Engineering bacteria for bioremediation of persistent organochlorine pesticide lindane (γ-hexachlorocyclohexane)

A global systematic review and meta-analysis of innovative technologies for 1,2,4-trichlorobenzene remediation in soil and water

The 1,2,4-trichlorobenzene (1,2,4-TCB) is a persistent organic pollutant, which poses a serious concern due to its long-lasting and detrimental impact on soil and water quality. This study uses meta-analysis to investigate the effectiveness of various remediation methods for 1,2,4-TCB in water and soil. In water, the intimate coupling of photocatalysis and biodegradation (ICPB) demonstrated the highest removal rate (80%), followed by photocatalysis (PC, 69%), bioremediation (B, 53%), and photolysis (P, 42%). Optimal conditions for 1,2,4-TCB removal in water included short remediation times (< 5 days), higher temperatures (≥ 25 °C), neutral pH, and specific free radicals (H+ > •OH > •O2-). In soil, short-term remediation methods and suspended cultures showed higher removal rates. Topsoil depth layers (≤ 10 cm) exhibited better removal rates than subsoil (> 10 cm). Key factors influencing remediation effectiveness in water were hydraulic retention time (HRT), salinity, and water table depth, while in soil, remediation time and soil depth layer were the most significant. This research highlights the importance of optimizing remediation methods and environmental conditions to remove 1,2,4-TCB from contaminated sites effectively. Further investigation is needed to understand the underlying mechanisms and optimal conditions for these remediation methods, particularly in soil. Effective remediation of 1,2,4-TCB requires a tailored approach considering specific environmental conditions and challenges in water and soil. The ICPB shows promise, especially in aquatic environments. However, further research is essential to optimize these methods, particularly for soil remediation.

Cyanobacteria-Pesticide Interactions and Their Implications for Sustainable Rice Agroecosystems

Modern agricultural practices rely heavily on fertilizers and pesticides to boost crop yields, essential for feeding the growing global population. However, their extensive use poses significant environmental risks. Chemical-based fertilizers and pesticides persist in ecosystems, potentially harming ecological stability. Wetland rice farming utilizing nitrogen-fixing cyanobacteria has emerged as an ecofriendly alternative, drawing attention due to its capacity to mitigate pesticide-related issues. Cyanobacteria, capable of fixing atmospheric nitrogen, thrive in low-nitrogen conditions and can aid plant growth. Some species can also biodegrade pesticides, offering a means to clean up contaminated environments. Researchers are exploring ways to leverage cyanobacteria's nitrogen fixation and biodegradation abilities for ecofriendly biofertilizers and environmental cleanup. This approach presents promise for sustainable agriculture and environmental preservation. The current study delves into multiple studies to investigate global pesticide usage levels, primary categorization, and persistence patterns. It also investigates cyanobacterial distribution and their interactions with pesticides in wetland rice ecosystems, aiming to enable their use in sustainable agriculture. Additionally, the review provides a thorough summary of the literature's findings about the potential of cyanobacteria in pesticide degradation.

A synthetic biology approach for the treatment of pollutants with microalgae

The increase in global population and industrial development has led to a significant release of organic and inorganic pollutants into water streams, threatening human health and ecosystems. Microalgae, encompassing eukaryotic protists and prokaryotic cyanobacteria, have emerged as a sustainable and cost-effective solution for removing these pollutants and mitigating carbon emissions. Various microalgae species, such as C. vulgaris, P. tricornutum, N. oceanica, A. platensis, and C. reinhardtii, have demonstrated their ability to eliminate heavy metals, salinity, plastics, and pesticides. Synthetic biology holds the potential to enhance microalgae-based technologies by broadening the scope of treatment targets and improving pollutant removal rates. This review provides an overview of the recent advances in the synthetic biology of microalgae, focusing on genetic engineering tools to facilitate the removal of inorganic (heavy metals and salinity) and organic (pesticides and plastics) compounds. The development of these tools is crucial for enhancing pollutant removal mechanisms through gene expression manipulation, DNA introduction into cells, and the generation of mutants with altered phenotypes. Additionally, the review discusses the principles of synthetic biology tools, emphasizing the significance of genetic engineering in targeting specific metabolic pathways and creating phenotypic changes. It also explores the use of precise engineering tools, such as CRISPR/Cas9 and TALENs, to adapt genetic engineering to various microalgae species. The review concludes that there is much potential for synthetic biology based approaches for pollutant removal using microalgae, but there is a need for expansion of the tools involved, including the development of universal cloning toolkits for the efficient and rapid assembly of mutants and transgenic expression strains, and the need for adaptation of genetic engineering tools to a wider range of microalgae species.

Strategies for mitigation of pesticides from the environment through alternative approaches: A review of recent developments and future prospects

Chemical-based peticides are having negative impacts on both the healths of human beings and plants as well. The World Health Organisation (WHO), reported that each year, >25 million individuals in poor nations are having acute pesticide poisoning cases along with 20,000 fatal injuries at global level. Normally, only ∼0.1% of the pesticide reaches to the intended targets, and rest amount is expected to come into the food chain/environment for a longer period of time. Therefore, it is crucial to reduce the amounts of pesticides present in the soil. Physical or chemical treatments are either expensive or incapable to do so. Hence, pesticide detoxification can be achieved through bioremediation/biotechnologies, including nano-based methodologies, integrated approaches etc. These are relatively affordable, efficient and environmentally sound methods. Therefore, alternate strategies like as advanced biotechnological tools like as CRISPR Cas system, RNAi and genetic engineering for development of insects and pest resistant plants which are directly involved in the development of disease- and pest-resistant plants and indirectly reduce the use of pesticides. Omics tools and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation of pesticides also discussed from the literatures. Overall, the review focuses on the most recent advancements in bioremediation methods to lessen the effects of pesticides along with the role of microorganisms in pesticides elimination. Further, pesticide detection is also a big challenge which can be done by using HPLC, GC, SERS, and LSPR ELISA etc. which have also been described in this review.

Bacterial remediation of pesticide polluted soils: Exploring the feasibility of site restoration

For decades, reclamation of pesticide contaminated sites has been a challenging avenue. Due to increasing agricultural demand, the application of synthetic pesticides could not be controlled in its usage, and it has now adversely impacted the soil, water, and associated ecosystems posing adverse effects on human health. Agricultural soil and pesticide manufacturing sites, in particular, are one of the most contaminated due to direct exposure. Among various strategies for soil reclamation, ecofriendly microbial bioremediation suffers inherent challenges for large scale field application as interaction of microbes with the polluted soil varies greatly under climatic conditions. Methodically, starting from functional or genomic screening, enrichment isolation; functional pathway mapping, production of tensioactive metabolites for increasing the bioavailability and bio-accessibility, employing genetic engineering strategies for modifications in existing catabolic genes to enhance the degradation activity; each step-in degradation study has challenges and prospects which can be addressed for successful application. The present review critically examines the methodical challenges addressing the feasibility for restoring and reclaiming pesticide contaminated sites along with the ecotoxicological risk assessments. Overall, it highlights the need to fine-tune the available processes and employ interdisciplinary approaches to make microbe assisted bioremediation as the method of choice for reclamation of pesticide contaminated sites.

Pharmaceutical residues: One of the significant problems in achieving 'clean water for all' and its solution

With the rapid emergence of various metabolic and multiple-drug-resistant infectious diseases, new pharmaceuticals are continuously being introduced in the market. The excess production and use of pharmaceuticals and their untreated/unmetabolized release in the environment cause the contamination of aquatic ecosystem, and thus, compromise the environment and human-health. The present review provides insights into the classification, sources, occurrence, harmful impacts, and existing technologies to curb these problems. A comprehensive detail of various biological and nanotechnological strategies for the removal of pharmaceutical residues from water is critically discussed focusing on their efficiencies, and current limitations to design improved-technologies for their lab-to-field applications. Furthermore, the review highlights and suggests the scope of integrated bionanotechnological methods for enhanced removal of pharmaceutical residues from water to fulfill the United Nations Sustainable Development Goal (UN-SDG) for providing clean potable water for all.

IDENTIFICATION OF POTENTIAL SOIL DEGRADING MICROBIALS CONTAMINATED WITH INSECTICIDES

The high use of insecticides can cause soil contamination in the rice field environment, so a solution is needed to reduce the contamination and the negative impact on human health. One of the efforts that can be done to overcome this problem was by bioremediation. The bioremediation technique was chosen due to it is eco- friendly, efficient, and cost-effective in its application. However, bioremediation relies on the capacity of living organisms to absorb, accumulate, translocate and detoxify pollutants in a polluted environment. The objective of this study is to explore microbes that can be used as bioremediation agents in soil exposed to various types of insecticide contamination. The results of this study was as many as ±56 species of microbes can be used as bioremediation agents for various types of insecticides so that bioremediation needs to be carried out in order to avoid pesticide residues on soil and agricultural products.

Fungal and bacterial assisted bioremediation of environmental toxicant (N-[2-[3-chloro-5-(trifluoromethyl)-2-pyridinyl] ethyl]-2-(trifluoromethyl) benzamide) holding benzamidic genesis elucidating the eco-friendly strategy

Fluopyram (FLP) containing benzamidic genesis utilized for seed detoxification and as a foliar application is associated with low profound toxicity in mammals but long-term toxicology investigations have revealed that FLP can stimulate tumor growth. FLP attenuation has been the first time scrutinized employing microorganisms originally identified from soils. Biodegrative assays of four fungal strains; Aspergillus fumigatus (AFu), Aspergillus terreus (AT), Aspergillus flavus (AF), Aspergillus niger (AN), and three bacterial strains: Streptococcus pneumoniae (SP) Streptococcus pyogenes (SPy), and Escherichia coli (EC), were employed. Ten milligrams per liter FLP concentration was made employing separately microbe and analyzed for 35 days. The analytical technique was inclusive of ultraviolet-visible spectrophotometric and high-performance liquid chromatography procedure endeavored to test FLP biodegradation. SP and AT exhibited maximal potentiality to metabolize FLP. HPLC is indicative of several metabolites formations. FLP degradation by AFu, EC, SPy, AN, AF, AT, SP was observed to be 24.2%, 82.7%, 89.8%, 90.7%, 91.3%, 95.4%, and 99.3%, explicating the efficacy of all strains employed in FLP degradation. Current investigations are indicative of significant bioremediation strategies for xenobiotic mitigation. Furthermore, the current examinations are inclusive of the augmentation of biodegradative assays to be utilized on a large scale for efficient environmental management cost-effectively and sustainably.

Microbe mediated remediation of dyes, explosive waste and polyaromatic hydrocarbons, pesticides and pharmaceuticals

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Environmental pollutants dyes, pesticides, pharmaceuticals, explosive waste and polyaromatic hydrocarbons.

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Environmental pollutants toxicity.

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Possible microbial biodegradation pathways of environmental pollutants.

Industrialization and human activities have led to serious effects on environment. With the progress taking place in the biodegradation field, it is important to summarize the latest advancement. In this review, we intend to provide insights on the recent progress on the biodegradation of environmental contaminants such as dyes, pesticides, pharmaceuticals, explosive waste and polyaromatic hydrocarbons by microorganisms. Along with the biodegradation of environmental contaminants, toxicity effects have also been discussed.

Effective Remediation Strategy for Xenobiotic Zoxamide by Pure Bacterial Strains, Escherichia coli, Streptococcus pyogenes, and Streptococcus pneumoniae

Zoxamide, a class IV hazardous fungicide, is perilous for the environment due to its highly persistent nature. Up till the current date, there are no reports on the biodegradation of zoxamide. The scarcity of knowledge in this domain led to the present research to evaluate the biodegradation of this benzamide fungicide by three bacterial strains, Escherichia coli (EC), Streptococcus pyogenes (SPy), and Streptococcus pneumoniae (SP). Biotransformation of zoxamide was scrutinized in nutrient broth assemblies for a period of 28 days followed by UV-visible spectrophotometer and GC-MS analysis of the metabolites. The results exhibited a low to medium biodegradation potential of the bacterial cells to metabolize zoxamide. The highest biotransformation percentage was observed by E. coli to be 29.8%. The order of half-life calculated for the degradation results was EC (42.5) < SPy (58.7) < SP (67.9) days. GC-MS analysis indicated the formation of several metabolites including, 2-(3,5-dichloro-4-methylphenyl)-4-ethyl-4-methyl-4H-1,3-oxazin-5(6H)-one, 3,5-dichloro-N-(3-hydroxy-1-ethyl-1-methyl--2-oxopropyl)-4-methylbenzamide and 3,5-dichloro-4-methylbenzamide. The research could influence the biotreatment strategies for the environmentally friendly eradication of xenobiotics.

In silico Prediction of Protein-Protein Interaction Network Induced by Manganese II in Meyerozyma guilliermondii

Recently, there has been an increasing interest in the use of yeast to produce biosorbent materials, because yeast is economical to use, adaptable to a variety of conditions, and amenable to morphological manipulations to yield better raw biomaterials. Previous studies from our laboratory have shown that Meyerozyma guilliermondii, a non-pathogenic haploid yeast (ascomycete), exhibits excellent biosorption capacity for Mn²⁺, as demonstrated by kinetic analyses. Shotgun/bottom-up analyses of soluble fractions revealed a total of 1257 identified molecules, with 117 proteins expressed in the absence of Mn²⁺ and 69 expressed only in the presence of Mn²⁺. In this article, we describe the first in silico prediction and screening of protein–protein interactions (PPIs) in M. guilliermondii using experimental data from shotgun/bottom-up analyses. We also present the categorization of biological processes (BPs), molecular functions (MFs), and metabolic pathways of 71 proteins upregulated in the M. guilliermondii proteome in response to stress caused by an excess of Mn²⁺ ions. Most of the annotated proteins were related to oxidation–reduction processes, metabolism, and response to oxidative stress. We identified seven functional enrichments and 42 metabolic pathways; most proteins belonged to pathways related to metabolic pathways (19 proteins) followed by the biosynthesis of secondary metabolites (10 proteins) in the presence of Mn²⁺. Using our data, it is possible to infer that defense mechanisms minimize the impact of Mn²⁺ via the expression of antioxidant proteins, thus allowing adjustment during the defense response. Previous studies have not considered protein interactions in this genus in a manner that permits comparisons. Consequently, the findings of the current study are innovative, highly relevant, and provide a description of interactive complexes and networks that yield insight into the cellular processes of M. guilliermondii. Collectively, our data will allow researchers to explore the biotechnological potential of M. guilliermondii in future bioremediation processes.

Soil microalgae and cyanobacteria: the biotechnological potential in the maintenance of soil fertility and health

The soil microbiota plays a major role in maintaining the nutrient balance, carbon sink, and soil health. Numerous studies reported on the function of microbiota such as plant growth-promoting bacteria and fungi in soil. Although microalgae and cyanobacteria are ubiquitous in soil, very less attention has been paid on the potential of these microorganisms. The indiscriminate use of various chemicals to enhance agricultural productivity led to serious consequences like structure instability, accumulation of toxic contaminants, etc., leading to an ecological imbalance between soil, plant, and microbiota. However, the significant role of microalgae and cyanobacteria in crop productivity and other potential options has been so far undermined. The intent of the present critical review is to highlight the significance of this unique group of microorganisms in terms of maintaining soil fertility and soil health. Beneficial soil ecological applications of these two groups in enhancing plant growth, establishing interrelationships among other microbes, and detoxifying chemical agents such as insecticides, herbicides, etc. through mutualistic cooperation by synthesizing enzymes and phytohormones are presented. Since recombinant technology involving genomic integration favors the development of useful traits in microalgae and cyanobacteria for their potential application in improvement of soil fertility and health, the merits and demerits of various such advanced methodologies associated in harnessing the biotechnological potential of these photosynthetic microorganisms for sustainable agriculture were also discussed.

Porous zeolite imidazole framework-wrapped urchin-like Au-Ag nanocrystals for SERS detection of trace hexachlorocyclohexane pesticides via efficient enrichment

A core-shell configuration of the zeolite imidazole framework (ZIF-8) wrapped urchin-like Au-Ag alloyed nanocrystals (UAANs) were designed and fabricated via adding the pre-formed plasmonic nanoparticles into the ZIF-8 precursor solution with hexadecyltrimethyl ammonium bromide (CTAB). The UAANs are about 100 nm in size with high-density tips. The ZIF-8 shell layer is nanoporous and can be controlled in thickness from 10 nm to 40 nm by the CTAB concentration. Importantly, such ZIF-8 wrapped UAANs can be used as the highly efficient surface enhanced Raman scattering (SERS) substrates for detection of the trace hexachlorocyclohexane (HCH) molecules. The ZIF-8 shell layer with an appropriate thickness (-∼20 nm) can evidently increase the SERS performance of the UAANs to the trace γ-HCH and α-HCH. Such wrapping-enhanced SERS effect significantly increases, by a power function, with the decreasing HCH concentration, especially in the concentration below 10^-6 M, which is attributed to the ever-increasing enrichment effect to the HCH molecules. The detection limit is down below 1.5 ppb. This work presents a highly efficient substrate for the SERS-based detection of the trace HCH, and also displays the potential application in the SERS detection of volatile small molecules.

Cadmium sulphide quantum dots with tunable electronic properties by bacterial precipitation

We present a new method to fabricate semiconducting, transition metal nanoparticles (NPs) with tunable bandgap energies using engineered Escherichia coli. These bacteria overexpress the Treponema denticola cysteine desulfhydrase gene to facilitate precipitation of cadmium sulphide (CdS) NPs. Analysis with transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy reveal that the bacterially precipitated NPs are agglomerates of mostly quantum dots, with diameters that can range from 3 to 15 nm, embedded in a carbon-rich matrix. Additionally, conditions for bacterial CdS precipitation can be tuned to produce NPs with bandgap energies that range from quantum-confined to bulk CdS. Furthermore, inducing precipitation at different stages of bacterial growth allows for control over whether the precipitation occurs intra- or extracellularly. This control can be critically important in utilizing bacterial precipitation for the environmentally-friendly fabrication of functional, electronic and catalytic materials. Notably, the measured photoelectrochemical current generated by these NPs is comparable to values reported in the literature and higher than that of synthesized chemical bath deposited CdS NPs. This suggests that bacterially precipitated CdS NPs have potential for applications ranging from photovoltaics to photocatalysis in hydrogen evolution.

A fusant of Amycolatopsis sp. M3-1 and Pseudomonas sp. Nai8 with high capacity of degrading novel pyrimidynyloxybenzoic herbicide ZJ0273 and naphthalene

ZJ0273 (propyl 4-(2-(4, 6-demethoxy pyrimidin-2-yloxy) benzylamino) benzoate) is a novel pyrimidynyloxybenzoic-based herbicide developed in China for oilseed crop. This study was aimed to construct new strains capable of degrading naphthalene and ZJ0273 by protoplast fusion between Amycolatopsis sp. M3-1 and Pseudomonas sp. Nai8. Eight recombinant strains were successfully produced, and the strains could simultaneously utilize ZJ0273 and naphthalene as the sole carbon and energy source, respectively. One of recombinant strains, MN6 with higher degrading efficiency, was chosen for further study. Under the condition of pH 7.0, 30 °C, ZJ0273 and naphthalene degradation percent by the recombinant strain MN6 could reach 65.10% (20 days) and 88.46% (48 h), respectively. According to the identified six metabolites (M1-M6) by LC-MS/MS, biodegradation pathway of ZJ0273 was proposed. ZJ0273 biodegradation catalyzed by the recombinant strain MN6 involved continuous biocatalytic reactions such as de-estering, hydrolysis, acylation, C-N cleavage, de-methyl, and ether cleavage reactions.

In silico analysis and experimental validation of lipoprotein and novel Tat signal peptides processing in Anabaena sp. PCC7120

Signal peptide (SP) plays a pivotal role in protein translocation. Lipoprotein- and twin arginine translocase (Tat) dependent signal peptides were studied in All3087, a homolog of competence protein of Synechocystis PCC6803 and in two putative alkaline phosphatases (ALPs, Alr2234 and Alr4976), respectively. In silico analysis of All3087 is shown to possess the characteristics feature of competence proteins such as helix-hairpin-helix, N and C-terminal HKD endonuclease domain, calcium binding domain and N-terminal lipoprotein signal peptide. The SP recognition-cleavage site in All3087 was predicted (AIA-AC) using SignalP while further in-depth analysis using Pred-Lipo and WebLogo analysis for consensus sequence showed it as IAA-C. Activities of putative ALPs were confirmed by heterologous overexpression, activity assessment and zymogram analysis. ALP activity in Anabaena remains cell bound in log-phase, but during late log/stationary phase, an enhanced ALP activity was detected in extracellular milieu. The enhancement of ALP activity during stationary phase was not only due to inorganic phosphate limitation but also contributed by the presence of novel bipartite Tat-SP. The Tat signal transported the folded active ALPs to the membrane, followed by anchoring into the membrane and successive cleavage enabling transportation of the ALPs to the extracellular milieu, because of bipartite architecture and processing of transit Tat-SP.

Fate of β-hexachlorocyclohexane in the mixed microbial cultures (MMCs) three-stage polyhydroxyalkanoates (PHA) production process from cheese whey

This work aimed to study the fate and effect of β-hexachlorocyclohexane (β-HCH) during several steps of PHA production and purification, by using an artificially contaminated cheese whey (CW) as the feedstock. Most of β-HCH (around 90%) was adsorbed on CW solids and it was removed after the acidogenic fermentation step, when residual CW solids are separated along with anaerobic biomass from the liquid-phase. Purification steps also contributed strongly to the removal of residual β-HCH; overall, the PHA production process removed about 99.9% of initial β-HCH content. Moreover, it has been shown that β-HCH has neither detrimental effect on acidogenic fermentation nor on PHA accumulation, that were performed by using unacclimated mixed microbial cultures.

Cyanobacterial heat-shock response: role and regulation of molecular chaperones

Cyanobacteria constitute a morphologically diverse group of oxygenic photoautotrophic microbes which range from unicellular to multicellular, and non-nitrogen-fixing to nitrogen-fixing types. Sustained long-term exposure to changing environmental conditions, during their three billion years of evolution, has presumably led to their adaptation to diverse ecological niches. The ability to maintain protein conformational homeostasis (folding–misfolding–refolding or aggregation–degradation) by molecular chaperones holds the key to the stress adaptability of cyanobacteria. Although cyanobacteria possess several genes encoding DnaK and DnaJ family proteins, these are not the most abundant heat-shock proteins (Hsps), as is the case in other bacteria. Instead, the Hsp60 family of proteins, comprising two phylogenetically conserved proteins, and small Hsps are more abundant during heat stress. The contribution of the Hsp100 (ClpB) family of proteins and of small Hsps in the unicellular cyanobacteria (Synechocystis and Synechococcus) as well as that of Hsp60 proteins in the filamentous cyanobacteria (Anabaena) to thermotolerance has been elucidated. The regulation of chaperone genes by several cis-elements and trans-acting factors has also been well documented. Recent studies have demonstrated novel transcriptional and translational (mRNA secondary structure) regulatory mechanisms in unicellular cyanobacteria. This article provides an insight into the heat-shock response: its organization, and ecophysiological regulation and role of molecular chaperones, in unicellular and filamentous nitrogen-fixing cyanobacterial strains.