Extracellular polymeric substances (EPS) secreted by bacteria play a role in influencing the mineralization and growth of CaCO3 minerals. However, the specific roles of different EPS forms in bacterially influenced carbonate mineralization remain inadequately understood. Therefore, this study conducted CaCO3 mineralization simulation experiments using bound EPS (BEPS) and soluble EPS (SEPS) separately extracted from Synechococcus sp. PCC7942 and Bacillus cereus LV-1 cultures. The precipitates obtained from mineralization experiments with BEPSPCC7942, SEPSPCC7942, BEPSLV-1, and SEPSLV-1, as well as the control group (CK), were predominantly calcite with minor aragonite, suggesting that high SI and pH facilitated the crystallization of these phases. The mole percentage of aragonite in the EPS-treated groups was lower than that in the CK groups. Compared to the CK group, BEPSPCC7942, SEPSPCC7942, and BEPSLV-1 promoted the formation of rhombohedral crystals with blurred edges, and SEPSLV-1 produced rhombohedral minerals with smooth surfaces. The ratios of large to small crystals in the EPS experiments were lower than those of the CK experiments. Negatively charged EPS can attach to specific crystal faces, thereby inhibiting the growth of certain CaCO3 crystal facets, leading to the formation of rhombohedral crystals with blurred edges and providing additional nucleation sites, which results in the formation of smaller crystals.
Aquatic ecosystems heavily impacted by heavy metal contamination are a serious issue for the environment. Therefore, the adoption of an affordable and effective bioremediation method will help to address this problem. The objective of this study was to examine the bioremediation potential of the thermophilic dead biomass of three isolates (GS1, BS1, and GWII) for the detoxification of manganese (Mn2+), copper (Cu2+), and chromium (Cr6+). These isolates were collected from water and soil sediment samples of Gauri Kund and Tapt Kund geothermal springs. The bacterial isolates were characterized as neutrophilic to alkali-tolerant and exhibited maximal growth at the optimum temperature of 55 degrees C under laboratory environment conditions. The results showed distinct affinities of the dead biomass for each thermophilic isolate for metal bioremediation. The sediment isolate GS1 (Gauri Kund) exhibits the highest metal removal affinities for Mn2+ (44.95%) and Cr6+ (53.89%), respectively, while BS1 (Tapt Kund) exhibits the highest metal-specific affinity for Cu2+ (53.51%). These findings highlight the significance of thermophilic dead biomass as a viable alternative for addressing microbial pathogenicity, metabolic dependence, and metal toxicity. Therefore, this method has proven to be a highly effective substitute for conventional treatment approaches.
Hydraulic concrete structures are prone to surface cracking due to sustained loads, fluctuating water levels, and environmental factors, which weaken the bearing capacity of concrete. This study investigates the repair of concrete cracks using enzyme-induced calcium carbonate precipitation (EICP) and either chitosan (CS) or sodium alginate (SA). Enzyme activity, mineralization reaction, ultrasonic, compressive strength, splitting tensile strength, XRD, FTIR, and SEM tests were conducted to assess the repaired performance of concrete. A Laplace model was developed for predicting splitting tensile strength, ultrasonic transit time and compressive strength. It was found that the optimal enzyme activity was achieved at enzyme concentration of 110 g/L, urea concentration of 0.3 mol/L, pH of 8, and a standing time of 0-10 minutes. The optimal EICP mineralization conditions were reached at enzyme concentration of 110 g/L, cementation solution concentration of 0.3 mol/L, pH of 8, skim milk powder content of 1.2%, and enzyme-cementation ratio of 1:0.75. EICP treatment significantly reduced ultrasonic transit time, and markedly enhanced the compressive and splitting tensile strengths. The optimal additive contents for CS and SA were identified as 0.2% and 0.6%, respectively. These findings offer a technical support for the effective repair of cracks in hydraulic concrete.
Soil salinity disrupts rhizobacterial communities, threatening agricultural productivity. This study used amplicon-based microbiome analysis to characterize bacterial diversity in rhizosphere soils from high- and low-saline areas of Bangladesh. The physicochemical properties were measured by pH, moisture content, temperature, and electrical conductivity (EC) to understand the soil salinity level in both areas. 16S rRNA gene amplicon sequencing was used to analyze microbial diversity and functional potential. The EC of high-saline soil was greater than 9.00 dS/m, whereas in low-saline soil it was less than 0.35 dS/m. 16S rRNA gene amplicon sequencing analysis showed that the phylum Firmicutes was abundant in both regions. However, alpha-diversity measured by the ACE, Shannon, and Chao1 indices was higher in low-saline areas than in high-saline areas. Moreover, beta diversity analysis revealed distinct community structures and differences in bacterial communities. Analysis of common taxa showed that 798 species were more prevalent in low-saline regions, compared to 196 species in high-saline areas, indicating adaptation to different salinity levels. Pathway abundance analysis highlights distinct metabolic functions between the two areas, with high-saline rhizobacteria favoring HEXITOLDEGSUPER-PWY and ASPASN-PWY. These findings offer insight into how bacteria respond to soil salinity and may help guide sustainable agricultural strategies for saline environments.
Biocarbonation of reactive magnesia cement (RMC) is an innovative and potentially sustainable technique for soil improvement. This study aims to optimize the ratios of key parameters: microbial dosage (10%-30%), RMC content (3%-10%), and urea content (0-4 mol/L). On this basis, the long-term performance was evaluated through dry-wet cycle tests. Experimental results indicated that a linear relationship existed between microbial dosage and RMC content. The optimal urea concentration was determined to be 1 mol/L. Moreover, the unconfined compressive strength (UCS) increased with the augmentation of RMC content, reaching up to 4.2 MPa, which was 142.77%-250% higher than that of PC (Portland cement) and MICP (Microbial induced carbonate precipitation) samples. Additionally, the mass and strength losses of the sample with 8% RMC content after 8 dry-wet cycles were only 0.62% and 5.58%, respectively- reduced by up to 70% compared with PC and MICP samples. The micro-tests results showed that the strength of the samples can be attributed to the synergistic effect of hydrated magnesia carbonates (HMCs) and Mg(OH)2. During the dry-wet cycle, the residual RMC in the sample would continue to hydrate and fill the pores. The obtained findings have demonstrated that the biocarbonation of RMC has engineering feasibility.
Eolian sand will cause friction and erosion to the land surface when subject to wind force, which has an adverse effect on transportation, agriculture and atmospheric environment. In this paper, microbially induced calcite precipitation (MICP) and basalt fiber reinforcement (BFR) methods were used to stabilize the eolian sand. To evaluate the wind erosion resistance of eolian sand, the wind-tunnel model tests were conducted to investigate the effects of wind velocity, erosion angle and erosion time on the threshold friction velocity, cumulative mass loss, wind erosion modulus, cemented thickness and surface morphology. Based on the test results, an erosion modulus model considering the wind velocity and erosion angle was constructed. The test results indicated that the threshold friction velocity of eolian sand decreased with increasing of wind erosion angle, whereas the cumulative mass loss increased with increasing of wind velocity and wind erosion angle. Under the maximum wind velocity and erosion angle, the mass loss of MICP-BFR treated sand was reduced by 90.06% compared with that of loose sand. Wind erosion modulus followed the order of loose sand > MICP treated sand > MICP-BFR treated sand. The cemented thickness of MICP treated sand exhibited uniform distribution, whereas that of MICP-BFR treated sand presented relatively uniform with an average thickness of 2 cm. The model prediction results coincided with the measurement results, indicating that the model is applicable to predict the erosion modulus of eolian sand. The research results can provide a reference for wind prevention and sand solidification in desert areas.
The Niger Delta region of Nigeria is one of the most oil-rich ecosystems globally but has suffered extensive environmental degradation due to decades of petroleum exploration, extraction, and accidental spills. Microbial bioremediation offers an effective and sustainable alternative for hydrocarbon removal, yet detailed understanding of the diversity, functionality, and dynamics of native microbial communities in these environments remains limited. This study utilized shotgun metagenomic sequencing to comprehensively characterize the microbial consortia inhabiting petroleum hydrocarbon-contaminated creek sediments. High-throughput sequencing revealed dominance of hydrocarbonoclastic bacteria, including Alcanivorax, Pseudomonas, Bacillus, and Acinetobacter, alongside fungal genera such as Aspergillus, Penicillium, and Trichoderma. Functional annotation indicated enrichment of key genes involved in alkane and aromatic hydrocarbon degradation, biosurfactant production, and stress response pathways, highlighting the intrinsic bioremediation potential of these communities. Some of the genes revealed were; HSA: 1739(DLG1), PTR: 460968(DLG1), PPS: 100987596(DLG1), GGO: 101132886(DLG1), PON: 100444925(DLG1), NLE: 100603856(DLG1), MCC: 709572(DLG1), MCF: 102123600(DLG1), 102143830(PATJ), CSAB: 103241973(DLG1), RRO: 104676365(DLG1). Multivariate analyses showed strong correlations between physicochemical parameters and microbial composition, emphasizing the influence of environmental factors on biodegradation efficiency. These findings provide a comprehensive metagenomic blueprint for designing targeted, community-based bioremediation strategies, contributing to sustainable restoration of oil-contaminated aquatic ecosystems in the Niger Delta.
Since the dawn of human civilization, discovery of metals, especially iron (Fe), has played a pivotal role in the growth and diversification of human societies and industries. Steel, a metallurgical engineering marvel, is considered the backbone of any economy. Despite the immense importance and demand, Fe supply chains are highly compromised. The dominance of low-grade ores and highly positive carbon footprint of Fe ore processing presses demand green technologies like biomining. Understanding the intricate mechanisms by which microbes encourage mineral dissolution is pivotal in bioleaching. This study addresses a critical knowledge gap by examining the ability of Pseudomonas aeruginosa to mobilize Fe from mineral (ferrihydrite, goethite, and hematite) and rock surfaces (basalt glass and crystalline basalt), selected to mimic the mineralogy of critical and oxide Fe ores, such as laterites. Fe acquisition poses challenges to P. aeruginosa due to its limited availability in diverse environments. To overcome this limitation, bacteria employ sophisticated strategies, including synthesizing and secreting siderophores, small molecules with a high affinity for Fe, to scavenge and uptake Fe effectively. In this study, we investigated the role of siderophores in facilitating Fe uptake from various Fe sources by P. aeruginosa. Experimental setups involved incubating Fe oxides and basalt separately in sterilized Teflon flasks containing an Fe-limiting growth medium, each inoculated with a P. aeruginosa strain. Results demonstrated a significant increase in extracted Fe when siderophores were present, indicating a siderophore-driven process in Fe mobilization. Our findings highlight the complex regulatory network governing Fe mobilization in P. aeruginosa, emphasizing the interplay between quorum sensing (QS) and the Fe sequestration system. Unraveling these molecular mechanisms advances our understanding of microbial Fe acquisition strategies and opens avenues for understanding the innovative survival strategies employed by bacteria in Fe-limiting environments. Such studies are important for scaling up ferredox (a biohydrometallurgical concept for oxide ores) biomining processes for industrial use.
Manganese (Mn) plays an important role in marine biogeochemical cycling; however, the mechanisms of microbial Mn oxidation in deep-sea environments remain poorly understood. This study investigated the Mn tolerance and precipitation capabilities of a novel bacterial isolate, Staphylococcus ureilyticus GOM10, isolated from deep-sea water in the Gulf of Mexico. Using a multidisciplinary approach combining microbiological, microscopic, spectroscopic, genomic, and geochemical modeling techniques, we elucidated the genetic pathways underlying Mn oxidation in GOM10. Scanning electron microscopy and energy-dispersive X-ray spectroscopy confirmed the presence of Mn-bearing precipitates associated with the bacterial cells. The strain demonstrated tolerance to Mn(II) concentrations up to 150 mM and could oxidize Mn(II) at a rate of 5.2-29.2 nM h(-1). Genomic analysis revealed genes related to Mn transport and oxidation, including superoxide dismutase (SOD), peroxidases, and Mn-dependent regulators, suggesting that the Mn oxidation mechanism involves the generation of reactive oxygen species (ROS). The proposed oxidation pathway couples Mn(II) oxidation with cellular protection against oxidative stress. Our findings highlight the importance of investigating alternative pathways, such as ROS-mediated oxidation, for a more comprehensive understanding of Mn biomineralization in deep-sea environments. This study provides insights into microbial adaptations in deep-sea environments and the potential role of heterotrophic bacteria in Mn cycling.
We report the successful extraction and characterization of microbial DNA from vertebrate fossil-bearing Pleistocene sediments at Hathnora, India's sole archaic hominin site, situated in the central Narmada Valley. Recent paleontological salvage excavations at the central Narmada Valley site uncovered multiple elephant fossils eroding from the Baneta Formation's fine-grained deposits. Sediment samples from the same stratum were collected for microbial DNA analysis. Initial kit-based DNA extraction attempts using bead beating and column-based methods or nanoparticles were hindered by high humic acid content, which compromised DNA recovery and PCR amplification. We optimized and compared eight alternative DNA extraction methods. This paper presents the results of these trials, highlighting their relative merits. Our optimized approach yielded high-quality sedaDNA (260/280 ratio of 1.9) suitable for V3-V4 amplicon sequencing and downstream taxonomic profiling. The resulting amplicon-based metagenomics analysis enabled some insights into the evolutionary dynamics of microbial communities in tropical sediment environments; an aspect useful for paleoenvironmental reconstruction.
Microbially Induced Calcite Precipitation (MICP) is a biomineralization process driven by ureolytic microorganisms that mediates calcium carbonate formation in porous environments. This study bridges the research gap between experimental and modeling/simulation approach by investigating a key parameter (porosity) that has not been thoroughly explored in prior MICP studies. This study presents a spatio-temporal reactive transport model to investigate long-term porosity evolution during MICP over a 180-day simulation period. The modeling framework integrates microbial kinetics, substrate transport, and calcite precipitation to capture coupled biogeochemical interactions. Results reveal a pronounced time-dependent and spatially heterogeneous reduction in porosity, particularly near the injection interface where microbial activity and reactant availability are highest. During the initial duration (0-5 days), porosity decreased slightly from 0.30 to 0.295, followed by substantial pore clogging over extended durations (10-180 days), with porosity reaching 0.12 in highly mineralized regions. The evolution pattern reflects nonlinear feedback between microbial growth, urea hydrolysis, and mineral precipitation. Regression analysis yielded the R-2 of 0.9644, indicating a strong correlation between treatment duration and porosity reduction. The findings provide highly promising insights into microbe-mineral-pore interactions governing long-term biomineralization in porous systems.
Soil microbial community plays a pivotal role in structuring the physical, chemical, and biological characteristics of ecosystem. Metagenomic sequencing was used to delineate the abundance and involvement of root associated bacterial community in the remediation of textile sludge using phyto and rhizoremediation approach. The contaminated textile sludge was enriched with Klebsiella sp. VITAJ23 belonging to Proteobacteria and experimental soil used as control revealed the predominance of Firmicutes. Phyto and rhizoremediation study was designed for a period of 60 d for the removal of toxicity in textile sludge. Rhizoremediation treatment exhibited taxonomic shifts associated with detoxification, with Firmicutes emerging as the dominant indigenous microbial phylum following the degradation of toxic compounds present in textile sludge. Members of the phyla Firmicutes, Actinobacteria, and Proteobacteria accounted for 50-82% of the total diversity in all the tested samples. The most abundant beneficial microbes included members of Bacillus, Lysobacter, Rhizobium, Mesorhizobium, and Bradyrhizobium in the soils after phyto and rhizoremediation treatments. The unweighted PCoA analysis revealed that studied categories belonged to principal coordinate 1 (36.25%), which was also confirmed by heatmap analysis and diversity indices. These results emphasize on the effectiveness of metagenomic analysis to study the impact and taxonomic shift in microbial community pattern in contaminated environment upon treatment with effective strain VITAJ23. This study can pave way in understanding the application of indigenous bacteria for the remediation of dyes without affecting the soil microbial population. However, acclimatization of bacteria during onsite bioremediation is a major hurdle to be addressed.
Microbially induced calcite precipitation (MICP) is a biomediated soil improvement technique that enhances sand strength through microbial calcite deposition. The unconfined compressive strength (UCS) of MICP-treated sand is a key performance indicator of this process. In this study, a deep neural network (DNN) model was developed to predict UCS and benchmarked against four machine learning models: linear regression (LR), decision tree (DT), random forest (RF), and support vector regression (SVR). A comprehensive database of 443 UCS test results was compiled from laboratory experiments and literature, incorporating geotechnical, biological, and chemical input parameters, including mean grain size, uniformity coefficient, initial void ratio, urease activity (UA), urea concentration, calcium concentration, treatment cycles (TC), and calcium carbonate content (CCC). Model performance was assessed using mean absolute error (MAE), root mean square error (RMSE), R2, and extended robustness metrics (VAF, RSR, NMBE, A20, SI, and Willmott's d-index). The results showed that the DNN consistently outperformed all other models, achieving the highest predictive accuracy and reliability. Furthermore, SHapley Additive exPlanations (SHAP) analysis confirmed the dominant influence of CCC, TC, calcium concentration, and UA on UCS predictions, providing mechanistic interpretability of the model outputs. These findings demonstrate that DNN-based models are powerful and interpretable tools for predicting UCS of MICP-treated sand, with strong potential for supporting design and optimization in bio-mediated ground improvement.
Concrete is a major contributor to carbon emissions worldwide. In response to this climate impact, scientists are actively working to develop more sustainable alternatives to traditional concrete. One potential alternative is bio-enzyme-based concrete, or BBE, made using Bacillus aerophilus from fermented soybeans, watermelons, and palm jaggery solution. BBE transform carbon dioxide into crystals of calcium carbonate, allowing concrete to heal itself when cracked and decreasing emissions in the process. BBE-mortar has better mechanical properties than Portland cement mortar and is also cheaper and more sustainable. Cocci-shaped bacterial spores are also evident in SEM images taken at day 28 where the bacteria initiate the healing of the cracks. These bacteria reduce levels of CO2 in the process as they precipitate calcium and barium deposits, resulting in negative carbon emissions during construction. In fact, EDS analysis shows high levels of barium, calcium, and iron in the bacterial concrete, which absorb CO2 from the atmosphere with compounds to form precipitates such as BaCO3, CaCO3, and FeCO3. Among other advancements, this technology renders concrete "self-healing", massively cuts carbon emissions, and allows construction to have a lighter ecological footprint - potentially revolutionizing construction for sustainability.
Volcanic rocks have diverse landforms, morphology and textures hosting a diversity of life. Colonization modifies rock structure and chemistry by bioweathering. We consider interactions between biological crusts and rock by bioweathering features on different Xitle volcano geoforms (300 AD, Mexico). We analyzed five representative, contrasting sites (scoria cone crater, lava tube, promontory, crevice wall and flat ropey lobe), assessing altitude, local climate, surrounding vegetation and rock properties. We documented initial physical / chemical bioweathering steps using different microscopies. We found physical bioweathering: surface penetration, fractures, mineral detachment, vesicle infilling, particle entrapment, endolithic colonization. Element mapping detected Ca, Na, Al, Mg concentrations in lichen thallus, also Si and Cl in lava tube bacterial biofilms. Vesicle boundary glass had K and Na concentration. Microprobe analysis detected no rock alteration near biocrusts. Different biological groups exert different bioweathering types and intensity. Lichens are the strongest bioweathering agents, associated with all features. Mosses are only associated with vesicle infilling and particle entrapment, while bacterial biofilms are associated with endolithic colonization and biofilm lithification. We see chemical limited alteration from biological communities, the lava surface being resistant both chemically and structurally, supporting highly biodiverse communities without modification over Xitle's time scales and conditions.
Microbial solidification technology can effectively enhance the strength of sandy soil, but it will cause obvious brittleness. There are a large number of discarded clothes, which are prone to cause environmental pollution. This paper proposed a method combining the reinforcement of discarded clothing fiber with microbial solidification. Polyester and pure cotton clothing fibers with mass fractions of 0%, 0.1%, 0.2%, 0.3% and 0.4% were uniformly mixed with standard sand, and then the sand samples were solidified based on microbially induced carbonate precipitation (MICP) technology. The results showed that discarded clothing fiber not only enhanced the mechanical strength of MICP-treated sand samples, but also increased the ductility of the sand samples. An appropriate amount of fiber was randomly distributed in the sand samples to form a network structure, which could restrain the displacement of sand particles, increase the strength and improve the brittleness of MICP-treated sand samples. Taking all indicators into account, the reinforcing effect of polyester clothing fiber was superior to that of pure cotton clothing fiber, and the optimal fiber content was 0.3%. This research provides an effective method for recycling discarded clothes and promotes the application of fiber-reinforced MICP-treated sand in practical engineering.
