaerobic oxidation of methane, to nitrogen cycling processes, such as ammonification, ureolysis, and denitrification. Moreover, the peritidal zone where temperate microbialites are mostly found today, is under the influence of both freshwater and seawater, arguing for successive biogeochemical processes leading to mineral saturation, and questioning interpretations of fossil records. This study investigates microbialites in three tide pools from the peritidal zone of Fongchueisha, Hengchun, Taiwan, to address the influence of salinity on microbial community composition and carbonate precipitation mechanisms. Microbial samples were collected across varying salinity gradients at multiple time points and analyzed using next-generation sequencing (NGS) of bacterial 16S and eukaryotic 18S rRNA genes. Our results indicate that dominant bacterial groups, including Cyanobacteria and Alphaproteobacteria, were largely influenced by salinity variations, albeit pH exhibited stronger correlation with community composition. Combining our results on geochemistry and taxonomic diversity over time, we inferred a shift in the trophic mode under high salinity conditions, during which the use of urea and amino acids as a nitrogen source outcompetes diazotrophy, ureolysis and ammonification of amino acids reinforcing carbonate precipitation dynamics by triggering an increase in both pH and dissolved inorganic carbon.

Modifying the antibacterial performance of Cu surfaces by topographic patterning in the micro- and nanometer scale

Antimicrobial surfaces are a promising approach to reduce the spread of pathogenic microorganisms in various critical environments. To achieve high antimicrobial functionality, it is essential to consider the material-specific bactericidal mode of action in conjunction with bacterial surface interactions. This study investigates the effect of altered contact conditions on the antimicrobial efficiency of Cu surfaces against Escherichia coli and Staphylococcus aureus. The fabrication of line-like periodic surface patterns in the scale range of single bacterial cells was achieved utilizing ultrashort pulsed direct laser interference patterning. These patterns create both favorable and unfavorable topographies for bacterial adhesion. The variation in bacteria/surface interaction is monitored in terms of strain-specific bactericidal efficiency and the role of corrosive forces driving quantitative Cu ion release. The investigation revealed that bacterial deactivation on Cu surfaces can be either enhanced or decreased by intentional topography modifications, independent of Cu ion emission, with strain-specific deviations in effective pattern scales observed. The results of this study indicate the potential of targeted topographic surface functionalization to optimize antimicrobial surface designs, enabling strain-specific decontamination strategies.

Application of Sporosarcina pasteurii for the biomineralization of calcite in the treatment of waste concrete fines

In this study, we explored and described various parameters of microbially induced calcite precipitation (MICP) using the alkaliphilic bacterium Sporosarcina pasteurii DSM 33, which exhibits ureolytic activity, to stabilize and strengthen waste concrete fines (WCF). Bacterial cell concentration, single and repeated addition of bacterial suspension, and pH adjustment were tested in stage 1 of the experimental agenda in order to tune parameters for sample preparation in stage 2 focused on the effect of MICP treatment duration (14, 30, 60, and 90 days). Two types of WCF materials differing in their physicochemical properties were used for the stabilization. The results of the EDS and XRD analyses confirmed the presence of CaCO3 crystals, which increased by about 10-12% over time, affecting the porosity, compactness, and strength of the formed composites. The XRD results also indicated that the WCF properties significantly influence the formation of the type of CaCO3 crystals, supported also by microscopy observations. This study highlights the potential of MICP technology to make concrete recycling more sustainable, aligning with the concept of a circular economy; however, the interplay between the WCF materials of various properties and bacterial activity must be further scrutinized.

Mechanisms of manganese-tolerant Bacillus brevis MM2 mediated oxytetracycline biodegradation process

Addressing the environmental threat of oxytetracycline (OTC) contamination, this study harnesses the bioremediation capabilities of Bacillus brevis MM2, a manganese-oxidizing bacterium from acid mine drainage. We demonstrate the strain's exceptional efficiency in degrading OTC under high manganese conditions, with complete removal achieved within 24 h. The degradation is facilitated by the production of Bio-MnOx, utilizing their high redox potential and large specific surface area, which significantly enhance the adsorption and oxidation of OTC. Advanced characterization techniques, including X-ray diffraction, scanning electron microscopy, High Resolution-Transmission Electronic Microscope and X-ray photoelectron spectroscopy, provide a detailed analysis of the structural and functional properties of Bio-MnOx. The study also reveals the crucial role of Mn(III) intermediates and reactive oxygen species in the OTC degradation process, with quenching experiments validating their substantial impact on efficiency. Laccase activity, a key manganese-oxidizing enzyme, is assessed spectrophotometrically, further highlighting the enzymatic contribution to Mn(II) oxidation and OTC breakdown. This research contributes valuable insights and approaches for the targeted bioremediation of OTC-contaminated aquatic environments, offering a promising strategy for combating pollution from antibiotics and analogous compounds.

The competitive and selective adsorption of heavy metals by struvite in the Pb(II)-Cd(II)-Zn(II) composite system and its environmental significance

The prevalence of struvite and other phosphate minerals in eutrophic environments has a significant effect on the transport and transformation of environmental heavy metals, but their competitive immobilization characteristics and mechanisms for heavy metals remain unclear. Three different sources of struvite (BS, CSHS, and CSS) were obtained respectively by biosynthesis and chemical synthesis with or without humic acid to investigate their competitive immobilization characteristics and mechanism of heavy metals in the Pb(II)-Cd(II)-Zn(II) composite system. The results showed that the immobilization of heavy metals by struvite is physico-chemical adsorption and the affinity (in descending order) is Pb(II) >> Cd(II)/Zn(II). Cd(II) promotes the immobilization of Pb(II)/Zn(II) by BS. The order of the selective strength by struvite for Pb(II) is BS >> CSS ≈ CSHS. The study indicates that the difference between struvite holding heavy metal ions is related to the material composition and heavy metal types, and BS shows best selective immobilization for Pb(II) in the Pb(II)-Cd(II)-Zn(II) composite system. This study provides a theoretical basis for understanding the environmental geochemical role and eco-environmental effects of struvite.

Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms

BACKGROUND

Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave's Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave.

RESULTS

The cave's biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique "CaveCurd" community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO2 content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces.

CONCLUSIONS

The Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave's ancient rock paintings.

Microbially induced calcium carbonate precipitation in fossil consolidation treatments: Preliminary results inducing exogenous Myxococcus xanthus bacteria in a miocene Cheirogaster richardi specimen

This research paper proposes Microbially Induced Calcium Carbonate Precipitation (MICP) as an innovative approach for palaeontological heritage conservation, specifically on deteriorated carbonate fossils. Due to its efficiency in bioconsolidation of carbonate ornamental rocks, Myxococcus xanthus inoculation on carbonate fossils was studied in this research. Treatment was tested on nine fossil samples from decontextualized fragments of Cheirogaster richardi specimens (Can Mata site, Hostalets de Pierola, Catalonia, Spain). The main objective was to evaluate whether treatment with Myxococcus xanthus improved fossil surface cohesion and hardness and mechanical strength without significant physicochemical and aesthetic changes to the surface. Chemical compatibility of the treatment, penetration capacity and absence of noticeable changes in substrate porosity were considered as important issues to be evaluated. Samples were analysed, before and after treatment, by scanning electron microscopy, weight control, spectrophotometry, X-ray diffraction analysis, water absorption analysis, pH and conductivity control, Vickers microindentation and tape test. Results show that hardness increases by a factor of almost two. Cohesion also increases and surface disaggregated particles are bonded together by a calcium carbonate micrometric layer with no noticeable changes in surface roughness. Colour and gloss variations are negligible, and pH, conductivity and weight hardly change. Slight changes in porosity were observed but without total pore clogging. To sum up, results indicate that Myxococcus xanthus biomineralisation is an effective consolidation treatment for carbonate fossils and highly compatible with carbonate substrates. Furthermore, bacterial precipitation of calcium carbonate is a safe and eco-friendly consolidation treatment.

An experimental study on post-mortem dissolution and overgrowth processes affecting coccolith assemblages: A rapid and complex process

Coccolith dissolution together with post-mortem morphological features are immensely important phenomena that can affect assemblage compositions, complicate taxonomic identification as well as provide valuable palaeoenvironmental insights. This study summarizes the effects of pH oscillations on post-mortem coccolith morphologies and the abundances and compositions of calcareous nannoplankton assemblages in three distinct types of material-(i) Cretaceous chalk, (ii) Miocene marls, and (iii) late Holocene calcareous ooze. Two independent experimental runs within a semi-enclosed system setting were realized to observe assemblage alterations. One experiment was realized with the presence of bacteria and, in contrast, the second one inhibited their potential effect on the studied system. The pH was gradually decreased within the range of 8.3-6.4 using a reaction of CO₂ with H₂ O forming weak carbonic acid (H₂ CO₃ ), thereby affecting [ CO 3 2 - ]. Further, a subsequent overgrowth study was carried out during spontaneous degassing accompanied by a gradual pH rise. The experiment revealed that the process and intensity of coccolith corrosion and subsequent overgrowth build-ups are influenced by a plethora of different factors such as (i) pH and associated seawater chemistry, (ii) mineral composition of the sediment, (iii) the presence of coccoliths within a protective substrate (faecal pellets, pores, pits), and (iv) the presence/absence of bacteria. Nannoplankton assemblages with corroded coccoliths or with coccoliths with overgrowth build-ups showed that the observed relative abundances of taxa experienced alteration from the original compositions. Additionally, extreme pH oscillations may result in enhanced morphological changes that make coccoliths unidentifiable structures, and might even evoke the absence of coccoliths in the fossil record.

Deep Paleoproteotyping and Microtomography Revealed No Heart Defect nor Traces of Embalming in the Cardiac Relics of Blessed Pauline Jaricot

Scientific examination of the heart of Blessed Pauline Jaricot-a French missionary figure-was carried out in 2022. As tandem mass spectrometry proteotyping has proven to be valuable to obtain the broad taxonomic repertoire of a given sample without any a priori information, we aimed at exploring the conditions of preservation of the relics and possible conditions of death. Metaproteomics and high-resolution microtomography imaging approaches were combined. A dataset comprising 6731 high-resolution MS/MS spectra was acquired and 968 of these spectra could be assigned to specific peptidic biomolecules. Based on the taxonomical information encompassed by the identified peptide sequences, 5 phyla were identified amongst eukaryota (94% of the biomass): Ascomycota (55%), with the species Aspergillus versicolor, Trichophyton mentagrophytes and Aspergillus glaucus, corresponding to expected cadaverous fungal flora; Chordata (42%), represented by a unique species, Homo sapiens; Streptophyta (3%); and Arthropoda (traces). Bacteria (6% of the biomass) were poorly represented. No trace of embalming substance could be retrieved, nor any pathogens. Imaging evidenced no heart defect nor embalming traces. No evidence that was inconsistent with natural and spontaneous conservation could be retrieved. This study prefigures the power of modern molecular techniques such as paleoproteotyping coupled to microtomography to gain insight into historical relics.

Correlation tests between relative light unit and colony forming unit for improving adenosine triphosphate bioluminescence analysis in bacterial consolidation treatments on palaeontological heritage

In this article bacterial carbonate mineralization treatments are proposed as a novel strategy for decayed fossils and palaeontological heritage conservation; specifically, by means of inoculation of Myxococcus xanthus, a bacterium of proven effectiveness in ornamental stone bioconsolidation. Bioconsolidation treatments can be very effective, stable, nontoxic, environmentally friendly, and chemically compatible with fossil heritage. The method reproduces what nature has been doing for millennia with fossils that have been permineralized by bacterial calcium carbonate precipitation. There is, however, some concern that bacterial inoculation could lead to the growth of undesirable microbiota, which could subsequently damage the fossil substrate. Because of this, the use of bacteria on heritage items must be meticulously monitored and analysis strategies should be carried out to detect bacteria viability during and after treatments. For this purpose, adenosine triphosphate assay is proposed in this article as a fast, affordable, portable, and easy-to-use system for conservators. as ATP assay results are relative and difficult to relate to colony forming unit, this study aims to improve their applicability by examining the correlation between ATP analysis and total viable bacteria count in the specific case of M. xanthus. This research provides reference and correlatable data to obtain an approximate estimation of M. xanthus viable bacterial colonies based on relative light unit data.

Role of intracellular energy metabolism in Mn(Ⅱ) removal by the novel bacterium Stenotrophomonas sp. MNB17

Microorganism-mediated Mn(Ⅱ) removal has gained increasing attention as a valuble bioremediation approach. In this study, a novel strain Stenotrophomonas sp. MNB17 - obtained from marine sediments - was found to show Mn(Ⅱ) removal efficiencies of 98.51-99.38% within 7 days and 92.24% within 20 days at Mn(Ⅱ) concentrations of 10-40 mM and 50 mM, respectively. On day 7, 80.44% of 50 mM Mn(Ⅱ) was oxidized to Mn(Ⅲ/Ⅳ), whereas only 2.11-2.86% of 10-40 mM Mn(Ⅱ) was oxidized. This difference in the proportion of Mn-oxides suggested that the strain MNB17 could remove soluble Mn(Ⅱ) via distinct mechanisms under different Mn(Ⅱ) concentrations. At 10 mM Mn(Ⅱ), indirect mechanisms were employed by strain MNB17 to remove Mn(Ⅱ). The sufficient energy generated by increased cellular respiration led to enhanced ammonification, and MnCO₃ was the main component of the Mn-precipitates (97.27%). Meanwhile, intracellular fatty acids were degraded and served as an important carbon source for respiration. At 50 mM Mn(Ⅱ), most of the soluble Mn(Ⅱ) was oxidized, and Mn-oxides dominated the Mn-precipitates (80.44%). Mn(Ⅱ) oxidation likely contributed to electrons for energy production, as the down-regulation of respiratory pathways resulted in a deficit of electron supply, which warrants futher study. The exogenous addition of tricarboxylic acid cycle substrates (malate, α-ketoglutarate, oxaloacetate, succinate, and fumarate) was found to accelerate Mn(Ⅱ) removal as MnCO₃ at a concentration of 50 mM. Overall, this study reports a novel strain MNB17 with the biotechnological potential of Mn(Ⅱ) removal and elucidates the function of cellular energy metabolism during the Mn(Ⅱ) removal process. In addition, it demonstrates the potential of aerobic respiration-related substrates in accelerating the removal of high concentrations of Mn(Ⅱ) for the first time.

Classical and Nonclassical Nucleation and Growth Mechanisms for Nanoparticle Formation

All solid materials are created via nucleation. In this evolutionary process, nuclei form in solution or at interfaces and expand by monomeric growth, oriented attachment, and phase transformation. Nucleation determines the location and size of nuclei, whereas growth controls the size, shape, and aggregation of newly formed nanoparticles. These physical properties of nanoparticles can determine their functionalities, reactivities, and porosities, as well as their fate and transport. Recent advances in nanoscale analytical technologies allow in situ real-time observations, enabling us to uncover the molecular nature of nuclei and the critical controlling factors for nucleation and growth. Although a single theory cannot yet fully explain such evolving processes, we have started to better understand how both classical and nonclassical theories can work together, and we have begun to recognize the importance of connecting these theories. This review discusses the recent convergence of knowledge about the nucleation and the growth of nanoparticles. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Understanding the mechanisms of biological struvite biomineralisation

The mechanisms of struvite production through biomineralisation were investigated for five microorganisms (Bacillus pumilus, Brevibacterium antiquum, Myxococcus xanthus, Halobacterium salinarum and Idiomarina loihiensis). After 72-96 h of incubation, the microbial strains tested increased the solution pH from 7.5 to 7.7 to 8.4-8.7, and removed ortho-phosphate (63-71%) and magnesium (94-99%) by biomineralisation. The minerals formed were identified as struvite (i.e. bio-struvite). Within the initial 24 h of incubation, microbial growth rates of 0.16-0.28 1/h were measured, and bio-struvite production was observed when the solution supersaturation index with respect to struvite achieved 0.6-0.8 units. The crystals produced by B. pumilus, H. salinarum and M. xanthus were thin trapezoidal-platy shaped and presented a gap size about 200 μm for intervals between cumulative volume undersize distribution at 50% and 90%. While B. antiquum and I. loihiensis produced crystals of coffin-lid/long-bar shape and a narrow size gap around 100 μm for intervals between cumulative volume percentage of 50% and 90%, indicating homogeneous crystal size distribution. Intracellular supersaturation of struvite phase was achieved within B. antiquum and I. loihiensis cells, corresponding to observation of intracellular vesicle-like structures occupied with electron-dense granules/materials. This study suggests that B. antiquum and I. loihiensis produced bio-struvite through biologically controlled mineralisation. This mechanism is the preferred for recovering nutrients from streams such as wastewater because it allows a link between manipulation of microbial growth conditions and bio-struvite production, even in highly complex streams like wastewater.

Attachment on mortar surfaces by cyanobacterium Gloeocapsa PCC 73106 and sequestration of CO2 by microbially induced calcium carbonate

Cyanobacterial carbonate precipitation induced by cells and extracellular polymeric substances (EPS) enhances mortar durability. The percentage of cell/EPS attachment regulates the effectiveness of the mortar restoration. This study investigates the cell coverage on mortar and microbially induced carbonate precipitation. Statistical analysis of results from scanning electron and fluorescence microscopy shows that the cell coverage was higher in the presence of UV-killed cells than living cells. Cells are preferably attached to cement paste than sand grains, with a difference of one order of magnitude. The energy-dispersive X-ray spectroscopy analyses and Raman mapping suggest cyanobacteria used atmospheric CO2 to precipitate carbonates.

Microbially Induced Desaturation and Carbonate Precipitation through Denitrification: A Review

Microbially induced carbonate precipitation (MICP) has been proposed as a sustainable approach to solve various environmental, structural, geotechnical and architectural issues. In the last decade, a ubiquitous microbial metabolism, nitrate reduction (also known as denitrification) got attention in MICP research due to its unique added benefits such as simultaneous corrosion inhibition in concrete and desaturation of porous media. The latter even upgraded MICP into a more advanced concept called microbially induced desaturation and precipitation (MIDP) which is being investigated for liquefaction mitigation. In this paper, we present the findings on MICP through denitrification by covering applications under two main titles: (i) applications solely based on MICP, such as soil reinforcement, development of microbial self-healing concrete, restoration of artwork and historical monuments, and industrial wastewater treatment, (ii) an application based on MIDP: liquefaction mitigation. After explaining the denitrification process in detail and describing the MICP and MIDP reaction system occurring through denitrification metabolism, the most recent advances in each potential field of application are collected, addressing the novel findings and limitations, to provide insights toward the practical applications in situ. Finally, the research needs required to deal with the defined challenges in application-oriented upscaling and optimization of MICP through denitrification are suggested. Overall, collected research findings revealed that MICP through denitrification possesses a great potential to replace conventionally used petrochemical-based, labour intensive, destructive and economically unfeasible techniques used in construction industry with a bio-based, labourless, low-carbon technology. This worldwide applicable bio-based technology will facilitate the sustainable development and contribute to the carbon-emission-reduction.

A green decontamination technology through selective biomineralization of algicidal microorganisms for enhanced astaxanthin production from Haematococcus pluvialis at commercial scale

Currently, there is a lack of an efficient, environmentally-benign and sustainable industrial decontamination strategy to steadily achieve improved astaxanthin production from Haematococcus pluvialis under large-scale outdoor conditions. Here, this study demonstrates for the first time that a CaCO₃ biomineralization-based decontamination strategy (CBDS) is highly efficient in selectively eliminating algicidal microorganisms, such as bacteria and fungi, during large-scale H. pluvialis cultivation under autotrophic and mixotrophic conditions, thereby augmenting the astaxanthin productivity. Under outdoor AT and MT conditions, the average astaxanthin productivity of H. pluvialis using CBDS in a closed photobioreactor system was substantially increased by 14.85- (1.19 mg L^-1 d^-1) and 13.65-fold (2.43 mg L^-1 d^-1), respectively, compared to the contaminated H. pluvialis cultures. Given the exponentially increasing demand of astaxanthin, a natural anti-viral, anti-inflammatory, and antioxidant drug, CBDS will be a technology of interest in H. pluvialis-based commercial astaxanthin production which has been hindered by the serious biological contaminations.

Myxobacteria and their products: current trends and future perspectives in industrial applications

Myxobacteria belong to a group of bacteria that are known for their well-developed communication system and synchronized or coordinated movement. This typical behavior of myxobacteria is mediated through secondary metabolites. They are capable of producing secondary metabolites belonging to several chemical classes with unique and wide spectrum of bioactivities. It is predominantly significant that myxobacteria specialize in mechanisms of action that are very rare with other producers. Most of the metabolites have been explored for their medical and pharmaceutical values while a lot of them are still unexplored. This review is an attempt to understand the role of potential metabolites produced by myxobacteria in different applications. Different myxobacterial metabolites have demonstrated antibacterial, antifungal, and antiviral properties along with cytotoxic activity against various cell lines. Beside their metabolites, these myxobacteria have also been discussed for better exploitation and implementation in different industrial sectors.

Microbiologically Induced Carbonate Precipitation in the Restoration and Conservation of Cultural Heritage Materials

Microbiologically induced carbonate precipitation (MICP) is a well-known biogeochemical process that allows the formation of calcium carbonate deposits in the extracellular environment. The high concentration of carbonate and calcium ions on the bacterial surface, which serves as nucleation sites, promotes the calcium carbonate precipitation filling and binding deteriorated materials. Historic buildings and artwork, especially those present in open sites, are susceptible to enhanced weathering resulting from environmental agents, interaction with physical-chemical pollutants, and living organisms, among others. In this work, some published variations of a novel and ecological surface treatment of heritage structures based on MICP are presented and compared. This method has shown to be successful as a restoration, consolidation, and conservation tool for improvement of mechanical properties and prevention of unwanted gas and fluid migration from historical materials. The treatment has revealed best results on porous media matrixes; nevertheless, it can also be applied on soil, marble, concrete, clay, rocks, and limestone. MICP is proposed as a potentially safe and powerful procedure for efficient conservation of worldwide heritage structures.

Arsenic mobilization affected by extracellular polymeric substances (EPS) of the dissimilatory iron reducing bacteria isolated from high arsenic groundwater

The factors that control arsenic (As) mobilization by dissimilatory iron reduction (DIR) are complicated. The association between As mobilization and extracellular polymeric substance (EPS) of dissimilatory iron reducing bacteria (DIRB) remained unclear. In this study, three DIRB were isolated from high arsenic groundwater to understand the effects of EPS on As mobilization. In the laboratory settings, strain Klebsiella oxytoca IR-ZA released As into aqueous phase from As-bearing ferrihydrite, while strain Shewanella putrefaciens IAR-S1 and S. xiamenensis IR-S2 re-sequestrated As by forming secondary minerals during ferrihydrite reduction. Characterization of EPS contents with Fourier Transform Infrared Spectroscopy and high-performance liquid chromatography suggested that mannan and succinic acid were the main different EPS contents of the DIRB. The biomineralization processes were tightly regulated by EPS compositions. Mannan secreted by IAR-S1 and IR-S2 promoted while succinic acid secreted by IR-ZA suppressed the biomineralization and As immobilization. Energy-dispersive X-ray Spectroscopy mapping indicated that As in the secondary minerals was wrapped with EPS. X-ray diffraction and room temperature Mössbauer spectroscopy showed these secondary minerals were vivianite and magnetite, respectively. The amount of As mobilized into aqueous phase was strongly affected by available anions (H₂PO₄^- and HCO₃^-). Our results indicated that the EPS of DIRB significantly influenced As mobilization.

Understanding the biochemical characteristics of struvite bio-mineralising microorganisms and their future in nutrient recovery

The biochemical properties of selected microorganisms (Bacillus pumilus, Brevibacterium antiquum, Myxococcus xanthus, Halobacterium salinarum and Idiomarina loihiensis), known for their ability to produce struvite through biomineralisation, were investigated. All five microorganisms grew at mesophilic temperature ranges (22-34 °C), produced urease (except I. loihiensis) and used bovine serum albumin as a carbon source. I. loihiensis was characterised as a facultative anaerobe able to use O₂ and NO₃ as an electron acceptor. A growth rate of 0.15 1/h was estimated for I. loihiensis at pH 8.0 and NaCl 3.5% w/v. The growth rates for the other microorganisms tested were 0.14-0.43 1/h at pH 7-7.3 and NaCl ≤1% w/v. All the microorganisms produced struvite, as identified by morphological and X-ray Powder Diffraction (XRD) analysis, under aerobic conditions. The biological struvite yield was between 1.5 and 1.7 g/L of media, the ortho-phosphate removal and recovery were 55-76% and 46-54%, respectively, the Mg²⁺ removal and recovery was 92-98% and 83-95%, respectively. Large crystals (>300 μm) were observed, with coffin-lid and long-bar shapes being the dominant morphology of biological struvite crystals. The characterisation of the biochemical properties of the studied microorganisms is critical for reactor and process design, as well as operational conditions, to promote phosphorus recovery from waste streams.

Microbially induced calcium carbonate precipitation: a widespread phenomenon in the biological world

Biodeposition of minerals is a widespread phenomenon in the biological world and is mediated by bacteria, fungi, protists, and plants. Calcium carbonate is one of those minerals that naturally precipitate as a by-product of microbial metabolic activities. Over recent years, microbially induced calcium carbonate precipitation (MICP) has been proposed as a potent solution to address many environmental and engineering issues. However, for being a viable alternative to conventional techniques as well as being financially and industrially competitive, various challenges need to be overcome. In this review, the detailed metabolic pathways, including ammonification of amino acids, dissimilatory reduction of nitrate, and urea degradation (ureolysis), along with the potent bacteria and the favorable conditions for precipitation of calcium carbonate, are explained. Moreover, this review highlights the potential environmental and engineering applications of MICP, including restoration of stones and concrete, improvement of soil properties, sand consolidation, bioremediation of contaminants, and carbon dioxide sequestration. The key research and development questions necessary for near future large-scale applications of this innovative technology are also discussed.

Alkaliphiles: The Emerging Biological Tools Enhancing Concrete Durability

Concrete is one of the most commonly used building materials ever used. Despite it is a very important and common construction material, concrete is very sensitive to crack formation and requires repair. A variety of chemical-based techniques and materials have been developed to repair concrete cracks. Although the use of these chemical-based repair systems are the best commercially available choices, there have also been concerns related to their use. These repair agents suffer from inefficiency and unsustainability. Most of the products are expensive and susceptible to degradation, exhibit poor bonding to the cracked concrete surfaces, and are characterized by different physical properties such as thermal expansion coefficients which are different to that of concrete. Moreover, many of these repair agents contain chemicals that pose environmental and health hazards. Thus, there has been interest in developing concrete crack repair agents that are efficient, long lasting, safe, and benign to the environment and exhibit physical properties which resemble that of the concrete. The search initiated by these desires brought the use of biomineralization processes as tools in mending concrete cracks. Among biomineralization processes, microbially initiated calcite precipitation has emerged as an interesting alternative to the existing chemical-based concrete crack repairing system. Indeed, results of several studies on the use of microbial-based concrete repair agents revealed the remarkable potential of this approach in the fight against concrete deterioration. In addition to repairing existing concrete cracks, microorganisms have also been considered to make protective surface coating (biodeposition) on concrete structures and in making self-healing concrete.Even though a wide variety of microorganisms can precipitate calcite, the nature of concrete determines their applicability. One of the important factors that determine the applicability of microbes in concrete is pH. Concrete is highly alkaline in nature, and hence the microbes envisioned for this application are alkaliphilic or alkali-tolerant. This work reviews the available information on applications of microbes in concrete: repairing existing cracks, biodeposition, and self-healing. Moreover, an effort is made to discuss biomineralization processes that are relevant to extend the durability of concrete structures. Graphical Abstract.

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

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

Calcite formation induced by Ensifer adhaerens, Microbacterium testaceum, Paeniglutamicibacter kerguelensis, Pseudomonas protegens and Rheinheimera texasensis

A wide range of bacterial species are able to induce calcium carbonate precipitation. Using our own laboratory-preserved strains, we have newly discovered that Ensifer sp. MY11e, Microbacterium sp. TMd9a1, Paeniglutamicibacter sp. MSa1a, Pseudomonas sp. GTc3, and Rheinheimera sp. ATWe6 can induce the formation of calcite crystals on an agar medium. Type strains of their closely related species (Ensifer adhaerens, Microbacterium testaceum, Paeniglutamicibacter kerguelensis, Pseudomonas protegens, and Rheinheimera texasensis) could also induce calcite formation. Although the initial pH value of the agar medium was 6.1, the pH of the agar media containing calcite, induced by cultivation of the 10 bacterial strains, increased to 8.0-8.4. The ammonification (oxidative deamination) of amino acids may been responsible for this increase in pH. The crystals formed both on and around the bacterial colonies. Furthermore, when these strains (excepting two Microbacterium strains) were cultivated on a cellulose acetate membrane filter (0.20 μm pore size) resting on the surface of the agar medium (i.e., in the membrane filter culture method), the crystals formed on the agar medium separate from the bacterial cells. These results indicate that the bacterial cells did not necessarily become nucleation sites for these crystals. We also investigated whether the studied strains could be applied to the biocementation of sand, and found that only two Ensifer strains were able to form large sand lumps.

Methanogens predominate in natural corrosion protective layers on metal sheet piles

Microorganisms are able to cause, but also to inhibit or protect against corrosion. Corrosion inhibition by microbial processes may be due to the formation of mineral deposition layers on metal objects. Such deposition layers have been found in archaeological studies on ancient metal objects, buried in soil, which were hardly corroded. Recent field investigations showed that natural mineral deposition layers can be found on sheet piles in soil. We investigated the microbial communities of these deposition layers and the adjacent soil. Our data, from five different sampling sites, all show striking differences between microbial communities of the deposition layer versus the adjacent soil over the depth profile. Bacterial species dominated in top soil while archaeal sequences increased in abundance with depth. All mineral deposition layers from the steel surface were dominated by Euryarchaeota, of which almost all sequences were phylogenetically related with the Methanobacteria genus. The mineral layer consisted of carbonate precipitates. Based on 16S rDNA gene sequencing data we hypothesize that the methanogens directly extract electrons from the metal surface, thereby, initially inducing mild corrosion, but simultaneously, inducing carbonate precipitation. This, will cause encrustation of the archaea, which drastically slow down their activity and create a natural protective layer against further corrosion.

Bacterial magnetosome and its potential application

Bacterial magnetosome, synthetized by magnetosome-producing microorganisms including magnetotactic bacteria (MTB) and some non-magnetotactic bacteria (Non-MTB), is a new type of material comprising magnetic nanocrystals surrounded by a phospholipid bilayer. Because of the special properties such as single magnetic domain, excellent biocompatibility and surface modification, bacterial magnetosome has become an increasingly attractive for researchers in biology, medicine, paleomagnetism, geology and environmental science. This review briefly describes the general feature of magnetosome-producing microorganisms. This article also highlights recent advances in the understanding of the biochemical and magnetic characteristics of bacterial magnetosome, as well as the magnetosome formation mechanism including iron ions uptake, magnetosome membrane formation, biomineralization and magnetosome chain assembly. Finally, this review presents the potential applications of bacterial magnetosome in biomedicine, wastewater treatment, and the significance of mineralization of magnetosome in biology and geology.

Diversity and Biomineralization Potential of the Epilithic Bacterial Communities Inhabiting the Oldest Public Stone Monument of Cluj-Napoca (Transylvania, Romania)

In this study, we investigated the biomineralization potential and diversity of the epilithic bacterial communities dwelling on the limestone statue of Saint Donatus, the oldest public monument of Cluj-Napoca city (Transylvania region, NW Romania). Their spatial distribution together with phylogenetic and metabolic diversity, as well as their capacity to precipitate calcium carbonate was evaluated by combining molecular and phenotypic fingerprinting methods with X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron-microscopy analyses. The results of real-time quantitative PCR, molecular fingerprinting and community-level physiological profiling showed that diverse and abundant bacterial assemblages that differ in relation to their collection site colonized the statue. The cultivation and molecular identification procedures allowed the characterization of 79 bacterial isolates belonging to Proteobacteria (73.4%), Firmicutes (19%), and Actinobacteria (7.6%). Amongst them, the 22 strains identified as being capable of calcium carbonate precipitation were found to belong mostly to Bacillus and Pseudomonas genera. We found that bacteria acted as nucleation sites, inducing the formation of nanoscale aggregates that were shown to be principally composed of vaterite. Furthermore, we expanded the current knowledge on culturable diversity of carbonatogenic bacteria by providing evidence for biogenic vaterite/calcite formation mediated by: Pseudomonas synxantha, P. graminis, Brevibacterium iodinum, Streptomyces albidoflavus, and Stenotrophomonas chelatiphaga. Overall, this study highlights the need to evaluate the carbonatogenetic potential of all the bacterial communities present on stone artwork prior to designing an efficient conservation treatment based on biomineralization.

Formations of calcium carbonate minerals by bacteria and its multiple applications

Biomineralization is a naturally occurring process in living organisms. In this review, we discuss microbially induced calcium carbonate precipitation (MICP) in detail. In the MICP process, urease plays a major role in urea hydrolysis by a wide variety of microorganisms capable of producing high levels of urease. We also elaborate on the different polymorphs and the role of calcium in the formation of calcite crystal structures using various calcium sources. Additionally, the environmental factors affecting the production of urease and carbonate precipitation are discussed. This MICP is a promising, eco-friendly alternative approach to conventional and current remediation technologies to solve environmental problems in multidisciplinary fields. Multiple applications of MICP such as removal of heavy metals and radionuclides, improve the quality of construction materials and sequestration of atmospheric CO₂ are discussed. In addition, we discuss other applications such as removal of calcium ions, PCBs and use of filler in rubber and plastics and fluorescent particles in stationary ink and stationary markers. MICP technology has become an efficient aspect of multidisciplinary fields. This report not only highlights the major strengths of MICP, but also discusses the limitations to application of this technology on a commercial scale.

Carbonate Precipitation through Microbial Activities in Natural Environment, and Their Potential in Biotechnology: A Review

Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed.

Metabolism-Induced CaCO3 Biomineralization During Reactive Transport in a Micromodel: Implications for Porosity Alteration

The ability of Pseudomonas stutzeri strain DCP-Ps1 to drive CaCO3 biomineralization has been investigated in a microfluidic flowcell (i.e., micromodel) that simulates subsurface porous media. Results indicate that CaCO3 precipitation occurs during NO3(-) reduction with a maximum saturation index (SIcalcite) of ∼1.56, but not when NO3(-) was removed, inactive biomass remained, and pH and alkalinity were adjusted to SIcalcite ∼ 1.56. CaCO3 precipitation was promoted by metabolically active cultures of strain DCP-Ps1, which at similar values of SIcalcite, have a more negative surface charge than inactive strain DCP-Ps1. A two-stage NO3(-) reduction (NO3(-) → NO2(-) → N2) pore-scale reactive transport model was used to evaluate denitrification kinetics, which was observed in the micromodel as upper (NO3(-) reduction) and lower (NO2(-) reduction) horizontal zones of biomass growth with CaCO3 precipitation exclusively in the lower zone. Model results are consistent with two biomass growth regions and indicate that precipitation occurred in the lower zone because the largest increase in pH and alkalinity is associated with NO2(-) reduction. CaCO3 precipitates typically occupied the entire vertical depth of pores and impacted porosity, permeability, and flow. This study provides a framework for incorporating microbial activity in biogeochemistry models, which often base biomineralization only on SI (caused by biotic or abiotic reactions) and, thereby, underpredict the extent of this complex process. These results have wide-ranging implications for understanding reactive transport in relevance to groundwater remediation, CO2 sequestration, and enhanced oil recovery.

A mineralogical characterization of biogenic calcium carbonates precipitated by heterotrophic bacteria isolated from cryophilic polar regions

Precipitation of calcium carbonate (CaCO3(s) ) can be driven by microbial activity. Here, a systematic approach is used to identify the morphological and mineralogical characteristics of CaCO3(s) precipitated during the heterotrophic growth of micro-organisms isolated from polar environments. Focus was placed on establishing mineralogical features that are common in bioliths formed during heterotrophic activity, while in parallel identifying features that are specific to bioliths precipitated by certain microbial phylotypes. Twenty microbial isolates that precipitated macroscopic CaCO3(s) when grown on B4 media supplemented with calcium acetate or calcium citrate were identified. A multimethod approach, including scanning electron microscopy, high-resolution transmission electron microscopy, and micro-X-ray diffraction (μ-XRD), was used to characterize CaCO3(s) precipitates. Scanning and transmission electron microscopy showed that complete CaCO3(s) crystal encrustation of Arthrobacter sp. cells was common, while encrustation of Rhodococcus sp. cells did not occur. Several euhedral and anhedral mineral formations including disphenoid-like epitaxial plates, rhomboid-like aggregates with epitaxial rhombs, and spherulite aggregates were observed. While phylotype could not be linked to specific mineral formations, isolates tended to precipitate either euhedral or anhedral minerals, but not both. Three anhydrous CaCO3(s) polymorphs (calcite, aragonite, and vaterite) were identified by μ-XRD, and calcite and aragonite were also identified based on TEM lattice-fringe d value measurements. The presence of certain polymorphs was not indicative of biogenic origin, although several mineralogical features such as crystal-encrusted bacterial cells, or casts of bacterial cells embedded in mesocrystals are an indication of biogenic origin. In addition, some features such as the formation of vaterite and bacterial entombment appear to be linked to certain phylotypes. Identifying phylotypes consistent with certain mineralogical features is the first step toward discovering a link between these crystal features and the precise underlying molecular biology of the organism precipitating them.

Assessment of a biostimulated or bioaugmented calcification system with Bacillus pasteurii in a simulated soil environment

To evaluate how native soil microorganism and nutrients interact in a bioaugmented or biostimulated calcification process, batch experiments were conducted in saturated soil extract either amended with Bacillus pasteurii and/or NB-NH4Cl media (nutrient broth, 3.0 g/L; NH4Cl, 10.0 g/L; NaHCO3, 2.12 g/L). The NB-NH4Cl medium was chosen out of three potential candidates, where B. pasteurii precipitated the maximum amount of calcium (>95 %) as calcite in 12 h of incubation. The addition of B. pasteurii into saturated soil extract marginally improved the calcification to 4.26 % compared to the unamended control (3.2 %). Calcification with B. pasteurii in autoclaved soil extract was even better (18.75 %). However, the addition of the NB-NH4Cl medium into the soil extract could significantly improve the calcification irrespective of whether B. pasteurii was added (88.46 %) or not (77.04 %). It suggests that soil microbial activity was not limiting even though soil nutrient was inadequate. It also indicates a possible negative interaction between soil microorganisms and B. pasteurii under nutrient-limited conditions.

Influence of substrate mineralogy on bacterial mineralization of calcium carbonate: implications for stone conservation

The influence of mineral substrate composition and structure on bacterial calcium carbonate productivity and polymorph selection was studied. Bacterial calcium carbonate precipitation occurred on calcitic (Iceland spar single crystals, marble, and porous limestone) and silicate (glass coverslips, porous sintered glass, and quartz sandstone) substrates following culturing in liquid medium (M-3P) inoculated with different types of bacteria (Myxococcus xanthus, Brevundimonas diminuta, and a carbonatogenic bacterial community isolated from porous calcarenite stone in a historical building) and direct application of sterile M-3P medium to limestone and sandstone with their own bacterial communities. Field emission scanning electron microscopy (FESEM), atomic force microscopy (AFM), powder X-ray diffraction (XRD), and 2-dimensional XRD (2D-XRD) analyses revealed that abundant highly oriented calcite crystals formed homoepitaxially on the calcitic substrates, irrespective of the bacterial type. Conversely, scattered spheroidal vaterite entombing bacterial cells formed on the silicate substrates. These results show that carbonate phase selection is not strain specific and that under equal culture conditions, the substrate type is the overruling factor for calcium carbonate polymorph selection. Furthermore, carbonate productivity is strongly dependent on the mineralogy of the substrate. Calcitic substrates offer a higher affinity for bacterial attachment than silicate substrates, thereby fostering bacterial growth and metabolic activity, resulting in higher production of calcium carbonate cement. Bacterial calcite grows coherently over the calcitic substrate and is therefore more chemically and mechanically stable than metastable vaterite, which formed incoherently on the silicate substrates. The implications of these results for technological applications of bacterial carbonatogenesis, including building stone conservation, are discussed.