Laboratory research aimed at closing the gaps in microbial bioremediation

Transgenic Arabidopsis thaliana plants expressing bacterial γ-hexachlorocyclohexane dehydrochlorinase LinA

BACKGROUND

γ-Hexachlorocyclohexane (γ-HCH), an organochlorine insecticide of anthropogenic origin, is a persistent organic pollutant (POP) that causes environmental pollution concerns worldwide. Although many γ-HCH-degrading bacterial strains are available, inoculating them directly into γ-HCH-contaminated soil is ineffective because of the low survival rate of the exogenous bacteria. Another strategy for the bioremediation of γ-HCH involves the use of transgenic plants expressing bacterial enzyme for γ-HCH degradation through phytoremediation.

RESULTS

We generated transgenic Arabidopsis thaliana expressing γ-HCH dehydrochlroninase LinA from bacterium Sphingobium japonicum strain UT26. Among the transgenic Arabidopsis T2 lines, we obtained one line (A5) that expressed and accumulated LinA well. The A5-derived T3 plants showed higher tolerance to γ-HCH than the non-transformant control plants, indicating that γ-HCH is toxic for Arabidopsis thaliana and that this effect is relieved by LinA expression. The crude extract of the A5 plants showed γ-HCH degradation activity, and metabolites of γ-HCH produced by the LinA reaction were detected in the assay solution, indicating that the A5 plants accumulated the active LinA protein. In some A5 lines, the whole plant absorbed and degraded more than 99% of γ-HCH (10 ppm) in the liquid medium within 36 h.

CONCLUSION

The transgenic Arabidopsis expressing active LinA absorbed and degraded γ-HCH in the liquid medium, indicating the high potential of LinA-expressing transgenic plants for the phytoremediation of environmental γ-HCH. This study marks a crucial step toward the practical use of transgenic plants for the phytoremediation of POPs.

scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling

IMPORTANCE

A central question in microbial ecology is which member of a community performs a particular metabolism. Several sophisticated isotope labeling techniques are available for analyzing the metabolic function of populations and individual cells in a community. However, these methods are generally either insufficiently sensitive or throughput-limited and thus have limited applicability for the study of complex environmental samples. Here, we present a novel approach that combines highly sensitive radioisotope tracking, microfluidics, high-throughput sorting, and single-cell genomics to simultaneously detect and identify individual microbial cells based solely on their in situ metabolic activity, without prior information on community structure.

Bioremediation of the herbicide glyphosate in polluted soils by plant-associated microbes

Most productive lands worldwide base their crop production on the use of glyphosate (GLY)-resistant plants, and consequently, widespread use of this herbicide has led to environmental issues that need to be solved. Soil bioremediation technologies based on degradation of GLY by microorganisms are strategies that have been considered useful to solve this environmental problem. Recently, a further step has been taken considering the use of bacteria that interact with plants, either alone or both bacteria and plant together, for the removal of GLY herbicide. Plant-interacting microorganisms with plant growth-promoting traits can also enhance plant growth and contribute to successful bioremediation strategies.

Acidophilic microorganisms in remediation of contaminants present in extremely acidic conditions

Acidophiles are a group of microorganisms that thrive in acidic environments where pH level is far below the neutral value 7.0. They belong to a larger family called extremophiles, which is a group that thrives in various extreme environmental conditions which are normally inhospitable to other organisms. Several human activities such as mining, construction and other industrial processes release highly acidic effluents and wastes into the environment. Those acidic wastes and wastewaters contain different types of pollutants such as heavy metals, radioactive, and organic, whose have adverse effects on human being as well as on other living organisms. To protect the whole ecosystem, those pollutants containing effluents or wastes must be clean properly before releasing into environment. Physicochemical cleanup processes under extremely acidic conditions are not always successful due to high cost and release of toxic byproducts. While in case of biological methods, except acidophiles, no other microorganisms cannot survive in highly acidic conditions. Therefore, acidophiles can be a good choice for remediation of different types of contaminants present in acidic conditions. In this review article, various roles of acidophilic microorganisms responsible for removing heavy metals and radioactive pollutants from acidic environments were discussed. Bioremediation of various acidic organic pollutants by using acidophiles was also studied. Overall, this review could be helpful to extend our knowledge as well as to do further relevant novel studies in the field of acidic pollutants remediation by applying acidophilic microorganisms.

A systematic review on the implementation of advanced and evolutionary biotechnological tools for efficient bioremediation of organophosphorus pesticides

Ever since the concept of bioremediation was introduced, microorganisms, microbial enzymes and plants have been used as principal elements for Organophosphate pesticide (OPP) bioremediation. The enzyme systems and genetic profile of these microbes have been studied deeply in past years. Plant growth promoting rhizobacteria (PGPR) are considered as one of the potential candidates for OPP bioremediation and has been widely used to stimulate the phytoremediation potential of plants. Constructed wetlands (CWs) in OPP biodegradation have brought new prospects to microcosm and mesocosm based remediation strategies. Application of synthetic biology has provided a new dimension to the field of OPP bioremediation by introducing concepts like, gene manipulation andediting, expression and regulation of catabolic enzymes, implementation of whole-cell based and enzyme based biosensor systems for the detection and monitoring of OPP pollution in both terrestrial and aquatic environment. System biology and bioinformatics tools have rendered significant knowledge regarding the genetic, enzymatic and biochemical aspects of microbes and plants thereby, helping researchers to analyze the mechanism of OPP biodegradation. Structural biology has provided significant conceptual information regarding OPP biodegradation pathways, structural and functional characterization of metabolites and enzymes, enzyme-pollutant interactions, etc. Therefore, this review discussed the prospects and challenges of most advanced and high throughput strategies implemented for OPP biodegradation. The review also established a comparative analysis of various bioremediation techniques and highlighted the interdependency among them. The review highly suggested the simultaneous implementation of more than one remediation strategy or a combinational approach creating an advantageous hybrid technique for OPP bioremediation.

Sustainable strategies for combating hydrocarbon pollution: Special emphasis on mobil oil bioremediation

The global rise in industrialization and vehicularization has led to the increasing trend in the use of different crude oil types. Among these mobil oil has major application in automobiles and different machines. The combustion of mobil oil renders a non-usable form that ultimately enters the environment thereby causing problems to environmental health. The aliphatic and aromatic hydrocarbon fraction of mobil oil has serious human and environmental health hazards. These components upon interaction with soil affect its fertility and microbial diversity. The recent advancement in the omics approach viz. metagenomics, metatranscriptomics and metaproteomics has led to increased efficiency for the use of microbial based remediation strategy. Additionally, the use of biosurfactants further aids in increasing the bioavailability and thus biodegradation of crude oil constituents. The combination of more than one approach could serve as an effective tool for efficient reduction of oil contamination from diverse ecosystems. To the best of our knowledge only a few publications on mobil oil have been published in the last decade. This systematic review could be extremely useful in designing a micro-bioremediation strategy for aquatic and terrestrial ecosystems contaminated with mobil oil or petroleum hydrocarbons that is both efficient and feasible. The state-of-art information and future research directions have been discussed to address the issue efficiently.

Metabolic Engineering of Escherichia coli for Methyl Parathion Degradation

Organophosphate compounds are widely used in pesticides to control weeds, crop diseases, and insect pests. Unfortunately, these synthetic compounds are hazardous and toxic to all types of living organisms. In the present work, Escherichia coli was bioengineered to achieve methyl parathion (MP) degradation via the introduction of six synthetic genes, namely, opdS, pnpAS, pnpBS, pnpCS, pnpDS, and pnpES, to obtain a new transformant, BL-MP. MP and its subsequent decomposition intermediates were completely degraded by this transformant to enter the metabolites of multiple anabolic pathways. The MP-degraded strain created in this study may be a promising candidate for the bioremediation of MP and potential toxic intermediates.

Photocatalytic Material–Microbe Hybrids: Applications in Environmental Remediations

Environmental pollution has become one of the most urgent global issues that we have to face now. Searching new technologies to solve environmental issues is of great significance. By intimately coupling photocatalytic materials with microbes, the emerging photocatalytic material–microbe hybrid (PMH) system takes advantages of the high-efficiency, broad-spectrum light capture capability of the photocatalytic material and the selectivity of microbial enzymatic catalysis to efficiently convert solar energy into chemical energy. The PMH system is originally applied for the solar-to-chemical production. Interestingly, recent studies demonstrate that this system also has great potential in treating environmental contaminations. The photogenerated electrons produced by the PMH system can reductively decompose organic pollutants with oxidative nature (e.g., refractory azo dyes) under anaerobic circumstances. Moreover, based on the redox reactions occurring on the surface of photocatalysts and the enzymatic reactions in microbes, the PMH system can convert the valences of multiple heavy metal ions into less toxic or even nontoxic status simultaneously. In this review, we introduce the recent advances of using the PMH system in treating environmental pollutions and compare this system with another similar system, the traditional intimately coupled photocatalysis and biodegradation (ICPB) system. Finally, the current challenges and future directions in this field are discussed as well.

Recent Developments in Microbe-Plant-Based Bioremediation for Tackling Heavy Metal-Polluted Soils

Soil contamination with heavy metals (HMs) is a serious concern for the developing world due to its non-biodegradability and significant potential to damage the ecosystem and associated services. Rapid industrialization and activities such as mining, manufacturing, and construction are generating a huge quantity of toxic waste which causes environmental hazards. There are various traditional physicochemical techniques such as electro-remediation, immobilization, stabilization, and chemical reduction to clean the contaminants from the soil. However, these methods require high energy, trained manpower, and hazardous chemicals make these techniques costly and non-environment friendly. Bioremediation, which includes microorganism-based, plant-based, microorganism-plant associated, and other innovative methods, is employed to restore the contaminated soils. This review covers some new aspects and dimensions of bioremediation of heavy metal-polluted soils. The bioremediation potential of bacteria and fungi individually and in association with plants has been reviewed and critically examined. It is reported that microbes such as Pseudomonas spp., Bacillus spp., and Aspergillus spp., have high metal tolerance, and bioremediation potential up to 98% both individually and when associated with plants such as Trifolium repens, Helianthus annuus, and Vallisneria denseserrulata. The mechanism of microbe's detoxification of metals depends upon various aspects which include the internal structure, cell surface properties of microorganisms, and the surrounding environmental conditions have been covered. Further, factors affecting the bioremediation efficiency and their possible solution, along with challenges and future prospects, are also discussed.

Port Sediments: Problem or Resource? A Review Concerning the Treatment and Decontamination of Port Sediments by Fungi and Bacteria

Contamination of marine sediments by organic and/or inorganic compounds represents one of the most critical problems in marine environments. This issue affects not only biodiversity but also ecosystems, with negative impacts on sea water quality. The scientific community and the European Commission have recently discussed marine environment and ecosystem protection and restoration by sustainable green technologies among the main objectives of their scientific programmes. One of the primary goals of sustainable restoration and remediation of contaminated marine sediments is research regarding new biotechnologies employable in the decontamination of marine sediments, to consider sediments as a resource in many fields such as industry. In this context, microorganisms—in particular, fungi and bacteria—play a central and crucial role as the best tools of sustainable and green remediation processes. This review, carried out in the framework of the Interreg IT-FR Maritime GEREMIA Project, collects and shows the bioremediation and mycoremediation studies carried out on marine sediments contaminated with ecotoxic metals and organic pollutants. This work evidences the potentialities and limiting factors of these biotechnologies and outlines the possible future scenarios of the bioremediation of marine sediments, and also highlights the opportunities of an integrated approach that involves fungi and bacteria together.

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.

Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation

Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.

Optimization studies on biodegradation of atrazine by Bacillus badius ABP6 strain using response surface methodology

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Atrazine is widely used herbicide that causes harmful effects to living organisms.

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A bacterial isolate Bacillus badius ABP6 strain was used in the study.

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Optimization parameters showed better influence on the Biodegradation process of atrazine.

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Response surface methodology is a promising approach for Biodegradation enhancement by optimizing process parameters.

In this study, the optimization of distinctive environmental factors such as pH, temperature, agitation-speed and atrazine-concentration on atrazine degradation by utilizing Bacillus badius ABP6 strain, has been done through response-surface-methodology (RSM). The optimum-conditions after analysis for the maximum atrazine degradation were: pH 7.05, temperature 30.4 °C, agitation-speed 145.7 rpm, and atrazine-concentration 200.9 ppm. The prescribed model was approved for high F-value (95.92), very low P-value (<0.01) and non- significant lack of fit (0.1627). It was observed that under the optimized-conditions, the R² value of regression models for all the response variables was 0.9897 and the maximum atrazine degradation i.e. 89.7 % was found. Finally for graphical representation, the validated optimum-conditions of variables and responses were simulated using three dimensional plots (3D). The confirmation of the model is successful to suggest the optimization parameters of atrazine degradation under in-situ condition by bacterial isolate employing response-surface-methodology optimization tool of Design expert software (new version 10.0.1).

Metal and organic pollutants bioremediation by extremophile microorganisms

Extremophiles comprise microorganisms that are able to grow and thrive in extreme environments, including in an acidic or alkaline pH, high or low temperatures, high concentrations of pollutants, and salts, among others. These organisms are promising for environmental biotechnology due to their unique physiological and enzymatic characteristics, which allow them to survive in harsh environments. Due to the stability and persistence of these microorganisms under adverse environmental conditions, they can be used for the bioremediation of environments contaminated with extremely recalcitrant pollutants. Here, we provide an overview of extremophiles and the role of "omics" in the field of bioremediation of environmental pollutants, including hydrocarbons, textile dyes and metals.

Augmentation of Atrazine biodegradation by two Bacilli immobilized on α-Fe2O3 magnetic nanoparticles

In this study, a novel immobilizing carrier with α-Fe₂O₃ magnetic nanoparticles was developed and used for immobilization of atrazine-degrading bacterial isolates of Bacillus spp. Since the free cells of microorganisms generally not succeed to degrade pollutants; thus, extra treatments are alluring to make strides biodegradation. Scanning electron microscope (SEM) images appeared that after immobilization the bacterial cells were totally retained and entirely distributed on the surface of α-Fe₂O₃ magnetic nanoparticles_. The performance of α-Fe₂O₃ immobilized cells in atrazine (ATZ) degradation was compared with the free cells, which was about 90.56% in 20 days. Experimental results exhibited that ATZ could be degraded at a broad range of physicochemical parameters viz. pH (4.0 to 9.0), temperature (20 to 45 °C), ATZ concentration (50 to 300 mg L⁻¹) and agitation speed (50 to 300 rpm), which underlines that α-Fe₂O₃ immobilized cells could tolerate a higher range of ATZ concentration as compared to free cells. This research demonstrated that α-Fe₂O₃ could be applied as a potential carrier in cell immobilization and biodegradation of ATZ herbicide with greater efficiency.

Bacterial Catabolism of Biphenyls: Synthesis and Evaluation of Analogues

A series of alkylated 2,3-dihydroxybiphenyls has been prepared on the gram scale by using an effective Directed ortho Metalation-Suzuki-Miyaura cross-coupling strategy. These compounds have been used to investigate the substrate specificity of the meta-cleavage dioxygenase BphC, a key enzyme in the microbial catabolism of biphenyl. Isolation and characterization of the meta-cleavage products will allow further study of related processes, including the catabolism of lignin-derived biphenyls.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Extremophilic Microfactories: Applications in Metal and Radionuclide Bioremediation

Metals and radionuclides (M&Rs) are a worldwide concern claiming for resilient, efficient, and sustainable clean-up measures aligned with environmental protection goals and global change constraints. The unique defense mechanisms of extremophilic bacteria and archaea have been proving usefulness towards M&Rs bioremediation. Hence, extremophiles can be viewed as microfactories capable of providing specific and controlled services (i.e., genetic/metabolic mechanisms) and/or products (e.g., biomolecules) for that purpose. However, the natural physiological plasticity of such extremophilic microfactories can be further explored to nourish different hallmarks of M&R bioremediation, which are scantly approached in the literature and were never integrated. Therefore, this review not only briefly describes major valuable extremophilic pathways for M&R bioremediation, as it highlights the advances, challenges and gaps from the interplay of ‘omics’ and biological engineering to improve extremophilic microfactories performance for M&R clean-up. Microfactories’ potentialities are also envisaged to close the M&R bioremediation processes and shift the classical idea of never ‘getting rid’ of M&Rs into making them ‘the belle of the ball’ through bio-recycling and bio-recovering techniques.

Phytoremediation: State-of-the-art and a key role for the plant microbiome in future trends and research prospects

Phytoremediation is increasingly adopted as a more sustainable approach for soil remediation. However, significant advances in efficiency are still necessary to attain higher levels of environmental and economic sustainability. Current interventions do not always give the expected outcomes in field settings due to an incomplete understanding of the multicomponent biological interactions. New advances in -omics are gradually implemented for studying microbial communities of polluted land in situ. This opens new perspectives for the discovery of biodegradative strains and provides us new ways of interfering with microbial communities to enhance bioremediation rates. This review presents retrospectives and future perspectives for plant microbiome studies relevant to phytoremediation, as well as some knowledge gaps in this promising research field. The implementation of phytoremediation in soil clean-up management systems is discussed, and an overview of the promoting factors that determine the growth of the phytoremediation market is given. Continuous growth is expected since elimination of contaminants from the environment is demanded. The evolution of scientific thought from a reductionist view to a more holistic approach will boost phytoremediation as an efficient and reliable phytotechnology. It is anticipated that phytoremediation will prove the most promising for organic contaminant degradation and bioenergy crop production on marginal land.

Global transcriptional response of solvent-sensitive and solvent-tolerant Pseudomonas putida strains exposed to toluene

Pseudomonas putida strains are generally recognized as solvent tolerant, exhibiting varied sensitivity to organic solvents. Pan-genome analysis has revealed that 30% of genes belong to the core-genome of Pseudomonas. Accessory and unique genes confer high degree of adaptability and capabilities for the degradation and synthesis of a wide range of chemicals. For the use of these microbes in bioremediation and biocatalysis, it is critical to understand the mechanisms underlying these phenotypic differences. In this study, RNA-seq analysis compared the short- and long-term responses of the toluene-sensitive KT2440 strain and the highly tolerant DOT-T1E strain. The sensitive strain activates a larger number of genes in a higher magnitude than DOT-T1E. This is expected because KT2440 bears one toluene tolerant pump, while DOT-T1E encodes three of these pumps. Both strains activate membrane modifications to reduce toluene membrane permeability. The KT2440 strain activates the TCA cycle to generate energy, while avoiding energy-intensive processes such as flagellar biosynthesis. This suggests that KT2440 responds to toluene by focusing on survival mechanisms. The DOT-T1E strain activates toluene degradation pathways, using toluene as source of energy. Among the unique genes encoded by DOT-T1E is a 70 kb island composed of genes of unknown function induced in response to toluene.

A comparison of the response of twoBurkholderia fungorumstrains grown as planktonic cells versus biofilm to dibenzothiophene and select polycyclic aromatic hydrocarbons

In natural environments, bacteria often exist in close association with surfaces and interfaces by establishing biofilms. Here, we report on the ability of Burkholderia fungorum strains DBT1 and 95 to survive in high concentrations of hydrocarbons, and we compare their growth as a biofilm vs. planktonic cells. The 2 compounds tested were dibenzothiophene (DBT) and a mixture of naphthalene, phenanthrene, and pyrene (5:2:1) as representative compounds of thiophenes and polycyclic aromatic hydrocarbons (PAHs), respectively. The results showed that both strains were able to degrade DBT and to survive in the presence of up to a 2000 mg·L−1concentration of this compound both as a biofilm and as free-living cells. Moreover, B. fungorum DBT1 showed reduced tolerance towards the mixed PAHs (2000 mg·L−1naphthalene, 800 mg·L−1phenanthrene, and 400 mg·L−1pyrene) both as a biofilm and as free-living cells. Conversely, biofilms of B. fungorum 95 enhanced resistance against these toxic compounds compared with planktonic cells (P < 0.05). Visual observation through confocal laser scanning microscopy showed that exposure of biofilms to DBT and PAHs altered their structure: high concentrations of DBT triggered an aggregation of biofilm cells. These findings provide new perspectives on the effectiveness of using DBT-degrading bacterial strains in bioremediation of hydrocarbon-contaminated sites.

Potential of Polycyclic Aromatic Hydrocarbon-Degrading Bacterial Isolates to Contribute to Soil Fertility

Restoration of polycyclic aromatic hydrocarbon- (PAH-) polluted sites is presently a major challenge in agroforestry. Consequently, microorganisms with PAH-degradation ability and soil fertility improvement attributes are sought after in order to achieve sustainable remediation of polluted sites. This study isolated PAH-degrading bacteria from enriched cultures of spent automobile engine-oil polluted soil. Isolates' partial 16S rRNA genes were sequenced and taxonomically classified. Isolates were further screened for their soil fertility attributes such as phosphate solubilization, atmospheric nitrogen fixation, and indoleacetic acid (IAA) production. A total of 44 isolates were obtained and belong to the genera Acinetobacter, Arthrobacter, Bacillus, Flavobacterium, Microbacterium, Ochrobactrum, Pseudomonas, Pseudoxanthomonas, Rhodococcus, and Stenotrophomonas. Data analysed by principal component analysis showed the Bacillus and Ochrobactrum isolates displayed outstanding IAA production. Generalized linear modelling statistical approaches were applied to evaluate the contribution of the four most represented genera (Pseudomonas, Acinetobacter, Arthrobacter, and Rhodococcus) to soil fertility. The Pseudomonas isolates were the most promising in all three soil fertility enhancement traits evaluated and all isolates showed potential for one or more of the attributes evaluated. These findings demonstrate a clear potential of the isolates to participate in restorative bioremediation of polluted soil, which will enhance sustainable agricultural production and environmental protection.

Sugarcane bagasse as support for immobilization of Bacillus pumilus HZ-2 and its use in bioremediation of mesotrione-contaminated soils

The degrading microorganisms isolated from environment usually fail to degrade pollutants when used for bioremediation of contaminated soils; thus, additional treatments are needed to enhance biodegradation. In the present study, the potential of sugarcane bagasse as bacteria-immobilizing support was investigated in mesotrione biodegradation. A novel isolate Bacillus pumilus HZ-2 was applied in bacterial immobilization, which was capable of degrading over 95 % of mesotrione at initial concentrations ranging from 25 to 200 mg L(-1) within 4 days in flask-shaking tests. Scanning electron microscope (SEM) images showed that the bacterial cells were strongly absorbed and fully dispersed on bagasse surface after immobilization. Specially, 86.5 and 82.9 % of mesotrione was eliminated by bacteria immobilized on bagasse of 100 and 60 mesh, respectively, which indicated that this immobilization was able to maintain a high degrading activity of the bacteria. Analysis of the degradation products determined 2-amino-4-methylsulfonylbenzoic acid (AMBA) and 4-methylsulfonyl-2-nitrobenzoic acid (MNBA) as the main metabolites in the biodegradation pathway of mesotrione. In the sterile soil, approximately 90 % of mesotrione was degraded after supplementing 5.0 % of molasses in bacteria-bagasse composite, which greatly enhanced microbial adaptability and growth in the soil environment. In the field tests, over 75 % of mesotrione in soil was degraded within 14 days. The immobilized preparation demonstrated that mesotrione could be degraded at a wide range of pH values (5.0-8.0) and temperatures (25-35 °C), especially at low concentrations of mesotrione (5 to 20 mg kg(-1)). These results showed that sugarcane bagasse might be a good candidate as bacteria-immobilizing support to enhance mesotrione degradation by Bacillus p. HZ-2 in contaminated soils.

Bacterial sugar utilization gives rise to distinct single-cell behaviours

Inducible utilization pathways reflect widespread microbial strategies to uptake and consume sugars from the environment. Despite their broad importance and extensive characterization, little is known how these pathways naturally respond to their inducing sugar in individual cells. Here, we performed single-cell analyses to probe the behaviour of representative pathways in the model bacterium Escherichia coli. We observed diverse single-cell behaviours, including uniform responses (d-lactose, d-galactose, N-acetylglucosamine, N-acetylneuraminic acid), 'all-or-none' responses (d-xylose, l-rhamnose) and complex combinations thereof (l-arabinose, d-gluconate). Mathematical modelling and probing of genetically modified pathways revealed that the simple framework underlying these pathways - inducible transport and inducible catabolism - could give rise to most of these behaviours. Sugar catabolism was also an important feature, as disruption of catabolism eliminated tunable induction as well as enhanced memory of previous conditions. For instance, disruption of catabolism in pathways that respond to endogenously synthesized sugars led to full pathway induction even in the absence of exogenous sugar. Our findings demonstrate the remarkable flexibility of this simple biological framework, with direct implications for environmental adaptation and the engineering of synthetic utilization pathways as titratable expression systems and for metabolic engineering.

Metaproteomics to unravel major microbial players in leaf litter and soil environments: challenges and perspectives

Soil- and litter-borne microorganisms vitally contribute to biogeochemical cycles. However, changes in environmental parameters but also human interferences may alter species composition and elicit alterations in microbial activities. Soil and litter metaproteomics, implying the assignment of soil and litter proteins to specific phylogenetic and functional groups, has a great potential to provide essential new insights into the impact of microbial diversity on soil ecosystem functioning. This article will illuminate challenges and perspectives of current soil and litter metaproteomics research, starting with an introduction to an appropriate experimental design and state-of-the-art proteomics methodologies. This will be followed by a summary of important studies aimed at (i) the discovery of the major biotic drivers of leaf litter decomposition, (ii) metaproteomics analyses of rhizosphere-inhabiting microbes, and (iii) global approaches to study bioremediation processes. The review will be closed by a brief outlook on future developments and some concluding remarks, which should assist the reader to develop successful concepts for soil and litter metaproteomics studies.

Occurrence and suitability of pharmaceuticals and personal care products as molecular markers for raw wastewater contamination in surface water and groundwater

This study aimed to provide the first and comprehensive data on the occurrence of 17 target pharmaceuticals and personal care products (PPCPs) in urban water environment in Singapore. Meanwhile, this study also verified the suitability of these PPCPs as specific markers of raw wastewater contamination in receiving water bodies in highly urbanized areas where both surface water and groundwater are not impacted by the discharge of treated wastewater effluents. Analytical results of wastewater showed that among 17 target PPCPs examined, only 5 PPCPs were detected in 100 % of raw wastewater samples, including acetaminophen (ACT), carbamazepine (CBZ), caffeine (CF), diethyltoluamide (DEET), and salicylic acid (SA). Similarly, these PPCPs were found in most surface water and groundwater. Interestingly, the three PPCPs (ACT, CBZ, and SA) were only detected in surface water and groundwater in the sampling sites close to relatively older sewer systems, while they were absent in background samples that were collected from the catchment with no known wastewater sources. This suggests that ACT, CBZ, and SA can be used as specific molecular markers of raw wastewater in surface water and groundwater. This study also confirmed that CF and DEET were not really associated with wastewater sources, thus cannot serve well as specific molecular markers of wastewater contamination in receiving water bodies. To the best knowledge of the authors, the use of ACT and SA as specific molecular markers of raw wastewater contamination in urban surface waters and groundwater was first reported. Further studies on the use of ACT, CBZ, and SA along with other chemical/microbial markers are recommended to identify and differentiate contamination sources of surface waters/groundwater.

Identification of Burkholderia multivorans ATCC 17616 genetic determinants for fitness in soil by using signature-tagged mutagenesis

To identify bacterial genetic determinants for fitness in a soil environment, signature-tagged mutagenesis (STM) was applied to a soil bacterium, Burkholderia multivorans ATCC 17616. This strain was randomly mutagenized by each of 36 different signature-tagged plasposons, and 36 mutants with different tags were grouped as a set. A total of 192 sets consisting of 6912 independent mutants were each inoculated into soil and incubated. Two-step STM screening based on quantitative real-time PCR of total DNAs extracted from the resulting soil samples using the tag-specific primers led to the selection of 39 mutant candidates that exhibited a reduction in relative competitive fitness during incubation in the soil, and 32 plasposon-insertion sites were determined. Among them, mutants having plasposon insertion in fur, deaD or hrpA exhibited reduced fitness during incubation in soil when compared with the control strain. The deficiency in the soil fitness of the fur mutant was recovered by the introduction of the wild-type fur gene, indicating that the fur gene is one of the genetic determinants for fitness in the soil.

Further characterization of o-nitrobenzaldehyde degrading bacterium Pseudomonas sp. ONBA-17 and deduction on its metabolic pathway

A previously reported o-nitrobenzaldehyde (ONBA) degrading bacterium Pseudomonas sp. ONBA-17 was further identified and characterized. Based on results of DNA base composition and DNA-DNA hybridization, the strain was identified as P. putida. Its degradation effect enhanced with increase of inoculum amount and no lag phase was observed. Higher removal rate was achieved under shaking conditions. All tested ONBA with different initial concentrations could be completely degraded within 5 d. In addition, degradative enzyme(s) involved was confirmed as intra-cellular distributed and constitutively expressed. Effects of different compounds on relative activity of degradative enzyme(s) within cell-free extract were also evaluated. Finally, 2-nitrobenzoic acid and 2, 3-dihydroxybenzoic acid were detected as metabolites of ONBA degradation by P. putida ONBA-17, and relevant metabolic pathway was preliminary proposed. This study might help with future research in better understanding of nitroaromatics biodegradation.

Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome

Pseudomonas putida DOT-T1E is an organic solvent tolerant strain capable of degrading aromatic hydrocarbons. Here we report the DOT-T1E genomic sequence (6 394 153 bp) and its metabolic atlas based on the classification of enzyme activities. The genome encodes for at least 1751 enzymatic reactions that account for the known pattern of C, N, P and S utilization by this strain. Based on the potential of this strain to thrive in the presence of organic solvents and the subclasses of enzymes encoded in the genome, its metabolic map can be drawn and a number of potential biotransformation reactions can be deduced. This information may prove useful for adapting desired reactions to create value-added products. This bioengineering potential may be realized via direct transformation of substrates, or may require genetic engineering to block an existing pathway, or to re-organize operons and genes, as well as possibly requiring the recruitment of enzymes from other sources to achieve the desired transformation.

Funding Information Work in our laboratory was supported by Fondo Social Europeo and Fondos FEDER from the European Union, through several projects (BIO2010-17227, Consolider-Ingenio CSD2007-00005, Excelencia 2007 CVI-3010, Excelencia 2011 CVI-7391 and EXPLORA BIO2011-12776-E).

Bioremediation, an environmental remediation technology for the bioeconomy

Bioremediation differs from other industrial biotechnologies in that, although bioremediation contractors must profit from the activity, the primary driver is regulatory compliance rather than manufacturing profit. It is an attractive technology in the context of a bioeconomy but currently has limitations at the field scale. Ecogenomics techniques may address some of these limitations, but a further challenge would be acceptance of these techniques by regulators.