Inoculation of Sinorhizobium saheli YH1 Leads to Reduced Metal Uptake for Leucaena leucocephala Grown in Mine Tailings and Metal-Polluted Soils

Application of rhizobium inoculation in regulating heavy metals in legumes: A meta-analysis

Rhizobium inoculation has been widely applied to alleviate heavy metal (HM) stress in legumes grown in contaminated soils, but it has generated inconsistent results with regard to HM accumulation in plant tissues. Here, we conducted a meta-analysis to assess the performance of Rhizobium inoculation for regulating HM in legumes and reveal the general influencing factors and processes. The meta-analysis showed that Rhizobium inoculation in legumes primarily increased the total HM uptake by stimulating plant biomass growth rather than HM phytoavailability. Inoculation had no significant effect on the average shoot HM concentration (p > 0.05); however, it significantly increased root HM uptake by 61 % and root HM concentration by 7 % (p < 0.05), indicating safe agricultural production while facilitating HM phytostabilisation. Inoculation decreased shoot HM concentrations and increased root HM uptake in Vicia, Medicago and Glycine, whereas it increased shoot HM concentrations in Sulla, Cicer and Vigna. The effects of inoculation on shoot biomass were suppressed by nitrogen fertiliser and native microorganisms, and the effect on shoot HM concentration was enhanced by high soil pH, organic matter content, and phosphorous content. Inoculation-boosted shoot nutrient concentration was positively correlated with increased shoot biomass, whereas the changes in pH and organic matter content were insufficient to significantly affect accumulation outcomes. Nitrogen content changes in the soil were positively correlated with changes in root HM concentration and uptake, whereas nitrogen translocation changes in the tissues were positively correlated with changes in HM translocation. Phosphorus solubilisation could improve HM phytoavailability at the expense of slight biomass promotion. These results suggest that the diverse growth-promoting characteristics of Rhizobia influence the trade-off between biomass-HM phytoavailability and HM translocation, impacting HM accumulation outcomes. Our findings can assist in optimising the utilisation of legume-Rhizobium systems in HM-contaminated soils.

PGPR-Enabled bioremediation of pesticide and heavy metal-contaminated soil: A review of recent advances and emerging challenges

The excessive usage of agrochemicals, including pesticides, along with various reckless human actions, has ensued discriminating prevalence of pesticides and heavy metals (HMs) in crop plants and the environment. The enhanced exposure to these chemicals is a menace to living organisms. The pesticides may get bioaccumulated in the food chain, thereby leading to several deteriorative changes in the ecosystem health and a rise in the cases of some serious human ailments including cancer. Further, both HMs and pesticides cause some major metabolic disturbances in plants, which include oxidative burst, osmotic alterations and reduced levels of photosynthesis, leading to a decline in plant productivity. Moreover, the synergistic interaction between pesticides and HMs has a more serious impact on human and ecosystem health. Various attempts have been made to explore eco-friendly and environmentally sustainable methods of improving plant health under HMs and/or pesticide stress. Among these methods, the employment of PGPR can be a suitable and effective strategy for managing these contaminants and providing a long-term remedy. Although, the application of PGPR alone can alleviate HM-induced phytotoxicities; however, several recent reports advocate using PGPR with other micro- and macro-organisms, biochar, chelating agents, organic acids, plant growth regulators, etc., to further improve their stress ameliorative potential. Further, some PGPR are also capable of assisting in the degradation of pesticides or their sequestration, reducing their harmful effects on plants and the environment. This present review attempts to present the current status of our understanding of PGPR's potential in the remediation of pesticides and HMs-contaminated soil for the researchers working in the area.

Microbial mediated remediation of heavy metals toxicity: mechanisms and future prospects

Heavy metal pollution has become a serious concern across the globe due to their persistent nature, higher toxicity, and recalcitrance. These toxic metals threaten the stability of the environment and the health of all living beings. Heavy metals also enter the human food chain by eating contaminated foods and cause toxic effects on human health. Thus, remediation of HMs polluted soils is mandatory and it needs to be addressed at higher priority. The use of microbes is considered as a promising approach to combat the adverse impacts of HMs. Microbes aided in the restoration of deteriorated environments to their natural condition, with long-term environmental effects. Microbial remediation prevents the leaching and mobilization of HMs and they also make the extraction of HMs simple. Therefore, in this context recent technological advancement allowed to use of bioremediation as an imperative approach to remediate polluted soils. Microbes use different mechanisms including bio-sorption, bioaccumulation, bioleaching, bio-transformation, bio-volatilization and bio-mineralization to mitigate toxic the effects of HMs. Thus, keeping in the view toxic HMs here in this review explores the role of bacteria, fungi and algae in bioremediation of polluted soils. This review also discusses the various approaches that can be used to improve the efficiency of microbes to remediate HMs polluted soils. It also highlights different research gaps that must be solved in future study programs to improve bioremediation efficency.

Advances in amelioration of air pollution using plants and associated microbes: An outlook on phytoremediation and other plant-based technologies

Globally, air pollution is an unfortunate aftermath of rapid industrialization and urbanization. Although the best strategy is to prevent air pollution, it is not always feasible. This makes it imperative to devise and implement techniques that can clean the air continuously. Plants and microbes have a natural potential to transform or degrade pollutants. Hence, strategies that use this potential of living biomass to remediate air pollution seem to be promising. The simplest future trend can be planting suitable plant-microbe species capable of removing air pollutants like SO2, CO2, CO, NOX and particulate matter (PM) along roadsides and inside the buildings. Established wastewater treatment strategies such as microbial fuel cells (MFC) and constructed wetlands (CW) can be suitably modified to ameliorate air pollution. Green architecture involving green walls and green roofs is facile and aesthetic, providing urban ecosystem services. Certain microbe-based bioreactors such as bioscrubbers and biofilters may be useful in small confined spaces. Several generative models have been developed to assist with planning and managing green spaces in urban locales. The physiological limitations of using living organisms can be circumvent by applying biotechnology and transgenics to improve their potential. This review provides a comprehensive update on not just the plants and associated microbes for the mitigation of air pollution, but also lists the technologies that are available and/or can be modified and used for air pollution control. The article also gives a detailed analysis of this topic in the form of strengths-weaknesses-opportunities-challenges (SWOC). The strategies mentioned in this review would help to attain corporate Environmental Social and Governance (ESG) and Sustainable Development Goals (SDGs), while reducing carbon footprint in the urban scenario. The review aims to emphasise that urbanization is possible while tackling air pollution using facile, green techniques involving plants and associated microbes.

Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review

Comprehending the structure and function of rhizobacteria components and their regulation are crucial for sustainable agricultural management. However, obtaining comprehensive species information for most bacteria in the natural environment, particularly rhizobacteria, presents a challenge using traditional culture methods. To obtain diverse and pure cultures of rhizobacteria, this study primarily reviews the evolution of rhizobacteria culturomics and associated culture methods. Furthermore, it explores new strategies for enhancing the application of culturomics, providing valuable insights into efficiently enriching and isolate target bacterial strains/groups from the environment. The findings will help improve rhizobacteria's culturability and enrich the functional bacterial library.

Mitigation of heavy metal stress in the soil through optimized interaction between plants and microbes

Agricultural as well as industrial processes, such as mining and textile activities, are just a few examples of anthropogenic activities that have a long-term negative impact on the environment. Each of the aforementioned factors increases the concentration of heavy metals in soil. Heavy metal contamination in soil causes a wide range of environmental issues and is harmful to microbes, plants, and animals. Because of their non-biodegradability and toxic effects, preventing additional metal contamination and remediating the vast majority of contaminated sites around the world is critical. Hence, this review focuses on the effects of metal contamination on soil microbes, as well as plant-microbe interactions. Plant-associated probiotics reduce metal accumulation; the introduction of beneficial microbes is regarded as one of the most promising approaches to improving metal stress tolerance; thus, the study focuses on plant-microbe interactions as well as their actual implications via phytoremediation. Plant-microbe interaction can play an important role in acclimating vegetation (plants) to metalliferous conditions and should thus be studied to improve microbe-aided metal tolerance in plants. Plant-interacted microbes reduce metal accumulation in plant cells and metal bioaccumulation in the soil through a variety of processes. A novel phytobacterial approach, such as genetically modified microbes, is now being used to improve heavy metal cleanup as well as stress tolerance among plants. This review examines our current understanding of such negative consequences of heavy metal stresses, signaling responses, and the role of plant-associated microbiota in heavy metal stress tolerance and interaction.

Assessment of PGP traits of Bacillus cereus NDRMN001 and its influence on Cajanus cajan (L.) Millsp. phytoremediation potential on metal-polluted soil under controlled conditions

The current study looked at the plant growth-promoting (PGP) traits of the pre-isolated and metal-tolerant Bacillus cereus NDRMN001 as well as their stimulatory effect on the physiology, biomolecule content, and phytoremediation potential of Cajanus cajan (L.) Millsp. on metal-polluted soil. The bauxite mine, which is surrounded by farmland (1 km away), has been severely polluted by metals such as Cd (31.24 ± 1.68), Zn (769.57 ± 3.46), Pb (326.85 ± 3.43), Mn (2519.6 ± 5.71), and Cr (302.34 ± 1.62 mg kg^-1) that exceeded Indian standards. The metal-tolerant B. cereus NDRMN001 had excellent PGP activities such as synthesis of hydrogen cyanide (HCN), siderophore, indole acetic acid (IAA), N₂ fixation, and P solubilization. Furthermore, the optimal growth conditions (temperature of 30°C, pH 6.5, 6% glucose, 9% tryptophan, and 1.5% tricalcium phosphate) for effective synthesis and expression of PGP traits in B. cereus NDRMN001 were determined. Such metal-tolerant B. cereus NDRMN001 traits can significantly reduce metals in polluted soil, and their PGP traits significantly improve plant growth in polluted soil. Hence, this strain (B. cereus NDRMN001) significantly improved the growth and phytoremediation potential of C. cajan (L.) Millsp on metal-polluted soil without [study I: 2 kg of sieved and autoclaved metal-polluted soil seeded with bacterium-free C. cajan (L.) Millsp. seeds] and with [study II: 2 kg of sieved and autoclaved metal-polluted soil seeded with B. cereus NDRMN001-coated C. cajan (L.) Millsp. seeds] B. cereus NDRMN001 amalgamation. Fertile soil was used as control. The physiological parameters, biomolecule contents, and the phytoremediation (Cr: 7.74, Cd: 12.15, Zn: 16.72, Pb: 11.47, and Mn: 14.52 mg g^-1) potential of C. cajan (L.) Millsp. were significantly effective in study II due to the metal-solubilizing and PGP traits of B. cereus NDRMN001. These results conclude that the test bacteria B. cereus NDRMN001 considerably improved the phytoremediation competence of C. cajan (L.) Millsp. on metal-polluted soil in a greenhouse study.

Plant growth-promoting bacteria in phytoremediation of metal-polluted soils: Current knowledge and future directions

Soil metal contamination is a major concern due to the ever-rising number of areas afflicted worldwide and the detrimental effects of metals to the environment and human health. Due to their non-biodegradability and toxicity, it is paramount to prevent further metal contamination and remediate the thousands of contaminated sites across the planet. Yet, conventional reclamation based on physical and chemical methods is often expensive, impractical, and triggers secondary pollution issues. Hence, microbe-aided phytoremediation has been gaining significant traction due to its environment-friendly character, cost-effectiveness, and the breakthroughs achieved during the past few decades. Microorganisms are an essential part of natural ecosystems and play a crucial role in their restoration. Indeed, plant-microbe associations in metal-polluted soils are pivotal for plants to tolerate metal toxicity and thrive in these harsh environments. Therefore, improving the understanding of this intricate relationship is invaluable for boosting phytoremediation. In this review, we focus on the potential of plant growth promoting bacteria (PGPB) for enhancing phytoremediation of metal-polluted soils. We discuss the mechanisms employed by microbes to promote plant growth and assist the removal or immobilization of metals in soil, thereby enhancing phytoextraction and phytostabilization, respectively. Microbe-mediated metal removal and detoxification through processes entailing adsorption, chelation, transformation, and precipitation, to list but a few, are also critically examined. Moreover, this work covers the direct and indirect mechanisms used by PGPB to facilitate plant acquisition of nutrients like nitrogen and phosphorus, supply and regulate phytohormones, and exert control over antagonistic microorganisms. Lastly, we provide an outlook on the future directions of microbe-aided phytoremediation and phytomining. Clearly, to fully validate and comprehend the potential of PGPB-aided phytoremediation, a considerable shift from bench-scale to field research is necessary. What's more, it is envisaged that recent advancements in genetic engineering may soon help furthering the efficiency of microbe-assisted phytoremediation.

Effects of Co-application of Cadmium-Immobilizing Bacteria and Organic Fertilizers on Houttuynia cordata and Microbial Communities in a Cadmium-Contaminated Field

Cadmium pollution is a serious threat to the soil environment. The application of bio-based fertilizers in combination with beneficial microbial agents is a sustainable approach to solving Cd pollution in farm soil. The present study investigated the effects of co-application of a Cd-immobilizing bacterial agent and two fermented organic fertilizers (fermentative edible fungi residue; fermentative cow dung) on Houttuynia cordata and its microbial communities in a Cd-polluted field. It showed that both the application of the Cd-immobilizing bacterial agent alone and the combined application of bio-based soil amendments and the bacterial agent effectively reduced >20% of the uptake of Cd by the plant. Soil nitrogen level was significantly raised after the combined fertilization. The multivariate diversity analysis and co-occurrence network algorithm showed that a significant shift of microbial communities took place, in which the microbial populations tended to be homogeneous with reduced microbial richness and increased diversity after the co-application. The treatment of fermentative cow dung with the addition of the bacterial agent showed a significant increase in the microbial community dissimilarity (R = 0.996, p = 0.001) compared to that treated with cow dung alone. The co-application of the bacterial agent with both organic fertilizers significantly increased the abundance of Actinobacteria and Bacteroidetes. The FAPROTAX soil functional analysis revealed that the introduction of the microbial agent could potentially suppress human pathogenic microorganisms in the field fertilized with edible fungi residue. It also showed that the microbial agent can reduce the nitrite oxidation function in the soil when applied alone or with the organic fertilizers. Our study thus highlights the beneficial effects of the Cd-immobilizing bacterial inoculant on H. cordata and provides a better understanding of the microbial changes induced by the combined fertilization using the microbial agent and organic soil amendments in a Cd-contaminated field.

Nickel mine soil is a potential source for soybean plant growth promoting and heavy metal tolerant rhizobia

Mine soil is not only barren but also contaminated by some heavy metals. It is unclear whether some rhizobia survived under extreme conditions in the nickel mine soil. Therefore, this study tries to isolate some effective soybean plant growth promoting and heavy metal resistant rhizobia from nickel mine soil, and to analyze their diversity. Soybean plants were used to trap rhizobia from the nickel mine soil. A total of 21 isolates were preliminarily identified as rhizobia, which were clustered into eight groups at 87% similarity level using BOXA1R-PCR fingerprinting technique. Four out of the eight representative isolates formed nodules on soybean roots with effectively symbiotic nitrogen-fixing and plant growth promoting abilities in the soybean pot experiment. Phylogenetic analysis of 16S rRNA, four housekeeping genes (atpD-recA-glnII-rpoB) and nifH genes assigned the symbiotic isolates YN5, YN8 and YN10 into Ensifer xinjiangense and YN11 into Rhizobium radiobacter, respectively. They also showed different tolerance levels to the heavy metals including cadmium, chromium, copper, nickel, and zinc. It was concluded that there were some plant growth promoting and heavy metal resistant rhizobia with the potential to facilitate phytoremediation and alleviate the effects of heavy metals on soybean cultivation in nickel mine soil, indicating a novel evidence for further exploring more functional microbes from the nickel mine soil.

Effects of Co-application of Cadmium-Immobilizing Bacteria and Organic Fertilizers on Houttuynia cordata and Microbial Communities in a Cadmium-Contaminated Field

Cadmium pollution is a serious threat to the soil environment. The application of bio-based fertilizers in combination with beneficial microbial agents is a sustainable approach to solving Cd pollution in farm soil. The present study investigated the effects of co-application of a Cd-immobilizing bacterial agent and two fermented organic fertilizers (fermentative edible fungi residue; fermentative cow dung) on Houttuynia cordata and its microbial communities in a Cd-polluted field. It showed that both the application of the Cd-immobilizing bacterial agent alone and the combined application of bio-based soil amendments and the bacterial agent effectively reduced >20% of the uptake of Cd by the plant. Soil nitrogen level was significantly raised after the combined fertilization. The multivariate diversity analysis and co-occurrence network algorithm showed that a significant shift of microbial communities took place, in which the microbial populations tended to be homogeneous with reduced microbial richness and increased diversity after the co-application. The treatment of fermentative cow dung with the addition of the bacterial agent showed a significant increase in the microbial community dissimilarity (R = 0.996, p = 0.001) compared to that treated with cow dung alone. The co-application of the bacterial agent with both organic fertilizers significantly increased the abundance of Actinobacteria and Bacteroidetes. The FAPROTAX soil functional analysis revealed that the introduction of the microbial agent could potentially suppress human pathogenic microorganisms in the field fertilized with edible fungi residue. It also showed that the microbial agent can reduce the nitrite oxidation function in the soil when applied alone or with the organic fertilizers. Our study thus highlights the beneficial effects of the Cd-immobilizing bacterial inoculant on H. cordata and provides a better understanding of the microbial changes induced by the combined fertilization using the microbial agent and organic soil amendments in a Cd-contaminated field.

Changes of root microbial populations of natively grown plants during natural attenuation of V-Ti magnetite tailings

Mine tailings contain dangerously high levels of toxic metals which pose a constant threat to local ecosystems. Few naturally grown native plants can colonize tailings site and the existence of their root-associated microbial populations is poorly understood. The objective of this study was to give further insights into the interactions between native plants and their microbiota during natural attenuation of abandoned V-Ti magnetite mine tailings. In the present work, we first examined the native plants' potential for phytoremediation using plant/soil analytical methods and then investigated the root microbial communities and their inferred functions using 16 S rRNA-based metagenomics. It was found that in V-Ti magnetite mine tailings the two dominant plants Bothriochloa ischaemum and Typha angustifolia were able to increase available nitrogen in the rhizosphere soil by 23.3% and 53.7% respectively. The translocation factors (TF) for both plants indicated that B. ischaemum was able to accumulate Pb (TF = 1.212), while T. angustifolia was an accumulator of Mn (TF = 2.502). The microbial community structure was more complex in the soil associated with T. angustifolia than with B. ischaemum. The presence of both plants significantly reduced the population of Acinetobacter. Specifically, B. ischaemum enriched Massilia, Opitutus and Hydrogenophaga species while T. angustifolia significantly increased rhizobia species. Multivariate analyses revealed that among all tested soil variables Fe and total organic carbon (TOC) could be the key factors in shaping the microbial structure. The putative functional analysis indicated that soil sample of B. ischaemum was abundant with nitrate/nitrite reduction-related functions while that of T. angustifolia was rich in nitrogen fixing functions. The results indicate that these native plants host a diverse range of soil microbes, whose community structure can be shaped by plant types and soil variables. It is also possible that these plants can be used to improve soil nitrogen content and serve as bioaccumulators for Pb or Mn for phytoremediation purposes.

Rhizobia population was favoured during in situ phytoremediation of vanadium-titanium magnetite mine tailings dam using Pongamia pinnata

Mine tailings contain toxic metals and can lead to serious pollution of soil environment. Phytoremediation using legumes has been regarded as an eco-friendly way for the rehabilitation of tailings-laden lands but little is known about the changes of microbial structure during the process. In the present study, we monitored the dynamic change of microbiota in the rhizosphere of Pongamia pinnata during a 2-year on-site remediation of vanadium-titanium magnetite tailings. After remediation, overall soil health conditions were significantly improved as increased available N and P contents and enzyme activities were discovered. There was also an increase of microbial carbon and nitrogen contents. The Illumina sequencing technique revealed that the abundance of taxa under Proteobacteria was increased and rhizobia-related OTUs were preferentially enriched. A significant difference was discovered for sample groups before and after remediation. Rhizobium and Nordella were identified as the keystone taxa at genus rank. The functional prediction indicated that nitrogen fixation was enhanced, corresponding well with qPCR results which showed a significant increase of nifH gene copy numbers by the 2nd year. Our findings for the first time elucidated that legume phytoremediation can effectively cause microbial communities to shift in favour of rhizobia in heavy metal contaminated soil.