Rhizospheric mechanisms of Bacillus subtilis bioaugmentation-assisted phytostabilization of cadmium-contaminated soil

Simultaneous Cd immobilization and oxidative stress alleviation in Brassica chinensis by a novel phosphate-solubilizing strain Sutcliffiella horikoshii P1

Microbial remediation of cadmium (Cd) pollution offers economically green and operationally simple advantages, particularly in environments with mild contamination. The acquisition of efficient strains and coupling between bacterial response and plant fitness are current research emphases in the remediation process. In this study, a novel phosphate-solubilizing strain with outstanding Cd-resistance, Sutcliffiella (S.) horikoshii P1 was isolated. Cd removal efficiency reached 98.85 % by the strain within 24 h at an initial concentration of 5 mg/L. Distribution analysis revealed that the dominant mechanism of Cd removal by the strain varies with Cd concentrations. Notably, the seed soaking of Brassica chinensis with S. horikoshii P1 could improve seed germination rate and growth potential regardless of the presence of Cd stress. Morphological and biochemical trait analysis revealed that the inoculated strain also increased fresh weight and reduced the Cd phytoavailability of Brassica chinensis by producing active substances and alleviating plant oxidative stress. Pot experiment demonstrated that the transport factor (TF) and bioconcentration factor (BCF) decreased by 22.76 % and 33.59 %, respectively, and Cd content in edible parts met food safety standards. Whole-genome sequencing analysis demonstrated that functional genes related to heavy metal resistance and transport (cadC, czcD, znuA, etc.), and gene clusters involved in siderophore secretion may regulate Cd immobilization and the plant growth-promoting effect of S. horikoshii P1. The results underscored the feasibility and effectiveness of Sutcliffiella horikoshii in addressing Cd contamination and promoting plant growth, providing a basis for the future application in agricultural safe production.

Newly isolated bacterium and arbuscular mycorrhizal fungus effectively reduce the root cadmium concentration and increase the root biomass of Ophiopogon japonicus

Soil cadmium (Cd) contamination is one of the major challenges in food production. This has led to above-maximum threshold accumulation of Cd in O. japonicus roots. This research identifies Pseudomonas tianjinensis S2 (PL), a newly isolated bacterium, and Corymbiglomus tortuosum (Ct), an arbuscular mycorrhizal fungus (AMF), as effective agents for reducing Cd concentration in the roots of O. japonicus. Compared to the control (CK) treatment, the root Cd levels decreased by 62.27 % and 46.13 %, respectively, significantly enhancing root biomass. We also noticed the involvement of -OH, -CH, and CC functional groups in Cd chelation in both treatments, and the formation of precipitates, including C2H2CdO4, C4H6CdO4, Cd(OH)2, and Cd3(PO4)2, in both PL and Ct treatments. Moreover, the proportion of residual Cd in soil increased by 21.21 % and 10.61 % for the PL and Ct treatments, respectively, compared to the CK. The findings suggest that P. tianjinensis S2 is more effective than C. tortuosum for high Cd-contaminated fields, while the fungal inoculant is suitable for lower contamination levels, offering valuable strategies for bioremediation. Therefore, we suggest further research to focus on elucidating the effect of a P. tianjinensis S2 and C. tortuosum combination on O. japonicus root growth and Cd accumulation.

Biofilm-overproducing Bacillus amyloliquefaciens strain B9ΔywcC reduces cadmium uptake in lettuce by upregulating the expression of proteins associated with root surface biofilm formation and cell membrane homeostasis

In this study, Bacillus amyloliquefaciens strain B9 and its biofilm-overproducing B9ΔywcC mutant (ΔywcCM) were characterized for their effects on Cd accumulation in Italian lettuce and the underlying molecular mechanisms under hydroponic conditions. Both B9 and ΔywcCM significantly reduced Cd contents in lettuce tissues compared with the controls. Furthermore, ΔywcCM exhibited significantly decreased Cd accumulation and increased root surface biofilm biomass and biofilm-mediated Cd immobilization compared with B9. Proteomic analysis of lettuce root surface biofilms revealed that ΔywcCM significantly upregulated the expression of several proteins compared to B9. These included IolC and IolD (associated with inositol metabolism), GlpK (associated with glycerol metabolism), TyrS (associated with tRNA synthesis and transport), and LepA and PepT (associated with protein translation and modification), which are associated with biofilm formation; ArgS and AspS (associated with tRNA synthesis and transport), LepA (associated with protein translation and modification), and GcvT (associated with aminomethyltransferase), which are involved in cell membrane homeostasis. Furthermore, ΔywcCM significantly upregulated the expression of iolD, iolI, and pepT in the root surface biofilms relative to B9. These findings demonstrated that the biofilm-overproducing ΔywcCM enhances root surface biofilm formation and stability, thereby promoting Cd immobilization and reducing Cd accumulation in lettuce leaves grown in Cd-contaminated solutions.

Potential of pigeon pea [Cajanus cajan (L.) Millsp.] associated with endophytic bacterium Bacillus cereus PEB-9 to remediate cadmium-contaminated soil

Phytoremediation associated with plant-beneficial bacteria has gained considerable attention for its efficiency in remediating cadmium (Cd)-contaminated soil. In this study, we isolated an endophytic bacterium, PEB-9, from pigeon pea, which was identified as Bacillus cereus and exhibited strong plant growth-promoting traits along with high Cd resistance in vitro. Pot experiments demonstrated that PEB-9 inoculation increased in pigeon pea biomass (11.45-19.29 %), Cd accumulation (43.89-69.90 %), and the Cd transfer factor (4.17-16.89 %) in Cd-stress soil (2-10 mg/kg), with soil remediation efficiency improving by 11.1-15.4 %. Under Cd stress, PEB-9-treated pigeon pea exhibited significant improvement in the activities of superoxide dismutase, peroxidase, and catalase, while a notable decrease in malondialdehyde content, indicating a reduction in Cd cytotoxicity. Additionally, the chlorophyll content in PEB-9-treated plants was significantly higher than that in the control group. Furthermore, PEB-9 inoculation enhanced bioavailable Cd, soil enzymes activity and nutrient content, including available nitrogen, phosphorus, and organic matter, while also boosting the relative abundance of stress-resistant bacterial groups, such as Proteobacteria and Actinobacteria. Correlation analysis indicated that soil nutrient changes induced by PEB-9 significantly influenced bacterial community structure, thereby regulating plant physiological responses, and improving Cd remediation efficacy of pigeon pea. These findings offer a valuable basis for the practical implementation of PEB-9 in remediating Cd-contaminated soils.

Bacillus Subtilis as an Excellent Microbial Treatment Agent for Environmental Pollution: A Review

The use of microorganisms in environmental biotreatment is gaining attention, particularly Bacillus subtilis (B. subtilis), recognized for its effectiveness in wastewater treatment and soil remediation. Its success stems from its diverse biological activities and adaptability, which improve environmental quality and ecological balance. This paper reviews the remediation capabilities and mechanisms of B. subtilis, focusing on its applications in water purification and soil pollution management. B. subtilis facilitates pollutant degradation and adsorption through enzyme production, organic acids, unique cell wall properties, and interactions with other microorganisms. The article addresses current challenges and future directions, emphasizing the need for enhanced cultivation, screening, and genetic engineering of functional strains. Understanding the interactions of these strains with other microorganisms and studying their ecological and toxicological impacts are essential for optimizing microbial remediation, providing both theoretical and practical foundations for bioremediation efforts.

Co-exposure impact of nickel oxide nanomaterials and Bacillus subtilis on soybean growth and nitrogen assimilation dynamics

Nickel oxide nanoparticles (NiO-NPs) pose potential threats to agricultural production. Bacillus subtilis has emerged as a stress-mitigating microbe that alleviates the phytotoxicity caused by NiO-NPs. However, the mechanisms underlying its effectiveness, particularly in root-nodule symbiosis and biological N2-fixation (BNF), remain unclear. Here, we tested the combined exposure of NiO-NPs (50 mg kg-1) and B. subtilis on soybean (Glycine max L.) growth and BNF. Combined exposure increased root length, shoot length, root biomass, and shoot biomass by 19% to 26%, while Ni (200 mg kg-1) reduced them by 38% to 53% compared to the control. NiO-NPs at 100 and 200 mg kg-1 significantly (P < 0.05) reduced nodule formation by 16% and 58% and Nitrogen assimilation enzyme activities levels (urease, nitrate reductase, glutamine synthetase, and glutamate synthetase) by 13% to 57%. However, co-exposure with B. subtilis improved nodule formation by 22% to 44%. Co-exposure of NiO-NPs (200 mg kg-1) with B. subtilis increased peroxidase, catalase, and glutathione peroxidase activity levels by 20%, 16%, and 14% while reducing malondialdehyde (14%) and hydrogen peroxide (12%) levels compared to NiO-NPs alone. Additionally, co-exposure of NiO-NPs (100 and 200 mg kg-1) with B. subtilis enhanced the relative abundance of Stenotrophomonas, Gemmatimonas, and B. subtilis, is associated with N2-cycling and N2-fixation potential. This study confirms that B. subtilis effectively mitigates NiO-NP toxicity in soybean, offering a sustainable method to enhance BNF and crop growth and contribute to addressing global food insecurity.

Nitrogen enrichment stimulates nutrient cycling genes of rhizosphere soil bacteria in the Phoebe bournei young plantations

Anthropogenic nitrogen (N) deposition is expected to increase substantially and continuously in terrestrial ecosystems, endangering the balance of N and phosphorus (P) in P-deficient subtropical forest soil. Despite the widely reported responses of the microbial community to simulated N deposition, there is limited understanding of how N deposition affects the rhizosphere soil processes by mediating functional genes and community compositions of soil bacteria. Here, five levels of simulated N deposition treatments (N0, 0 g m-2·yr-1; N1, 100 g m-2·yr-1; N2, 200 g m-2·yr-1; N3, 300 g m-2·yr-1; and N4, 400 g m-2·yr-1) were performed in a 10-year-old Phoebe bournei plantation. Quantitative microbial element cycling smart chip technology and 16S rRNA gene sequencing were employed to analyze functional gene compositions involved in carbon (C), N, and P cycling, as well as rhizosphere bacterial community composition. N deposition significantly influenced C cycling relative abundance of genes in the rhizosphere soil, especially those involved in C degradation. Low and moderate levels (100-300 g m-2·yr-1) of N deposition promoted the relative abundance of the C decomposition-related genes (e.g., amyA, abfA, pgu, chiA, cex, cdh, and glx), whereas high N deposition (400 g m-2·yr-1) suppressed enzyme (e.g., soil invertase, soil urease, and soil acid phosphatase) activities, affecting the C cycling processes in the rhizosphere. Simulated N deposition affected the functional genes associated with C, N, and P cycling by mediating soil pH and macronutrients. These findings provide new insights into the management of soil C sequestration in P. bournei young plantations as well as the regulation of C, N, and P cycling and microbial functions within ecosystems.

Effective soil remediation with fungal Co-inoculation and king grass for robust cadmium and chromium phytoextraction

Bioremediation, an economical and environmentally friendly approach, provides a sustainable solution for mitigating heavy metal contamination in soils. This study identifies four fungal strains-Trichoderma harzianum DAA8, Trichoderma reesei DAA9, Rhizomucor variabilis DFB3, and Trichoderma asperellum LDA4-that exhibit tolerance to cadmium (Cd) and chromium (Cr). These strains were isolated from soils impacted by heavy metal contamination in mining regions. Rigorous examinations of these strains led us to determine their Minimum Inhibitory Concentrations (MICs) and optimal absorption-reduction conditions. Our microscopic data and GC-MS analysis indicate that these strains can accumulate Cd and Cr by generating compounds, such as ketones and imines, in heavy metal environments. We evaluated the remediation efficacy of both single and co-cultures of Rhizomucor variabilis DFB3 and Trichoderma asperellum LDA4 in conjunction with king grass, a plant known for its heavy metal accumulation capabilities. Our findings indicated an impressive 41.9% increase in plant biomass and 47.2% and 64.4% increase in Cd and Cr accumulation respectively. The removal rates of Cd and Cr were 16.5% and 19.0%, respectively, following the co-inoculation of Rhizomucor variabilis DFB3 and Trichoderma asperellum LDA4. These rates represent increases of 37.1% and 33.7% compared to the removal rates achieved with king grass alone. This study not only advances strategies to manage Cd-Cr contamination but also sets a pathway for efficient heavy metal soil remediation using a microbial-plant combined technique.

Insights into the critical roles of water-soluble organic matter and humic acid within kitchen compost in influencing cadmium bioavailability

Compost has demonstrated potential as a cadmium (Cd) remediation agent, while it still remains unclear about the core components in driving the bioactive transformation of Cd. To address this issue, this study isolated three components-kitchen compost powder (KC), humic acid (HA), and water-soluble organic matter (DOM)-from kitchen compost to regulate soil properties, bacterial community structures and functions, and Cd migration risks. The results revealed that the addition of 20% KC and HA reduced the bioavailability factor of Cd by 47.20% and 16.74%, respectively, with HA contributing 35.47% of the total reduction achieved with KC. Conversely, the application of DOM increased the Cd risk through a reduction in soil pH and an increase in the abundance of Cd-activating bacteria, which adversely affected the stability of Cd complexes. However, the porous structure and organic matter in KC and HA provided adsorption sites for Cd passivation and promoted the growth of Cd-fixing bacteria. This study effectively identifies both the positive and negative effects of key compost components on Cd migration and provides scientific guidance for applying kitchen compost in soil management.

Bacillus altitudinis Mediated Lead Bioremediation for Enhanced Growth of Rice Seedlings

Lead (Pb) is a hazardous environmental pollutant that threatens soil health, water quality, and agricultural productivity. Plant growth-promoting rhizobacteria (PGPRs) mediated bioremediation is considered as an eco-friendly approach for agro-environmental sustainability. This study investigated the Pb bioremediation potential of Bacillus altitudinis (IHBT-705). The results revealed that IHBT-705 strain tolerated upto 15 mM of Pb, possessed 96% Pb bioaccumulation efficiency, and also maintained its plant growth-promoting (PGP) traits under Pb stress. Furthermore, IHBT-705 strain treated with 15 mM Pb solution (IHBT-W) and soil containing 15 mM Pb treated with IHBT-705 inoculum (IHBT-S) ameliorated the detrimental effects of Pb stress. Both IHBT-W and IHBT-S treatment significantly improved the shoot length, root length, total roots, chlorophyll content, and antioxidants enzyme activity of the rice seedlings as compared to the seedlings treated with 15 mM Pb solution (Pb-W) and soil containing 15 mM Pb (Pb-S). Also, IHBT-W and IHBT-S treatment decreased the Pb content in the rice plant by 97 and 96% over their respective Pb-W and Pb-S plants. Overall, our research underscores the remarkable Pb bioremediation potential of IHBT-705, offering a promising avenue for dual function, i.e. improving soil health and promoting plant growth under Pb contamination.

Co-application of Parthenium biochar and urea effectively mitigate cadmium toxicity during wheat growth

Environmental contamination by cadmium (Cd), a highly toxic heavy metal, poses significant health risks to plants and humans. Biochar has been effectively used to promote plant growth and productivity under Cd stress. This study presents an innovative application of biochar derived from the invasive weed Parthenium hysterophorus to promote plant growth and productivity under Cd stress. Our study includes detailed soil and plant analyses, providing a holistic perspective on how biochar and urea amendments influence soil properties, nutrient availability, and plant physiological responses. To address these, we established seven treatments: the control, Cd alone (5 mg kg-1), biochar alone (5 %), urea alone (3 g kg-1), biochar with Cd, urea with Cd, and a combination of biochar and urea with Cd. Cd stress alone significantly reduced plant growth indicators such as shoot and root length, fresh and dry biomass, chlorophyll content, and grain yield. However, the supplementation of biochar, urea, or their combination significantly increased shoot length (by 48%, 34%, and 65%), root length (by 73%, 46%, and 70%), and fresh shoot biomass (by 4%, 31%, and 4%), respectively. This improvement is attributed to enhanced soil properties and improved nutrient absorption. The biochar-urea combination also enhanced Cd tolerance by improving total chlorophyll content by 14 %, 13 %, and 16 % compared to the control, respectively. Similaly, these treatments significantly (p < 0.05) boosted the activity of antioxidant enzymes such as catalase, peroxidase, and superoxide dismutase by 51 %, 30 %, and 51 %, respectively, thereby mitigating oxidative stress as a defensive mechanism. The Cd tolerance was improved by biochar, urea, and their combinations, which reduced Cd content in the shoots (by 60.5 %, 38.9 %, and 51.3 %), roots (by 47.5 %, 23.9 %, and 57.6 %), and grains (by 58.1 %, 30.2 %, and 38.3 %) relative to Cd stress alone, respectively. The synergistic effects of biochar and urea are achieved through improved soil properties, nutrient availability, activating antioxidant defense mechanisms, and minimizing the accumulation of metal ions in plant tissues, thereby enhancing plant defenses against Cd stress. Conclusively, converting invasive Parthenium weed into biochar and combining it with urea offers an environmentally friendly solution to manage its spreading while effectively mitigating Cd stress in crops.

Inoculation with Bacillus thuringiensis reduces uptake and translocation of Pb/Cd in soil-wheat system: A life cycle study

Microbial inoculation is an important strategy to reduce the supply of heavy metals (HMs) in soil-crop systems. However, the mechanisms of microbial inoculation for the availability of HMs in soil and their accumulation/transfer in crops remain unclear. Here, the inhibitory effect of inoculation with Bacillus thuringiensis on the migration and accumulation of Pb/Cd in the soil-wheat system during the whole growth period was investigated by pot experiments. The results showed that inoculation with Bacillus thuringiensis increased soil pH and available nutrients (including carbon, nitrogen, and phosphorus), and enhanced the activities of nutrient-acquiring enzymes. Dominance analysis showed that dissolved organic matter (DOM) is the key factor affecting the availability of HMs. The content of colored spectral clusters and humification characteristics of DOM were significantly improved by inoculation, which is conducive to reducing the availability of Pb/Cd, especially during the flowering stage, the decrease was 12.8 %. Inoculation decreased Pb/Cd accumulation in the shoot and the transfer from root to shoot, with the greatest decreases at the jointing and seedling stages (27.0-34.1 % and 6.9-11.8 %), respectively. At the maturity stage, inoculation reduced the Pb/Cd accumulation in grain (12.9-14.7 %) and human health risk (4.1-13.2 %). The results of Pearson correlation analysis showed that the availability of Pb/Cd was positively correlated with the humification of DOM. Least square path model analysis showed that Bacillus thuringiensis could significantly reduce Pb/Cd accumulation in the grain and human health risks by regulating DOM spectral characteristics, the availability of HMs in soil and metals accumulation/transport in wheat at different growth stages. This study revealed the inhibition mechanism of Bacillus thuringiensis on migration of Pb/Cd in a soil-wheat system from a viewpoint of a full life cycle, which offers a valuable reference for the in-situ remediation of HM-contaminated soil and the safe production of food crops in field.

Potential of the plant growth-promoting rhizobacterium Rhodococcus qingshengii LMR356 in mitigating lead stress impact on Sulla spinosissima L

Mining-related lead (Pb) pollution of the soil poses serious hazards to ecosystems and living organisms, including humans. Improved heavy metal phytoremediation efficacy, achieved by using phytostabilizing plants assisted by plant-growth-promoting (PGP) microorganisms, has been presented as an effective strategy for remediating polluted soils. The objective of this research was to examine the response and potential of the plant-growth-promoting bacterium LMR356, a Rhodococcus qingshengii strain isolated from an abandoned mining soil, under lead stress conditions. Compared to non-contaminated culture media, the presence of lead induced a significant decrease in auxin production (from 21.17 to 2.65 μg mL-1) and phosphate solubilization (from 33.60 to 8.22 mg L-1), whereas other PGP traits increased drastically, such as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity (from 38.17 to 71.37 nmol mg-1 h-1 α-ketobutyrate), siderophore production (from 69 to 83%), exopolysaccharide production (from 1952.28 to 3637.72 mg mL-1), biofilm formation, and motility. We, therefore, investigated the behavior of Sulla spinosissima L. in the presence or absence of this strain under a variety of experimental conditions. Under hydroponic conditions, Sulla plants showed endurance to varying lead concentrations (500-1000 μM). Inoculation of plants with Rhodococcus qingshengii strain LMR356 enhanced plant tolerance, as demonstrated by the increase in plant biomass (ranging from 14.41 to 79.12%) compared to non-inoculated Pb-stressed and non-stressed control plants. Antioxidant enzyme activities (increasing by -42.71 to 126.8%) and chlorophyll (383.33%) and carotenoid (613.04%) content were also augmented. In addition to its impact on plant lead tolerance, strain LMR356 showed a growth-promoting effect on Sulla plants when cultivated in sterilized non-contaminated sand. Parameters such as plant biomass (16.57%), chlorophyll (24.14%), and carotenoid (30%) contents, as well as ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT) activities, were all elevated compared to non-inoculated plants. Furthermore, when the same plant species was cultivated in highly polluted soil, inoculation increased plant biomass and improved its physiological properties. These findings demonstrate that LMR356 is a phytobeneficial bacterial strain capable of enhancing Sulla growth under normal conditions and improving its heavy metal tolerance in multi-polluted soils. Thus, it can be considered a promising biofertilizer candidate for growing Sulla spinosissima L. or other selected plants intended for application in restoration and stabilization initiatives aimed at reviving and safeguarding environmentally compromised and polluted soils after mining activities.

The Effect of Two Siderophore-Producing Bacillus Strains on the Growth Promotion of Perennial Ryegrass under Cadmium Stress

Cadmium (Cd) is a highly toxic and cumulative environmental pollutant. Siderophores are heavy metal chelators with high affinity to heavy metals, such as Cd. Ryegrass (Lolium perenne L.) has a potential remediation capacity for soils contaminated by heavy metals. Consequently, using ryegrass alongside beneficial soil microorganisms that produce siderophores may be an effective means to remediate soils contaminated with Cd. In this study, the Bacillus strains WL1210 and CD303, which were previously isolated from the rhizospheres of Nitraria tangutorum in Wulan and Peganum harmala L. in Dachaidan, Qinghai, China, respectively, both arid and sandy environments, were evaluated for heavy metal pollution mitigation. Our quantitative analyses have discerned that the two bacterial strains possess commendable attributes of phosphorus (P) solubilization and potassium (K) dissolution, coupled with the capacity to produce phytohormones. To assess the heavy metal stress resilience of these strains, they were subjected to a cadmium concentration gradient, revealing their incremental growth despite cadmium presence, indicative of a pronounced tolerance threshold. The subsequent phylogenetic analysis, bolstered by robust genomic data from conserved housekeeping genes, including 16S rDNA, gyr B gene sequencing, as well as dnaK and recA, delineated a species-level phylogenetic tree, thereby confirming the strains as Bacillus atrophaeus. Additionally, we identified the types of iron-carrier-producing strains as catechol (WL1210) and carboxylic acid ferrophilin (CD303). A genomic analysis uncovered functional genes in strain CD303 associated with plant growth and iron carrier biosynthesis, such as fnr and iscA. Ryegrass seed germination assays, alongside morphological and physiological evaluations under diverse heavy metal stress, underscored the strains' potential to enhance ryegrass growth under high cadmium stress when treated with bacterial suspensions. This insight probes the strains' utility in leveraging alpine microbial resources and promoting ryegrass proliferation.

Biochar-bacteria-plant combined potential for remediation of oil-contaminated soil

Oil pollution is a common type of soil organic pollution that is harmful to the ecosystem. Bioremediation, particularly microbe-assisted phytoremediation of oil-contaminated soil, has become a research hotspot in recent years. In order to explore more appropriate bioremediation strategies for soil oil contamination and the mechanism of remediation, we compared the remediation effects of three plants when applied in combination with a microbial agent and biochar. The combined remediation approach of Tagetes erecta, microbial agent, and biochar exhibited the best plant growth and the highest total petroleum hydrocarbons degradation efficiency (76.60%). In addition, all of the remediation methods provided varying degrees of restoration of carbon and nitrogen contents of soils. High-throughput sequencing found that microbial community diversity and richness were enhanced in most restored soils. Some soil microorganisms associated with oil degradation and plant growth promotion such as Cavicella, C1_B045, Sphingomonas, MND1, Bacillus and Ramlibacter were identified in this study, among which Bacillus was the major component in the microbial agent. Bacillus was positively correlated with all soil remediation indicators tested and was substantially enriched in the rhizosphere of T. erecta. Functional gene prediction of the soil bacterial community based on the KEGG database revealed that pathways of carbohydrate metabolism and amino acid metabolism were up-regulated during remediation of oil-contaminated soils. This study provides a potential method for efficient remediation of oil-contaminated soils and thoroughly examines the biochar-bacteria-plant combined remediation mechanisms of oil-contaminated soil, as well as the combined effects from the perspective of soil bacterial communities.

Uncovering the mechanisms of how corn steep liquor and microbial communities minimize cadmium translocation in Chinese cabbage

Corn steep liquor-assisted microbial remediation has been proposed as a promising strategy to remediate cadmium (Cd)-contaminated soil. In this study, we determined Bacillus subtilis (K2) with a high cadmium (Cd) accumulation ability and Cd resistance. However, studies on this strategy used in the Cd uptake of Chinese cabbage are lacking, and the effect of the combined incorporation of corn steep liquor and K2 on the functions and microbial interactions of soil microbiomes is unclear. Here, we study the Cd uptake and transportation in Chinese cabbage by the combination of K2 and corn steep liquor (K2 + C7) in a Cd-contaminated soil and corresponding microbial regulation mechanisms. Results showed that compared to inoculant K2 treatment alone, a reduction of Cd concentration in the shoots by 14.4% and the dry weight biomass of the shoots and the roots in Chinese cabbage increased by 21.6% and 30.8%, respectively, under K2 + C7 treatment. Meanwhile, hydrogen peroxide (H2O2) and malondialdehyde (MDA) levels were decreased by enhancing POD and SOD activity, thereby reversing Cd-induced oxidative damage. Importantly, inoculation of K2 would decrease the diversity of the microbial community while enhancing the abundance of dominant species. These findings provide a promising strategy for reducing the Cd accumulation in Chinese cabbage and recovering soil ecological functions.

Effects of organic fertilizers on plant growth and the rhizosphere microbiome

Application of organic fertilizers is an important strategy for sustainable agriculture. The biological source of organic fertilizers determines their specific functional characteristics, but few studies have systematically examined these functions or assessed their health risk to soil ecology. To fill this gap, we analyzed 16S rRNA gene amplicon sequencing data from 637 soil samples amended with plant- and animal-derived organic fertilizers (hereafter plant fertilizers and animal fertilizers). Results showed that animal fertilizers increased the diversity of soil microbiome, while plant fertilizers maintained the stability of soil microbial community. Microcosm experiments verified that plant fertilizers were beneficial to plant root development and increased carbon cycle pathways, while animal fertilizers enriched nitrogen cycle pathways. Compared with animal fertilizers, plant fertilizers harbored a lower abundance of risk factors such as antibiotic resistance genes and viruses. Consequently, plant fertilizers might be more suitable for long-term application in agriculture. This work provides a guide for organic fertilizer selection from the perspective of soil microecology and promotes sustainable development of organic agriculture.IMPORTANCEThis study provides valuable guidance for use of organic fertilizers in agricultural production from the perspective of the microbiome and ecological risk.

Bacteria-loaded biochar for the immobilization of cadmium in an alkaline-polluted soil

The combination of biochar and bacteria is a promising strategy for the remediation of Cd-polluted soils. However, the synergistic mechanisms of biochar and bacteria for Cd immobilization remain unclear. In this study, the experiments were conducted to evaluate the effects of the combination of biochar and Pseudomonas sp. AN-B15, on Cd immobilization, soil enzyme activity, and soil microbiome. The results showed that biochar could directly reduce the motility of Cd through adsorption and formation of CdCO3 precipitates, thereby protecting bacteria from Cd toxicity in the solution. In addition, bacterial growth further induces the formation of CdCO3 and CdS and enhances Cd adsorption by bacterial cells, resulting in a higher Cd removal rate. Thus, bacterial inoculation significantly enhances Cd removal in the presence of biochar in the solution. Moreover, soil incubation experiments showed that bacteria-loaded biochar significantly reduced soil exchangeable Cd in comparison with other treatments by impacting soil microbiome. In particular, bacteria-loaded biochar increased the relative abundance of Bacillus, Lysobacter, and Pontibacter, causing an increase in pH, urease, and arylsulfatase, thereby passivating soil exchangeable Cd and improving soil environmental quality in the natural alkaline Cd-contaminated soil. Overall, this study provides a systematic understanding of the synergistic mechanisms of biochar and bacteria for Cd immobilization in soil and new insights into the selection of functional strain for the efficient remediation of the contaminated environments by bacterial biochar composite.

Cadmium-tolerant Bacillus cereus 2-7 alleviates the phytotoxicity of cadmium exposure in banana plantlets

Bananas are the world's important fruit and staple crop in the developing countries. Cadmium (Cd) contamination in soils results in the decrease of crop yield and food safety. Bioremediation is an environmental-friendly and effective measure using Cd-tolerant plant growth promoting rhizobacteria (PGPR). In our study, a Cd-resistant PGPR Bacillus cereus 2-7 was isolated and identified from a discarded gold mine. It could produce multiple plant growth promoting biomolecules such as siderophores, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC)-deaminase and phosphatase. The extracellular accumulation was a main manner of Cd removal. Surplus Cd induced the expression of Cd resistance/transport genes of B. cereus 2-7 to maintain the intracellular Cd homeostasis. The pot experiment showed that Cd contents decreased by 50.31 % in soil, 45.43 % in roots, 56.42 % in stems and 79.69 % in leaves after the strain 2-7 inoculation for 40 d. Bacterial inoculation alleviated the Cd-induced oxidative stress to banana plantlets, supporting by the increase of chlorophyll contents, plant height and total protein contents. The Cd remediation mechanism revealed that B. cereus 2-7 could remodel the rhizosphere bacterial community structure and improve soil enzyme activities to enhance the immobilization of Cd. Our study provides a Cd-bioremediation strategy using Cd-resistant PGPR in tropical and subtropical area.

Comparative analysis of metabolic mechanisms in the remediation of Cd-polluted alkaline soil in cotton field by biochar and biofertilizer

To screen environmentally friendly and efficient Cd pollution remediation material, the effects of BC and BF on soil Cd bio-availability and cotton Cd absorption were analyzed under Cd exposure. Besides, the differences in metabolic mechanisms by which biochar (BC) and biofertilizer (BF) affect Cd-contaminated soil and cotton were also analyzed. The results showed that the application of BC and BF increased cotton dry matter accumulation, boll number, and single boll weight, and reduced the Cd content in cotton roots, stems, leaves, and bolls. At harvest, the Cd content in cotton roots in the BC and BF groups reduced by 15.23% and 16.33%, respectively, compared with that in the control. This was attributed to the conversion of carbonate-bound Cd (carbon-Cd) and exchangeable Cd (EX-Cd) by BC and BF into residual Cd (Res-Cd). It should be noted that the soil available Cd (Ava-Cd) content in the BF group was lower than that in the BC group. The metabolomic analysis results showed that for BC vs BF, the relative abundance of differential metabolites Caffeic acid, Xanthurenic acid, and Shikimic acid in soil and cotton roots were up-regulated. Mantel test found that cotton root exudate l-Histinine was correlated with the enrichment of Cd in various organs of cotton. Therefore, the application of BC and BF can alleviate Cd stress by reducing soil Ava-Cd content and cotton's Cd uptake, and BF is superior to BC in reducing Cd content in soil and cotton organs. This study will provide a reference for the development of efficient techniques for the remediation of Cd-polluted alkaline soil, and provide a basis for subsequent metagenomics analysis.

Coal slime as a good modifier for the restoration of copper tailings with improved soil properties and microbial function

In recent years, the solid wastes from the coal industry have been widely used as soil amendments. Nevertheless, the impact of utilizing coal slime for copper tailing restoration in terms of plant growth, physicochemical characteristics of the tailing soil, and microbial succession remains uncertain.Herein, the coal slime was employed as a modifier into copper tailings. Their effect on the growth and physiological response of Ryegrass, and the soil physicochemical properties as well as the bacterial community structure were investigated. The results indicated that after a 30-day of restoration, the addition of coal slime at a ratio of 40% enhanced plant growth, with a 21.69% rise in chlorophyll content, and a 62.44% increase in peroxidase activity. The addition of 40% coal slime also increased the content of nutrient elements in copper tailings. Following a 20-day period of restoration, the concentrations of available copper and available zinc in the modified tailings decreased by 39.6% and 48.51%, respectively, with 40% of coal slime added. In the meantime, there was an observed augmentation in the species diversity of the bacterial community in the modified tailings. The alterations in both community structure and function were primarily influenced by variations in pH value, available nitrogen, phosphorus, potassium, and available copper. The addition of 40% coal slime makes the physicochemical properties and microbial community evolution of copper tailings reach a balance point. The utilization of coal slime has the potential to enhance the physicochemical characteristics of tailings and promote the proliferation of microbial communities, hence facilitating the soil evolution of two distinct solid waste materials. Consequently, the application of coal slime in the restoration of heavy metal tailings is a viable approach, offering both cost-effectiveness and efficacy as an enhancer.

Bioremediation of Heavy Metals by the Genus Bacillus

Environmental contamination with heavy metals is one of the major problems caused by human activity. Bioremediation is an effective and eco-friendly approach that can reduce heavy metal contamination in the environment. Bioremediation agents include bacteria of the genus Bacillus, among others. The best-described species in terms of the bioremediation potential of Bacillus spp. Are B. subtilis, B. cereus, or B. thuringiensis. This bacterial genus has several bioremediation strategies, including biosorption, extracellular polymeric substance (EPS)-mediated biosorption, bioaccumulation, or bioprecipitation. Due to the above-mentioned strategies, Bacillus spp. strains can reduce the amounts of metals such as lead, cadmium, mercury, chromium, arsenic or nickel in the environment. Moreover, strains of the genus Bacillus can also assist phytoremediation by stimulating plant growth and bioaccumulation of heavy metals in the soil. Therefore, Bacillus spp. is one of the best sustainable solutions for reducing heavy metals from various environments, especially soil.

Microbial community assembly of the hyperaccumulator plant Sedum plumbizincicola in two contrasting soil types with three levels of cadmium contamination

Microbial communities are closely related to plant performance and numerous studies have shown their involvement with the growth and development of host plants, resistance to pathogen invasion and adaptation to environmental stress. Here we described in detail the ecological process of the microbial community assembly in hyperaccumulator plant Sedum plumbizincicola. We divided the microbiota into four ecological compartments (bulk soil, rhizosphere, root endosphere and aboveground endosphere). The results showed that host selection strongly controlled the aggregation of microbial community. So that microbes occupied different niches from the bulk soil to the aboveground endosphere, and bacterial diversity and network complexity decreased gradually. Soil types were the second influencing factor, especially for the microbial community in the root endosphere. The SourceTracker analysis further confirmed the vertical migration of microbes from bulk soil to aboveground endosphere. In addition, under the condition of heavy metal pollution, the microbial community of S. plumbizincicola tended to form a microbial pool dominated by Proteobacteria and Actinobacteria. Ellin6067, Sphingomonas, Ralstonia, SC-I-84_uncultured bacterium, Burkholderiaceae_Undibacterium and Pedosphaeraceae_uncultured bacterium etc. were identified as the vital biomarker taxa. Among these genera, the relative abundance of last three was significantly positively correlated with the activation and transfer of cadmium, and they mainly enriched in paddy soil. This study provides evidence for the mechanism by which the microbial community assembly occurs and experience for regulating the microbial community and increasing the accumulation efficiency of potentially toxic metals in S. plumbizincicola.

Current Trends in Bioaugmentation Tools for Bioremediation: A Critical Review of Advances and Knowledge Gaps

Bioaugmentation is widely used in soil bioremediation, wastewater treatment, and air biofiltration. The addition of microbial biomass to contaminated areas can considerably improve their biodegradation performance. Nevertheless, analyses of large data sets on the topic available in literature do not provide a comprehensive view of the mechanisms responsible for inoculum-assisted stimulation. On the one hand, there is no universal mechanism of bioaugmentation for a broad spectrum of environmental conditions, contaminants, and technology operation concepts. On the other hand, further analyses of bioaugmentation outcomes under laboratory conditions and in the field will strengthen the theoretical basis for a better prediction of bioremediation processes under certain conditions. This review focuses on the following aspects: (i) choosing the source of microorganisms and the isolation procedure; (ii) preparation of the inoculum, e.g., cultivation of single strains or consortia, adaptation; (iii) application of immobilised cells; (iv) application schemes for soil, water bodies, bioreactors, and hydroponics; and (v) microbial succession and biodiversity. Reviews of recent scientific papers dating mostly from 2022-2023, as well as our own long-term studies, are provided here.

Bioorganic fertilizer promotes pakchoi growth and shapes the soil microbial structure

As a functional probiotic, Bacillus subtilis can promote crop growth and improve nutrient utilization by various mechanisms, so it has been made into bioorganic fertilizer as a replacement for chemical fertilizer. However, the effects of B. subtilis bioorganic fertilizer application on the yield and quality of commercial crops of Brassica chinensis L., the soil physicochemical properties and the microflora have not been clarified. In this study, pot experiments were conducted using Brassica chinensis L. plants with four fertilization treatments: control without fertilization (CK), chemical fertilizer (CF), organic fertilizer (OF), and bioorganic fertilizer containing B. subtilis (BF). After 30 days of pot experiment, the results showed that BF efficiently improved plant height and biomass (1.20- and 1.93-fold, respectively); as well as significantly increasing soil available potassium and pH value. Using high-throughput sequencing, we examined the bacterial and fungal communities in the soil, and found that their diversity was remarkablely reduced in the BF treatment compared to CK group. A principal coordinate analysis also showed a clear separation of bacterial and fungal communities in the BF and CK groups. After application of B. subtilis bioorganic fertilizer, some beneficial bacteria (such as Bacillus and Ammoniphilus) and fungi (Trichoderma and Mortierella) were enriched. A network analysis indicated that bacteria were the dominant soil microbes and the presence of B. subtilis stimulated the colonization of beneficial microbial communities. In addition, predictive functional profiling demonstrated that the application of bioorganic fertilizer enhanced the function of mineral element metabolism and absorption and increased the relative abundance of saprotrophs. Overall, the application of bioorganic fertilizer effectively changed the soil microflora, improved the soil available potassium and pH value, and boosted the yield of Brassica chinensis L. This work has valuable implications for promoting the safe planting of facility vegetables and the sustainable development of green agriculture.

The potential of Bacillus subtilis and phosphorus in improving the growth of wheat under chromium stress

AIM

Hexavalent chromium (Cr⁺⁶ ) is one of the most toxic heavy metals that have deteriorating effects on the growth and quality of the end product of wheat. Consequently, this research was designed to evaluate the role of Bacillus subtilis and phosphorus fertilizer on wheat facing Cr⁺⁶ stress.

METHODS AND RESULTS

The soil was incubated with Bacillus subtilis and phosphorus fertilizer before sowing. The statistical analysis of the data showed that the co-application of B. subtilis and phosphorus yielded considerably more significant (p < 0.05) results compared with an individual application of the respective treatments. The co-treatment improved the morphological, physiological and biochemical parameters of plants compared with untreated controls. The increase in shoot length, root length, shoot fresh weight and root fresh weight was 38.17%, 29.31%, 47.89% and 45.85%, respectively, compared with untreated stress-facing plants. The application of B. subtilis and phosphorus enhanced osmolytes content (proline 39.98% and sugar 41.30%), relative water content and stability maintenance of proteins (86.65%) and cell membranes (66.66%). Furthermore, augmented production of antioxidants by 67.71% (superoxide dismutase), 95.39% (ascorbate peroxidase) and 60.88% (catalase), respectively, were observed in the Cr⁺⁶ - stressed plants after co-application of B. subtilis and phosphorus.

CONCLUSION

It was observed that the accumulation of Cr⁺⁶ was reduced by 54.24%, 59.19% and 90.26% in the shoot, root and wheat grains, respectively. Thus, the combined application of B. subtilis and phosphorus has the potential to reduce the heavy metal toxicity in crops.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study explored the usefulness of Bacillus subtilis and phosphorus application on wheat in heavy metal stress. It is a step toward the combinatorial use of plant growth-promoting rhizobacteria with nutrients to improve the ecosystems' health.