The utilization of biomineralization technique based on microbial induced phosphate precipitation in remediation of potentially toxic ions contaminated soil: A mini review

Immobilization of Pb(II) by Bacillus megaterium-based microbial-induced phosphate precipitation (MIPP) considering bacterial phosphorolysis ability and Ca-mediated alleviation of lead toxicity

Inappropriate handling of lead (Pb)-containing wastewater that is produced as a result of smelting activities threatens the surrounding environment and human health. The microbial-induced phosphate precipitation (MIPP) technology was applied to immobilize Pb2+ in an aqueous solution considering bacterial phosphorolysis ability and Ca-mediated alleviation of lead toxicity. Pb immobilization was accompanied by sample characterization in order to explore the inherent mechanism that affected the immobilization efficiency. Results showed that Ca2+ use elevated the immobilization efficiency through the prevention of bacterial physisorption and chemisorption, an enhancement to the phosphatase activity and the degree of SGP hydrolysis, and the provision of nucleation sites for Pb2+ to attach. The formation of the Pb-GP complex helped the bacteria to maintain its activity at the commencement of catalyzing SGP hydrolysis. The nucleated minerals that were precipitated in a columnar shape through a directional stacking manner under MIPP featured higher chemical stability compared to non-nucleated minerals. As a result, there were three pathways, namely, bacterial physisorption, bacterial chemisorption, and substrate chelation, applied for Pb immobilization. The immobilization efficiency of 99.6% is achieved by precipitating bioprecipitates including Pb5(PO4)3Cl, Pb10(PO4)6Cl2, and Ca2Pb3(PO4)3Cl. The findings accentuate the potential of applying the MIPP technology to Pb-containing wastewater remediation.

Efficient uranium sequestration ability and mechanism of live and inactivated strain of Streptomyces sp. HX-1 isolated from uranium wastewater

Prokaryotes are effective biosorbents for the recovery of uranium and other heavy metals. However, the potential mechanism of uranium bioaccumulation by filamentous strain (actinobacteria) remains unclear. This study demonstrates the potential for and mechanism of uranium bioaccumulation by living (L-SS) and inactivated (I-SS) Streptomyces sp. HX-1 isolated from uranium mine waste streams. Uranium accumulation experiments showed that L-SS and I-SS had efficient uranium adsorption potentials, with removal rates of 92.93 and 97.42%, respectively. Kinetic and equilibrium data indicated that the bioaccumulation process was consistent with the pseudo-second-order kinetic, Langmuir, and Sips isotherm models. FTIR indicated that the main functional groups of L-SS and I-SS binding uranium were uranyl, carboxyl, and phosphate groups. Moreover, the results of XRD, XPS, SEM-EDS, and TEM-EDS analyses revealed for the first time that L-SS has biomineralization and bioreduction capacity against uranium. L-SS mineralize U(VI) into NH4UO2PO4 and [Formula: see text] through the metabolic activity of biological enzymes (phosphatases). In summary, Streptomyces sp. HX-1 is a novel and efficient uranium-fixing biosorbent for the treatment of uranium-contaminated wastewater.

Phosphate and illite colloid pose a synergistic risk of enhanced uranium transport in groundwater: A challenge for phosphate immobilization remediation of uranium contaminated environmental water

The phosphorus-containing reagents have been proposed to remediate the uranium contaminated sites due to the formation of insoluble uranyl phosphate mineralization products. However, the colloids, including both pseudo and intrinsic uranium colloids, could disturb the environmental fate of uranium due to its nonnegligible mobility. In this work, the transport pattern and micro-mechanism of uranium coupled to phosphate and illite colloid (IC) were investigated by combining column experiments and micro-spectroscopic evidences. Results showed that uranium transport was facilitated in granular media by forming the intrinsic uranyl phosphate colloid (such as Na-autunite) when the pH > 3.5 and CNa+ < 10 mM. Meanwhile, the mobility of uranium depended greatly on the typical water chemistry parameters governing the aggregation and deposit of intrinsic uranium colloids. However, the attachment of phosphate on illite granule increased the repulsive force and enhanced the dispersion stability of IC in the IC-U(VI)-phosphate ternary system. The non-preequilibrium transport and retention profiles, HRTEM-mapping, as well as TRLFS spectra revealed that the IC enhanced uranium mobility by forming the ternary IC-uranyl phosphate hybrid, and acted as the coagulation preventing agent for uranyl phosphate particles. This observed facilitation of uranium transport resulted from the formation of intrinsic uranyl phosphate colloids and IC-uranyl phosphate hybrids should be taken into consideration when evaluating the potential risk of uranium migration and optimizing the in-situ mineralization remediation strategy for uranium contaminated environmental water.

Penicillium oxalicum induced phosphate precipitation enhanced cadmium (Cd) immobilization by simultaneously accelerating Cd biosorption and biomineralization

Soil cadmium (Cd) is immobilized by the progressing biomineralization process as microbial induced phosphate precipitation (MIPP), which is regulated by phosphate (P) solubilizing microorganisms and P sources. However, little attention has been paid to the implications of Cd biosorption during MIPP. In this study, the newly isolated Penicillium oxalicum could immobilize 5.4-12.6 % of Cd2+, while the presence of hydroxyapatite (HAP) considerably enhanced Cd2+ immobilization in P. oxalicum and reached over 99 % Cd2+ immobilization efficiency within 7 days. Compared to P. oxalicum mono inoculation, MIPP dramatically boosted Cd biosorption and biomineralization efficiency by 71 % and 16 % after 96 h cultivation, respectively. P. oxalicum preferred to absorbing Cd2+ and reaching maximum Cd2+ biosorption efficiency of 87.8 % in the presence of HAP. More surface groups in P. oxalicum and HAP mineral involved adsorption which resulted in the formation of Cd-apatite [Ca8Cd2(PO4)6(OH)2] via ion exchange. Intracellular S2-, secreted organic acids and soluble P via HAP solubilization complexed with Cd2+, progressively mineralized into Cd5(PO4)3OH, Cd(H2PO4)2, C4H6CdO4 and CdS. These results suggested that Cd2+ immobilization was enhanced simultaneously by the accelerated biosorption and biomineralization during P. oxalicum induced P precipitation. Our findings revealed new mechanisms of Cd immobilization in MIPP process and offered clues for remediation practices at metal contaminated sites.

Unearthing Earth's secrets: Exploring the environmental legacy of contaminants in soil, water, and sediments

The Earth's history is documented in human civilizations, soil layers, river movement, and quiet sediments throughout millennia. This investigation explores the significant legacy of environmental toxins in these key planet components. Understanding how ancient activity shaped the terrain is crucial as mankind faces environmental issues. This interdisciplinary study uses environmental science, archaeology, and geology to uncover Earth's mysteries. It illuminates the dynamic processes that have built our globe by studying pollutants and soil, water, and sediments. This research follows human actions, both intentional and unintentional, from ancient civilizations through contemporary industrialization and their far-reaching effects. Environmental destiny examines how contaminants affect ecosystems and human health. This study of past contamination helps solve modern problems including pollution cleanup, sustainable land management, and water conservation. This review studies reminds us that our previous activities still affect the ecosystem in a society facing rapid urbanisation and industrialization. It emphasises the importance of environmental stewardship and provides a framework for making educated choices to reduce toxins in soil, water, and sediments. Discovery of Earth's secrets is not only a historical curiosity; it's a necessary step towards a sustainable and peaceful cohabitation with our home planet.

Comprehensive bioremediation effect of phosphorus-mineralized bacterium Enterobacter sp. PMB-5 on cadmium contaminated soil-crop system

Phosphate-mineralizing bacteria (PMBs) have been widely studied by inducing phosphate heavy metal precipitation, but current researches neglect to study their effects on soil-microbe-crop systems on cadmium (Cd) contaminated. Based on this, a strain PMB, Enterobacter sp. PMB-5, was inoculated into Cd contaminated pots to detect soil characteristics, Cd occurrence forms, soil biological activities, plant physiological and biochemical indicators. The results showed that the inoculation of strain PMB-5 significantly increased the available phosphorus content (85.97%-138.64%), Cd-residual fraction (11.04%-29.73%), soil enzyme activities (31.94%-304.63%), plant biomass (6.10%-59.81%), while decreased the state of Cd-HOAc (11.50%-31.17%) and plant bioconcentration factor (23.76%-44.24%). These findings indicated that strain PMB-5 could perform the function of phosphorus solubilization to realize the immobilization of Cd in the complex soil environment. Moreover, SEM-EDS, FTIR, XPS, and XRD analysis revealed that strain PMB-5 does not significantly alter the soil morphology, structure, elemental distribution, and chemical composition, which suggested that remediation of Cd contamination using strain PMB-5 would not further burden the soil. This research implies that PMB-5 could be a safe and effective bioinoculant for remediating Cd-contaminated soils, contributing to the sustainable management of soil health in contaminated environments.

Different survival strategies of the phosphate-mineralizing bacterium Enterobacter sp. PMB-5 in response to cadmium stress: Biomineralization, biosorption, and bioaccumulation

The phosphate-mineralizing bacteria (PMBs) has shown great potential as a sustainable solution to support pollution remediation through its induced mineralization capacity. However, few studies have been conducted on the mechanism of cadmium (Cd) tolerance in PMBs. In this study, a PMB strain, Enterobacter sp. PMB-5, screened from Cd-contaminated rhizosphere soil, has high resistance to Cd (540 - 1220 mg/L) and solubilized phosphate (232.08 mg/L). The removal experiments showed that the strain PMB-5 removed 71.69-98.24% and 34.83-76.36% of Cd with and without biomineralization, respectively. The characterization result of SEM, EDS, TEM, XPS and XRD revealed that PMB-5 induced Cd to form amorphous phosphate precipitation through biomineralization and adopted different survival strategies, including biomineralization, bioaccumulation, and biosorption to resistance Cd in the microbial induced phosphate precipitation (MIPP) system and the non-MIPP system, respectively. Moreover, the results of whole genome sequencing and qRT-PCR indicated that phosphorus metabolism genes such as pst, pit, phn, ugp, ppk, etc. and heavy metal tolerance genes (including ion transport, ion efflux, redox, antioxidant stress), such as czcD, zntA, mgtA, mgtC, katE, SOD2, dsbA, cysM, etc. were molecular for the PMB-5 mineralization and Cd tolerance of PMB-5. Together, our findings suggested Enterobacter sp. PMB-5 is a potential target for developing more effective bioinoculants for Cd contamination remediation.

Microbial induced carbonate precipitation for remediation of heavy metals, ions and radioactive elements: A comprehensive exploration of prospective applications in water and soil treatment

Improper disposal practices have caused environmental disruptions, possessing by heavy metal ions and radioactive elements in water and soil, where the innovative and sustainable remediation strategies are significantly imperative in last few decades. Microbially induced carbonate precipitation (MICP) has emerged as a pioneering technology for remediating contaminated soil and water. Generally, MICP employs urease-producing microorganisms to decompose urea (NH2CONH2) into ammonium (NH4+and carbon dioxide (CO2), thereby increasing pH levels and inducing carbonate precipitation (CO32-), and effectively removing remove contaminants. Nonetheless, the intricate mechanism underlying heavy metal mineralization poses a significant challenge, constraining its application in contaminants engineering, particularly in the context of prolonged heavy metal leaching over time and its efficacy in adverse environmental conditions. This review provides a comprehensive idea of recent development of MICP and its application in environmental engineering, examining metabolic pathways, mineral precipitation mechanisms, and environmental factors as well as providing future perspectives for commercial utilization. The use of ureolytic bacteria in MICP demonstrates cost-efficiency, environmental compatibility, and successful pollutant abatement over tradition bioremediation techniques, and bio-synthesis of nanoparticles. limitations such as large-scale application, elevated Ca2+levels in groundwater, and gradual contaminant release need to be overcome. The possible future research directions for MICP technology, emphasizing its potential in conventional remediation, CO2 sequestration, bio-material synthesis, and its role in reducing environmental impact for long-term economic benefits.

Effect of Phanerochaete chrysosporium induced phosphate precipitation on bacterial diversity during the soil remediation process

Biomineralization by phosphate minerals and phosphate solubilizing fungi (PSF) has attracted great interest as a novel remediation method for heavy metal(loid) co-contaminated soil. It was very essential to investigate the microenvironment response with the application of amendments. In this study, three grain sizes of hydroxyapatites (HAP) and Phanerochaete chrysosporium (P. chrysosporium) were used to investigate the change in heavy metal(loid) fractions, soil physicochemical properties, and bacterial community during the remediation of Mangchang and Dabaoshan acidic mine soils. The results showed that the residual fractions in the two soils increased significantly after 35 days of remediation, especially that of As and Zn in Dabaoshan soils were presented at over 87%. In addition, soil pH, organic matter (OM), and available phosphorous (AP) were almost improved. 16S rRNA sequencing analysis indicated that the introduction of culture medium and P. chrysosporium alone changed bacterial abundance, but the addition of HAP changed the bacterial diversity and community composition by altering environmental conditions. The amendments in the research showed good performance on immobilizing heavy metal(loid)s and reducing their bioavailability. Moreover, the research suggested that environmental factors and soil inherent properties could influence the microbial community structure and composition.

The influence of cysteine in transformation of Cd fractionation and microbial community structure and functional profile in contaminated paddy soil

Remediating cadmium (Cd) contaminated paddy soil is vital for agroecology, food safety, and human health. Soil washing is more feasible to reduce remediation method due to its high efficiency. However, green, low-cost and more efficient washing agents are still required. In this study, we investigated the ability of cysteine as a washing agent for soil washing to remove Cd from contaminated paddy soil. Through a batch experiment, we evaluated the removal efficiency of cysteine as a washing agent by comparing their removal rate with that of a microbial inoculant and sulphuric acid as other washing agents. The transformation of Cd fractionation and microbial community structure and functional profile in paddy soils after cysteine leaching was studied by using sequential extraction and high-throughput sequencing. Results showed that cysteine had better efficiency in the removal of Cd from paddy soil in comparison to sulphuric acid and the microbial inoculant, and could achieve a maximum removal rate of 97 % Cd in paddy soil. Cysteine decreased the proportion of Cd in the exchangeable fraction, carbonate bound fraction, iron and manganese bound fraction, and organic matter bound fraction and was best for the removal of the residual fraction, which contributed to its higher Cd removal ability. Considering the economic benefits of the reagents used, cysteine was shown to be economically feasible for use as a leaching agent. In addition, cysteine could significantly increase the relative abundance of Thermochromatium, Sideroxydans, Streptacidiphilus, and Frankia which promoted the nitrogen and sulfur metabolism in the paddy soil. In summary, this study revealed that cysteine was readily available, cheap, non-toxic, highly efficient, and even has fertilizing properties, making it eco-friendly and ideal for remediation of Cd-contaminated paddy soils. Besides, the health of paddy soils would also benefit from cysteine's promotion of microbial nitrogen and sulfur metabolism.

Nutrients in overlying water affect the environmental behavior of heavy metals in coastal sediments

Excessive nutrients in aquatic ecosystems are the main driving factors for eutrophication and water quality deterioration. However, the influence of nutrients in overlying water on sediment heavy metals is not well understood. In this study, the effects of nitrate nitrogen (NO3-N) addition and phosphate addition in the overlying water on the environmental behaviors of chromium (Cr), copper (Cu), and cadmium (Cd) in coastal river sediments were investigated. Fresh estuary sediments and synthetic saltwater were used in microcosm studies conducted for 13 d. To determine the biological effect, unsterilized and sterilized treatments were considered. The results showed that the diffusion of Cr and Cu was inhibited in the unsterilized treatments with increased NO3-N. However, under the NO3-N sterilized treatments, Cr and Cu concentrations in the overlying water increased. This was mostly related to changes in the microbial regulation of dissolved organic carbon and pH in the unsterilized treatments. Further, in the unsterilized treatments, NO3-N addition considerably increased the concentrations of the acid-soluble (Cr, Cu, and Cd increased by 5%-8%, 29%-41%, and 31%-42%, respectively) and oxidizable (Cr, Cu, and Cd increased by 10%, 5%, and 14%, respectively) fractions. Additionally, compared with that in the unsterilized treatments, Cu and Cd concentrations in P-3 treatments decreased by 7% and 63%, respectively. By producing stable metal ions, microorganisms reduced the amount of unstable heavy metals in the sediment and heavy metal concentration in the overlying water, by considerably enhancing the binding ability of phosphate and heavy metal ions. This study provides a theoretical basis for investigating the coupling mechanisms between heavy metals and nutrients.

Characterization and genome analysis of Neobacillus mesonae NS-6, a ureolysis-driven strain inducing calcium carbonate precipitation

In this study, a highly promising bacterium was isolated from sandstone oil in the Ordos Basin, named strain NS-6 which exhibited exceptional urease production ability and demonstrated superior efficiency in inducing the deposition of calcium carbonate (CaCO3). Through morphological and physiochemical characteristics analysis, as well as 16S rRNA sequencing, strain NS-6 was identified as Neobacillus mesonae. The activity of urease and the formation of CaCO3 increased over time, reaching a maximum of 7.9 mmol/L/min and 184 mg (4.60 mg/mL) respectively at 32 h of incubation. Scanning Electron Microscopy (SEM) revealed CaCO3 crystals ranging in size from 5 to 6 μm, and Energy Dispersive X-ray (EDX) analysis verified the presence of calcium, carbon, and oxygen within the crystals. X-ray Diffraction (XRD) analysis further confirmed the composition of these CaCO3 crystals as calcite and vaterite. Furthermore, the maximum deposition of CaCO3 by strain NS-6 was achieved using response surface methodology (RSM), amounting to 193.8 mg (4.845 mg/mL) when the concentration of calcium ions was 0.5 mmol/L supplemented with 0.9 mmol/L of urea at pH 8.0. Genome-wide analysis revealed that strain NS-6 possesses a chromosome of 5,736,360 base pairs, containing 5,442 predicted genes, including 3,966 predicted functional genes and 1,476 functionally unknown genes. Genes like ureA, ureB, and ureC related to urea catabolism were identified by gene annotation, indicating that strain NS-6 is a typical urease-producing bacterium and possesses a serial of genes involved in metabolic pathways that mediated the deposition of CaCO3 at genetic level.

Natural surfactant mediated bioremediation approaches for contaminated soil

The treatment of environmental pollution by employing microorganisms is a promising technology, termed bioremediation, which has several advantages over the other established conventional remediation techniques. Consequently, there is an urgent inevitability to develop pragmatic techniques for bioremediation, accompanied by the potency of detoxifying soil environments completely. The bioremediation of contaminated soils has been shown to be an alternative that could be an economically viable way to restore polluted soil. The soil environments have long been extremely polluted by a number of contaminants, like agrochemicals, polyaromatic hydrocarbons, heavy metals, emerging pollutants, etc. In order to achieve a quick remediation overcoming several difficulties the utility of biosurfactants became an excellent advancement and that is why, nowadays, the biosurfactant mediated recovery of soil is a focus of interest to the researcher of the environmental science field specifically. This review provides an outline of the present scenario of soil bioremediation by employing a microbial biosurfactant. In addition to this, a brief account of the pollutants is highlighted along with how they contaminate the soil. Finally, we address the future outlook for bioremediation technologies that can be executed with a superior efficiency to restore a polluted area, even though its practical applicability has been cultivated tremendously over the few decades.

Effects of dissolved organic matter derived from cow manure on heavy metal(loid)s and bacterial community dynamics in mercury-thallium mining waste slag

Organic amendments in aided phytostabilization of waste slag containing high levels of heavy metal (loid)s (HMs) are an important way to control the release of HMs in situ. However, the effects of dissolved organic matter (DOM) derived from organic amendments on HMs and microbial community dynamics in waste slag are still unclear. Here, the effect of DOM derived from organic amendments (cow manure) on the geochemical behaviour of HMs and the bacterial community dynamics in mercury (Hg)-thallium (Tl) mining waste slag were investigated. The results showed that the Hg-Tl mining waste slag without the addition of DOM continuously decreased the pH and increased the EC, Eh, SO42-, Hg, and Tl levels in the leachate with increasing incubation time. The addition of DOM significantly increased the pH, EC, SO42-, and arsenic (As) levels but decreased the Eh, Hg, and Tl levels. The addition of DOM significantly increased the diversity and richness of the bacterial community. The dominant bacterial phyla (Proteobacteria, Firmicutes, Acidobacteriota, Actinobacteriota, and Bacteroidota) and genera (Bacillus, Acinetobacter, Delftia, Sphingomonas, and Enterobacter) were changed in association with increases in DOM content and incubation time. The DOM components in the leachate were humic-like substances (C1 and C2), and the DOC content and maximum fluorescence intensity (FMax) values of C1 and C2 in the leachate decreased and first increased and then decreased with increasing incubation time. The correlations between HMs and DOM and the bacterial community showed that the geochemical behaviours of HMs in Hg-Tl mining waste slag were directly influenced by DOM-mediated properties and indirectly influenced by DOM regulation of bacterial community changes. Overall, these results indicated that DOM properties associated with bacterial community changes increased As mobilization but decreased Hg and Tl mobilization from Hg-Tl mining waste slag.

Stabilization of Pb(II) in wastewater and tailings by commercial bacteria through microbially induced phosphate precipitation (MIPP)

Microbially induced phosphate precipitation (MIPP) is an effective and eco-friendly method for Pb(II) stabilization. The phosphate-solubilizing microorganisms (PSM) for MIPP are commonly isolated from Pb(II)-contaminated sites through a series of intricate and time-consuming enrichment and purification processes. This research used ready-made commercial bacteria to develop a simple MIPP process. Bacillus subtilis (BS, CCTCC AB 98002) was selected from two commercial PSM strains owing to more effective Pb(II) removal. Compared to the most isolated microorganisms, BS released more than twice as much inorganic phosphorus (Pi) as well as had a high-level Pb(II) tolerance. BS could remove >99% of Pb(II) from 500 mg/L Pb(II)-containing water at the optimal 0.05 M sodium glycerophosphate (SGP), pH 7-9, and ≤0.03 M MgCl₂, outperforming most isolated microorganisms. In addition, BS could mitigate the contamination risk of the lead‑zinc tailings, by reducing the readily leachable Pb(II) concentration from 0.81 mg/L (over the regulatory limit of 0.1 mg/L) to 0.00042 mg/L. The unstable Pb(II) in the solution and tailings was ultimately stabilized to Pb₅(PO₄)₃Cl after the SGP phosphorlysis and phosphate precipitation processes. In conclusion, commercial BS is a superior alternative to isolated microorganisms for MIPP on Pb(II) stabilization. The simple-processed and high-effective BS-based MIPP provides the MIPP method a new insight for widespread implementation in the remediation of heavy metals-containing wastewater, soil, and waste.

Synergistic remediation of lead pollution by biochar combined with phosphate solubilizing bacteria

Pb(II) is extreme toxic to biological cells, which limits the restoration of Pb(II) by functional strains. This study examined a Pb(II)-tolerant phosphate solubilizing bacteria(PSB) Ochrobactrum sp. J023 combined with corn stover biochar to enhance the immobilization of Pb(II). The results showed that the removal rate of Pb(II) by biochar combined with phosphate-solubilizing bacteria was as high as 71.30 %. SEM-EDS showed that more disordered crystals appeared on the surface of biochar treated with bacteria. XRD analysis indicated that the mineralization products of Pb(II) in biochar combined strain system were mainly in Pb₅(PO₄)₃OH and Pb₅(PO₄)₃Cl. FT-IR analysis revealed that there were more phosphate groups involved in the mineralization process when biochar was added. XPS verified the formation of PbO or lead-containing precipitates in this system, and the amount of lead precipitates was larger. The mechanism of lead fixation by strain combined with biochar can be regarded that the strain regulates the microenvironment of the biochar surface, enhances the release of phosphate and promotes the generation of stable pyroxite. Moreover, biochar composition and porous structure not only provide nutrient elements for strains, but also protect and promote the metabolism of strains. Biochar adsorption also reduces the loss of available phosphorus, which helps PSB to fix Pb sustainably and effectively. This suggests that the synergistic effect of PSB-biochar can not only effectively reduce the mobility and bioavailability of Pb(II), but also increase the sustainability of remediation. Therefore, the combination of phosphate solubilizing bacteria and biochar is a promising approach to the remediation of heavy metal pollution.

Penicillium oxalicum augments soil lead immobilization by affecting indigenous microbial community structure and inorganic phosphate solubilization potential during microbial-induced phosphate precipitation

Phosphate-solubilizing microorganisms (PSMs) are critically important for increasing soil phosphate (P) and decreasing lead (Pb) bioavailability during microbial-induced phosphate precipitation (MIPP). However, their relative contributions to the indigenous soil microbial communities and P-cycling genes during the MIPP process remain unclear. In this study, inoculation of the PSM P. oxalicum in hydroxyapatite-cultured and Pb-contaminated soil increased soil phosphatase activities, available P (AP) concentrations and reduced available Pb levels. Metagenomics revealed a 3.9-44.0% increase in the abundance of P-cycling genes by P. oxalicum inoculation. No P-cycling genes were assigned to Penicillium. While P. oxalicum increased the complexity of microbial community co-occurrence networks, and improved the directly interrelationships between Penicillium and genera containing P-cycling gene. These results suggesting that P. oxalicum obviously positively affected the regulation of indigenous P-cycling functional communities during the MIPP process. Inorganic P solubilization genes (gcd, ppa, and ppx) have been shown to affect soil AP, suggesting that inorganic P solubilization is the major driver of Pb immobilization improvement following P. oxalicum inoculation. These results enhance our understanding of the significant ecological role of PSMs in governing soil P-cycling and alleviating Pb²⁺ biotoxicity during the MIPP process.

Enhanced Cd(II) biomineralization induced by microalgae after cultivating modification in high-phosphorus culture

In this study, high-phosphorus beared microalgae was prepared by cultivating modification in high-phosphorus culture, and used for the enhanced Cd(II) biomineralization in soil. Batch experiment results showed that Chlorella sorokiniana FK was modified successfully in highly phosphate culture. Both intracellular P (Poly-P, 29.7 mg/kg) and surface P (phosphoryl based functional groups, 3.7 mol/kg) were greatly enhanced, and the Cd(II) removal capacity surged to 45.98 mg/g at equilibrium in the Langmuir simulation. The EXAFS analysis indicated that Cd tended to form a more stable bidentate complex (RPO₄)₂Cd when bounding with phosphate groups on the surface of the high-phosphorus microalgae. Moreover, high-phosphorus beared microalgae not only had higher immobilization amount of Cd(II), but also promoted immobilized Cd from adsorbed state to mineralized state. After high-phosphate cultured, increased density of P-related groups provided more adsorption sites, while the decomposition of intracellular Poly-P released phosphate ions into cell surface microenvironment, which combined and promoted the formation of Cd₃(PO₄)₂/Cd(H₂PO₄)₂ on cell surface. Cd-contaminated soil remediation experiments applying high-surface-phosphate beared microalgae further showed that more Cd stabilized as a residue fraction within 49 days. This study proposes that the high-phosphate culture strategy is a good way to improve the immobilization of heavy metals in soil induced by microorganisms.

Biogeochemical behavior and pollution control of arsenic in mining areas: A review

Arsenic (As) is one of the most toxic metalloids that possess many forms. As is constantly migrating from abandoned mining area to the surrounding environment in both oxidation and reducing conditions, threatening human health and ecological safety. The biogeochemical reaction of As included oxidation, reduction, methylation, and demethylation, which is closely associated with microbial metabolisms. The study of the geochemical behavior of arsenic in mining areas and the microbial remediation of arsenic pollution have great potential and are hot spots for the prevention and remediation of arsenic pollution. In this study, we review the distribution and migration of arsenic in the mining area, focus on the geochemical cycle of arsenic under the action of microorganisms, and summarize the factors influencing the biogeochemical cycle of arsenic, and strategies for arsenic pollution in mining areas are also discussed. Finally, the problems of the risk control strategies and the future development direction are prospected.

Lactic acid bacteria induce phosphate recrystallization for the in situ remediation of uranium-contaminated topsoil: Principle and application

Uranium (U) contamination often occurs in the topsoil (arable layer), and is a serious threat to crop growth. However, conventional microbial reduction methods are sensitive to oxygen and cannot be used to treat aerobic topsoils. In this study, phosphate-solubilizing microorganisms (PSM) were isolated from U-contaminated topsoil and used for soil remediation. Microbial metabolites and products were analyzed, and the pathways and mechanisms of PSM immobilization were revealed. The results showed that strain PSM8 had the highest phosphate-solubilizing capacity (dissolved P was 208 ± 5 mg/L) and the highest U removal rate (97.3 ± 0.1%). Multi-technical analyses indicated that bacterial surface functional groups adsorbed (UO₂)²⁺ ions on the cell surface, glycolysis produced 3-10 mg/L of lactic acid (pH 4.7-6.0), and lactic acid solubilized Ca₃(PO₄)₂ to form stable chernikovite (a type of uranyl phosphate) on the cell surface. The coupled application of Ca₃(PO₄)₂ and strain PSM8 significantly reduced the bioavailability of soil U (62 ± 11%), converting U from the exchangeable to the residual phase and P from the steady to the available form. In addition, pot experiments showed that soil remediation promoted crop growth and significantly reduced U uptake and toxicity to photosynthetic systems. These findings demonstrate that PSM and Ca₃(PO₄)₂ are good coupled fertilizers for U-contaminated agricultural soil.

Phosphate capture from biogas slurry with magnesium-doped biochar composite derived from Lycium chinensis branch filings: performance, mechanism, and effect of coexisting ions

The performance, mechanisms, and effects of various coexisting ions on phosphorus (P) adsorptive capture in biogas slurry using MgO-doped biochar (MBC) were investigated. The results revealed that in comparison to the pristine biochar, the introduction of MgO significantly improved the P adsorptive capture feasibility of MBC. In addition, the process of P capture by MBC was not affected by the initial pH of the solution. The process of P capture could reach equilibrium within 120 min and be simulated using both the pseudo-first-order and the pseudo-second-order kinetic models. In addition, the highest P capture capacity calculated from the Langmuir isotherm model was approximately 129.35 mg/g. The coexisting of cations including NH₄⁺, Ca²⁺, Cu²⁺, Cd²⁺, Pb²⁺, Zn²⁺, and Cr³⁺ in higher concentrations of promoted P adsorptive capture through precipitation and ionic atmosphere effects. The presence of coexisting ions including SO₄^2-, HCO₃^-, and fulvic acid (FA) had a certain inhibitory effect on the P adsorptive capture through competitive adsorption with phosphate. The existence of monovalent ions such as K⁺, Na⁺, Cl^-, and NO₃^- had no significant effect on P adsorptive capture. The adsorptive capture of P by MBC was affected by various processes including electrostatic attraction and surface complexation, and the presence of different coexisting substances had different impacts on the P adsorption. Adding to these, the P in the biogas slurry was completely adsorbed by the MBC during the experiment, indicating that MBC is a promising composite in the engineering application for the capture of P from wastewater.

Recent advances in soil remediation technology for heavy metal contaminated sites: A critical review

With the increasing development of industry and urbanization, heavy metal contaminated sites have become progressively conspicuous, particularly by unreasonable emissions from electroplating, nonferrous metals smelting, mine tailing, etc. In recent years, soil remediation technologies for heavy metal contaminated sites have developed rapidly. New and effective remediation technologies have emerged successively, and more successful practical applications have appeared. Therefore, systematical summarization of the current progress is essential. As a result, in this paper, some mainstream soil remediation technologies for heavy metal contaminated sites, including physical remediation (soil thermal desorption and soil replacement), bioremediation (phytoremediation and microbial remediation), chemical remediation (chemical leaching, chemical stabilization, electrokinetic remediation-permeable reactive barrier, and chemical oxidation/reduction), as well as various combined remediation are comprehensively reviewed. The influencing factors, advantages, disadvantages, remediation mechanism, and practical applications are also deeply discussed. Besides, the corresponding remediation strategies are put forward for the remediation of heavily polluted sites such as the chemical industry, smelting, and tailing areas. Overall, this review will be beneficial for the in-depth understanding and provide references for the reasonable selection and development of soil remediation technology for heavy metal contaminated sites.

Prospects for Using Phosphate-Solubilizing Microorganisms as Natural Fertilizers in Agriculture

Phosphates are known to be essential for plant growth and development, with phosphorus compounds being involved in various physiological and biochemical reactions. Phosphates are known as one of the most important factors limiting crop yields. The problem of phosphorus deficiency in the soil has traditionally been solved by applying phosphate fertilizers. However, chemical phosphate fertilizers are considered ineffective compared to the organic fertilizers manure and compost. Therefore, increasing the bioavailability of phosphates for plants is one of the primary goals of sustainable agriculture. Phosphate-solubilizing soil microorganisms can make soil-insoluble phosphate bioavailable for plants through solubilization and mineralization. These microorganisms are currently in the focus of interest due to their advantages, such as environmental friendliness, low cost, and high biological efficiency. In this regard, the solubilization of phosphates by soil microorganisms holds strong potential in research, and inoculation of soils or crops with phosphate-solubilizing bacteria is a promising strategy to improve plant phosphate uptake. In this review, we analyze all the species of phosphate-solubilizing bacteria described in the literature to date. We discuss key mechanisms of solubilization of mineral phosphates and mineralization of organic phosphate-containing compounds: organic acids secreted by bacteria for the mobilization of insoluble inorganic phosphates, and the enzymes hydrolyzing phosphorus-containing organic compounds. We demonstrate that phosphate-solubilizing microorganisms have enormous potency as biofertilizers since they increase phosphorus bioavailability for the plant, promote sustainable agriculture, improve soil fertility, and raise crop yields. The use of phosphate-solubilizing microbes is regarded as a new frontier in increasing plant productivity.

Insight into functional microorganisms in wet–dry conversion to alleviate the toxicity of chromium fractions in red soil

Soil contamination with potentially toxic element such as chromium (Cr) poses a threat to the environment and human health. The environmental toxicity of Cr is related not only to the total Cr content but also to the distribution of Cr fractions. In this study, laboratory simulation experiments were conducted to explore the characteristics of Cr fractions and responses of the functional microbial community during dynamic leaching and static drying processes. The results showed that acid-soluble Cr and reducible Cr transformed into other relatively stable fractions under dry conditions, and ammonium nitrogen promoted the transformation. Nitrate-nitrogen was significantly positively correlated with Cr fractions in the wet stage (p < 0.05), while ammonium nitrogen showed the same relation in the dry process. Analysis of the microbial community showed that the bacterial and fungal genera Flavihumibacter, Altererythrobacter, Methylobacillus, Flavisolibacter, Lysobacter, and Cladosporium were related to the Cr fractions (acid-soluble Cr, reducible Cr, and oxidizable Cr) under wet conditions, while the microbial genera Ellin6067, MND1, and Ramlibacter were related to Cr fractions under dry conditions. Moreover, the proliferation of the functional microbial genera Methylobacillus, Ellin6067, and MND1 related to Cr fractions in the wet–dry conversion process alleviated the environmental toxicity of Cr. These findings provide useful information for the remediation of Cr-contaminated soils by monitoring the distribution fractions of Cr and the functional microbial community under wet–dry conditions.

Effect of the phosphate solubilization and mineralization synergistic mechanism of Ochrobactrum sp. on the remediation of lead

Phosphate-solubilizing bacteria (PSB) promotes the formation of mineralized precipitation through phosphorous dissolution and mineralization, forming stable lead (Pb(II)) minerals and reducing the migration of Pb(II) in the environment. In this study, a Pb-tolerant strain Ochrobactrum sp. J023 from a contaminated soil around a battery factory in Jiangsu Province, China, was screened for experiments to investigate the phosphate solubilization and mineralization mechanism of this strain. The organic acids and the acid phosphatase produced by the bacteria have a synergistic effect on phosphate dissolution. When the pH of the culture medium decreased to the lowest 4.55, the amount of soluble phosphate and the activity of acid phosphatase reached the maximum 161.29 mg L^-1 and 61.98 U mL^-1, and there was a significant correlation between the concentration of soluble phosphate and the activity of acid phosphatase (R = 0.832**, P < 0.05). It was found that acetic acid played the most important role in the secreted organic acids. During the mineralization reaction, the extracellular polymeric substances (EPS) chelates part of the Pb(II) on the surface of the cell wall, preventing the metal Pb from penetrating into the cell, thus providing protection to the strain. Meanwhile, due to the nucleation sites provided by cell surface groups (carboxyl and phosphate groups), a large number of metal ions are absorbed to promote the formation of crystallization. The final mineralized product of Pb(II) by strain J023 was pyroxite (Pb₅(PO₄)₃X, where X = Cl, OH). The mechanism of phosphate dissolution and mineralization proposed by us is that the organic acids and acid phosphatases secreted by phosphate-solubilizing bacteria promote the increase of PO₄^3- concentration in the solution, the complexation of metal cations and cell surface groups will induce the formation of mineralized precipitation under the catalysis of enzyme. Therefore, it is a promising strategy for bioremediation of lead pollution by screening functional strains with strong abilities of phosphate solubility and mineralization.

Surface biomineralization of uranium onto Shewanella putrefaciens with or without extracellular polymeric substances

The influence of extracellular polymeric substances (EPS) on the interaction between uranium [U(VI)] and Shewanella putrefaciens (S. putrefaciens), especially the U(VI) biomineralization process occurring on whole cells and cell components of S. putrefaciens was investigated in this study. The removal efficiency of U(VI) by S. putrefaciens was decreased by 22% after extraction of EPS. Proteins were identified as the main components of EPS by EEM analysis and were determined to play a major role in the biosorption of uranium. SEM-EDS results showed that U(VI) was distributed around the whole cell as 500-nanometer schistose structures, which consisted primarily of U and P. However, similar uranium lamellar crystal were wrapped only on the surface of EPS-free S. putrefaciens cells. FTIR and XPS analysis indicated that phosphorus- and nitrogen-containing groups played important roles in complexing U (VI). XRD and U L_III-edge EXAFS analyses demonstrated that the schistose structure consisted of hydrogen uranyl phosphate [H₂(UO₂)₂(PO₄)₂•8H₂O]. Our study provides new insight into the mechanisms of induced uranium crystallization by EPS and cell wall membranes of living bacterial cells under aerobic conditions.

The roles of intracellular and extracellular calcium in Bacillus subtilis biofilms

In nature, bacteria reside in biofilms– multicellular differentiated communities held together by an extracellular matrix. This work identified a novel subpopulation—mineral-forming cells—that is essential for biofilm formation in Bacillus subtilis biofilms. This subpopulation contains an intracellular calcium-accumulating niche, in which the formation of a calcium carbonate mineral is initiated. As the biofilm colony develops, this mineral grows in a controlled manner, forming a functional macrostructure that serves the entire community. Consistently, biofilm development is prevented by the inhibition of calcium uptake. Our results provide a clear demonstration of the orchestrated production of calcite exoskeleton, critical to morphogenesis in simple prokaryotes.

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The orchestrated formation of calcite scaffolds supports the morphogenesis of microbial biofilms

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A novel subpopulation—mineral-forming cells—is essential for biofilm formation

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This subpopulation contains an intracellular calcium-accumulating niche, supporting the formation of calcium carbonate

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Intracellular calcium homeostasis and calcium export are associated with a functional biofilm macrostructure

Mineralization of lead by Phanerochaete chrysosporium microcapsules loaded with hydroxyapatite

In this study, microcapsules assembled with Phanerochaete chrysosporium (P. chrysosporium, PC) and hydroxyapatite (HAP) were successfully prepared and applied for Pb(II) immobilization in aqueous solution. The effect of different conditions on Pb(II) removal was investigated, such as pH, temperature, dosages of microcapsules and HAP, and initial concentrations of Pb(II). The removal efficiency of Pb(II) was in order of HAP+PC > HAP > PC > CK (control check) at the Pb(II) initial concentration of 100 mg L^-1, which were 87.7%, 82.82%, 63.67% and 2.06%, respectively. Under HAP+PC treatment, P. chrysosporium secreted plentiful organic acids like formic, oxalic and citric acids, when the addition dose of HAP increased from 5 g L^-1 to 15 g L^-1, the production of formic acid increased remarkably from 32.37 g L^-1 to 66.02 g L^-1. After reaction, P. chrysosporium kept a good biological activity evidenced by the live/dead stain test. The characterization results indicated that the insoluble apatite could transform to soluble phosphate due to the secreted organic acids, then reacted with Pb(II) to form pyromorphite [Pb₁₀(PO₄)₆Cl₂] and lead phosphate hydroxide [Pb₁₀(PO₄)₆(OH)₂]. The overall results clearly demonstrated that combining P. chrysosporium with HAP could be used as a promising technology to accelerate lead immobilization.

Vertical distribution of the toxic metal(loid)s chemical fraction and microbial community in waste heap at a nonferrous metal mining site

Over the past few decades, nonferrous mining has produced numerous waste rock and part of the waste that has not been properly treated was generally dumped at roadsides and hill slopes. However, the vertical distributions of toxic metal(loid)s and composition of microbial communities in waste heap and the under-laid pristine soil are rarely studied. In this work, the fraction-related distributions of toxic metal(loid)s were investigated at a waste heap profile and the indigenous microbial assemblages were also analyzed by Illumina sequencing of 16 s rRNA genes. Results showed that compared to the under-laid pristine soil, content of toxic metal(loid)s, especially Cd, As and Pb, in waste rock layer were higher. Most of As in subsoil existed as non-specifically sorbed and specifically-sorbed fractions, which could be ascribed to the migration from the upper layer. The mobility was significantly correlated with Eh, EC, clay content, CEC and the total content of metal(loid)s. Phyla Proteobacteria, Acidobacteria and Firmicutes dominated the microbial communities. The microbial community compositions at the genus level were similar, but their relative abundances were mainly influenced by pH, CEC, Eh, SOM, and bioavailability content of toxic metal(loid)s. Besides, microbial functions of elements (S, Fe, Mn and As) oxidation/reduction and metabolites (siderophore, biosurfactant, organic acid, phosphatase and urease) potentially were used for pollutants bioremediation.

Remediation of soil cadmium pollution by biomineralization using microbial-induced precipitation: a review

In recent years, with industrial pollution and the application of agricultural fertilizers with high cadmium (Cd) content, soil Cd pollution has become increasingly serious. A large amount of Cd is discharged into the environment, greatly endangering the stability of the ecological environment and human health. The use of microorganisms to induce Cd precipitation and mineralization is an important bioremediation method. Itis highly efficient, has a low cost, enables environmental protection, and convenient to operate. This article summarizes the pollution status, pollution source, biological toxicity and existing forms of Cd, as well as the biomineralization mechanism of microbial induced Cd(II) precipitation, mainly including microbial-induced carbonate precipitation, microbial-induced phosphate precipitation and microbial-induced sulfide precipitation. Factors affecting the bioremediation of Cd, such as pH, coexisting ions, and temperature, are introduced. Finally, the key points and difficulties of future microbe-induced Cd(II) biomineralization research are highlighted, providing a scientific basis and theoretical guidance for the application of microbe-induced Cd(II) immobilization in soil.

Phosphorus-modified biochar cross-linked Mg-Al layered double-hydroxide composite for immobilizing uranium in mining contaminated soil

The decommissioning of uranium mill tailings (UMTs) is usually accompanied by uranium (U) contamination in soil, which poses a serious threat to human health and ecological safety. In this study, a novel phosphorus-modified bamboo biochar (PBC) cross-linked Mg-Al layered double-hydroxide (LDH) composite ("PBC@LDH") was successfully prepared by phosphate pre-impregnation and a hydrothermal method with Mg-Al LDH. Physicochemical analysis revealed that phosphorus-containing functional groups and Mg-Al LDH were grafted onto the pristine biochar (BC) matrix. Laboratory-scale incubation and column leaching experiments were performed on the prepared BC, PBC, and PBC@LDH. The results showed that, at a dosage of 10%, the PBC@LDH composite had a commendable ability to immobilize U in soil. After 40 days of incubation with the stabilizer, the more mobile U was converted into immobilized species. Furthermore, during a column leaching experiment with simulated acid rain, the cumulative loss and leaching efficiency of U were remarkably reduced by PBC@LDH treatment compared with the control, reaching 53% and 54%, respectively. Surface complexation, co-precipitation, and reduction described the adsorption and immobilization mechanisms. In conclusion, this research demonstrates that the PBC@LDH composite offers a potentially effective amendment for the remediation of U contaminated soil.

Roles of Phosphate Solubilizing Microorganisms from Managing Soil Phosphorus Deficiency to Mediating Biogeochemical P Cycle

Phosphorus (P) is a vital element in biological molecules, and one of the main limiting elements for biomass production as plant-available P represents only a small fraction of total soil P. Increasing global food demand and modern agricultural consumption of P fertilizers could lead to excessive inputs of inorganic P in intensively managed croplands, consequently rising P losses and ongoing eutrophication of surface waters. Despite phosphate solubilizing microorganisms (PSMs) are widely accepted as eco-friendly P fertilizers for increasing agricultural productivity, a comprehensive and deeper understanding of the role of PSMs in P geochemical processes for managing P deficiency has received inadequate attention. In this review, we summarize the basic P forms and their geochemical and biological cycles in soil systems, how PSMs mediate soil P biogeochemical cycles, and the metabolic and enzymatic mechanisms behind these processes. We also highlight the important roles of PSMs in the biogeochemical P cycle and provide perspectives on several environmental issues to prioritize in future PSM applications.

Spatial Distribution of Toxic Metal(loid)s and Microbial Community Analysis in Soil Vertical Profile at an Abandoned Nonferrous Metal Smelting Site

In this study soils at different depths were collected in a Zn smelting site located in Zhuzhou City, China, in order to understand toxic metal(loid)s distribution and microbial community in vertical soil profile at a smelting site. Except Soil properties and metal(loid)s content, the richness and diversity of microbial communities in soil samples were analyzed via high-throughput Illumina sequencing of 16s rRNA gene amplicons. The results showed that the content of As, Pb, Cu, Cd, Zn, and Mn was relatively high in top soil in comparison to subsoil, while the concentration of Cr in subsoil was comparable with that in top soil due to its relative high background value in this soil layer. The bioavailability of Cd, Mn, Zn, and Pb was relative higher than that of As, Cr, and Cu. The diversity of soil microbial communities decreased with increasing depth, which might be ascribed to the decrease in evenness with increase in depth duo to the influence by environmental conditions, such as pH, TK (total potassium), CEC (cation exchange capacity), ORP (oxidation reduction potential), and Bio-Cu (bioavailable copper). The results also found Acidobacteria, Proteobacteria, Firmicutes, and Chloroflexi were dominant phyla in soil samples. At the genus level, Acinetobacter, Pseudomonas, and Gp7 were dominant soil microorganism. Besides, Environmental factors, such as SOM (soil organic matter), pH, Bio-Cu, Bio-Cd (bioavailable cadmium), and Bio-Pb (bioavailable lead), greatly impacted microbial community in surface soil (1-3 m), while ORP, TK, and AN concentration influenced microbial community in the subsoil (4-10 m).