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

Impact of soil density on biomineralization using EICP and MICP techniques for earthen sites consolidation

Enzyme-induced calcium carbonate precipitation (EICP) and microbially-induced calcium carbonate precipitation (MICP) techniques represent emerging trends in soil stabilization. However, the impact of soil density on biomineralization, particularly in historical earthen sites, remains unclear. This study compares the consolidation effects of EICP and MICP on cylindrical samples (10 cm × 5 cm) with three densities (1.5 g/cm3, 1.6 g/cm3, and 1.7 g/cm3) derived from the soil near the UNESCO World Cultural Heritage Site of Suoyang Ancient City, Gansu Province, China. Results showed that calcium carbonate production increased across all densities through bio-cementation, with higher densities producing more calcium carbonate. MICP-treated specimens exhibited larger increases in calcium carbonate production compared to those treated with EICP. Specimens with a density of 1.7 g/cm³ showed a wave velocity increase of 3.26% (EICP) and 7.13% (MICP), and an unconfined compressive strength increase of 8% (EICP) and 26% (MICP). These strength increases correlated with the generation of calcium carbonate. The findings suggest that biomineralization can be effectively utilized for in situ consolidation of earthen sites, emphasizing the importance of considering soil density in biologically-based conservation technologies. Furthermore, MICP shows potential advantages over EICP in providing stronger, compatible and more sustainable soil reinforcement.

Biomineral deposits and coatings on stone monuments as biodeterioration fingerprints

Biominerals deposition processes, also called biomineralisation, are intimately related to biodeterioration on stone surfaces. They include complex processes not always completely well understood. The study of biominerals implies the identification of organisms, their molecular mechanisms, and organism/rock/atmosphere interactions. Sampling restrictions of monument stones difficult the biominerals study and the in situ demonstrating of biodeterioration processes. Multidisciplinary works are required to understand the whole process. Thus, studies in heritage buildings have taken advantage of previous knowledge acquired thanks to laboratory experiments, investigations carried out on rock outcrops and within caves from some years ago. With the extrapolation of such knowledge to heritage buildings and the advances in laboratory techniques, there has been a huge increase of knowledge regarding biomineralisation and biodeterioration processes in stone monuments during the last 20 years. These advances have opened new debates about the implications on conservation interventions, and the organism's role in stone conservation and decay. This is a review of the existing studies of biominerals formation, biodeterioration on laboratory experiments, rocks, caves, and their application to building stones of monuments.

Insights in MICP dynamics in urease-positive Staphylococcus sp. H6 and Sporosarcina pasteurii bacterium

Microbially induced calcite precipitation (MICP) is an efficient and eco-friendly technique that has attracted significant interest for resolving various problems in the soil (erosion, improving structural integrity and water retention, etc.), remediation of heavy metals, production of self-healing concrete or restoration of different concrete structures. The success of most common MICP methods depends on microorganisms degrading urea which leads to the formation of CaCO3 crystals. While Sporosarcina pasteurii is a well-known microorganism for MICP, other soil abundant microorganisms, such as Staphylococcus bacteria have not been thoroughly studied for its efficiency in bioconsolidation though MICP is a very important proccess which can ensure soil quality and health. This study aimed to analyze MICP process at the surface level in Sporosarcina pasteurii and a newly screened Staphylococcus sp. H6 bacterium as well as show the possibility of this new microorganism to perform MICP. It was observed that Staphylococcus sp. H6 culture precipitated 157.35 ± 3.3 mM of Ca2+ ions from 200 mM, compared to 176 ± 4.8 mM precipitated by S. pasteurii. The bioconsolidation of sand particles was confirmed by Raman spectroscopy and XRD analysis, which indicated the formation of CaCO3 crystals for both Staphylococcus sp. H6 and S. pasteurii cells. The water-flow test suggested a significant reduction in water permeability in bioconsolidated sand samples for both Staphylococcus sp. H6 and S. pasteurii. Notably, this study provides the first evidence that CaCO3 precipitation occurs on the surface of Staphylococcus and S. pasteurii cells within the initial 15-30 min after exposure to the biocementation solution. Furthermore, Atomic force microscopy (AFM) indicated rapid changes in cell roughness, with bacterial cells becoming completely coated with CaCO3 crystals after 90 min incubation with a biocementation solution. To our knowledge, this is the first time where atomic force microscopy was used to visualize the dynamic of MICP on cell surface.

New insights into Saccharomyces cerevisiae induced calcium carbonate precipitation

Our previous study reported that Saccharomyces cerevisiae could induce calcium carbonate (CaCO3) precipitation, but the associated mechanism was unclear. In the present study, Saccharomyces cerevisiae was cultured under various conditions, including the presence of different organic acids and initial pH, and the yields of CaCO3 formation induced by the different organic acids were compared. The metabolism of organic acid by the metabolites of S. cerevisiae was also assessed in vitro. The SEM-EDS and XRD results showed that only acetate acid, pyruvic acid, and α-ketoglutaric acid could induce CaCO3 formation, and the weight order of the produced CaCO3 was pyruvic acid, acetate acid, α-ketoglutaric acid. In addition, the presence of only yeast metabolites and the initial neutral or alkaline environment also limited the CaCO3 formation. These results illustrated that organic acid oxidation intracellularly, especially the tricarboxylic acid cycle, was the major mechanism, and the CaCO3 yield was related to the amount of CO2 produced by the metabolism of organic acids. These findings will deepen the knowledge of the mineralization capacity of S. cerevisiae and provide a theoretical basis for the future application of yeast as an alternative microorganism in MICP.

Baseline investigation on soil solidification through biocementation using airborne bacteria

Microbial induced carbonate precipitation (MICP) through the ureolysis metabolic pathway is one of the most studied topics in biocementation due to its high efficiency. Although excellent outcomes have proved the potential of this technique, microorganisms face some obstacles when considering complicated situations in the real field, such as bacterial adaptability and survivability issues. This study made the first attempt to seek solutions to this issue from the air, exploring ureolytic airborne bacteria with resilient features to find a solution to survivability issues. Samples were collected using an air sampler in Sapporo, Hokkaido, a cold region where sampling sites were mostly covered with dense vegetation. After two rounds of screening, 12 out of 57 urease-positive isolates were identified through 16S rRNA gene analysis. Four potentially selected strains were then evaluated in terms of growth pattern and activity changes within a range of temperatures (15°C-35°C). The results from sand solidification tests using two Lederbergia strains with the best performance among the isolates showed an improvement in unconfined compressive strength up to 4-8 MPa after treatment, indicating a high MICP efficiency. Overall, this baseline study demonstrated that the air could be an ideal isolation source for ureolytic bacteria and laid a new pathway for MICP applications. More investigations on the performance of airborne bacteria under changeable environments may be required to further examine their survivability and adaptability.

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.

Biosynthesis of Calcite Nanocrystal by a Novel Polyextremophile Bhargavaea cecembensis-Related Strain Isolated from Sandy Soil

Urease-producing bacteria are abundant in soils, which can precipitate calcium carbonate nanocrystals by enzymatic hydrolysis of urea in the presence of calcium ions. This process is known as microbially induced calcium carbonate precipitation (MICP), and it has received much attention in recent years as an eco-friendly technology. Therefore, the purpose of the present study was to isolate local extremophile bacterial strains capable of producing calcium carbonate. Among a total of 44 isolated urease-producing strains from sandy soils, one strain with a high level of urease activity (8.16 U/ml) and production of a large amount of calcium carbonate (410 mg/100 ml) was selected for further investigation. 16S rRNA gene sequencing showed that this strain had 99.66% sequence identity to Bhargavaea cecembensis. The SEM-EDX and XRD analyses indicated that irregular vaterite and aggregated nanocalcite were the dominant polymorphs produced by this strain. The size of these nanocalcite crystals ranged between 25 and 42 nm. The selected strain showed high levels of tolerance to different conditions of temperature, pH, and salinity. This strain grows at high temperatures up to 50 °C, alkaline pH (9-11), and high concentrations of NaCl (20-25% w/v). Flow cytometry analysis demonstrated 96% cell viability of the isolated strain after desiccation stress. Bhargavaea was first reported in 2009 as a new genus, and it belongs to the Firmicutes. So far, there has been no report on its MICP potential. The present study is the first one to report nanocrystal calcium carbonate precipitation in polyextremophile Bhargavaea cecembensis, which makes it a suitable candidate for bio-cementation under extreme circumstances.

Improvement of microstructure of cementitious composites by microbially-induced calcite precipitation

In this study, microstructural improvement of cementitious composites was achieved by bacterial CaCO₃ precipitation using three bacterial species, namely Sporosarcina pasteurii, Bacillus cereus, and Actinobacteria sp. M135-3, respectively. The final product was comparatively investigated regarding the physical effects of urease activity of different cells on the mortar in the long term.Microstructural improvement was determined by evaluating the pore structure by determining the increase in strength, decrease in water absorption, and capillary water absorption rate of the cement mortars having different microorganism concentrations (10⁶-10⁹ bacteria/ml). These measurements were taken on bacteria-containing and control samples on the 2nd, 7th, 28th, and 56th days, respectively. In addition, calcite and vaterite as calcium carbonate polymorphs formed by the precipitation of calcium carbonate by three types of bacteria were identified by Scanning electron microscopy and energy dispersive X-ray spectroscopy (SEM/EDS), X-ray diffraction (XRD) and Thermogravimetric analysis - Differential scanning calorimetry (TGA-DSC) analyzes.The bacteria-containing mortar samples showed that bacterial species and concentrations directly affect cementitious composites' mechanical and physical properties. Composite samples containing bacteria resulted in statistically significant microstructural improvements measured by higher mechanical strength, lower water absorption value, and capillary water absorption rate compared to control samples, especially at early ages. However, the effect of microbial calcite formation diminishes at later ages, especially at 56-days, attributed to the bacteria cells losing their vitality and integrity and forming spaces inside the mortars.

Insight on bacteria communities in outdoor bronze and marble artefacts in a changing environment

Epilithic bacteria play a fundamental role in the conservation of cultural heritage (CH) materials. On stones, bacterial communities cause both degradation and bioprotection actions. Bronze biocorrosion in non-burial conditions is rarely studied. Only few studies have examined the relationship between bacteria communities and the chemical composition of patinas (surface degradation layers). A better comprehension of bacterial communities growing on our CH is fundamental not only to understand the related decay mechanisms but also to foresee possible shifts in their composition due to climate change. The present study aims at (1) characterizing bacterial communities on bronze and marble statues; (2) evaluating the differences in bacterial communities' composition and abundance occurring between different patina types on different statues; and (3) providing indications about a representative bacterial community which can be used in laboratory tests to better understand their influence on artefact decay. Chemical and biological characterization of different patinas were carried out by sampling bronze and marble statues in Bologna and Ravenna (Italy), using EDS/Raman spectroscopy and MinION-based 16SrRNA sequencing. Significant statistical differences were found in bacterial composition between marble and bronze statues, and among marble patinas in different statues and in the same statue. Marble surfaces showed high microbial diversity and were characterized mainly by Cyanobacteria, Proteobacteria and Deinococcus-Thermus. Bronze patinas showed low taxa diversity and were dominated by copper-resistant Proteobacteria. The copper biocidal effect is evident in greenish marble areas affected by the leaching of copper salts, where the bacterial community is absent. Here, Ca and Cu oxalates are present because of the biological reaction of living organisms to Cu ions, leading to metabolic product secretions, such as oxalic acid. Therefore, a better knowledge on the interaction between bacteria communities and patinas has been achieved.

Evidencing the role of carbonic anhydrase in the formation of carbonate minerals by bacterial strains isolated from extreme environments in Qatar

Calcium carbonate, one of the most abundant minerals in the geological records is considered as primary source of the carbon reservoir. The role of microorganisms in the biotic precipitation of calcium carbonate has been extensively investigated, especially at extreme life conditions. In Qatar, Sabkhas which are microbial ecosystems housing biomineralizing bacteria, have been carefully studied as unique sites of microbial dolomite formation. Dolomite (CaMg(CO₃)₂ is an important carbonate mineral forming oil reservoir rocks; however, dolomite is rarely formed in modern environments. The enzyme carbonic anhydrase is present in many living organisms, performs interconversion between CO₂ and the bicarbonate ion. Thus, carbonic anhydrase is expected to accelerate both carbonate rock dissolution and CO₂ uptake at the same time, serving as carbonite source to carbonites-forming bacteria. This study gathered cross-linked data on the potential role of the carbonic anhydrase excreted by mineral-forming bacteria, isolated from two different extreme environments in Qatar. Dohat Faishakh Sabkha, is a hypersaline coastal Sabkha, from where various strains of the bacterium Virgibacillus were isolated. Virgibacillus can -not only-mediate carbonate mineral formation, but also contributes to magnesium incorporation into the carbonate minerals, leading to the formation of high magnesium calcite. The latter is considered as precursor for dolomite formation. In addition, bacterial strains isolated from marine sediments, surrounding coral reef in Qatar sea, would provide additional knowledge on the role of carbonic anhydrase in mineral formation. Here, the quantification of the two mostly described activities of carbonic anhydrase; esterase and hydration reactions were performed. Mineral-forming strains were shown to exhibit high activities as opposed to the non-forming minerals, which confirms the relation between the presence of active carbonic anhydrase combined with elevated metabolic activity and the biomineralizing potential of the bacterial strains. The highest specific intracellular carbonic anhydrase activity; as both esterase and hydration (i.e., 66 ± 3 and 583000 ± 39000 WAU/10⁸ cells respectively), was evidenced in mineral-forming strains as opposed to non-mineral forming strains (i.e., 6 ±. 0.5 and 1223 ± 61 WAU/10⁸cells) respectively. These findings would contribute to the understanding of the mechanism of microbially mediated carbonate precipitation. This role may be both in capturing CO₂ as source of carbonate, and partial solubilization of the formed minerals allowing incorporation of Mg instead of calcium, before catalyzing again the formation of more deposition of carbonates.

Biomineralization in Cave Bacteria—Popcorn and Soda Straw Crystal Formations, Morphologies, and Potential Metabolic Pathways

Caves are extreme, often oligotrophic, environments that house diverse groups of microorganisms. Many of these microbes can perform microbiologically induced carbonate precipitation (MICP) to form crystalline secondary cave deposits known as speleothems. The urease family is a group of enzymes involved in MICP that catalyze the breakdown of urea, which is a source of energy, into ammonia and carbonate. Carbonate anions are effluxed to the extracellular surface of the bacterium where it then binds to environmental calcium to form calcium carbonate which then continues to grow in crystal form. Here, we studied bacterial communities from speleothems collected from the Iron Curtain Cave (ICC) in Chilliwack, B.C., Canada, to characterize these organisms and determine whether urease-positive (U+) bacteria were present in the cave and their potential impact on speleothem formation. The ICC is a carbonate cave located on the northside of Chipmunk Ridge, presenting a unique environment with high iron content sediment and limestone structures throughout. With six pools of water throughout the cave, the environment is highly humid, with temperatures ranging between 4 and 12°C depending on the time of year. Ninety-nine bacterial strains were isolated from popcorn (PCS) and soda straw (SSS) speleothems. These isolates were screened for urease enzymatic activity, with 11 candidates found to be urease-positive. After incubation, species-specific crystal morphologies were observed. Popcorn speleothem provided more bacterial diversity overall when compared to soda straw speleothem when examined under a culture-based method. Nearly twice as many U+ isolates were isolated from popcorn speleothems compared to soda straw speleothems. The U+ candidates were identified to the genus level by 16S rRNA analysis, and two isolates underwent whole-genome sequencing. Two novel species were identified as Sphingobacterium sp. PCS056 and Pseudarthrobacter sp. SSS035. Both isolates demonstrated the most crystal production as well as the most morphologically dissimilar crystal shapes in broth culture and were found to produce crystals as previously observed in both agar and broth media. The results from this study are consistent with the involvement of urease-positive bacteria isolated from the ICC in the formation of cave speleothems. 16S rRNA sequencing revealed a diverse set of microbes inhabiting the speleothems that have urease activity. Whole-genome sequencing of the two chosen isolates confirmed the presence of urease pathways, while revealing differences in urease pathway structure and number. This research contributes to understanding microbial-associated cave formation and degradation, with applications to cave conservation, microbiota composition, and their role in shaping the cave environment.

Experimental Study on High-Temperature Damage Repair of Concrete by Soybean Urease Induced Carbonate Precipitation

In this study, the effects of soybean-urease-induced carbonate precipitation on a high-temperature damage repair of concrete were explored. C50 concrete specimens were exposed to high temperatures from 300 to 600 °C, then cooled to an ambient temperature and repaired by two different methods. The influences of the damage temperature and repair methods on surface film thickness, average infrared temperature increase, water absorption, and compressive strength were investigated. Scanning electron microscopy (SEM) images were carried out to further study the mechanism involved. The results revealed that the white sediments on the surface of the repaired specimens were calcium carbonate (CaCO₃) and calcium oxalate (CaC₂O₄). The surface film thickness reached up to 1.94 mm after repair. The average infrared temperature increase in the repaired specimens at different damage temperatures was averagely reduced by about 80% compared with that before the repair. It showed more obvious repair effects at higher temperatures in water absorption and compressive strength tests; the compressive strength of repaired specimens was 194% higher than that before repairs at 600 °C. A negative pressure method was found to be more effective than an immersion method. This study revealed the utilization of SICP on repairing high-temperature damage of concrete is feasible theoretically.

A review on the applications of microbially induced calcium carbonate precipitation in solid waste treatment and soil remediation

Improper disposal and accumulation of solid waste can cause a number of environmental problems, such as the heavy metal contamination of soil. Microbially induced calcium carbonate precipitation (MICP) is considered as a promising technology to solve many environmental problems. Calcium-based solid waste can be utilized as an alternative source of calcium for the MICP process, and carbonate-based biominerals can be used for soil remediation, solid waste treatment, remediation of construction concrete, and generation of bioconcrete. This paper describes the metabolic pathways and mechanisms of microbially induced calcium carbonate precipitation and highlights the value of MICP for solid waste treatment and soil remediation applications. The factors affecting the effectiveness of MICP are discussed and analyzed through an overview of recent studies on the application of MICP in environmental engineering. The paper also summarizes the current challenges for the large-scale application of this innovative technology. In prospective study, MICP can be an effective alternative to conventional technologies in solid waste treatment, soil remediation and CO₂ sequestration, as it can reduce negative environmental impacts and provide long-term economic benefits.

Self-Healing Construction Materials: The Geomimetic Approach

A person spends most of his life in rooms built from various building materials; therefore, the optimization of the human environment is an important and complex task that requires interdisciplinary approaches. Within the framework of the new theory of geomimetics in the building science of materials, the concepts of technogenic metasomatism, the affinity of microstructures, and the possibilities of creating composites that respond to operational loads and can self-heal defects have been created. The article aims to introduce the basic principles of the science of geomimetics in terms of the design and synthesis of building materials. The study’s novelty lies in the concept of technogenic metasomatism and the affinity of microstructures developed by the authors. Novel technologies have been proposed to produce a wide range of composite binders (including waterproof and frost-resistant gypsum binders) using novel forms of source materials with high free internal energy. The affinity microstructures for anisotropic materials have been formulated, which involves the design of multilayered composites and the repair of compounds at three levels (nano-, micro-, macro-). The proposed theory of technogenic metasomatism in the building science of materials represents an evolutionary stage for composites that are categorized by their adaptation to evolving circumstances in the operation of buildings and structures. Materials for three-dimensional additive technologies in construction are proposed, and examples of these can be found in nature. Different ways of applying our concept for the design of building materials in future works are proposed.

Bioconservation of Historic Stone Buildings—An Updated Review

Cultural heritage buildings of stone construction require careful restorative actions to maintain them as close to the original condition as possible. This includes consolidation and cleaning of the structure. Traditional consolidants may have poor performance due to structural drawbacks such as low adhesion, poor penetration and flexibility. The requirement for organic consolidants to be dissolved in volatile organic compounds may pose environmental and human health risks. Traditional conservation treatments can be replaced by more environmentally acceptable, biologically-based, measures, including bioconsolidation using whole bacterial cells or cell biomolecules; the latter include plant or microbial biopolymers and bacterial cell walls. Biocleaning can employ microorganisms or their extracted enzymes to remove inorganic and organic surface deposits such as sulfate crusts, animal glues, biofilms and felt tip marker graffiti. This review seeks to provide updated information on the innovative bioconservation treatments that have been or are being developed.

Ammonium monoethyloxalate (AmEtOx): a new agent for the conservation of carbonate stone substrates

Ammonium monoethyloxalate (AmEtOx) is proposed as a consolidanting agent for carbonate stones such as biomicritic limestone and marble, resulting in the formation of a microcrystalline passivating phase of calcium oxalate (whewellite and weddellite).