Bacteria-induced mineral precipitation: a mechanistic review

Advanced bacteria-based biomaterials for environmental applications

A large amount of anthropogenic CO2 emissions are derived from Portland cement production, contributing to global warming, which threatens human health and exposes flora and fauna to ecological imbalance. With concerns about the high maintenance and repair costs of concrete, the development of microbially induced calcium carbonate precipitation (MICP)-based self-healing concrete has been extensively examined. Bacterial carriers for microcrack healing could enhance the concrete's self-healing capacity by maintaining bacterial activity and viability. To reduce cement consumption, the development of sustainable engineered living materials (ELMs) based on MICP has become a promising new research topic that combines synthetic biology and material science, and they can potentially serve as alternatives to traditional construction materials. This review aims to describe bacterial carriers and the ongoing development of advanced ELMs based on MICP. We also highlight the emerging issues linked to applying MICP technology at the commercial scale, including economic challenges and environmental concerns.

Bio-inspired synthesis of nanocrystalline calcite demonstrating significant improvement in mechanical properties of concrete: a construction-nanobiotechnology approach

The bioinspired synthesis of construction material, known as biocement, represents a significant advancement in addressing the environmental sustainability issues associated with traditional cement use in the built environment. Biocement is produced through the process of microbially induced bio-mineralization (MIBM), which offers a promising alternative or supplement to conventional cement, potentially reducing its consumption. Despite extensive literature on the application of biocement in construction biotechnology, the fundamental mechanisms underlying its ability to enhance concrete quality remain poorly understood. This study focuses on the kinetics of biomineral synthesis by two Bacillus species; Bacillus megaterium RB05 and Bacillus foraminis DRG5, to identify the most effective strain for biomineralization. Bioconcrete specimens were created by adding inoculum containing Bacillus megaterium RB05 cells with a nutrient solution to the concrete mixture in a layer-by-layer approach. After 28 days of water curing, nanoparticles of CaCO3, ranging in size from 27 to 82 nm, were produced in the bioconcrete specimens. The resulting concrete, containing nanocrystalline biogenic calcite, demonstrated significant improvements in mechanical properties. Specifically, compressive and tensile strengths of the bioconcrete, tested using a universal testing machine (UTM), increased by 7.69 ± 0.08% and 22 ± 0.1%, respectively, after 72 h of curing. Additionally, the biocement was found to exhibit an organic-inorganic hybrid nature, as identified by TEM, EDAX, FESEM, FTIR, and XRD analyses. The enhanced mechanical properties were attributed to the high surface-to-volume ratio and hybrid nature of the calcite nanoparticles. The findings of this investigation are encouraging, suggesting the potential development of future green and self-sustainable construction materials or bioconcrete.

Understanding microbial biomineralization at the molecular level: recent advances

Microbial biomineralization is a phenomenon involving deposition of inorganic minerals inside or around microbial cells as a direct consequence of biogeochemical cycling. The microbial metabolic processes often create environmental conditions conducive for the precipitation of silicate, carbonate or phosphate, ferrate forms of ubiquitous inorganic ions. Till date the fundamental mechanisms underpinning two of the major types of microbial biomineralization such as, microbially controlled and microbially induced remains poorly understood. While microbially-controlled mineralization (MCM) depends entirely on the genetic makeup of the cell, microbially-induced mineralization (MIM) is dependent on factors such as cell morphology, cell surface structures and extracellular polymeric substances (EPS). In recent years, the organic template-mediated nucleation of inorganic minerals has been considered as an underlying mechanism based on the principles of solid-state bioinorganic chemistry. The present review thus attempts to provide a comprehensive and critical overview on the recent progress in holistic understanding of both MCM and MIM, which involves, organic-inorganic biomolecular interactions that lead to template formation, biomineral nucleation and crystallization. Also, the operation of specific metabolic pathways and molecular operons in directing microbial biomineralization have been discussed. Unravelling these molecular mechanisms of biomineralization can help in the biomimetic synthesis of minerals for potential therapeutic applications, and facilitating the engineering of microorganisms for commercial production of biominerals.

Mechanism of bacteriophage-induced vaterite formation

This study shows how bacterial viruses (bacteriophages, phages) interact with calcium carbonate during precipitation from aqueous solution. Using electron microscopy, epifluorescence microscopy, X-ray diffraction, and image analysis, we demonstrate that bacteriophages can strongly influence the formation of the vaterite phase. Importantly, bacteriophages may selectively bind both amorphous calcium carbonate (ACC) and vaterite, and indirectly affect the formation of structural defects in calcite crystallites. Consequently, the surface properties of calcium carbonate phases precipitating in the presence of viruses may exhibit different characteristics. These findings may have significant implications in determining the role of bacterial viruses in modern microbially-rich carbonate sedimentary environments, as well as in biomedical technologies. Finally, the phage-vaterite system, as a biocompatible material, may serve as a basis for the development of promising drug delivery carriers.

Enrichment of Terbium(III) under synergistic effect of biosorption and biomineralization by Bacillus sp. DW015 and Sporosarcina pasteurii

Biosorption and biomineralization are commonly used for the immobilization of metal ions. Biosorption is commonly used as a green method to enrich rare earth ions from wastewater. However, little attention has been paid to the facilitating role of biomineralization in the enrichment of rare earth ions. In this study, a strain of Bacillus sp. DW015, isolated from ion adsorption type rare earth ores and a urease-producing strain Sporosarcina pasteurii were used to enrich rare earth elements (REEs) from an aqueous solution. The results indicate that biomineralization accelerates the enrichment of Terbium(III) compared to biosorption alone. Kinetic analysis suggests that the main mode of action of DW015 was biosorption, following pseudo-second-order kinetics (R2 = 0.998). The biomineralization of DW015 did not significantly contribute to the enrichment of Tb(III), whereas excessive biomineralization of S. pasteurii led to a decrease in the enrichment of Tb(III). A synergistic system of biosorption and biomineralization was established by combining the two bacteria, with the optimal mixed bacteria (S. pasteurii:DW015) ratio being 1:19. This study provides fundamental support for the synergistic effect of biosorption and biomineralization and offers a new reference for future microbial-based enrichment methods.

IMPORTANCE

A weak microbially induced calcium carbonate precipitation (MICP) promotes the enrichment of Tb(III) by bacteria, while a strong MICP leads to the release of Tb(III). However, existing explanations cannot elucidate these mechanisms. In this study, the morphology of the bioprecipitation and the degree of Tb(III) enrichment were analyzed by X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive spectroscopy (EDS). The data revealed that MICP could drive stable attachment of Tb(III) onto the cell surface, forming a Tb-CaCO3 mixed solid phase. Excessive rapid rate of calcite generation could disrupt the Tb(III) adsorption equilibrium, leading to the release of Tb(III). Therefore, in order for Tb(III) to be stably embedded in calcite, it is necessary to have a sufficient number of adsorption sites on the bacteria and to regulate the rate of MICP. This study provides theoretical support for the process design of MICP for the enrichment of rare earth ions.

Microbial consortium involved in ferromanganese and francolite biomineralization in an anchialine environment (Zinzulùsa Cave, Castro, Italy)

Tidally-influenced subterranean settings represent natural geomicrobiological laboratories, relatively unexplored, that facilitate the investigation of new biomineralization processes. The unusual water chemistry of Zinzulùsa Cave and its oligotrophic and aphotic conditions have allowed the development of a unique ecosystem in which complex bacterial activities induce rare biomineralization processes. A diversified microbial community develops on centimeter-thick crusts that form in the submerged part of the cave. The crusts are formed of Ca-phosphate minerals, mostly carbonate-fluoroapatite (francolite), covered by a black crust, few microns in thickness, composed of ferromanganiferous oxides (hematite and vernadite). Diffuse coccoidal and filamentous bacteria and amorphous organic matter are mixed with the minerals. The micromorphologies and comparative 16S rRNA gene-based metabarcoding analyses identify a "core microbiota" also common to other natural environments characterized by FeMn and Ca-phosphate mineralization. The microbiota is characterized by nitrifying, sulfide/sulfur/thiosulfate-oxidizing and sulfate/thiosulfate/sulfur-reducing bacteria. In addition, manganese-oxidizing bacteria include the recently described "Ca. Manganitrophus noduliformans" and an abundance of bacteria belonging to the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum, as well as Haliangiales (fruiting body-forming bacteria) and Hyphomicrobiales (stalked and budding bacteria) that are known to produce extracellular polymers that trap iron and manganese oxides. 16S rRNA gene metabarcoding analysis showed the presence of bacteria able to utilize many organic P substrates, including Ramlibacter, and SEM images revealed traces of fossilized microorganisms resembling "cable bacteria", which may play a role in Ca-phosphate biomineralization. Overall, the data indicate biomineralization processes induced by microbial metabolic activities for both ferromanganiferous oxide and francolite components of these crusts.

Recovery of terbium by Lysinibacillus sp. DW018 isolated from ionic rare earth tailings based on microbial induced calcium carbonate precipitation

Microbial induced calcium carbonate precipitation (MICP) is considered as an environmentally friendly microbial-based technique to remove heavy metals. However, its application in removal and recovery of rare earth from wastewaters remains limited and the process is still less understood. In this study, a urease-producing bacterial strain DW018 was isolated from the ionic rare earth tailings and identified as Lysinibacillus based on 16S rRNA gene sequencing. Its ability and possible mechanism to recover terbium was investigated by using X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), and fourier transform infrared spectroscopy (FTIR). The results showed that the urease activity of DW018 could meet the biomineralization requirements for the recovery of Tb3+ from wastewaters. The recovery rate was as high as 98.28% after 10 min of treatment. The optimal conditions for mineralization and recovery were determined as a bacterial concentration of OD600 = 1.0, a temperature range of 35 to 40°C, and a urea concentration of 0.5%. Notably, irrespective of CaCO3 precipitation, the strain DW018 was able to utilize MICP to promote the attachment of Tb3+ to its cell surface. Initially, Tb3+ existed in amorphous form on the bacterial surface; however, upon the addition of a calcium source, Tb3+ was encapsulated in calcite with the growth of CaCO3 at the late stage of the MICP. The recovery effect of the strain DW018 was related to the amino, hydroxyl, carboxyl, and phosphate groups on the cell surface. Overall, the MICP system is promising for the green and efficient recovery of rare earth ions from wastewaters.

Understanding the role of zinc ions on struvite nucleation and growth in the context of infection urinary stones

Taking into account that in recent decades there has been an increase in the incidence of urinary stones, especially in highly developed countries, from a wide range of potentially harmful substances commonly available in such countries, we chose zinc for the research presented in this article, which is classified by some sources as a heavy metal. In this article, we present the results of research on the influence of Zn2+ ion on the nucleation and growth of struvite crystals-the main component of infection urinary stones. The tests were carried out in an artificial urine environment with and without the presence of Proteus mirabilis bacteria. In the latter case, the activity of bacterial urease was simulated chemically, by systematic addition of an aqueous ammonia solution. The obtained results indicate that Zn2+ ions compete with Mg2+ ions, which leads to the gradual replacement of Mg2+ ions in the struvite crystal lattice with Zn2+ ions to some extent. This means co-precipitation of Mg-struvite (MgNH4PO4·6H2O) and Znx-struvite (Mg1-xZnxNH4PO4·6H2O). Speciation analysis of chemical complexes showed that Znx-struvite precipitates at slightly lower pH values than Mg-struvite. This means that Zn2+ ions shift the nucleation point of crystalline solids towards a lower pH. Additionally, the conducted research shows that Zn2+ ions, in the range of tested concentrations, do not have a toxic effect on bacteria; on the contrary, it has a positive effect on cellular metabolism, enabling bacteria to develop better. It means that Zn2+ ions in artificial urine, in vitro, slightly increase the risk of developing infection urinary stones.

Revitalizing contaminated lands: A state-of-the-art review on the remediation of mine-tailings using phytoremediation and genomic approaches

The mining industry has historically served as a critical reservoir of essential raw materials driving global economic progress. Nevertheless, the consequential by-product known as mine tailings has consistently produced a substantial footprint of environmental contamination. With annual discharges of mine tailings surpassing 10 billion tons globally, the need for effective remediation strategies is more pressing than ever as traditional physical and chemical remediation techniques are hindered by their high costs and limited efficacy. Phytoremediation utilizing plants for remediation of polluted soil has developed as a promising and eco-friendly approach to addressing mine tailings contamination. Furthermore, sequencing of genomic DNA and transcribed RNA extracted from mine tailings presents a pivotal opportunity to provide critical supporting insights for activities directed towards the reconstruction of ecosystem functions on contaminated lands. This review explores the growing prominence of phytoremediation and metagenomics as an ecologically sustainable techniques for rehabilitating mine-tailings. The present study envisages that plant species such as Solidago chilensis, Festuca arundinacea, Lolium perenne, Polygonum capitatum, Pennisetum purpureum, Maireana brevifolia, Prosopis tamarugo etc. could be utilized for the remediation of mine-tailings. Furthermore, a critical evaluation of the organic and inorganic ammendments that optimize conditions for the remediation of mine tailings is also provided. The focus of this review extends to the exploration of environmental genomics to characterize microbial communities in mining sites. By delving into the multifaceted dimensions of phytoremediation and genomics for mine tailings, this study contributes to the ongoing efforts to revitalize contaminated lands for a sustainable and environmentally friendly future.

Comparison of calcium carbonate production by bacterial isolates from recycled aggregates

The new technology of microbially induced calcium carbonate precipitation (MICP) has been applied in construction materials as a strategy to enhance their properties. In pursuit of solutions that are more localized and tailored to the study's target, this work focused on isolating and selecting bacteria capable of producing CaCO3 for posterior application in concrete aggregates. First, eleven bacterial isolates were obtained from aggregates and identified as genera Bacillus, Lysinibacillus, Exiguobacterium, and Micrococcus. Then, the strains were compared based on the quantity and nature of calcium carbonate they produced using thermogravimetric analysis, X-ray diffraction, and scanning electron microscopy with energy dispersive spectroscopy. Bacillus sp. dominated the cultured isolates and, along with Lysinibacillus sp., exhibited the highest CaCO3 conversion (up to 80%). On the other hand, Exiguobacterium and Micrococcus genera showed the poor ability to MICP (21.3 and 20.3%, respectively). Calcite and vaterite were the dominant carbonate polymorphs, with varying proportions. Concrete aggregates have proven to be a source of microorganisms capable of producing stable calcium carbonates with a high conversion rate. This indicates the feasibility of using microorganisms derived from local sources for application in construction materials as a sustainable way to enhance their characteristics.

Enhancing La(III) biosorption and biomineralization with Micromonospora saelicesensis: Involvement of phosphorus and formation of monazite nano-minerals

The release of rare earth elements (REEs) from mining wastes and their applications has significant environmental implications, necessitating the development of effective prevention and reclamation strategies. The mobility of REEs in groundwater due to microorganisms has garnered considerable attention. In this study, a La(III) resistant actinobacterium, Micromonospora saelicesensis KLBMP 9669, was isolated from REE enrichment soil in GuiZhou, China, and evaluated for its ability to adsorb and biomineralize La(III). The findings demonstrated that M. saelicesensis KLBMP 9669 immobilized La(III) through the physical and chemical interactions, with immobilization being influenced by the initial La(III) concentration, biomass, and pH. The adsorption kinetics followed a pseudo-second-order rate model, and the adsorption isotherm conformed to the Langmuir model. La(III) adsorption capacity of this strain was 90 mg/g, and removal rate was 94 %. Scanning electron microscope (SEM) coupled with energy dispersive X-ray spectrometer (EDS) analysis revealed the coexistence of La(III) with C, N, O, and P. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) investigations further indicated that carboxyl, amino, carbonyl, and phosphate groups on the mycelial surface may participate in lanthanum adsorption. Transmission electron microscopy (TEM) revealed that La(III) accumulation throughout the M. saelicesensis KLBMP 9669, with some granular deposits on the mycelial surface. Selected area electron diffraction (SAED) confirmed the presence of LaPO4 crystals on the M. saelicesensis KLBMP 9669 biomass after a prolonged period of La(III) accumulation. This post-sorption nano-crystallization on the M. saelicesensis KLBMP 9669 mycelial surface is expected to play a crucial role in limiting the bioimmobilization of REEs in geological repositories.

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols

Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. We created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.

DNA sequencing, microbial indicators, and the discovery of buried kimberlites

Population growth and technological advancements are placing growing demand on mineral resources. New and innovative exploration technologies that improve detection of deeply buried mineralization and host rocks are required to meet these demands. Here we used diamondiferous kimberlite ore bodies as a test case and show that DNA amplicon sequencing of soil microbial communities resolves anomalies in microbial community composition and structure that reflect the surface expression of kimberlites buried under 10 s of meters of overburden. Indicator species derived from laboratory amendment experiments were employed in an exploration survey in which the species distributions effectively delineated the surface expression of buried kimberlites. Additional indicator species derived directly from field observations improved the blind discovery of kimberlites buried beneath similar overburden types. Application of DNA sequence-based analyses of soil microbial communities to mineral deposit exploration provides a powerful illustration of how genomics technologies can be leveraged in the discovery of critical new resources.

Microbial communities in paddy soils: differences in abundance and functionality between rhizosphere and pore water, the influence of different soil organic carbon, sulfate fertilization and cultivation time, and contribution to arsenic mobility and speciation

Abiotic factors and rhizosphere microbial populations influence arsenic accumulation in rice grains. Although mineral and organic surfaces are keystones in element cycling, localization of specific microbial reactions in the root/soil/pore water system is still unclear. Here, we tested if original unplanted soil, rhizosphere soil and pore water represented distinct ecological microniches for arsenic-, sulfur- and iron-cycling microorganisms and compared the influence of relevant factors such as soil type, sulfate fertilization and cultivation time. In rice open-air-mesocosms with two paddy soils (2.0% and 4.7% organic carbon), Illumina 16S rRNA gene sequencing demonstrated minor effects of cultivation time and sulfate fertilization that decreased Archaea-driven microbial networks and incremented sulfate-reducing and sulfur-oxidizing bacteria. Different compartments, characterized by different bacterial and archaeal compositions, had the strongest effect, with higher microbial abundances, bacterial biodiversity and interconnections in the rhizosphere vs pore water. Within each compartment, a significant soil type effect was observed. Higher percentage contributions of rhizosphere dissimilatory arsenate- and iron-reducing, arsenite-oxidizing, and, surprisingly, dissimilatory sulfate-reducing bacteria, as well as pore water iron-oxidizing bacteria in the lower organic carbon soil, supported previous chemistry-based interpretations of a more active S-cycling, a higher percentage of thioarsenates and lower arsenic mobility by sorption to mixed Fe(II)Fe(III)-minerals in this soil.

Preliminary indication of the role of AHL-dependent quorum sensing systems in calcium carbonate precipitation in Gram-negative bacteria

Numerous microbial species participate in precipitation of carbonates in various natural environments, including soils, geological formations, freshwater biofilms and oceans. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and adaptive aspects remain poorly known. Many Gram-negative bacteria use cell-to-cell communication systems relying on N-acylhomoserine lactone (AHLs) signal molecules to express certain phenotypic traits in a density-dependent manner, a phenomenon referred as to quorum-sensing (QS). In this work, bacterial isolates collected from cave and rhizosphere soil were analyzed to study the occurrence of the AHL-mediated QS in bacterial calcium carbonate (CaCO3) precipitation. To test the production of AHLs signal molecules, we cross-streaked Gram-negative calcifying strains, selected among the environmental strains studied, with the AHL-negative mutant Chromobacterium subtsugae strain CV026. Only Burkholderia ambifaria LMG 11351 was able to restore violacein production in CV026 among the tested strains. The constructed AHL-negative mutant of B. ambifaria LMG 11351 could not precipitate CaCO3 on B-4 agar. Scanning Electron Microscopy (SEM) analysis on CaCO3 crystals obtained in vitro shows crystals of different morphologies, calcified biofilms and bacteria in close contact with the precipitated crystals. In the inner layers of the bioliths deposited by B. ambifaria LMG 11351, a stream-like organization of the Burkholderia imprints was not detected by SEM. Our data provide preliminary evidence that the activation of AHL-regulated genes may be a prerequisite for in vitro bacterial carbonatogenesis, in some cases, confirming the specific role of bacteria as CaCO3 precipitating agents. We enhance the understanding of bacterial CaCO3 biomineralization and its potential biotechnology implications for QS-based strategies to enhance or decrease CaCO3 precipitation through specific bacterial processes. The AHL-negative mutant of B. ambifaria LMG 11351 (a well-known plant growth-promoting bacterium) could also be used to study plant-bacteria interactions. The adaptive role of bacterial CaCO3 biomineralization was also discussed.

Study of diversity of mineral-forming bacteria in sabkha mats and sediments of mangrove forest in Qatar

The involvement of microorganisms in carbonate minerals and modern dolomite formation in evaporitic environments occupied with microbial mats (i.e., sabkha) and in mangrove forests is evidenced, while its potential diversity requires further elucidation. Microorganisms can create supersaturated microenvironments facilitating the formation of various carbonate minerals through specific metabolic pathways. This is particularly important in arid environments, where deposition and sedimentary structures can occur. This study investigated the biodiversity of halophilic, heterotrophic, and aerobic mineral-forming bacteria in mangrove forests and living and decaying mats of Qatari sabkha. The diversity study was performed at the protein level using MALDI-TOF mass spectrometry protein profiles combined with principal component analysis (PCA), which revealed a high diversity of isolated strains at the taxonomy and protein profile levels. The diversity of the minerals formed in pure cultures was evidenced by SEM/EDS and XRD analysis. Different types of carbonate minerals (calcium carbonate, magnesium carbonates, and high-magnesium calcites) were formed in pure cultures of the studied strains, which might explain their occurrence in the bulk composition of the sediments from where the strains were isolated. These results illuminate the diversity of biological mineral-formation processes in the extreme environments of Qatari sabkhas and mangroves, explaining the high diversity of minerals in these environments.

Will tomorrow's mineral materials be grown?

Biomineralization, the capacity to form minerals, has evolved in a great diversity of bacterial lineages as an adaptation to different environmental conditions and biological functions. Microbial biominerals often display original properties (morphology, composition, structure, association with organics) that significantly differ from those of abiotically formed counterparts, altogether defining the 'mineral phenotype'. In principle, it should be possible to take advantage of microbial biomineralization processes to design and biomanufacture advanced mineral materials for a range of technological applications. In practice, this has rarely been done so far and only for a very limited number of biomineral types. This is mainly due to our poor understanding of the underlying molecular mechanisms controlling microbial biomineralization pathways, preventing us from developing bioengineering strategies aiming at improving biomineral properties for different applications. Another important challenge is the difficulty to upscale microbial biomineralization from the lab to industrial production. Addressing these challenges will require combining expertise from environmental microbiologists and geomicrobiologists, who have historically been working at the forefront of research on microbe-mineral interactions, alongside bioengineers and material scientists. Such interdisciplinary efforts may in the future allow the emergence of a mineral biomanufacturing industry, a critical tool towards the development more sustainable and circular bioeconomies.

Microbially Induced Calcium Carbonate Precipitation by Sporosarcina pasteurii: a Case Study in Optimizing Biological CaCO3 Precipitation

Current production of traditional concrete requires enormous energy investment that accounts for approximately 5 to 8% of the world's annual CO2 production. Biocement is a building material that is already in industrial use and has the potential to rival traditional concrete as a more convenient and more environmentally friendly alternative. Biocement relies on biological structures (enzymes, cells, and/or cellular superstructures) to mineralize and bind particles in aggregate materials (e.g., sand and soil particles). Sporosarcina pasteurii is a workhorse organism for biocementation, but most research to date has focused on S. pasteurii as a building material rather than a biological system. In this review, we synthesize available materials science, microbiology, biochemistry, and cell biology evidence regarding biological CaCO3 precipitation and the role of microbes in microbially induced calcium carbonate precipitation (MICP) with a focus on S. pasteurii. Based on the available information, we provide a model that describes the molecular and cellular processes involved in converting feedstock material (urea and Ca2+) into cement. The model provides a foundational framework that we use to highlight particular targets for researchers as they proceed into optimizing the biology of MICP for biocement production.

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.

Microbial Influence on the Mobility of +3 Actinides from a Salt-Based Nuclear Waste Repository

Biologically enhanced transport of radionuclides is one of several processes that can affect the performance of a nuclear waste repository. In this work, several microbial isolates from the Waste Isolation Pilot Plant (WIPP) were tested for their influence on the concentration of neodymium, as an analog for +3 actinides, in simple sodium chloride solutions and in anoxic WIPP brines. Batch sorption experiments were carried out over a period of 4-5 weeks. In many cases, the effect on neodymium in solution was immediate and extensive and assumed to be due to surface complexation. However, over time, the continued loss of Nd from the solution was more likely due to biologically induced precipitation and/or mineralization and possible entrapment in extracellular polymeric substances. The results showed no correlation between organism type and the extent of its influence on neodymium in solution. However, a correlation was observed between different test matrices (simple NaCl versus high-magnesium brine versus high-NaCl brine). Further experiments were conducted to test these matrix effects, and the results showed a significant effect of magnesium concentration on the ability of microorganisms to remove Nd from solution. Possible mechanisms include cation competition and the alteration of cell surface structures. This suggests that the aqueous chemistry of the WIPP environs could play a larger role in the final disposition of +3 actinides than the microbiology.

Unraveling disparate roles of organisms, from plants to bacteria, and viruses on built cultural heritage

The different organisms, ranging from plants to bacteria, and viruses that dwell on built cultural heritage can be passive or active participants in conservation processes. For the active participants, particular attention is generally given to organisms that play a positive role in bioprotection, bioprecipitation, bioconsolidation, bioremediation, biocleaning, and biological control and to those involved in providing ecosystem services, such as reducing temperature, pollution, and noise in urban areas. The organisms can also evolve or mutate in response to changes, becoming tolerant and resistant to biocidal treatments or acquiring certain capacities, such as water repellency or resistance to ultraviolet radiation. Our understanding of the capacities and roles of these active organisms is constantly evolving as bioprotection/biodeterioration, and biotreatment studies are conducted and new techniques for characterizing species are developed. This brief review article aims to shed light on interesting research that has been abandoned as well as on recent (some ongoing) studies opening up new scopes of research involving a wide variety of organisms and viruses, which are likely to receive more attention in the coming years. KEY POINTS: • Organisms and viruses can be active or passive players in heritage conservation • Biotreatment and ecosystem service studies involving organisms and viruses are shown • Green deal, health, ecosystem services, and global change may shape future research.

The iron "redox battery" in sandy sediments: Its impact on organic matter remineralization and phosphorus cycling

Permeable sandy sediments cover 50-60 % of the global continental shelf and are important bioreactors that regulate organic matter (OM) turnover and nutrient cycling in the coastal ocean. In sands, the dynamic porewater advection can cause rapid mass transfer and variable redox conditions, thus affecting OM remineralization pathways, as well as the recycling of iron and phosphorus. In this study, North Sea sands were incubated in flow-through reactors (FTRs) to investigate biogeochemical processes under porewater advection and changing redox conditions. We found that the average rate of anaerobic OM remineralization was 12 times lower than the aerobic pathway, and Fe(III) oxyhydroxides were found to be the major electron acceptors during 34 days of anoxic incubation. Reduced Fe accumulated in the solid phase (expressed as Fe(II)) before significant release of Fe²⁺ into the porewater, and most of the reduced Fe (~96 %) remained in the solid phase throughout the anoxic incubation. Fe(II) retained in the solid phase, either through the formation of authigenic Fe(II)-bearing minerals or adsorption, was easily re-oxidized upon exposure to O₂. Excessive P release (apart from OM remineralization) started at the beginning of the anoxic incubation and accelerated after the release of Fe²⁺ with a constant P/Fe²⁺ ratio of 0.26. After 34 days of anoxic incubation, porewater was re‑oxygenated and > 99 % of released P was coprecipitated through Fe²⁺ oxidation (so-called "Fe curtain"). Our results demonstrate that Fe(III)/Fe(II) in the solid phase can serve as a relatively immobile and rechargeable "redox battery" under dynamic porewater advection. This Fe "redox battery" is characteristic for permeable sediments and environments with variable redox conditions, making Fe an important player in OM turnover. We also suggest that P liberated before Fe²⁺ release can escape the "Fe curtain" in surface sediments, thus potentially increasing net benthic P efflux from permeable sediments under variable redox conditions.

Active Sulfate-Reducing Bacterial Community in the Camel Gut

The diversity and activity of sulfate-reducing bacteria (SRB) in the camel gut remains largely unexplored. An abundant SRB community has been previously revealed in the feces of Bactrian camels (Camelus bactrianus). This study aims to combine the 16S rRNA gene profiling, sulfate reduction rate (SRR) measurement with a radioactive tracer, and targeted cultivation to shed light on SRB activity in the camel gut. Fresh feces of 55 domestic Bactrian camels grazing freely on semi-arid mountain pastures in the Kosh-Agach district of the Russian Altai area were analyzed. Feces were sampled in early winter at an ambient temperature of -15 °C, which prevented possible contamination. SRR values measured with a radioactive tracer in feces were relatively high and ranged from 0.018 to 0.168 nmol S cm^-3 day^-1. The 16S rRNA gene profiles revealed the presence of Gram-negative Desulfovibrionaceae and spore-forming Desulfotomaculaceae. Targeted isolation allowed us to obtain four pure culture isolates belonging to Desulfovibrio and Desulforamulus. An active SRB community may affect the iron and copper availability in the camel intestine due to metal ions precipitation in the form of sparingly soluble sulfides. The copper-iron sulfide, chalcopyrite (CuFeS₂), was detected by X-ray diffraction in 36 out of 55 analyzed camel feces. In semi-arid areas, gypsum, like other evaporite sulfates, can be used as a solid-phase electron acceptor for sulfate reduction in the camel gastrointestinal tract.

Relationship between Bacterial Contribution and Self-Healing Effect of Cement-Based Materials

The civil research community has been attracted to self-healing bacterial-based concrete as a potential solution in the economy 4.0 era. This concept provides more sustainable material with a longer lifetime due to the reduction of crack appearance and the need for anthropogenic impact. Regardless of the achievements in this field, the gap in the understanding of the importance of the bacterial role in self-healing concrete remains. Therefore, understanding the bacterial life cycle in the self-healing effect of cement-based materials and selecting the most important relationship between bacterial contribution, self-healing effect, and material characteristics through the process of microbiologically (bacterially) induced carbonate precipitation is just the initial phase for potential applications in real environmental conditions. The concept of this study offers the possibility to recognize the importance of the bacterial life cycle in terms of application in extreme conditions of cement-based materials and maintaining bacterial roles during the self-healing effect.

Manipulating Bacterial Biofilms Using Materiobiology and Synthetic Biology Approaches

Bacteria form biofilms on material surfaces within hours. Biofilms are often considered problematic substances in the fields such as biomedical devices and the food industry; however, they are beneficial in other fields such as fermentation, water remediation, and civil engineering. Biofilm properties depend on their genome and the extracellular environment, including pH, shear stress, and matrices topography, stiffness, wettability, and charges during biofilm formation. These surface properties have feedback effects on biofilm formation at different stages. Due to emerging technology such as synthetic biology and genome editing, many studies have focused on functionalizing biofilm for specific applications. Nevertheless, few studies combine these two approaches to produce or modify biofilms. This review summarizes up-to-date materials science and synthetic biology approaches to controlling biofilms. The review proposed a potential research direction in the future that can gain better control of bacteria and biofilms.

A critical review of mineral-microbe interaction and coevolution: mechanisms and applications

The mineral-microbe interactions play important roles in environmental change, biogeochemical cycling of elements, and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation, and precipitation of minerals through their activity, resulting in either genetically-controlled or metabolism-induced biomineralization. Through these interactions minerals and microbes coevolve through Earth history. The mineral-microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral-microbe interactions for the benefit of humankind.

Microbial communities in carbonate precipitates from drip waters in Nerja Cave, Spain

Research on cave microorganisms has mainly focused on the microbial communities thriving on speleothems, rocks and sediments; however, drip water bacteria and calcite precipitation has received less attention. In this study, microbial communities of carbonate precipitates from drip waters in Nerja, a show cave close to the sea in southeastern Spain, were investigated. We observed a pronounced difference in the bacterial composition of the precipitates, depending on the galleries and halls. The most abundant phylum in the precipitates of the halls close to the cave entrance was Proteobacteria, due to the low depth of this sector, the direct influence of a garden on the top soil and the infiltration of waters into the cave, as well as the abundance of members of the order Hyphomicrobiales, dispersing from plant roots, and other Betaproteobacteria and Gammaproteobacteria, common soil inhabitants. The influence of marine aerosols explained the presence of Marinobacter, Idiomarina, Thalassobaculum, Altererythrobacter and other bacteria due to the short distance from the cave to the sea. Nineteen out of forty six genera identified in the cave have been reported to precipitate carbonate and likely have a role in mineral deposition.

Authigenic Minerals of the Derbent and South Caspian Basins (Caspian Sea): Features of Forms, Distribution and Genesis under Conditions of Hydrogen Sulfide Contamination

This paper presents the results of complex lithological, mineralogical, and geochemical studies of bottom sediments of deep-water basins of the Caspian Sea (Derbent and South Caspian Basins) in areas contaminated by hydrogen sulfide. In the course of complex studies, numerous manifestations of authigenic mineral formation associated with the stage of early diagenesis have been established. Authigenic minerals belonging to the groups of sulfates (gypsum, barite), chlorides (halite), carbonates (calcite, low Mg-calcite; kutnohorite), and sulfides (framboidal pyrite), as well as their forms and composition, have been identified by a complex of analytical methods (X-ray diffractometry (XRD), scanning electron microscopy (SEM) with energy-dispersive X-ray spectroscopy (EDS); atomic absorption spectroscopy (AAS); coulometric titration (CT)); the nature of their distribution in bottom sediments has been assessed. Carbonates and sulfates are predominant authigenic minerals in the deep-water basins of the Caspian Sea. As a part of the study, differences have been established in the composition and distribution of associations of authigenic minerals in the bottom sediments in the deep-water basins. These are mineral associations characteristic of the uppermost part of the sediments (interval 0–3 cm) and underlying sediments. In the Derbent Basin, in sediments of the interval 3–46 cm, an authigenic association is formed from gypsum, calcite, magnesian calcite, siderite, and framboidal pyrite. An association of such authigenic minerals as gypsum and calcite is formed in sediments of the 0–3 cm interval. In the South Caspian Basin, in sediments of the interval 3–35 cm, an association of such authigenic minerals as gypsum, halite, calcite, magnesian calcite, and framboidal pyrite is formed. The association of such authigenic minerals as gypsum, halite, calcite, magnesian calcite, kutnohorite, and framboidal pyrite is characteristic of sediments of the 0–3 cm interval. We consider the aridity of the climate in the South Caspian region to be the main factor that determines the appearance of such differences in the uppermost layer of sediments of the basins. Judging by the change in the composition of authigenic associations, the aridity of the South Caspian increased sharply by the time of the accumulation of the upper layer of sediments (interval 0–3 cm). Taking into account lithological, mineralogical and geochemical data, the features of the processes of authigenic mineral formation in the deep-water basins of the Caspian Sea under conditions of hydrogen sulfide contamination have been determined. Analysis of the results obtained and published data on the conditions of sedimentation in the Caspian Sea showed that hydrogen sulfide contamination recorded in the bottom layer of the water column of the deep-water basins of the Caspian Sea may affect the formation of authigenic sulfides (framboidal pyrite), sulfates (gypsum), and carbonates (calcite and kutnohorite) associated with the activity of sulfate-reducing bacteria in reducing conditions.

The Effect of Bacteria on Early Age Strength of CEM I and CEM II Cementitious Composites

Despite being associated with lower carbon emissions, CEM II cementitious materials exhibit reduced early age strength compared to that of CEM I. Several studies have demonstrated early age strength improvements by incorporating bacterial cells in concrete. In this study, live vegetative bacteria and dead bacteria killed in two different ways were used to explore whether changes in strength are related to the bacteria’s viability or their surface morphology. Compressive and flexural strength tests were performed at mortars with and without bacteria for both CEM I and CEM II cement. Their microstructure, porosity and mineralogy were also examined. No net strength gain was recorded for either CEM I or CEM II bacterial mortars compared to non-bacterial controls, although changes in the porosity were reported. It is proposed that two phenomena, one causing strength-reduction and one causing strength-gain, took place in the bacterial specimens, simultaneously. It is suggested that each phenomenon is dependent on the alkalinity of the cement matrix, which differs between CEM I and CEM II mortars at early age. Nevertheless, in neither case could it be recommended that the addition of bacteria is an effective way of increasing the early age strength of mortars.

Genetic optimisation of bacteria-induced calcite precipitation in Bacillus subtilis

Background

Microbially induced calcite precipitation (MICP) is an ancient property of bacteria, which has recently gained considerable attention for biotechnological applications. It occurs as a by-product of bacterial metabolism and involves a combination of chemical changes in the extracellular environment, e.g. pH increase, and presence of nucleation sites on the cell surface or extracellular substances produced by the bacteria. However, the molecular mechanisms underpinning MICP and the interplay between the contributing factors remain poorly understood, thus placing barriers to the full biotechnological and synthetic biology exploitation of bacterial biomineralisation.

Results

In this study, we adopted a bottom-up approach of systematically engineering Bacillus subtilis, which has no detectable intrinsic MICP activity, for biomineralisation. We showed that heterologous production of urease can induce MICP by local increases in extracellular pH, and this can be enhanced by co-expression of urease accessory genes for urea and nickel uptake, depending on environmental conditions. MICP can be strongly enhanced by biofilm-promoting conditions, which appeared to be mainly driven by production of exopolysaccharide, while the protein component of the biofilm matrix was dispensable. Attempts to modulate the cell surface charge of B. subtilis had surprisingly minor effects, and our results suggest this organism may intrinsically have a very negative cell surface, potentially predisposing it for MICP activity.

Conclusions

Our findings give insights into the molecular mechanisms driving MICP in an application-relevant chassis organism and the genetic elements that can be used to engineer de novo or enhanced biomineralisation. This study also highlights mutual influences between the genetic drivers and the chemical composition of the surrounding environment in determining the speed, spatial distribution and resulting mineral crystals of MICP. Taken together, these data pave the way for future rational design of synthetic precipitator strains optimised for specific applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01704-1.