Thermophilic degradation of environmental pollutants

Ocean Stratification Impacts on Dissolved Polycyclic Aromatic Hydrocarbons (PAHs): From Global Observation to Deep Learning

Ocean stratification plays a crucial role in many biogeochemical processes of dissolved matter, but our understanding of its impact on widespread organic pollutants, such as polycyclic aromatic hydrocarbons (PAHs), remains limited. By analyzing dissolved PAHs collected from global oceans and marginal seas, we found different patterns in vertical distributions of PAHs in relation to ocean primary productivity and stratification index. Notably, a significant positive logarithmic relationship (R2 = 0.50, p < 0.05) was observed between the stratification index and the PAH stock. To further investigate the impact of ocean stratification on PAHs, we developed a deep learning neural network model. This model incorporated input variables determining the state of the seawater or the stock of PAHs. The modeled PAH stocks displayed substantial agreement with the observed values (R2 ≥ 0.92), suggesting that intensified stratification could prompt the accumulation of PAHs in the water column. Given the amplified effect of global warming, it is imperative to give more attention to increased ocean stratification and its impact on the environmental fate of organic pollutants.

Bioremediation of polycyclic aromatic hydrocarbons contaminated soils: recent progress, perspectives and challenges

The life of all creatures is supported directly or indirectly by soil, which is a significant environmental matrix. The soil has been polluted partly due to increased human activities and population growth, releasing several foreign substances and persistent contaminants. When toxic substances like polycyclic aromatic hydrocarbons (PAHs) are disposed of, the characteristics of the soil are changed, microbial biodiversity is impacted, and items are destroyed. Because of the mutagenicity, carcinogenicity, and toxicity of petroleum hydrocarbons, the restoration and cleanup of PAH-polluted areas represent a severe technological and environmental challenge for long-term growth and development. Although there are several ways to clean up PAH-contaminated soils, much attention is paid to intriguing bacteria, fungus, and their enzymes. Various factors influence PAH breakdown, including pH, temperature, airflow, moisture level, nutrient availability, and degrading microbial populations. This review discusses how PAHs affect soil characteristics and shows that secondary metabolite and carbon dioxide decomposition are produced due to microbial breakdown processes. Furthermore, the advantages of bioremediation strategies were assessed for correct evaluation and considered dependable on each legislative and scientific research level, as analyzed in this review.

Detoxification of Aflatoxin B1 by a Potential Probiotic Bacillus amyloliquefaciens WF2020

Microbial degradation is considered as an attractive method to eliminate exposure to aflatoxin B1 (AFB1), the most toxic mycotoxin that causes great economic losses and brings a serious threat to human and animal health, in food and feed. In this study, Bacillus amyloliquefaciens WF2020, isolated from naturally fermented pickles, could effectively degrade AFB1 ranging from 1 to 8 μg/ml, and the optimum temperature and pH value were 37–45°C and 8.0, respectively. Moreover, B. amyloliquefaciens WF2020 was considered to be a potential probiotic due to the synthesis of active compounds, absence of virulence genes, susceptibility to various antibiotics, and enhanced lifespan of Caenorhabditis elegans. Extracellular enzymes or proteins played a major role in AFB1 degradation mediated by B. amyloliquefaciens WF2020 into metabolites with low or no mutagenicity and toxicity to C. elegans. AFB1 degradation by the cell-free supernatant was stable up to 70°C, with an optimal pH of 8.0, and the cell-free supernatant could still degrade AFB1 by 37.16% after boiling for 20 min. Furthermore, B. amyloliquefaciens WF2020 caused a slight defect in fungal growth and completely inhibited AFB1 production when co-incubated with Aspergillus flavus. Additionally, B. amyloliquefaciens WF2020 suppressed the expression of 10 aflatoxin pathway genes and 2 transcription factors (alfR and alfS), suggesting that B. amyloliquefaciens WF2020 might inhibit AFB1 synthesis in A. flavus. These results indicate that B. amyloliquefaciens WF2020 and/or its extracellular enzymes or proteins have a promising potential to be applied in protecting food and feed from AFB1 contamination.

A thermophile Hydrogenibacillus sp. strain efficiently degrades environmental pollutants polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants threatening ecosystems and human health. Here, we isolated and characterized a new strain, Hydrogenibacillus sp. N12, which is a thermophilic PAH-degrader. Strain N12 utilizes naphthalene as a sole carbon and energy source above 60°C and co-metabolizes many other PAHs as well. The metabolites were identified in the catabolism of naphthalene by gas chromatography-mass spectrometry (GC-MS) and stable isotopic analysis. Based on the identified metabolites, we proposed two possible metabolic pathways, one via salicylic acid and the other via phthalic acid. Whole-genome sequencing reveals that strain N12 possesses a small chromosome of 2.6 Mb. Combining genetic and transcriptional information, we reveal a new gene cluster for the naphthalene degradation. The genes, designated as narAaAb that are predicted to encode the alpha and beta subunits of naphthalene dioxygenase, were subsequently subcloned into Escherichia coli and the enzyme activity was detected by whole-cell transformation. Capacity to degrade several other tricyclic-PAHs was also characterized, suggesting co-existence of other constitutively expressed enzyme systems in strain N12 in addition to the naphthalene degradation gene cluster. Our study provides insights into the potential of the thermophilic PAH-degrader in biotechnology and environmental management applications.

Enhanced Sinks of Polycyclic Aromatic Hydrocarbons Due to Kuroshio Intrusion: Implications on Biogeochemical Processes in the Ocean-Dominated Marginal Seas

The biogeochemical processes of polycyclic aromatic hydrocarbons (PAHs) in the South China Sea (SCS) are influenced by the exchanges of water masses, energies, and materials between this marginal sea and the Pacific Ocean. To investigate the impact of oceanic water intrusion on semivolatile compounds, we collected seawater samples in the Western Pacific, northern, and central SCS in 2017 and analyzed for dissolved PAHs. PAH concentrations in the water columns of the Pacific Ocean and SCS were 1.7-11 and 1.1-7.3 ng L^-1, respectively, showing spatial distinctions in terms of the composition and source characteristics. A common depletion for three-ring PAHs was found in the northern SCS by comparing the modeling results of conservative mixing by Kuroshio intrusion. Kuroshio water increased the levels of temperature, dissolved oxygen, and nutrients when intruding into the northern SCS and was likely to enhance the bioavailability of PAHs and stimulate their biodegradation process. In the water column, the most effective layer under the Kuroshio intrusion impact is different for three- and four-ring PAHs, where the three-ring PAHs' depletion was most significant at the surface; however, for four-ring PAHs, that was at the deep chlorophyll maximum layer. This study highlighted the effect of ocean currents on PAHs for their water-column processes both from physical and biogeochemical perspectives.

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.

Microbial Degradation of Zearalenone by a Novel Microbial Consortium, NZDC-6, and Its Application on Contaminated Corncob by Semisolid Fermentation

A novel microbial consortium (NZDC-6) was screened and characterized to detoxify the estrogenic mycotoxin zearalenone (ZEA), which commonly contaminates maize and is a major threat to food and health security. We found NZDC-6 to be thermophilic and highly effective, with a 90.3% ZEA degradation ratio at an optimum temperature of 60 °C. NZDC-6 was also effective at degrading the more estrogenic ZEA cognates, α-zearalenol (α-ZAL) and β-zearalenol (β-ZAL), with >90% degradation ratios. To evaluate a practical application, ZEA-contaminated corncobs were treated with NZDC-6 via semisolid fermentation. Measurements of physicochemical parameters and 16S microbial diversity and redundancy analysis (RDA) indicated that ZEA removal was most efficient at a low corncob solid content (< 5%), as a high solid content overwhelmed the microbial metabolic load, leading to increased dissolved oxygen and lowered pH. Our results demonstrate that the control of environmental variables is crucial for effective ZEA microbial removal in practical applications.

Polycyclic Aromatic Hydrocarbons: A Critical Review of Environmental Occurrence and Bioremediation

The degree of polycyclic aromatic hydrocarbon contamination of environmental matrices has increased over the last several years due to increase in industrial activities. Interest has surrounded the occurrence and distribution of polycyclic aromatic hydrocarbons for many decades because they pose a serious threat to the health of humans and ecosystems. The importance of the need for sustainable abatement strategies to alleviate contamination therefore cannot be overemphasised, as daily human activities continue to create pollution from polycyclic aromatic hydrocarbons and impact the natural environment. Globally, attempts have been made to design treatment schemes for the remediation and restoration of contaminated sites. Several techniques and technologies have been proposed and tested over time, the majority of which have significant limitations. This has necessitated research into environmentally friendly and cost-effective clean-up techniques. Bioremediation is an appealing option that has been extensively researched and adopted as it has been proven to be relatively cost-effective, environmentally friendly and is publicly accepted. In this review, the physicochemical properties of some priority polycyclic aromatic hydrocarbons, as well as the pathways and mechanisms through which they enter the soil, river systems, drinking water, groundwater and food are succinctly examined. Their effects on human health, other living organisms, the aquatic ecosystem, as well as soil microbiota are also elucidated. The persistence and bioavailability of polycyclic aromatic hydrocarbons are discussed as well, as they are important factors that influence the rate, efficiency and overall success of remediation. Bioremediation (aerobic and anaerobic), use of biosurfactants and bioreactors, as well as the roles of biofilms in the biological treatment of polycyclic aromatic hydrocarbons are also explored.

Benzo(a)pyrene degradation and microbial community responses in composted soil

Benzo(a)pyrene degradation was compared in soil that was either composted, incubated at a constant temperature of 22 °C, or incubated under a temperature regime typical of a composting process. After 84 days, significantly more (61%) benzo(a)pyrene was removed from composted soil compared to soils incubated at a constant temperature (29%) or at composting temperatures (46%). Molecular fingerprinting approaches indicated that in composted soils, bacterial community changes were driven by both temperature and organic amendment, while fungal community changes were primarily driven by temperature. Next-generation sequencing data revealed that the bacterial community in composted soil was dominated by Actinobacteria (order Actinomycetales), Firmicutes (class Bacilli), and Proteobacteria (classes Gammaproteobacteria and Alphaproteobacteria), regardless of whether benzo(a)pyrene was present or not. The relative abundance of unclassified Actinomycetales (Actinobacteria) was significantly higher in composted soil when degradation was occurring, indicating a potential role for these organisms in benzo(a)pyrene metabolism. This study provides baseline data for employing straw-based composting strategies for the removal of high molecular weight PAHs from soil and contributes to the knowledge of how microbial communities respond to incubation conditions and pollutant degradation.

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.

Extracellular Polyhydroxyalkanoate Depolymerase by Acidovorax sp. DP5

Bacteria capable of degrading polyhydroxyalkanoates (PHA) by secreting extracellular depolymerase enzymes were isolated from water and soil samples collected from various environments in Malaysia. A total of 8 potential degraders exhibited clear zones on poly(3-hydroxybutyrate) [P(3HB)] based agar, indicating the presence of extracellular PHA depolymerase. Among the isolates, DP5 exhibited the largest clearing zone with a degradation index of 6.0. The highest degradation activity of P(3HB) was also observed with depolymerase enzyme of DP5 in mineral salt medium containing P(3HB). Based on biochemical characterization and 16S rRNA cloning and sequencing, isolate DP5 was found to belong to the genus Acidovorax and subsequently named as Acidovorax sp. DP5. The highest extracellular depolymerase enzyme activity was achieved when 0.25% (w/v) of P(3HB) and 1 g/L of urea were used as carbon and nitrogen source, respectively, in the culture media. The most suitable assay condition of the depolymerase enzyme in response to pH and temperature was tested. The depolymerase produced by strain Acidovorax sp. DP5 showed high percentage of degradation with P(3HB) films in an alkaline condition with pH 9 and at a temperature of 40°C.

Biodegradation of Toluene Under Seasonal and Diurnal Fluctuations of Soil-Water Temperature

An increasing interest in bioremediation of hydrocarbon polluted sites raises the question of the influence of seasonal and diurnal changes on soil-water temperature on biodegradation of BTEX, a widespread group of (sub)-surface contaminants. Therefore, we investigated the impact of a wide range of varying soil-water temperature on biodegradation of toluene under aerobic conditions. To see the seasonal impact of temperature, three sets of batch experiments were conducted at three different constant temperatures: 10°C, 21°C, and 30°C. These conditions were considered to represent (1) winter, (2) spring and/or autumn, and (3) summer seasons, respectively, at many polluted sites. Three additional sets of batch experiments were performed under fluctuating soil-water temperature cases (21<>10°C, 30<>21°C, and 10<>30°C) to mimic the day-night temperature patterns expected during the year. The batches were put at two different temperatures alternatively to represent the day (high-temperature) and night (low-temperature) times. The results of constant- and fluctuating-temperature experiments show that toluene degradation is strongly dependent on soil-water temperature level. An almost two-fold increase in toluene degradation time was observed for every 10°C decrease in temperature for constant-temperature cases. Under fluctuating-temperature conditions, toluene degraders were able to overcome the temperature stress and continued thriving during all considered weather scenarios. However, a slightly longer time was taken compared to the corresponding time at daily mean temperature conditions. The findings of this study are directly useful for bioremediation of hydrocarbon-polluted sites having significant diurnal and seasonal variations of soil-water temperature.

An Overview of Biodegradation of LNAPLs in Coastal (Semi)-arid Environment

Contamination of soil and water due to the release of light non-aqueous phase liquids (LNAPLs) is a ubiquitous problem. The problem is more severe in arid and semi-arid coastal regions where most of the petroleum production and related refinery industries are located. Biological treatment of these organic contaminated resources is receiving increasing interests and where applicable, can serve as a cost-effective remediation alternative. The success of bioremediation greatly depends on the prevailing environmental variables, and their remediation favoring customization requires a sound understanding of their integrated behavior on fate and transport of LNAPLs under site-specific conditions. The arid and semi-arid coastal sites are characterized by specific environmental extremes; primarily, varying low and high temperatures, high salinity, water table dynamics, and fluctuating soil moisture content. An understanding of the behavior of these environmental variables on biological interactions with LNAPLs would be helpful in customizing the bioremediation for restoring problematic sites in these regions. Therefore, this paper reviews the microbial degradation of LNAPLs in soil-water, considering the influences of prevailing environmental parameters of arid and semi-arid coastal regions. First, the mechanism of biodegradation of LNAPLs is discussed briefly, followed by a summary of popular kinetic models used by researchers for describing the degradation rate of these hydrocarbons. Next, the impact of soil moisture content, water table dynamics, and soil-water temperature on the fate and transport of LNAPLs are discussed, including an overview of the studies conducted so far. Finally, based on the reviewed information, a general conclusion is presented with recommendations for future research subjects on optimizing the bioremediation technique in the field under the aforesaid environmental conditions. The present review will be useful to better understand the feasibility of bioremediation technology, in general, and its applicability for remediating LNAPLs polluted lands under aforesaid environments, in particular.

Characterization of a moderate thermophilic Nocardia species able to grow on polycyclic aromatic hydrocarbons

AIMS

Our goal was the characterization of a new moderate thermophilic polycyclic aromatic hydrocarbon (PAH)-utilizing Nocardia strain.

METHODS AND RESULTS

A thermophilic bacterium, strain TSH1, was isolated from a contaminated soil. The macroscopic and microscopic features fit well with the description of Nocardia species. The results of 16S rRNA gene analysis showed 100% match to the type strain of N. otitidiscaviarum DSM 43242(T). Strain TSH1 showed the same mycolic acid pattern as the type strain of N. otitidiscaviarum but its fatty acid profile did not permit identification to the species level. The carbon utilization profile of strain TSH1 was different from N. otitidiscaviarum. The results of hydrophobicity measurements showed that PAHs-grown cells were significantly more hydrophobic than LB-grown cells. Furthermore, biosurfactant production was detected during bacterial growth on different culture media.

CONCLUSIONS

Strain TSH1 is capable of growing on a range of PAHs. When grown in PAHs-supplemented media, strain TSH1 showed a high affinity for the organic phase, suggesting that it can develop a hydrophobic surface.

SIGNIFICANCE AND IMPACT OF THE STUDY

High cell surface hydrophobicity and capability of strain TSH1 to degrade different PAHs at 50 degrees C may make it an ideal candidate to treat PAH-contaminated desert soils.

Bacterial diversity of a cyanobacterial mat degrading petroleum compounds at elevated salinities and temperatures

Cyanobacterial mats of the Arabian Gulf coast of Saudi Arabia experience extreme conditions of temperature and salinity. Because they are exposed to continuous oil pollution, they form ideal models for biodegradation under extreme conditions. We investigated the bacterial diversity of these mats using denaturing gradient gel electrophoresis and 16S rRNA cloning, and tested their potential to degrade petroleum compounds at various salinities (fresh water to 16%) and temperatures (5 to 50 degrees C). Cloning revealed that c. 15% of the obtained sequences were related to unknown, possibly novel bacteria. Bacteria belonging to Beta-, Gamma- and Deltaproteobacteria, Cytophaga-Flavobacterium-Bacteroides group and Spirochetes, were detected. The biodegradation of petroleum compounds at different salinities by mat microorganisms showed that pristine and n-octadecane were optimally degraded at salinities between 5 and 12% (weight per volume NaCl) whereas the optimum degradation of phenanthrene and dibenzothiophene was at 3.5% salinity. The latter compounds were also degradable at 8% salinity. The same compounds were degraded at temperatures between 15 and 40 degrees C but not at 5 and 50 degrees C. The optimum temperature of degradation was 28-40 degrees C for both aliphatics and aromatics. We conclude that the studied microbial mats from Saudi Arabia are rich in novel halotolerant and thermotolerant microorganisms with the potential to degrade petroleum compounds at elevated salinities and temperatures.

A novel heat-stable lipolytic enzyme from Sulfolobus acidocaldarius DSM 639 displaying similarity to polyhydroxyalkanoate depolymerases

A fragment of genomic DNA from Sulfolobus acidocaldarius DSM 639 encoding a lipolytic enzyme was cloned and sequenced. The 314-amino acid polypeptide displays a maximum sequence similarity (43%) to a putative polyhydroxyalkanoate depolymerase from Pseudomonas oleovorans and contains the pentapeptide G-X1-S-X2-G which is typical of serine hydrolases. The protein is highly thermostable and is able to hydrolyse a variety of lipid substrates thus providing a promising tool for potential biotechnological applications.