A critical review on microbes-based treatment strategies for mitigation of toxic pollutants

Dendrochemical analysis of heavy metals in Magnolia champaca tree rings in Mizoram, Northeast India

Heavy metals are among the important environmental pollutants, yet their impact in remote areas remains underexplored because of limited studies on their monitoring. This study presents the first dendrochemical analysis from Mizoram, using Magnolia champaca tree rings to assess heavy metal concentration trends at a natural forest site (Site-I) and a roadside plantation (Site-II) for about two and half decades (from 1993 to 2019). The concentrations of Zn, Pb, Fe, Cu, Ni, and Mn were analyzed in tree rings to reconstruct pollution history. The results revealed a significant difference between the two sites, with roadside tree cores exhibiting greater variability and steadily increasing heavy metal concentrations as compared to natural forest. The mean concentrations of metals in natural forest samples were in the order: Fe (18.22 mg kg⁻1) > Mn (12.01 mg kg⁻1) > Ni (7.23 mg kg⁻1) > Cu (3.71 mg kg⁻1) > Pb (0.398 mg kg⁻1) > Zn (0.411 mg kg⁻1). In contrast, roadside samples showed considerably higher metal concentrations in the order: Mn (39.92 mg kg⁻1) > Fe (22.9 mg kg⁻1) > Ni (11.61 mg kg⁻1) > Cu (10.28 mg kg⁻1) > Zn (6.723 mg kg⁻1) > Pb (3.17 mg kg⁻1). Notably, M. champaca samples collected from the roadside contained elevated levels of Pb, Fe, Cu, and Ni, exceeding the permissible limits for plant parts as prescribed by the WHO. The study underscores the potential of species as a bioindicator of heavy metal pollution. These findings are crucial for informing soil management, pollution control, and understanding nutrient-metal cycling in trees. Further research is needed to explore the plant-soil interactions and behaviours of heavy metals in these environments.

Enhancing remediation efficiency of cadmium-contaminated soil: integrating forage-microorganism systems with agronomic strategies

Soil contamination due to heavy metals, especially cadmium (Cd), poses a growing concern. This study seeks to develop an economical and non-polluting sustainable remediation program for Cd-contaminated soil to address this issue. This study pioneered the exploration of Cd accumulation patterns in three forage species: Lolium multiflorum Lamk (LMJS), Sorghum bicolor × sudanense (SSBJ), and Sorghum sudanense (Piper) Stapf (SUJS) to identify their optimal harvest periods in Cd-contaminated soils. Additionally, a consortium of beneficial microorganisms (combinations of C, F, and H; C: 10% Bacillus subtilis; F: 20% Bacillus subtilis + 10% Bacillus cereus + 20% Citrobacter; H: 20% Deinococcus radiodurans + 10% Bacillus cereus) was implemented, with a focus on developing an efficient forage-microbial co-remediation system. Subsequently, agronomic strategies (mowing or chelating agents) were employed to improve the Cd enrichment capacity of the combined forage-microbe remediation system, offering sustainable field remediation strategies. The results indicate that the SSBJ + F combined remediation system was mowed on the 60th day (stubble left at 35 cm, light mowing) and harvested on the 120th day as the optimal choice. The bioaccumulation quantity (BCQ) unit accumulation in Cd-contaminated soil at a concentration of 10 mg/kg reached 0.397 mg/kg, and the annual Cd removal rate was 9.23%, representing a 29.63% increase compared to the control group. The results of this study provide valuable insights into the development of practical, field-applicable remedial measures for cadmium-contaminated soils while minimizing environmental impacts.

Unappreciated role of secondary metabolism-derived small mediators in degrading bisphenol A and antibiotics by a laccase-expressing fungus

Fungal laccase producers can effectively address bisphenol A (BPA) and antibiotic-contaminated water. However, the role of small mediators produced by fungal secondary metabolism in enhancing the removal of refractory contaminants is often overlooked. In this work, an efficient laccase-producing strain, Trametes hirsuta La-7, was activated to simultaneously treat BPA and antibiotics. Coexisting tetracycline, ciprofloxacin, sulfadiazine, or roxithromycin inhibited fungal cell growth, reducing laccase biosynthesis but largely increasing the formation of syringaldehyde (SYR), 4-hydroxybenzoic acid (HBA), and vanillin (VAN) through a complex regulatory network. These specialized metabolites (i.e., small mediators) acted as diffusible electron carriers for laccase, enabling the oxidative decomposition of the four antibiotics with high redox potentials. According to laccase-mediator-regulated radical random polymerization and decomposition, the identified intermediates of copollutants were parallelly concentrated in oligomeric coupling products and oxidative cleavage species. By inoculating logarithmic phase cell pellets in conjunction with an artificially added small mediator (SYR, HBA, or VAN), the removal efficiencies of BPA and the four antibiotics within 5 d reached 100% and 69-100% in artificial wastewater, respectively. The low and ultimately non-biotoxic intermediate products generated in the fungus-mediator systems mitigated the eco-environmental risks of the parent compounds. This work highlights the previously underappreciated role of secondary metabolism-derived small mediators in enhancing the degradation of BPA and antibiotics by a laccase-expressing fungus and is beneficial to the rational design of a robust fungus-mediator system for environmental bioremediation.

Hepatotoxicity of N-nitrosodin-propylamine in larval zebrafish by upregulating the Wnt pathway

N-nitrosodin-propylamine is an organic compound mainly used in organic synthesis. As a typical pollutant, the accidental release of N-nitrosodin-propylamine may cause environmental pollution, especially water environment pollution. In the present study, we used the zebrafish model for the first time to evaluate the developmental toxicity of this drug in the liver. Zebrafish larvae fertilized at 72hpf showed a range of toxic responses after 72hpf exposure to the drug. These include increased mortality, delayed absorption of yolk sac nutrients, shorter body length, abnormal liver morphology, gene disruption, and altered expression of various indicators with increasing dose. Studies on the mechanism of toxicity showed that N-nitrosodin-propylamine exposure increased the level of oxidative stress, increased the level of apoptosis in hepatocytes, and up-regulated the transcriptional expression level of Wnt signaling pathway genes. Astaxanthin and IWR-1 can effectively save the liver toxicity in zebrafish caused by N-nitrosodin-propylamine. Our study showed that the drug exposure induced hepatotoxicity in zebrafish larvae through the up-regulation of Wnt signaling pathway, oxidative stress and apoptosis.

Assessment of heavy metal pollution in soil-parent material relationship across ecosystems

The works of assessing the pollution posed by metals in agricultural areas in developing countries are limited. This study aims to assess metal concentrations and pollution indices of parent materials and soils representing the mantle and oceanic crust units of the ophiolite in the Eastern Mediterranean region, specifically in Kahramanmaraş Province. A total of 88 samples, comprising 44 soil (0-30 cm) and 44 parent material (90 + cm), were collected from the study area. Arsenic (As), mercury (Hg), selenium (Se), uranium (U), molybdenum (Mo), tin (Sn), and cesium (Cs) concentrations were analyzed in these samples, along with the reference metal, iron (Fe). Pollution levels were assessed using enrichment factor (EF) and contamination factor (CF) calculations. Results showed that elemental concentrations (Hg, Se, U, Mo, Sn, and Cs) in soils from the mantle and oceanic crust generally reflected those of the parent material. However, the average As concentration in soils from oceanic crust and mantle units was notably elevated, showing a 3 to fourfold increase compared to the parent material. Based on pollution index values, soils from these units demonstrated a moderate level of enrichment (2 < EF < 5) for As, while other elements (Hg, Se, U, Mo, Sn, and Cs) fell into the low enrichment class (EF < 2). Furthermore, the CF index indicated significant contamination (3 < CF < 6) for As. These findings suggest As contamination in soils from different units of the ophiolite (mantle and oceanic crust), potentially resulting from agricultural chemicals like pesticides and fertilizers.

A synergistic approach combining computational fluid dynamics simulation with hydrolysis-acidification for dye wastewater treatment

Wastewater treatment is effectively conducted using anaerobic biological methods. Nevertheless, the efficiency of these methods can be hindered by challenges like short-circuits and dead zones, particularly in treating persistent contaminants. This work utilized computational fluid dynamics (CFD) simulations to enhance water distribution, ensuring uniform interactions between solid and liquid phases, and thus mitigating issues related to short-circuits and dead zones. Such enhancements notably amplified the anaerobic biological process's efficiency. Furthermore, dye biodegradability was improved through the application of the hydrolysis acidification technique. Optimal hydraulic retention time for the hydrolysis-acidification reactor, established at 9 h, was determined via sludge cultivation and domestication for stable operation. During stable operation, an elevation in effluent volatile fatty acids was observed, alongside a COD removal rate fluctuating between 15% and 29%. Approximately 50% was noted as the rate of color removal. Simultaneously, a noticeable decrease in effluent pH occurred, with total nitrogen removal approximating 8%. An estimated BOD5/COD ratio of 0.32 was recorded. The incorporation of microbial agents led to an enhanced COD removal, ranging from 28% to 33%, thereby stabilizing the effluent BOD5/COD ratio at around 0.35. This research highlights the advantages of optimizing water distribution in anaerobic reactors, particularly when combined with hydrolysis-acidification techniques, effectively addressing issues of short-circuits and dead zones.

Insight into bacterial role attribution in dissolved organic matter humification during rice straw composting with microbial inoculation

This study aims to investigate the effect of microbial role distribution in microbial carbon pumps on dissolved organic matter (DOM) humification during rice straw composting with microbial inoculation. Three composting groups were designed, named CK (control), B4 (with Bacillus subtilis, OR058594) and Z1 (with Aspergillus fumigatus, AF202956.1). As a result of inoculation, the composition of microbial communities was changed, so that the microorganisms that promoted DOM humification were concentrated in the responders in the microbial carbon pump. DOM was divided into three components in three composting treatments: C1, C2 and C3. After inoculation with Bacillus subtilis, the C2 component was significantly affected, while after inoculation with Aspergillus fumigatus, the C3 component was significantly affected. The results of physicochemical factors affecting the transformation of DOM fluorescence components indicated that C1, C2 and C3 were related to the abundance of the cellulose-degrading enzyme-encoding gene GH7 in CK and B4 composting. However, the C2 was susceptible to organic matter in Z1 composting. This study explored the distribution of microbial communities from a new perspective, which provided new information for analyzing DOM humification and treating agricultural straws to achieve clean conditions for environmental friendliness.

Biological roles of soil microbial consortium on promoting safe crop production in heavy metal(loid) contaminated soil: A systematic review

Heavy metal(loid) (HM) pollution of agricultural soils is a growing global environmental concern that affects planetary health. Numerous studies have shown that soil microbial consortia can inhibit the accumulation of HMs in crops. However, our current understanding of the effects and mechanisms of inhibition is fragmented. In this review, we summarise extant studies and knowledge to provide a comprehensive view of HM toxicity on crop growth and development at the biological, cellular and the molecular levels. In a meta-analysis, we find that microbial consortia can improve crop resistance and reduce HM uptake, which in turn promotes healthy crop growth, demonstrating that microbial consortia are more effective than single microorganisms. We then review three main mechanisms by which microbial consortia reduce the toxicity of HMs to crops and inhibit HMs accumulation in crops: 1) reducing the bioavailability of HMs in soil (e.g. biosorption, bioaccumulation and biotransformation); 2) improving crop resistance to HMs (e.g. facilitating the absorption of nutrients); and 3) synergistic effects between microorganisms. Finally, we discuss the prospects of microbial consortium applications in simultaneous crop safety production and soil remediation, indicating that they play a key role in sustainable agricultural development, and conclude by identifying research challenges and future directions for the microbial consortium to promote safe crop production.

Is a non-cytotoxic and non-genotoxic novel bioinspired dipeptide structure synthesis possible for theragnostic applications?

The diagnosis and treatment of the diseases in a certain coordination is a subject that has been emphasized in recent years. Theragnostics approaches allow simultaneous diagnosis and treatment of chronic diseases such as cancer. An ideal theragnostic should be biocompatible and can be used safely in humans. Although several types of theragnostics have been developed, none of yet satisfied these criteria. Bioinspired materials with noble metal centers encapsulating therapeutic and imaging agents were shown to possess theragnostic activities. In this study, it was aimed to synthesize, characterize, and evaluate the cytotoxic and genotoxic effects of self-assembly of diphenylalanine (Phe-Phe) dipeptides presence of mercury (Hg2+) ions to be used for theragnostic. Cytotoxicity and genotoxicity studies were done in mouse fibroblast (NIH/3T3) cells by 3-(4,5-Dimethylthiazol-2-yl)- 2,5-diphenyltetrazolium bromide (MTT) and single cell gel electrophoresis (Comet) assays, respectively. It was found that cell viability decreased in a dose-dependent manner in 24-, 48-, and 72-h treatment. Also, Phe-Phe dipeptides did not cause any significant changes in DNA damage at the concentrations of 1, 2, and 5 mg/mL in 4- and 24-h exposures. In the 48-h exposure, Phe-Phe peptide exposure at concentrations of 2 and 5 mg/mL caused a significant increase in DNA damage and in the 72-h of exposure, a significant increase in DNA damage was observed at all studied concentrations. According to the results of the study, it can be said that Phe-Phe dipeptides presence of Hg2+ ions are biocompatible and can be used safely for theragnostic purposes.

Soil microbial responses to simultaneous contamination of antimony and arsenic in the surrounding area of an abandoned antimony smelter in Southwest China

Soil contamination with heavy metal(loid)s may influence microbial activities in the soil, and consequently jeopardize soil health. Microbial responses to soil contamination play an important role in ecological risk assessment. This study investigated the effect of heavy metal(loid)s contamination on microbial community structure and abundance in the surrounding soil of an abandoned antimony (Sb) smelter in Qinglong county, Guizhou province, Southwest China. A total of 46 soil samples were collected from ten sampling sites (labelled as A-I, and CK) across the study area at depths of 0-2, 2-10, 10-20, 20-30, 30-40, and 40-50 cm. The soil samples were analyzed for total and bioavailable heavy metal(loid) concentrations, bacterial, fungal, and archaeal community structures, diversities, and functions, together with soil basic physicochemical properties. Much greater ecological risk of Sb and arsenic (As) was present in the surface soil (0-2 cm) compared to that in the subsoils. The activities of dominant microorganisms tended to be associated with soil pH and heavy metal(loid)s (i.e., Sb, As, lead (Pb), cadmium (Cd), and chromium (Cr)). Bacteria associated with IMCC26256, Rhizobiales, Burkholderiales, and Gaiellales, and archaea associated with Methanocellales were estimated to be tolerant to high concentrations of Sb and As in the soil. In addition, the magnitude of soil microbial responses to Sb and As contamination was in the order of archaea > bacteria > fungi. In contrast to the negligible response of fungi and negative response of bacteria to Sb and As contamination, there was a strongly positive correlation between archaeal activity and total Sb and As concentrations in the soil. Our findings provide a theoretical basis for the remediation of Sb smelter-affected soil.

Global Situation of Bioremediation of Leachate-Contaminated Soils by Treatment with Microorganisms: A Systematic Review

This systematic review presents the current state of research in the last five years on contaminants in soils, especially in leachates from solid waste landfills, with emphasis on biological remediation. In this work, the pollutants that can be treated by microorganisms and the results obtained worldwide were studied. All the data obtained were compiled, integrated, and analyzed by soil type, pollutant type, bacterial type, and the countries where these studies were carried out. This review provides reliable data on the contamination of soils worldwide, especially soils contaminated by leachate from municipal landfills. The extent of contamination, treatment objectives, site characteristics, cost, type of microorganisms to be used, and time must be considered when selecting a viable remediation strategy. The results of this study can help develop innovative and applicable methods for evaluating the overall contamination of soil with different contaminants and soil types. These findings can help develop innovative, applicable, and economically feasible methods for the sustainable management of contaminated soils, whether from landfill leachate or other soil types, to reduce or eliminate risk to the environment and human health, and to achieve greater greenery and functionality on the planet.

Current Trends in Bioaugmentation Tools for Bioremediation: A Critical Review of Advances and Knowledge Gaps

Bioaugmentation is widely used in soil bioremediation, wastewater treatment, and air biofiltration. The addition of microbial biomass to contaminated areas can considerably improve their biodegradation performance. Nevertheless, analyses of large data sets on the topic available in literature do not provide a comprehensive view of the mechanisms responsible for inoculum-assisted stimulation. On the one hand, there is no universal mechanism of bioaugmentation for a broad spectrum of environmental conditions, contaminants, and technology operation concepts. On the other hand, further analyses of bioaugmentation outcomes under laboratory conditions and in the field will strengthen the theoretical basis for a better prediction of bioremediation processes under certain conditions. This review focuses on the following aspects: (i) choosing the source of microorganisms and the isolation procedure; (ii) preparation of the inoculum, e.g., cultivation of single strains or consortia, adaptation; (iii) application of immobilised cells; (iv) application schemes for soil, water bodies, bioreactors, and hydroponics; and (v) microbial succession and biodiversity. Reviews of recent scientific papers dating mostly from 2022-2023, as well as our own long-term studies, are provided here.

Metabolic pathway of Cr(VI) reduction by bacteria: A review

Heavy metal wastes, particularly hexavalent chromium [Cr(VI)], are generated from anthropogenic activities, and their increasing abundance has been a research concern due to their toxicity, genotoxicity, carcinogenicity and mutagenicity. Exposure to these dangerous pollutants could lead to chronic infections and even mortality in humans and animals. Bioremediation using microorganisms, particularly bacteria, has gained considerable interest because it can remove contaminants naturally and is safe to the surrounding environment. Bacteria, such as Pseudomonas putida and Bacillus subtilis, can reduce the toxic Cr(VI) to the less toxic trivalent chromium Cr(III) through mechanisms including biotransformation, biosorption and bioaccumulation. These mechanisms are mostly linked to chromium reductase and nitroreductase enzymes, which are involved in the Cr(VI) reduction pathway. However, relevant data on the nitroreductase route remain insufficient. Thus, this work proposes an alternative metabolic pathway of nitroreductase, wherein nitrate activates the reaction and indirectly reduces toxic chromium. This nitroreductase pathway occurs concurrently with the chromium reduction pathway.

Diagnostic strategy for the combined effects of microplastics and potentially toxic elements on microbial communities in catchment scale

Combined effects of potentially toxic materials (PTMs) released from production activities on microbial communities in environmental flimsy area are poorly recognised. Microplastics (MPs) and potentially toxic elements (PTEs) were investigated in soils and river sediments in a headwater catchment from the Qinghai-Tibet Plateau. Their co-effects on microbial communities and the controlling factors affecting communities were further explored. Results showed that MPs and PTEs significantly accumulated in soils and sediments. Among which fragment-shaped MPs and copper (Cu) dominated, with mean contents of 1.11 × 10⁴ and 1.81 × 10⁴ items kg^-1 and 13.80 and 7.33 mg kg^-1 in soils and sediments, respectively. Distribution index (0.54) suggested that fiber-shaped MPs preferred to transport into rivers and deposited in sediments. The film mulching contributed significantly to the occurrence of fragment-shaped MPs, while Cu may be derived from industrial wastewater. The antagonistic effect between fiber-shaped MPs and zinc (Zn) on soil microbial structure was found based on their obtuse angle in canonical correlation analysis. While the synergistic effect between total phosphorus (TP) and Cu on diversity was detected by interaction detector model (q(TP ∩ Cu) >q(TP) >q(Cu), p < 0.05). Soil TP and Cu were identified as controlling factors influencing diversity through random forest model and factor detector (q(TP) = 0.49, q(Cu) = 0.36, p < 0.05), which may be related to direct nutrient supply and microbial resistance, respectively. The negative effects of MPs on structure might be counteracted by increasing Zn content, while the co-existence of TP and Cu further increased diversity. A diagnostic framework, which involves background data collection, sampling analysis, characterisation and relationship investigation, was proposed to explore the co-effects of complex pollution and factors on communities. This study may provide strategies to mitigate the negative effects on microorganisms in the environment.

Tricks and tracks in waste management with a special focus on municipal landfill leachate: Leads and obstacles

Landfilling is the most widely used disposal method for municipal solid waste around the world. The main disadvantage of this strategy is formation of leachate, among other aspects. Landfill leachate contains highly toxic and bio-refractory substances that are detrimental to the environment and human health. Hence, the risk(s) of discharging potentially harmful landfill leachate into the environment need to be assessed and measured in order to make effective choices about landfill leachate management and treatment. In view of this, the present review aims to investigate (a) how landfill leachate is perceived as an emerging concern, and (b) the stakeholders' mid- to long-term policy priorities for implementing technological and integrative solutions to reduce the harmful effects of landfill leachate. Because traditional methods alone have been reported ineffective, and in response to emerging contaminants and stringent regulations, new effective and integrated leachate treatments have been developed. This study gives a forward-thinking of the accomplishments and challenges in landfill leachate treatment during the last decade. It also provides a comprehensive compilation of the formation and characterization of landfill leachate, the geo-environmental challenges that it raises, as well as the resource recovery and industrial linkage associated with it in order to provide an insight into its sustainable management.

Recent advances in carbon-based nanomaterials for the treatment of toxic inorganic pollutants in wastewater

Wastewater contains inorganic pollutants, generated by industrial and domestic sources, such as heavy metals, antibiotics, and chemical pesticides, and these pollutants cause many environmental problems.

Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.

Trichoderma - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture

The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.