Bioremediation: environmental clean-up through pathway engineering

Unlocking the genomic potential of Red Sea coral probiotics

The application of beneficial microorganisms for corals (BMC) decreases the bleaching susceptibility and mortality rate of corals. BMC selection is typically performed via molecular and biochemical assays, followed by genomic screening for BMC traits. Herein, we present a comprehensive in silico framework to explore a set of six putative BMC strains. We extracted high-quality DNA from coral samples collected from the Red Sea and performed PacBio sequencing. We identified BMC traits and mechanisms associated with each strain as well as proposed new traits and mechanisms, such as chemotaxis and the presence of phages and bioactive secondary metabolites. The presence of prophages in two of the six studied BMC strains suggests their possible distribution within beneficial bacteria. We also detected various secondary metabolites, such as terpenes, ectoines, lanthipeptides, and lasso peptides. These metabolites possess antimicrobial, antifungal, antiviral, anti-inflammatory, and antioxidant activities and play key roles in coral health by reducing the effects of heat stress, high salinity, reactive oxygen species, and radiation. Corals are currently facing unprecedented challenges, and our revised framework can help select more efficient BMC for use in studies on coral microbiome rehabilitation, coral resilience, and coral restoration.

24-Epibrassinolide alleviates diazinon oxidative damage by escalating activities of antioxidant defense systems in maize plants

Excessive use of pesticides against pests has contaminated agricultural crops and raised global concerns about food safety. This research investigates the alleviation effects of 24-epibrassinolide (EBL) seed priming on diazinon (DZ) pesticide toxicity. The experiment was conducted with eight groups including control, DZ, EBL (10 µM), EBL (0.1 µM), EBL (0.01 µM), EBL (10 µM) + DZ, EBL (0.1 µM) + DZ, and EBL (0.01 µM) + DZ. Plants grown with the lowest concentration of EBL (0.01 µM) exhibited an upward increase in the activity of SOD, CAT, POD, APX, GR, and GST enzymes under DZ toxicity stress. In contrast, higher concentrations of EBL showed some inhibitory effects on the activity of antioxidant enzymes. In addition, low concentrations of EBL elevated the free radical scavenging capacity (DPPH), iron-reducing antioxidant power (FRAP), photosynthesis rate (Pn), stomatal conductance (Gs) and proline, and protein contents. EBL also reduced lipid peroxidation (MDA levels) in the DZ-exposed plants, leading to membrane integrity. The favorable effects of EBL were more evident when plants were exposed to pesticides than normal growth conditions. The results indicated that EBL seed priming intensifies the antioxidant enzymes system activity, and helps maize plants against toxic effects of DZ under proper concentration.

Chromium in plant-soil nexus: Speciation, uptake, transport and sustainable remediation techniques

Heavy metal (HM) pollution has become a serious global problem due to the non-biodegradable nature of the HMs and their persistence in the environment. Agricultural soil is a non-renewable resource that requires careful management so that it can fulfill the increasing demand for agricultural food production. However, different anthropogenic activities have resulted in a large-scale accumulation of HMs in soil which is detrimental to soil and plant health. Due to their ubiquity, increased bioavailability, toxicity, and non-biodegradable nature, HM contamination has formed a roadblock in the way of achieving food security, safety, and sustainability in the future. Chromium (Cr), specifically Cr(VI) is a highly bioavailable HM with no proven role in the physiology of plants. Chromium has been found to be highly toxic to plants, with its toxicity also influenced by chemical speciation, which is in turn controlled by different factors, such as soil pH, redox potential, organic matter, and microbial population. In this review, the different factors that influence Cr speciation were analyzed and the relationship between biogeochemical transformations of Cr and its bioavailability which may be beneficial for devising different Cr remediation strategies has been discussed. Also, the uptake and transport mechanism of Cr in plants, with particular reference to sulfate and phosphate transporters has been presented. The biological solutions for the remediation of Cr contaminated sites which offer safe and viable alternatives to old-style physical and chemical remediation strategies have been discussed in detail. This review provides theoretical guidance in developing suitable approaches for the better management of these remediation strategies.

Development of multifarious carrier materials and impact conditions of immobilised microbial technology for environmental remediation: A review

Microbial technology is the most sustainable and eco-friendly method of environmental remediation. Immobilised microorganisms were introduced to further advance microbial technology. In immobilisation technology, carrier materials distribute a large number of microorganisms evenly on their surface or inside and protect them from external interference to better treat the targets, thus effectively improving their bioavailability. Although many carrier materials have been developed, there have been relatively few comprehensive reviews. Therefore, this paper summarises the types of carrier materials explored in the last ten years from the perspective of structure, microbial activity, and cost. Among these, carbon materials and biofilms, as environmentally friendly functional materials, have been widely applied for immobilisation because of their abundant sources and favorable growth conditions for microorganisms. The novel covalent organic framework (COF) could also be a new immobilisation material, due to its easy preparation and high performance. Different immobilisation methods were used to determine the relationship between carriers and microorganisms. Co-immobilisation is particularly important because it can compensate for the deficiencies of a single immobilisation method. This paper emphasises that impact conditions also affect the immobilisation effect and function. In addition to temperature and pH, the media conditions during the preparation and reaction of materials also play a role. Additionally, this study mainly reviews the applications and mechanisms of immobilised microorganisms in environmental remediation. Future development of immobilisation technology should focus on the discovery of novel and environmentally friendly carrier materials, as well as the establishment of optimal immobilisation conditions for microorganisms. This review intends to provide references for the development of immobilisation technology in environmental applications and to further the improve understanding of immobilisation technology.

Biosynthesis of value-added bioproducts from hemicellulose of biomass through microbial metabolic engineering

Hemicellulose is the second most abundant carbohydrate in lignocellulosic biomass and has extensive applications. In conventional biomass refinery, hemicellulose is easily converted to unwanted by-products in pretreatment and therefore can't be fully utilized. The present study aims to summarize the most recent development of lignocellulosic polysaccharide degradation and fully convert it to value-added bioproducts through microbial and enzymatic catalysis. Firstly, bioprocess and microbial metabolic engineering for enhanced utilization of lignocellulosic carbohydrates were discussed. The bioprocess for degradation and conversion of natural lignocellulose to monosaccharides and organic acids using anaerobic thermophilic bacteria and thermostable glycoside hydrolases were summarized. Xylose transmembrane transporting systems in natural microorganisms and the latest strategies for promoting the transporting capacity by metabolic engineering were summarized. The carbon catabolite repression effect restricting xylose utilization in microorganisms, and metabolic engineering strategies developed for co-utilization of glucose and xylose were discussed. Secondly, the metabolic pathways of xylose catabolism in microorganisms were comparatively analyzed. Microbial metabolic engineering for converting xylose to value-added bioproducts based on redox pathways, non-redox pathways, pentose phosphate pathway, and improving inhibitors resistance were summarized. Thirdly, strategies for degrading lignocellulosic polysaccharides and fully converting hemicellulose to value-added bioproducts through microbial metabolic engineering were proposed.

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Hemicellulose is the main carbohydrate of biomass and has valuable applications.

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Hemicellulose is underutilized in conventional biomass refinery and pretreatment.

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Microbial and enzymatic catalysis were applied for hemicellulose utilization.

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Xylose is converted to value-added bioproducts by metabolic engineering.

Klebsiella oxytoca: an efficient pyrene-degrading bacterial strain isolated from petroleum-contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are the hazardous xenobiotic agents of oil production. One of the methods to eliminate hazardous compounds is bioremediation, which is the most efficient and cost-effective method to eliminate the harmful byproducts of crude petroleum processing. In this study, five pure bacterial isolates were isolated from petroleum-contaminated soil, four of which showed a robust growth on the PAH pyrene, as a sole carbon source. Various methods viz mass spectroscopy, biochemical assays, and 16S RNA sequencing employed to identify the isolates ascertained the consistent identification of Klebsiella oxytoca by all three methods. Scanning electron microscopy and Gram staining further demonstrated the characterization of the K. oxytoca. High-performance liquid chromatography of the culture supernatant of K. oxytoca grown in pyrene containing media showed that the cells started utilizing pyrene from the 6th day onwards and by the 12th day of growth, 70% of the pyrene was completely degraded. A genome search for the genes predicted to be involved in pyrene degradation using Kyoto Encyclopedia of Genes and Genomes (KEGG) confirmed their presence in the genome of K. oxytoca. These results suggest that K. oxytoca would be a suitable candidate for removing soil aromatic hydrocarbons.

Health hazards of hexavalent chromium (Cr (VI)) and its microbial reduction

Industrial effluents/wastewater are the main sources of hexavalent chromium (Cr (VI)) pollutants in the environment. Cr (VI) pollution has become one of the world’s most serious environmental concerns due to its long persistence in the environment and highly deadly nature in living organisms. To its widespread use in industries Cr (VI) is highly toxic and one of the most common environmental contaminants. Cr (VI) is frequently non-biodegradable in nature, which means it stays in the environment for a long time, pollutes the soil and water, and poses substantial health risks to humans and wildlife. In living things, the hexavalent form of Cr is carcinogenic, genotoxic, and mutagenic. Physico-chemical techniques currently used for Cr (VI) removal are not environmentally friendly and use a large number of chemicals. Microbes have many natural or acquired mechanisms to combat chromium toxicity, such as biosorption, reduction, subsequent efflux, or bioaccumulation. This review focuses on microbial responses to chromium toxicity and the potential for their use in environmental remediation. Moreover, the research problem and prospects for the future are discussed in order to fill these gaps and overcome the problem associated with bacterial bioremediation’s real-time applicability.

Bacteria with a mouth: Discovery and new insights into cell surface structure and macromolecule transport

A bacterium with a "mouth"-like pit structure isolated for the first time in the history of microbiology was a Gram-negative rod, containing glycosphingolipids in the cell envelope, and named Sphingomonas sp. strain A1. The pit was dynamic, with repetitive opening and closing during growth on alginate, and directly included alginate concentrated around the pit, particularly by flagellins, an alginate-binding protein localized on the cell surface. Alginate incorporated into the periplasm was subsequently transferred to the cytoplasm by cooperative interactions of periplasmic solute-binding proteins and an ATP-binding cassette transporter in the cytoplasmic membrane. The mechanisms of assembly, functions, and interactions between the above-mentioned molecules were clarified using structural biology. The pit was transplanted into other strains of sphingomonads, and the pitted recombinant cells were effectively applied to the production of bioethanol, bioremediation for dioxin removal, and other tasks. Studies of the function of the pit shed light on the biological significance of cell surface structures and macromolecule transport in bacteria.

Microbial Response to Phytostabilization in Mining Impacted Soils Using Maize in Conjunction with Biochar and Compost

Even after remediation, mining impacted soils can leave behind a landscape inhospitable to plant growth and containing residual heavy metals. While phytostabilization can be used to restore such sites by limiting heavy metal spread, it is reliant on soil capable of supporting plant growth. Manure-based biochars, coupled with compost, have demonstrated the ability to improve soil growth conditions in mine impacted soils, however there is a paucity of information regarding their influence on resident microbial populations. The objective of this study was to elucidate the impact of these soil amendments on microbial community structure and function in mine impacted soils placed under phytostabilization management with maize. To this aim, a combination of phospholipid fatty acid (PLFA) and enzymatic analyses were performed. Results indicate that microbial biomass is significantly increased upon addition of biochar and compost, with maximal microbial biomass achieved with 5% poultry litter biochar and compost (62.82 nmol g-1 dry soil). Microbial community structure was impacted by biochar type, rate of application, and compost addition, and influenced by pH (r2 = 0.778), EC (r2 = 0.467), and Mg soil concentrations (r2 = 0.453). In three of the four enzymes analyzed, poultry litter biochar treatments were observed with increased activity rates that were often significantly greater than the unamended control. Overall, enzyme activities rates were influenced by biochar type and rate, and addition of compost. These results suggest that using a combination of biochar and compost can be utilized as a management tool to support phytostabilization strategies in mining impacted soils.

Geothermal heating: Is it a boon or a bane for bioremediation?

There has been a worldwide interest in renewable energy technologies, as a means of decreasing reliance on fossil fuels, minimizing climate change effects, and reducing greenhouse emissions. One such technology is geothermal heating where the constant subsurface temperature is used to cool or heat building interiors via heat pumps. In Canada, the use of geothermal heating has become a popular option for heating and cooling buildings, and it is anticipated that, in the near term, most large buildings will include geothermal heating as part of their climate control strategy. However, little is known about the environmental impacts of geothermal heating on the subsurface environment. The present review will examine the effect of geothermal heating on groundwater flow and remediation efforts, whereby the heat generated by geothermal systems may help with urban pollution. "Geothermal Remediation" could leverage the subsurface heating resulting from geothermal systems to accelerate biodegradation of certain petroleum-based pollutants at brown-field sites, while providing building(s) with sustainable heating and cooling. This idea coincides with the rising momentum towards sustainable and green remediation in Europe and the United States. To ensure that Geothermal Remediation is achievable, the effect of heat on bioremediation needs to be examined. This review provides an insight into what we know about heat effects on bioremediation activities and subsurface transport.

A crucial review on polycyclic aromatic Hydrocarbons - Environmental occurrence and strategies for microbial degradation

Over the last century, contamination of polycyclic aromatic hydrocarbons (PAHs) has risen tremendously due to the intensified industrial activities like petrochemical, pharmaceutical, insecticides and fertilizers applications. PAHs are a group of organic pollutants with adverse effects on both humans and the environment. These PAHs are widely distributed in various ecosystems including air, soil, marine water and sediments. Degradation of PAHs generally occurs through processes like photolysis, adsorption, volatilization, chemical degradation and microbial degradation. Microbial degradation of PAHs is done by the utilization of diverse microorganisms like algae, bacteria, fungi which are readily compatible with biodegrading/bio transforming PAHs into H₂O, CO₂ under aerobic, or CH₄ under anaerobic environment. The rate of PAHs degradation using microbes is mainly governed by various cultivation conditions like temperature, pH, nutrients availability, microbial population, chemical nature of PAHs, oxygen and degree of acclimation. Several microbial species including Selenastrum capricornutum, Ralstonia basilensis, Acinetobacter haemolyticus, Pseudomonas migulae, Sphingomonas yanoikuyae and Chlorella sorokiniana are known to degrade PAHs via biosorption and enzyme-mediated degradation. Numerous bacterial mediated PAHs degradation methods are studied globally. Among them, PAHs degradation by bacterial species like Pseudomonas fluorescence, Pseudomonas aeruginosa, Rhodococcus spp., Paenibacillus spp., Mycobacterium spp., and Haemophilus spp., by various degradation modes like biosurfactant, bioaugmentation, biostimulation and biofilms mediated are also investigated. In contrarily, PAHs degradation by fungal species such as Pleurotus ostreatus, Polyporus sulphureus, Fusarium oxysporum occurs using the activity of its ligninolytic enzymes such as lignin peroxidase, laccase, and manganese peroxidase. The present review highlighted on the PAHs degradation activity by the algal, fungal, bacterial species and also focused on their mode of degradation.

Research progress in bioremediation of petroleum pollution

With the enhancement of environmental protection awareness, research on the bioremediation of petroleum hydrocarbon environmental pollution has intensified. Bioremediation has received more attention due to its high efficiency, environmentally friendly by-products, and low cost compared with the commonly used physical and chemical restoration methods. In recent years, bacterium engineered by systems biology strategies have achieved biodegrading of many types of petroleum pollutants. Those successful cases show that systems biology has great potential in strengthening petroleum pollutant degradation bacterium and accelerating bioremediation. Systems biology represented by metabolic engineering, enzyme engineering, omics technology, etc., developed rapidly in the twentieth century. Optimizing the metabolic network of petroleum hydrocarbon degrading bacterium could achieve more concise and precise bioremediation by metabolic engineering strategies; biocatalysts with more stable and excellent catalytic activity could accelerate the process of biodegradation by enzyme engineering; omics technology not only could provide more optional components for constructions of engineered bacterium, but also could obtain the structure and composition of the microbial community in polluted environments. Comprehensive microbial community information lays a certain theoretical foundation for the construction of artificial mixed microbial communities for bioremediation of petroleum pollution. This article reviews the application of systems biology in the enforce of petroleum hydrocarbon degradation bacteria and the construction of a hybrid-microbial degradation system. Then the challenges encountered in the process and the application prospects of bioremediation are discussed. Finally, we provide certain guidance for the bioremediation of petroleum hydrocarbon-polluted environment.

Bioremediation of lignin derivatives and phenolics in wastewater with lignin modifying enzymes: Status, opportunities and challenges

Lignin modifying enzymes from fungi and bacteria are potential biocatalysts for sustainable mitigation of different potentially toxic pollutants in wastewater. Notably, the paper and pulp industry generates enormous amounts of wastewater containing high amounts of complex lignin-derived chlorinated phenolics and sulfonated pollutants. The presence of these compounds in wastewater is a critical issue from environmental and toxicological perspectives. Some chloro-phenols are harmful to the environment and human health, as they exert carcinogenic, mutagenic, cytotoxic, and endocrine-disrupting effects. In order to address these most urgent concerns, the use of oxidative lignin modifying enzymes for bioremediation has come into focus. These enzymes catalyze modification of phenolic and non-phenolic lignin-derived substances, and include laccase and a range of peroxidases, specifically lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). In this review, we explore the key pollutant-generating steps in paper and pulp processing, summarize the most recently reported toxicological effects of industrial lignin-derived phenolic compounds, especially chlorinated phenolic pollutants, and outline bioremediation approaches for pollutant mitigation in wastewater from this industry, emphasizing the oxidative catalytic potential of oxidative lignin modifying enzymes in this regard. We highlight other emerging biotechnical approaches, including phytobioremediation, bioaugmentation, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based technology, protein engineering, and degradation pathways prediction, that are currently gathering momentum for the mitigation of wastewater pollutants. Finally, we address current research needs and options for maximizing sustainable biobased and biocatalytic degradation of toxic industrial wastewater pollutants.

Recent Advances in Enzymes for the Bioremediation of Pollutants

Nowadays, pollution of the environment is a huge problem for humans and other organisms' health. Conventional methods of pollutant removal like membrane filtration or ion exchange are not efficient enough to lower the number of pollutants to standard levels. Biological methods, because of their higher efficiency and biocompatibility, are preferred for the remediation of pollutants. These cost-effective and environment-friendly methods of reducing pollutants are called bioremediation. In bioremediation methods, enzymes play the most crucial role. Enzymes can remedy different types of organic and inorganic pollutants, including PAHs, azo dyes, polymers, organocyanides, lead, chromium, and mercury. Different enzymes isolated from various species have been used for the bioremediation of pollutants. Discovering new enzymes and new subtypes with specific physicochemical characteristics would be a promising way to find more efficient and cost-effective tools for the remediation of pollutants.

Deployment of Engineered Microbes: Contributions to the Bioeconomy and Considerations for Biosecurity

Engineering at microscopic scales has an immense effect on the modern bioeconomy. Microbes contribute to such disparate markets as chemical manufacturing, fuel production, crop optimization, and pharmaceutical synthesis, to name a few. Due to new and emerging synthetic biology technologies, and the sophistication and control afforded by them, we are on the brink of deploying engineered microbes to not only enhance traditional applications but also to introduce these microbes to sectors, contexts, and formats not previously attempted. In microbially managed medicine, microbial engineering holds promise for increasing efficacy, improving tissue penetration, and sustaining treatment. In the environment, the most effective areas for deployment are in the management of crops and protection of ecosystems. However, caution is warranted before introducing engineered organisms to new environments where they may proliferate without control and could cause unforeseen effects. We summarize ideas and data that can inform identification and assessment of the risks that these tools present to ensure that realistic hazards are described and unrealistic ones do not hinder advancement. Further, because modes of containment are crucial complements to deployment, we describe the state of the art in microbial biocontainment strategies, current gaps, and how these gaps might be addressed through technological advances in synthetic engineering. Collectively, this work highlights engineered microbes as a foundational and expanding facet of the bioeconomy, projects their utility in upcoming deployments outside the laboratory, and identifies knowns and unknowns that will be necessary considerations and points of focus in this endeavor.

New insights into the degradation of synthetic pollutants in contaminated environments

The environment is contaminated by synthetic contaminants owing to their extensive applications globally. Hence, the removal of synthetic pollutants (SPs) from the environment has received widespread attention. Different remediation technologies have been investigated for their abilities to eliminate SPs from the ecosystem; these include photocatalysis, sonochemical techniques, nanoremediation, and bioremediation. SPs, which can be organic or inorganic, can be degraded by microbial metabolism at contaminated sites. Owing to their diverse metabolisms, microbes can adapt to a wide variety of environments. Several microbial strains have been reported for their bioremediation potential concerning synthetic chemical compounds. The selection of potential strains for large-scale removal of organic pollutants is an important research priority. Additionally, novel microbial consortia have been found to be capable of efficient degradation owing to their combined and co-metabolic activities. Microbial engineering is one of the most prominent and promising techniques for providing new opportunities to develop proficient microorganisms for various biological processes; here, we have targeted the SP-degrading mechanisms of microorganisms. This review provides an in-depth discussion of microbial engineering techniques that are used to enhance the removal of both organic and inorganic pollutants from different contaminated environments and under different conditions. The degradation of these pollutants is investigated using abiotic and biotic approaches; interestingly, biotic approaches based on microbial methods are preferable owing to their high potential for pollutant removal and cost-effectiveness.

Comparison of Structure and Adsorption Properties of Mesoporous Silica Functionalized with Aminopropyl Groups by the Co-Condensation and the Post Grafting Methods

The adsorptive potential has been evaluated for the aminopropyl functionalized mesoporous silica materials obtained by co-condensation and post grafting methods. Nitrogen sorption, small angle neutron and X-ray scattering (SANS and SAXS) demonstrated high surface area and well-ordered hexagonal pore structure suitable for applications as adsorbents of metals from waste waters. A comparison of Cr(VI) adsorption properties of the materials prepared by different functionalization methods has been performed. The obtained results demonstrated the adsorption capacity due to the affinity of the chromium ions to the amino groups, and showed that co-condensation of tetraethoxysilane (TEOS) and 3-aminopropyl triethoxysilane (APTES) resulted in higher metal sorption capacity of the materials compared to post-synthesis grafting of aminopropyl groups onto the mesoporous silica particles.

Chemical-Assisted Microbially Mediated Chromium (Cr) (VI) Reduction Under the Influence of Various Electron Donors, Redox Mediators, and Other Additives: An Outlook on Enhanced Cr(VI) Removal

Chromium (Cr) (VI) is a well-known toxin to all types of biological organisms. Over the past few decades, many investigators have employed numerous bioprocesses to neutralize the toxic effects of Cr(VI). One of the main process for its treatment is bioreduction into Cr(III). Key to this process is the ability of microbial enzymes, which facilitate the transfer of electrons into the high valence state of the metal that acts as an electron acceptor. Many underlying previous efforts have stressed on the use of different external organic and inorganic substances as electron donors to promote Cr(VI) reduction process by different microorganisms. The use of various redox mediators enabled electron transport facility for extracellular Cr(VI) reduction and accelerated the reaction. Also, many chemicals have employed diverse roles to improve the Cr(VI) reduction process in different microorganisms. The application of aforementioned materials at the contaminated systems has offered a variety of influence on Cr(VI) bioremediation by altering microbial community structures and functions and redox environment. The collective insights suggest that the knowledge of appropriate implementation of suitable nutrients can strongly inspire the Cr(VI) reduction rate and efficiency. However, a comprehensive information on such substances and their roles and biochemical pathways in different microorganisms remains elusive. In this regard, our review sheds light on the contributions of various chemicals as electron donors, redox mediators, cofactors, etc., on microbial Cr(VI) reduction for enhanced treatment practices.

Futuristic avenues of metabolic engineering techniques in bioremediation

Bioremediation is a promising technology for the treatment of environmental contaminants and paving new avenues for the betterment of the environment. Over the last some years, several approaches have been employed to optimize the genetic machinery of microorganisms relevant to bioremediation. Metabolic engineering is one of them that provides a new insight for bioremediation. This review envisages the critical role of these techniques toward exploring the possibilities of the creation of a new pathway, leading to pathway expansion to new substrates by assembling of catabolic modules from different origins in the same microbial cell. The recombinant DNA technology and gene editing tools were also explored for the construction of metabolically engineered microbial strains for the degradation of complex pollutants. Moreover, the importance of CRISPR-Cas system for knock-in and knock-out of genes was described by using recent studies. Further, the idea of the cocultivation of more than one metabolic engineered microbial communities is also discussed, which can be crucial in the bioremediation of multiple and complex pollutants. Finally, this review also elucidates the effective application of metabolic engineering in bioremediation through these techniques and tools.

Extremophilic Microorganisms for the Treatment of Toxic Pollutants in the Environment

As concerns about the substantial effect of various hazardous toxic pollutants on the environment and public health are increasing, the development of effective and sustainable treatment methods is urgently needed. In particular, the remediation of toxic components such as radioactive waste, toxic heavy metals, and other harmful substances under extreme conditions is quite difficult due to their restricted accessibility. Thus, novel treatment methods for the removal of toxic pollutants using extremophilic microorganisms that can thrive under extreme conditions have been investigated during the past several decades. In this review, recent trends in bioremediation using extremophilic microorganisms and related approaches to develop them are reviewed, with relevant examples and perspectives.

Bioremediation potential of Cd by transgenic yeast expressing a metallothionein gene from Populus trichocarpa

Cadmium (Cd) is an extremely toxic environmental pollutant with high mobility in soils, which can contaminate groundwater, increasing its risk of entering the food chain. Yeast biosorption can be a low-cost and effective method for removing Cd from contaminated aqueous solutions. We transformed wild-type Saccharomyces cerevisiae (WT) with two versions of a Populus trichocarpa gene (PtMT2b) coding for a metallothionein: one with the original sequence (PtMT2b 'C') and the other with a mutated sequence, with an amino acid substitution (C3Y, named here: PtMT2b 'Y'). WT and both transformed yeasts were grown under Cd stress, in agar (0; 10; 20; 50 μM Cd) and liquid medium (0; 10; 20 μM Cd). Yeast growth was assessed visually and by spectrometry OD₆₀₀. Cd removal from contaminated media and intracellular accumulation were also quantified. PtMT2b 'Y' was also inserted into mutant strains: fet3fet4, zrt1zrt2 and smf1, and grown under Fe-, Zn- and Mn-deficient media, respectively. Yeast strains had similar growth under 0 μM, but differed under 20 μM Cd, the order of tolerance was: WT < PtMT2b 'C' < PtMT2b 'Y', the latter presenting 37% higher growth than the strain with PtMT2b 'C'. It also extracted ~80% of the Cd in solution, and had higher intracellular Cd than WT. Mutant yeasts carrying PtMT2b 'Y' had slightly higher growth in Mn- and Fe-deficient media than their non-transgenic counterparts, suggesting the transgenic protein may chelate these metals. S. cerevisiae carrying the altered poplar gene offers potential for bioremediation of Cd from wastewaters or other contaminated liquids.

Role of Microorganisms in the Remediation of Wastewater in Floating Treatment Wetlands: A Review

This article provides useful information for understanding the specific role of microbes in the pollutant removal process in floating treatment wetlands (FTWs). The current literature is collected and organized to provide an insight into the specific role of microbes toward plants and pollutants. Several aspects are discussed, such as important components of FTWs, common bacterial species, rhizospheric and endophytes bacteria, and their specific role in the pollutant removal process. The roots of plants release oxygen and exudates, which act as a substrate for microbial growth. The bacteria attach themselves to the roots and form biofilms to get nutrients from the plants. Along the plants, the microbial community also influences the performance of FTWs. The bacterial community contributes to the removal of nitrogen, phosphorus, toxic metals, hydrocarbon, and organic compounds. Plant–microbe interaction breaks down complex compounds into simple nutrients, mobilizes metal ions, and increases the uptake of pollutants by plants. The inoculation of the roots of plants with acclimatized microbes may improve the phytoremediation potential of FTWs. The bacteria also encourage plant growth and the bioavailability of toxic pollutants and can alleviate metal toxicity.

Aerobic biodegradation of high explosive hexahydro-1,3,5- trinitro-1,3,5-triazine by Janibacter cremeus isolated from contaminated soil

OBJECTIVE

To evaluate the ability of Janibacter cremeus a soil bacterium isolated from explosive contaminated site in degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and to study enzyme responsible for degradation.

RESULTS

The isolate exhibited 88% degradation of RDX in 30 days of incubation. The biodegradation process followed the first order kinetics. The half- life of RDX was calculated to be 11.088 days. The RDX degradation process was complemented by concomitant release of nitrite ions with 0.78 mol of nitrite released per mole of RDX. The metabolites; Trinitroso- RDX, diamino-RDX, trimino-RDX, bis- (hydroxymethyl) nitramine and methylenedintramine derivative, viz, methylene- N- (hydroxy- methyl)- hydroxylamine- N-(hydroxymethyl) nitroamine corresponding to the molecular weights 174, 162, 132, 122 and 167 Da respectively were also detected. Nitroreductase enzyme was found to be responsible for RDX degradation.

CONCLUSION

J. cremeus could degrade RDX as sole source of nitrogen, via three different pathways wherein, Nitroreductase enzyme was found to play a major role. The efficient degradation of RDX makes J. cremeus suitable in treatment of contaminated water and soil at field scale levels.

Genetic Engineering-Facilitated Coassembly of Synthetic Bacterial Cells and Magnetic Nanoparticles for Efficient Heavy Metal Removal

Heavy-metal pollution is becoming a worldwide problem severely threatening our health and ecosystem. In this study, we constructed a genetic-engineering-driven coassembly of synthetic bacterial cells and magnetic nanoparticles (MNPs) for capturing heavy metals. The Escherichia coli cells were genetically engineered by introducing a de novo synthetic heavy-metal-capturing gene (encoding a protein SynHMB containing a six-histidine tag, two cystine-rich peptides, and a metallothionein sequence) and a synthetic type VI secretory system (T6SS) cluster of Pseudomonas putida, endowing the synthetic cells (SynEc2) with high ability of displaying the heavy-metal-capturing SynHMB on cell surface. MNPs were synthesized by a coprecipitation method and further modified by polyethylenimine (PEI) and diethylenetriaminepentaacetic acid (DTPA). Owing to the surface exposure of six-histidine tag on the synthetic bacteria and carboxyl groups on the modified MNPs (MNP@SiO₂-PEI-DTPA), the synthetic bacterial cells and MNPs coassembled to form biotic/abiotic complex exhibiting a self-developing characteristic. In the culture medium containing both Cd²⁺ and Pb²⁺, the coassemblies captured these heavy metals with high removal efficiency (>90% even at 50 mg/L of Cd²⁺ and 50 mg/L of Pb²⁺) and were conveniently recycled by artificial magnetic fields. Moreover, the coassemblies realized coremoval of organic carbon pollutants with the removal efficiency of >80%. This study builds a novel biotic/abiotic coassembling platform facilitated by genetic engineering and sheds light on development of artificial magnetic biological systems for efficient treatment of environmental pollution.

Heterologous expression of the tetracycline resistance gene tetX to enhance degradability and safety in doxycycline degradation

Microbial remediation has the potential to inexpensively yet effectively decontaminate and restore contaminated environments, but the virulence of pathogens and risk of resistance gene transmission by microorganisms during antibiotic removal often limit its implementation. Here, a cloned tetX gene with clear evolutionary history was expressed to explore doxycycline (DOX) degradation and resistance variation during the degradation process. Phylogenetic analysis of tetX genes showed high similarity with those of pathogenic bacteria, such as Riemerella sp. and Acinetobacter sp. Successful tetX expression was performed in Escherichia coli and confirmed by SDS-PAGE and Western blot. Our results showed that 95.0 ± 1.0% of the DOX (50 mg/L) was degraded by the recombinant strain (ETD-1 with tetX) within 48 h, which was significantly higher than that for the control (38.9 ± 8.7%) and the empty plasmid bacteria (8.8 ± 5.1%) (P < 0.05). The tetX gene products in ETD-1 cell extracts also exhibited an efficient DOX degradation ability, with a degradation rate of 80.5 ± 1.2% at 168 h. Furthermore, there was no significant proliferation of the tetX resistance gene during DOX degradation (P > 0.05). The efficient and safe DOX-degrading capacity of the recombinant strain ETD-1 makes it valuable and promising for antibiotic removal in the environment.

Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds

Aromatic hydrocarbons (AH) are widely distributed in nature, and many of them have been reported as relevant environmental pollutants and valuable carbon sources for different microorganisms. In this work, high-throughput sequencing of a metagenomic fosmid library was carried out to evaluate the functional and taxonomic diversity of genes involved in aromatic compounds degradation in oil-impacted mangrove sediments. In addition, activity-based approach and gas chromatography were used to assess the degradation potential of fosmid clones. Results indicated that AH degradation genes, such as monooxygenases and dioxygenases, were grouped into the following categories: anaerobic degradation of aromatic compounds (20.34%), metabolism of central aromatic intermediates (35.40%) and peripheral pathways for catabolism of aromatic compounds (22.56%). Taxonomic affiliation of genes related to aromatic compounds metabolism revealed the prevalence of the classes Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. Aromatic hydrocarbons (phenol, naphthalene, phenanthrene, pyrene and benzopyrene) were used as the only carbon source to screen clones with degradation potential. Of the 2500 clones tested, 48 showed some respiratory activity in at least one of the five carbon sources used. The hydrocarbon degradation ability of the top ten fosmid clones was confirmed by GC-MS. Further, annotation of assembled metagenomic fragments revealed ORFs corresponding to proteins and functional domains directly or indirectly involved in the aromatic compound metabolism, such as catechol 2,3-dioxygenase and ferredoxin oxidoreductase. Finally, these data suggest that the indigenous mangrove sediment microbiota developed essential mechanisms towards ecosystem remediation of petroleum hydrocarbon impact.

Biomimetic strategies to design metallic proteins for detoxification of hazardous heavy metal

Discharge of hazardous heavy metals in to the environment poses a serious threat to the ecosystem owing to its non-degradability and indestructability. Physical and chemical techniques for the removal of heavy metals from industrial effluent is expensive and causes secondary pollution. On the other hand, biological processes using microorganisms play a vital role due to their large surface area to volume ratio, which increases the interactions with metal ions present in the environment. Here, we developed a third generation biological tool for the removal of heavy metal (copper) from the effluent through the biosynthesis of intracellular and surface displayed metallic proteins with novel metal co-ordination chemistry. We evaluated the cell viability for maximum heavy metal adsorption and metal tolerance of synthesized congener metallic proteins. Finally, to eliminate the cost associated with incorporation of metal binding aminoacid, we have introduced a genetic circuit in order to evolve a novel magnetotactic bacterium. The bioreactor studies of the consortia of metallic protein expressing cells immobilized on functionalized granular activated carbon revealed that 97% of copper was adsorbed from the industrial effluent. It is evident that the use of congener metallic proteins will be a futuristic approach for the treatment of wastewater facilitating environmental detoxification.

Biosorption and biotransformation of hexavalent chromium [Cr(VI)]: A comprehensive review

Chromium (VI) is one of the most common environmental contaminant due to its tremendous industrial applications. It is non-biodegradable as it is a heavy metal, and hence, of major concern. Therefore, it is pertinent that the remediation method should be such that brings chromium within permissible limits before the effluent is discharged. Several different strategies are adopted by microorganisms for Cr (VI) removal mostly involving biosorption and biotransformation or both. These mechanisms are based on the surface nature of the biosorbent and the availability of reductants. This review article focuses on chromium pollution problem, its chemistry, sources, effects, remediation strategies by biological agents and detailed chromium detoxification mechanism in microbial cell. A summary of applied in situ and ex situ chromium bioremediation technologies is also listed. This can be helpful for developing technologies to be more efficient for Cr (VI) removal thereby bridging the gap between laboratory findings and industrial application for chromium remediation.

Impact of heavy metal on activity of some microbial enzymes in the riverbed sediments: Ecotoxicological implications in the Ganga River (India)

We studied the extracellular enzyme activity (EEA) in the riverbed sediment along a 518km gradient of the Ganga River receiving carbon and nutrient load from varied human sources. Also, we tested, together with substrate-driven stimulation, if the heavy metal accumulated in the sediment inhibits enzyme activities. Because pristine values are not available, we considered Dev Prayag, a least polluted site located 624km upstream to main study stretch, as a reference site. There were distinct increases in enzyme activities in the sediment along the study gradient from Dev Prayag, however, between-site differences were in concordance with sediment carbon(C), nitrogen (N) and phosphorus (P). Fluorescein diacetate hydrolysis (FDAase), β-glucosidase (Glu) and protease activities showed positive correlation with C, N and P while alkaline phosphatase was found negatively correlated with P. Enzyme activities were found negatively correlated with heavy metal, although ecological risk index (E_Rⁱ) varied with site and metal species. Dynamic fit curves showed significant positive correlation between heavy metal and microbial metabolic quotient (qCO₂) indicating a decrease in microbial activity in response to increasing heavy metal concentrations. This study forms the first report linking microbial enzyme activities to regional scale sediment heavy metal accumulation in the Ganga River, suggests that the microbial enzyme activities in the riverbed sediment were well associated with the proportion of C, N and P and appeared to be a sensitive indicator of C, N and P accumulation in the river. Heavy metal accumulated in the sediment inhibits enzyme activities, although C rich sediment showed relatively low toxicity due probably to reduced bioavailability of the metal. The study has relevance from ecotoxicological as well as from biomonitoring perspectives.

Contemporary enzyme based technologies for bioremediation: A review

The persistent disposal of xenobiotic compounds like insecticides, pesticides, fertilizers, plastics and other hydrocarbon containing substances is the major source of environmental pollution which needs to be eliminated. Many contemporary remediation methods such as physical, chemical and biological are currently being used, but they are not sufficient to clean the environment. The enzyme based bioremediation is an easy, quick, eco-friendly and socially acceptable approach used for the bioremediation of these recalcitrant xenobiotic compounds from the natural environment. Several microbial enzymes with bioremediation capability have been isolated and characterized from different natural sources, but less production of such enzymes is a limiting their further exploitation. The genetic engineering approach has the potential to get large amount of recombinant enzymes. Along with this, enzyme immobilization techniques can boost the half-life, stability and activity of enzymes at a significant level. Recently, nanozymes may offer the potential bioremediation ability towards a broad range of pollutants. In the present review, we have described a brief overview of the microbial enzymes, different enzymes techniques (genetic engineering and immobilization of enzymes) and nanozymes involved in bioremediation of toxic, carcinogenic and hazardous environmental pollutants.

Effects of cadmium-resistant fungi Aspergillus aculeatus on metabolic profiles of bermudagrass [Cynodondactylon (L.)Pers.] under Cd stress

Plants' tolerance to heavy metal stress may be induced by the exploitation of microbes. The objectives of this study were to investigate the effect of cadmium (Cd)-resistant fungus, Aspergillus aculeatus, on tolerance to Cd and alteration of metabolites in bermudagrass under Cd stress, and identify the predominant metabolites associated with Cd tolerance. Two genotypes of bermudagrass with contrasting Cd tolerance (Cd-sensitive 'WB92' and Cd-tolerant 'WB242') were exposed to 0, 50, 150 and 250 mg kg^-1 Cd for 21 days. Physiological responses of bermudagrass to Cd stress were evaluated based on the relative growth rate (RGR) and normalized relative transpiration rate (NRT). Plants inoculated with A. aculeatus exhibited higher RGR and NRT under Cd stress than those of non-inoculated plants, regardless of genotypes. A total of 32 Cd-responsive metabolites in leaves and 21 in roots were identified in the two genotypes, including organic acids, amino acids, sugars, and fatty acids and others. Interestingly, under Cd stress, the leaves of inoculated 'WB92' accumulated less citric acid, aspartic acid, glutamic acid, sucrose, galactose, but more sorbose and glucose, while inoculated 'WB242' leaves had less citric acid, malic acid, sucrose, sorbose, but more fructose and glucose, compared to non-inoculated plants. In 'WB92' roots, the A. aculeatus reduced mannose content, but increased trehalose and citric acid content, while in 'WB242', it decreased sucrose, but enhanced citric acid content, compared to Cd regime. The results of this study suggest that A. aculeatus may induce accumulation of different metabolites associated with Cd tolerance in bermudagrass.

Removal Capacities of Polycyclic Aromatic Hydrocarbons (PAHs) by a Newly Isolated Strain from Oilfield Produced Water

The polycyclic aromatic hydrocarbon (PAH)-degrading strain Q8 was isolated from oilfield produced water. According to the analysis of a biochemical test, 16S rRNA gene, house-keeping genes and DNA-DNA hybridization, strain Q8 was assigned to a novel species of the genus Gordonia. The strain could not only grow in mineral salt medium (MM) and utilize naphthalene and pyrene as its sole carbon source, but also degraded mixed naphthalene, phenanthrene, anthracene and pyrene. The degradation ratio of these four PAHs reached 100%, 95.4%, 73.8% and 53.4% respectively after being degraded by Q8 for seven days. A comparative experiment found that the PAHs degradation efficiency of Q8 is higher than that of Gordonia alkaliphila and Gordonia paraffinivorans, which have the capacities to remove PAHs. Fourier transform infrared spectra, saturate, aromatic, resin and asphaltene (SARA) and gas chromatography-mass spectrometry (GC-MS) analysis of crude oil degraded by Q8 were also studied. The results showed that Q8 could utilize n-alkanes and PAHs in crude oil. The relative proportions of the naphthalene series, phenanthrene series, thiophene series, fluorene series, chrysene series, C21-triaromatic steroid, pyrene, and benz(a)pyrene were reduced after being degraded by Q8. Gordonia sp. nov. Q8 had the capacity to remediate water and soil environments contaminated by PAHs or crude oil, and provided a feasible way for the bioremediation of PAHs and oil pollution.

Isolation of Pseudomonas fluorescens species highly resistant to pentachlorobenzene

Polychlorinated aromatic compounds, including pentachlorobenzenes and hexachlorobenzenes, are recalcitrant industrial pollutants that cause adverse effects on living cells. In this paper, the isolation of Pseudomonas fluorescens species with high resistance to pentachlorobenzene (PeCB) is reported. It was found that, in contrast to its slightly negative effect on P. fluorescens growth, PeCB readily inhibited the cell growth of Serratia spp. and Escherichia coli strains, thus indicating that inhibition of bacterial growth by PeCB is species-dependent. Analysis of a P. fluorescens isolate revealed that the exposure to PeCB induced production of reactive oxygen species and led to an increase in the level of alkyl hydroperoxide reductase C (AhpC), an important enzyme enhancing the cell tolerance to organic hydroperoxides usually accumulated under oxidative stress. The putative mechanism conferring PeCB resistance to P. fluorescens and the potential use of P. fluorescens in bioremediation are discussed.

Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals

Actinobacteria exhibit cosmopolitan distribution since their members are widely distributed in aquatic and terrestrial ecosystems. In the environment they play relevant ecological roles including recycling of substances, degradation of complex polymers, and production of bioactive molecules. Biotechnological potential of actinobacteria in the environment was demonstrated by their ability to remove organic and inorganic pollutants. This ability is the reason why actinobacteria have received special attention as candidates for bioremediation, which has gained importance because of the widespread release of contaminants into the environment. Among organic contaminants, pesticides are widely used for pest control, although the negative impact of these chemicals in the environmental balance is increasingly becoming apparent. Similarly, the extensive application of heavy metals in industrial processes lead to highly contaminated areas worldwide. Several studies focused in the use of actinobacteria for cleaning up the environment were performed in the last 15 years. Strategies such as bioaugmentation, biostimulation, cell immobilization, production of biosurfactants, design of defined mixed cultures and the use of plant-microbe systems were developed to enhance the capabilities of actinobacteria in bioremediation. In this review, we compiled and discussed works focused in the study of different bioremediation strategies using actinobacteria and how they contributed to the improvement of the already existing strategies. In addition, we discuss the importance of omic studies to elucidate mechanisms and regulations that bacteria use to cope with pollutant toxicity, since they are still little known in actinobacteria. A brief account of sources and harmful effects of pesticides and heavy metals is also given.

Genetic identification of arsenate reductase and arsenite oxidase in redox transformations carried out by arsenic metabolising prokaryotes - A comprehensive review

Arsenic (As) contamination in water is a cause of major concern to human population worldwide, especially in Bangladesh and West Bengal, India. Arsenite (As(III)) and arsenate (As(V)) are the two common forms in which arsenic exists in soil and groundwater, the former being more mobile and toxic. A large number of arsenic metabolising microorganisms play a crucial role in microbial transformation of arsenic between its different states, thus playing a key role in remediation of arsenic contaminated water. This review focuses on advances in biochemical, molecular and genomic developments in the field of arsenic metabolising bacteria - covering recent developments in the understanding of structure of arsenate reductase and arsenite oxidase enzymes, their gene and operon structures and their mechanism of action. The genetic and molecular studies of these microbes and their proteins may lead to evolution of successful strategies for effective implementation of bioremediation programs.

Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review

Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.

Genetically engineered Pseudomonas putida X3 strain and its potential ability to bioremediate soil microcosms contaminated with methyl parathion and cadmium

A multifunctional Pseudomonas putida X3 strain was successfully engineered by introducing methyl parathion (MP)-degrading gene and enhanced green fluorescent protein (EGFP) gene in P. putida X4 (CCTCC: 209319). In liquid cultures, the engineered X3 strain utilized MP as sole carbon source for growth and degraded 100 mg L(-1) of MP within 24 h; however, this strain did not further metabolize p-nitrophenol (PNP), an intermediate metabolite of MP. No discrepancy in minimum inhibitory concentrations (MICs) to cadmium (Cd), copper (Cu), zinc (Zn), and cobalt (Co) was observed between the engineered X3 strain and its host strain. The inoculated X3 strain accelerated MP degradation in different polluted soil microcosms with 100 mg MP kg(-1) dry soil and/or 5 mg Cd kg(-1) dry soil; MP was completely eliminated within 40 h. However, the presence of Cd in the early stage of remediation slightly delayed MP degradation. The application of X3 strain in Cd-contaminated soil strongly affected the distribution of Cd fractions and immobilized Cd by reducing bioavailable Cd concentrations with lower soluble/exchangeable Cd and organic-bound Cd. The inoculated X3 strain also colonized and proliferated in various contaminated microcosms. Our results suggested that the engineered X3 strain is a potential bioremediation agent showing competitive advantage in complex contaminated environments.

Hairy root induction and phytoremediation of textile dye, Reactive green 19A-HE4BD, in a halophyte, Sesuvium portulacastrum (L.) L

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Hairy roots induction from A. rhizogenes NCIM 5140 strain in Sesuvium.

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Textile dye degradation and color removal using hairy roots.

In this study, we report phytoremediation of textile dyes using hairy roots derived through Agrobacterium rhizogenes (NCIM 5140) infection of in vitro leaf and stem explants of a halophyte Sesuvium portulacastrum (L.) L. Leaf explants showed higher frequency of hairy root induction (70%) than stem explants (30%), and maximum number of roots (leaf 42.3 ± 2.4 and stem 50.3 ± 1.7). Transformed nature of hairy roots was ascertained by amplifying 970 bp region of T-DNA of Ri plasmid. Hairy roots were screened for phytoremediation of various textile dyes and results showed that HRs were able to degrade Reactive green 19A HE4BD upto 98% within 5 days of incubation. Spectrophotometric analysis showed decrease in dye concentration while HPLC and FTIR analysis confirmed its degradation. Seed germination assay demonstrated non-toxic nature of the extracted metabolites. This is the first report on induction of hairy root culture in Sesuvium portulacastrum and phytoremediation of textile dyes.

Structural and kinetic characterization of recombinant 2-hydroxymuconate semialdehyde dehydrogenase from Pseudomonas putida G7

The first enzyme in the oxalocrotonate branch of the naphthalene-degradation lower pathway in Pseudomonas putida G7 is NahI, a 2-hydroxymuconate semialdehyde dehydrogenase which converts 2-hydroxymuconate semialdehyde to 2-hydroxymuconate in the presence of NAD(+). NahI is in family 8 (ALDH8) of the NAD(P)(+)-dependent aldehyde dehydrogenase superfamily. In this work, we report the cloning, expression, purification and preliminary structural and kinetic characterization of the recombinant NahI. The nahI gene was subcloned into a T7 expression vector and the enzyme was overexpressed in Escherichia coli ArcticExpress as a hexa-histidine-tagged fusion protein. After purification by affinity and size-exclusion chromatography, dynamic light scattering and small-angle X-ray scattering experiments were conducted to analyze the oligomeric state and the overall shape of the enzyme in solution. The protein is a tetramer in solution and has nearly perfect 222 point group symmetry. Protein stability and secondary structure content were evaluated by a circular dichroism spectroscopy assay under different thermal conditions. Furthermore, kinetic assays were conducted and, for the first time, KM (1.3±0.3μM) and kcat (0.9s(-1)) values were determined at presumed NAD(+) saturation. NahI is highly specific for its biological substrate and has no activity with salicylaldehyde, another intermediate in the naphthalene-degradation pathway.

Differential Expression of Antioxidant Enzymes During Degradation of Azo Dye Reactive black 8 in Hairy roots of Physalis minima L

The enzymes involved in the protection of plant metabolism in presence of azo dye was characterized by studying activities of the role of antioxidant enzymes in the hairy roots (HRs) of Physalis minima L. during degradation of an azo dye, Reactive Black 8 (RB8). When the HRs were exposed to RB8 (30 mg L(-1)), a  nine fold increase in SOD activity was observed after 24 h, while 22 and 50 fold increase in activity was observed for POX and APX respectively after 72 h, whereas there was no significant change in activity of CAT. The activation of different antioxidant enzymes at different time intervals under dye stress suggests the synchronized functioning of antioxidant machinery to protect the HRs from oxidative damage. FTIR analysis confirmed the degradation of dye and the non-toxic nature of metabolites formed after dye degradation was confirmed by phytotoxicity study.

Identification of cadmium-resistant fungi related to Cd transportation in bermudagrass [Cynodon dactylon (L.) Pers]

Phytoremediation utilizing plants and microbes has been increasingly adopted as a green technology for cleaning up heavy metal polluted soils. Cd polluted soil and native bermudagrass from Liuyang and Zhuzhou in Hunan province of China were collected to investigate microbial diversity and isolate Cd resistant fungi, and then to determine the effect of Cd resistant fungi on Cd tolerance and transportation of bermudagrass. The functional diversity of microorganisms was evaluated using the BIOLOG Eco method. Cd-resistant fungi strain was isolated and identified as Aspergillus aculeatus based on the ribosomal internal transcribed spacer region sequence analysis. Bermudagrass was exposed to control, Cd only, and Cd plus A. aculeatus (Cd + A. aculeatus) with growth matrix (sawdust/sand = 3/1 in volume). Results indicated that Cd + A. aculeatus treated bermudagrass exhibited a higher photosynthetic activity compared to Cd only treated plants. Inoculation of A. aculeatus resulted in a decrease in stem and leaf Cd concentrations, to a greater extent for Cd-sensitive than for Cd-tolerant genotype. However, inoculation of A. aculeatus increased root Cd concentration under Cd stress conditions, significantly elevated soil pH, and decreased soil water-soluble Cd concentration. These results suggested that A. aculeatus might be potentially applied to improve Cd tolerance and to reduce Cd transportation to shoot of bermudagrass.

Characterization and potential application in mercury bioremediation of highly mercury-resistant marine bacterium Bacillus thuringiensis PW-05

Bacillus thuringiensis PW-05 was isolated from the Odisha coast and was found to resist 50 ppm of Hg as HgCl2 as well as higher concentrations of CdCl2, ZnSO4, PbNO3 and Na2HAsO4. Resistance towards several antibiotics, viz amoxycillin, ampicillin, methicillin, azithromycin and cephradine (CV) was also observed. The mer operon possessed by most of the mercury-resistant bacteria was also found in this isolate. Atomic absorption spectroscopy revealed that the isolate can volatilize >90 % of inorganic mercury. It showed biofilm formation in the presence of 50 ppm HgCl2 and can produce exopolysaccharide under same conditions. The isolate was found to volatilize mercury efficiently under a wide range of environmental parameters, i.e. pH (7 to 8), temperature (25 °C to 40 °C) and salinity (5 to 25 ppt). merA gene expression has been confirmed by real-time reverse transcriptase PCR study. Fourier transform infrared study revealed that -SH and -COOH groups play a major role in the process of adaptation to Hg. Hence, this isolate B. thuringiensis PW-05 shows an interesting potential for bioremediation of mercury.

Aerobic degradation of N-methyl-4-nitroaniline (MNA) by Pseudomonas sp. strain FK357 isolated from soil

N-Methyl-4-nitroaniline (MNA) is used as an additive to lower the melting temperature of energetic materials in the synthesis of insensitive explosives. Although the biotransformation of MNA under anaerobic condition has been reported, its aerobic microbial degradation has not been documented yet. A soil microcosms study showed the efficient aerobic degradation of MNA by the inhabitant soil microorganisms. An aerobic bacterium, Pseudomonas sp. strain FK357, able to utilize MNA as the sole carbon, nitrogen, and energy source, was isolated from soil microcosms. HPLC and GC-MS analysis of the samples obtained from growth and resting cell studies showed the formation of 4-nitroaniline (4-NA), 4-aminophenol (4-AP), and 1, 2, 4-benzenetriol (BT) as major metabolic intermediates in the MNA degradation pathway. Enzymatic assay carried out on cell-free lysates of MNA grown cells confirmed N-demethylation reaction is the first step of MNA degradation with the formation of 4-NA and formaldehyde products. Flavin-dependent transformation of 4-NA to 4-AP in cell extracts demonstrated that the second step of MNA degradation is a monooxygenation. Furthermore, conversion of 4-AP to BT by MNA grown cells indicates the involvement of oxidative deamination (release of NH2 substituent) reaction in third step of MNA degradation. Subsequent degradation of BT occurs by the action of benzenetriol 1, 2-dioxygenase as reported for the degradation of 4-nitrophenol. This is the first report on aerobic degradation of MNA by a single bacterium along with elucidation of metabolic pathway.