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Biotransformation of soil organochlorine pesticides (OCP) is often impeded by a lack of nutrients relevant for bacterial growth and/or co-metabolic OCP biotransformation. By providing space-filling mycelia, fungi promote contaminant biodegradation by facilitating bacterial dispersal and the mobilization and release of nutrients in the mycosphere. We here tested whether mycelial nutrient transfer from nutrient-rich to nutrient-deprived areas facilitates bacterial OCP degradation in a nutrient-deficient habitat. The legacy pesticide hexachlorocyclohexane (HCH), a non-HCH-degrading fungus ( Fusarium equiseti K3), and a co-metabolically HCH-degrading bacterium ( Sphingobium sp. S8) isolated from the same HCH-contaminated soil were used in spatially structured model ecosystems. Using 13 C-labeled fungal biomass and protein-based stable isotope probing (protein-SIP), we traced the incorporation of 13 C fungal metabolites into bacterial proteins while simultaneously determining the biotransformation of the HCH isomers. The relative isotope abundance (RIA, 7.1–14.2%), labeling ratio (LR, 0.13–0.35), and the shape of isotopic mass distribution profiles of bacterial peptides indicated the transfer of 13 C-labeled fungal metabolites into bacterial proteins. Distinct 13 C incorporation into the haloalkane dehalogenase (linB) and 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase (LinC), as key enzymes in metabolic HCH degradation, underpin the role of mycelial nutrient transport and fungal-bacterial interactions for co-metabolic bacterial HCH degradation in heterogeneous habitats. Nutrient uptake from mycelia increased HCH removal by twofold as compared to bacterial monocultures. Fungal-bacterial interactions hence may play an important role in the co-metabolic biotransformation of OCP or recalcitrant micropollutants (MPs).

Fungi are usually involved in degradation/deterioration of many anthropogenic wastes due to their verse enzyme secretions and adaptive capabilities. In this study, five dominant fungal strains were isolated from an aged lindane polluted site, they were all mixed (100 mg each) together with pent mushroom compost (SMC) and applied to lindane polluted soil (5 kg) at 10, 20, 30, 40% and control 0% (soil with no treatment), these were used to grow M. maximus Jacq for 3 months. To establish lindane degradation, deductions such as Degradation rate (K1), Half-life (t1/2) and Degradation efficiency (DE) were made based on the analyzed lindane concentrations before and after the experiment. We also tested the presence and expressions of phosphoesterases (mpd and opd-A) and catechol 1,2-dioxygenases (efk2 and efk4) genes in the strains. The stains were identified as Aspergillus niger (KY693970); Talaromyces atroroseus (KY488464), Talaromyces purpurogenus (KY488468), Yarrowia lipolytica (KY488469) and Aspergillus flavus (KY693973) through morphological and molecular methods. Combined rhizospheric action of M. maximus and fungi speed up lindane degradation rate, initially detected lindane concentration of 45 mg/kg was reduced to 11.26, 9.34 and 11.23 mg/kg in 20, 30 and 40% treatments respectively making 79.76, 85.93 and 88.67% degradation efficiencies. K1 of 1.29 was recorded in control while higher K1 of 1.60, 1.96 and 2.18 /day were recorded in 20, 30 and 40% treatments respectively. The best t1/2 of 0.32 and 0.35 /day were recorded in 40 and 30% compared to control (0.54 /day). All the strains were also affirmed to possess the tested genes; opd was overexpressed in all the strains except KY693973 while mpd was overexpressed in KY693970, KY488464 but moderately expressed in KY488468, KY488469 and KY693973. However, efk genes were under-expressed in most of the strains except KY488469 and KY693973 which showed moderate expression of efk4. This work suggests that the synergistic association of the identified rhizospheric fungi and M. maximus roots could be used to remove lindane in soil at a limited time period and this combination could be used at large scale.

This review elucidates different bioremediation approaches used for degradation of HCH from contaminated sites. It highlights the significance of degradative pathways, microbial diversity and impact of different environmental factors for developing viable bioremediation strategies. The application of innovative biotechnological approaches and a thorough understanding of HCH biodegradation pathways show great promise for the creation of long-term solutions to HCH pollution and the restoration of polluted soil ecosystems. Bioremediation technologies viz. biostimulation, bioaugmentation, phytoremediation have been considered till date for treating HCH-contaminated sites. Different bacterial and fungal strains have been reported for degradation of HCH residues. However, these methods are limited to γ-HCH degradation, at laboratory scale and achieving lower success rate for large scale demonstration trials. This review presents a theoretical background for degradation of different HCH isomers in soil through plants, microbes and through their cooperative interactions. This work briefly overviews the substantial contamination of the environment by HCH residues, along with spontaneous evolution of degradation pathways through various HCH degrading microbes. Bioremediation mechanism and pathways of HCH degradation through plants and microbes have been discussed thoroughly. Through molecular and genetic investigations, the complex metabolic pathways used by these microbes, including reductive dechlorination, hydrolysis, and ring cleavage, has been clarified. This study seeks to give a thorough summary of recent discoveries and developments in bioremediation methods for soil HCH degradation. Numerous microbial consortia, including fungi, plants, and bacteria have been recognised as important participants in the transformation of HCH.

Hexachlorocyclohexane (HCH) was extensively used as a pesticide until the 1990s. It was synthesized by benzene photochlorination, resulting in a mixture of stereoisomers, which included α‐, β‐, γ‐, and δ‐HCH, among others. It was later discovered that only the γ‐HCH isomer (also called lindane) had insecticidal properties, so it began to be purified from this mixture, while the remaining HCH isomers (representing around 85%–90% of industrial HCH production) were disposed of in dumpsites, generating environmental issues. Several works have studied microbial‐driven biodegradation and physiological responses to γ‐HCH, but information concerning the other isomers is scarce. Since previous research showed that the cyanobacterium Anabaena sp. PCC 7120 is effective at removing lindane; this study focused on its responses to the α‐, β‐, and δ‐HCH isomers. The results showed that Anabaena tolerates α‐ and γ‐HCH well, with little impact on growth, while β‐ and δ‐HCH are more poorly tolerated and negatively affect growth and cell physiology. It was also found that, in the presence of Anabaena sp. PCC 7120, both α‐ and γ‐HCH are completely eliminated from supernatants while β‐ and δ‐HCH are partially eliminated. Additionally, the linC gene was found to be expressed at twice the normal level in the presence of α‐ and γ‐HCH at 2 mg/mL. Overall, this study reveals how Anabaena responds to key HCH isomers found in contaminated sites and supports its potential use in bioremediation. This study investigates the physiological responses of Anabaena sp. PCC 7120 to HCH isomers, emphasizing both its tolerance to these compounds and its ability to biodegrade them. The findings support the potential application of Anabaena in the bioremediation of environments contaminated with specific HCH isomers.

Background Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes ( S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6). Results Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN ) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity. Conclusion The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS 6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.

Haloalkane dehalogenase, LinB, is a member of the α/β hydrolase family of enzymes. It has a wide range of halogenated substrates, but, has been mostly studied in context of degradation of hexachlorocyclohexane (HCH) isomers, especially β-HCH (5–12% of total HCH isomers), which is the most recalcitrant and persistent among all the HCH isomers. LinB was identified to directly act on β-HCH in a one or two step transformation which decreases its toxicity manifold. Thereafter, many studies focused on LinB including its structure determination using X-ray crystallographic studies, structure comparison with other haloalkane dehalogenases, substrate specificity and kinetic studies, protein engineering and site-directed mutagenesis studies in search of better catalytic activity of the enzyme. LinB was mainly identified and characterized in bacteria belonging to sphingomonads. Detailed sequence comparison of LinB from different sphingomonads further revealed the residues critical for its activity and ability to catalyze either one or two step transformation of β-HCH. Association of LinB with IS6100 elements is also being discussed in detail in sphingomonads. In this review, we summarized vigorous efforts done by different research groups on LinB for developing better bioremediation strategies against HCH contamination. Also, kinetic studies, protein engineering and site directed mutagenesis studies discussed here forms the basis of further exploration of LinB’s role as an efficient enzyme in bioremediation projects.

Micropollutants, such as heavy metals and pesticides, inhibit microbial growth, threatening ecosystems. Yet, the mechanism behind mycoremediation of the pesticide lindane and multiple metals (Cd, Total Cr, Cu, Ni, Pb, Zn) remains poorly understood. In our study, we investigated cellular responses in Aspergillus fumigatus PD-18 using LC-MS/MS, identifying 2190 proteins, 1147 of which were consistently present under both stress conditions. Specifically, Cu-Zn superoxide dismutase and heat shock proteins were up-regulated to counter oxidative stress and protein misfolding. Proteins involved in intracellular trafficking, secretion, and vesicular transport; RNA processing and modification showed enhanced abundance and regulating stress response pathways. Additionally, haloalkane dehalogenase and homogentisate 1,2-dioxygenase played pivotal roles in lindane mineralization. Bioinformatics analysis highlighted enriched pathways such as Glyoxylate and dicarboxylate metabolism and Purine metabolism, that are crucial for combating adverse environments. We identified the hub protein 26 S proteasome regulatory subunit complex as potential biomarker and remedial targets for mycoremediation of wastewater, suggesting practical applications for environmental remediation.

Streptomyces sp. MC1, a bacterium isolated from an environment contaminated with organic and inorganic pollutants, can reduce chromium and degrade lindane, making it a promising candidate for bioremediation. However, a major challenge in bioremediation trials is monitoring bacteria survival in soil. To assess the survival of Streptomyces sp. MC1 during bioremediation, we introduced fluorescence tagging and a selectable marker into this strain by intergeneric conjugation from Escherichia coli. Conjugation assays were performed using two E. coli strains (ET12567/pUZ8002 or S17-1) and Streptomyces sp. MC1 (spores or mycelium). The integrative plasmid pSC001, carrying a gene encoding the monomeric green fluorescent protein (mGFP), was used. Various donor and recipient concentrations were tested and the presence of MgCl2 or CaCl2 during conjugation was also evaluated. Optimal conditions included low concentrations of both Streptomyces sp. MC1 spores and E. coli S17-1, with MgCl2 in the medium. Exconjugants were analyzed, confirming plasmid site-specific integration and mGFP expression. In bioremediation assays with soils co-contaminated with Cr(VI) and lindane, fluorescence-tagged Streptomyces sp. MC1 successfully demonstrated survival over 28 days. Our results, combined with the availability of the Streptomyces sp. MC1 genome sequence, will facilitate further characterization of this strain’s features and accelerate its development for bioremediation applications.

This study introduces an indigenous bacterial strain, Exiguobacterium sp. (L.O), isolated from sugarcane fields in Sevur, Tamil Nadu, which has adapted to prolonged exposure to dimethoate. The strain demonstrated the capability to utilize 150 ppm of dimethoate as its sole carbon source, achieving a remarkable degradation rate of 95.87% within 5 days in mineral salt media. Gas chromatography–mass spectrometry (GC–MS) analyses identified the presence of intermediate by-products formed during degradation, like methyl diethanol amine and aspartyl glycine ethyl ester. Notably, phosphorothioic O, O, S-acid, an expected end product in the degradation of dimethoate, was also identified, further confirming the strain’s effective metabolic breakdown of the pesticide. Further degradation study and analysis of changes in functional group was performed by FTIR, and a hypothetical degradation pathway was elucidated showing the course of dimethoate metabolism by the strain. Exiguobacterium sp. (L.O) also displayed significant plant growth-promoting traits, including the production of HCN, IAA, and ammonia and the formation of biofilms, which enhance its utility in agricultural applications. The ecotoxicity study revealed the degradation by-products exhibited reduced toxicity compared to the parent compound dimethoate, highlighting the strain’s potential not only for bioremediation but also for supporting sustainable agricultural practices. This research presents a novel application of Exiguobacterium sp. (L.O), integrating the bioremediation of the organophosphate pesticide dimethoate with agricultural enhancement. This approach is critical for addressing the challenges associated with pesticide pollution in agricultural practices. This study is likely the first to demonstrate the application of this strain in the degradation of dimethoate, as suggested by an extensive review of the literature.

The biotransformation of hexachlorocyclohexane isomers (HCH) by two Dehalococcoides mccartyi strains (195 and BTF08) and an enrichment culture was investigated and compared to conversion by the obligate anaerobic strain Clostridium pasteurianum strain DSMZ 525. The D. mccartyi strains preferentially transformed γ-HCH over α-HCH and δ-HCH isomers while β-HCH biotransformation was not significant. In case of the enrichment culture, γ-HCH was preferentially transformed over the δ-HCH, β-HCH and α-HCH isomers. Major observed metabolites in both cases were tetrachlorocyclohexene and as end products monochlorobenzene (MCB) and benzene. Dechlorination of the γ-HCH isomer was linked to an increase in cell numbers for strain 195. γ-HCH transformation was linked to considerable carbon stable isotope fractionation with the enrichment factor εc = − 5.5 ± 0.8‰ for D. mccartyi strain 195, εc = − 3.1 ± 0.4‰ for the enrichment culture and εc = − 4.1 ± 0.6‰ for co-metabolic transformation by C. pasteurianum.