Impact of bacterial activity on turnover of insoluble hydrophobic substrates (phenanthrene and pyrene)-Model simulations for prediction of bioremediation success

Microbes and microbial strategies in carcinogenic polycyclic aromatic hydrocarbons remediation: a systematic review

Degradation, detoxification, or removal of the omnipresent polycyclic aromatic hydrocarbons (PAHs) from the ecosphere as well as their prevention from entering into food chain has never appeared simple. In this context, cost-effective, eco-friendly, and sustainable solutions like microbe-mediated strategies have been adopted worldwide. With this connection, measures have been taken by multifarious modes of microbial remedial strategies, i.e., enzymatic degradation, biofilm and biosurfactant production, application of biochar-immobilized microbes, lactic acid bacteria, rhizospheric-phyllospheric-endophytic microorganisms, genetically engineered microorganisms, and bioelectrochemical techniques like microbial fuel cell. In this review, a nine-way directional approach which is based on the microbial resources reported over the last couple of decades has been described. Fungi were found to be the most dominant taxa among the CPAH-degrading microbial community constituting 52.2%, while bacteria, algae, and yeasts occupied 37.4%, 9.1%, and 1.3%, respectively. In addition to these, category-wise CPAH degrading efficiencies of each microbial taxon, consortium-based applications, CPAH degradation-related molecular tools, and factors affecting CPAH degradation are the other important aspects of this review in light of their appropriate selection and application in the PAH-contaminated environment for better human-health management in order to achieve a sustainable ecosystem.

Microbial-assisted phytodegradation for the amelioration of pyrene-contaminated soil using Pseudomonas aeruginosa and Aspergillus oryzae with alfalfa and sunflower

Environmental pollution caused by polycyclic aromatic hydrocarbons (PAHs) jeopardizes nature. PAHs are the most toxic, mutagenic, and carcinogenic pollutants and their cleanup is important for the environment. In the current research, to assess and evaluate three remediation strategies for pyrene removal from the soil, a pot experiment was performed: (a) bioremediation with Pseudomonas aeruginosa and Aspergillus oryzae, (b) phytoremediation with sunflower (Helianthus annuus) and alfalfa (Medicago sativa L.) and (c) microbial-assisted phytoremediation for the treatment of pyrene (700 mg kg-1). Results depict that P. aeruginosa significantly promoted the growth and tolerance of taken plants and reduced pyrene concentration in soil. Compared with those planted in pyrene-contaminated soil without inoculation. The highest percentage of pyrene removal was observed in P. aeruginosa inoculated alfalfa (91%), alfalfa inoculated with A. oryzae (83.96%), and without inoculation (78.20%). Moreover, alfalfa planted in P. aeruginosa augmented soil had the highest dehydrogenase activity (37.83 μg TPF g-1 soil h-1), and fluorescein diacetate hydrolysis (91.67 μg fluorescein g-1 dry soil). DHA and FDA are the indicators of bioaugmentation influence on the indigenous microbial activity of contaminated soil. As a result of the findings, the rhizospheric association of plants and microbes is beneficial for pyrene removal. Therefore, P. aeruginosa-assisted phytodegradation might be a more successful remediation technique for pyrene-contaminated soil than bioremediation and phytodegradation solely.

Multi-Approach Characterization of Novel Pyrene-Degrading Mycolicibacterium austroafricanum Isolates Lacking nid Genes

Polycyclic aromatic hydrocarbons (PAHs) are chemical compounds that are widespread in the environment, arising from the incomplete combustion of organic material, as well as from human activities involving petrol exploitation, petrochemical industrial waste, gas stations, and environmental disasters. PAHs of high molecular weight, such as pyrene, have carcinogenic and mutagenic effects and are considered pollutants. The microbial degradation of PAHs occurs through the action of multiple dioxygenase genes (nid), which are localized in genomic island denominate region A, and cytochrome P450 monooxygenases genes (cyp) dispersed in the bacterial genome. This study evaluated pyrene degradation by five isolates of Mycolicibacterium austroafricanum using 2,6-dichlorophenol indophenol (DCPIP assay), gas chromatography/mass spectrometry (CG/MS), and genomic analyses. Two isolates (MYC038 and MYC040) exhibited pyrene degradation indexes of 96% and 88%, respectively, over a seven-day incubation period. Interestingly, the genomic analyses showed that the isolates do not have nid genes, which are involved in PAH biodegradation, despite their ability to degrade pyrene, suggesting that degradation may occur due to the presence of cyp150 genes, or even genes that have not yet been described. To the best of our knowledge, this is the first report of isolates without nid genes demonstrating the ability to degrade pyrene.

Bioremediation of Polycyclic Aromatic Hydrocarbons in Contaminated Soils Using Vermicompost

Bioremediation of polycyclic aromatic hydrocarbons (PAHs) in contaminated soils are reported in many literatures. Composting, in addition to bioremediation, can simultaneously increase soil organic matter content and soil fertility and is thus regarded as one of the most cost-effective methods of soil remediation. In this study, biodegradation of phenanthrene (PHE) and pyrene (PYR) is reported by microbial consortia enriched by vermicompost. After soil samples preparation and grinding, the samples were contaminated with 100, 200, and 300 mg/kg of PHE and PYR concentrations and inoculated with three concentrations (2, 4, and 6 wt.%) of vermicompost. PHE and PYR concentrations were analyzed by HPLC during bioremediation. After 70 days, two highly capable microbial consortia were used to remove the pollutants in bioaugmentation conditions. Analysis of their microbial composition revealed that the consortia contain several Proteobacteria phylum bacterial species, and the most common genera were Pseudomonas and Citrobacter. Decontamination rates for PHE and PYR were estimated to be 89% and 83% over 45 days, respectively. Biodegradation kinetics revealed that microbial degradation followed a first-order kinetics. This study provides clear evidence on the biodegradation of PHE and PYR, paving the way for the development of bioremediation technologies for the recovery of polluted ecosystems.

Scientific concepts and methods for moving persistence assessments into the 21st century

The evaluation of a chemical substance's persistence is key to understanding its environmental fate, exposure concentration, and, ultimately, environmental risk. Traditional biodegradation test methods were developed many years ago for soluble, nonvolatile, single-constituent test substances, which do not represent the wide range of manufactured chemical substances. In addition, the Organisation for Economic Co-operation and Development (OECD) screening and simulation test methods do not fully reflect the environmental conditions into which substances are released and, therefore, estimates of chemical degradation half-lives can be very uncertain and may misrepresent real environmental processes. In this paper, we address the challenges and limitations facing current test methods and the scientific advances that are helping to both understand and provide solutions to them. Some of these advancements include the following: (1) robust methods that provide a deeper understanding of microbial composition, diversity, and abundance to ensure consistency and/or interpret variability between tests; (2) benchmarking tools and reference substances that aid in persistence evaluations through comparison against substances with well-quantified degradation profiles; (3) analytical methods that allow quantification for parent and metabolites at environmentally relevant concentrations, and inform on test substance bioavailability, biochemical pathways, rates of primary versus overall degradation, and rates of metabolite formation and decay; (4) modeling tools that predict the likelihood of microbial biotransformation, as well as biochemical pathways; and (5) modeling approaches that allow for derivation of more generally applicable biotransformation rate constants, by accounting for physical and/or chemical processes and test system design when evaluating test data. We also identify that, while such advancements could improve the certainty and accuracy of persistence assessments, the mechanisms and processes by which they are translated into regulatory practice and development of new OECD test guidelines need improving and accelerating. Where uncertainty remains, holistic weight of evidence approaches may be required to accurately assess the persistence of chemicals. Integr Environ Assess Manag 2022;18:1454-1487. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Coupling of desorption of phenanthrene from marine sediments and biodegradation of the sediment washing solution in a novel biochar immobilized-cell reactor

The recurrent dredging of marine sediments needs the use of ex-situ technologies such as sediment washing (SW) to effectively remove polycyclic aromatic hydrocarbons. Notwithstanding, the large volumes of generated spent SW effluents require adequate treatment by employing highly-efficient, inexpensive and environmentally-friendly solutions. This study proposes the phenanthrene (PHE) desorption from sediments using Tween® 80 (TW80) as extracting agent and the treatment of the resulting spent SW solution in a biochar (BC) immobilized-cell bioreactor. The SW process reached the highest PHE removal of about 91% using a surfactant solution containing 10,800 mg L^-1 of TW80. The generated amount of spent PHE-polluted SW solution can be controlled by keeping a solid to liquid ratio of 1:4. A PHE degradation of up to 96% was subsequently achieved after 43 days of continuous reactor operation, aerobically treating the TW80 solution in the BC immobilized-cell bioreactor with a hydraulic retention time of 3.5 days. Brevundimonas, Chryseobacterium, Dysgonomonas, Nubsella, and both uncultured Weeksellaceae and Xanthobacteraceae genera were mainly involved in PHE biodegradation. A rough economic study showed a total cost of 342.60 € ton^-1 of sediment, including the SW operations, TW80 and BC supply and the biological treatment of the SW solution.

Negative role of biochars in the dissipation and vegetable uptake of polycyclic aromatic hydrocarbons (PAHs) in an agricultural soil: Cautions for application of biochars to remediate PAHs-contaminated soil

Biochars were studied for their impacts on the dissipation and vegetable uptake of polycyclic aromatic hydrocarbons (PAHs) in an agricultural soil. The health risks of PAHs taken up by vegetables were assessed by growing Chinese cabbage in both unamended soil and biochar-amended soils. In the unamended soil, the total 16 PAHs (Σ16PAHs) content decreased by 77.38% after planting the vegetable. The dissipation percentages of low-molecular-weight PAHs (LMW-PAHs), medium-molecular-weight PAHs (MMW-PAHs), and high-molecular-weight PAHs (HMW-PAHs) were 82.37%, 72.65%, and 68.63%, respectively. A significant negative correlation was determined between the dissipation percentages of PAHs in soil and the logK_ow of PAHs (p < 0.01), indicating that the affinity of PAHs for soil particles was one of an important limiting factors on the dissipation of PAHs. The uptake of PAHs by plant was significantly reduced with the increase in the molecular weight of the PAHs (76.55% for LWM-PAHs, 17.13% for MMW-PAHs, and 6.05% for HMW-PAHs). Addition of biochars to the soil decreased the dissipation of Σ16PAHs (73.59-77.01%), mostly due to a decrease in the dissipation of LMW-PAHs and MMW-PAHs. This finding was due to the immobilization of LMW-PAHs and MMW-PAHs within the biochar micropores. A marked reduction of Proteobacteria in biochar-amended soils also resulted in the decreased biodegradation of PAHs. Four of six biochars significantly increased the concentrations of Σ16PAHs in plant by 30.10-74.22%. Generally, biochars significantly increased the uptake of LMW-PAHs by plant but had little influence on the plant uptake of MMW-PAHs and HMW-PAHs. Three of six biochars notably increased the incremental lifetime cancer risk values based on the exposure of PAHs by vegetable consumption.

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.

Rhizoremediation as a green technology for the remediation of petroleum hydrocarbon-contaminated soils

Rhizoremediation is increasingly becoming a green and sustainable alternative to physico-chemical methods for remediation of contaminated environments through the utilization of symbiotic relationship between plants and their associated soil microorganisms in the root zone. The overall efficiency can be enhanced by identifying suitable plant-microbe combinations for specific contaminants and supporting the process with the application of appropriate soil amendments. This approach not only involves promoting the existing activity of plants and soil microbes, but also introduces an adequate number of microorganisms with specific catabolic activity. Here, we reviewed recent literature on the main mechanisms and key factors in the rhizoremediation process with a particular focus on soils contaminated with total petroleum hydrocarbon (TPH). We then discuss the potential of different soil amendments to accelerate the remediation efficiency based on biostimulation and bioaugmentation processes. Notwithstanding some successes in well-controlled environments, rhizoremediation of TPH under field conditions is still not widespread and considered less attractive than physico-chemical methods. We catalogued the major pitfalls of this remediation approach at the field scale in TPH-contaminated sites and, provide some applicable situations for the future successful use of in situ rhizoremediation of TPH-contaminated soils.

Microbial Turnover of Glyphosate to Biomass: Utilization as Nutrient Source and Formation of AMPA and Biogenic NER in an OECD 308 Test

Environmental fate assessment of chemicals involves standardized simulation tests with isotope-labeled molecules to balance transformation, mineralization, and formation of nonextractable residues (NER). Methods to predict microbial turnover and biogenic NER have been developed, having limited use when metabolites accumulate, the chemicals are not the only C source, or provide for other macroelements. To improve predictive capability, we extended a recently developed method for microbial growth yield estimation to account for incomplete degradation and multiple-element assimilation and combined it with a dynamic model for fate description in soils and sediments. We evaluated the results against the unique experimental data of 13C3-15N co-labeled glyphosate turnover with AMPA formation in water-sediment systems (OECD 308). Balancing 13C- and 15N- fluxes to biomass showed a pronounced shift of glyphosate transformation from full mineralization to AMPA formation. This may be explained by various hypotheses, for example, the limited substrate turnover inherent to the batch conditions of the test system causing microbial starvation or inhibition by P release. Modeling results indicate initial N overload due to the lower C/N ratio in glyphosate compared to average cell composition leading to subsequent C demand and accumulation of AMPA.

In situ long-term modeling of phenanthrene dynamics in an aged contaminated soil using the VSOIL platform

Management and remediation actions of polycyclic aromatic hydrocarbons (PAH) contaminated sites require an accurate knowledge of the dynamics of these chemicals in situ under real conditions. Here we developed, under the Virtual Soil Platform, a global model for PAH that describes the principal physical and biological processes controlling the dynamics of PAH in soil under real climatic conditions. The model was applied first to simulate the observed dynamics of phenanthrene in situ field experimental plots of industrial contaminated soil. In a second step, different long-term scenarios of climate change or bioavailability increase were applied. Our results show that the model can adequately predict the fate of phenanthrene and can contribute to clarify some of unexplored aspects regarding the behavior of phenanthrene in soil like its degradation mechanism and stabilization. Tested prospective scenarios showed that bioavailability increase (through the addition of solvent or surfactants) resulted in significant increase in substrate transfer rate, hence reducing remediation time. Regarding climate change effect, the model indicated that phenanthrene concentration decreased by 54% during 40years with a natural attenuation and both scenarios chosen for climatic boundaries provided very similar results.

Rhizospheric microorganisms as a solution for the recovery of soils contaminated by petroleum: A review

Petroleum is currently the world's main energy source, and its demand is expected to increase in coming years. Its intense exploitation can lead to an increase in the number of environmental accidents, such as spills and leaks, and an increase in the generation of environmental liabilities resulting from refining. Due to its hydrophobic characteristics and slow process of biodegradation, petroleum can remain in the environment for a long time and its toxicity can cause a negative impact on both terrestrial and aquatic ecosystems, with the main negative effects related to its carcinogenic potential for both animals and humans. The objective of the present review is to discuss environmental contamination by oil, conventional treatment techniques and bioremediation an alternative tool for recovery petroleum-contaminated soils, focusing on the rhizodegradation process, plant growth-promoting rhizobacteria (PGPR), a phytoremediation strategy in which the microorganisms that colonize the roots of phytoremediatior plants are responsible for the biodegradation of petroleum. These microorganisms can be selected and tested individually or in the form of consortia to evaluate their potential for oil degradation, or even to measure the use of biosurfactants produced by them to constitute tools for the development of environmental recovery strategies and biotechnological application.

Prediction of the Formation of Biogenic Nonextractable Residues during Degradation of Environmental Chemicals from Biomass Yields

Degradation tests with radio or stable isotope labeled compounds enable the detection of the formation of nonextractable residues (NER). In PBT and vPvB assessment, remobilisable NER are considered as a potential risk while biogenic NER from incorporation of labeled carbon into microbial biomass are treated as degradation products. Relationships between yield, released CO₂ (as indicator of microbial activity and mineralization) and microbial growth can be used to estimate the formation of biogenic NER. We provide a new approach for calculation of potential substrate transformation to microbial biomass (theoretical yield) based on Gibbs free energy and microbially available electrons. We compare estimated theoretical yields of biotechnological substrates and of chemicals of environmental concern with experimentally determined yields for validation of the presented approach. A five-compartment dynamic model is applied to simulate experiments of ¹³C-labeled 2,4-D and ibuprofen turnover. The results show that bioNER increases with time, and that most bioNER originates from microbial proteins. Simulations with precalculated input data demonstrate that precalculation of yields reduces the number of fit parameters considerably, increases confidence in fitted kinetic data, and reduces the uncertainty of the simulation results.

A unified approach for including non-extractable residues (NER) of chemicals and pesticides in the assessment of persistence

All chemicals form non-extractable residues (NER) to various extents in environmental media like soil, sediment, plants and animals. NER can be quantified in environmental fate studies using isotope-labeled (such as ¹⁴C or ¹³C) tracer compounds. Previous NER definitions have led to a mismatch of legislation and state of knowledge in research: the residues are assumed to be either irreversibly bound degradation products or at least parts of these residues can be released. In the latter assumption, soils and sediments are a long-term source of slowly released residues. We here present a conceptual experimental and modeling approach to characterize non-extractable residues and provide guidance how they should be considered in the persistence assessment of chemicals and pesticides. Three types of NER can be experimentally discriminated: sequestered and entrapped residues (type I), containing either the parent substance or xenobiotic transformation products or both and having the potential to be released, which has indeed been observed. Type II NER are residues that are covalently bound to organic matter in soils or sediments or to biological tissue in organisms and that are considered being strongly bound with very low remobilization rates like that of humic matter degradation rates. Type III NER comprises biogenic NER (bioNER) after degradation of the xenobiotic chemical and anabolic formation of natural biomolecules like amino acids and phospholipids, and other biomass compounds. We developed the microbial turnover to biomass (MTB) model to predict the formation of bioNER based on the structural properties of chemicals. Further, we proposed an extraction sequence to obtain a matrix containing only NER. Finally, we summarized experimental methods to distinguish the three NER types. Type I NER and type II NER should be considered as potentially remobilizable residues in persistence assessment but the probability of type II release is much lower than that of type I NER, i.e., type II NER in soil are "operationally spoken" irreversibly bound and can be released only in minute amounts and at very slow rates, if at all. The potential of remobilization can be evaluated by chemical, physical and biological methods. BioNER are of no environmental concern and, therefore, can be assessed as such in persistence assessment. The general concept presented is to consider the total amount of NER minus potential bioNER as the amount of xenoNER, type I + II. If a clear differentiation of type I and type II is possible, for the calculation of half-life type I NER are considered as not degraded parent substance or transformation product(s). On the contrary, type II NER may generally be considered as (at least temporarily) removed. Providing proof for type II NER is the most critical issue in NER assessment and requires additional research. If no characterization and additional information on NER are available, it is recommended to assess the total amount as potentially remobilizable. We propose our unified approach of NER characterization and evaluation to be implemented into the persistence and environmental hazard assessment strategies for REACH chemicals and biocides, human and veterinary pharmaceuticals, and pesticides, irrespective of the different regulatory frameworks.

Biological and analytical techniques used for detection of polyaromatic hydrocarbons

Polycyclic aromatic hydrocarbons contain two or more fused benzene rings that are considered as cosmo-pollutants ubiquitously found in the environment. The identification and monitoring of polycyclic aromatic hydrocarbons (PAHs) are of great interests for rapid and on-site detection. Therefore, many analytical and biological techniques have been proposed for the qualitative and quantitative assessments of PAHs. Non-biological analytical techniques such as infrared, Raman, and fluorescence spectroscopies are commonly exploited as non-destructive techniques while gas chromatography (GC) and high-performance liquid chromatography (HPLC) with multiple detectors are extensively employed for the separation and detection of an analyte. Even though spectroscopy and chromatography are more accurate, convenient, and feasible techniques, often, these methods are expensive and sophisticated which require high maintenance cost. On the other hand, biological approaches, i.e., immunoassay, PCR, and microarray, offer comprehensive high-throughput specificity and sensitivity for a similar analyte. Biosensor- and immunoassay-mediated detections of PAHs have opened up new avenues in terms of low cost, rapid determination, and higher sensitivity. In this review, we have discussed the strengths and limitations of biological and analytical techniques that were explored for precise evaluation and were trusted at both the legislation and research levels.

Microbial growth yield estimates from thermodynamics and its importance for degradation of pesticides and formation of biogenic non-extractable residues

In biodegradation studies with isotope-labelled pesticides, fractions of non-extractable residues (NER) remain, but their nature and composition is rarely known, leading to uncertainty about their risk. Microbial growth leads to incorporation of carbon into the microbial mass, resulting in biogenic NER. Formation of microbial mass can be estimated from the microbial growth yield, but experimental data is rare. Instead, we suggest using prediction methods for the theoretical yield based on thermodynamics. Recently, we presented the Microbial Turnover to Biomass (MTB) method that needs a minimum of input data. We have estimated the growth yield of 40 organic chemicals (31 pesticides) using the MTB and two existing methods. The results were compared to experimental values, and the sensitivity of the methods was assessed. The MTB method performed best for pesticides. Having the theoretical yield and using the released CO₂ as a measure for microbial activity, we predicted a range for the formation of biogenic NER. For the majority of the pesticides, a considerable fraction of the NER was estimated to be biogenic. This novel approach provides a theoretical foundation applicable to the evaluation and prediction of biogenic NER formation during pesticide degradation experiments, and may also be employed for the interpretation of NER data from regulatory studies.

Enhanced Accessibility of Polycyclic Aromatic Hydrocarbons (PAHs) and Heterocyclic PAHs in Industrially Contaminated Soil after Passive Dosing of a Competitive Sorbate

To assess the exposure to polycyclic aromatic hydrocarbons (PAHs) it is important to understand the binding mechanisms between specific soil constituents and the organic pollutant. In this study, sorptive bioaccessibility extraction (SBE) was applied to quantify the accessible PAH fraction in industrially contaminated soil with and without passive dosing of a competitive sorbate. SBE experiments revealed an accessible PAH fraction of 41 ± 1% (∑16 US EPA PAHs + 5 further PAHs). The passive dosing of toluene below its saturation level revealed competitive binding and resulted in an average increase of the accessible fraction to 49 ± 2%, whereby primarily the accessibility of higher molecular weight PAHs (log K_ow > 6) was affected. Competitive binding was verified using the same soil with only desorption-resistant PAHs present. In this experiment, passive dosing of toluene resulted in desorption of 13 ± 0.4% PAH. We explain increased PAH desorption after addition of toluene by competitive adsorption to high-affinity sorption sites while acknowledging that toluene could additionally have increased PAH mobility within the soil matrix. Findings suggest that the presence of copollutants at contaminated sites deserves specific considerations as these may increase accessibility and thereby exposure and mobility of PAHs.

Perspectives and Challenges in Microbial Communities Metabolic Modeling

Bacteria have evolved to efficiently interact each other, forming complex entities known as microbial communities. These "super-organisms" play a central role in maintaining the health of their eukaryotic hosts and in the cycling of elements like carbon and nitrogen. However, despite their crucial importance, the mechanisms that influence the functioning of microbial communities and their relationship with environmental perturbations are obscure. The study of microbial communities was boosted by tremendous advances in sequencing technologies, and in particular by the possibility to determine genomic sequences of bacteria directly from environmental samples. Indeed, with the advent of metagenomics, it has become possible to investigate, on a previously unparalleled scale, the taxonomical composition and the functional genetic elements present in a specific community. Notwithstanding, the metagenomic approach per se suffers some limitations, among which the impossibility of modeling molecular-level (e.g., metabolic) interactions occurring between community members, as well as their effects on the overall stability of the entire system. The family of constraint-based methods, such as flux balance analysis, has been fruitfully used to translate genome sequences in predictive, genome-scale modeling platforms. Although these techniques have been initially developed for analyzing single, well-known model organisms, their recent improvements allowed engaging in multi-organism in silico analyses characterized by a considerable predictive capability. In the face of these advances, here we focus on providing an overview of the possibilities and challenges related to the modeling of metabolic interactions within a bacterial community, discussing the feasibility and the perspectives of this kind of analysis in the (near) future.

Characteristics of PAH tar oil contaminated soils-Black particles, resins and implications for treatment strategies

Tar oil contamination is a major environmental concern due to health impacts of polycyclic aromatic hydrocarbons (PAH) and the difficulty of reaching acceptable remediation end-points. Six tar oil-contaminated soils with different industrial histories were compared to investigate contamination characteristics by black particles. Here we provide a simple method tested on 6 soils to visualize and identify large amounts of black particles (BP) as either solid aggregates of resinified and weathered tar oil or various wood/coke/coal-like materials derived from the contamination history. These materials contain 2-10 times higher PAH concentrations than the average soil and were dominantly found in the sand fraction containing 42-86% of the total PAH. The PAH contamination in the different granulometric fractions was directly proportional to the respective total organic carbon content, since the PAH were associated to the carbonaceous particulate materials. Significantly lower (bio)availability of PAH associated to these carbonaceous phases is widely recognized, thus limiting the efficiency of remediation techniques. We provide a conceptual model of the limited mass transfer of PAH from resinated tar oil phases to the water phase and emphasize the options to physically separate BP based on their lower bulk density and slower settling velocity.

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.

Effects of cytotoxicity of erythromycin on PAH-degrading strains and degrading efficiency

The MIC of erythromycin of pyrene degrading strain ofMycobacterium gilvumCP13.