Effects of physicochemical factors on PAH degradation by Planomicrobium alkanoclasticum

Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants that are mutagenic, carcinogenic, and toxic to living organisms. Here, the ability and effectiveness of selected bacteria isolated from an oil‐contaminated area in biodegrading PAHs were evaluated, and the optimal conditions conducive to bacterial PAH biodegradation were determined. Of six bacterial isolates identified based on their 16S rRNA sequences, Planomicrobium alkanoclasticum could subsist on and consume nearly all hydrocarbons according to the 2,6‐dichlorophenolindophenol assay. The efficacy of this isolate at PAH biodegradation was then empirically confirmed. After 30 days of incubation, P. alkanoclasticum degraded 90.8% of the 16 PAH compounds analyzed and fully degraded eight of them. The optimum P. alkanoclasticum growth conditions were 35°C, pH 7.5, and NaNO₃ as the nitrogen source. Under these biostimulant conditions, P. alkanoclasticum degraded 91.4% of the total PAH concentration and completely decomposed seven PAHs after 15 days incubation. Hence, P. alkanoclasticum is an apt candidate for the biodegradation of PAHs and the bioremediation of sites contaminated by them.     

Factors affecting polycyclic aromatic hydrocarbon biodegradation by Aspergillus flavus

This study investigated the ability of fungi isolated from highly contaminated soil to biodegrade polycyclic aromatic hydrocarbon (PAH) compounds, as well as the effect of several parameters on the biodegradation ability of these fungi. The isolated fungi were identified using ITS rDNA sequencing and tested using 2,6‐dichlorophinolendophenol to determine their preliminary ability to degrade crude oil. The top‐performing fungi, Aspergillus flavus and Aspergillus fumigatus, were selected to test their ability to biodegrade PAH compounds as single isolates. After 15 days of incubation, A. flavus degraded 82.7% of the total PAH compounds, with the complete degradation of six compounds, whereas A. fumigatus degraded 68.9% of the total PAHs, with four aromatic compounds completely degraded. We also tested whether different temperatures, pH, and nitrogen sources influenced the growth of A. flavus and the degradation rate. The degradation process was optimal at a temperature of 30°C, pH of 5.5, and with nitrogen in the form of yeast extract. Finally, the ability of the fungal candidate, A. flavus, to degrade PAH compounds under these optimum conditions was studied. The results showed that 95.87% of the total PAHs, including 11 aromatic compounds, were completely degraded after 15 days of incubation. This suggests that A. flavus is a potential microorganism for the degradation of PAH compounds in aqueous cultures.     

Literature overview: Microbial metabolism of high molecular weight polycyclic aromatic hydrocarbons

High molecular weight polycyclic aromatic hydrocarbons (HMW PAHs) increase in hydrophobicity with increases in their molecular weight and ring angularity. Microbial strategies to deal with PAH hydrophobicity include biofilm formation, enzyme induction, and biosurfactants, the effect of which is variable on PAH metabolism depending on the surfactant type and concentration, substrate, and microbial strain(s). Aerobic HMW PAH metabolism proceeds via mineralization, partial degradation, and cometabolic transformations. Generally, bacteria and nonlignolytic fungi metabolize PAHs via initial PAH ring oxidation by dioxygenases to form cis‐dihydrodiols, which are transformed to catechol compounds by dehydrogenases and other mono‐ and dioxygenases to substituted catechol and noncatechol compounds, all ortho‐ or metacleaved and further oxidized to simpler compounds. However, lignolytic fungi form quinones and acids to CO₂. This review discusses the pathways for HMW PAH microbial metabolism. © 2008 Wiley Periodicals, Inc.     

Microbial Communities in Composite Biofilms Participating in the Degradation of PCB

A moorland soil site polluted with PCB showed a high diversity ofmetabolically active bacteria. Beside frequent types of 16S rRNAsequences similar to those of the species ofSphingomonasand the Acidobacterium phylum an unusual high number ofsequences from the genus Burkholderia were found. Burkholderia was also the main genus in isolates enriched onbiphenyl or various chlorobenzoates. In microcosm experimentssterilized surfaces exposed to PCB polluted soil always showed thepresence of clay aggregates formed by bacteria attached to thesubstratum. The bacteria use the PCB loaded clay colloids astransport medium for the water insoluble substrate to get accessto the carbon source. This is a novel mechanism of how bacteria dealwith hydrophobic substrates.     

The Effect of Interaction Between White-rot Fungi and Indigenous Microorganisms on Degradation of Polycyclic Aromatic Hydrocarbons in Soil

White-rot fungi applied for soil bioremediation have to compete with indigenous soil microorganisms. The effect of competition on both indigenous soil microflora and white-rot fungi was evaluated with regard to degradation of polycyclic aromatic hydrocarbons (PAH) with different persistence in soil. Sterile and non-sterile soil was artificially contaminated with ¹⁴C-labeled PAH consisting of three (anthracene), four (pyrene, benz[a]anthracene) and five fused aromatic rings (benzo[a]pyrene, dibenz[a,h]anthracene). The two fungi tested,Dichomitus squalens and Pleurotus ostreatus, produced similar amounts of ligninolytic enzymes in soil, but PAH mineralization by P. ostreatus was significantly higher. Compared to the indigenous soil microflora, P.ostreatus mineralized 5-ring PAH to a larger extent, while the indigenous microflora was superior in mineralizing 3-ring and 4-ring PAH. In coculture the special capabilities of both soil microflora and P. ostreatus were partly restricted due to antagonistic interactions, but essentially preserved. Thus, soil inoculation with P. ostreatus significantly increased the mineralization of high-molecular-weight PAH, and at the same time reduced the mineralization of anthracene and pyrene. Regarding the mineralization of low-molecular-weight PAH, the stimulation of indigenous soil microorganisms by straw amendment was more efficient than application of white-rot fungi.     

Utilisation of Supernatants of Pure Cultures of Streptomyces thermocarboxydus NH50 to Reduce Chromium Toxicity and Mobility in Contaminated Soils

Chromium is a heavy metal used in various industrial sectors. Improper handling and storage of chromium-laden effluents or wastes can lead to the pollution of the environment. The most toxic form is the more mobile one: hexavalent chromium Cr(VI). The reduction of Cr(VI) results in the immobilisation of chromium into its less toxic trivalent form Cr(III). This phenomenon may prevent the contamination of groundwater when the soil in the vadose zone is contaminated. Many bacteria have been isolated from contaminated soils and described to reduce Cr(VI) into Cr(III). A new Cr(VI)-reducing strain, identified as a Streptomyces thermocarboxydus,has been isolated and studied in our laboratories for its ability to reduce Cr(VI). This aerobic bacterium, in contrast to other genera described which mediate reduction via enzymes, produces reducing agents into the culture supernatants. Cr(VI) reduction by these substances is accelerated by the presence of small concentration of cupric ions (Cu²⁺). The reducing agent(s) can be easily recovered from the bacterial cultures and used as cell-free solution to treat contaminated soils by an in situ or ex situ processes.     

Root Exudates Impact on Phenanthrene Availability

In order to improve and optimize phytoremediation of PAH we propose to focus on the rhizospheric processes controlling PAH degradation. In this paper the effect of root exudates on PAH availability is studied. Model organic compounds (malic acid, malonic acid and EDTA) representing root exudates have been tested for their effect on phenanthrene sorption on a reference non polluted agricultural soil material. Phenanthrene adsorption isotherms were first obtained with batch experiments. Results showed linear isotherms and phenanthrene sorption was enhanced as the concentration of organic compounds in the solution increased. Column leaching experiments were then used to simulate the effect of root exudation following the soil pollution. Inlet solutions containing the different organic acids used were flowed through the column containing the artificially polluted soil material. Elution curves showed that the phenanthrene was less easily eluted when the solution injected contained the organic acids. However, magnitude of the phenomena did not fit with adsorption constants obtained in batch experiments. Phenanthrene desorption appeared limited by sequestration but organic acids seemed able to partially disturb the soil material structure to limit the sequestration effect.     

Biodegradation of Aliphatic and Aromatic Hydrocarbons: Specificity among Bacteria Isolated from Refinery Waste Sludge

Indigenous microorganisms, enriched and isolated from refinery waste sludge, were observed to possess a broad range of metabolic activities for mixtures of several classes of substrates of petroleum hydrocarbons, such as monoaromatic and polycyclic aromatic hydrocarbons (PAHs) and n- and branched alkanes. Three of the best-growing bacterial isolates selectively enriched with these compounds were identified by 16S rDNA sequencing as belonging to the genera Enterobacter and Ochrobactrum. Two of them, Enterobacter sp. strain EK3.1 and Ochrobactrum sp. strain EK6 utilise a hydrocarbon mixture of the branched alkane 2,6,10,14-tetramethylpentadecane and the PAHs acenaphthylene and acenaphthene. Enterobacter sp. strain EK4 can grow with a mixture of 2,6,10,14-tetramethylpentadecane, toluene, acenaphthylene and acenaphthene as carbon sources. Nucleic acid fingerprint analysis, by terminal restriction fragment length polymorphism (T-RFLP) of the PCR-amplified 16S rRNA genes, of the autochthonous bacterial community in contaminated soil samples showed complex and different community structures under different treatments of refinery waste sludge in landfarm areas. The characteristic peaks of the T-RFLP profiles of the individual, isolated degrading bacteria Enterobacter spp. and Ochrobactrum sp. were detected in the T-RFLP fingerprint of the bacterial community of the four months old treated landfarm soil, suggesting the enrichment of bacteria belonging to the same operational taxonomic units, as well as their importance in degrading activity.     

Reducing salinity and organic contaminants in the Pearl Harbor dredged material using soil amendments and plants

Phytoremediation is an emerging technique that can be used to economically remediate sites contaminated with trace elements and/or man‐made organic contaminants. This technique was used on Pearl Harbor (Oahu, Hawaii) dredged material (PHDM) containing polycyclic aromatic hydrocarbons (PAHs) and some heavy metals. The dredged material was first amended with a high‐calcium soil (Waialua Mollisol) and a biosolids‐based compost at different proportions to yield varying salinity levels. A mixture that yielded an electrical conductivity (EC, a measure of salinity) of the saturated paste extract of 15 to 20 dS/m was identified and used to evaluate the salt tolerance of five plant species. Relative germination and one‐month‐old biomass indicated that common bermuda grass (Cynodon dactylon), seashore paspalum (Paspalum vaginatum), beach pea (Vigna marina), and cow pea (Vigna unguiculata) can produce at least 40 percent of biomass of the control at an EC of approximately 18 dS/m, suggesting the four plants are relatively salt tolerant. In contrast, Desmodium intortum either did not germinate or died within two weeks after germination at the same salinity level. A subsequent greenhouse experiment, using mixtures of the PHDM (0 or 25 percent dry weight), organic amendments (10 percent leucaena green manure or biosolids‐based compost), and a Mollisol (65 or 90 percent dry weight) in 6‐liter pots containing 4 kilograms of material yielded the following results: (1) A combination of transplanted seashore paspalum, seeded bermuda grass, and seeded beach pea was effective in taking up sodium (Na), thereby reducing salinity and making the medium more amenable to diversified microbes and plants, which may be effective PAH degraders; (2) total PAH concentration was reduced by about 30 percent after three months of active plant growth, but degradation of individual PAH members varied significantly, however; (3) leguminous green manure, as a soil amendment, was more effective than compost for use in bio‐ and/or phytoremediations; and (4) soil amendments, when applicable, could supplement living plants in reducing organic contaminants, such as PAHs. © 2002 Wiley Periodicals, Inc.     

Biosorption study of potential fungi for copper remediation from Peninsular Malaysia

The ability to grow in heavy metal contaminated areas and absorb heavy metals from the environment make fungi a potentially viable biological‐based technology for remediating hazardous heavy metals in soil. In this study, 10 fungi from a copper (Cu)‐polluted area in Malaysia were isolated, with the four highest growth fungi identified as Simplicillium subtropicum, Fusarium solani, Aspergillus tamari, and Aspergillus niger. Results from toxicity and biosorption testing showed that A. niger and F. solani grew the fastest in the presence of Cu, but exhibited lower Cu uptake per unit of biomoass. In contrast, A. tamarii and S. subtropicum had lower growth rates, but showed better uptake of Cu per unit of biomass. S. subtropicum was identified as the best species for bioremediation because it had the highest Cu uptake and positive growth measured in the presence of Cu at concentrations below 100 mg/L. A niger proved to be most suitable for bioremediation if the concentration of Cu exceeds 100 mg/L.     

Kinetic Study of Naphthalene Biodegradation in Aerobic Slurry Phase Microcosms for the Optimisation of the Process

The research was focused on the slurry-phase biodegradation of naphthalene. The biodegradation process was optimised with preliminary experiments in slurry aerobic microcosms. From soil samples collected on a contaminated site, a Pseudomonas putida strain, called M8, capable to degrade naphthalene was selected. Microcosms were prepared with M8 strain by mixing non-contaminated soil and mineral M9 medium. Different experimental conditions were tested varying naphthalene concentration, soil:water ratio and inoculum density. The disappearance of hydrocarbon, the production of carbon dioxide, and the ratio of total heterotrophic and naphthalene-degrading bacteria were monitored at different incubation times. The kinetic equation that best fitted the disappearance of contaminant with time was determined. The results showed that the isolated strain enhanced the biodegradation rate with respect to the natural biodegradation.     

Contaminated land clean-up using composted wastes and impacts of VOCs on land

This paper describes experiments that demonstrate the effects and potential for remediation of a former steelworks site in Wales polluted with polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs). Under field conditions, PAH-contaminated soil was composted in-vessel, with or without organic feedstocks, receiving forced aeration for 80 days followed by 4 months maturation. Treatments compared PAH removal in contaminated soil to contaminated soil mixed with three different organic waste mixes after composting and after composts were spread to land. After composting, PAH concentrations declined in all treatments, by up to 38%. Sixteen months after the composts were landspread and vegetation was established, only those containing contaminated soil with organic additions exhibited further PAH removal, by up to 29%. Composting resulted in a decline in the relative concentration of small PAHs, whereas the landspreading-vegetation phase saw a decline in the relative concentration of medium PAHs in two of the three composts exhibiting PAH removal. Under controlled glasshouse conditions, vegetated soil columns of differing depths were exposed to VOCs from beneath. VOC vapour affected both shoot and root growth and soil microbial activity; effects varied with distance from the VOC source. This work demonstrated that on-site remediation of aged PAH-contaminated land can be successfully initiated by in-vessel co-composting followed by land spreading and vegetation, within a practical timeframe.     

A New Perspective on Sustainable Soil Remediation—Case Study Suggests Novel Fungal Genera Could Facilitate in situ Biodegradation of Hazardous Contaminants

Deciding upon a cost effective and sustainable method to address soil pollution is a challenge for many remedial project managers. High pressure to quickly achieve cleanup goals pushes for energy‐intensive remedies that rapidly address the contaminants of concern with established technologies, often leaving little room for research and development especially for slower treatment technologies, such as bioremediation, for the more heavily polluted sites. In this case study, new genomic approaches have been leveraged to assess fungal biostimulation potential in soils polluted with particularly persistent hydrophobic contaminants. This new approach provides insights into the genetic functions available at a given site in a way never before possible. In particular, this article presents a case study where next‐generation sequencing has been used to categorize fungi in soils from the Atlantic Wood Industries Superfund site in Portsmouth, Virginia. Data suggest that original attempts to harness fungi for bioremediation may have focused on fungal genera poorly suited to survive under heavily polluted site conditions, and that more targeted approaches relying on native indigenous fungi which are better equipped to survive under site‐specific conditions may be more appropriate. ©2016 Wiley Periodicals, Inc.     

Enhancing Performance of Sphingobacterium spiritivorum in Bioremediation Phenanthrene Contaminated Sand

Many biodegradation studies have focused on survival of isolated bacteria to increase the bacteria population and subsequently enhance the efficiency of polycyclic aromatic hydrocarbon (PAH) biodegradation. However, there is limited research on enhancing the performance of isolated bacteria through reinoculation. Thus, this study was designed to evaluate the effects of reinoculation on the performance of Sphingobacterium spiritivorum in degradation of phenanthrene contaminated sand. Experiments were performed in three different reactors. Inoculation was performed once (day 0) in reactor 1. In reactor 2, inoculation was performed twice (day 0 and day 5). The bacteria was isolated from reactor 2 and inoculated into reactor 3. The study results show reactor 3 having the highest degradation rate (13.61 mg/kg/day) and percentage removal (95.36 percent). In contrast, without reinoculation in reactor 1, 68.93 percent of phenanthrene was removed. Thus, the performance of S. spiritivorum in phenanthrene degradation can be enhanced through reinoculation. © 2014 Wiley Periodicals, Inc.     

混合菌修复石油污染土壤

选取4种从石油污染土壤中分离出的石油降解菌（包括根瘤菌（A）、节细菌（B）、嗜盐菌（C）和芽孢杆菌（D））,对模拟石油污染土壤进行了微生物修复实验。考察了4种菌单独使用时的石油降解率,确定了混合菌的最佳配比和菌群的最优培养条件,并对比了微生物修复前后土壤的各项性质。实验结果表明：4种菌均可提高微生物修复石油污染土壤的修复效果,使用D菌时石油降解率最高;当混合菌的w（A）∶w（B）∶w（C）∶w（D）=12∶2∶21∶65时,在培养条件为混合菌接种量122.0 mL/kg、土壤含水率14%（w）、鸡粪加入量90 g/kg、麦糠加入量150 g/kg和表面活性剂加入量22 mL/kg的情况下,土壤的修复效果最好,40 d后石油降解率达66.95%;经混合菌修复的石油污染土壤,其肥力明显升高,脱氢酶、过氧化酶和脲酶的活性均升高,微生物数量也有明显增加。     

Biodegradation of Polycyclic Aromatic Hydrocarbons by Exopolymers Synthesized by Moderately Halophilic Bacteria: Chemical Composition and Functional Properties

Three strains of halophilic bioemulsifier-producing bacteria; Bacillus sp. 2BSG-PDA-16, Bacillus sp. DV2-37 and Bacillus licheniformis ABRII6 were isolated from crude oil polluted water samples. Characteristics of exopolymers produced by these strains in media supplemented with various hydrocarbons instead of glucose were studied. Yield production, chemical composition, emulsifying, rheological and flocculating properties of exopolymers varied according to the strain and the carbon source. The highest amount of exopolymers synthesized by Bacillus sp. 2BSG-PDA-16, Bacillus sp. DV2-37 and B. licheniformis ABRII6 was 11, 18.5 and 12.4 g/l, respectively from media amended with glucose, while the most active emulsifiers were those obtained from media added with crude oil. Furthermore, all exopolymers produced were capable of emulsifying crude oil more efficiently than the three chemical surfactants tested as control (Tween 20, Tween 80 and Triton X-100). Respect to chemical composition, exopolymers produced on hydrocarbons always have lower content of carbohydrates and proteins than exopolymers produced in medium amended with glucose, however they showed higher amounts of uronic acids, sulfates and acetyl residues. The rheological study suggested that the exopolymers have characteristics of the pseudoplastic fluids. Efficiency of bacterial strains to remove PAH seems to agree with their potential applicability in oil bioremediation technology.     

Contributions of common sources of polycyclic aromatic hydrocarbons to soil contamination

Asphalt products, particularly sealants, are prepared using petroleum products that contain a com‐plex mixture of aliphatic and aromatic hydrocarbons, including polycyclic aromatic hydrocarbons (PAHs). Clearly, these products are ubiquitous in urban environments, which raises an issue regard‐ing the potential for PAHs to be transported from parking lots to underlying or adjacent soil, surface‐water bodies, or groundwater. Based on a literature review, there are limited studies focus‐ing on this issue; however, the studies that have been published have fascinating conclusions. The literature shows, as expected, that asphalt‐based products contain PAHs. The highest PAH concen‐trations are present in asphalt sealants, particularly those manufactured using coal tar. Furthermore, due to the low solubility and high partition coefficients of PAHs, the potential for PAHs to leach from asphalt surfaces is negligible, which has been confirmed by leachability studies. Thus, there is little risk that PAHs will be present in stormwater runoff or leach into groundwater from asphalt‐paved areas in a dissolved form. However, asphalt pavement and sealants produce particulate matter that can contain concentrations of PAHs in the sub‐percent range (100s to 1,000s mg/kg total PAHs) that is transported in stormwater runoff. Some studies show that this can cause soil and sediment con‐tamination with total PAH concentrations in the range of 1 to 10 mg/kg. From a remediation per‐spective, many site cleanups are conducted to remediate the presence of PAHs to cleanup goals below 1 mg/kg or, in some cases, 0.1 mg/kg or lower. From a total risk perspective, remediating sites to low PAH cleanup goals may be unwarranted in light of the risk of transportable PAHs produced from paved parking surfaces. In other words, is it reasonable to conduct a cleanup to remediate low PAH concentrations and then redevelop the area with asphalt pavement and sealant, which may pose a greater PAH‐related risk? © 2006 Wiley Periodicals, Inc.     

Bioremediation of Chromate by Sulfate-Reducing Bacteria, Cytochromes c3 and hydrogenases

The treatment of soils and ground waters polluted by heavy metals is of economical and environmental interest. Reduction of Cr(VI) to the less toxic Cr(III) associated to its precipitation is a potentially useful process for bioremediation. In order to develop ecological processes using micro-organisms, we have compared various sulfate-reducing bacteria for enzymatic reduction of chromate. The best Cr(VI) reductase activity was obtained with Desulfomicrobium norvegicum. Despite morphological changes induced by the presence of chromate, this strain can grow in the presence of up to 500 M Cr(VI) and can decontaminate waters polluted by Cr(VI) when seeded in bioreactors. We have demonstrated the ability of several metalloenzymes (cytochromes c ₃ and hydrogenases) to reduce chromate. Biophysical investigations of the chromate/protein interaction in order to get further informations on the mechanism of metal reduction by cytochromes c ₃ are under the way.     

Three Different Topics for Bioremediation Application on Soils and Waters Contaminated with Aromatic Compounds, by Using Immobilized Bacteria

Molecular techniques and modelling are presented as powerful tools required in the performance of efficient soil and water bioremediation systems. An Escherichia coli CC118-D strain was constructed by inserting the Klebsiella pneumoniae hpa B gene, coding for the unstable 3,4-dihydroxyphenylacetate 2,3-dioxygenase, into its chromosome. When the constructed strain was immobilized, both enzyme stability and viability increased along the studied period, in absence of antibiotic. We proposed this strategy as an approach to overcoming plasmid instability and to enhance enzyme activity and stability, avoiding antibiotic utilization. A model was developed to understand and predict the behaviour of bacteria and pollutants in a bioreactor system, considering: fluid dynamics, molecular/cellular scale processes and biofilm formation.     

Bacteria Degrading PCBs and CBs Isolated from Long-Term PCB Contaminated Soil

Bacteria able to degrade polychlorinated biphenyls (PCBs) and chlorobenzoic acids (CBs) were isolated from soil that had been contaminated with PCBs for 15–30 years. Contaminated soil in which PCB content ranged between 10–470 mg/kg was naturally vegetated with different plants including ash (Fraxinus excelsior), birch (Betula pendula), black locust (Robinia pseudoacacia), Austrian pine (Pinus nigra) and goat willow (Salix caprea) trees as well as a variety of grasses and forbs. Bacteria able to use biphenyl as a sole source of carbon and energy were found in the root zone of all plants, but occurred in the largest numbers beneath pine and black locust. Bacteria able to degrade chlorobenzoic acids were isolated from the same location contaminated with PCBs. Strains that were taxonomically identified by 16S rDNA as Pandoraea were able to use 2-CB, 3-CB, 2,3-CB, 2,5-CB as sole carbon sources, and the strain Arthrobacter utilised 4-CB.