Effect of culture medium on biocalcification by Pseudomonas Putida, Lysinibacillus Sphaericus and Bacillus Subtilis

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.

Novel method to achieve crystallinity of calcite by Bacillus subtilis in coupled and non-coupled calcium-carbon sources

Bacteria mineralization is a promising biotechnological approach to apply in biomaterials development. In this investigation, we demonstrate that Bacillus subtilis 168 induces and influences CaCO₃ composites precipitation. Crystals were formed in calcium-carbon non-coupled (glycerol + CaCl₂, GLY; or glucose + CaCl₂, GLC) and coupled (calcium lactate, LAC; or calcium acetate, ACE) agar-sources, only maintaining the same Ca²⁺ concentration. The mineralized colonies showed variations in morphology, size, and crystallinity form properties. The crystals presented spherulitic growth in all conditions, and botryoidal shapes in GLC one. Birefringence and diffraction patterns confirmed that all biogenic carbonate crystals (BCC) were organized as calcite. The CaCO₃ in BCC was organized as calcite, amorphous calcium carbon (ACC) and organic matter (OM) of biofilm; all of them with relative abundance related to bacteria growth condition. BCC-GLY presented greatest OM composition, while BCC-ACE highest CaCO₃ content. Nucleation mechanism and OM content impacted in BCC crystallinity.

Role of Fungi in the Formation of Patinas on Feilaifeng Limestone, China

Feilaifeng is a cultural heritage site that contains unique Buddhist statues which date back to the Five Dynasties period (907 AD-960 AD). The site was inscribed on world heritage list by UNESCO in 2011. Various patinas, which may be caused by fungi, have covered the surface of the limestone and have severely diminished the esthetic value of the statues and altered the limestone structure. Culture-dependent method was used to isolate and identify the fungi. After incubation on modified B4 medium, the calcifying fungi were identified by optical microscopy and scanning electron microscopy combined with X-ray energy-dispersive analysis. Aspergillus, Penicillium, and Colletotrichum were observed as the biomineralizing fungi. X-ray diffraction showed that the patina consisted of calcite (CaCO₃), but the crystals synthesized by the identified fungi were whewellite (CaC₂O₄·H₂O) for Aspergillus and Penicillium, and vaterite (CaCO₃) for Colletotrichum. In addition, the metabolites of Colletotrichum suppressed the transformation of vaterite to calcite, but Mg²⁺ could inhibit the function of the metabolites. The different crystal form between the patina and the products of fungi may suggest two different pathways of patina formation and provide important reference data for studies of the mechanisms of biomineralization, cleaning of the patina, and protection of the Feilaifeng statues.

Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems in Natural and in Vitro Biomineralization Conditions

Natural mineral formations are a window into important processes leading to carbon storage and mineralized carbonate structures formed through abiotic and biotic processes. In the current study, we made an attempt to undertake a comprehensive approach to characterize the mineralogical, mechanical, and microbial properties of different kinds of speleothems from karstic caves; with an aim to understand the bio-geo-chemical processes in speleothem structures and their impact on nanomechanical properties. We also investigated the biomineralization abilities of speleothem surface associated microbial communities in vitro. Mineralogical profiling using techniques such as X-ray powder Diffraction (XRD) and Tescan Integrated Mineral Analyzer (TIMA) demonstrated that calcite was the dominant mineral in the majority of speleothems with Energy Dispersive X-ray Analysis (EDS) indicating a few variations in the elemental components. Differing proportions of polymorphs of calcium carbonate such as aragonite and vaterite were also recorded. Significant variations in trace metal content were recorded through Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Scanning Electron Microscopy (SEM) analysis revealed differences in morphological features of the crystals which varied from triangular prismatic shapes to etched spiky forms. Microbial imprints and associations were seen in a few sections. Analysis of the associated microbial diversity showed significant differences between various speleothems at Phylum level; although Proteobacteria and Actinobacteria were found to be the predominant groups. Genus level microbial associations showed a relationship with the geochemistry, mineralogical composition, and metal content of the speleothems. The assessment of nanomechanical properties measured by Nanoindentation revealed that the speleothems with a dominance of calcite were stronger than the speleothems with mixed calcium carbonate polymorphs and silica content. The in vitro metabolic activity of the microbial communities associated with the surfaces of the speleothems resulted in calcium carbonate crystal precipitation. Firmicutes and Proteobacteria dominated these populations, in contrast to the populations seen in natural systems. The precipitation of calcium carbonate crystals in vitro indicated that microbial metabolic activity may also play an important role in the synthesis and dissociation of biominerals in the natural environment. Our study provides novel evidence of the close relationship between mineralogy, microbial ecology, geochemistry, and nanomechanical properties of natural formations.

Non-ureolytic calcium carbonate precipitation by Lysinibacillus sp. YS11 isolated from the rhizosphere of Miscanthus sacchariflorus

Although microbially induced calcium carbonate precipitation (MICP) through ureolysis has been widely studied in environmental engineering fields, urea utilization might cause environmental problems as a result of ammonia and nitrate production. In this study, many non-ureolytic calcium carbonate-precipitating bacteria that induced an alkaline environment were isolated from the rhizosphere of Miscanthus sacchariflorus near an artificial stream and their ability to precipitate calcium carbonate minerals with the absence of urea was investigated. MICP was observed using a phase-contrast microscope and ion-selective electrode. Only Lysinibacillus sp. YS11 showed MICP in aerobic conditions. Energy dispersive X-ray spectrometry and X-ray diffraction confirmed the presence of calcium carbonate. Field emission scanning electron microscopy analysis indicated the formation of morphologically distinct minerals around cells under these conditions. Monitoring of bacterial growth, pH changes, and Ca²⁺ concentrations under aerobic, hypoxia, and anaerobic conditions suggested that strain YS11 could induce alkaline conditions up to a pH of 8.9 and utilize 95% of free Ca²⁺ only under aerobic conditions. Unusual Ca²⁺ binding and its release from cells were observed under hypoxia conditions. Biofilm and extracellular polymeric substances (EPS) formation were enhanced during MICP. Strain YS11 has resistance at high pH and in high salt concentrations, as well as its spore-forming ability, which supports its potential application for self-healing concrete.

Non-ureolytic calcium carbonate precipitation by Lysinibacillus sp. YS11 isolated from the rhizosphere of Miscanthus sacchariflorus

Although microbially induced calcium carbonate precipitation (MICP) through ureolysis has been widely studied in environmental engineering fields, urea utilization might cause environmental problems as a result of ammonia and nitrate production. In this study, many non-ureolytic calcium carbonate-precipitating bacteria that induced an alkaline environment were isolated from the rhizosphere of Miscanthus sacchariflorus near an artificial stream and their ability to precipitate calcium carbonate minerals with the absence of urea was investigated. MICP was observed using a phase-contrast microscope and ion-selective electrode. Only Lysinibacillus sp. YS11 showed MICP in aerobic conditions. Energy dispersive X-ray spectrometry and X-ray diffraction confirmed the presence of calcium carbonate. Field emission scanning electron microscopy analysis indicated the formation of morphologically distinct minerals around cells under these conditions. Monitoring of bacterial growth, pH changes, and Ca²⁺ concentrations under aerobic, hypoxia, and anaerobic conditions suggested that strain YS11 could induce alkaline conditions up to a pH of 8.9 and utilize 95% of free Ca²⁺ only under aerobic conditions. Unusual Ca²⁺ binding and its release from cells were observed under hypoxia conditions. Biofilm and extracellular polymeric substances (EPS) formation were enhanced during MICP. Strain YS11 has resistance at high pH and in high salt concentrations, as well as its spore-forming ability, which supports its potential application for self-healing concrete.

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.

Biomineralization processes of calcite induced by bacteria isolated from marine sediments

Biomineralization is a known natural phenomenon associated with a wide range of bacterial species. Bacterial-induced calcium carbonate precipitation by marine isolates was investigated in this study. Three genera of ureolytic bacteria, Sporosarcina sp., Bacillus sp. and Brevundimonas sp. were observed to precipitate calcium carbonate minerals. Of these species, Sporosarcina sp. dominated the cultured isolates. B. lentus CP28 generated higher urease activity and facilitated more efficient precipitation of calcium carbonate at 3.24 ± 0.25 × 10⁻⁴ mg/cell. X-ray diffraction indicated that the dominant calcium carbonate phase was calcite. Scanning electron microscopy showed that morphologies of the minerals were dominated by cubic, rhombic and polygonal plate-like crystals. The dynamic process of microbial calcium carbonate precipitation revealed that B. lentus CP28 precipitated calcite crystals through the enzymatic hydrolysis of urea, and that when ammonium ion concentrations reached 746 mM and the pH reached 9.6, that favored calcite precipitation at a higher level of 96 mg/L. The results of this research provide evidence that a variety of marine bacteria can induce calcium carbonate precipitation, and may influence the marine carbonate cycle in natural environments.

Biocalcification using B. pasteurii for strengthening brick masonry civil engineering structures

Microbiologically induced calcite precipitation in bricks by bacterium Bacillus pasteurii (NCIM 2477) using a media especially optimized for urease production (OptU) was demonstrated in this study. Effect of biocalcification activity on compressive strength and water absorption capacity of bricks was investigated. Various other parameters such as pH, growth profile, urease activity, urea breakdown and calcite precipitated were monitored during the 28 days curing period. Efficiency of B. pasteurii to form microbial aided calcite precipitate in OptU media resulted into 83.9% increase in strength of the bricks as compared to only 24.9% with standard media, nutrient broth (NB). In addition to significant increase in the compressive strength, bricks treated with B. pasteurii grown in OptU media resulted in 48.9 % reduction in water absorption capacity as compared to control bricks immersed in tap water. Thus it was successfully demonstrated that microbial calcification in optimized media by Bacillus pasteurii has good potential for commercial application to improve the life span of structures constructed with bricks, particularly structures of heritage importance.

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.