Effects of Bacillus subtilis and nanohydroxyapatite on the metal accumulation and microbial diversity of rapeseed (Brassica campestris L.) for the remediation of cadmium-contaminated soil

A new strategy for sustainable agricultural development: Meta-analysis of the efficient interaction of plant growth-promoting rhizobacteria with nanoparticles

Nanoparticles (NPs) and plant growth-promoting rhizobacteria (PGPR) are two kinds of additives that have obvious promotion effect on plant growth and development, but the effectiveness and influencing factors of their cooperation remain incompletely understood. Here, we conducted a global meta-analysis of 68 published studies to explore the potential effects of simultaneous exposure to NPs and PGPR on plants and the factors influencing the benefits of their cooperation. The results indicated that either individual or combined applications of PGPR and NPs were effective at promoting plant growth and development, but the advantages of cooperation were more obvious, especially for plants under stress conditions. Our results also illustrated that PGPRs species affected the efficiency of cooperation with NPs, with the Bacillus spp. and Pseudomonas spp. having the most significant positive effects. Exposure to NPs of 7-15 d and foliar application had the most significant effects on plant biomass, photosynthetic capacity and nutrient accumulation. Effects on plant antioxidant systems were associated with NPs type, size, application dose and exposure way, but were not significantly related to exposure duration. Our results emphasize the effectiveness of cooperation between PGPR and NPs, which provides a theoretical basis for the development of nano-biofertilizers (NBFs), and also provides support for the application and promotion of NBFs in agricultural production.

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.

Significance of zinc-solubilizing plant growth-promoting rhizobacterial strains in nutrient acquisition, enhancement of growth, yield, and oil content of canola (Brassica napus L.)

The present study was conducted with the aim to isolate, characterize, and identify the promising zinc-solubilizing rhizobacteria found naturally in the rhizosphere of canola (Brassica napus L.) plants. The study investigated the roles of these strains in nutrient acquisition and assimilation of extracellular molecules such as hormones and secondary metabolites. Ten isolated promising zinc-solubilizing strains (CLS1, CLS2, CLS3, CLS6, CLS8, CLS9, CLS11, CLS12, CLS13, and CLS15) were selected and characterized biochemically. Almost all the tested strains were Gram-positive, could fix nitrogen, and were positive for indole acetic acid, HCN, exopolysaccharides, and siderophore production. These effective zinc-solubilizing strains were identified through 16S rRNA gene sequencing. Based on the amount of solubilized zinc and halo zone diameter, four potent strains (CLS1, CLS2, CLS3, and CLS9) were selected for pot and field evaluation. Among all the identified bacterial genera isolated from the rhizosphere of the same host plant at different sampling sites, Priestia aryabhattai was found most abundant and found at all three sampling sites. The strains Priestia megaterium, Staphylococcus succinus, and Bacillus cereus were found at two different sites. Bacillus subtilis was found at only one site. These strains have a number of plant growth-stimulating characteristics as well as the ability to colonize plant roots successfully. The results indicated that inoculation of all these four zinc-solubilizing tested strains enhanced the plant growth, oil contents, and yield attributes of canola as compared to non-inoculated control with fertilizer levels. Staphylococcus succinus (CLS1) was first reported as a zinc solubilizer and associated with canola. Priestia aryabhattai (CLS2) and Priestia megaterium (CLS9) were found to be the best strains, with the most pronounced beneficial effect on canola growth and yield traits in both pot and field conditions. The site-specific dominance of these strains observed in this study may contribute toward decision-making for the development of specific inocula for canola. Therefore, identification of these strains could help in providing adequate amount of soluble zinc along with enhanced plant growth, yield, and oil content of canola.

Integrated genomics and transcriptomics reveal the extreme heavy metal tolerance and adsorption potentiality of Staphylococcus equorum

In this study, we successfully isolated 11 species of cadmium-tolerant bacterium from Pu-erh rhizosphere soil, of which Staphylococcus equorum PU1 showed the highest cadmium tolerance, with a minimum inhibitory concentration (MIC) value of 500 mg/L. The cadmium removal efficiency of PU1 in 400 mg/L cadmium medium reached 58.7 %. Based on the Nanopore PromethION and Illumina NovaSeq platforms, we successfully obtained the complete PU1 genome with a size of 2,705,540 bp, which encoded 2729 genes. We further detected 82 and 44 indel mutations in the PU1 genome compared with the KS1039 and KM1031 genomes from the database. Transcriptional analysis showed that the expression of 11 genes in PU1 increased with increasing cadmium concentrations (from 0 to 200, then to 400 mg/L), which encoded cadmium resistance, cadmium transport, and mercury resistance genes. In addition, some genes showed differential expression patterns with changes in cadmium concentration, including quinone oxidoreductase-like protein, ferrous iron transport protein, and flavohemoprotein. Gene Ontology (GO) functions, including oxidation reduction process and oxidoreductase activity functions, and KEGG pathways, including glycolysis/gluconeogenesis and biosynthesis of secondary metals, were also considered closely related to the extreme cadmium tolerance of PU1. This study provides novel insight into the cadmium tolerance mechanism of bacteria.

Biofortification Technology for the Remediation of Cadmium-Contaminated Farmland by the Hyperaccumulator Sedum alfredii under Crop Rotation and Relay Cropping Mode

Soil cadmium (Cd) extraction for hyperaccumulators is one of the most important technologies for the remediation of Cd-contaminated farmland soil. However, a phytoremediation model using a single hyperaccumulator cannot guarantee normal agricultural production in contaminated areas. To solve this problem, a combination of efficient remediation and safe production has been developed. Based on two-period field experiments, this study explored the effect of biofortification on soil Cd remediation using the fruit tree Sedum alfredii Hance and oil sunflower crop rotation and relay cropping mode. BioA and BioB treatments could markedly improve the efficiency of Cd extraction and remediation, and the maximum increase in Cd accumulation was 243.29%. When BioB treatment was combined with papaya-S. alfredii and oil sunflower crop rotation and relay cropping mode, the highest soil Cd removal rate in the two periods was 40.84%, whereas the Cd concentration of papaya fruit was lower than safety production standards (0.05 mg/kg). These results demonstrate that biofortification measures can significantly improve the Cd extraction effect of S. alfredii crop rotation and relay cropping restoration modes, which has guiding significance for Cd pollution remediation and safe production in farmland.

Soil bacteria around a derelict tailings pile with different metal pollution gradients: community composition, metal tolerance and influencing factors

Bacteria play a vital role in ecological processes of soil contaminated by heavy metals. Here, soil sampling was carried out around a tailings pile contaminated to different degrees by cadmium (Cd), lead (Pb) and arsenic (As). The bacteria in the soil were cultured, separated and purified on Luria-Bertani medium, and the changes in bacterial communities in soils with different pollution levels were analysed with 16S rRNA sequencing. Bacillus pacificus strain MZ520364 was found to be highly tolerant to Cd, Pb and As, and single-metal and multimetal tolerance experiments were further conducted with this strain. The results obtained from alpha diversity and operational taxonomic unit (OTU) statistical analyses showed a significant difference in bacterial composition among soils with different metal pollution levels, and the highest bacterial diversity was found at the most severely polluted site. Evidence from variance partitioning analysis (VPA) and the Spearman correlation heatmap analysis showed that the leading factors affecting bacterial community composition were cation exchange content (CEC), pH, total Zn, total As, and available As concentrations in soil. Additionally, in the single-metal treatments, B. pacificus MZ520364 could tolerate 600 mg/L Cd²⁺, 1000 mg/L Pb²⁺ or 700 mg/L As³⁺. When Cd, Pb and As coexisted, the best growth of B. pacificus MZ520364 was present at 120 mg/L Cd²⁺, 200 mg/L Pb²⁺ and 150 mg/L As³⁺. The effect of Cd, Pb and As on the growth of the strain followed the order of Cd > As > Pb, and the heavy metal combination showed more toxicity than single metals. In summary, our results revealed the ecological impact of soil physicochemical properties on the diversity and richness of soil bacterial communities and suggested that B. pacificus MZ520364 may be used for the remediation of Cd-Pb-As co-contaminated soil.

Effects of Amendments and Indigenous Microorganisms on the Growth and Cd and Pb Uptake of Coriander (Coriandrum sativum L.) in Heavy Metal-Contaminated Soils

Heavy metal (HM) contamination of soils is a worldwide problem with adverse consequences to the environment and human health. For the safe production of vegetables in contaminated soil, efficient soil amendments need to be applied such as nano-hydroxyapatite (n-HAP) and poly γ-glutamic acid (γ-PGA), which can mitigate heavy metal uptake and enhance crop yield. However, the combined effects of soil amendments and indigenous microorganisms (IMOs) on HMs immobilisation and accumulation by crops have received little attention. We established a pot experiment to investigate the effects of IMOs combined with n-HAP and γ-PGA on coriander (Coriandrum sativum L.) growth and its Cd and Pb uptake in two acidic soils contaminated with HMs. The study demonstrated that applying n-HAP, with and without IMOs, significantly increased shoot dry biomass and reduced plant Cd and Pb uptake and diethylenetriaminepentaacetic acid (DTPA) extractable Cd and Pb concentrations in most cases. However, γ-PGA, with and without IMOs, only reduced soil DTPA-extractable Pb concentrations in slightly contaminated soil with 0.29 mg/kg Cd and 50.9 mg/kg Pb. Regardless of amendments, IMOs independently increased shoot dry biomass and soil DTPA-extractable Cd concentrations in moderately contaminated soil with 1.08 mg/kg Cd and 100.0 mg/kg Pb. A synergistic effect was observed with a combined IMOs and n-HAP treatment, where DTPA-extractable Cd and Pb concentrations decreased in slightly contaminated soil compared with the independent IMOs and n-HAP treatments. The combined treatment of γ-PGA and IMOs substantially increased shoot dry biomass in moderately contaminated soil. These results indicate that solo n-HAP enhanced plant growth and soil Cd and Pb immobilisation, and mitigated Cd and Pb accumulation in shoots. However, the combination of n-HAP and IMOs was optimal for stabilising and reducing HMs' uptake and promoting plant growth in contaminated soil, suggesting its potential for safe crop production.

Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde

The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.

A comprehensive review on nanobiotechnology for bioremediation of heavy metals from wastewater

Removal of contaminants from wastewater is a big concern for the scientific community. Heavy metals are one of the major contaminants present in wastewater. Heavy metals such as Cd²⁺ , Pb²⁺ , Mn²⁺ , and so forth, are highly toxic and pose a serious threat to the environment due to their nonbiodegradable nature. With the advent of nanobiotechnology, heavy metal contaminants can be mitigated with the help of nanomaterials produced by eco-friendly methods. Specially designed bionanomaterials often exhibit properties such as increased shelf life, self-healing nature, adaptability in different environments, and cost-effectiveness, thus showing advantages over nanomaterials produced by physicochemical methods. Due to their high specificity and adsorption capacity, bionanomaterials can remove heavy metals present even in a very low concentration in wastewater. The use of bionanotechnology in their remediation paves a way for environmental sustainability and helps in cost reduction. This paper intends to discuss the nanobiotechnological approach for the remediation of heavy metals from wastewater. Furthermore, the paper also reviews some important nanomaterials and their potential applications in the depollution of heavy-metal contaminated wastewater.

High-throughput sequencing clarifies the spatial structures of microbial communities in cadmium-polluted rice soils

Soil microbial communities are affected by environmental factors. Contamination with heavy metals such as cadmium (Cd) can decrease soil microbial species richness and substantially alter soil microbial species composition. Investigations of the microbial communities in Cd-contaminated soils are necessary to obtain data for soil bioremediation efforts. However, depth-associated variations in microbial community composition and structure in Cd-contaminated paddy soils are not well understood. Here, the effects of various degrees of long-term Cd pollution on soil microorganisms were investigated at different soil depths within the plough layer using 16S rRNA gene amplicon sequencing. We found that, in Cd-polluted soils, microbial communities were more similar between the surface soil and the underlying soil. In addition, microbial community richness and/or diversity were significantly reduced in the Cd-polluted underlying soil as compared with the non-polluted underlying soil. However, species richness in the surface layer was significantly greater in the mildly and severely Cd-polluted soils. The soil microbial communities in the same soil layer differed significantly between the non-polluted and polluted soils. Furthermore, Cd contamination affected the microbial communities of different soil layers differently. Soil pH had a synergistic effect on microbial community abundance and composition. The potential functions of the soil microbiota were mainly related to environmental processing, genetic processing, and metabolic pathways. Notably, our identification of the phyla that were differently abundant among sites with different levels of Cd pollution will provide experimental guidance for further explorations of the effects of Cd on soil microbes in natural environments. Our results not only demonstrate that long-term Cd pollution leads to a marked reduction in microbial richness and diversity in the underlying soil layer, but they also help to clarify how long-term heavy metal contamination affects the soil bacterial community.