Cadmium-tolerant bacteria reduce the uptake of cadmium in rice: potential for microbial bioremediation

Contribution of Cd passivating functional bacterium H27 to tobacco growth under Cd stress

The cadmium (Cd) embedded in tobacco not only affects yield and quality but also harms human health. Microbial remediation has attracted widespread attention due to its low cost and minimal risk of secondary pollution. Therefore, researching microbes capable of inhibiting crop absorption of heavy metals or removing heavy metals from the environment has significant practical implications. This study screened a strain named H27 with a Cd immobilization efficiency of up to 76.60%. Static cultivation experiments showed that immobilization of Cd by H27 is achieved through intracellular absorption, hydroxyl, carboxyl, and phosphate group reactions on the cell wall. The bacterium can also secrete extracellular substances to adsorb Cd and increase the environmental pH, reducing the bioavailability of Cd. H27 reduced the accumulation of Cd in the stems of hydroponically grown tobacco by 55.23% and decreased the expression of three Cd transport genes, HAM2, IRT1, and NRAMP1, in the roots. Additionally, H27 increased the mineralization rate of organic matter, increased the content of humic acid in the soil, promoted the formation of smaller soil particles, and enhanced the adsorption and fixation of Cd by soil components while simultaneously raising the pH of rhizosphere and non-rhizosphere soils in tobacco growth environments. Both hydroponic and potted experiments showed that H27 alleviated the inhibitory effect of Cd on tobacco growth, significantly reducing Cd accumulation in various parts of tobacco and lowering the transfer coefficient of Cd within the tobacco plant. This study aims to effectively reduce the Cd content in tobacco using microbes, mitigate the harm of heavy metals in cigarettes to human health, and provide theoretical and practical basis for the application of microbial techniques to control heavy metal absorption in tobacco.

Stress mitigation mechanism of rice leaf microbiota amid atmospheric deposition of heavy metals

Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.

As(III)-oxidizing and plant growth-promoting bacteria increase the starch biosynthesis-related enzyme activity, 2-AP levels, and grain quality of arsenic-stressed rice plants

BACKGROUND

Grain quality is an important index of rice production, particularly when plants are grown under stress. Arsenic (As) contamination in paddy fields severely affects rice grain yield and quality. Here, the effects of As and combinations of As(III)-oxidizing bacteria (Pseudomonas stutzeri 4.25, 4.27, and 4.44) and plant growth-promoting bacteria (Delftia acidovorans KKU2500-12 and Cupriavidus taiwanensis KKU2500-3) on enzymes related to starch accumulation in grains and the grain quality of Khao Dawk Mali 105 rice cultivated in As-contaminated soil under greenhouse conditions were investigated.

RESULTS

Arsenic affected the activities of starch biosynthesis-related enzymes, and decreases of up to 76.27%, 71.53%, 49.74%, 73.39%, and 47.46% in AGPase, SSS, GBSS, SBE, and SDBE activities, respectively, and 9.42-61.07% in starch accumulation in grains were detected after growth in As-contaminated soil. However, the KKU2500-3/4.25 and KKU2500-3/4.44 combinations yielded the greatest enzyme activities in grains, and compared with the results observed in uninoculated seedlings, increases in starch accumulation of up to 51.16% and 23.81% were found in the inoculated seedlings after growth in medium- and high-As-contaminated soils, at 10-17 and 10-24 days after anthesis, respectively. The bacteria increased the 2-AP content in rice under As stress, possibly via the induction of proline, a 2-AP substrate. Bacterium-inoculated rice had significantly greater 2-AP levels than uninoculated rice, and 2.16-9.93% and 26.57-42.04% increases were detected in rice plants grown in medium- and high-As-contaminated soils, respectively.

CONCLUSIONS

Arsenic toxicity can be mitigated in rice growing under greenhouse conditions by maintaining starch biosynthesis, accumulating amylose, and increasing 2-AP content. The effectiveness of these bacteria should be validated in paddy fields; hence, safe rice grains with a good starch content and aroma could be produced.

Calcium polypeptide mitigates Cd toxicity in rice via reducing oxidative stress and regulating pectin modification

KEY MESSAGE

Calcium polypeptide plays a key role during cadmium stress responses in rice, which is involved in increasing peroxidase activity, modulating pectin methylesterase activity, and regulating cell wall by reducing malondialdehyde content. Cadmium (Cd) contamination threatens agriculture and human health globally, emphasizing the need for sustainable methods to reduce cadmium toxicity in crops. Calcium polypeptide (CaP) is a highly water-soluble small molecular peptide acknowledged for its potential as an organic fertilizer in promoting plant growth. However, it is still unknown whether CaP has effects on mitigating Cd toxicity. Here, we investigated the effect of CaP application on the ability to tolerate toxic Cd in rice. We evaluated the impact of CaP on rice seedlings under varying Cd stress conditions and investigated the effect mechanism of CaP mitigating Cd toxicity by Fourier transform infrared spectroscopy (FTIR), fluorescent probe dye, immunofluorescent labeling, and biochemical analysis. We found a notable alleviation of Cd toxicity by reduced malondialdehyde content and increased peroxidase activity. In addition, our findings reveal that CaP induces structural alterations in the root cell wall by modulating pectin methylesterase activity. Altogether, our results confirm that CaP not only promoted biomass accumulation but also reduced Cd concentration in rice. This study contributes valuable insights to sustainable strategies for addressing Cd contamination in agricultural ecosystems.

Microbial mechanisms in nitrogen fertilization: Modulating the re-mobilization of clay mineral-bound cadmium in agricultural soils

Soil cadmium (Cd) can affect crop growth and food safety, and through the enrichment in the food chain, it ultimately poses a risk to human health. Reducing the re-mobilization of Cd caused by the release of protons and acids by crops and microorganisms after stabilization is one of the significant technical challenges in agricultural activities. This study aimed to investigate the re-mobilization of stabilized Cd within the clay mineral-bound fraction of soil and its subsequent accumulation in crops utilizing nitrogen ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3--N), at 60 and 120 mg kg-1. Furthermore, the study harvested root exudates at various growth stages to assess their direct influence on the re-mobilization of stabilized Cd and to evaluate the indirect effects mediated by soil microorganisms. The results revealed that, in contrast to the NO3--N treatment, the NH4+-N treatment significantly enhanced the conversion of clay mineral-bound Cd in the soil to NH4NO3-extractable Cd. It also amplified the accumulation of Cd in edible amaranth, with concentrations in roots and shoots rising from 1.7-6.0 mg kg-1 to 4.3-9.8 mg kg-1. The introduction of NH4+-N caused a decrease in the pH value of the rhizosphere soil and stimulated the production and secretion organic and amino acids, such as oxalic acid, lactic acid, stearic acid, succinic acid, and l-serine, from the crop roots. Furthermore, compared to NO3--N, the combined interaction of root exudates with NH4+-N has a more pronounced impact on the abundance of microbial genes associated with glycolysis pathway and tricarboxylic acid cycle, such as pkfA, pfkB, sucB, sucC, and sucD. The effects of NH4+-N on crops and microorganisms ultimately result in a significant increase in the re-mobilization of stabilized Cd. However, the simulated experiments showed that microorganisms only contribute to 3.8-6.6 % of the re-mobilization of clay mineral-bound Cd in soil. Therefore, the fundamental strategy to inhibit the re-mobilization of stabilized Cd in vegetable cultivation involves the regulation of proton and organic acid secretion by crops.

Endophytic bacteria for Cd remediation in rice: Unraveling the Cd tolerance mechanisms of Cupriavidus metallidurans CML2

The utility of endophytic bacteria in Cadmium (Cd) remediation has gained significant attention due to their ability to alleviate metal-induced stress and enhance plant growth. Here, we investigate C. metallidurans CML2, an endophytic bacterial strain prevalent in rice, showing resilience against 2400 mg/L of Cd(II). We conducted an in-depth integrated morphological and transcriptomic analysis illustrating the multifarious mechanisms CML2 employs to combat Cd, including the formation of biofilm and CdO nanoparticles, upregulation of genes involved in periplasmic immobilization, and the utilization of RND efflux pumps to extract excess Cd ions. Beyond Cd, CML2 exhibited robust tolerance to an array of heavy metals, including Mn2+, Se4+, Ni2+, Cu2+, and Hg2+, demonstrating effective Cd(II) removal capacity. Furthermore, CML2 has exhibited plant growth-promoting properties through the production of indole-3-acetic acid (IAA) at 0.93 mg/L, soluble phosphorus compounds at 1.11 mg/L, and siderophores at 22.67%. Supportively, pot experiments indicated an increase in root lengths and a decrease in Cd bioaccumulation in rice seedlings inoculated with CML2, consequently reducing Cd translocation rates from 43% to 31%. These findings not only contribute to the understanding of Cd resistance mechanisms in C. metallidurans, but also underscore CML2's promising application in Cd remediation within rice farming ecosystems.

Factors influencing cadmium accumulation in plants after inoculation with rhizobacteria: A meta-analysis

Rhizobacteria have the potential to enhance phytoremediation by generating substances that stimulate plant development and influence the effectiveness of cadmium (Cd) remediation by adjusting Cd availability via metal solubilization. Furthermore, rhizobacterial inoculation affects plants' metal tolerance and uptake by controlling the expression of several metal transporters, channels, and metal chelator genes. A meta-analysis was conducted to quantitatively assess the effects of rhizobacteria on Cd accumulation in plants using 207 individual observations from 47 articles. This meta-analysis showed an average Cd concentration increase of 8.09 % in plant cells under rhizobacteria treatment. The effects of different plant-microbial interactions on the bioaccumulation of Cd in plants varied. Selecting the proper rhizobacteria-plant association is essential to affect Cd buildup in plant roots and shoots. A more extended planting period (>30 days) and a suitable soil pH (<6, 7-8) would aid in the phytoextraction of Cd from the soil. This study comprehensively and quantitatively investigated the effects of plants, rhizobacteria, soil pH, planting period, experimental sites, and plant organs on plant Cd accumulation. According to the analysis of explanatory factors, plant species, planting period, soil pH, and rhizobacteria species have a more decisive influence on Cd accumulation than other factors. The results provide information for future research on the successful remediation of soils contaminated with Cd. More investigations are required to elucidate the intricate interactions between plant roots and microorganisms.

An Overview of Bacteria-Mediated Heavy Metal Bioremediation Strategies

Contamination-free groundwater is considered a good source of potable water. Even in the twenty-first century, over 90 percent of the population is reliant on groundwater resources for their lives. Groundwater influences the economical state, industrial development, ecological system, and agricultural and global health conditions worldwide. However, different natural and artificial processes are gradually polluting groundwater and drinking water systems throughout the world. Toxic metalloids are one of the major sources that pollute the water system. In this review work, we have collected and analyzed information on metal-resistant bacteria along with their genetic information and remediation mechanisms of twenty different metal ions [arsenic (As), mercury (Hg), lead (Pb), chromium (Cr), iron (Fe), copper (Cu), cadmium (Cd), palladium (Pd), zinc (Zn), cobalt (Co), antimony (Sb), gold (Au), silver (Ag), platinum (Pt), selenium (Se), manganese (Mn), molybdenum (Mo), nickel (Ni), tungsten (W), and uranium (U)]. We have surveyed the scientific information available on bacteria-mediated bioremediation of various metals and presented the data with responsible genes and proteins that contribute to bioremediation, bioaccumulation, and biosorption mechanisms. Knowledge of the genes responsible and self-defense mechanisms of diverse metal-resistance bacteria would help us to engineer processes involving multi-metal-resistant bacteria that may reduce metal toxicity in the environment.

Genotypic variation in grain cadmium concentration in wheat: Insights into soil pollution, agronomic characteristics, and rhizosphere microbial communities

Soil cadmium (Cd) pollution poses a serious threat to both the productivity and quality of wheat. This study aimed to investigate the genotypic variation in grain Cd concentration in wheat through field and pot experiments. Among 273 wheat genotypes, a significant genotypic difference was found in grain Cd concentration, ranging from 0.01 to 0.14 mg kg-1. Two contrasting genotypes, X321 (a low grain Cd accumulator) and X128 (a high grain Cd accumulator), were selected for pot experiments. X321 exhibited a 17.9% greater reduction in yield and a 10.2% lower shoot-to-grain Cd translocation rate than X128 under Cd treatment. Grain Cd content showed a positive correlation with soil available Cd content and a negative correlation with Cu content. Soil catalase activity significantly decreased in X128 under Cd stress, whereas no difference was found in X321. The grains of X321 exhibited a more compact spatial distribution of starch grains and protein matrix than those of X128. Moreover, the size of A-type starch in X128 was larger than in X321. Meanwhile, X128 contained much B-type starch, with some surface pits observed on A-type granules under Cd stress. Cd treatment increased the abundance of rhizosphere microorganism communities, with Ellin6067 and Ramlibacter being enriched in X128 under Cd treatment, which might facilitate Cd uptake. The accumulation of Cd in grains demonstrated a strong positive correlation with the rhizosphere bacterial diversity (correlation coefficient = 0.78). These findings provide new insights into the basis of grain Cd accumulation in wheat and have potential implications for developing new verities with low Cd accumulation to ensure food safety and minimize human exposure.

Cadmium-Tolerant Bacterium Strain Cdb8-1 Contributed to the Remediation of Cadmium Pollution through Increasing the Growth and Cadmium Uptake of Chinese Milk Vetch (Astragalus sinicus L.) in Cadmium-Polluted Soils

Cadmium (Cd) pollution has attracted global attention because it not only jeopardizes soil microbial ecology and crop production, but also threatens human health. As of now, microbe-assisted phytoremediation has proven to be a promising approach for the revegetation of Cd-contaminated soil. Therefore, it is important to find such tolerant microorganisms. In the present study, we inoculated a bacteria strain tolerant to Cd, Cdb8-1, to Cd-contaminated soils and then explored the effects of Cdb8-1 inoculation on the performance of the Chinese milk vetch. The results showed plant height, root length, and fresh and dry weight of Chinese milk vetch grown in Cdb8-1-inoculated soils increased compared to the non-inoculated control group. The inoculation of Cd-contaminated soils with Cdb8-1 also enhanced their antioxidant defense system and decreased the H2O2 and malondialdehyde (MDA) contents, which alleviated the phytotoxicity of Cd. The inoculation of Cdb8-1 in Cd-contaminated soils attenuated the contents of total and available Cd in the soil and augmented the BCF and TF of Chinese milk vetch, indicating that the combined application of Cd-tolerant bacteria Cdb8-1 and Chinese milk vetch is a potential solution to Cd-contaminated soils.

Full-Length Transcriptome Sequencing Analysis and Characterization of WRKY Transcription Factors Responsive to Cadmium Stress in Arabis paniculata

Arabis paniculata is a newly discovered hyperaccumulator known for its ability to accumulate multiple metals. WRKY proteins play a significant role in plant responses to various stresses, including cadmium (Cd) stress. However, there is limited research on the molecular biology of Arabis paniculata, especially regarding the WRKY family. In this study, we conducted third-generation sequencing for functional annotation and structural analysis of Arabis paniculata. We obtained 41,196 high-quality isoforms from the full-length transcriptome, with an average length of 1043 bp. A total of 26,670 genes were predicted against NR, Swissprot, KOG, and KEGG databases. Functional comparison using the KOG database revealed excellent annotation in 25 functional categories, with general function prediction (1822 items) being the most predominant. MISA analysis identified 12,593 SSR loci, with single nucleotide repeats being the largest category (44.83% of the total). Moreover, our predictions provide insights into 20,022 coding sequences (CDS), 811 transcription factors, and 17,963 LncRNAs. In total, 34 WRKY gene sequences were identified in Arabis paniculata. Bioinformatics analysis revealed diverse numbers of amino acids in these WRKYs (113 to 545 aa), and a conserved WRKYGQK sequence within the N-terminus of the WRKY protein. Furthermore, all WRKYs were found to be localized in the nucleus. Phylogenetic analysis classified the WRKY genes into three categories: I (14 members), II (17 members), and III (3 members). Category II was subsequently divided into four sub-categories: II-a (8 members), II-b (1 member), II-c (1 member), and II-d (7 members). Our quantitative real-time polymerase chain reaction (qRT-PCR) experiments revealed that ApWRKY23 and ApWRKY34 exhibited the highest expression levels at the 24-h time point, suggesting their potential role as the candidate genes for Cd stress response. These findings contribute to our understanding of the genomic information of Arabis paniculata and provide a basis for the analysis of its genetic diversity. Additionally, this study paves the way for a comprehensive exploration of the molecular mechanisms underlying the WRKY genes in Arabis paniculata under Cd stress conditions.

Risk assessment of toxic and hazardous metals in paddy agroecosystem by biochar-for bio-membrane applications

Toxic and carcinogenic metal (loid)s, such arsenic (As) and cadmium (Cd), found in contaminated paddy soils pose a serious danger to environmental sustainability. Their geochemical activities are complex, making it difficult to manage their contamination. Rice grown in Cd and As-polluted soils ends up in people's bellies, where it can cause cancer, anemia, and the deadly itai sickness. Solving this issue calls for research into eco-friendly and cost-effective remediation technology to lower rice's As and Cd levels. This research delves deeply into the origins of As and Cd in paddy soils, as well as their mobility, bioavailability, and uptake mechanisms by rice plants. It also examines the current methods and reactors used to lower As and Cd contamination in rice. Iron-modified biochar (Fe-BC) is a promising technology for reducing As and Cd toxicity in rice, improving soil health, and boosting rice's nutritional value. Biochar's physiochemical characteristics are enhanced by the addition of iron, making it a potent adsorbent for As and Cd ions. In conclusion, Fe-BC's biomembrane properties make them an attractive option for remediating As- and Cd-contaminated paddy soils. More efficient mitigation measures, including the use of biomembrane technology, can be developed when sustainable agriculture practices are combined with these technologies.

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.

Alleviation of Cadmium Toxicity in Thai Rice Cultivar (PSL2) Using Biofertilizer Containing Indigenous Cadmium-Resistant Microbial Consortia

Biofertilizer as an amendment has growing awareness. Little attention has been paid to bioremediation potential of indigenous heavy-metal-resistant microbes, especially when isolated from long-term polluted soil, as a bioinoculant in biofertilizers. Biofertilizers are a type of versatile nutrient provider and soil conditioner that is cost-competitive and highly efficient with nondisruptive detoxifying capability. Herein, we investigated the effect of biofertilizers containing indigenous cadmium (Cd)-resistant microbial consortia on rice growth and physiological response. The Thai rice cultivar PSL2 (Oryza sativa L.) was grown in Cd-enriched soils amended with 3% biofertilizer. The composition of the biofertilizers' bacterial community at different taxonomic levels was explored using 16S rRNA gene Illumina MiSeq sequencing. Upon Cd stress, the test biofertilizer had maximum mitigating effects as shown by modulating photosynthetic pigment, MDA and proline content and enzymatic antioxidants, thereby allowing increased shoot and root biomass (46% and 53%, respectively) and reduced grain Cd content, as compared to the control. These phenomena might be attributed to increased soil pH and organic matter, as well as enriched beneficial detoxifiers, i.e., Bacteroidetes, Firmicutes and Proteobacteria, in the biofertilizers. The test biofertilizer was effective in alleviating Cd stress by improving soil biophysicochemical traits to limit Cd bioavailability, along with adjusting physiological traits such as antioxidative defense. This study first demonstrated that incorporating biofertilizer derived from indigenous Cd-resistant microbes could restrict Cd contents and consequently enhance plant growth and tolerance in polluted soil.

Community-based mechanisms underlying the root cadmium uptake regulated by Cd-tolerant strains in rice (Oryza sativa. L)

In recent years, the problem of Cd pollution in paddy fields has become more and more serious, which seriously threatens the safe production of food crops and human health. Using microorganisms to reduce cadmium pollution in rice fields is a green, safe and efficient method, the complicated interactions between the microbes in rice roots throughout the process of cadmium absorption by rice roots are poorly understood. In this investigation, a hydroponic pot experiment was used to examine the effects of bacteria R3 (Herbaspirillum sp) and T4 (Bacillus cereus) on cadmium uptake and the endophytic bacterial community in rice roots. The results showed that compared with CK (Uninoculated bacterial liquid), the two strains had significant inhibitory or promotive effects on cadmium uptake in rice plant, respectively. Among them, the decrease of cadmium content in rice plants by R3 strain reached 78.57-79.39%, and the increase of cadmium content in rice plants by T4 strain reached 140.49-158.19%. Further investigation showed that the cadmium content and root cadmium enrichment coefficient of rice plants were significantly negatively correlated with the relative abundances of Burkholderia and Acidovorax, and significantly positively correlated with the relative abundances of Achromobacter, Agromyces and Acidocella. Moreover, a more complex network of microbes in rice roots inhibited rice plants from absorbing cadmium. These results suggest that cadmium uptake by rice plants is closely related to the endophytic bacterial community of roots. This study provides a reference scheme for the safe production of crops in cadmium contaminated paddies and lays a solid theoretical foundation for subsequent field applications.

Ability of Cupriavidus necator H16 to resist, bioremove, and accumulate some hazardous metal ions in water

Bacterial biomasses are suitable and inexpensive biosorbents for the removal of metal ions. The Gram-negative betaproteobacterium Cupriavidus necator H16 is found in soil and freshwater environments. In this study, C. necator H16 was used to remove chromium (Cr), arsenic (As), aluminum (Al), and cadmium (Cd) ions from water. Minimum inhibition concentration (MIC) values of C. necator to Cr, As, Al, and Cd were found as 76, 69, 341, and 275 mg/L, respectively. The highest rates of Cr, As, Al, and Cd bioremoval were 45, 60, 54, and 78%, respectively. pH levels between 6.0 and 8.0 and an average temperature of 30 °C were optimum for the most efficient bioremoval. Scanning electron microscopy (SEM) images of Cd-treated cells showed that the morphology of the cells was significantly impaired compared to the control. Shifts in the Fourier transform infrared spectroscopy analysis (FTIR) spectra of the Cd-treated cell walls also confirmed the presence of active groups. As a result, it can be said that C. necator H16 has a moderate bioremoval efficiency for Cr, As, and Al and a high bioremoval efficiency for Cd.

Extracellular vesicles as a strategy for cadmium secretion in bacteria SH225

Cadmium (Cd), as one of the most carcinogenic substances, poses a great threat to human health. With the development of microbial remediation technology, the necessity for urgent research into the mechanism of Cd toxicity to bacteria has arisen. In this study, a highly Cd-tolerant strain (up to 225 mg/L) was isolated and purified from Cd-contaminated soil, which was identified by 16S rRNA as a strain of Stenotrophomonas sp., thus manually designated as SH225. By testing OD₆₀₀ of the strain, we indicated that Cd concentrations below 100 mg/L had no discernible impact on the biomass of SH225. When the Cd concentration was over 100 mg/L, the cell growth was significantly inhibited, while the number of extracellular vesicles (EVs) was greatly elevated. After extraction, cell-secreted EVs were confirmed to contain large amounts of Cd cations, highlighting the crucial function of EVs in the Cd detoxification of SH225. Meanwhile, the TCA cycle was vastly enhanced, suggesting that the cells provided adequate energy supply for EVs transport. Thus, these findings emphasized the crucial role played by vesicles and TCA cycle in Cd detoxification.

Isolation and identification of the molybdenum-resistant strain Raoultella ornithinolytica A1 and its effect on MoO42- in the environment

The mining and leakage of molybdenum (Mo) can cause environmental contamination which has not been realized until recently. Bacteria that can mitigate Mo-contamination was enriched and isolated. The low temperature and different pH conditions were considered to analysis its feasibility in Northern China which suffers from a long time of low temperatures every year. The result showed that the removal rate of MoO₄^2- by Raoultella ornithinolytica A1 reached 30.46% at 25 °C and pH 7.0 in Luria-Bertani medium (LB). Meanwhile, A1 also showed some efficiency in the reduction of MoO₄^2- in low phosphate molybdate medium (LPM), which reached optimum at the MoO₄^2- concentration of 10 mM. The results of FTIR indicated that the cell wall performed an essential role in the MoO₄^2- removal process, which was illustrated by the distribution of Mo in A1 (Mo bound to cell wall accounted for 92.29% of the total MoO₄^2- removed). In addition, low temperature (10 °C) effect the removal rate of MoO₄^2- by - 8.38 to 11.66%, indicating the potential for the in-situ microbial remediation of Mo-contaminated environments in low temperature areas.

Low Cd-accumulating rice grain production through inoculation of germinating rice seeds with a plant growth-promoting endophytic bacterium

This study investigated the effects of the plant growth-promoting endophytic bacterium Cupriavidus taiwanensis KKU2500-3 on the growth of KDML105 rice plants and cadmium (Cd) accumulation in grains. The rice plants were cultivated in soils with 20 and 50 ppm Cd under greenhouse conditions for two consecutive years. At both levels, Cd reduced rice growth and development. Under Cd stress, KKU2500-3 colonized the root surface and interior of rice plants at the early growth stage, and this colonization remained until the late stage. The colonized bacteria increased the pigment contents but reduced the root-to-aboveground translocation of Cd. In soil with 20 ppm Cd, the phytochelatin content of the bacteria-inoculated rice was lower (32.3-89.3%) than that of uninoculated rice. In soil with 50 ppm Cd, the bacteria-inoculated rice exhibited higher glutathione reductase (5-63%) and proline (5-115%) levels, a higher reduced glutathione (GSH)/0.5 oxidized glutathione (GSSG) ratio (4-212%) and decreased lipid peroxidation (1-19%) compared with uninoculated rice. The root-to-grain translocation factor of inoculated rice in soil with 50 ppm Cd was significantly lower than that of inoculated rice in soil with 20 ppm Cd, and this finding was consistent with the 38.6% and 75.1% reductions in Cd accumulation observed in grains from soils with 20 and 50 ppm Cd, respectively. The Cd content of KDML105 grains grown in soil with 50 ppm Cd was 0.36 ppm, which is below the Codex standard for polished rice (0.4 ppm). The levels of available P, Zn, and SO₄^2- also affect Cd availability in soil, and colonized KKU2500-3 showed varying responses to different Cd levels. Thus, bacterial inoculation, the Cd level and soil properties play important roles in Cd accumulation in KDML105 rice grains. The role of C. taiwanensis KKU2500-3 on the production of low-Cd-accumulating rice in paddy fields contaminated with a range of Cd levels should be further investigated.

A Coculture of Enterobacter and Comamonas Species Reduces Cadmium Accumulation in Rice

The accumulation of cadmium (Cd) in plants is strongly impacted by soil microbes, but its mechanism remains poorly understood. Here, we report the mechanism of reduced Cd accumulation in rice by coculture of Enterobacter and Comamonas species. In pot experiments, inoculation with the coculture decreased Cd content in rice grain and increased the amount of nonbioavailable Cd in Cd-spiked soils. Fluorescence in situ hybridization and scanning electron microscopy detection showed that the coculture colonized in the rhizosphere and rice root vascular tissue and intercellular space. Soil metagenomics data showed that the coculture increased the abundance of sulfate reduction and biofilm formation genes and related bacterial species. Moreover, the coculture increased the content of organic matter, available nitrogen, and potassium and increased the activities of arylsulfatase, β-galactosidase, phenoloxidase, arylamidase, urease, dehydrogenase, and peroxidase in soils. In subsequent rice transcriptomics assays, we found that the inoculation with coculture activated a hypersensitive response, defense-related induction, and mitogen-activated protein kinase signaling pathway in rice. Heterologous protein expression in yeast confirmed the function of four Cd-binding proteins (HIP28-1, HIP28-4, BCP2, and CID8), a Cd efflux protein (BCP1), and three Cd uptake proteins (COPT4, NRAM5, and HKT6) in rice. Succinic acid and phenylalanine were subsequently proved to inhibit rice divalent Cd [Cd(II)] uptake and activate Cd(II) efflux in rice roots. Thus, we propose a model that the coculture protects rice against Cd stress via Cd immobilization in soils and reducing Cd uptake in rice. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

A cadmium-tolerant endophytic bacterium reduces oxidative stress and Cd uptake in KDML105 rice seedlings by inducing glutathione reductase-related activity and increasing the proline content

The effect of the endophytic Cupriavidus taiwanensis KKU2500-3 on the Cd toxicity of KDML105 rice seedlings was investigated in a 10 μM CdCl2 hydroponic system. As demonstrated after bacterial inoculation of germinating rice seeds, KKU2500-3 colonized all rice plant parts. In RB (Rice + KKU2500-3) and RBC (Rice + KKU2500-3+Cd), KKU2500-3 effectively colonized and was detected at a markedly higher number in the root surface and interior than in shoots and leaves. The activities of antioxidant enzymes ascorbate peroxidase (APOX), glutathione reductase (GR), and superoxide dismutase (SOD) and the proline content in inoculated rice were higher in roots and aboveground tissues. RBC exhibited a higher reduced-to-oxidized glutathione ratio in roots and leaves (3-55%) but a lower malondialdehyde content (8-78%). Phytochelatins (PCs) were detected in all rice tissues, but their levels in RBC were 13-70% lower than those in RC (Rice + Cd), demonstrating that the induction of PCs in rice was unrelated to KKU2500-3. The Cd levels in roots and shoots were lower in RBC than RC, and the root-to-shoot Cd translocation factor was 0.6-62.2% lower. At 30 DAT, the Cd levels in RBC roots and shoots were 30.2% and 73.7% lower, respectively, than those in RC. Colonized KKU2500-3 activated GR and increased the proline content to overcome rice Cd toxicity. These effects may trap Cd in plant cells and reduce its translocation. Hence, KKU2500-3 synergistically interacts with rice to detoxify Cd at early growth stages, and KDML105 rice grains with low Cd accumulation could be produced if this interaction is maintained until late growth stages.

Insights on strain 115 plant growth-promoting bacteria traits and its contribution in lead stress alleviation in pea (Pisum sativum L.) plants

The present study aims to characterize the plant growth-promoting bacterial traits of Bacillus simplex (strain 115). This bacterium was inoculated in hydroponically conditions to improve pea (Pisum sativum L.) growth submitted to lead (Pb) toxicity. Root nodulation system was developed enough in 23-day-old plants attesting the interaction between the two organisms. In addition to its phosphate solubilization and siderophore production traits that reached 303.8 μg P mL-1 and 49.6 psu respectively, the Bacillus strain 115 exhibited Pb bio-sorption ability. Inoculation of Pb-stressed pea with strain 115 showed roots and shoots biomass recovery (+ 70% and + 61%, respectively). Similarly, water and protein contents were increased in Pb-treated plants after bacterial inoculation. In the presence of strain 115, Pb relative toxicity level decreased (- 39.3% compared to Pb stress only). Moreover, catalase and superoxide dismutase activities were upregulated in Pb-exposed plants (+ 56% and + 51%, respectively). After inoculation with strain 115, catalase and superoxide dismutase activities were restored by - 38% and - 44% respectively. Simultaneously, oxidant stress indicator (H2O2 and 4-hydroxynonenal) and osmo-regulators (proline and glycine-betaine) contents as well as lipoxygenase activity decreased significantly in Pb-treated plants after Bacillus strain's inoculation. Taken together, the results give some evidences for the plant growth-promoting capacity of strain 115 in helping alleviation of Pb stress.

Responses to arsenic stress of rice varieties coinoculated with the heavy metal-resistant and rice growth-promoting bacteria Pseudomonas stutzeri and Cupriavidus taiwanensis

Arsenic (As)-contaminated rice paddy fields are spreading globally, and thus, rice grains with low As accumulation at a safe level for consumption is profoundly needed. Rice is highly susceptible to As accumulation, and the responses to As vary among rice varieties. Here, combinations of the As^III-oxidizing bacteria Pseudomonas stutzeri strains 4.25, 4.27, or 4.44 and Cupriavidus taiwanensis KKU2500-3 were investigated with respect to their responses to As toxicity and rice growth promotion during the early growth stage. All bacterial strains enhanced antioxidant enzyme activities, including SOD, CAT, APX, GPX, and GR, under As stress in vitro. Uninoculated and coinoculated rice seedlings of three rice varieties (KDML105, RD6, RD10) were cultivated in hydroponic solution without and with a combination of toxic As^III and less toxic As^V for 30 days. Compared with uninoculated seedlings, the inoculated seedlings showed higher growth parameters and lower As contents in roots, shoots and throughout the plants. The bioconcentration factor (BCF) and translocation factor were reduced in inoculated seedlings. The effective response of rice to As toxicity influenced by bacteria was highest in KDML105, followed by RD6 and RD10. The root sulfide content was correlated with As accumulation in roots, shoots, and total seedlings and the BCFs. P. stutzeri 4.44 and C. taiwanensis KKU2500-3 were the most promising combinations for application in KDML105 cultivation under As-contaminated conditions. Understanding the basic response of rice coinoculated with effective bacteria at the early stage will provide guidelines for rice cultivation under As conditions at other scales.

Biochar amendment reduces cadmium uptake by stimulating cadmium-resistant PGPR in tomato rhizosphere

Biochar amendment in the soil can exert a positive effect in reducing heavy metal toxicity in plants. However, it remains unclear the extent to which this effect is associated with the modulation of plant growth-promoting rhizobacteria (PGPR). Here, we initially conducted a pot experiment using tomato (Solanum lycopersicum L.) as a model plant grown in soil spiked with cadmium. First, we found biochar amendment to result in reduced cadmium uptake in tomato plants and trackable changes in the tomato rhizosphere microbiome. Then, a rhizosphere transplant experiment validated the importance of this microbiome modulation for cadmium-toxicity amelioration. Sequence-based analyses targeted the isolation of representative isolates of PGPR, including Bacillus and Flavisolibacter spp. that displayed in vitro cadmium tolerance and biosorption capabilities (in addition to abilities to solubilize phosphate and produce indole acetic acid). Last, we performed a soil inoculation experiment and confirmed the effectiveness of these isolates in reducing cadmium toxicity in tomato plants. Besides, we found the inoculation of these taxa as single inoculant and in combination to result in increased activities of specific antioxidant enzymes in tomato tissues. Taken together, this study revealed the ecological and physiological mechanisms by which biochar amendment indirectly alleviate cadmium toxicity in tomato plants, in this case, via the modulation and activity of specific PGPR populations. This study provides new insights into strategies able to promote beneficial PGPR in the rhizosphere with potential application to ameliorate heavy metal toxicity in plants.

Metarhizium robertsii as a promising microbial agent for rice in situ cadmium reduction and plant growth promotion

The toxic chemical element cadmium (Cd) in paddy fields triggered increasing problems of growth inhibition and food security in rice consistently. In this study, we found Metarhizium robertsii, which is widely used as a bioinsecticide and biofertilizer in agriculture and recently found to be resistant to Cd, developed intraradical and extraradical symbiotic hyphae in rice seedlings, and successfully colonized in the rice rhizosphere soil to more than 10³ CFUs g^-1 soil at harvesting. M. robertsii colonization significantly reduced Cd accumulations in both hydroponically cultured seedlings and the matured rice cultured in Cd contaminated potting soil (2 ppm). Notably, Cd accumulation reduction of the roots, stems, leaves, husks and grains of the matured rice induced by the fungus were 44.3%, 32.1%, 35.3%, 31.9% and 24.7%, respectively. It was caused by the M. robertsii-induced suppression of Cd intake transporter gene osNramp5 in the rice roots, and the chemical stabilizing of Cd to the residual fraction in the rhizosphere soil. In addition, the colonization of M. robertsii significantly promoted the growth characters and the photosynthesis of the rice plants. This is achieved by the increase of endogenous hormone levels of indole-3-acetic, gibberellin A₃ and brassinolide induced by M. robertsii. Furthermore, the fungus enhanced the antioxidative capacities via increasing enzyme activities of catalase, peroxidase and the production of glutathione, ascorbic acid, proline in the rice plants. Our work provides theoretical basis for expanding the use of M. robertsii as in situ Cd accumulation reduction and detoxification agents for rice in contaminated paddy fields.

Tolerance and Cadmium (Cd) Immobilization by Native Bacteria Isolated in Cocoa Soils with Increased Metal Content

Twelve cadmium native bacteria previously isolated in soils of cocoa farms located in the western Colombian Andes (Santander), and tolerant to 2500 µM CdCl2 (120 mg Cd/L), were chosen in order to test their tolerance and Cd immobilization using liquid culture medium (Nutritive broth) at different concentrations of heavy metals. Furthermore, in the greenhouse experiments, the strains Exiguobacterium sp. (11-4A), Klebsiella variicola sp. (18-4B), and Enterobacter sp. (29-4B) were applied in combined treatments using CCN51 cacao genotype seeds grown in soil with different concentrations of Cd. All bacterial strains’ cell morphologies were deformed in TEM pictures, which also identified six strain interactions with biosorption and four strain capacities for bioaccumulation; FT-IR suggested that the amide, carbonyl, hydroxyl, ethyl, and phosphate groups on the bacteria biomass were the main Cd binding sites. In the pot experiments, the concentration of Cd was distributed throughout the cacao plant, but certain degrees of immobilization of Cd can occur in soil to prevent an increase in this level in roots with the presence of Klebsiella sp.

Cadmium-Tolerant Bacteria in Cacao Farms from Antioquia, Colombia: Isolation, Characterization and Potential Use to Mitigate Cadmium Contamination

Bioremediation of farm soil is a technique that merits in-depth research. There are few studies related to the use of bioremediation to reduce cadmium (Cd) availability in soils used for cacao production. This study investigates (1) field bioprospection and strain characterization using techniques including isothermal microcalorimetry to select a group of cadmium-tolerant bacteria (CdtB) for potential use as bioremediators of cacao soils and (2) the application of bacterial inoculum to compare the immobilization of Cd under field conditions. Bioprospection was carried out in four cacao farms from the Antioquia district in Colombia. Culturable CdtB strains were isolated using CdCl2 as a Cd source and identified using molecular techniques. The metabolic characterization of Cd immobilization was carried out using isothermal microcalorimetry with CdCl2 amendments. Five cadmium-tolerant bacteria were isolated and characterized as Bacillus spp. The strain CdtB14 showed better growth and Cd immobilization ability (estimated through heat ratios) than any strain isolated thus far, suggesting potential for future use in bioproduct development. Furthermore, the application of two previously characterized CdtB strains with zeolite powder was performed in the same farms where the bioprospection process was carried out. The application of the preformulated inoculum resulted in a decrease of 0.30 + 0.1 mg kg−1 of soil Cd in two out of the four assessed farms. The field results are preliminary and require data on the change in Cd in cacao beans to understand what this result means for Cd mitigation. This study is the first to combine bioprospecting and the performance of CdtB in laboratory and field experiments in cacao farms and shows the potential of bioremediation to mitigate Cd contamination in cacao.

Effective immobilization of heavy metals via reactive barrier by rhizosphere bacteria and their biofilms

As the portal of plants, rhizosphere microorganisms play an essential role in controlling the species, transformation, and bioavailability of heavy metals, yet the potential passivation mechanism is still unclear. In this study, two heavy metal resistant and growth-promoting rhizosphere bacteria were screened, and their mechanisms in dealing with external stress and immobilizing heavy metal were explored. The results showed that heavy metals inhibited the ability of Pseudomonas sp. H13 and Brevundomonas sp. H16 to promote plant growth, but stimulated the production of extracellular polysaccharides and inorganic labile sulfide, and enhanced biofilm formation, thereby significantly improved the removal efficiency of Cu²⁺, Zn²⁺, Cd²⁺, and Pb²⁺. Compared with H16, the biofilm of H13 disintegrated rapidly in the later stage, so more metal ions were adsorbed on the planktonic cells. The C-OH and PO groups related to polysaccharides play a crucial role in heavy metal adsorption, and the immobilization mechanism of the planktonic cell is mainly ion exchange and group complex, but for H16, intracellular enrichment cannot be ignored. Functional group complexes played a dominant role in biofilm, and the immobilized heavy metals were more difficult to release into the environment. This study highlighted the potential application prospects of biofilm bacteria in heavy metal remediation and explained the reactive barrier of rhizosphere bacteria to heavy metals.

Abscisic acid-catabolizing bacteria: A useful tool for enhancing phytoremediation

Bacteria-facilitated phytoextraction has been gaining recognition for the phytoremediation of heavy metal (HM)-contaminated soils. Nevertheless, it remains unclear whether catabolizing abscisic acid (ABA) in hyperaccumulating plants via rhizobacteria could facilitate HM phytoextraction. In this study, inoculation with the ABA-catabolizing bacterium, Rhodococcus qingshengii, increased HM (Cd, Zn, Pb, and Cu) concentrations in the shoots of hyperaccumulators Vetiveria zizanioides, Brassica juncea, Lolium perenne L., Solanum nigrum L., and Sedum alfredii Hance grown in mildly and severely contaminated soils by 28.8%-331.3%, 8.5%-393.4%, 21.2%-222.5%, 14.7%-115.5%, and 28.3%-174.2%, respectively, compared with non-inoculated plants. The fresh biomass of these hyperaccumulators was elevated by 16.5%-94.4%, compared to that of the bacteria-free control. Phytoremediation potential indices, including bioconcentration and translocation factors, also revealed that the bacteria markedly boosted the phytoextraction efficacy from soil. Furthermore, principal component analysis (PCA) suggested that the effects of bacteria on the concentrations of Cd and Zn in hyperaccumulators were significantly correlated with ABA metabolism, but not with Pb and Cu. Combined with the synergistic effects on plant biomass, the bacteria also improved the phytoextraction of Pb and Cu in hyperaccumulators. Overall, the application of microorganism-assisted remediation based on ABA-catabolizing bacteria might be an alternative strategy for enhancing phytoremediation efficiency in HM-contaminated soils.

Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of 'Omics' Technologies

Rice, the main staple food for about half of the world's population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial-rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.

Cadmium-Tolerant Rhizospheric Bacteria of the C3/CAM Intermediate Semi-Halophytic Common Ice Plant (Mesembryanthemum crystallinum L.) Grown in Contaminated Soils

The common ice plant, Mesembryanthemum crystallinum L., has recently been found as a good candidate for phytoremediation of heavy-metal polluted soils. This semi-halophyte is a C₃/CAM (Crassulacean acid metabolism) intermediate plant capable of tolerating extreme levels of cadmium in the soil. The aim of the work was to obtain and characterize novel, Cd-tolerant microbial strains that populate the root zone of M. crystallinum performing different types of photosynthetic metabolism and growing in Cd-contaminated substrates. The plants exhibiting either C₃ or CAM photosynthesis were treated for 8 days with different CdCl₂ doses to obtain final Cd concentrations ranging from 0.82 to 818 mg⋅kg^-1 of soil d.w. The CAM phase was induced by highly saline conditions. After treatment, eighteen bacterial and three yeast strains were isolated from the rhizosphere and, after preliminary Cd-resistance in vitro test, five bacterial strains were selected and identified with a molecular proteomics technique. Two strains of the species Providencia rettgeri (W6 and W7) were obtained from the C₃ phase and three (one Paenibacillus glucanolyticus S7 and two Rhodococcus erythropolis strains: S4 and S10) from the CAM performing plants. The isolates were further tested for Cd-resistance (treatment with either 1 mM or 10 mM CdCl₂) and salinity tolerance (0.5 M NaCl) in model liquid cultures (incubation for 14 days). Providencia rettgeri W7 culture remained fully viable at 1 mM Cd, whereas Rh. erythropolis S4 and S10 together with P. glucanolyticus S7 were found to be resistant to 10 mM Cd in the presence of 0.5 M NaCl. It is suggested that the high tolerance of the common ice plant toward cadmium may result from the synergic action of the plant together with the Cd/salt-resistant strains occurring within rhizospheral microbiota. Moreover, the isolated bacteria appear as promising robust microorganisms for biotechnological applications in bio- and phytoremediation projects.

Theobroma cacao L. agricultural soils with natural low and high cadmium (Cd) in Santander (Colombia), contain a persistent shared bacterial composition shaped by multiple soil variables and bacterial isolates highly resistant to Cd concentrations

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This study report statistically significant differences in beta-diversity correlated with soil properties, including Cd concentrations.

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Culture-dependent techniques allowed the isolation of bacterial strains tolerating high Cd concentrations up to 120 mgL⁻¹ for potencial Cd biosorption or intracellular sequestration.

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The combination of different approaches provides a baseline about the bacterial composition and Cd tolerant strains found in these soils influence for lower Cd accumulation in cocoa crops.

Heavy metals can be found in soil as natural components or as product of contaminations events; plants growing in soils are prone to bioaccumulate heavy metals on their biomass. Theobroma cacao L. can bioaccumulate cadmium (Cd) in the seed and could be in derived food products, it considered a human health risk; therefore, removal of Cd is desirable but not vet technically and economically feasible; only to avoid Cd in cocoa is by selecting lands plots exhibiting lower Cd concentrations in soils, imposing a serious limitation to farmers and regulators. The study of bacterial communities and isolation bacteria with tolerance and mechanisms to counteract the translocation of Cd to the parts of cocoa plant exhibits high relevance in Colombia economy and especially to companies producing chocolate and derivatives. Here, we explore bacterial communities associated with soils having relatively high natural Cd concentrations in a large agricultural cocoa plot located in the Santander region. We characterized the bacterial communities’ compositions by amplicon 16S rRNA sequencing from metagenomics soil DNA and by culturing-based enumeration and isolation approaches.

Culture-dependent techniques allowed the isolation of bacteria tolerant to Cd concentration, complement the information for Colombia, and expand the number of strains characterized with adaptive capacity against Cd with tolerance in a concentration of 120 mg/L, which represents the first capacity for Exiguobacterium sp., Ralstonia sp., Serratia sp., Dermacoccus sp., Klebsiella sp., Lactococcus sp. and Staphylococcus sp. In addition to confirming that there is a greater diversity of Cd-tolerant bacteria present in soils of farms cultivated with cocoa in Colombia. As for the results of new generation sequencing, they revealed that, the alpha-diversity in bacterial composition, according to the ANOVA, there are statistically significant differences of the bacterial communities present in the samples. Regarding Pearson correlation analysis, it was found the Shannon Simpson indices, have a positive correlation against OM, C, pH, Mn, C.E.C.I., Ca, P and negatively correlated with S; respect to bacterial community structure, a principal component analysis, which revealed that independent of the concentration of Cd present in soil samples, separates them according to pH value. Phyla to high abundance relative in all samples were Proteobacteria, Acidobacteriota, Actinobacteriota, Verrucomicrobiota, Myxococcota, Chloroflexi, Plactomycetota, Bacteroidota, Gemmatimonadota, Nitrospirota, Firmicutes and NB1_J; the bacteria genera with higher relative abundance (>0.5%) Nitrospira, candidatus Udaeobacter, Haliangium, Cupriavidus, MND1, Bacillus, Kitasatospora, Niveibacterium, Acidothermus, Burkholderia, Acidibacter, Terrimonas, Gaiella, candidatus Solibacter, Kitasatospora, Sphingomonas, Streptomyces, this genus with a relationship with the Cd tolerance process. After it, redundancy analysis was performed between the variation of the bacterial communities identified by dependent and independent techniques and edaphic soil variables, where their positive correlation was found against K, OM, C, Ca, pH (p<0.01) and P, C.E.C.I (p<0.05). For soil samples, the bacterial genera that make up the core community were identified, which are present in all samples as Nitrospira sp., Cupriavidus sp., Burkholderia sp., Haliangium sp., candidatus Udaeobacter, MND1, Kitasatospora, Acidothermus, Acidibacter, Streptomyces, Gaiella, candidatus Solibacter and Terramonas; the genera identified has a different and fundamental role in ecosystem functioning. The combination of different approaches offers new clues regarding the assessment of bacterial communities in soils cultivated with cocoa in soils with elevated Cd content in Colombia, and the ecological role and interplay of soil components and bacterial communities that contribute to modulate the effect of bioaccumulation in products.

Comparative Study of Heavy Metal Uptake and Analysis of Plant Growth Promotion Potential of Multiple Heavy Metal-Resistant Bacteria Isolated From Arable Land

Heavy metal-induced pollution is a serious environmental concern. This study was aimed at exploring indigenous heavy metal-resistant and plant growth promoting bacteria from arable land that might be useful for developing green strategies to counter the challenges related to bioremediation and sustainable agriculture. A thorough screening and characterization of all the twenty heavy metal-resistant bacterial isolates obtained in this study was done. Of these, three potent isolates were further analyzed to unravel their heavy metal resistance and uptake potentiality. Minimum inhibitory concentration determination depicted considerable tolerance (≥ 500 µg/mL) of the three isolates to Ni, Zn, Fe, Cd, Cu, etc. Growth kinetics of the isolates in presence of various heavy metals indicated differences between normal and metal-induced growth. pH tolerance and pigmentation ability of the isolates were also analyzed. Inductively Coupled Plasma-Mass Spectrometry study revealed maximum Cd uptake by the isolates during exponential phase of growth. One of the isolates demonstrated plant growth promotion ability detected using different in vitro qualitative screening tests. Molecular identification using 16S rRNA depicted the isolates as strains of Pseudomonas aeruginosa. This was the first study of heavy metal-resistant and plant growth promoting bacteria from this region. Further exploration of such multi metal-resistant indigenous bacteria may pave the way for designing effective strategies for bioremediation and sustainable agriculture.

Unveiling Endophytic Bacterial Community Structures of Different Rice Cultivars Grown in a Cadmium-Contaminated Paddy Field

Endophytic bacteria play potentially important roles in the processes of plant adaptation to the environment. Understanding the composition and dynamics of endophytic bacterial communities under heavy metal (HM) stress can reveal their impacts on host development and stress tolerance. In this study, we investigated root endophytic bacterial communities of different rice cultivars grown in a cadmium (Cd)-contaminated paddy field. These rice cultivars are classified into low (RBQ, 728B, and NX1B) and high (BB and S95B) levels of Cd-accumulating capacity. Our metagenomic analysis targeting 16S rRNA gene sequence data reveals that Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes, and Spirochaetes are predominant root endophytic bacterial phyla of the five rice cultivars that we studied. Principal coordinate analysis shows that the developmental stage of rice governs a larger source of variation in the bacterial communities compared to that of any specific rice cultivar or of the root Cd content. Endophytic bacterial communities during the reproductive stage of rice form a more highly interconnected network and exhibit higher operational taxonomic unit numbers, diversities, and abundance than those during the vegetative stage. Forty-five genera are significantly correlated with Cd content in rice root, notably including positive-correlating Geobacter and Haliangium; and negative-correlating Pseudomonas and Streptacidiphilus. Furthermore, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis shows that functional pathways, such as biosynthesis of siderophore and type II polyketide products, are significantly enhanced during the reproductive stage compared to those during the vegetative stage under Cd stress. The isolated endophytic bacteria from the Cd-contaminated rice roots display high Cd resistance and multiple traits that may promote plant growth, suggesting their potential application in alleviating HM stress on plants. This study describes in detail for the first time the assemblage of the bacterial endophytomes of rice roots under Cd stress and may provide insights into the interactions among endophytes, plants, and HM contamination.

Speciation, transportation, and pathways of cadmium in soil-rice systems: A review on the environmental implications and remediation approaches for food safety

Cadmium (Cd) contamination in paddy fields is a serious health concern because of its high toxicity and widespread pollution. Recently, much progress has been made in elucidating the mechanisms involved in Cd uptake, transport, and transformation from paddy soils to rice grains, aiming to mitigate the associated health risk; however, these topics have not been critically reviewed to date. Here, we summarized and reviewed the (1) geochemical distribution and speciation of Cd in soil-rice systems, (2) mobilization, uptake, and transport of Cd from soil to rice grains and the associated health risks, (3) pathways and transformation mechanisms of Cd from soil to rice grains, (4) transporters involved in reducing Cd uptake, transport, and accumulation in rice plants, (5) factors governing Cd bioavailability in paddy, and (6) comparison of remediation approaches for mitigating the environmental and health risks of Cd contamination in paddy fields. Briefly, this review presents the state of the art about the fate of Cd in paddy fields and its transport from soil to grains, contributing to a better understanding of the environmental hazards of Cd in rice ecosystems. Challenges and perspectives for controlling Cd risks in rice are thus raised. The summarized findings in this review may help to develop innovative and applicable methods for controlling Cd accumulation in rice grains and sustainably manage Cd-contaminated paddy fields.

Cadmium-tolerant bacteria: current trends and applications in agriculture

Cadmium (Cd) is considered a toxic heavy metal; nevertheless, its toxicity fluctuates for different organisms. Cadmium-tolerant bacteria (CdtB) are diverse and non-phylogenetically related. Because of their ecological importance these bacteria become particularly relevant when pollution occurs and where human health is impacted. The aim of this review is to show the significance, culturable diversity, metabolic detoxification mechanisms of CdtB and their current uses in several bioremediation processes applied to agricultural soils. Further discussion addressed the technological devices and the possible advantages of genetically modified CdtB for diagnostic purposes in the future.

The endophytic bacterium Bacillus koreensis 181-22 promotes rice growth and alleviates cadmium stress under cadmium exposure

Recently, cadmium (Cd) contamination in paddy soils has become a highly concerning pollution problem. Endophytic microbes in rice not only affect the plant growth but also contribute to ion absorption by the roots. Therefore, they are a promising, ecologically sound means of reducing the Cd transport from soils to shoots and grains of the plant. In this study, a Cd-resistant endophytic bacterium, named 181-22, with high Cd absorption capacity (90.8%) was isolated from the roots of rice planting in heavily Cd-contaminated paddy soils and was identified as Bacillus koreensis CGMCC 19,468. The strain significantly increased fresh weight of roots and shoots (44.4% and 42.7%) and dry weight of roots and shoots (71.3% and 39.9%) and decreased Cd content in the rice roots (12.8%), shoots (34.3%), and grains (39.1%) under Cd stress compared to uninoculated plant by colonizing rice roots via seed inoculation. Moreover, colonization of 181-22 reprogrammed rice physiology to alleviate Cd stress by increasing pigment and total protein content, regulating Cd-induced oxidative stress enzymes such as superoxide dismutase and catalase and reducing malondialdehyde. Thus, B. koreensis 181-22 has the potential to protect rice against Cd stress and can be used as a biofertilizer to bioremediate paddy soils contaminated with Cd. KEY POINTS: • Bacillus koreensis 181-22 colonized the inside of rice roots at high numbers via seed inoculation. • B. koreensis 181-22 promoted rice growth and decreased Cd accumulation in grains. • B. koreensis 181-22 regulated the physiological response to alleviated Cd stress in rice.

Unraveling the heavy metal resistance and biocontrol potential of Pseudomonas sp. K32 strain facilitating rice seedling growth under Cd stress

Heavy metal and metalloid toxicity in agricultural land needs special attention for crop production essential to feed increasing population globally. Plant growth-promoting rhizobacteria (PGPR) are native biological agents that have tremendous potential to augment crop production in contaminated fields. This study involves selection and identification (through 16S rRNA gene sequence and FAME analysis) of a potent Pseudomonas sp. (strain K32) isolated from a metal-contaminated rice rhizosphere, aimed to its application for sustainable agriculture. Apart from multi-heavy metal(loid) resistance (Cd²⁺, Pb²⁺ and As³⁺ upto 4000, 3800, 3700 μg/ml respectively) along with remarkable Cd bioaccumulation potential (∼90%), this strain showed IAA production, nitrogen-fixation and phosphate solubilization under Cd stress. This bioaccumulation efficiency coupled with PGP traits resulted in the significant enhancement of rice seedling growth under Cd stress. This positive impact of K32 strain was clearly manifested in morphological and biochemical improvements under Cd stress including successful root colonization with rice roots. Cd uptake was also reduced significantly in seedlings in presence of K32 strain. Together with all mentioned properties, K32 showed bio-control potential against plant pathogenic fungi viz. Aspergillus flavus, Aspergillus parasiticus, Paecilomyces sp., Cladosporium herbarum, Rhizopus stolonifer and Alternaria alternata which establish K32 strain a key player in effective bioremediation of agricultural fields. Biocontrol potential was found to be the result of enzymatic activities viz. chitinase, β-1,3-glucanase and protease which were estimated as 8.17 ± 0.44, 4.38 ± 0.35 and 7.72 ± 0.28 U/mg protein respectively.

Cadmium pollution of soil-rice ecosystems in rice cultivation dominated regions in China: A review

Cd accumulation in paddy soils and its subsequent transfer to the food chain are widespread environmental issues, which has been extensively investigated in China. However, most studies focused on regional scales and these results may not be applicable to present the Cd contamination status in soil-rice ecosystems at a national scale. Therefore, based on collected data from China's rice cultivation dominated regions, this study provides the Cd pollution level of paddy soils and rice grains in China. Results indicates that the Yangtze River basin, especially Hunan, required more attention due to the elevated Cd concentrations in soil-rice ecosystems. Moreover, this review summarizes the significant natural and anthropogenic sources, transport and accumulation mechanism as well as the influencing factors of Cd in soil-rice ecosystems. The wide occurrence of Cd contamination in paddy soils derived primarily from mining activities, intensive application of phosphates fertilizers and e-waste. Physicochemical characteristics of soil, soil microorganisms, temperature as well as the physiological features of rice plants all contribute to Cd accumulation in rice grains, which can be controlled to mitigate Cd accumulation in rice grains. This review will provide a scientific reference for Cd pollution control and management with respect to paddy field ecosystems in China and other countries.

Effects of Pseudomonas TCd-1 on rice (Oryza sativa) cadmium uptake, rhizosphere soils enzyme activities and cadmium bioavailability under cadmium contamination

Microbial remediation is a promising technique to reduce Cd accumulation in rice (Oryza sativa). In present study, a set of pot experiments were conducted to evaluate the effects of Cd-tolerate Pseudomonas TCd-1 inoculation on rice Cd uptake, soil enzyme activities and Cd bioavailability in the rhizosphere soils under Cd contaminated conditions. The results showed that at the ripening stage, with the inoculation of TCd-1, Cd contents in root, culm, leaf, hull and brown rice significantly reduced by 60.7%, 47.7%, 50.6%, 58.1% and 47.9%, respectively, and the cadmium bioconcentration factor (BCF) of rice lowered by 66.2% under 5 mg kg-1 Cd treatment. At the meantime, in the rhizosphere soils, pH increased by 0.05, the contents of exchangeable Cd (EX-Cd) and Fe-Mn oxides (OX-Cd) increased by 107.8% and 33.5%, whereas organic matter (OM-Cd) and residual (Res-Cd) decreased by 31.9% and 60.0%, respectively. The activity of acid phosphatase (ACP) increased by 28.3%, catalase (CAT), saccharase (SUC) activity decreased by 28.5% and 26.0%. Similarly, the Cd contents in root, culm, leaf, hull and brown rice reduced by 42.1%, 42.5%, 58.0%, 50.3%, and 68.8%, respectively, and the BCF lowered by 57.1%, under 10 mg kg-1 Cd treatment. Simultaneously, the soil pH increased by 0.06, the activities of CAT, SUC, urease (URE), ACP decreased by 26.4%, 34.6%, 63.8% and 15.3%, respectively. Furthermore, the correlation analysis showed that the inoculation of TCd-1 changed the correlation between rice Cd content and the biomass of roots, leaves, soil pH, CAT, PPO, URE activities, OM-Cd in rhizosphere soils. It suggested that Pseudomonas TCd-1 effectively reduced Cd uptake and Cd accumulation in rice was closely linked to the changes of soil pH, enzyme activities and Cd availability.

Efficacy of Indole Acetic Acid and Exopolysaccharides-Producing Bacillus safensis Strain FN13 for Inducing Cd-Stress Tolerance and Plant Growth Promotion in Brassica juncea (L.)

Untreated wastewater used for irrigating crops is the major source of toxic heavy metals and other pollutants in soils. These heavy metals affect plant growth and deteriorate the quality of edible parts of growing plants. Phytohormone (IAA) and exopolysaccharides (EPS) producing plant growth-promoting rhizobacteria can reduce the toxicity of metals by stabilizing them in soil. The present experiment was conducted to evaluate the IAA and EPS-producing rhizobacterial strains for improving growth, physiology, and antioxidant activity of Brassica juncea (L.) under Cd-stress. Results showed that Cd-stress significantly decreased the growth and physiological parameters of mustard plants. Inoculation with Cd-tolerant, IAA and EPS-producing rhizobacterial strains, however, significantly retrieved the inhibitory effects of Cd-stress on mustard growth, and physiology by up regulating antioxidant enzyme activities. Higher Cd accumulation and proline content was observed in the roots and shoot tissues upon Cd-stress in mustard plants while reduced proline and Cd accumulation was recorded upon rhizobacterial strains inoculation. Maximum decrease in proline contents (12.4%) and Cd concentration in root (26.9%) and shoot (29%) in comparison to control plants was observed due to inoculation with Bacillus safensis strain FN13. The activity of antioxidant enzymes was increased due to Cd-stress; however, the inoculation with Cd-tolerant, IAA-producing rhizobacterial strains showed a non-significant impact in the case of the activity of superoxide dismutase (SOD), peroxidase (POX) and catalase (CAT) in Brassica juncea (L.) plants under Cd-stress. Overall, Bacillus safensis strain FN13 was the most effective strain in improving the Brassica juncea (L.) growth and physiology under Cd-stress. It can be concluded, as the strain FN13 is a potential phytostabilizing biofertilizer for heavy metal contaminated soils, that it can be recommended to induce Cd-stress tolerance in crop plants.

Speciation and fate of toxic cadmium in contaminated paddy soils and rice using XANES/EXAFS spectroscopy

The present study was conducted to determine the Cd distribution and speciation in contaminated paddy soils and rice kernels using XANES/EXAFS spectroscopy. The morphology and crystallization of rice and soils were investigated using FE-SEM and XRD techniques. The EXAFS spectra of Cd in soil and rice kernels showed that cadmium oxides (CdO) in soil and rice kernels formed Cd clusters with Cd-O bond distances of 2.35 Å and 2.25 Å (coordination numbers of 2.3 and 3.8), respectively. The XRD patterns show that silica oxide (SiO₂, 2θ = 24.2) and aluminum oxide (Al₂O₃, 2θ = 35.7) were the main components detected. The FE-SEM analysis revealed that the surface characteristics and sizes of the rice kernels are smooth and uneven with particle sizes of 0.5-4 µm, while the soil particles are not uniform and aggregated. Furthermore, the distribution of toxic metals/metalloid (Cd, Pb, Cr, Ni, As, Cu, and Zn) accumulated in the contaminated paddy soils and rice crops were also examined. Interestingly, these results offered an insight into the accumulation mechanism and distribution of heavy metals in contaminated rice farming soils and rice crops.

Impacts of earthworm introduction and cadmium on microbial communities composition and function in soil

Heavy metal contamination of soil has become a public concern. Earthworms are key players in the functioning and service of soil ecosystems, with comprehension of their introduction in the polluted soil offering new insights into the protection of soil resources. In the present study, we evaluated the effects of earthworm (Eisenia fetida) introduction and Cd (0, 10, 30, and 60 mg kg^-1 of Cd) exposure upon soil microbial community using 16S rRNA gene amplicon sequencing. Our research demonstrated that Gemmatimonadetes and Deinococcus-Thermus upregulated significantly, while Chryseolinea showed an obvious decreasing trend after earthworm introduction. In Cd contaminated soil, many genera exhibited a greater presence of Cd-dependent bacteria, namely Cd-tolerant bacteria such as Altererythrobacter and Luteimonas, and a decrease of sensitive bacteria, such as Amaricoccus and Haliangium. Moreover, functional prediction analysis of soil microbiota indicated that earthworm introduction and Cd exposure changed functional pathways of soil microorganisms. The results obtained in this study are beneficial for understanding soil microbial community impacted by earthworm, and for exploring Cd resistant or tolerant bacteria, with potentially significant findings for soil biodiversity and Cd bioremediation.

Biofertilizer-induced response to cadmium accumulation in Oryza sativa L. grains involving exogenous organic matter and soil bacterial community structure

The accumulation of cadmium (Cd) in Oryza sativa L., the world's most significant staple crop, is a health threat to millions of people. The objective of this study was to evaluate the effectiveness of commercially available biofertilizers (with high (BF2) and low organic matter (OM) content (BF1)) on Cd accumulation in two types of soils and to determine the bacterial community responses by high-throughput sequencing. The study was conducted in the form of pot experiment in greenhouse in 2018. Four treatments were set: BF1, BF2, organic fertilizer (OF), and control (CK) and the amendments were applied before the rice cultivation. The results showed that the addition of biofertilizers immobilized or mobilized Cd in soils, depending on the soil type and the OM content in biofertilizers. The exogenous OM in biofertilizers was the driving factor for the difference in pH and Cd accumulation in rice grains. The application of biofertilizers with high OM content was effective in reducing Cd accumulation in the rice grains (19.7% lower than CK) by significantly increasing soil pH (from 6.02 to 6.67) in acid silt loam soil (TZ). The consumption of acid fermentation products by soil chemoorganotrophs and the complexation of organic anions in the biofertilizer treatment tended to buffer the pH drop in the drainage and decrease the Cd availability. However, in the weak acid silty clay loam soil (SX), the addition of biofertilizer with high OM significantly increased Cd accumulation in rice grains (21.9% higher than CK), probably owing to the release of acid substances, resulting from the significant increase of the predominant bacteria Chloroflexi. The addition of biofertilizer with low OM content did not significantly change Cd accumulation in rice grains or affect the soil microbial structures in both soils. In conclusion, the effects of biofertilizer on rice Cd accumulation were related to the OM content and soil bacterial community. Biofertilizers with high organic matter may not be suitable for amendments in the paddy soils with high clay content to reduce Cd accumulation in rice grains.

A newly isolated bacterium Comamonas sp. XL8 alleviates the toxicity of cadmium exposure in rice seedlings by accumulating cadmium

Cadmium (Cd) is a typical heavy-metal highly accumulating in crops and drinking water, thus posing a severe health risk for human health. In this study, we firstly isolated 24 Cd-resistant bacteria from the heavy-metals contaminated soil at Daye Iron Ore, in which Comamonas sp. XL8 exhibited a high resistance and strong accumulation capacity to Cd. After absorption, Comamonas sp. XL8 could biosynthesize intracellular Cd-nanoparticles (CdNPs), which has not been reported in characteristics of Comamonas genus before. We found that the gene expressions of cadA and bmtA related to Cd transportation and binding in strain XL8 were significantly upregulated with Cd exposure, suggesting that genes cadA and bmtA may contribute to the formation of CdNPs. Of particular note, the co-inoculation of Comamonas sp. XL8 and rice seedlings (Oryzae sativa L.) significantly decreased the oxidative stress-induced by Cd accumulation and subsequently alleviated toxicity of Cd exposure. Our results reveal the biochemical process of Cd accumulation in Comamonas sp. XL8 by forming CdNPs, showing that it has great potential for effective bioremediation of environmental Cd exposure.

Cadmium stress in paddy fields: Effects of soil conditions and remediation strategies

Cadmium (Cd) toxicity in paddy soil and accumulation in rice plants and grains have got global concern due to its health effects. This review highlights the effects of soil factors including soil organic matter, soil pH, redox potential, and soil microbes which influencing Cd uptake by rice plant. Therefore, a comprehensive review of innovative and environmentally friendly management practices for managing Cd stress in rice is lacking. Thus, this review discusses the effect of Cd toxicity in rice and describes management strategies to offset its effects. Moreover, future research thrusts to reduce its uptake by rice has also been highlighted. Through phytoremediation, Cd may be extracted and stabilized in the soil while through microbes Cd can be sequestrated inside the microbial bodies. Increased Cd uptake in hyperaccumulator plants to remediate and convert the toxic form of Cd into non-toxic forms. While in chemical remediation, Cd can be washed out, immobilized and stabilized in the soil through chemical amendments. The organic amendments may help through an increase in soil pH, adsorption in its functional groups, the formation of complexations, and the conversion of exchangeable to residual forms. Developing rice genotypes with restricted Cd uptake and reduced accumulation in grain through conventional and marker-assisted breeding are fundamental keys for safe rice production. In this regard, the use of molecular techniques including identification of QTLs, CRISPR/Cas9, and functional genomics may be quite helpful.