Microbial Interventions in Bioremediation of Heavy Metal Contaminants in Agroecosystem

Plants' molecular behavior to heavy metals: from criticality to toxicity

The contamination of soil and water with high levels of heavy metals (HMs) has emerged as a significant obstacle to agricultural productivity and overall crop quality. Certain HMs, although serving as essential micronutrients, are required in smaller quantities for plant growth. However, when present in higher concentrations, they become very toxic. Several studies have shown that to balance out the harmful effects of HMs, complex systems are needed at the molecular, physiological, biochemical, cellular, tissue, and whole plant levels. This could lead to more crops being grown. Our review focused on HMs' resources, occurrences, and agricultural implications. This review will also look at how plants react to HMs and how they affect seed performance as well as the benefits that HMs provide for plants. Furthermore, the review examines HMs' transport genes in plants and their molecular, biochemical, and metabolic responses to HMs. We have also examined the obstacles and potential for HMs in plants and their management strategies.

Effects of dissolved organic matter on distribution characteristics of heavy metals and their interactions with microorganisms in soil under long-term exogenous effects

Long-term waste accumulation (LTWA) in soil not only alters its physical and chemical properties but also affects heavy metals and microorganisms in polluted soil through the dissolved organic matter (DOM) it produces. However, research on the impact of DOM from LTWA on heavy metals and microorganisms in polluted soil is limited, which has resulted in an incomplete understanding of the mechanisms involved in LTWA soils remediation. This study focuses on the DOM generated by waste accumulation and analyses the physicochemical properties, microbial community structure, and vertical distribution of heavy metals in four types of LTWA soils at different depths (0-100 cm). A causal analysis is conducted using structural equation modelling. The results indicate that due to the retention effect of the soil and microorganisms, heavy metal pollution is concentrated on the soil surface layer (>30 cm). With increasing depth, there is a decrease in heavy metal concentration and an increase in microbial diversity and abundance. DOM plays a significant role in regulating the concentration of soil heavy metals and the diversity and abundance of microorganisms. The DOM from different soils gradually transforms into substances dominated by tyrosine, tryptophan, and fulvic acid, which sustain the normal life activities and gene expression of microorganisms. Bacteria such as Pseudarthrobacter, Desulfurivibrio, Thiobacillus, and Sulfurimonas, which are involved in energy transformation, along with genes such as water channel protein and YDIF, which enhance heavy metal metabolism, ensure that microbial communities can maintain basic life processes in polluted environments and gradually select for dominant species that are adapted to heavy metal pollution. These novel discoveries illuminate the potential for modulating the composition of DOM to amplify microbial activity, while concurrently offering insights into the migration patterns of various long-term exogenous pollutants. This foundational knowledge provides a foundation for the development of efficacious remediation strategies.

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

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

Use of plant growth-promoting bacteria to facilitate phytoremediation

Here, phytoremediation studies of toxic metal and organic compounds using plants augmented with plant growth-promoting bacteria, published in the past few years, were summarized and reviewed. These studies complemented and extended the many earlier studies in this area of research. The studies summarized here employed a wide range of non-agricultural plants including various grasses indigenous to regions of the world. The plant growth-promoting bacteria used a range of different known mechanisms to promote plant growth in the presence of metallic and/or organic toxicants and thereby improve the phytoremediation ability of most plants. Both rhizosphere and endophyte PGPB strains have been found to be effective within various phytoremediation schemes. Consortia consisting of several PGPB were often more effective than individual PGPB in assisting phytoremediation in the presence of metallic and/or organic environmental contaminants.

Exploring the biotechnological potential of Acinetobacter soli ANG344B: A novel bacterium for 2-phenylethanol production

A bacterium, Acinetobacter soli ANG344B, isolated from river water, exhibited an exceptional capacity to produce 2-phenylethanol (2-PE) using L-phenylalanine (L-Phe) as a precursor-a capability typically observed in yeasts rather than bacteria. Bioreactor experiments were conducted to evaluate the production performance, using glucose as the carbon source for cellular growth and L-Phe as the precursor for 2-PE production. Remarkably, A. soli ANG344B achieved a 2-PE concentration of 2.35 ± 0.26 g/L in just 24.5 h of cultivation, exhibiting a global volumetric productivity of 0.10 ± 0.01 g/L.h and a production yield of 0.51 ± 0.01 g2-PE/gL-Phe, a result hitherto reported only for yeasts. These findings position A. soli ANG344B as a highly promising microorganism for 2-PE production. Whole-genome sequencing of A. soli strain ANG344 revealed a genome size of 3.52 Mb with a GC content of 42.7 %. Utilizing the Rapid Annotation using Subsystem Technology (RAST) server, 3418 coding genes were predicted, including genes coding for enzymes previously associated with the metabolic pathway of 2-PE production in other microorganisms, yet unreported in Acinetobacter species. Through gene mapping, 299 subsystems were identified, exhibiting 30 % subsystem coverage. The whole genome sequence data was submitted to NCBI GeneBank with the BioProject ID PRJNA982713. These draft genome data offer significant potential for exploiting the biotechnological capabilities of A. soli strain ANG344 and for conducting further comparative genomic studies.

Graphene-based nanomaterials as potential candidates for environmental mitigation of pesticides

Over the years, bioaccumulation of hazardous chemicals in the food chain has become a critical issue, resulting in numerous health risks. Environmental mitigation aims to clean up contaminated sites and eliminate hazardous materials from the air, water, or soil to restore the site to its original and safe condition. Pesticides constitute one of the most dangerous environmental pollutants which are generally used to increase crop production. Addressing the removal or treatment of pesticides has become pivotal in mitigating environmental threats. Diverse remediation methods are employed to protect the environment and public health. Graphene-based materials have emerged as promising candidates with exceptional properties, including excellent adsorption capacity due to their high surface area, strong hydrophilicity, and tunable properties. Owing to these properties, they have been attracting major research attention in the field of design and fabrication of materials for the mitigation of pesticides from the environment such as from contaminated food, water and other samples. Various physical, chemical and biological extraction techniques are adopted to remove pesticides. This review article provides an insight into the potential role of graphene-based materials in the environmental remediation of pesticides. We have focused on the removal of Organophosphates, Organochlorines, Carbamates and Pyrethroids present in water, fruit, vegetable and other samples, highlighting the urgent need for environmental remediation. While graphene-based materials hold potential for pesticide remediation, addressing challenges in scalable production, assessing long-term sustainability, and mitigating potential environmental impacts are critical steps for successful large-scale applications.

Revitalizing contaminated lands: A state-of-the-art review on the remediation of mine-tailings using phytoremediation and genomic approaches

The mining industry has historically served as a critical reservoir of essential raw materials driving global economic progress. Nevertheless, the consequential by-product known as mine tailings has consistently produced a substantial footprint of environmental contamination. With annual discharges of mine tailings surpassing 10 billion tons globally, the need for effective remediation strategies is more pressing than ever as traditional physical and chemical remediation techniques are hindered by their high costs and limited efficacy. Phytoremediation utilizing plants for remediation of polluted soil has developed as a promising and eco-friendly approach to addressing mine tailings contamination. Furthermore, sequencing of genomic DNA and transcribed RNA extracted from mine tailings presents a pivotal opportunity to provide critical supporting insights for activities directed towards the reconstruction of ecosystem functions on contaminated lands. This review explores the growing prominence of phytoremediation and metagenomics as an ecologically sustainable techniques for rehabilitating mine-tailings. The present study envisages that plant species such as Solidago chilensis, Festuca arundinacea, Lolium perenne, Polygonum capitatum, Pennisetum purpureum, Maireana brevifolia, Prosopis tamarugo etc. could be utilized for the remediation of mine-tailings. Furthermore, a critical evaluation of the organic and inorganic ammendments that optimize conditions for the remediation of mine tailings is also provided. The focus of this review extends to the exploration of environmental genomics to characterize microbial communities in mining sites. By delving into the multifaceted dimensions of phytoremediation and genomics for mine tailings, this study contributes to the ongoing efforts to revitalize contaminated lands for a sustainable and environmentally friendly future.

In vitro and in vivo screening of bacterial species from contaminated soil for heavy metal biotransformation activity

Heavy metals (HMs) are widely used in various industries. High concentrations of HMs can be severely toxic to plants, animals and humans. Microorganism-based bioremediation has shown significant potential in degrading and detoxifying specific HM contaminants. In this study, we cultivated a range of bacterial strains in liquid and solid nutrient medium containing different concentrations of different HMs to select and analyze bacteria capable of transforming HMs. The bacterial strains most resistant to selected HMs and exhibiting the ability to remove HMs from contaminated soils were identified. Then, the bacterial species capable of utilizing HMs in soil model experiments were selected, and their ability to transform HMs was evaluated. This study has also generated preliminary findings on the use of plants for further removal of HMs from soil after microbial bioremediation. Alcaligenes faecalis, Delftia tsuruhatensis and Stenotrophomonas sp. were selected for their ability to grow in and utilize HM ions at the maximum permissible concentration (MPC) and two times the MPC. Lysinibacillus fusiformis (local microflora) can be used as a universal biotransformation tool for many HM ions. Brevibacillus parabrevis has potential for the removal of lead ions, and Brevibacillus reuszeri and Bacillus safensis have potential for the removal of arsenic ions from the environment. The bacterial species have been selected for bioremediation to remove heavy metal ions from the environment.

Microbial strategies for copper pollution remediation: Mechanistic insights and recent advances

Environmental contamination is aninsistent concern affecting human health and the ecosystem. Wastewater, containing heavy metals from industrial activities, significantly contributes to escalating water pollution. These metals can bioaccumulate in food chains, posing health risks even at low concentrations. Copper (Cu), an essential micronutrient, becomes toxic at high levels. Activities like mining and fungicide use have led to Copper contamination in soil, water, and sediment beyond safe levels. Copper widely used in industries, demands restraint of heavy metal ion release into wastewater for ecosystem ultrafiltration, membrane filtration, nanofiltration, and reverse osmosis, combat heavy metal pollution, with emphasis on copper.Physical and chemical approaches are efficient, large-scale feasibility may have drawbackssuch as they are costly, result in the production of sludge. In contrast, bioremediation, microbial intervention offers eco-friendly solutions for copper-contaminated soil. Bacteria and fungi facilitate these bioremediation avenues as cost-effective alternatives. This review article emphasizes on physical, chemical, and biological methods for removal of copper from the wastewater as well asdetailing microorganism's mechanisms to mobilize or immobilize copper in wastewater and soil.

Isolation, characterization, identification, genomics and analyses of bioaccumulation and biosorption potential of two arsenic-resistant bacteria obtained from natural environments

Arsenic (As) is a significant contaminant whose unrestrained entrance into different ecosystems has created global concern. At the cellular level, As forms unsteady intermediates with genetic materials and perturbs different metabolic processes and proper folding of proteins. This study was the first in this region to explore, isolate, screen systematically, and intensively characterize potent As-tolerant bacterial strains from natural environments near Raiganj town of Uttar Dinajpur, West Bengal. In this study, two potent Gram-negative bacterial strains with high tolerance to the poisonous form of As, i.e., As(III) and As(V), were obtained. Both the isolates were identified using biochemical tests and 16S rRNA gene sequencing. These bacteria oxidized toxic As(III) into less poisonous As(V) and depicted tolerance towards other heavy metals. Comparative metabolic profiling of the isolates in control and As-exposed conditions through Fourier-transform infrared spectroscopy showed metabolic adjustments to cope with As toxicity. The metal removal efficiency of the isolates at different pH showed that one of the isolates, KG1D, could remove As efficiently irrespective of changes in the media pH. In contrast, the efficiency of metal removal by PF14 was largely pH-dependent. The cell mass of both the isolates was also found to favourably adsorb As(III). Whole genome sequence analysis of the isolates depicted the presence of the arsRBC genes of the arsenic operon conferring resistance to As. Owing to their As(III) oxidizing potential, high As bioaccumulation, and tolerance to other heavy metals, these bacteria could be used to bioremediate and reclaim As-contaminated sites.

Unlocking the potential of co-application of steel slag and biochar in mitigation of arsenic-induced oxidative stress by modulating antioxidant and glyoxalase system in Abelmoschus esculentus L

This study investigates our hypothesis that how effect of arsenic stress on okra (Abelmoschus esculentus L.) can be alleviated through the use of waste materials such as steel slag (SS) and corncob biochar (BC). Different growth variables, biochemical parameters, oxidative stress markers, enzymatic and non-enzymatic antioxidants and glyoxylase enzyme activities were assessed. When okra was exposed to As, there was a noticeable decrease in seedling length, biomass, relative water content, various biochemical attributes, however, electrolyte leakage and lipid peroxidation in okra were enhanced. The supplementation of SS and BC-either individually or in combination-improved the growth parameters and reduced oxidative stress markers. Application of SS and BC also lowered As accumulation in roots and shoots of okra mitigating adverse effects of As exposure. Additionally, the activities of antioxidant and glyoxalase enzyme increased when SS and BC were present, concurrently reducing methylglyoxal content. Arsenic-induced stress led to oxidative damage, an enhancement in both enzymatic and non-enzymatic antioxidants, induced the synthesis of thiol and phytochelatins in roots and shoots. These may play a vital function in alleviating oxidative stress induced by As. Superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase activities were significantly enhanced in As-treated plants. These enhancement were further amplified when SS and BC were amended to As-treated okra. Therefore, synergistic application of SS and BC effectively protects okra against oxidative stress induced by As by increasing both antioxidant defense and glyoxalase systems. Both SS, an industrial byproduct, and BC, generated from agricultural waste, are cost-effective, environmentally friendly, safe, and non-toxic materials which can be used for crop production in As contaminated soil.

Heavy metal tolerance, and metal biosorption by exopolysaccharides produced by bacterial strains isolated from marine hydrothermal vents

The present study highlights heavy metal tolerance, EPS production, and biosorption capacity of four hydrothermal vent bacterial strains, namely Exiguobacterium aquaticum, Mammaliicoccus sciuri, Micrococcus luteus, and Jeotgalicoccus huakuii against As, Cd, Cr, Cu, Co, Pb and Ni. The biosorption assay showed high removal efficiency of As (83%) by E. aquaticum, Cd (95%) by M. sciuri, Cu (94%) by M. luteus, and Ni (89%) by J. huakuii and their produced EPS with these metals in aqueous solution were 84%, 85%, 98%, and 91%, respectively. The maximum EPS yield was attained by optimized medium composition consisting of 1% Xylose, and 1% NaCl at pH 7. In metal-amended conditions, the four bacterial strains showed induced EPS production in the initial concentrations. SEM with EDX and CLSM images showed that the growth and EPS production of bacterial strains were affected by metal ion concentrations. A phenol sulphuric acid method and BCA assay were used to identify both the carbohydrate and total protein content of four extracted EPS. A DPPH assay revealed that EPS influences free radical scavenging and has a highly enhanced synergistic effect with its antioxidant activity. FT-IR analysis of four extracted EPS showed the shifting of peaks in the functional groups of EPS before and after adsorption of metal ions. At pH 5 and after 60 min contact time metal removal efficiency and adsorption capacity increased as calculated for As, Cd, Cu, and Ni by four extracted EPS: (86%, 20 mg/g), (74%, 19 mg/g), (94%, 60 mg/g) and (89%, 32 mg/g) and (89%, 16 mg/g), (85%, 16 mg/g), (96%, 22 mg/g) and (91%, 16 mg/g), respectively. The Langmuir compared to the Freundlich model was found to better represent the adsorption by EPS providing maximum adsorption capacities for As (34.65 mg/g), Cd (52.88 mg/g), Cu (24.91 mg/g), and Ni (58.38 mg/g).

Microbial consortium and impact of industrial mining on the Natural High Background Radiation Area (NHBRA), India - Characteristic role of primordial radionuclides in influencing the community structure and extremophiles pattern

The present investigation is the first of its kind which aims to study the characteristics of microbial consortium inhabiting one of the natural high background radiation areas of the world, Chavara Coast in Kerala, India. The composition of the microbial community and their structural changes were evaluated under the natural circumstances with exorbitant presence of radionuclides in the sediments and after the radionuclide's recession due to mining effects. For this purpose, the concentration of radionuclides, heavy metals, net radioactivity estimation via gross alpha and beta emitters and other physiochemical characteristics were assessed in the sediments throughout the estuarine stretch. According to the results, the radionuclides had a significant effect in shaping the community structure and composition, as confirmed by the bacterial heterogeneity achieved between the samples. The results indicate that high radioactivity in the background environment reduced the abundance and growth of normal microbial fauna and favoured only the growth of certain extremophiles belonging to families of Piscirickettsiacea, Rhodobacteriacea and Thermodesulfovibrionaceae, which were able to tolerate and adapt towards the ionizing radiation present in the environment. In contrast, communities from Comamondacea, Sphingomonadacea, Moraxellacea and Erythrobacteracea were present in the sediments collected from industrial outlet, reinforcing the potent role of radionuclides in governing the community pattern of microbes present in the natural environment. The study confirms the presence of these novel and unidentified bacterial communities and further opens the possibility of utilizing their usefulness in future prospects.

Bioremediation of hazardous heavy metals by marine microorganisms: a recent review

Heavy metals (HMs) like Zn, Cu, Pb, Ni, Cd, and Hg, among others, play a role in several environmental problems. The marine environment is polluted by several contaminants, such as HMs. A variety of physico-chemical methods usually available for sanitation HMs remediation suffer from either limitation. Bioremediation is a promising way of dealing with HMs pollution. Microbes have the ability with various potencies to resist HMs tension. The current review discusses the main sources and influences of HMs, the role of marine microorganisms in HMs bioremediation, as well as the microbial mechanisms for HMs detoxification and transformation. This review paper aims to provide an overview of the bioremediation technologies that are currently available for the removal of HMs ions from industrial and urban effluent by aquatic organisms such as bacteria, fungi, and microalgae, particularly those that are isolated from marine areas. The primary goals are to outline various studies and offer helpful information about the most important aspects of the bioelimination techniques. The biotreatment practices have been primarily divided into three techniques based on this topic. They are biosorption, bioaccumulation, bioleaching, and biotransformation. This article gives the brief view on the research studies about bioremediation of HMs using marine microorganisms. The current review also deals with the critical issues and recent studies based on the HMs biodetoxification using aquatic microorganisms.

Application of biochar on soil bioelectrochemical remediation: behind roles, progress, and potential

Bioelectrochemical systems (BESs) that combine electrochemistry with biological methods have gained attention in the remediation of polluted environments, including wastewater, sludge, sediments, and soils. The most attractive advantage of BESs is that the solid electrode is used as an inexhaustible electron acceptor or donor, and biocurrent directly converted from organics can afford the reaction energy of contaminant breakdown, crossing the internal energy barrier of endothermic degradation, which achieves a continuous biodegradation process without the simultaneous use of exogenetic chemicals and bioelectricity recovery. However, soil BESs are hindered by expensive electrode materials, difficult pollutant and electron transfer, low microbial competitive activity, and biocompatibility in contamination remediation. Fortunately, introducing biochar into soil BESs could reveal a high potential in addressing these BES inadequacies. The characteristics of biochar, e.g., conductivity, transferability, high specific surface area, high porosity, large functional groups, and biocompatibility, can improve the performance of soil BESs. In fact, biochar not only carries electrons but also transfers nutrients, pollutants, and even bacteria by facilitating transmission in the bioelectric field of BESs. Consequently, the abilities of biochar make for better functionality of BESs. This review collates information on the roles, application, and progress of biochar in soil BESs, and future prospects are given. It is beneficial for environmental researchers and engineers to extend BES application in environmental remediation and to assist the progress of carbon sequestration and emission reduction based on the inertia of biochar and the blocking of electron flow to form methane.

Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan

Heavy metal (HMe) pollution in regions with mining and metallurgy activities is known to be a serious environmental problem worldwide. Hydrological processes contribute to the dissemination of HMes (drainage, precipitation, flow rate). The aim of the present study is to investigate the microbial community structure in ten river sediments sampled in different regions of East Kazakhstan, which are contaminated with HMes. The overall degree of sediment contamination with HMes (Cr, Cu, Zn, Pb, and Cd) was assessed using the pollution index Zc, which ranged from 0.43 to 21.6, with the highest in Ridder City (Zc = 21.6) and Ust-Kamenogorsk City, 0.8 km below the dam of the hydroelectric power station (Zc = 19.6). The tested samples considerably differed in organic matter, total carbon, nitrogen, and phosphorus content, as well as in the abundance of HMe-related functional gene families and antibiotic resistance genes. Metagenomic analysis of benthic microorganisms showed the prevalence of Proteobacteria (88.84-97.61%) and Actinobacteria (1.21-5.98%) at the phylum level in all samples. At the class level, Actinobacteria (21.68-57.48%), Betaproteobacteria (19.38-41.17%), and Alphaproteobacteria (10.0-39.78%) were the most common among the classified reads. To the best of our knowledge, this is the first study on the metagenomic characteristics of benthic microbial communities exposed to chronic HMe pressure in different regions of East Kazakhstan.

Microbial Removal of Heavy Metals from Contaminated Environments Using Metal-Resistant Indigenous Strains

Contamination of soil with heavy metals has become a matter of global importance due to its impact on agriculture, environmental integrity, and therefore human health and safety. Several microbial strains isolated from soil contaminated by long-term chemical and petrochemical activities were found to manifest various levels of tolerance to Cr, Pb, and Zn, out of which Bacillus marisflavi and Trichoderma longibrachiatum exhibited above-moderate tolerance. The concentrations of target heavy metals before and after bioremediation were determined using electrochemical screen-printed electrodes (SPE) modified with different nanomaterials. The morpho-structural SEM/EDX analyses confirmed the presence of metal ions on the surface of the cell, with metal uptake being mediated by biosorption with hydroxyl, carboxyl, and amino groups as per FTIR observations. T. longibrachiatum was observed to pose a higher bioremediation potential compared to B. marisflavi, removing 87% of Cr and 67% of Zn, respectively. Conversely, B. marisflavi removed 86% of Pb from the solution, compared to 48% by T. longibrachiatum. Therefore, the fungal strain T. longibrachiatum could represent a viable option for Cr and Zn bioremediation strategies, whereas the bacterial strain B. marisflavi may be used in Pb bioremediation applications.

Heavy Metal Tolerance of Microorganisms Isolated from Coastal Marine Sediments and Their Lead Removal Potential

In this study, 338 microorganisms, comprising 271 bacteria and 67 fungi, were isolated from sediment samples collected from underexplored Pacific and Caribbean regions of Colombia. Screening trials were conducted on selected strains (n = 276) to assess their tolerance to cadmium (Cd2+), lead (Pb2+), and zinc (Zn2+), leading to the identification of six bacteria capable of withstanding 750 mg·L-1 of each heavy metal ion. Three promising microorganisms, identified as Enterobacter sp. INV PRT213, Pseudomonas sp. INV PRT215, and Stenotrophomonas sp. INV PRT216 were selected for lead removal experiments using LB broth medium supplemented with 400 mg·L-1 Pb2+. Among these, Pseudomonas sp. INV PRT215 exhibited significant potential, removing 49% of initial Pb2+ after 240 min of exposure (16.7 g wet biomass·L-1, pH 5, 30 °C). Infrared spectra of Pb-exposed biomass showed changes in functional groups, including carbonyl groups of amides, carboxylate, phosphate, hydroxyl, and amine groups, compared to the not-exposed control. These changes suggested interactions between the metal and functional groups in the biomass. The findings of this study highlight the potential of microorganisms derived from coastal marine environments as promising candidates for future applications in bioremediation of polluted environments contaminated with heavy metals.

Application of the Aliivibrio fischeri bacterium bioassay for assessing single and mixture effects of antibiotics and copper

The Aliivibrio fischeri bioassay was successfully applied in order to evaluate the acute effect of sulfamethoxazole (SMX), ciprofloxacin (CIP), chlortetracycline (CTC) and copper (Cu), alone or in binary, ternary, and overall mixture. The toxicity results are reported in terms of both effective concentrations, which inhibited 50% of the bacterium bioluminescence (EC50%), and in Toxic Units (TUs). The TUs were compared with predicted values obtained using the Concentration Addition model (CA). Finally, the toxicity of water extracts from a soil contaminated by the three antibiotics (7 mg Kg-1 each) in the presence/absence of copper (30 mg Kg-1) was also evaluated. Copper was the most toxic chemical (EC50: 0.78 mg L-1), followed by CTC (EC50: 3.64 mg L-1), CIP (96 mg L-1) and SMX (196 mg L-1). Comparing the TU and CA values of the mixtures, additive effects were generally found. However, a synergic action was recorded in the case of the CIP+Cu co-presence and antagonistic effects in the case of CTC+Cu and the ternary mixture (containing each antibiotic at 0.7 mg L-1), were identified. Soil water extracts did not show any toxicity, demonstrating the buffering ability of the soil to immobilize these chemicals.

State-of-the-art adsorption and adsorptive filtration based technologies for the removal of trace elements: A critical review

Water and wastewater are contaminated with various types of trace elements that are released from industrial activities. Their presence, at concentrations above the permissible limit, will cause severe negative impacts on human health and the environment. Due to their cost-effectiveness, simple design, high efficiency, and selectivity, adsorption, and adsorptive filtration are techniques that have received lots of attention as compared to other water treatment techniques. Adsorption isotherms and kinetic studies help to understand the mechanisms of adsorption and adsorption rates, which can be used to develop and optimize different adsorbents. This state-of-the-art review provides and combines the advancements in different conventional and advanced adsorbents, biosorbents, and adsorptive membranes for the removal of trace elements from water streams. Herein, this review discusses the sources of different trace elements and their impact on human health. The review also covers the adsorption technique with a focus on various advanced adsorbents, their adsorption capacities, and adsorption isotherm modeling in detail. In addition, biosorption is critically discussed together with its mechanisms and biosorption isotherms. In the end, the application of various advanced adsorptive membranes is discussed and their comparison with adsorbents and biosorbents is systematically presented.

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.

Microbial Exudates as Biostimulants: Role in Plant Growth Promotion and Stress Mitigation

Microbes hold immense potential, based on the fact that they are widely acknowledged for their role in mitigating the detrimental impacts of chemical fertilizers and pesticides, which were extensively employed during the Green Revolution era. The consequence of this extensive use has been the degradation of agricultural land, soil health and fertility deterioration, and a decline in crop quality. Despite the existence of environmentally friendly and sustainable alternatives, microbial bioinoculants encounter numerous challenges in real-world agricultural settings. These challenges include harsh environmental conditions like unfavorable soil pH, temperature extremes, and nutrient imbalances, as well as stiff competition with native microbial species and host plant specificity. Moreover, obstacles spanning from large-scale production to commercialization persist. Therefore, substantial efforts are underway to identify superior solutions that can foster a sustainable and eco-conscious agricultural system. In this context, attention has shifted towards the utilization of cell-free microbial exudates as opposed to traditional microbial inoculants. Microbial exudates refer to the diverse array of cellular metabolites secreted by microbial cells. These metabolites enclose a wide range of chemical compounds, including sugars, organic acids, amino acids, peptides, siderophores, volatiles, and more. The composition and function of these compounds in exudates can vary considerably, depending on the specific microbial strains and prevailing environmental conditions. Remarkably, they possess the capability to modulate and influence various plant physiological processes, thereby inducing tolerance to both biotic and abiotic stresses. Furthermore, these exudates facilitate plant growth and aid in the remediation of environmental pollutants such as chemicals and heavy metals in agroecosystems. Much like live microbes, when applied, these exudates actively participate in the phyllosphere and rhizosphere, engaging in continuous interactions with plants and plant-associated microbes. Consequently, they play a pivotal role in reshaping the microbiome. The biostimulant properties exhibited by these exudates position them as promising biological components for fostering cleaner and more sustainable agricultural systems.

Structural-functional analysis and molecular characterization of arsenate reductase from Enterobacter cloacae RSC3 for arsenic biotransformation

Enterobacter cloacae RSC3 isolated from an industrial pesticide site transformed arsenate into arsenite. The arsenate is transported by membrane-bound phosphate transporter and transformed to arsenite by arsenate reductase (arsC). E. cloacae RSC3 produced an arsenate reductase enzyme with a maximum activity of 354 U after 72 h of incubation. Arsenate reductase was found to be active and stable at a wide range of temperatures (20 and 45 °C) and pH (5-10), with maximum activity at 35 °C and pH 7.0. The arsenate reductase protein was further characterised molecularly using different bioinformatics tools. The 3D structure of ArsC protein was predicted by homology modelling and validated by the Ramachandran plot with 91.9% residues in the most favoured region. ArsC protein of E. cloacae RSC3 revealed structural homology with ArsC from PDB ID: 1S3C. The gene ontology results also showed that the ArsC protein had a molecular functionality of the arsenate reductase (glutaredoxin) activity and the biological function of cellular response to DNA damage stimulus. Molecular docking analysis of 3D structures using AutoDock vina-1.5.7 server predicted four ligand binding active site residues at Gln70, Asp68, Leu68, and Leu63. Strong ArsC-arsenate ion interaction was observed with binding energy -1.03 kcal/mol, indicating significant arsenate reductase activity and specificity of ArsC protein. On the basis of molecular dynamics simulation analysis, the RMSD and RMSF values revealed the stability of ArsC protein from E. cloacae RSC3.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03730-9.

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.

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.

Biochar as a Green Sorbent for Remediation of Polluted Soils and Associated Toxicity Risks: A Critical Review

Soil contamination with organic contaminants and various heavy metals has become a global environmental concern. Biochar application for the remediation of polluted soils may render a novel solution to soil contamination issues. However, the complexity of the decontaminating mechanisms and the real environment significantly influences the preparation and large-scale application of biochar for soil ramification. This review paper highlights the utilization of biochar in immobilizing and eliminating the heavy metals and organic pollutants from contaminated soils and factors affecting the remediation efficacy of biochar. Furthermore, the risks related to biochar application in unpolluted agricultural soils are also debated. Biochar production conditions (pyrolysis temperature, feedstock type, and residence time) and the application rate greatly influence the biochar performance in remediating the contaminated soils. Biochars prepared at high temperatures (800 °C) contained more porosity and specific surface area, thus offering more adsorption potential. The redox and electrostatic adsorption contributed more to the adsorption of oxyanions, whereas ion exchange, complexation, and precipitation were mainly involved in the adsorption of cations. Volatile organic compounds (VOCs), dioxins, and polycyclic aromatic hydrocarbons (PAHs) produced during biochar pyrolysis induce negative impacts on soil alga, microbes, and plants. A careful selection of unpolluted feedstock and its compatibility with carbonization technology having suitable operating conditions is essential to avoid these impurities. It would help to prepare a specific biochar with desired features to target a particular pollutant at a specific site. This review provided explicit knowledge for developing a cost-effective, environment-friendly specific biochar, which could be used to decontaminate targeted polluted soils at a large scale. Furthermore, future study directions are also described to ensure a sustainable and safe application of biochar as a soil improver for the reclamation of polluted soils.

Exploring the Extreme Acid Tolerance of a Dynamic Protein Nanocage

Encapsulins are microbial protein nanocages capable of efficient self-assembly and cargo enzyme encapsulation. Due to their favorable properties, including high thermostability, protease resistance, and robust heterologous expression, encapsulins have become popular bioengineering tools for applications in medicine, catalysis, and nanotechnology. Resistance against physicochemical extremes like high temperature and low pH is a highly desirable feature for many biotechnological applications. However, no systematic search for acid-stable encapsulins has been carried out, while the influence of pH on encapsulin shells has so far not been thoroughly explored. Here, we report on a newly identified encapsulin nanocage from the acid-tolerant bacterium Acidipropionibacterium acidipropionici. Using transmission electron microscopy, dynamic light scattering, and proteolytic assays, we demonstrate its extreme acid tolerance and resilience against proteases. We structurally characterize the novel nanocage using cryo-electron microscopy, revealing a dynamic five-fold pore that displays distinct "closed" and "open" states at neutral pH but only a singular "closed" state under strongly acidic conditions. Further, the "open" state exhibits the largest pore in an encapsulin shell reported to date. Non-native protein encapsulation capabilities are demonstrated, and the influence of external pH on internalized cargo is explored. Our results expand the biotechnological application range of encapsulin nanocages toward potential uses under strongly acidic conditions and highlight pH-responsive encapsulin pore dynamics.

Bioremediation of Heavy Metals by the Genus Bacillus

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

Current research trends on cosmetic microplastic pollution and its impacts on the ecosystem: A review

Since the advent of microplastics, it has become a vital component, directly or indirectly, in our daily lives. With advancements in their use, microplastics have become an integral part of personal care, cosmetics, and cleaning products (PCCPs) and emerged as a domestic source of environmental pollution. Over the years, researchers have ascertained the harmful effects of microplastics on the environment. In this context, the assessment and monitoring of microplastics in PCCPs require considerable attention. In addition, it raises concern regarding the need to develop innovative, sustainable, and environmentally safe technologies to combat microplastic pollution. Therefore, this review is an endeavor to uncover the fate, route and degradation mechanism of cosmetic microplastics. In addition, the major technological advancement in cosmetic microplastic removal and the steps directed toward mitigating cosmetic microplastic pollution are also discussed.

Hormesis Responses of Growth and Photosynthetic Characteristics in Lonicera japonica Thunb. to Cadmium Stress: Whether Electric Field Can Improve or Not?

"Hormesis" is considered a dose-response phenomenon mainly observed at hyperaccumulator plants under heavy metals stress. In this study, the effects of electric fields on hormesis responses in Lonicera japonica Thunb. under cadmium (Cd) treatments were investigated by assessing the plant growth and photosynthetic characteristics. Under Cd treatments without electric fields, the parameters of plant growth and photosynthetic characteristics increased significantly when exposed to 5 mg L^-1 Cd, and decreased slightly when exposed to 25 mg L^-1 Cd, showing an inverted U-shaped trend, which confirmed that low concentration Cd has a hormesis effect on L. japonica. Under electric fields, different voltages significantly promoted the inverted U-shaped trend of the hormesis effect on the plant, especially by 2 V cm^-1 voltage. Under 2 V cm^-1 voltage, the dry weight of the root and leaf biomass exposed to 5 mg L^-1 Cd increased significantly by 38.38% and 42.14%, and the photosynthetic pigment contents and photosynthetic parameters were also increased significantly relative to the control, indicating that a suitable electric field provides better improvements for the hormesis responses of the plant under Cd treatments. The synergistic benefits of the 5 mg L^-1 Cd and 2 V cm^-1 electric field in terms of the enhanced hormesis responses of growth and photosynthetic characteristics could contribute to the promoted application of electro-phytotechnology.

The capability of chloramphenicol biotransformation of Klebsiella sp. YB1 under cadmium stress and its genome analysis

Co-contamination by antibiotics and heavy metal is common in the environment, however, there is scarce information about antibiotics biodegradation under heavy metals stress. In this study, Klebsiella sp. Strain YB1 was isolated which is capable of biodegrading chloramphenicol (CAP) with a biodegradation efficiency of 22.41% at an initial CAP of 10 mg L^-1 within 2 days. CAP biodegradation which fitted well with the first-order kinetics. YB1 still degrades CAP under Cd stress, however 10 mg L^-1 Cd inhibited CAP biodegradation by 15.1%. Biotransformation pathways remained the same under Cd stress, but two new products (Cmpd 19 and Cmpd 20) were identified. Five parallel metabolism pathways of CAP were proposed with/without Cd stress, including one novel pathway (pathway 5) that has not been reported before. In pathway 5, the initial reaction was oxidation of CAP by disruption of C-C bond at the side chain of C1 and C2 with the formation of 4-nitrobenzyl alcohol and CY7, then these intermediates were oxidized into p-nitrobenzoic acid and CY1, respectively. CAP acetyltransferase and nitroreductase and 2,3/4,5-dioxygenase may play an important role in CAP biodegradation through genome analysis and prediction. This study deepens our understanding of mechanism of antibiotic degradation under heavy metal stress in the environment.

Peroxidases-based enticing biotechnological platforms for biodegradation and biotransformation of emerging contaminants

Rampant industrial boom, urbanization, and exponential population growth resulted in widespread environmental pollution, with water being one of the leading affected resources. All kinds of pollutants, including phenols, industrial dyes, antibiotics, pharmaceutically active residues, and persistent/volatile organic compounds, have a paramount effect, either directly or indirectly, on human health and aquatic entities. Strategies for affordable and efficient decontamination of these emerging pollutants have become the prime focus of academic researchers, industry, and government to constitute a sustainable human society. Classical treatment techniques for environmental contaminants are associated with several limitations, such as inefficiency, complex pretreatments, overall high process cost, high sludge generation, and highly toxic side-products formation. Enzymatic remediation is considered a green and ecologically friendlier method that holds considerable potential to mitigate any kinds of contaminating agents. Exploiting the potential of various peroxidases for pollution abatement is an emerging research area and has considerable advantages, such as efficiency and ease of handling, over other methods. This work is designed to provide recent progress in deploying peroxidases as green and versatile biocatalytic tools for the degradation and transformation of a spectrum of potentially hazardous environmental pollutants to broaden their scope for biotechnological and environmental purposes. More studies are required to explicate the degradation mechanisms, assess the toxicology levels of bio-transformed metabolites, and standardize the treatment strategies for economic viability.

Microbial degradation and transformation of benzo[a]pyrene by using a white-rot fungus Pleurotus eryngii F032

Polycyclic aromatic hydrocarbons (PAHs) are environmentally recalcitrant contaminants formed from naturally or incomplete combustion of organic materials and some of them are difficult to degrade due to their hydrophobicity and persistency. Benzo [a]pyrene (BaP), is one of PAHs that having five fused benzene and reported as mutagenic, carcinogenic and teratogenic compounds. Biodegradation is one of promising techniques due to its relatively low economic cost and microorganism is a natural capacity to consume hydrocarbons. In this investigation, Pleurotus eryngii F032 was grown in 20 mL of modified mineral salt broth (MSB) supplemented with BaP under static and agitated culture. Within 20 days, static culture removed 59% of BaP, whereas agitated culture removed the highest amount (73%). To expedite BaP elimination, the mechanism and behavior of BaP biosorption and biotransformation by Pleurotus eryngii F032 were additionally examined by gas chromatography-mass spectrometer (GC-MS). The optimal conditions for P. eryngii F032 to eliminate BaP were 25 °C, a C/N ratio of 8, pH 3 and 0.2% inoculum concentration. At an initial BaP content of 10 mg/L, more than 50% was effectively eliminated within 20 days under these conditions. Salinity, glucose, and rhamnolipids were the most important factors impacting BaP biodegradation. GC-MS found degradation products such as BaP-3,6-quinone, indicating plausible metabolic routes. Finally, it may be assumed that the primary mechanism by which white-rot fungi eliminate BaP is by the utilization of biotransformation enzymes such as laccase to mineralize the PAHs. Hence, Pleurotus eryngii F032 could be an ideal candidate to treat PAHs contaminated soils.

Response of soil microbial communities to natural radionuclides along specific-activity gradients

Understanding the response of soil microbial community to abnormal natural radionuclides is important to maintain soil ecological function, but the underlying mechanism of tolerance and survival of microbes is poorly studied. The effects of natural radionuclides on the topsoil microbial communities in anomalous natural radiation area were investigated in this work, and it was found that microbial community composition was significantly influenced by the specific-activities of natural radionuclides. The results revealed that relative abundances of 10 major microbial phyla and genera displayed different patterns along specific-activity gradients, including decreasing, increasing, hump-shaped, U-shaped, and similar sinusoidal or cosine wave trends, which indicated that the natural radionuclides were the predominant driver for change of microbial community structure. At the phylum and genus level, microbial communities were divided into two special groups according to the tolerance to natural radionuclides, such as ²³⁸U and ²³²Th, including tolerant and sensitive groups. Taken together, our findings suggest that the high specific-activities of natural radionuclides can obviously drive changes in microbial communities, providing a possibility for future studies on the microbial tolerance genes and bioremediation strains.

Mechanism of Microbial Detoxification of Heavy Metals: A Review

Heavy metal contamination from anthropogenic activities has an adverse effect on the environment due to its cytotoxicity, carcinogenicity and mutagenicity. Environment harbours microorganisms, some of which have been found to modify physico-chemical conditions of their surrounding environment through certain processes such as detoxification, metal homeostasis, precipitation, redox transformations etc. Investigations in the past have shown that short term contact with metals of certain bacteria causes the selection of resistant bacteria within weeks, while a prolonged exposure showed selected strains able to thrive better. Hence biotic methods could assist removal of heavy metals based on biosorption or bioaccumulation by microorganisms, which are cost-effective and environmental friendly in the long run. Microbial remediation is influenced by biotic and environmental factors as also the contamination site characteristics. The aim of this paper is to highlight and review some of the mechanisms of microbial remediation through techniques such as biostimulation, bioaugmentation etc.

Degradation of Xenobiotic Pollutants: An Environmentally Sustainable Approach

The ability of microorganisms to detoxify xenobiotic compounds allows them to thrive in a toxic environment using carbon, phosphorus, sulfur, and nitrogen from the available sources. Biotransformation is the most effective and useful metabolic process to degrade xenobiotic compounds. Microorganisms have an exceptional ability due to particular genes, enzymes, and degradative mechanisms. Microorganisms such as bacteria and fungi have unique properties that enable them to partially or completely metabolize the xenobiotic substances in various ecosystems.There are many cutting-edge approaches available to understand the molecular mechanism of degradative processes and pathways to decontaminate or change the core structure of xenobiotics in nature. These methods examine microorganisms, their metabolic machinery, novel proteins, and catabolic genes. This article addresses recent advances and current trends to characterize the catabolic genes, enzymes and the techniques involved in combating the threat of xenobiotic compounds using an eco-friendly approach.