Assessing ureolytic bacteria with calcifying abilities isolated from limestone caves for biocalcification

Microbially Induced Calcium Carbonate Precipitation Using Lysinibacillus sp.: A Ureolytic Bacterium from Uttarakhand for Soil Stabilization

Microbially induced calcium carbonate precipitation (MICP) is a soil remediation method that has emerged as a viable and long-term solution for enhancing soil mechanical qualities. The technique of MICP that has been extensively researched is urea hydrolysis, which occurs naturally in the environment by urease-producing bacteria as part of their fundamental metabolic processes. The objectives of the current study include screening and identifying native ureolytic bacteria from soil in Uttarakhand, optimizing growth factors for increased urease activity, and calcite precipitation by the bacteria using response surface methodology. Additionally, it was assessed how well the isolated bacteria in the medium biomineralized when using synthetic media and cheaper alternatives such as cow urine and eggshell as sources of urea and Ca2+, respectively. The isolated strain identified as Lysinibacillus sp. was found to be the very active strain after soil samples were screened for ureolytic bacteria. It was discovered that optimization studies with values of pH 8, urea concentration (0.8 M), inoculum concentration (3%), and incubation time (48 h) yielded a higher activity of 33.7 U/mL (threefold increase), and a higher calcium carbonate precipitation (enzyme activity: 10.96 U/mL, pH: 8.92, soluble Ca2⁺: 25.53 mM and insoluble Ca2⁺: 0.856 g). The calcite precipitation in broth media supplemented with ready-made substrates and alternative sources demonstrated a similar result of increased pH and ammonia release. Thus, the current study successfully paves the way for several possibilities to stabilize the slopy soils prone to landslides and erosion in Uttarakhand and pinpoint an economic approach through biomineralization.

Identification of phytase producing bacteria from acidifying Tithonia diversifolia: Potential for ruminant feed development

Phytate content in feed ingredients can negatively impact digestibility and palatability. To address this issue, it is necessary to study microbes capable of breaking down phytate content. This study aimed to isolate and characterize phytase-producing bacteria from decaying materials rich in phytic acid. The research was conducted in several stages. The first stage involved isolating phytase-producing bacteria from the acidification of Tithonia diversifolia using growth media containing Na-phytate. Bacterial isolates that produced clear zones were then tested for their activity and ability to produce several enzymes, specifically phytase, cellulase, and protease. The next step was to test the morphological characteristics of the bacterial isolate. The final stage of bacterial identification consisted of DNA isolation, followed by PCR amplification of the 16S rRNA gene, DNA sequence homology analysis, and construction of a phylogenetic tree. Based on research, three isolates were found to produce clear phytase zones: isolates R5 (20.3 mm), R7 (16.1 mm) and R8 (31.7 mm). All isolates were able to produce the enzymes phytase (5.45-6.54 U/ml), cellulase (2.60-2.92 U/ml), and protease (22.2-23.4 U/ml). Metagenomic testing identified isolate R7 and R8 as Alcaligenes faecalis and isolate R5 as Achromobacter xylosoxidans. The isolation and characterization of phytase-producing bacteria from Tithonia diversifolia acidification resulted in the identification of two promising candidates that can be applied as sources of phytase producers. Phytase-producing bacteria can be utilized to improve digestibility and palatability in animal feed.

Microbiological exploration of the Cueva del Viento lava tube system in Tenerife, Canary Islands

Cueva del Viento, located in the Canary Islands, Spain, is the Earth's sixth-longest lava tube, spanning 18,500 m, and was formed approximately 27,000 years ago. This complex volcanic cave system is characterized by a unique geomorphology, featuring an intricate network of galleries. Despite its geological significance, the geomicrobiology of Cueva del Viento remains largely unexplored. This study employed a combination of culture-dependent techniques and metabarcoding data analysis to gain a comprehensive understanding of the cave's microbial diversity. The 16S rRNA gene metabarcoding approach revealed that the coloured microbial mats (yellow, red and white) coating the cave walls are dominated by the phyla Actinomycetota, Pseudomonadota and Acidobacteriota. Of particular interest is the high relative abundance of the genus Crossiella, which is involved in urease-mediated biomineralization processes, along with the presence of genera associated with nitrogen cycling, such as Nitrospira. Culture-dependent techniques provided insights into the morphological characteristics of the isolated species and their potential metabolic activities, particularly for the strains Streptomyces spp., Paenarthrobacter sp. and Pseudomonas spp. Our findings underscore the potential of Cueva del Viento as an ideal environment for studying microbial diversity and for the isolation and characterization of novel bacterial species of biotechnological interest.

Sustainable utilization of biopolymers as green adhesive in soil improvement: a review

Throughout history, soil improvement has relied on various additives, from ancient practices using lime and other traditional compounds to modern methods employing geosynthetics and microbial treatments. However, conventional soil admixtures, while effective, often carry significant environmental drawbacks, especially in the case of additives like cement. In response to these environmental concerns, there has been a growing interest in the use of biopolymers as a sustainable alternative for ground improvement. This literature review centers on the properties and performance of biopolymers, addressing their increasing adoption in soil enhancement endeavors. It explores the historical context of soil improvement practices, highlights the contemporary environmental challenges posed by traditional additives, and underscores the emerging trend toward biopolymers as a green adhesive solution. The review further probes into specific biopolymers, examining their characteristics and elucidating how biopolymer-treated soils achieve the desired improvements. In essence, this review provides a comprehensive understanding of the historical evolution of soil improvement practices, the current environmental imperatives, and the promising role that biopolymers play in achieving sustainable soil enhancement. It serves as a valuable resource for researchers and practitioners seeking environmentally friendly alternatives in geotechnical engineering.

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.

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.

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.

Influence of Surface Roughness and Particle Characteristics on Soil–Structure Interactions: A State-of-the-Art Review

The study of soil–structure interface behavior contributes to the fundamental understanding of engineering performance and foundation design optimization. Previous research studies the effect of soil characteristics and surface roughness property on the soil–material interface mechanism via interface shear test. The reviews utilizing past established laboratory studies and more recent tests based on state-of-the-art technologies reveal that surface roughness significantly affects interface shear performances in the studies of soil–structure interactions, especially in peak shear strength development. A preliminary but original investigative study by the authors was also carried out using a sophisticated portable surface roughness gauge to define the material surface roughness properties in order to study the interface behavior parametrically. Additionally, using the authors’ own original research findings as a proof-of-concept innovation, particle image velocimetry (PIV) technology is applied using a digital single-lens reflex (DSLR) camera to capture sequential images of particle interactions in a custom-built transparent shear box, which validate the well-established four-stage soil shearing model. The authors also envisaged that machine learning, e.g., artificial neural network (ANN) and Bayesian inference method, amongst others, as well as numerical modeling, e.g., discrete element method (DEM), have the potential to also promote research advances on interface shear mechanisms, which will assist in developing a greater understanding in the complex study of soil–structure interactions.

Dairy manure pellets and palm oil mill effluent as alternative nutrient sources in cultivating Sporosarcina pasteurii for calcium carbonate bioprecipitation

Microbially induced carbonate precipitation (MICP) is a process that hydrolysis urea by microbial urease to fill the pore spaces of soil with induced calcium carbonate (CaCO₃ ) precipitates, which eventually results in improved or solidified soil. This research explored the possibility of using dairy manure pellets (DMP) and palm oil mill effluent (POME) as alternative nutrient sources for Sporosarcina pasteurii cultivation and CaCO₃ bioprecipitation. Different concentrations (20 to 80 g l^-1 ) of DMP and POME were used to propagate the cells of Sporosarcina pasteurii under laboratory conditions. The measured CaCO₃ contents for MICP soil specimens that were treated with bacterial cultures grown in DMP medium (60%, w/v) was 15.30 ±0.04g ml^-1 and POME medium (40%, v/v) was 15.49 ±0.05g ml^-1 after 21 days curing. The scanning electron microscopy showed that soil treated with DMP had rhombohedral structure-like crystals with smooth surfaces, while that of POME entailed ring-like cubical formation with rough surfaces Electron dispersive X-ray analysis was able to identify a high mass percentage of chemical element compositions (Ca, C, and O), while spectrum from Fourier-transform infrared spectroscopy confirmed the vibration peak intensities for CaCO₃ . Atomic force microscopy further showed clear topographical differences on the crystal surface structures that were formed around the MICP treated soil samples. These nutrient sources (DMP and POME) showed encouraging potential cultivation mediums to address high costs related to bacterial cultivation and biocementation treatment.

Microbiome of highly polluted coal mine drainage from Onyeama, Nigeria, and its potential for sequestrating toxic heavy metals

Drains from coal mines remain a worrisome point-source of toxic metal/metalloid pollutions to the surface- and ground-waters worldwide, requiring sustainable remediation strategies. Understanding the microbial community subtleties through microbiome and geochemical data can provide valuable information on the problem. Furthermore, the autochthonous microorganisms offer a potential means to remediate such contamination. The drains from Onyeama coal mine in Nigeria contained characteristic sulphates (313.0 ± 15.9 mg l⁻¹), carbonate (253.0 ± 22.4 mg l⁻¹), and nitrate (86.6 ± 41.0 mg l⁻¹), having extreme tendencies to enrich receiving environments with extremely high pollution load index (3110 ± 942) for toxic metals/metalloid. The drains exerted severe degree of toxic metals/metalloid contamination (Degree of contamination: 3,400,000 ± 240,000) and consequent astronomically high ecological risks in the order: Lead > Cadmium > Arsenic > Nickel > Cobalt > Iron > Chromium. The microbiome of the drains revealed the dominance of Proteobacteria (50.8%) and Bacteroidetes (18.9%) among the bacterial community, whereas Ascomycota (60.8%) and Ciliophora (12.6%) dominated the eukaryotic community. A consortium of 7 autochthonous bacterial taxa exhibited excellent urease activities (≥ 253 µmol urea min⁻¹) with subsequent stemming of acidic pH to > 8.2 and sequestration of toxic metals (approx. 100% efficiency) as precipitates (15.6 ± 0.92 mg ml⁻¹). The drain is a point source for metals/metalloid pollution, and its bioremediation is achievable with the bacteria consortium.

Isolation and Characterization of Urease-Producing Soil Bacteria

Urease is an enzyme produced by ureolytic microorganisms which hydrolyzes urea into ammonia and carbon dioxide. Microbial urease has wide applications in biotechnology, agriculture, medicine, construction, and geotechnical engineering. Urease-producing microbes can be isolated from different ecosystems such as soil, oceans, and various geological formations. The aim of this study was to isolate and characterize rapid urease-producing bacteria from Ethiopian soils. Using qualitative urease activity assay, twenty urease-producing bacterial isolates were screened and selected. Among these, three expressed urease at high rates as determined by a conductivity assay. The isolates were further characterized with respect to their biochemical, morphological, molecular, and exoenzyme profile characteristics. The active urease-producing bacterial isolates were found to be nonhalophilic to slightly halophilic neutrophiles and aerobic mesophiles with a range of tolerance towards pH (4.0-10.0), NaCl (0.25-5%), and temperature (20-40°C). According to the API ZYM assays, all three isolates were positive for alkaline phosphatase, leucine aryl amidase, acid phosphatase, and naphthol_AS_BI_phosphohydrolase. The closest described relatives of the selected three isolates (Isolate_3, Isolate_7, and Isolate_11) were Bacillus paramycoides, Citrobacter sedlakii, and Enterobacter bugandensis with 16S rRNA gene sequence identity of 99.0, 99.2, and 98.9%, respectively. From the study, it was concluded that the three strains appear to have a relatively higher potential for urease production and be able to grow under a wider range of growth conditions.

Strength and Microstructural Assessment of Reconstituted and Stabilised Soft Soils with Varying Silt Contents

The study of the strength of reconstituted and stabilised soft soils is very important in geotechnical engineering. The soil particles, such as clay, sand, and silt play important roles in determining the behaviour of soils. The behaviour of clay and sand particles are unique; however, the behaviour of silt particles lie in a transitional form between sand and clay. Therefore, this paper seeks to investigate (a) the effect of silt contents on the strength of soft soils; (b) the effect of silt content on the strength of cement-stabilised soft soils; and (c) the microstructure of the soft soil specimens stabilised by cement with varying particle size distribution. A series of tests consisting in consolidated, isotropic undrained (CIU) triaxial tests, unconfined compressive strength (UCS) tests, and scanning electron microscope (SEM) images were conducted in this study to achieve these objectives. In conclusion, the relationship between the silt content and critical state behaviour of soft soils (both clay and silt particles) are proposed. For the cement-stabilised specimens, the unconfined compressive strength increases with the increase in silt content when the cement content is 10%. However, the UCS decreases with the increase in silt content when cement content is 30%. With cement content ranging from 15–25%, the UCS increases at first with the increase of silt content but decreases once the silt content reaches a ‘saturation’ point.

Biopolymers as Green Binders for Soil Improvement in Geotechnical Applications: A Review

Soil improvement using biopolymers has attracted considerable attention in recent years, with the aim to reduce the harmful environmental effects of traditional materials, such as cement. This paper aims to provide a review on the environmental assessment of using biopolymers as binders in soil improvement, biopolymer-treated soil characteristics, as well as the most important factors affecting the behavior of the treated soil. In more detail, environmental benefits and concerns about the use of biopolymers in soil improvement as well as biopolymer–soil interaction are discussed. Various geotechnical properties are evaluated and compared, including the unconfined compressive strength, shear strength, erosion resistance, physical properties, and durability of biopolymer-treated soils. The influential factors and soil and environmental conditions affecting various geotechnical characteristics of biopolymer-treated soils are also discussed. These factors include biopolymer concentration in the biopolymer–soil mixture, moisture condition, temperature, and dehydration time. Potential opportunities for biopolymers in geotechnical engineering and the challenges are also presented.

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.

Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements

Lava caves differ from karstic caves in their genesis and mineral composition. Subsurface microbiology of lava tube caves in Canary Islands, a volcanic archipelago in the Atlantic Ocean, is largely unknown. We have focused the investigation in a representative lava tube cave, Fuente de la Canaria Cave, in La Palma Island, Spain, which presents different types of speleothems and colored microbial mats. Four samples collected in this cave were studied using DNA next-generation sequencing and field emission scanning electron microscopy for bacterial identification, functional profiling, and morphological characterization. The data showed an almost exclusive dominance of Bacteria over Archaea. The distribution in phyla revealed a majority abundance of Proteobacteria (37-89%), followed by Actinobacteria, Acidobacteria and Candidatus Rokubacteria. These four phyla comprised a total relative abundance of 72-96%. The main ecological functions in the microbial communities were chemoheterotrophy, methanotrophy, sulfur and nitrogen metabolisms, and CO2 fixation; although other ecological functions were outlined. Genome annotations of the especially representative taxon Ga0077536 (about 71% of abundance in moonmilk) predicted the presence of genes involved in CO2 fixation, formaldehyde consumption, sulfur and nitrogen metabolisms, and microbially-induced carbonate precipitation. The detection of several putative lineages associated with C, N, S, Fe and Mn indicates that Fuente de la Canaria Cave basalts are colonized by metabolically diverse prokaryotic communities involved in the biogeochemical cycling of major elements.