Beneficial role of bacterial endophytes in heavy metal phytoremediation

Diverse adaptation strategies of generalists and specialists to metal and salinity stress in the coastal sediments

Understanding the distinct roles and responses of bacterial community to environmental stressors is crucial for effective ecosystem management and conservation. Despite this, there is limited research on how environmental gradients specifically impact generalist and specialist subcommunities. This study investigates these subcommunities in the sediments of Jinzhou Bay, highlighting their distinct responses to environmental gradients. Generalists thrive in disturbed environments due to their broad ecological tolerances, while specialists show higher diversity in the stable, less contaminated upstream areas. At the genus level, Porphyrobacter and Subgroup_23 were identified as the dominant taxa of generalists, while Woeseia and Lutibacter were the dominant species of specialists. Physicochemical parameters, especially metals and salinity, significantly influence subcommunity composition. Generalists are adaptable to a wider range of factors, whereas specialists are affected by specific parameters, reflecting their narrower niches. The generalists exhibit a greater abundance of salinity tolerance genes compared to the specialists; however, this trend does not extend to metal resistance genes. Keystone taxa, primarily specialists, play crucial roles in maintaining community stability. Our results underscore the importance of considering both generalists and specialists in ecological assessments, offering insights for the management and conservation of bacterial microbial diversity in coastal ecosystems.

Taxonomic description of Micromonospora reichwaldensis sp. nov. and its biosynthetic and plant growth-promoting potential

Micromonospora strains proved to be a model organism for drug discovery and plant growth promotion (PGP). Strain DSM 115977 T was subjected to polyphasic taxonomic analysis and genome mining for biosynthetic gene clusters and PGP-associated genes in order to determine its taxonomic rank and assess its biosynthetic potential. The strain was found to form a novel species within the evolutionary radiation of the genus Micromonospora. The strain contained glucose, mannose, xylose, and ribose as whole-cell sugars and the isomer DL-diaminopimelic acid in its peptidoglycan. Strain DSM 115977T had iso-C15:0, iso-C16:0, C17:1cis 9, C17:0, iso-C17:0, and 10-methyl-C17:0 as fatty acid profile (>5%) and MK10-H4 and MK10-H6 as the predominant menaquinones (>10%). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, glycophospholipids, phosphoaminolipid, unidentified lipids, and phospholipids. The genome of the strain had a size of 7.0 Mbp with a DNA G + C content of 73.4%. It formed a well-supported sub-clade with its close phylogenomic neighbor, Micromonospora echinofusca DSM 43913T (98.7%). Digital DNA-DNA hybridization and average nucleotide identity derived from sequence comparisons between the strain and its close phylogenomic neighbors were below the thresholds of 70 and 95-96% for prokaryotic species demarcation, respectively. Based on these findings, strain DSM 115977T (Asg4T = KCTC 59188T) merits to be considered as the type strain of a new species for which the name Micromonospora reichwaldensis sp. nov. is proposed. Genome mining for biosynthetic gene clusters encoding specialized secondary metabolites highlighted its ability to produce potentially novel therapeutic compounds. The strain is rich in plant growth-promoting genes whose predicted products directly and indirectly affect the development and immune system of the plant.

IMPORTANCE

In view of the significant pharmaceutical, biotechnological, and ecological potentials of micromonosporae, it is particularly interesting to enhance the genetic diversity of this genus by focusing on the isolation of novel strain from underexplored habitats, with the promise that novel bacteria will lead to new chemical entities. In this report, modern polyphasic taxonomic study confirmed the assignment of strain DSM 115977T to a novel species for which the name Micromonospora reichwaldensis sp. nov. is proposed. The strain harbors in its genomic sequence several biosynthetic gene clusters for secondary metabolites and genes associated with plant growth-promoting features. The results of this study provide a very useful basis for launching more in-depth research into agriculture and/or drug discovery.

Sulfate-reducing bacteria block cadmium and lead uptake in rice by regulating sulfur metabolism

AIM

This study was dedicated to investigating the role of sulfur metabolic processes in sulfate-reducing bacteria in plant resistance to heavy metal contamination.

METHODS AND RESULTS

We constructed sulfate-reducing bacterial communities based on the functional properties of sulfate-reducing strains and then screened out the most effective sulfate-reducing bacterial community SYN1, that prevented Cd and Pb uptake in rice through a hydroponic experiment. This community lowered Cd levels in the roots and upper roots by 36.60% and 39.88%, respectively, and Pb levels by 35.96% and 51.54%. We also compared two treatment groups, inoculated with SYN1 and exogenously added GSH, and found that both enhanced the antioxidant response of the plants, increased the lignin and GSH contents and the expression of genes related to the phenylpropane biosynthesis pathway (OsCAD, Os4CL, OsCOMT, OsPOD, OsC3H, and OsPAL), and decreased the expression of heavy metal transporter genes (OsHMA2, OsIRT1) expression. There were no significant differences between the two treatments.

CONCLUSIONS

Sulfate-reducing bacteria produce GSH through the sulfur assimilation pathway, and GSH can directly chelate heavy metals or enhance plant antioxidant enzyme activities and regulate processes such as the uptake and translocation of heavy metals, thus enhancing plant resistance to heavy metal toxicity.

Two birds with one stone: Alleviating copper toxicity and inhibiting its upward transport in non-host rice (Oryza sativa L.) by inoculation of Cu-resistant endophytes from the hyperaccumulator Commelina communis

Endophytic bacteria derived from metal hyperaccumulators have demonstrated potential for improving copper (Cu) remediation in host plants; however, their potential application in non-host crops remains unclear. In this study, endophytic bacteria isolated from Commelina communis growing in mining areas and their mitigation effects on Cu toxicity in non-host rice were comprehensively evaluated. Among the isolated endophytes, Bacillus sp. D2 exhibited the highest Cu resistance, producing indole-3-acetic acid (IAA) at a concentration of 0.93 mg/L and exhibiting ACC deaminase activity of 13.88 μmol/mg·h under 200 mg/L Cu stress. Pot-experiment results revealed that Bacillus sp. D2 addition significantly increased the biomass and lengths of shoots under Cu stress conditions by 47.6% and 14.2%, respectively. Furthermore, Bacillus sp. D2 inoculation significantly reduced oxidative damage, enhanced antioxidant responses, and modulated plant hormone levels in Cu-exposed rice. Notably, Bacillus sp. D2 inoculation substantially decreased the upward translocation of Cu from underground roots to aboveground tissues. Moreover, Bacillus sp. D2 effectively alleviated Cu toxicity in rice plants by regulating the expression levels of genes involved in antioxidant systems (tAPx, Csd2, and FeSOD1), Cu transporters (AtPDR8 and HMA3), as well as metallothionein (MT2c). These results highlight the value of Bacillus sp. D2 as a bioinoculant for improving crop growth while reducing the risks associated with copper contamination in naturally Cu-contaminated soils.

Biocatalytic Potential of Pseudomonas Species in the Degradation of Polycyclic Aromatic Hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs), one of the major environmental pollutants, produced from incomplete combustion of materials like coal, oil, gas, wood, and charbroiled meat, that contaminate the air, soil, and water, necessitating urgent remediation. Understanding the metabolic pathways for PAHs degradation is crucial to preventing environmental damage and health issues. Biological methods are gaining increasing interest due to their cost-effectiveness and environmental friendliness. These methods are particularly suitable for remediating PAHs contamination and mitigating associated risks. The paper also outlines the processes for biodegrading PAHs, emphasizing the function of Pseudomonas spp., a kind of bacterium recognized for its capacity to degrade PAHs. To eliminate PAHs from the environment and reduce threats to human health and the environment, Pseudomonas spp. is essential. Understanding the mechanism of PAH breakdown by means of microbes could lead to effective clean-up strategies. The review highlights the enzymatic capabilities, adaptability, and genetic versatility of the genes like nah and phn of Pseudomonas spp., which are involved in PAHs degradation pathways. Scientific evidence supports using Pseudomonas spp. as biocatalysts for PAHs clean-up, offering cost-effective and eco-friendly solutions.

Isolation and evaluation of growth-promoting endophytic bacteria from Zanthoxylum dissitum Hemsl

The slow growth rate of Zanthoxylum dissitum Hemsl. (Zanthoxylum) is the important factor causing the scarcity of its available wild resource. It has been reported that the plant endophytes can promote the plant growth and the synthesis of secondary metabolitesby by enhancing the efficiency of nutrient absorption by plants and regulating plant hormones. It is important to explore the promoting effects of endophytes on the growth of Zanthoxylum. The application of high-throughput sequencing technology in this study revealed the presence of three phyla, five classes, seven orders, and eleven genera of endophytic bacteria in Zanthoxylum. The most prevalent phyla, classes, orders, and genera were identified respectively as Proteobacteria, Gammaproteobacteria, Burkholderiales, and Pseudomonas. In this study, an endophytic growth-promoting bacterium was isolated and identified as Sphingomonas sp. The results revealed that the bacterium exhibited robust nitrogen fixation, phosphorus solubilization, and effective siderophore production capabilities. The phosphate solubilization index (SI) was found to be (1.266 ± 0.0157). Following a 48-h incubation period in an inorganic phosphorus liquid medium (PKO), the concentration of auxin (IAA) and gibberellin (GA) reached their highest levels, at (138.145 ± 65.111) μg/mL and (805.74 ± 123.86) μg/mL, respectively. Moreover, the study showed that the endophytic bacteria markedly enhanced the germination potential and rate of sorghum seeds, and promoted significantly the growth of the tissue culture seedlings of Zanthoxylum.

Cyperus esculentus var. sativus Adapts to Multiple Heavy Metal Stresses Through the Assembly of Endophytic Microbial Communities

Interactions between plants and their endophytes alter their metabolic functions and ability to cope with abiotic stresses. In this study, high-throughput sequencing was used to analyze the species diversity and functions of endophytes in Cyperus esculentus var. sativus (CES) tubers under different heavy metal stress conditions. The results indicated that the number of observed endophytic species in the tubers increased under heavy metal stress (p < 0.05), leading to changes in species diversity and composition. The response of tuber endophytes to different metal concentrations varied, with certain endophytic bacteria and fungi, such as Pseudomonas, Novosphingobium, and Fusarium, showing increased abundance and becoming the dominant species in the tubers. Additionally, new endophytic genera, Actinophytocola and Monosporascus, emerged at specific metal concentrations (p < 0.05). Fatty acid salvage was enriched in the endophytes of CES, which may play an important role in assisting CES in responding to multiple heavy metal stresses. These findings showed that CES tuber endophytes undergo adaptive changes to support the ability of plants to cope with heavy metal stress.

Enhancing Miscanthus floridulus remediation of soil cadmium using Beauveria bassiana FE14: Plant growth promotion and microbial interactions

Soil heavy metal pollution presents substantial risks to food security and human health. This study focused on the efficiency of plant growth-promoting fungus-Beauveria bassiana FE14 and Miscanthus floridulus on the synergistic remediation of soil Cd contamination. Results revealed that B. bassiana FE14 significantly enhanced the growth of M. floridulus, substantially decreased Cd content in soil by 79.39 %, and modified enzyme activities (superoxide dismutase, peroxidase, and catalase) to alleviate Cd-induced oxidative stress in plants, determined by the physical and chemical indicators and enzyme activities of soil and plant. Based on microbiome analysis, this study also found significant changes in the composition, structure, and molecular ecological network of endophytic bacterial communities in roots, but this study had little effect on the bacterial and fungal communities in rhizosphere soil. In addition, the key genera (including Sphingomonas, unclassified_Comamonadaceae, Massilia, Bradyrhizobium, and Paraglomus) and key genes/enzymes (including cadC, zinc transporter, zinc and cadmium transporter, exoZ/Y/Z, catalase-peroxidase, superoxide dismutase, nitrite reductase, acid phosphatase, etc.) were involved in promoting plant growth and alleviating Cd stress. These findings revealed the potential of B. bassiana FE14 and M. floridulus working in synergy to enhance the phytoremediation efficiency of Cd-contaminated soils, thus presenting a promising approach for integrated plant-microbe remediation strategies.

Applying cross-scale regulations to Sedum plumbizincicola for strengthening the bioremediation of the agricultural soil that contaminated by electronic waste dismantling and revealing the underlying mechanisms by multi-omics

Electronic waste dismantling has induced the surrounding agricultural soils suffered from combined contamination of heavy metals and organic pollutants. Lower efficiency and complex mechanisms of bioremediation remain to be resolved. Here, we adopted regulations to Sedum plumbizincicola cross aboveground and belowground scales to strengthen the bioremediation efficiency. Results showed that the S. plumbizincicola intercropping with the Astragalus sinicusL. that inoculated with Rhizobium had the highest performance in reductions of Cd, PBDEs and PCBs from soils by 0.11 mg/kg, 67.93 μg/kg and 38.91 μg/kg, respectively. Rhizosphere soil metabolomics analysis demonstrated that reductions in Cd and PBDEs significantly associated with 2-Methylhippuric acid and L-Saccharopine, which were involved in phenylalanine metabolism, biosynthesis of amino acids and lysine. Metagenomics analysis revealed that these functional pathways were mediated by Frankia, Mycobacterium, Blastococcus, etc. microbial taxa, which were also significantly altered by regulations. Moreover, regulation regimes significantly affected transcription genes of S. plumbizincicola. Functional annotation revealed that cross-scale regulations significantly improved bioremediation efficiency through microorganisms and metabolites in the rhizosphere and transcription genes of S. plumbizincicola, which were illustrated to promote plant growth and tolerance to environmental stress. Our integration of multi-omics provides comprehensive and deep insights into molecular mechanisms in the cross-scale regulations of S. plumbizincicola, which would favor remediation techniques advances for the soil contaminated by electronic waste dismantling.

Evidence that beneficial microbial inoculation enhances heavy metal-contaminated soil remediation: Variations in plant endophyte communities

Microbial remediation of heavy metal (HM)-contaminated soil is a sustainable approach; however, the impact of microbial inoculation on the internal environment of plants remains understudied. Thus, Enterobacter sp. FM-1 (Enterobacter sp.) and the hyperaccumulator Bidens pilosa L. (B. pilosa L.) were used to study these effects. Through analyses of plant physiological and biochemical characteristics, the endophytic microbial community composition, microbial co-occurrence networks and functional predictions, the potential mechanisms by which Enterobacter sp. benefits the phytoremediation of HM-contaminated soil by B. pilosa L. were elucidated. Inoculation with Enterobacter sp. promoted the growth of B. pilosa L. and influenced the endophytic microbial community diversity in B. pilosa L. Interactions among endophytes facilitated the formation of microbial networks, with endophytic fungi playing a more prominent role than endophytic bacteria as the level of HM contamination increased. Functional predictions via PICRUSt2 revealed that endophytic bacteria are involved primarily in processes related to carbohydrate metabolism, ABC transporters, and amino acid metabolism. In conclusion, this study provides evidence for the beneficial role of microbes in improving the plant endosphere environment.

Response of the Endophytic Microbiome in Cotinus coggygria Roots to Verticillium Wilt Infection

Verticillium wilt caused by Verticillium dahliae Kleb. is a lethal soil-borne fungal disease of Cotinus coggygria. The plant endophytic microbiome plays an important role in maintaining plant health and disease resistance, but it is unclear how the endophytic microbiome of C. coggygria roots varies in response to Verticillium wilt occurrence. In this study, the endophytic microbial diversity, community composition, dominant species, and co-occurrence network of C. coggygria under Verticillium wilt-affected and healthy conditions were assessed using Illumina sequencing. Compared with healthy plants, the bacterial alpha diversity indices of Verticillium wilt-affected plants decreased significantly, while the fungal alpha diversity indices showed obvious increases. The relative abundance of dominant taxa including Proteobacteria, Actinobacteriota, Ascomycota, and Basidiomycota at the phylum level, as well as Gammaproteobacteria, Thermoleophilia, Dothideomycetes, and Agaricomycetes at the class level, differed significantly between Verticillium wilt-affected and healthy plants. Co-occurrence networks revealed that the fungal network of Verticillium wilt-affected roots was denser with more negative interactions, which may be relevant to functional changes from reciprocity to competition in the microbial community, in response to V. dahliae infection. The results enhanced our understanding on the relationships between the endophytic microbiome and Verticillium wilt, which could provide information for the management of this disease in C. coggygria.

Coating seeds with biocontrol bacteria-loaded sodium alginate/pectin hydrogel enhances the survival of bacteria and control efficacy against soil-borne vegetable diseases

Microbial seed coatings serve as effective, labor-saving, and ecofriendly means of controlling soil-borne plant diseases. However, the survival of microbial agents on seed surfaces and in the rhizosphere remains a crucial challenge. In this work, we embedded a biocontrol bacteria (Bacillus subtilis ZF71) in sodium alginate (SA)/pectin (PC) hydrogel as a seed coating agent to control Fusarium root rot in cucumber. The formula of SA/PC hydrogel was optimized with the highest coating uniformity of 90 % in cucumber seeds. SA/PC hydrogel was characterized using rheological, gel content, and water content tests, thermal gravimetric analysis, and Fourier transform infrared spectroscopy. Bacillus subtilis ZF71 within the SA/PC hydrogel network formed a biofilm-like structure with a high viable cell content (8.30 log CFU/seed). After 37 days of storage, there was still a high number of Bacillus subtilis ZF71 cells (7.23 log CFU/seed) surviving on the surface of cucumber seeds. Pot experiments revealed a higher control efficiency against Fusarium root rot in ZF71-SA/PC cucumber seeds (53.26 %) compared with roots irrigated with a ZF71 suspension. Overall, this study introduced a promising microbial seed coating strategy based on biofilm formation that improved performance against soil-borne plant diseases.

Genetic Adaptations and Mechanistic Insights Into Bacterial Bioremediation in Ecosystems

Metal pollution poses significant threats to the ecosystem and human health, demanding effective remediation strategies. Bioremediation, which leverages the unique metal-resistant genes found in bacteria, offers a cost-effective and efficient solution to heavy metal contamination. Genes such as Cad, Chr, Cop, and others provide pathways to improve the detoxification of the ecosystem. Through multiple techniques, genetic engineering makes bacterial genomes more capable of improving metal detoxification; nonetheless, there are still unanswered questions regarding the nature of new metal-resistant genes. This article examines bacteria's complex processes to detoxify toxic metals, including biosorption, bioaccumulation, bio-precipitation, and bioleaching. It also explores essential genes, proteins, signaling mechanisms, and bacterial biomarkers involved in breaking toxic metals.

Non-phytoremediation and phytoremediation technologies of integrated remediation for water and soil heavy metal pollution: A comprehensive review

Since the 1980s, there has been increasing concern over heavy metal pollution remediation. However, most research focused on the individual remediation technologies for heavy metal pollutants in either soil or water. Considering the potential migration of these pollutants, it is necessary to explore effective integrated remediation technologies for soil and water heavy metals. This review thoroughly examines non-phytoremediation technologies likes physical, chemical, and microbial remediation, as well as green remediation approaches involving terrestrial and aquatic phytoremediation. Non-phytoremediation technologies suffer from disadvantages like high costs, secondary pollution risks, and susceptibility to environmental factors. Conversely, phytoremediation technologies have gained significant attention due to their sustainable and environmentally friendly nature. Enhancements through chelating agents, biochar, microorganisms, and genetic engineering have demonstrated improved phytoremediation remediation efficiency. However, it is essential to address the environmental and ecological risks that may arise from the prolonged utilization of these materials and technologies. Lastly, this paper presents an overview of integrated remediation approaches for addressing heavy metal contamination in groundwater-soil-surface water systems and discusses the reasons for the research gaps and future directions. This paper offers valuable insights for comprehensive solutions to heavy metal pollution in water and soil, promoting integrated remediation and sustainable development.

Microbial Contributions to Heavy Metal Phytoremediation in Agricultural Soils: A Review

Phytoremediation is a sustainable technique that employs plants to reinforce polluted environments such as agroecosystems. In recent years, new strategies involving the plant microbiome as an adjuvant in remediation processes have been reported. By leveraging this microbial assistance to remediate soils contaminated with heavy metals such As, Pb, Cd, Hg, and Cr, plants can sequester, degrade, or stabilize contaminants more efficiently. Remarkably, some plant species are known for their hyper-accumulative traits in synergy with their microbial partners and can successfully mitigate heavy metal pollutants. This sustainable biotechnology based on plant-microbe associations not only aids in environmental cleanup but also enhances biodiversity, improves soil structure, and promotes plant growth and health, making it a promising solution for addressing agro-pollution challenges worldwide. The current review article emphasizes the potential of synergistic plant-microbe interactions in developing practical and sustainable solutions for heavy metal remediation in agricultural systems, which are essential for food security.

Endophyte-assisted non-host plant Tillandsia brachycaulos enhance indoor formaldehyde removal

This study investigated the use of endophyte-assisted Tillandsia brachycaulos to enhance formaldehyde removal in indoor environments. A formaldehyde-degrading endophyte from the root of Epipremnum aureum, Pseudomonas plecoglossicida, was identified and used for inoculation. Among the inoculation methods, spraying proved to be the most effective, resulting in a significant 35 % increase in formaldehyde removal after 36 hours. The results of the light exposure experiment (3000 Lux) demonstrate that an increase in light intensity reduces the efficiency of the Tillandsia brachycaulos-microbial system in degrading formaldehyde. In a 15-day formaldehyde fumigation experiment at 2 ppm in a normal indoor environment, the inoculated Tillandsia brachycaulos exhibited removal efficiency ranging from 42.53 % to 66.13 %, while the uninoculated declined from 31.62 % to 3.17 %. The Pseudomonas plecoglossicida (referred to as PP-1) became the predominant bacteria within the Tillandsia brachycaulos after fumigation. Moreover, the endophytic inoculation effectively increased the resistance and tolerance of Tillandsia brachycaulos to formaldehyde, as evidenced by lower levels of hydroxyl radical, malondialdehyde (MDA), free protein, and peroxidase activity (POD), as well as higher chlorophyll content compared to uninoculated Tillandsia brachycaulos. These findings indicate that the combination of endophytic bacteria and Tillandsia brachycaulos has significant potential for improving indoor air quality.

Phytoremediation efficiency of poplar hybrid varieties with diverse genetic backgrounds in soil contaminated by multiple toxic metals (Cd, Hg, Pb, and As)

Fifteen poplar varieties were used in a field trial to investigate the phytoremediation efficiency, stress resistance, and wood property of poplar hybrid varieties with diverse genetic backgrounds under the composite pollution of heavy metals. The coefficient of variation and clone repeatability for growth traits and Cd concentration were large. The Cd accumulation of poplar varieties 107 and QHQ reached 1.9 and 1.7 mg, respectively, followed by QHB, Ti, 69, and Pa, in which Cd accumulation reached 1.3 mg. Most of the intra-specific hybrid varieties (69, QH1, SL4, T3, and ZL46) had low Cd concentrations and small biomass, resulting in weak Cd accumulation and low phytoremediation efficiency for Cd-polluted soil. By contrast, the inter-sectional and inter-specific hybrid varieties exhibited better growth performance and accumulated higher concentrations of heavy metals than the intra-specific hybrids. The bioconcentration factor and translocation factor of Hg, As, and Pb were less than 1, indicating that poplars have low phytoremediation efficiency for these heavy metals. The hybrids between section Aigeiros and Tacamahaca (QHQ and QHB) and the inter-specific hybrid 107 within section Aigeiros were more resistant to composite heavy metal stress than the other poplar varieties were partially because of their high levels of free proline that exceeded 93 μg·g-1 FW. According to the correlation analysis of the concentrations of the different heavy metals, the poplar roots absorbed different heavy metals in a cooperative manner, indicating that elite poplar varieties with superior capacity for accumulating diverse heavy metals can be bred feasibly. Compared with the intra-specific hybrid varieties, the inter-sectional (QHQ and QHB) and inter-specific (107) hybrid varieties had higher pollution remediation efficiency, larger biomass, higher cellulose content, and lower lignin content, which is beneficial for pulpwood. Therefore, breeding and extending inter-sectional (QHQ and QHB) and inter-specific hybrid varieties can improve the phytoremediation of composite pollution.

The duality of sulfate-reducing bacteria: Reducing methylmercury production in rhizosphere but enhancing accumulation in rice plants

Sulfate-reducing bacteria (SRB) are known to alter methylmercury (MeHg) production in paddy soil, but the effect of SRB on MeHg dynamics in rhizosphere and rice plants remains to be fully elucidated. The present study investigated the impact of SRB on MeHg levels in unsterilized and γ-sterilized mercury-polluted paddy soils, with the aim to close this knowledge gap. Results showed that the presence of SRB reduced MeHg production by ∼22 % and ∼17 % in the two soils, but elevated MeHg contents by approximately 55 % and 99 % in rice grains, respectively. Similar trend at smaller scales were seen in roots and shoots. SRB inoculation exerted the most profound impact on amino acid metabolism in roots, with the relative response of L-arginine positively linking to MeHg concentrations in rhizosphere. The SRB-induced enrichment of MeHg in rice plants may be interpreted by the stronger presence of endophytic nitrogen-related microbes (e.g. Methylocaldum, Hyphomicrobium and Methylocystis) and TGA transcription factors interacting with glutathione metabolism and calmodulin. Our study provides valuable insights into the complex effects of SRB inoculation on MeHg dynamics in rice ecosystems, and may help to develop strategies to effectively control MeHg accumulation in rice grains.

Rhizophagus intraradices and Azospirillum brasilense improve growth of herbaceous plants and soil biological activity in revegetation of a recovering coal-mining area

We assessed, in a field experiment, the effects of arbuscular mycorrhizal fungi (Rhizophagus intraradices) and plant growth-promoting bacteria (Azospirillum brasilense) on the soil biological activity and the growth of key pioneer species used in the revegetation of coal-mining areas undergoing recovery. We applied four inoculation treatments to the pioneer plant species (Lablab purpureus, Paspalum notatum, Crotalaria juncea, Neonotonia wightii, Stylosanthes guianensis, Andropogon gayanus and Trifolium repens) used in the recovery process: NI (Control - Non-inoculated), AZO (A. brasilense), AMF (R. intraradices), and co-inoculation of AZO and AMF. On the 75th and 180th days, we measured plant dry mass, mycorrhizal colonization, N and P concentration, and accumulation in plant tissue. We collected soil to quantify glomalin content and soil enzyme activity. After 180 days, we did a phytosociological characterization of the remaining spontaneous plants.The both microorganisms, singly or co-inoculated, promoted increases in different fractions of soil glomalin, acid phosphatase activity, and fluorescein diacetate activity at 75 and 180 days. The inoculation was linked to higher plant biomass production (62-89%) and increased plant P and N accumulation by 34-75% and 70-85% at 180 days, compared with the non-inoculated treatment. Among the pioneer species sown Crotalaria juncea produced the highest biomass at the 75th and 180th days (67% and 76% of all biomass), followed by Lablab purpureus (3% and 0.5%), while the other species failed to establish. At 180 days, we observed twenty spontaneous plant species growing in the area, primarily from the Poaceae family (74%). That suggests that the pioneer species present in the area do not hinder the ecological succession process. Inoculation of R. intraradices and A. brasilense, isolated or combined, increases soil biological activity, growth, and nutrient accumulation in key pioneer plant species, indicating the potential of that technique for the recovery of lands degraded by coal mining.

R3 strain and Fe-Mn modified biochar reduce Cd absorption capacity of roots and available Cd content of soil by affecting rice rhizosphere and endosphere key flora

Microorganisms have a significant role in regulating the absorption and transportation of Cd in the soil-plant system. However, the mechanism by which key microbial taxa play a part in response to the absorption and transportation of Cd in rice under Cd stress requires further exploration. In this study, the cadmium-tolerant endophytic bacterium Herbaspirillum sp. R3 (R3) and Fe-Mn-modified biochar (Fe-Mn) were, respectively, applied to cadmium-contaminated rice paddies to investigate the effects of key bacterial taxa in the soil-rice system on the absorption and transportation of Cd in rice under different treatments. The results showed that both R3 and Fe-Mn treatments considerably decreased the content of cadmium in roots, stems and leaves of rice at the peak tillering stage by 17.24-49.28% in comparison to the control (CK). The cadmium content reduction effect of R3 treatment is better than that of Fe-Mn treatment. Further analysis revealed that the key bacterial taxa in rice roots under R3 treatment were Sideroxydans and Actinobacteria, and that their abundance showed a substantial positive correlation and a significant negative correlation with the capacity of rice roots to assimilate Cd from the surroundings, respectively. The significant increase in soil pH under Fe-Mn treatment, significant reduction in the relative abundances of Acidobacteria, Verrucomicrobia, Subdivision3 genera incertae sedis, Sideroxydans, Geobacter, Gp1, and Gp3, and the significant increase in the relative abundance of Thiobacillus among the soil bacterial taxa may be the main reasons for the decrease in available Cd content of the soil. In addition, both the R3 and Fe-Mn treatments showed some growth-promoting effects on rice, which may be related to their promotion of transformations of soil available nutrients. This paper describes the possible microbial mechanisms by which strain R3 and Fe-Mn biochar reduce Cd uptake in rice, providing a theoretical basis for the remediation of Cd contamination in rice and soil by utilizing key microbial taxa.

Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture

Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.

Mitigating heavy metal accumulation in tobacco: Strategies, mechanisms, and global initiatives

The threat of heavy metal (HM) pollution looms large over plant growth and human health, with tobacco emerging as a highly vulnerable plant due to its exceptional absorption capacity. The widespread cultivation of tobacco intensifies these concerns, posing increased risks to human health as HMs become more pervasive in tobacco-growing soils globally. The absorption of these metals not only impedes tobacco growth and quality but also amplifies health hazards through smoking. Implementing proactive strategies to minimize HM absorption in tobacco is of paramount importance. Various approaches, encompassing chemical immobilization, transgenic modification, agronomic adjustments, and microbial interventions, have proven effective in curbing HM accumulation and mitigating associated adverse effects. However, a comprehensive review elucidating these control strategies and their mechanisms remains notably absent. This paper seeks to fill this void by examining the deleterious effects of HM exposure on tobacco plants and human health through tobacco consumption. Additionally, it provides a thorough exploration of the mechanisms responsible for reducing HM content in tobacco. The review consolidates and synthesizes recent domestic and international initiatives aimed at mitigating HM content in tobacco, delivering a comprehensive overview of their current status, benefits, and limitations.

Bacteria associated with Comamonadaceae are key arsenite oxidizer associated with Pteris vittata root

Pteris vittata (P. vittata), an arsenic (As) hyperaccumulator commonly used in the phytoremediation of As-contaminated soils, contains root-associated bacteria (RAB) including those that colonize the root rhizosphere and endosphere, which can adapt to As contamination and improve plant health. As(III)-oxidizing RAB can convert the more toxic arsenite (As(III)) to less toxic arsenate (As(V)) under As-rich conditions, which may promote plant survial. Previous studies have shown that microbial As(III) oxidation occurs in the rhizospheres and endospheres of P. vittata. However, knowledge of RAB of P. vittata responsible for As(III) oxidation remained limited. In this study, members of the Comamonadaceae family were identified as putative As(III) oxidizers, and the core microbiome associated with P. vittata roots using DNA-stable isotope probing (SIP), amplicon sequencing and metagenomic analysis. Metagenomic binning revealed that metagenome assembled genomes (MAGs) associated with Comamonadaceae contained several functional genes related to carbon fixation, arsenic resistance, plant growth promotion and bacterial colonization. As(III) oxidation and plant growth promotion may be key features of RAB in promoting P. vittata growth. These results extend the current knowledge of the diversity of As(III)-oxidizing RAB and provide new insights into improving the efficiency of arsenic phytoremediation.

Diversity and functional traits of seed endophytes of Dysphania ambrosioides from heavy metal contaminated and non-contaminated areas

Seed endophytes played a crucial role on host plants stress tolerance and heavy metal (HM) accumulation. Dysphania ambrosioides is a hyperaccumulator and showed strong tolerance and extraordinary accumulation capacities of multiple HMs. However, little is known about its seed endophytes response to field HM-contamination, and its role on host plants HM tolerance and accumulation. In this study, the seed endophytic community of D. ambrosioides from HM-contaminated area (H) and non-contaminated area (N) were investigated by both culture-dependent and independent methods. Moreover, Cd tolerance and the plant growth promoting (PGP) traits of dominant endophytes from site H and N were evaluated. The results showed that in both studies, HM-contamination reduced the diversity and richness of endophytic community and changed the most dominant endophyte, but increased resistant species abundance. By functional trait assessments, a great number of dominant endophytes displayed multiple PGP traits and Cd tolerance. Interestingly, soil HM-contamination significantly increased the percentage of Cd tolerance isolates of Agrobacterium and Epicoccum, but significantly decreased the ration of Agrobacterium with the siderophore production ability. However, the other PGP traits of isolates from site H and N showed no significant difference. Therefore, it was suggested that D. ambrosioides might improve its HM tolerance and accumulation through harboring more HM-resistant endophytes rather than PGP endophytes, but to prove this, more work need to be conducted in the future.

Improving Lead Phytoremediation Using Endophytic Bacteria Isolated from the Pioneer Plant Ageratina adenophora (Spreng.) from a Mining Area

This study aimed to isolate and characterise endophytic bacteria from the pioneer plant Ageratina adenophora in a mining area. Seven strains of metal-resistant endophytic bacteria that belong to five genera were isolated from the roots of A. adenophora. These strains exhibited various plant growth-promoting (PGP) capabilities. Sphingomonas sp. ZYG-4, which exhibited the ability to secrete indoleacetic acid (IAA; 53.2 ± 8.3 mg·L-1), solubilize insoluble inorganic phosphates (Phosphate solubilization; 11.2 ± 2.9 mg·L-1), and regulate root ethylene levels (1-aminocyclopropane-1-carboxylic acid deaminase activity; 2.87 ± 0.19 µM α-KB·mg-1·h-1), had the highest PGP potential. Therefore, Sphingomonas sp. ZYG-4 was used in a pot experiment to study its effect on the biomass and Pb uptake of both host (Ageratina adenophora) and non-host (Dysphania ambrosioides) plants. Compared to the uninoculated control, Sphingomonas sp. ZYG-4 inoculation increased the biomass of shoots and roots by 59.4% and 144.4% for A. adenophora and by 56.2% and 57.1% for D. ambrosioides, respectively. In addition, Sphingomonas sp. ZYG-4 inoculation enhanced Pb accumulation in the shoot and root by 268.9% and 1187.3% for A. adenophora, and by 163.1% and 343.8% for D. ambrosioides, respectively, compared to plants without bacterial inoculation. Our research indicates that endophytic bacteria are promising candidates for enhancing plant growth and facilitating microbe-assisted phytoremediation in heavy metal-contaminated soil.

Exploring the potential of endophyte-plant interactions for improving crop sustainable yields in a changing climate

Climate change poses a major threat to global food security, significantly reducing crop yields as cause of abiotic stresses, and for boosting the spread of new and old pathogens and pests. Sustainable crop management as a route to mitigation poses the challenge of recruiting an array of solutions and tools for the new aims. Among these, the deployment of positive interactions between the micro-biotic components of agroecosystems and plants can play a highly significant role, as part of the agro-ecological revolution. Endophytic microorganisms have emerged as a promising solution to tackle this challenge. Among these, Arbuscular Mycorrhizal Fungi (AMF) and endophytic bacteria and fungi have demonstrated their potential to alleviate abiotic stresses such as drought and heat stress, as well as the impacts of biotic stresses. They can enhance crop yields in a sustainable way also by other mechanisms, such as improving the nutrient uptake, or by direct effects on plant physiology. In this review we summarize and update on the main types of endophytes, we highlight several studies that demonstrate their efficacy in improving sustainable yields and explore possible avenues for implementing crop-microbiota interactions. The mechanisms underlying these interactions are highly complex and require a comprehensive understanding. For this reason, omic technologies such as genomics, transcriptomics, proteomics, and metabolomics have been employed to unravel, by a higher level of information, the complex network of interactions between plants and microorganisms. Therefore, we also discuss the various omic approaches and techniques that have been used so far to study plant-endophyte interactions.

Physiological characteristics, rhizosphere soil properties, and root-related microbial communities of Trifolium repens L. in response to Pb toxicity

Trifolium repens L. (T. repens) is considered a potential phytoremediation species due to its large biomass and ability to accumulate and tolerate heavy metals. Lead (Pb) is an important heavy metal pollutant that can affect plant growth, photosynthesis, and enzyme activity. However, response mechanism of microorganisms in three root niches of metal tolerant plants to Pb is not completely understood. Therefore, in this study, a Pb poisoning model of T. repens was established with a Pb gradient (0, 1000 mg/kg, 2000 mg/kg, and 3000 mg/kg), and was used to evaluate growth and physiological responses, as well as enrichment and transport coefficients in T. repens, and explore the characteristics of rhizosphere soil and microbial composition of three root niches. We found that Pb stress caused oxidative injury, and inhibited photosynthesis in T. repens. 16S rDNA sequencing analysis showed that the richness of microbial communities in bulk soil was higher than that in rhizosphere soil both under Pb stress and Pb nonstress conditions. Moreover, Proteobacteria was dominant phylum in bulk and rhizosphere soils, and Proteobacteria and Cyanobacteria were dominant phylum in endophytic bacteria. For the first time, we systematically investigated the response of Pb from bulk soil to plant leaves. The results showed that microbial interaction existed between bulk and rhizosphere soil. Rhizosphere bacterium Haliangium was positively correlated with urease activity and soil nutrients. Endophytic bacterium Pseudomonas was positively correlated with plant biomass and played an important role in Pb tolerance of T. repens. In addition, endophytic bacteria formed complex correlation networks with growth and physiological indexes of both root and shoot, moreover the network in root was more complicated. Taken together, Pb stress dose-dependently inhibited the growth of plants. This study provided a theoretical basis for the further development of microbial cooperation with plant remediation of heavy metal contaminated soil.

Understanding the bacterial community structure associated with the Eichhornia crassipes rootzone

BACKGROUND

Plant microbiome acts as an interface between plants and their environment, aiding in the functioning of the ecosystem, such as protection against abiotic and biotic stress along with improving nutrient uptake. The rhizosphere is an essential interface for the interaction between plants and microbes and plays a substantial part in the removal as well as uptake of heavy metals and antibiotics from contaminated locations. Eichhornia crassipes is a promising plant that contains a rich community of microbes in its rhizosphere. Microorganism's association with plants embodies a crucial pathway via which humans can also be exposed to antibiotic-resistant genes and bacteria.

METHODS AND RESULTS

In our earlier study enhanced removal of ciprofloxacin was observed by plant growth-promoting Microbacterium sp. WHC1 in the presence of E. crassipes root exudates. Therefore, the V3-V4, hypervariable region of the 16 S rRNA gene was studied to assess the bacterial diversity and functional profiles of the microbiota associated with plant roots. Using the QIIME software program, 16 S rRNA data from the Next Generation Sequencing (NGS) platform was examined. Alpha diversity including Chao1, Observed Shannon, and Simpson index denote significantly higher bacterial diversity. Proteobacteria (79%) was the most abundant phylum which was present in the root samples followed by Firmicutes (8%) and Cyanobacteria (8%). Sulfuricurvum (36%) is the most abundant genus belonging to the family Helicobacteraceae and the species kujiense in the genus Sulfuricurvum is the most abundant species present in the root sample. Also, the bacterial communities in the rhizoplane of Eichhornia crassipes harbor the genes conferring resistance to beta-lactams, tetracycline, fluoroquinolones, and penams.

CONCLUSION

Metagenomic studies on the E. crassipes microbiome showed that the bacterial communities constituting the root exudates of the Eichhornia aid them to survive in a polluted environment.

ABA-metabolizing bacteria and rhamnolipids as valuable allies for enhancing phytoremediation efficiency in heavy metal-contaminated soils

Microbial-assisted phytoremediation has great potential to improve the efficiency of phytoremediation in heavy metal (HM)-contaminated soils. In this study, the synergistic effects of rhamnolipids and the abscisic acid (ABA)-metabolizing bacterium Rhodococcus qingshengii on the phytoremediation efficiency of Indian mustard (Brassica juncea) in HM-contaminated soils were investigated. The Cd, Zn, and Pb contents in plants treated with a combination of rhamnolipids and R. qingshengii were 48.4-77.1 %, 14.6-40.4 %, and 16.1-20.0 % higher, respectively, than in those treated with R. qingshengii alone, and 42.8-59.2 %, 13.1-48.2 %, and 7.3-67.5 % higher, respectively, than in those treated with rhamnolipids alone. In addition, the bioconcentration factors of each metal were improved, and the biomass further increased by 36.6-65.7 % compared to that of single treatments. Pearson's correlation analysis showed that rhamnolipids and R. qingshengii enhanced the accumulation of HMs in B. juncea by activating the available forms of HMs in the soil and regulating the ABA and indole-3-acetic acid in plants, respectively. The structural equation model indicated that R. qingshengii had a larger path coefficient than rhamnolipids in terms of HM content and plant biomass, suggesting that R. qingshengii may have a greater contribution to promoting the extraction of HMs from the soil under synergistic conditions. In conclusion, the combination of rhamnolipids and R. qingshengii has great potential to enhance the phytoremediation efficiency of hyperaccumulating plants in HM-contaminated soils.

Influence of biofertilizer on heavy metal bioremediation and enzyme activities in the soil to revealing the potential for sustainable soil restoration

Overuse of chemical fertilizer and pesticides in agricultural activity is frequently damaging to soil health and can accumulate heavy metals in the soil environment, causing harm to plants, humans, and the ecosystem. This study was done to evaluate the effectiveness of biofertilizers in reducing heavy metal levels in contaminated soil and enhancing the activity of soil enzymes that are crucial to plant growth and development. Two bacteria strains, Pseudomonas aeruginosa. and Bacillus firmus, were chosen to develop biofertilizers based on molasses. The pot experiment was setup using a completely randomized design with four treatments and five levels; Bacillus firmus and Pseudomonas aeruginosa were used separately, and they were combined for the biofertilizer dose (20, 40, 60, 80, and 100 mL). Utilizing contaminated soils taken from a greenhouse farm the effect of biofertilizer on heavy metal bioremediation and soil enzyme activity was examined. Methods of soil agrochemical analysis were used to determine the soil physiochemical properties and the concentrations of heavy metals Cu, Fe, Zn, Cd, Mo, Mn, were determined by inductively coupled plasma-mass spectrometry ICP-MS, following DTPA extraction methods. In results, soil pH decreased from 8.28 to 7.39, Ec increased from 0.91 to 1.12, organic matter increased from 18.88 to 20.63 g/kg, N increased gradually from 16.7 to 24.4 mg/kg, and K increased from 145.25 to 201.4 mg/kg. The effect of biofertilizer treatment on soil physiochemical characteristics was significantly positive. Application of biofertilizer significantly increased the heavy metal bioavailability and the activities of soil enzymes. Soil pH were positively correlated with soil Zn (0.99819*), APK (0.95869*) activity and negatively correlated with Fe (0.96759*) also statistically significant at (p < 0.05). The soil Cu positively correlated with Fe (0.99645*), Cd (0.97866*), β.D.GLU (0.99769*) and negatively correlated with PAK (- 0.9624*). Soil ARY had positive correlation with soil Mn (0.99683*), Cd (0.95695*), and negative correlation with PAK (- 0.99424*) at (p < 0.05). Soil enzyme activities were negatively correlated to heavy metals at a significant level. Collectively, the study highlights the potential of biofertilizers as a sustainable and effective approach to enhance soil health and remediate heavy metal-contaminated soils in greenhouses.

Synthesis, characterization, and reusability of novel nanobiocomposite of endophytic fungus Aspergillus flavus and magnetic nanoparticles (Fe3O4) with dye bioremediation potential

The incorrect disposal of textile dyes, such as Reactive Black 5 (RB5), causes several problems for living beings and the quality of the environment. Nanobiocomposites (NBC) produced from endophytic fungi (potentially remediation dyes-agents) and magnetic nanoparticles have high biotechnological potential due to their superparamagnetic behavior, which would allow their recovery through the magnetic field after the bioremediation process. This work aimed to obtain a new nanobiocomposite from the interaction of magnetite nanoparticles (Fe3O4) with the endophyte Aspergillus flavus (Af-CL-7) to evaluate its bioremediation capacity and to reduce the toxicity of RB5 and its reuse. Before obtaining the NBC, Af-CL-7 showed discoloration of RB5 and it was tolerant to all tested concentrations of this dye. The discovery of the nanobiocomposite textile dye bioremediator product presents a significant environmental advantage by addressing the issue of water pollution caused by textile dyes. The NBC called Af-Fe3O4 was successfully obtained with the magnetized endophyte, and their magnetic properties were verified by VSM analysis and by action of magnetic fields generated by Nd-Fe-B magnets SEM analyzes showed that the nanoparticles did not cause any damage to the hypha morphology, and TEM analyzes confirmed the presence of nanoparticles in the fungus wall and also inside the cell. The NBC Af-Fe3O4 and Af-CL-7 showed, respectively, 96.1% and 92.2% of RB5 discoloration in the first use, 91.1% e 86.2% of discoloration in the validation test, and 89.0% in NBC reuse. In the toxicological bioassay with Lactuca sativa seeds, NBC showed a positive reduction in the toxicity of RB5 after treatment, allowing the hypocotyl growth to be statistically similar to the control with water. Thus, we highlight the promising obtaining process of NBC that could be applied in bioremediation of contaminated waters, wherein the industrial economic cost will depend on the fermentation efficiency, biomass production and nanoparticle synthesis.

Recent progress on emerging technologies for trace elements-contaminated soil remediation

Abiotic stresses from potentially toxic elements (PTEs) have devastating impacts on health and survival of all living organisms, including humans, animals, plants, and microorganisms. Moreover, because of the rapid growing industrial activities together with the natural processes, soil contamination with PTEs has pronounced, which required an emergent intervention. In fact, several chemical and physical techniques have been employed to overcome the negative impacts of PTEs. However, these techniques have numerous drawback and their acceptance are usually poor as they are high cost, usually ineffectiveness and take longer time. In this context, bioremediation has emerged as a promising approach for reclaiming PTEs-contaminated soils through biological process using bacteria, fungus and plants solely or in combination. Here, we comprehensively reviews and critically discusses the processes by which microorganisms and hyperaccumulator plants extract, volatilize, stabilize or detoxify PTEs in soils. We also established a multi-technology repair strategy through the combination of different strategies, such as the application of biochar, compost, animal minure and stabilized digestate for stimulation of PTE remediation by hyperaccumulators plants species. The possible use of remote sensing of soil in conjunction with geographic information system (GIS) integration for improving soil bio-remediation of PTEs was discussed. By synergistically combining these innovative strategies, the present review will open very novel way for cleaning up PTEs-contaminated soils.

Root Exposure of Graphitic Carbon Nitride (g-C3N4) Modulates Metabolite Profile and Endophytic Bacterial Community to Alleviate Cadmium- and Arsenate-Induced Phytotoxicity to Rice (Oryza sativa L.)

To investigate the mechanisms by which g-C3N4 alleviates metal(loid)-induced phytotoxicity, rice seedlings were exposed to 100 and 250 mg/kg graphitic carbon nitride (g-C3N4) with or without coexposure to 10 mg/kg Cd and 50 mg/kg As for 30 days. Treatment with 250 mg/kg g-C3N4 significantly increased shoot and root fresh weight by 22.4-29.9%, reduced Cd and As accumulations in rice tissues by 20.6-26.6%, and elevated the content of essential nutrients (e.g., K, S, Mg, Cu, and Zn) compared to untreated controls. High-throughput sequencing showed that g-C3N4 treatment increased the proportion of plant-growth-promoting endophytic bacteria, including Streptomyces, Saccharimonadales, and Thermosporothrix, by 0.5-3.30-fold; these groups are known to be important to plant nutrient assimilation, as well as metal(loid) resistance and bioremediation. In addition, the population of Deinococcus was decreased by 72.3%; this genus is known to induce biotransformation As(V) to As(III). Metabolomics analyses highlighted differentially expressed metabolites (DEMs) involved in the metabolism of tyrosine metabolism, pyrimidines, and purines, as well as phenylpropanoid biosynthesis related to Cd/As-induced phytotoxicity. In the phenylpropanoid biosynthesis pathway, the increased expression of 4-coumarate (1.13-fold) and sinapyl alcohol (1.26-fold) triggered by g-C3N4 coexposure with Cd or As played a critical role in promoting plant growth and enhancing rice resistance against metal(loid) stresses. Our findings demonstrate the potential of g-C3N4 to enhance plant growth and minimize the Cd/As-induced toxicity in rice and provide a promising nanoenabled strategy for remediating heavy metal(loid)-contaminated soil.

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste

Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.

Plant growth-promoting rhizobacteria: A good companion for heavy metal phytoremediation

Phytoremediation is an environment-friendly approach regarded as a potential candidate for remediating heavy metal (HM)-contaminated soils. However, the low efficacy of phytoremediation is a major limitation that hampers its large-scale application. Therefore, developing strategies to enhance phytoremediation efficacy for contaminated soils is crucial. Plant growth-promoting rhizobacteria (PGPR) considerably contribute to phytoremediation intensification. To improve the efficiency of plant-microbe symbiosis for remediation, the mechanisms underlying PGPR-stimulated HM accumulation and tolerance in plants should be comprehensively understood. This review focuses on hyperaccumulators, PGPR, and the mechanisms by which PGPR enhance phytoremediation from four aspects: providing nutrients to plants, secreting plant hormones and specific enzymes, inducing systemic resistance, and altering the bioavailability of HMs in soils. It also provides a theoretical and technical basis for future research on PGPR synergism in promoting the phytoextraction efficiency in HM-contaminated soils.

Endophyte inoculation enhanced microbial metabolic function in the rhizosphere benefiting cadmium phytoremediation by Phytolaccaacinosa

Microbial metabolic activities in rhizosphere soil play a critical role in plant nutrient utilization and metal availability. However, its specific characteristics and influence on endophyte assisted phytoremediation remains unclear. In this study, an endophyte strain Bacillus paramycoides (B. paramycoides) was inoculated in the rhizosphere of Phytolacca acinosa (P. acinosa), and microbial metabolic characteristics of rhizosphere soils were analyzed using Biolog system to investigate how they influence phytoremediation performance of different types of cadmium contaminated soil. The results indicated that endophyte B. paramycoides inoculation enhanced bioavailable Cd percentage by 9-32%, resulting in the increased Cd uptake (32-40%) by P. acinosa. With endophyte inoculation, the utilization of carbon sources was significantly promoted by 4-43% and the microbial metabolic functional diversity increased by 0.4-36.8%. Especially, B. paramycoides enhanced the utilization of recalcitrant substrates carboxyl acids, phenolic compounds and polymers by 48.3-225.6%, 42.4-65.8% and 15.6-25.1%, respectively. Further, the microbial metabolic activities were significant correlated with rhizosphere soil microecology properties and impact phytoremediation performance. This study provided new insight into the microbial processes during endophyte assisted phytoremediation.

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

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.

The combined rhizoremediation by a triad: plant-microorganism-functional materials

The article describes new strategies for the remediation of soils contaminated with organic and inorganic pollutants. The aim of this study is to investigate the synergistic effects of combining plant-microorganism-functional materials for a more effective reduction of soil contamination with toxic chemicals. The innovative triad involves functional materials as a habitat for microorganisms, which helps to control the release of pollutants into the soil solution from the adsorbed form. This, in turn, reduces the toxic effect on microorganisms and plants. Microorganisms play a complex role, consisting of partial biodegradation of pollutants, stimulation of plant growth, and support for nutrient supply. Plants synthesize root exudates that facilitate microorganisms in biodegrading organic pollutants and stimulate their growth. The plant takes up pollutants through the root system, which can be further supported by endophytic microorganisms. The cooperation of the three players produces a synergistic effect that enhances the effectiveness of rhizodegradation supported by functional materials, which is more effective than using microorganisms, phytoremediation, or functional materials alone. The combination of physicochemical methods (functional materials) and microbiological methods (bacteria and fungi, rhizosphere, symbiotic and non-symbiotic) supported by plants (hyperaccumulators) is a promising approach for reducing chemicals from soil. Key examples of the synergistic effects of combining plant-microorganism-functional materials have been provided in this article.

Rhizospheric bacteria: the key to sustainable heavy metal detoxification strategies

The increasing rate of industrialization, anthropogenic, and geological activities have expedited the release of heavy metals (HMs) at higher concentration in environment. HM contamination resulting due to its persistent nature, injudicious use poses a potential threat by causing metal toxicities in humans and animals as well as severe damage to aquatic organisms. Bioremediation is an emerging and reliable solution for mitigation of these contaminants using rhizospheric microorganisms in an environmentally safe manner. The strategies are based on exploiting microbial metabolism and various approaches developed by plant growth promoting bacteria (PGPB) to minimize the toxicity concentration of HM at optimum levels for the environmental clean-up. Rhizospheric bacteria are employed for significant growth of plants in soil contaminated with HM. Exploitation of bacteria possessing plant-beneficial traits as well as metal detoxifying property is an economical and promising approach for bioremediation of HM. Microbial cells exhibit different mechanisms of HM resistance such as active transport, extra cellular barrier, extracellular and intracellular sequestration, and reduction of HM. Tolerance of HM in microorganisms may be chromosomal or plasmid originated. Proteins such as MerT and MerA of mer operon and czcCBA, ArsR, ArsA, ArsD, ArsB, and ArsC genes are responsible for metal detoxification in bacterial cell. This review gives insights about the potential of rhizospheric bacteria in HM removal from various polluted areas. In addition, it also gives deep insights about different mechanism of action expressed by microorganisms for HM detoxification. The dual-purpose use of biological agent as plant growth enhancement and remediation of HM contaminated site is the most significant future prospect of this article.

Arsenic (As) oxidation by core endosphere microbiome mediates As speciation in Pteris vittata roots

Pteris vittata is an arsenic(As)-hyperaccumulator that may be employed in phytoremediation of As-contaminated soils. P. vittata-associated microbiome are adapted to elevated As and may be important for host survival under stresses. Although P. vittata root endophytes could be critical for As biotransformation in planta, their compositions and metabolisms remain elusive. The current study aims to characterize the root endophytic community composition and As-metabolizing potentials in P. vittata. High As(III) oxidase gene abundances and rapid As(III) oxidation activity indicated that As(III) oxidation was the dominant microbial As-biotransformation processes compared to As reduction and methylization in P. vittata roots. Members of Rhizobiales were the core microbiome and the dominant As(III) oxidizers in P. vittata roots. Acquasition of As-metabolising genes, including both As(III) oxidase and As(V) detoxification reductase genes, through horizontal gene transfer was identified in a Saccharimonadaceae genomic assembly, which was another abundant population residing in P. vittata roots. Acquisition of these genes might improve the fitness of Saccharimonadaceae population to elevated As concentrations in P. vittata. Diverse plant growth promoting traits were encoded by the core root microbiome populations Rhizobiales. We propose that microbial As(III) oxidation and plant growth promotion are critical traits for P. vittata survival in hostile As-contaiminated sites.

Endophytic Plant Growth-Promoting Bacterium Bacillus subtilis Reduces the Toxic Effect of Cadmium on Wheat Plants

Heavy metal ions, in particular cadmium (Cd), have a negative impact on the growth and productivity of major crops, including wheat. The use of environmentally friendly approaches, in particular, bacteria that have a growth-stimulating and protective effect, can increase the resistance of plants. The effects of the pre-sowing seed treatment with the plant growth-promoting endophyte Bacillus subtilis 10-4 (BS) on cadmium acetate (Cd)-stressed Triticum aestivum L. (wheat) growth, photosynthetic pigments, oxidative stress parameters, roots' lignin content, and Cd ions accumulation in plants were analyzed. The results showed that the tested Cd-tolerant BS improved the ability of wheat seeds to germinate in the presence of different Cd concentrations (0, 0.1, 0.5, and 1 mM). In addition, the bacterial treatment significantly decreased the damaging effects of Cd stress (1 mM) on seedlings' linear dimensions (lengths of roots and shoots), biomass, as well as on the integrity and permeability of the cell walls (i.e., lipid peroxidation and electrolyte leakage) and resulted in reduced H₂O₂ generation. The pretreatment with BS prevented the Cd-induced degradation of the leaf photosynthetic pigments chlorophyll (Chl) a, Chl b, and carotenoids. Moreover, the bacterial treatment intensified the lignin deposition in the roots under normal and, especially, Cd stress conditions, thereby enhancing the barrier properties of the cell wall. This manifested in a reduced Cd ions accumulation in the roots and in the restriction of its translocation to the aboveground parts (shoots) of the bacterized plants under Cd stress in comparison with non-bacterized controls. Thus, the pre-sowing seed treatment with the endophyte BS may serve as an eco-friendly approach to improve wheat production in Cd-contaminated areas.

Effect of Heavy-Metal-Resistant PGPR Inoculants on Growth, Rhizosphere Microbiome and Remediation Potential of Miscanthus × giganteus in Zinc-Contaminated Soil

Microbial-assisted phytoremediation is considered a more effective approach to soil rehabilitation than the sole use of plants. Mycolicibacterium sp. Pb113 and Chitinophaga sp. Zn19, heavy-metal-resistant PGPR strains originally isolated from the rhizosphere of Miscanthus × giganteus, were used as inoculants of the host plant grown in control and zinc-contaminated (1650 mg/kg) soil in a 4-month pot experiment. The diversity and taxonomic structure of the rhizosphere microbiomes, assessed with metagenomic analysis of rhizosphere samples for the 16S rRNA gene, were studied. Principal coordinate analysis showed differences in the formation of the microbiomes, which was affected by zinc rather than by the inoculants. Bacterial taxa affected by zinc and the inoculants, and the taxa potentially involved in the promotion of plant growth as well as in assisted phytoremediation, were identified. Both inoculants promoted miscanthus growth, but only Chitinophaga sp. Zn19 contributed to significant Zn accumulation in the aboveground part of the plant. In this study, the positive effect of miscanthus inoculation with Mycolicibacterium spp. and Chitinophaga spp. was demonstrated for the first time. On the basis of our data, the bacterial strains studied may be recommended to improve the efficiency of M. × giganteus phytoremediation of zinc-contaminated soil.

Bioaccumulation and Bioremediation of Heavy Metals in Fishes-A Review

Heavy metals, the most potent contaminants of the environment, are discharged into the aquatic ecosystems through the effluents of several industries, resulting in serious aquatic pollution. This type of severe heavy metal contamination in aquaculture systems has attracted great attention throughout the world. These toxic heavy metals are transmitted into the food chain through their bioaccumulation in different tissues of aquatic species and have aroused serious public health concerns. Heavy metal toxicity negatively affects the growth, reproduction, and physiology of fish, which is threatening the sustainable development of the aquaculture sector. Recently, several techniques, such as adsorption, physio-biochemical, molecular, and phytoremediation mechanisms have been successfully applied to reduce the toxicants in the environment. Microorganisms, especially several bacterial species, play a key role in this bioremediation process. In this context, the present review summarizes the bioaccumulation of different heavy metals into fishes, their toxic effects, and possible bioremediation techniques to protect the fishes from heavy metal contamination. Additionally, this paper discusses existing strategies to bioremediate heavy metals from aquatic ecosystems and the scope of genetic and molecular approaches for the effective bioremediation of heavy metals.

Cadmium stimulated cooperation between bacterial endophytes and plant intrinsic detoxification mechanism in Lonicera japonica thunb

Due to the intimate association between plant physiology and metabolism, the internal colonizing microbe (endophytes) community must be adjusted to support plant productivity in response to cell damage in plants under stress. However, how endophytes coordinate their activities with plant intrinsic mechanisms such as antioxidative systems and detoxification pathways during Cd accumulation remains unknown. In this hydroponic pot study, we investigated how exposure of Lonicera japonica. thunb. to different levels of Cd (0.5, 2.5, 5, 10, and 20 mg kg^-1) affected plant growth, metabolic pathways, and endophyte community structure and function. Although Cd accumulation increased at 5 mg kg^-1 Cd, the biomass and height of L. japonica increased in association with elevated endophyte-involved plant detoxification activities. Endophytes, such as Sphingomonas, Klenkia, and Modestobacter, expressed major antioxidative regulators (superoxide dismutase and ascorbate acid) to detoxify Cd in L. japonica. Furthermore, L. japonica and its endophytes synergistically regulated the toxic effects of Cd accumulation via multiple plant metabolic defensive pathways to increase resistance to metal-induced stress.

Inoculation of Exogenous Complex Bacteria to Enhance Resistance in Alfalfa and Combined Remediation of Heavy Metal-Contaminated Soil

Heavy metals are considered to be one of the main sources of soil contamination. In this study, three tolerant bacteria were isolated from the heavy metal-contaminated soil in mining area, and immobilized bacteria were constructed using corn straw as the carrier. The combined remediation effect of immobilized bacteria and alfalfa in pot experiments was explored in heavy metal-contaminated soil. Under heavy metal stress, inoculation with immobilized bacteria significantly promoted the growth of alfalfa, in which the dry weights of roots, stems, and leaves increased by 19.8, 6.89, and 14.6%, respectively (P < 0.05). Also, inoculation with immobilized bacteria improved the antioxidant capacity of plants and the activity of soil enzymes and improved soil quality (P < 0.05). Microbial-phytoremediation technology effectively reduced the heavy metal content in the soil, and can restore the soil contaminated by heavy metals. The results will help to further understand the mechanism of microbial inoculation to reduce the toxicity of heavy metals, and provide guidance for the cultivation of forage grasses in heavy metal-contaminated soils.

Endophytes in Agriculture: Potential to Improve Yields and Tolerances of Agricultural Crops

Endophytic fungi and bacteria live asymptomatically within plant tissues. In recent decades, research on endophytes has revealed that their significant role in promoting plants as endophytes has been shown to enhance nutrient uptake, stress tolerance, and disease resistance in the host plants, resulting in improved crop yields. Evidence shows that endophytes can provide improved tolerances to salinity, moisture, and drought conditions, highlighting the capacity to farm them in marginal land with the use of endophyte-based strategies. Furthermore, endophytes offer a sustainable alternative to traditional agricultural practices, reducing the need for synthetic fertilizers and pesticides, and in turn reducing the risks associated with chemical treatments. In this review, we summarise the current knowledge on endophytes in agriculture, highlighting their potential as a sustainable solution for improving crop productivity and general plant health. This review outlines key nutrient, environmental, and biotic stressors, providing examples of endophytes mitigating the effects of stress. We also discuss the challenges associated with the use of endophytes in agriculture and the need for further research to fully realise their potential.

A comprehensive review on chromium (Cr) contamination and Cr(VI)-resistant extremophiles in diverse extreme environments

Chromium (Cr) compounds are usually toxins and exist abundantly in two different forms, Cr(VI) and Cr(III), in nature. Their contamination in any environment is a major problem. Many extreme environments including cold climate, warm climate, acidic environment, basic/alkaline environment, hypersaline environment, radiation, drought, high pressure, and anaerobic conditions have accumulated elevated Cr contamination. These harsh physicochemical conditions associated with Cr(VI) contamination damage biological systems in various ways. However, several unique microorganisms belonging to phylogenetically distant taxa (bacteria, fungi, and microalgae) owing to different and very distinct physiological characteristics can withstand extremities of Cr(VI) in different physicochemical environments. These challenging situations offer great potential and extended proficiencies in extremophiles for environmental and biotechnological applications. On these issues, the present review draws attention to Cr(VI) contamination from diverse extreme environmental regions. The study gives a detailed account on the ecology and biogeography of Cr(VI)-resistant microorganisms in inhospitable environments, and their use for detoxifying Cr(VI) and other applications. The study also focuses on physiological, multi-omics, and genetic engineering approaches of Cr(VI)-resistant extremophiles.

Trends in Harnessing Plant Endophytic Microbiome for Heavy Metal Mitigation in Plants: A Perspective

Plant microbiomes represent dynamic entities, influenced by the environmental stimuli and stresses in the surrounding conditions. Studies have suggested the benefits of commensal microbes in improving the overall fitness of plants, besides beneficial effects on plant adaptability and survival in challenging environmental conditions. The concept of 'Defense biome' has been proposed to include the plant-associated microbes that increase in response to plant stress and which need to be further explored for their role in plant fitness. Plant-associated endophytes are the emerging candidates, playing a pivotal role in plant growth, adaptability to challenging environmental conditions, and productivity, as well as showing tolerance to biotic and abiotic stresses. In this article, efforts have been made to discuss and understand the implications of stress-induced changes in plant endophytic microbiome, providing key insights into the effects of heavy metals on plant endophytic dynamics and how these beneficial microbes provide a prospective solution in the tolerance and mitigation of heavy metal in contaminated sites.

Current status and future prospect of managing lead (Pb) stress through microbes for sustainable agriculture

Soil is an important residence under various biotic and abiotic conditions. Contamination of soil by various means has hazardous effects on both plants and humans. Soil contamination by heavy metals occurs due to various man-made activities, including improper industrial and agricultural practices. Among the heavy metals, after arsenic, lead (Pb) was found to be the second most toxic metal and potent pollutants that accumulate in sediments and soils. Pb is not considered an essential element for promoting plant growth but is readily absorbed and accumulated in different plant parts. Many parameters such as pH, root exudation, soil particle size, cation exchange capacity, and other physicochemical parameters are involved in Pb uptake in plants. Excess amounts of Pb pose a threat to plant growth and cause toxicity such as chlorosis, blackening of the root system, and stunted growth. Pb toxicity may inhibit photosynthesis, disturb water balance and mineral nutrition, and alter the hormonal status, structure, and membrane permeability of plants. Therefore, this review addresses the effects of Pb toxicity and its impact on plant growth, including the morphological, physiological, and biological effects of Pb toxicity, the mechanisms behind different strategies promoting plant growth, and in combating Pb-induced stress. The bioremediation strategy for Pb removal from Pb-contaminated soil also plays an important role in combating Pb toxicity using bacterial community. Pb-contaminated soil may be remediated using different technologies such as rhizofiltration and phytoremediation, which tend to have a great capacity to curb Pb-contamination within the soil.