Isolation and characterization of a novel oxygenase that catalyzes the first step of n-alkane oxidation in Acinetobacter sp. strain M-1

Metagenomic analyses of a consortium for the bioremediation of hydrocarbons polluted soils

A bacterial consortium was isolated from a soil in Noblejas (Toledo, Spain) with a long history of mixed hydrocarbons pollution, by enrichment cultivation. Serial cultures of hydrocarbons polluted soil samples were grown in a minimal medium using diesel (1 mL/L) as the sole carbon and energy source. The bacterial composition of the Noblejas Consortium (NC) was determined by sequencing 16S rRNA gene amplicon libraries. The consortium contained around 50 amplicon sequence variants (ASVs) and the major populations belonged to the genera Pseudomonas, Enterobacter, Delftia, Stenotrophomonas, Achromobacter, Acinetobacter, Novosphingobium, Allorhizobium-Neorhizobium-Rhizobium, Ochrobactrum and Luteibacter. All other genera were below 1%. Metagenomic analysis of NC has shown a high abundance of genes encoding enzymes implicated in aliphatic and (poly) aromatic hydrocarbons degradation, and almost all pathways for hydrocarbon degradation are represented. Metagenomic analysis has also allowed the construction of metagenome assembled genomes (MAGs) for the major players of NC. Metatranscriptomic analysis has shown that several of the ASVs are implicated in hydrocarbon degradation, being Pseudomonas, Acinetobacter and Delftia the most active populations.

Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean

Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome-assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon-degrading microbes with clade-specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all Cycloclasticus. Furthermore, all Bermanella encoded and expressed genes for non-gaseous n-alkane degradation; however, DWH Bermanella encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume member in the SAR324 and UBA11654 have the capacity for aromatic hydrocarbon degradation. In contrast, Colwellia were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provides missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment.IMPORTANCEMicrobial degradation of hydrocarbons is a critically important process promoting ecosystem health, yet much of what is known about this process is based on physiological experiments with a few hydrocarbon substrates and cultured microbes. Thus, the ability to degrade the diversity of hydrocarbons that comprise oil and gas by microbes in the environment, particularly in the ocean, is not well characterized. Therefore, this study aimed to utilize non-cultivation-based 'omics data to explore novel genomes of uncultured marine microbes involved in degradation of oil and gas. Analyses of newly assembled metagenomic data and previously existing genomes from other marine data sets, with metagenomic and metatranscriptomic read recruitment, revealed globally distributed hydrocarbon-degrading marine microbes with clade-specific substrate degradation potentials that have not been previously reported. This new understanding of oil and gas degradation by uncultured marine microbes suggested that the global ocean harbors a diversity of hydrocarbon-degrading bacteria, which can act as primary agents regulating ecosystem health.

Variations in cuticular hydrocarbons of Calliphora vicina (Diptera: Calliphoridae) empty puparia: Insights for estimating late postmortem intervals

Necrophagous flies, particularly blowflies, serve as vital indicators in forensic entomology and ecological studies, contributing to minimum postmortem interval estimations and environmental monitoring. The study investigates variations in the predominant cuticular hydrocarbons (CHCs) viz. n-C25, n-C27, n-C28, and n-C29 of empty puparia of Calliphora vicina Robineau-Desvoidy, 1830, (Diptera: Calliphoridae) across diverse environmental conditions, including burial, above-ground and indoor settings, over 90 days. Notable trends include a significant decrease in n-C25 concentrations in buried and above-ground conditions over time, while n-C27 concentrations decline in buried and above-ground conditions but remain stable indoors. Burial conditions show significant declines in n-C27 and n-C29 concentrations over time, indicating environmental influences. Conversely, above-ground conditions exhibit uniform declines in all hydrocarbons. Indoor conditions remain relatively stable, with weak correlations between weathering time and CHC concentrations. Additionally, machine learning techniques, specifically Extreme Gradient Boosting (XGBoost), are employed for age estimation of empty puparia, yielding accurate predictions across different outdoor and indoor conditions. These findings highlight the subtle responses of CHC profiles to environmental stimuli, underscoring the importance of considering environmental factors in forensic entomology and ecological research. The study advances the understanding of insect remnant degradation processes and their forensic implications. Furthermore, integrating machine learning with entomological expertise offers standardized methodologies for age determination, enhancing the reliability of entomological evidence in legal contexts and paving the way for future research and development.

Deciphering the impact of microenvironmental factors on cuticular hydrocarbon degradation in Lucilia sericata empty Puparia: Bridging ecological and forensic entomological perspectives using machine learning models

Blow flies (Calliphoridae) play essential ecological roles in nutrient recycling by consuming decaying organic matter. They serve as valuable bioindicators in ecosystem management and forensic entomology, with their unique feeding behavior leading to the accumulation of environmental pollutants in their cuticular hydrocarbons (CHCs), making them potential indicators of exposure history. This study focuses on CHC degradation dynamics in empty puparia of Lucilia sericata under different environmental conditions for up to 90 days. The three distinct conditions were considered: outdoor-buried, outdoor-above-ground, and indoor environments. Five predominant CHCs, n-Pentacosane (n-C25), n-Hexacosane (n-C26), n-Heptacosane (n-C27), n-Octacosane (n-C28), and n-Nonacosane (n-C29), were analyzed using Gas Chromatography-Mass Spectrometry (GC-MS). The findings revealed variations in CHC concentrations over time, influenced by environmental factors, with significant differences at different time points. Correlation heatmap analysis indicated negative correlations between weathering time and certain CHCs, suggesting decreasing concentrations over time. Machine learning techniques Support Vector Machine (SVM), Multilayer Perceptron (MLP), and eXtreme Gradient Boosting (XGBoost) models explored the potential of CHCs as age indicators. SVM achieved an R-squared value of 0.991, demonstrating high accuracy in age estimation based on CHC concentrations. MLP also exhibited satisfactory performance in outdoor conditions, while SVM and MLP yielded unsatisfactory results indoors due to the lack of significant CHC variations. After comprehensive model selection and performance evaluations, it was found that the XGBoost model excelled in capturing the patterns in all three datasets. This study bridges the gap between baseline and ecological/forensic use of empty puparia, offering valuable insights into the potential of CHCs in environmental monitoring and investigations. Understanding CHCs' stability and degradation enhances blow flies' utility as bioindicators for pollutants and exposure history, benefiting environmental monitoring and forensic entomology.

Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments

Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.

Main Factors Determining the Scale-Up Effectiveness of Mycoremediation for the Decontamination of Aliphatic Hydrocarbons in Soil

Soil contamination constitutes a significant threat to the health of soil ecosystems in terms of complexity, toxicity, and recalcitrance. Among all contaminants, aliphatic petroleum hydrocarbons (APH) are of particular concern due to their abundance and persistence in the environment and the need of remediation technologies to ensure their removal in an environmentally, socially, and economically sustainable way. Soil remediation technologies presently available on the market to tackle soil contamination by petroleum hydrocarbons (PH) include landfilling, physical treatments (e.g., thermal desorption), chemical treatments (e.g., oxidation), and conventional bioremediation. The first two solutions are costly and energy-intensive approaches. Conversely, bioremediation of on-site excavated soil arranged in biopiles is a more sustainable procedure. Biopiles are engineered heaps able to stimulate microbial activity and enhance biodegradation, thus ensuring the removal of organic pollutants. This soil remediation technology is currently the most environmentally friendly solution available on the market, as it is less energy-intensive and has no detrimental impact on biological soil functions. However, its major limitation is its low removal efficiency, especially for long-chain hydrocarbons (LCH), compared to thermal desorption. Nevertheless, the use of fungi for remediation of environmental contaminants retains the benefits of bioremediation treatments, including low economic, social, and environmental costs, while attaining removal efficiencies similar to thermal desorption. Mycoremediation is a widely studied technology at lab scale, but there are few experiences at pilot scale. Several factors may reduce the overall efficiency of on-site mycoremediation biopiles (mycopiles), and the efficiency detected in the bench scale. These factors include the bioavailability of hydrocarbons, the selection of fungal species and bulking agents and their application rate, the interaction between the inoculated fungi and the indigenous microbiota, soil properties and nutrients, and other environmental factors (e.g., humidity, oxygen, and temperature). The identification of these factors at an early stage of biotreatability experiments would allow the application of this on-site technology to be refined and fine-tuned. This review brings together all mycoremediation work applied to aliphatic petroleum hydrocarbons (APH) and identifies the key factors in making mycoremediation effective. It also includes technological advances that reduce the effect of these factors, such as the structure of mycopiles, the application of surfactants, and the control of environmental factors.

Bioengineering for the Microbial Degradation of Petroleum Hydrocarbon Contaminants

Petroleum hydrocarbons are relatively recalcitrant compounds, and as contaminants, they are one of the most serious environmental problems. n-Alkanes are important constituents of petroleum hydrocarbons. Advances in synthetic biology and metabolic engineering strategies have made n-alkane biodegradation more designable and maneuverable for solving environmental pollution problems. In the microbial degradation of n-alkanes, more and more degradation pathways, related genes, microbes, and alkane hydroxylases have been discovered, which provide a theoretical basis for the further construction of degrading strains and microbial communities. In this review, the current advances in the microbial degradation of n-alkanes under aerobic condition are summarized in four aspects, including the biodegradation pathways and related genes, alkane hydroxylases, engineered microbial chassis, and microbial community. Especially, the microbial communities of “Alkane-degrader and Alkane-degrader” and “Alkane-degrader and Helper” provide new ideas for the degradation of petroleum hydrocarbons. Surfactant producers and nitrogen providers as a “Helper” are discussed in depth. This review will be helpful to further achieve bioremediation of oil-polluted environments rapidly.

Bio-photoelectrochemical degradation, and photocatalysis process by the fabrication of copper oxide/zinc cadmium sulfide heterojunction nanocomposites: Mechanism, microbial community and antifungal analysis

In this work, the fabrication of the CuO on ZnCdS as a heterojunction nanocomposites were conducted by hydrothermal method and the synthesis method was confirmed by the XRD, XPS, EDS, UV-vis spectrum analysis. The CuO/ZnCdS was used as a photocathode in the bio-photoelectrochemical system (BPES) for tetracycline (TC) degradation under solar irradiation. The CuO/ZnCdS photocathode indicated substantial photocatalytic efficiency for TC degradation, due to the fast separation and transfer of photogenerated carriers. The ESR test evaluates the mechanism of degradation, and shows that ·OH, and ·O₂^- were contributed to TC degradation. The TC degradation was 1.59 times higher than the unilluminated process (98.72% vs 61.71). The photocatalysis test shows that the TC was degraded about 90.5% in 1.5 h. Then, the synthesized CuO/ZnCdS nanocomposites were studied for the biological application such as antifungal activities. CuO/ZnCdS nanocomposites depicted substantial antimicrobial activity versus Candida-albicans by in vitro process. Therefore, this study suggests the novel system for the antibiotics degradation, and as antifungal application.

A review on biosurfactant producing bacteria for remediation of petroleum contaminated soils

The discharge of potentially toxic petroleum hydrocarbons into the environment has been a matter of concern, as these organic pollutants accumulate in many ecosystems due to their hydrophobicity and low bioavailability. Petroleum hydrocarbons are neurotoxic and carcinogenic organic pollutants, extremely harmful to human and environmental health. Traditional treatment methods for removing hydrocarbons from polluted areas, including various mechanical and chemical strategies, are ineffective and costly. However, many indigenous microorganisms in soil and water can utilise hydrocarbon compounds as sources of carbon and energy and hence, can be employed to degrade hydrocarbon contaminants. Therefore, bioremediation using bacteria that degrade petroleum hydrocarbons is commonly viewed as an environmentally acceptable and effective method. The efficacy of bioremediation can be boosted further by using potential biosurfactant-producing microorganisms, as biosurfactants reduce surface tension, promote emulsification and micelle formation, making hydrocarbons bio-available for microbial breakdown. Further, introducing nanoparticles can improve the solubility of hydrophobic hydrocarbons as well as microbial synthesis of biosurfactants, hence establishing a favourable environment for microbial breakdown of these chemicals. The review provides insights into the role of microbes in the bioremediation of soils contaminated with petroleum hydrocarbons and emphasises the significance of biosurfactants and potential biosurfactant-producing bacteria. The review partly focusses on how nanotechnology is being employed in different critical bioremediation processes.

Bioremediation of Soil from Petroleum Contamination

Petroleum is the most common global fossil fuel. It is a complex multi-component system mainly composed of various hydrocarbons such as alkanes, cycloalkanes, mono-, bi- and polyaromatic compounds, resins and asphaltenes. In spite of humanity’s need for petroleum, it negatively affects the environment due to its toxicity. The ecological problem is especially serious at petroleum mining sites or during petroleum transportation. Since it is not possible to replace petroleum with less toxic fuel, ways to reduce the toxic impact of petroleum hydrocarbons on the environment need to be developed. This review addresses bioremediation, a biological approach to petroleum degradation, which is mainly performed by microbes. The pathways of degradation of alkanes, alkenes and aromatic hydrocarbons are presented in detail. The effects of temperature, aeration and the presence of biogenic elements on microbial degradation of petroleum are discussed. Plant–microbe interactions involved with the bioremediation of petroleum-polluted soils are specifically addressed. The data presented in this review point to the great potential of bioremediation practices for cleaning soils of petroleum.

Bacterial Utilisation of Aliphatic Organics: Is the Dwarf Planet Ceres Habitable?

The regolith environment and associated organic material on Ceres is analogous to environments that existed on Earth 3-4 billion years ago. This has implications not only for abiogenesis and the theory of transpermia, but it provides context for developing a framework to contrast the limits of Earth's biosphere with extraterrestrial environments of interest. In this study, substrate utilisation by the ice-associated bacterium Colwellia hornerae was examined with respect to three aliphatic organic hydrocarbons that may be present on Ceres: dodecane, isobutyronitrile, and dioctyl-sulphide. Following inoculation into a phyllosilicate regolith spiked with a hydrocarbon (1% or 20% organic concentration wt%), cell density, electron transport activity, oxygen consumption, and the production of ATP, NADPH, and protein in C. hornerae was monitored for a period of 32 days. Microbial growth kinetics were correlated with changes in bioavailable carbon, nitrogen, and sulphur. We provide compelling evidence that C. hornerae can survive and grow by utilising isobutyronitrile and, in particular, dodecane. Cellular growth, electron transport activity, and oxygen consumption increased significantly in dodecane at 20 wt% compared to only minor growth at 1 wt%. Importantly, the reduction in total carbon, nitrogen, and sulphur observed at 20 wt% is attributed to biotic, rather than abiotic, processes. This study illustrates that short-term bacterial incubation studies using exotic substrates provide a useful indicator of habitability. We suggest that replicating the regolith environment of Ceres warrants further study and that this dwarf planet could be a valid target for future exploratory missions.

Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives

Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.

Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review

Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature's own hydrocarbon sensors, and once functionally characterised, these components can be used to create rapid, inexpensive and sensitive biosensors for use in applications such as bioremediation and metabolic engineering. Many bacterial monooxygenases have been identified, yet the regulation of only a few of these have been investigated in detail. A wealth of genetic and functional diversity of regulatory enzymes and promoter elements still remains unexplored and unexploited, both in published genome sequences and in yet-to-be-cultured bacteria. In this review we examine in detail the current state of research on monooxygenase gene regulation, and on the development of transcription-factor-based microbial biosensors for detection of alkanes and alkenes. A new framework for the systematic characterisation of the underlying genetic components and for further development of biosensors is presented, and we identify focus areas that should be targeted to enable progression of more biosensor candidates to commercialisation and deployment in industry and in the environment.

Exploring the diversity and hydrocarbon bioremediation potential of microbial community in the waste sludge of Duliajan oil field, Assam, India

Microbial community analysis of crude oil containing sludge collected from Duliajan oil field, Assam, India, showed the predominance of hydrocarbon-degrading bacteria such as Pseudomonas (20.1%), Pseudoxanthomonas (15.8%), Brevundimonas (1.6%), and Bacillus (0.8%) alongwith anaerobic, fermentative, nitrogen-fixing, nitrate-, sulfate-, and metal-reducing, syntrophic bacteria, and methanogenic archaea. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated gene collection for potential hydrocarbon degradation, lipid, nitrogen, sulfur, and methane metabolism. The culturable microbial community was predominated by Pseudomonas and Bacillus with the metabolic potential for utilizing diverse hydrocarbons, crude oil, and actual petroleum sludge as sole carbon source during growth and tolerating various environmental stresses prevailing in such contaminated sites. More than 90% of the isolated strains could produce biosurfactant and exhibit catechol 2,3-dioxygenase activity. Nearly 30% of the isolates showed alkane hydroxylase activity with the maximum specific activity of 0.54 μmol min^-1 mg^-1. The study provided better insights into the microbial diversity and functional potential within the crude oil containing sludge which could be exploited for in situ bioremediation of contaminated sites.

Current Advances in the Bacterial Toolbox for the Biotechnological Production of Monoterpene-Based Aroma Compounds

Monoterpenes are plant secondary metabolites, widely used in industrial processes as precursors of important aroma compounds, such as vanillin and (-)-menthol. However, the physicochemical properties of monoterpenes make difficult their conventional conversion into value-added aromas. Biocatalysis, either by using whole cells or enzymes, may overcome such drawbacks in terms of purity of the final product, ecological and economic constraints of the current catalysis processes or extraction from plant material. In particular, the ability of oxidative enzymes (e.g., oxygenases) to modify the monoterpene backbone, with high regio- and stereo-selectivity, is attractive for the production of "natural" aromas for the flavor and fragrances industries. We review the research efforts carried out in the molecular analysis of bacterial monoterpene catabolic pathways and biochemical characterization of the respective key oxidative enzymes, with particular focus on the most relevant precursors, β-pinene, limonene and β-myrcene. The presented overview of the current state of art demonstrates that the specialized enzymatic repertoires of monoterpene-catabolizing bacteria are expanding the toolbox towards the tailored and sustainable biotechnological production of values-added aroma compounds (e.g., isonovalal, α-terpineol, and carvone isomers) whose implementation must be supported by the current advances in systems biology and metabolic engineering approaches.

The tale of a versatile enzyme: Alpha-amylase evolution, structure, and potential biotechnological applications for the bioremediation of n-alkanes

As the primary source of a wide range of industrial products, the study of petroleum-derived compounds is of pivotal importance. However, the process of oil extraction and refinement is among the most environmentally hazardous practices, impacting almost all levels of the ecological chain. So far, the most appropriate strategy to overcome such an issue is through bioremediation, which revolves around the employment of different microorganisms to degrade hazardous compounds, generating less environmental impact and lower monetary costs. In this sense, a myriad of organisms and enzymes are considered possible candidates for the bioremediation process. Amidst the potential candidates is α-amylase, an evolutionary conserved starch-degrading enzyme. Notably, α-amylase was not only seen to degrade n-alkanes, a subclass of alkanes considered the most abundant petroleum-derived compounds but also low-density polyethylene, a dangerous pollutant produced from petroleum. Thus, due to its high conservation in both eukaryotic and prokaryotic lineages, in addition to the capability to degrade different types of hazardous compounds, the study of α-amylase becomes a rising interest. Nevertheless, there are no studies that review all biotechnological applications of α-amylase for bioremediation. In this work, we critically review the potential biotechnological applications of α-amylase, focusing on the biodegradation of petroleum-derived compounds. Evolutionary aspects are discussed, as well for all structural information and all features that could impact on the employment of this protein in the biotechnological industry, such as pH, temperature, and medium conditions. New perspectives and critical assessments are conducted regarding the application of α-amylase in the bioremediation of n-alkanes.

A novel membrane-aerated biofilter for the enhanced treatment of nitroaniline wastewater: Nitroaniline biodegradation performance and its influencing factors

Nitroaniline (NA) wastewater is known to be highly toxic and biodegradation-resistant. Based on the principles of molecular oxygen supply and biofilm formation, a novel membrane-aerated biofilter (MABF) combining membrane aeration with a biofilter was established for the first time to treat NA wastewater containing the same concentrations of p-nitroaniline (PNA) and o-nitroaniline (ONA). The NA wastewater treatment performance of the MABF was investigated, and the NA biodegradation characteristics were evaluated. When the influent NA concentration was 120 mg/L, the PNA and ONA removal rates reached 100% and 86.56%, respectively. The NA removal loading reached 111.62 g/m³·d, and the total nitrogen (TN) removal rate reached 82.97%. The synergistic effects of the diverse microorganisms in the membrane-aerated and nonaerated zones of the MABF enhanced the removal of NA and nitrogen. This MABF is an economically efficient and environmentally friendly technology for treating wastewater containing toxic and hazardous organic compounds.

A Rotational Slurry Bioreactor Accelerates Biodegradation of A-Fuel in Oil-Contaminated Soil Even under Low Temperature Conditions

An effective bioaugmentation system for oil-contaminated soil under low-temperature conditions was developed with a rotational slurry bioreactor. Mixtures of two Rhodococcus oil-degraders, strain A and C, which are officially permitted to be used in bioaugmentation in Japan, were inoculated and A-fuel oil was added to a final concentration of 2500 and 5000 mg/kg-slurry. Decomposition tests were carried out for the inoculated samples and non-inoculated samples by rotating at 15 °C, the annual average temperature of Japan. The residue of A-fuel oil and the number of bacteria were measured every two days. After 6 days of treatment, more than 95% of the oil was removed in the inoculated samples, which was more than three times faster than a previous degradation experiment without rotation. A semi-continuous treatment was performed by removing 90% of the treated slurry, then adding the same amount of contaminated slurry into the system without additional degraders. Ninety-four percent of A-fuel oil was successfully degraded after 6 days by this repeated treatment. This could drastically reduce the cost of preparing the degraders. Strikingly, semi-continuous treatment showed oil removal in the non-inoculated samples, indicating that the rotational slurry conditions could efficiently promote biodegradation by indigenous degraders. Our rotational slurry bioreactor accelerated the removal of oil contamination without adding further degraders provides an efficient and cost-effective method of removal of A-fuel oil using a semi-continuous system, which can be used in practical applications in areas with a cooler climate.

Tolerance of Fucus vesiculosus exposed to diesel water-accommodated fraction (WAF) and degradation of hydrocarbons by the associated bacteria

The viability and physiological state of brown macroalgae Fucus vesiculosus and its associated epiphytic bacteria exposed to diesel water-accommodated fraction (WAF), as well as the capacity of this association to deplete petroleum hydrocarbons (HCs) were experimentally tested. After a 6-day exposure treatment, the algal-surface associated bacteria were identified as primarily hydrocarbon-oxidising bacteria (HOB), and the algal-HOB association was able to deplete petroleum hydrocarbons from the diesel WAF by 80%. The HOB density on the algal surface exposed to diesel WAF was 350% higher compared to the control (i.e. HOB density on the algal surface exposed to ambient seawater), which suggest that they actively proliferated in the presence of hydrocarbons and most likely consumed hydrocarbons as their primary organic substrate. Exposure to diesel WAF did not affect the metabolic activity of F. vesiculosus. Higher lipid peroxidation was observed in F. vesiculosus exposed to diesel WAF while catalase concentration decreased only during the first day of exposure. Results suggest F. vesiculosus is tolerant to oil pollution and the algal-HOB association can efficiently deplete petroleum hydrocarbons in oil-contaminated seas.

Characterization and Transcriptional Regulation of n-Alkane Hydroxylase Gene Cluster of Rhodococcus jostii RHA1

Gram-positive actinomycete Rhodococcus jostii RHA1 is able to grow on C10 to C19 n-alkanes as a sole source of carbon and energy. To clarify, the n-alkane utilization pathway-a cluster of 5 genes (alkBrubA1A2BalkU) which appeared to be involved in n-alkane degradation-was identified and the transcriptional regulation of these genes was characterized. Reverse transcription-PCR analyses revealed that these genes constituted an operon and were transcribed in the presence of n-alkane. Inactivation of alkB led to the absence of the ability to utilize n-undecane. The alkB mutation resulted in reduction of growth rates on C10 and C12 n-alkanes; however, growths on C13 to C19 n-alkanes were not affected by this mutation. These results suggested that alkB was essential for the utilization of C10 to C12 n-alkanes. Inactivation of alkU showed the constitutive expression of alkB. Purified AlkU is able to bind to the putative promoter region of alkB, suggesting that AlkU played a role in repression of the transcription of alk operon. The results of this study indicated that alkB was involved in the medium-chain n-alkanes degradation of strain RHA1 and the transcription of alk operon was negatively regulated by alkU-encoded regulator. This report is important to understand the n-alkane degradation pathway of R. jostii, including the transcriptional regulation of alk gene cluster.

Indole Degradation in a Model System and in Poultry Manure by Acinetobacter spp

Indole degradation in a model system and in poultry manure was studied using an enrichment culture of two Acinetobacter species; Acinetobacter toweneri NTA1-2A and Acinetobacter guillouiae TAT1-6A. Degradation of indole was quantified using reverse phase high performance liquid chromatography (HPLC). The two strains were capable of degrading initial concentrations of indole ranging from 58.58–300 mg/L. The degradation efficiency was 66.36% (NTA1-2A), 94.87% (TAT1-6A), and 96.00% (mix) in 6 days when the initial concentration <300 mg/L. The strains were tested for enzymatic activity using 120 mg/L indole. The enzyme extracts of NTA1-2A and TAT1-6A from culture medium degraded indole completely, and no appreciable change of indole concentration was witnessed in the control group. The NTA1-2A, TAT1-6A, and the mix of strains were also used for in vivo poultry manure fermentation and removed 78.67%, 83.28%, and 83.70% of indole, respectively in 8 d. The strains showed a statistically significant difference (p < 0.05) in indole removal efficiency compared with the control, but no significant difference between the two strains and the mix in indole removal capacity. We concluded that A. toweneri NTA1-2A and A. guillouiae TAT1-6A are promising strains to remove indole and its derivatives to control the notorious odor in poultry and other livestock industries.

Isolation and characterization of two Acinetobacter species able to degrade 3-methylindole

3-Methylindole (3MI) or Skatole is a volatile lipophilic organic compound produced by anoxic metabolism of L-tryptophan and associated with animal farming and industrial processing wastes. Pure cultures of bacteria capable of utilizing 3MI were isolated from chicken manure using enrichment culture techniques. The bacteria were identified as Acinetobacter toweneri NTA1-2A and Acinetobacter guillouiae TAT1-6A, based on 16S rDNA gene amplicon sequence data. The optimal temperature and pH for degradation of 3MI were established using single factor experiments. Strain tolerance was assessed over a range of initial concentrations of 3MI, and the effects of initial concentration on subsequent microbial 3MI degradation were also measured. During the degradation experiment, concentrations of 3MI were quantified by reverse-phase high-performance liquid chromatography (HPLC). The strains were capable of degrade initial concentrations of 3MI ranging from 65–200 mg/L. The degradation efficiency was >85% in 6 days for both strains when the initial concentration is less than 200 mg/L. The strains were tested for enzymatic activity using 65 mg/L 3MI. The enzyme extracts of NTA1-2A and TAT1-6A from the 3MI medium degraded 71.46% and 60.71% of 3MI respectively, but no appreciable change in 3MI concentration in the control group was witnessed. Our experiment revealed betaine and choline were identified as 3MI degradation metabolites by both strains while nitroso-pyrrolidine and beta-alaninebetaine formed by NTA1-2A and TAT1-6A strains respectively. The NTA1-2A and TAT1-6A strains removed 84.32% and 81.39% 3MI respectively from chicken manure during fermentation in 8 days and showed a statistically significant difference (P < 0.05) compared with the control group. The optimum temperature and pH were 31°C and 6 respectively, for 3MI degradation by A. toweneri NTA1-2A and A. guillouiae TAT1-6A. We concluded that A. toweneri NTA1-2A and A. guillouiae TAT1-6A are potential strains of interest to degrade 3MI and control odorant in poultry and other livestock industries.

Implications of co-contamination with aged heavy metals and total petroleum hydrocarbons on natural attenuation and ecotoxicity in Australian soils

The bioremediation of historic industrial contaminated sites is a complex process. Co-contamination, often with lead which was commonly added to gasoline until 16 years ago is one of the biggest challenges affecting the clean-up of these sites. In this study, the effect of heavy metals, as co-contaminant, together with total petroleum hydrocarbons (TPH) is reported, in terms of remaining soil toxicity and the structure of the microbial communities. Contaminated soil samples from a relatively hot and dry climate in Western Australia were collected (n = 27). Analysis of soils showed the presence of both contaminants, TPHs and heavy metals. The Microtox test confirmed that their co-presence elevated the remaining ecotoxicity. Toxicity was correlated with the presence of lead, zinc and TPH (0.893, 0.599 and 0.488), respectively, assessed using Pearson Correlation coefficient factor. Next Generation Sequencing of soil bacterial 16S rRNA, revealed a lack of dominate genera; however, despite the variation in soil type, a few genera including Azospirillum spp. and Conexibacter were present in most soil samples (85% and 82% of all soils, respectively). Likewise, many genera of hydrocarbon-degrading bacteria were identified in all soil samples. Streptomyces spp. was presented in 93% of the samples with abundance between 7% and 40%. In contrast, Acinetobacter spp. was found in only one sample but was a dominant member of (45%) of the microbial community. In addition, some bacterial genera were correlated to the presence of the heavy metals, such as Geodermatophilus spp., Rhodovibrio spp. and Rubrobacter spp. which were correlated with copper, lead and zinc, respectively. This study concludes that TPH and heavy metal co-contamination significantly elevated the associated toxicity. This is an important consideration when carrying out risk assessment associated with natural attenuation. This study also improves knowledge about the dynamics of microbial communities in mixed contamination scenarios.

Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility

Environmental pollution with petroleum toxic products has afflicted various ecosystems, causing devastating damage to natural habitats with serious economic implications. Some crude oil components may serve as growth substrates for microorganisms. A number of bacterial strains reveal metabolic capacities to biotransform various organic compounds. Some of the hydrocarbon degraders are highly biochemically specialized, while the others display a versatile metabolism and can utilize both saturated aliphatic and aromatic hydrocarbons. The extended catabolic profiles of the latter group have been subjected to systematic and complex studies relatively rarely thus far. Growing evidence shows that numerous bacteria produce broad biochemical activities towards different hydrocarbon types and such an enhanced metabolic potential can be found in many more species than the already well-known oil-degraders. These strains may play an important role in the removal of heterogeneous contamination. They are thus considered to be a promising solution in bioremediation applications. The main purpose of this article is to provide an overview of the current knowledge on aerobic bacteria involved in the mineralization or transformation of both n-alkanes and aromatic hydrocarbons. Variant scientific approaches enabling to evaluate these features on biochemical as well as genetic levels are presented. The distribution of multidegradative capabilities between bacterial taxa is systematically shown and the possibility of simultaneous transformation of complex hydrocarbon mixtures is discussed. Bioinformatic analysis of the currently available genetic data is employed to enable generation of phylogenetic relationships between environmental strain isolates belonging to the phyla Actinobacteria, Proteobacteria, and Firmicutes. The study proves that the co-occurrence of genes responsible for concomitant metabolic bioconversion reactions of structurally-diverse hydrocarbons is not unique among various systematic groups.

Survival and Energy Producing Strategies of Alkane Degraders Under Extreme Conditions and Their Biotechnological Potential

Many petroleum-polluted areas are considered as extreme environments because of co-occurrence of low and high temperatures, high salt, and acidic and anaerobic conditions. Alkanes, which are major constituents of crude oils, can be degraded under extreme conditions, both aerobically and anaerobically by bacteria and archaea of different phyla. Alkane degraders possess exclusive metabolic pathways and survival strategies, which involve the use of protein and RNA chaperones, compatible solutes, biosurfactants, and exopolysaccharide production for self-protection during harsh environmental conditions such as oxidative and osmotic stress, and ionic nutrient-shortage. Recent findings suggest that the thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus uses a novel alkylsuccinate synthase for long-chain alkane degradation, and the thermophilic Candidatus Syntrophoarchaeum butanivorans anaerobically oxidizes butane via alkyl-coenzyme M formation. In addition, gene expression data suggest that extremophiles produce energy via the glyoxylate shunt and the Pta-AckA pathway when grown on a diverse range of alkanes under stress conditions. Alkane degraders possess biotechnological potential for bioremediation because of their unusual characteristics. This review will provide genomic and molecular insights on alkane degraders under extreme conditions.

Anaerobic Oxidation of Ethane, Propane, and Butane by Marine Microbes: A Mini Review

The deep ocean and its sediments are a continuous source of non-methane short-chain alkanes (SCAs) including ethane, propane, and butane. Their high global warming potential, and contribution to local carbon and sulfur budgets has drawn significant scientific attention. Importantly, microbes can use gaseous alkanes and oxidize them to CO₂, thus acting as effective biofilters. A relative decrease of these gases with a concomitant ¹³C enrichment of propane and n-butane in interstitial waters vs. the source suggests microbial anaerobic oxidation. The reported uncoupling of sulfate-reduction (SR) from anaerobic methane oxidation supports their microbial consumption. To date, strain BuS5 isolated from the sediments of Guaymas Basin, Gulf of California, is the only pure culture that can anaerobically degrade propane and n-butane. This organism belongs to a metabolically diverse cluster within the Deltaproteobacteria called Desulfosarcina/Desulfococcus. Other phylotypes involved in gaseous alkane degradation were identified based on stable-isotope labeling and fluorescence in-situ hybridization. A novel syntrophic association of the archaeal genus, Candidatus Syntrophoarchaeum, and a thermophilic SR bacterium, HotSeep-1 was recently discovered from the Guaymas basin, Gulf of California that can anaerobically oxidize n-butane. Strikingly, metagenomic data and the draft genomes of ca. Syntrophoarchaeum suggest that this organism uses a novel mechanism for n-butane oxidation, distinct from the well-established fumarate addition mechanism. These recent findings indicate that a lot remains to be understood about our understanding of anaerobic SCA degradation. This mini-review summarizes our current understanding of microbial anaerobic SCA degradation, and provides an outlook for future research.

Metabolic and stress responses of Acinetobacter oleivorans DR1 during long-chain alkane degradation

Acinetobacter oleivorans DR1 can utilize C₁₂–C₃₀ alkanes as a sole carbon source but not short‐chain alkanes (C₆, C₁₀). Two copies of each alkB‐, almA‐ and ladA‐type alkane hydroxylase (AH) are present in the genome of DR1 cells. Expression and mutational analyses of AHs showed that alkB1 and alkB2 are the major AH‐encoding genes under C₁₂–C₃₀, and the roles of other almA‐ and ladA genes are negligible. Our data suggested that AlkB1 is responsible for long‐chain alkane utilization (C₂₄–C₂₆), and AlkB2 is important for medium‐chain alkane (C₁₂–C₁₆) metabolism. Phylogenetic analyses revealed large incongruities between phylogenies of 16S rRNA and each AH gene, which implies that A. oleivorans DR1 has acquired multiple alkane hydroxylases through horizontal gene transfer. Transcriptomic and qRT‐PCR analyses suggested that genes participating in the synthesis of siderophore, trehalose and poly 3‐hydroxybutyrate (PHB) were expressed at much higher levels when cells used C₃₀ than when used succinate as a carbon source. The following biochemical assays supported our gene expression analyses: (i) quantification of siderophore, (ii) measurement of trehalose and (iii) observation of PHB storage. Interestingly, highly induced both ackA gene encoding an acetate kinase A and pta gene encoding a phosphotransacetylase suggested unusual ATP synthesis during C₃₀ alkane degradation, which was demonstrated by ATP measurement using the ΔackA mutant. Impaired growth of the ΔaceA mutant indicated that the glyoxylate shunt pathway is important when C₃₀ alkane is utilized. Our data provide insight into long‐chain alkane degradation in soil microorganisms.

Phylogenomic analysis of integral diiron membrane histidine motif-containing enzymes in ciliates provides insights into their function and evolutionary relationships

The Integral Membrane Histidine Motif-containing Enzymes (IMHME) are a class of binuclear non-heme iron proteins widely distributed among prokaryotes and eukaryotes. They are characterized by a conserved tripartite motif consisting of eight to ten histidine residues. Their known function is the activation of the dioxygen moiety to serve as efficient catalysts for reactions of hydroxylation, desaturation or reduction. To date most studies on IMHME were carried out in metazoan, phototrophic or parasitic organisms, whereas genome-wide analysis in heterotrophic free living protozoa, such as the Ciliophora phylum, has not been undertaken. In the seven fully sequenced genomes available we retrieved 118 putative sequences of the IMHME type, albeit with large differences in number among the ciliates: 11 sequences in Euplotes octocarinatus, 7 in Ichthyophthirius multifiliis, 13 in Oxytricha trifallax, 18 in Stylonychia lemnae, 25 in Tetrahymena thermophila, 31 in Paramecium tetraurelia and 13 in Pseudocohnilembus persalinus. The pool of putative sequences was classified in 16 orthologous groups from which 11 were related to fatty acid desaturase (FAD) and 5 to the fatty acid hydroxylase (FAH) superfamilies. Noteworthy, a large diversity on the number and type of FAD / FAH proteins were found among the ciliates, a feature that, in principle, may be attributed to peculiarities of the evolutionary process, such as gene expansion and reduction, but also to horizontal gene transfer, as we demonstrate in this work. We identified twelve putative enzymatic activities, from which four were newly assigned activities: sphingolipid Δ4-desaturase, ω3/Δ15 fatty acid desaturase, a large group of alkane 1-monooxygenases, and acylamide-delta-3(E)-desaturase, although unequivocal allocation would require additional experiments. We also combined the phylogenetics analysis with lipids analysis, thereby allowing the detection of two enzymatic activities not previously reported: a C-5 sterol desaturase in P. tetraurelia and a delta-9 fatty acid desaturase in Cohnilembus reniformis. The analysis revealed a significant lower number of FAD's sequences in the spirotrichea ciliates than in the oligohymenophorea, emphasizing the importance of fatty acids trophic transfer among aquatic organisms as a source of variation in metabolic activity, individual and population growth rates, and reproduction.

Isolation, identification and diesel-oil biodegradation capacities of indigenous hydrocarbon-degrading strains of Cellulosimicrobium cellulans and Acinetobacter baumannii from tarball at Terengganu beach, Malaysia

In this study, we isolated two indigenous hydrocarbon-degrading bacteria from tarball found in Rhu Sepuluh beach, Terengganu, Malaysia. These bacteria were identified based on their physiological characteristic and 16S rRNA gene sequence analysis, and they showed 99% similarity with Cellulosimicrobium cellulans DSM 43879 and Acinetobacter baumannii ATCC 19606 respectively. Their hydrocarbon-degrading capabilities were tested using diesel-oil as sole carbon source. Results analysed using GC-MS, showed diesel-oil alkanes were degraded an average 64.4% by C. cellulans and 58.1% by A. baumannii with medium optical density reaching 0.967 (C. cellulans) and 1.515 (A. baumannii) in minimal salt media at 32°C for 10days. Individual diesel-oil alkanes were degraded between 10%-95.4% by C. cellulans and 0.2%-95.9% by A. baumannii. Both strains utilized diesel-oil for growth. The study suggests both strains are part of indigenous hydrocarbon-degrading bacteria in tarball with potential for bioremediation of oil-polluted marine environment.

Biodegradation of Phenol by Bacteria Strain Acinetobacter Calcoaceticus PA Isolated from Phenolic Wastewater

A phenol-degrading bacterium strain PA was successfully isolated from the effluent of petrochemical wastewater. Based on its morphological, physiological and biochemical characteristics, the strain PA was characterized as a Gram-negative, strictly aerobic, nonmotile and short rod-shaped bacterium that utilizes phenol as a sole carbon and energy source. 16S rDNA sequence analysis revealed that this strain is affiliated to Acinetobacter calcoaceticus in the group of Gammaproteobacteria. The strain was efficient in removing 91.6% of the initial 800 mg∙L⁻¹ phenol within 48 h, and had a tolerance of phenol concentration as high as 1700 mg∙L⁻¹. These results indicated that A. calcoaceticus possesses a promising potential in treating phenolic wastewater.

Biofiltration of gasoline and diesel aliphatic hydrocarbons

The ability of a biofilm to switch between the mixtures of mostly aromatic and aliphatic hydrocarbons was investigated to assess biofiltration efficiency and potential substrate interactions. A switch from gasoline, which consisted of both aliphatic and aromatic hydrocarbons, to a mixture of volatile diesel n-alkanes resulted in a significant increase in biofiltration efficiency, despite the lack of readily biodegradable aromatic hydrocarbons in the diesel mixture. This improved biofilter performance was shown to be the result of the presence of larger size (C₉-C(12)) linear alkanes in diesel, which turned out to be more degradable than their shorter-chain (C₆-C₈) homologues in gasoline. The evidence obtained from both biofiltration-based and independent microbiological tests indicated that the rate was limited by biochemical reactions, with the inhibition of shorter chain alkane biodegradation by their larger size homologues as corroborated by a significant substrate specialization along the biofilter bed. These observations were explained by the lack of specific enzymes designed for the oxidation of short-chain alkanes as opposed to their longer carbon chain homologues.

Engineering transcription factors to improve tolerance against alkane biofuels in Saccharomyces cerevisiae

BACKGROUND

Biologically produced alkanes can be used as 'drop in' to existing transportation infrastructure as alkanes are important components of gasoline and jet fuels. Despite the reported microbial production of alkanes, the toxicity of alkanes to microbial hosts could pose a bottleneck for high productivity. In this study, we aimed to improve the tolerance of Saccharomyces cerevisiae, a model eukaryotic host of industrial significance, to alkane biofuels.

RESULTS

To increase alkane tolerance in S. cerevisiae, we sought to exploit the pleiotropic drug resistance (Pdr) transcription factors Pdr1p and Pdr3p, which are master regulators of genes with pleiotropic drug resistance elements (PDREs)-containing upstream sequences. Wild-type and site-mutated Pdr1p and Pdr3p were expressed in S. cerevisiae BY4741 pdr1Δ pdr3Δ (BYL13). The point mutations of PDR1 (F815S) and PDR3 (Y276H) in BYL13 resulted in the highest tolerance to C10 alkane, and the expression of wild-type PDR3 in BYL13 led to the highest tolerance to C11 alkane. To identify and verify the correlation between the Pdr transcription factors and tolerance improvement, we analyzed the expression patterns of genes regulated by the Pdr transcription factors in the most tolerant strains against C10 and C11 alkanes. Quantitative PCR results showed that the Pdr transcription factors differentially regulated genes associated with multi-drug resistance, stress responses, and membrane modifications, suggesting different extents of intracellular alkane levels, reactive oxygen species (ROS) production and membrane integrity. We further showed that (i) the expression of Pdr1mt1 + Pdr3mt reduced intracellular C10 alkane by 67 % and ROS by 53 %, and significantly alleviated membrane damage; and (ii) the expression of the Pdr3wt reduced intracellular C11 alkane by 72 % and ROS by 21 %. Alkane transport assays also revealed that the reduction of alkane accumulation was due to higher export (C10 and C11 alkanes) and lower import (C11 alkane).

CONCLUSIONS

We improved yeast's tolerance to alkane biofuels by modulating the expression of the wild-type and site-mutated Pdr1p and Pdr3p, and extensively identified the correlation between Pdr transcription factors and tolerance improvement by analyzing gene patterns, alkane transport, ROS, and membrane integrity. These findings provide valuable insights into manipulating transcription factors in yeast for improved alkane tolerance and productivity.

Plasmid-encoded tetracycline efflux pump protein alters bacterial stress responses and ecological fitness of Acinetobacter oleivorans

Acquisition of the extracellular tetracycline (TC) resistance plasmid pAST2 affected host gene expression and phenotype in the oil-degrading soil bacterium, Acinetobacter oleivorans DR1. Whole-transcriptome profiling of DR1 cells harboring pAST2 revealed that all the plasmid genes were highly expressed under TC conditions, and the expression levels of many host chromosomal genes were modulated by the presence of pAST2. The host energy burden imposed by replication of pAST2 led to (i) lowered ATP concentrations, (ii) downregulated expression of many genes involved in cellular growth, and (iii) reduced growth rate. Interestingly, some phenotypes were restored by deleting the plasmid-encoded efflux pump gene tetH, suggesting that the membrane integrity changes resulting from the incorporation of efflux pump proteins also resulted in altered host response under the tested conditions. Alteration of membrane integrity by tetH deletion was shown by measuring permeability of fluorescent probe and membrane hydrophobicity. The presence of the plasmid conferred peroxide and superoxide resistance to cells, but only peroxide resistance was diminished by tetH gene deletion, suggesting that the plasmid-encoded membrane-bound efflux pump protein provided peroxide resistance. The downregulation of fimbriae-related genes presumably led to reduced swimming motility, but this phenotype was recovered by tetH gene deletion. Our data suggest that not only the plasmid replication burden, but also its encoded efflux pump protein altered host chromosomal gene expression and phenotype, which also alters the ecological fitness of the host in the environment.

Characterization of the medium- and long-chain n-alkanes degrading Pseudomonas aeruginosa strain SJTD-1 and its alkane hydroxylase genes

A gram-negative aliphatic hydrocarbon-degrading bacterium SJTD-1 isolated from oil-contaminated soil was identified as Pseudomonas aeruginosa by comparative analyses of the 16S rRNA sequence, phenotype, and physiological features. SJTD-1 could efficiently mineralize medium- and long-chain n-alkanes (C12-C30) as its sole carbon source within seven days, showing the most optimal growth on n-hexadecane, followed by n-octadecane, and n-eicosane. In 36 h, 500 mg/L of tetradecane, hexadecane, and octadecane were transformed completely; and 2 g/L n-hexadecane was degraded to undetectable levels within 72 h. Two putative alkane-degrading genes (gene 3623 and gene 4712) were characterized and our results indicated that their gene products were rate-limiting enzymes involved in the synergetic catabolism of C12-C16 alkanes. On the basis of bioinformatics and transcriptional analysis, two P450 monooxygenases, along with a putative AlmA-like oxygenase, were examined. Genetically defective mutants lacking the characteristic alkane hydroxylase failed to degrade n-octadecane, thereby suggesting a different catalytic mechanism for the microbial transformation of alkanes with chain lengths over C18.

Culturable populations of Acinetobacter can promptly respond to contamination by alkanes in mangrove sediments

This study evaluated the potential of bacterial isolates from mangrove sediments to degrade hexadecane, an paraffin hydrocarbon that is a large constituent of diesel and automobile lubricants. From a total of 18 oil-degrading isolates obtained by an enrichment technique, four isolates showed a great potential to degrade hexadecane. The strain MSIC01, which was identified by 16S rRNA gene sequencing as Acinetobacter sp., showed the best performance in degrading this hydrocarbon, being capable of completely degrading 1% (v/v) hexadecane within 48 h without releasing biosurfactants. Its hydrophobic surface probably justifies its potential to degrade high concentrations of hexadecane. Thus, the sediments from the studied mangrove harbour bacterial communities that are able to use oil as a carbon source, which is a particularly interesting feature due to the risk of oil spills in coastal areas. Moreover, Acinetobacter sp. MSIC01 emerged as a promising candidate for applications in bioremediation of contaminated mangrove sediments.

Transcriptome response to alkane biofuels in Saccharomyces cerevisiae: identification of efflux pumps involved in alkane tolerance

BACKGROUND

Hydrocarbon alkanes have been recently considered as important next-generation biofuels because microbial production of alkane biofuels was demonstrated. However, the toxicity of alkanes to microbial hosts can possibly be a bottleneck for high productivity of alkane biofuels. To tackle this toxicity issue, it is essential to understand molecular mechanisms of interactions between alkanes and microbial hosts, and to harness these mechanisms to develop microbial host strains with improved tolerance against alkanes. In this study, we aimed to improve the tolerance of Saccharomyces cerevisiae, a model eukaryotic host of industrial significance, to alkane biofuels by exploiting cellular mechanisms underlying alkane response.

RESULTS

To this end, we first confirmed that nonane (C9), decane (C10), and undecane (C11) were significantly toxic and accumulated in S. cerevisiae. Transcriptome analyses suggested that C9 and C10 induced a range of cellular mechanisms such as efflux pumps, membrane modification, radical detoxification, and energy supply. Since efflux pumps could possibly aid in alkane secretion, thereby reducing the cytotoxicity, we formed the hypothesis that those induced efflux pumps could contribute to alkane export and tolerance. In support of this hypothesis, we demonstrated the roles of the efflux pumps Snq2p and Pdr5p in reducing intracellular levels of C10 and C11, as well as enhancing tolerance levels against C10 and C11. This result provided the evidence that Snq2p and Pdr5p were associated with alkane export and tolerance in S. cerevisiae.

CONCLUSIONS

Here, we investigated the cellular mechanisms of S. cerevisiae response to alkane biofuels at a systems level through transcriptome analyses. Based on these mechanisms, we identified efflux pumps involved in alkane export and tolerance in S. cerevisiae. We believe that the results here provide valuable insights into designing microbial engineering strategies to improve cellular tolerance for highly efficient alkane biofuel production.

Structural insights into diversity and n-alkane biodegradation mechanisms of alkane hydroxylases

Environmental microbes utilize four degradation pathways for the oxidation of n-alkanes. Although the enzymes degrading n-alkanes in different microbes may vary, enzymes functioning in the first step in the aerobic degradation of alkanes all belong to the alkane hydroxylases. Alkane hydroxylases are a class of enzymes that insert oxygen atoms derived from molecular oxygen into different sites of the alkane terminus (or termini) depending on the type of enzymes. In this review, we summarize the different types of alkane hydroxylases, their degrading steps, and compare typical enzymes from various classes with regard to their three-dimensional structures, in order to provide insights into how the enzymes mediate their different roles in the degradation of n-alkanes and what determines their different substrate ranges. Through the above analyzes, the degrading mechanisms of enzymes can be elucidated and molecular biological methods can be utilized to expand their catalytic roles in the petrochemical industry or in bioremediation of oil-contaminated environments.

Characterization of a novel Rieske-type alkane monooxygenase system in Pusillimonas sp. strain T7-7

The cold-tolerant bacterium Pusillimonas sp. strain T7-7 is able to utilize diesel oils (C5 to C30 alkanes) as a sole carbon and energy source. In the present study, bioinformatics, proteomics, and real-time reverse transcriptase PCR approaches were used to identify the alkane hydroxylation system present in this bacterium. This system is composed of a Rieske-type monooxygenase, a ferredoxin, and an NADH-dependent reductase. The function of the monooxygenase, which consists of one large (46.711 kDa) and one small (15.355 kDa) subunit, was further studied using in vitro biochemical analysis and in vivo heterologous functional complementation tests. The purified large subunit of the monooxygenase was able to oxidize alkanes ranging from pentane (C5) to tetracosane (C24) using NADH as a cofactor, with greatest activity on the C15 substrate. The large subunit also showed activity on several alkane derivatives, including nitromethane and methane sulfonic acid, but it did not act on any aromatic hydrocarbons. The optimal reaction condition of the large subunit is pH 7.5 at 30°C. Fe(2+) can enhance the activity of the enzyme evidently. This is the first time that an alkane monooxygenase system belonging to the Rieske non-heme iron oxygenase family has been identified in a bacterium.

Simultaneous degradation of phenol and n-hexadecane by Acinetobacter strains

Three phenol- and alkanes-degrading bacterial strains were isolated from a freshwater sample. Upon the 16S rRNA gene analysis, phenotype and physiological features, the three strains were designated as Acinetobacter sp. with both phenol hydroxylase gene (phe) and alkane monooxygenase gene (alkM) detected. They could simultaneously degrade phenol and n-hexadecane for growth, but prefer phenol than n-hexadecane. Between phenol (400mgl(-1)) and n-hexadecane (400mgl(-1)), n-hexadecane enhanced phenol degradation in mineral salt medium (MSM), while phenol affects negatively the n-hexadecane degradation. However, combination of phenol (400mgl(-1)) and n-hexadecane (400mgl(-1)) in MSM led to higher growth of the strains than the phenol and n-hexadecane separately. The transcription levels of phe and alkM genes supported the physiological properties of the strains.

Identification of a novel Baeyer-Villiger monooxygenase from Acinetobacter radioresistens: close relationship to the Mycobacterium tuberculosis prodrug activator EtaA

This work demonstrates that Acinetobacter radioresistens strain S13 during the growth on medium supplemented with long‐chain alkanes as the sole energy source expresses almA gene coding for a Baeyer‐Villiger monooxygenase (BVMO) involved in alkanes subterminal oxidation. Phylogenetic analysis placed the sequence of this novel BVMO in the same clade of the prodrug activator ethionamide monooxygenase (EtaA) and it bears only a distant relation to the other known class I BVMO proteins. In silico analysis of the 3D model of the S13 BVMO generated by homology modelling also supports the similarities with EtaA by binding ethionamide to the active site. In vitro experiments carried out with the purified enzyme confirm that this novel BVMO is indeed capable of typical Baeyer‐Villiger reactions as well as oxidation of the prodrug ethionamide.

Diversity of flavin-binding monooxygenase genes (almA) in marine bacteria capable of degradation long-chain alkanes

Many bacteria have been reported as degraders of long-chain (LC) n-alkanes, but the mechanism is poorly understood. Flavin-binding monooxygenase (AlmA) was recently found to be involved in LC-alkane degradation in bacteria of the Acinetobacter and Alcanivorax genera. However, the diversity of this gene and the role it plays in other bacteria remains unclear. In this study, we surveyed the diversity of almA in marine bacteria and in bacteria found in oil-enrichment communities. To identify the presence of this gene, a pair of degenerate PCR primers were was designed based on conserved motifs of the almA gene sequences in public databases. Using this approach, we identified diverse almA genes in the hydrocarbon-degrading bacteria and in bacterial communities from the surface seawater of the Xiamen coastal area, the South China Sea, the Indian Ocean, and the Atlantic Ocean. As a result, almA was positively detected in 35 isolates belonging to four genera, and a total of 39 different almA sequences were obtained. Five isolates were confirmed to harbor two to three almA genes. From the Xiamen coastal area and the Atlantic Ocean oil-enrichment communities, a total of 60 different almA sequences were obtained. These sequences mainly formed two clusters in the phylogenetic tree, named Class I and Class II, and these shared 45-56% identity at the amino acid level. Class I contained 11 sequences from bacteria represented by the Salinisphaera and Parvibaculum genera. Class II was larger and more diverse, and it was composed of 88 sequences from Proteobacteria, Gram-negative bacteria, and the enriched bacterial communities. These communities were represented by the Alcanivorax and Marinobacter genera, which are the two most popular genera hosting the almA gene. AlmA was also detected across a wide geographical range, as determined by the origin of the bacterial host. Our results demonstrate the diversity of almA and confirm its high rate of occurrence in hydrocarbon-degrading bacteria, indicating that this gene plays an important role in the degradation of LC alkanes in marine environments.

Abundance and diversity of n-alkane-degrading bacteria in a forest soil co-contaminated with hydrocarbons and metals: a molecular study on alkB homologous genes

Unraveling functional genes related to biodegradation of organic compounds has profoundly improved our understanding of biological remediation processes, yet the ecology of such genes is only poorly understood. We used a culture-independent approach to assess the abundance and diversity of bacteria catalyzing the degradation of n-alkanes with a chain length between C(5) and C(16) at a forest site co-contaminated with mineral oil hydrocarbons and metals for nearly 60 years. The alkB gene coding for a rubredoxin-dependent alkane monooxygenase enzyme involved in the initial activation step of aerobic aliphatic hydrocarbon metabolism was used as biomarker. Within the area of study, four different zones were evaluated: one highly contaminated, two intermediately contaminated, and a noncontaminated zone. Contaminant concentrations, hydrocarbon profiles, and soil microbial respiration and biomass were studied. Abundance of n-alkane-degrading bacteria was quantified via real-time PCR of alkB, whereas genetic diversity was examined using molecular fingerprints (T-RFLP) and clone libraries. Along the contamination plume, hydrocarbon profiles and increased respiration rates suggested on-going natural attenuation at the site. Gene copy numbers of alkB were similar in contaminated and control areas. However, T-RFLP-based fingerprints suggested lower diversity and evenness of the n-alkane-degrading bacterial community in the highly contaminated zone compared to the other areas; both diversity and evenness were negatively correlated with metal and hydrocarbon concentrations. Phylogenetic analysis of alkB denoted a shift of the hydrocarbon-degrading bacterial community from Gram-positive bacteria in the control zone (most similar to Mycobacterium and Nocardia types) to Gram-negative genotypes in the contaminated zones (Acinetobacter and alkB sequences with little similarity to those of known bacteria). Our results underscore a qualitative rather than a quantitative response of hydrocarbon-degrading bacteria to the contamination at the molecular level.

Are alkane hydroxylase genes (alkB) relevant to assess petroleum bioremediation processes in chronically polluted coastal sediments?

The diversity of alkB-related alkane hydroxylase sequences and the relationship between alkB gene expression and the hydrocarbon contamination level have been investigated in the chronically polluted Etang-de-Berre sediments. For this purpose, these sediments were maintained in microcosms and submitted to a controlled oil input miming an oil spill. New degenerated PCR primers targeting alkB-related alkane hydroxylase sequences were designed to explore the diversity and the expression of these genes using terminal restriction fragment length polymorphism fingerprinting and gene library analyses. Induction of alkB genes was detected immediately after oil addition and their expression detected only during 2 days, although the n-alkane degradation was observed throughout the 14 days of incubation. The alkB gene expression within triplicate microcosms was heterogeneous probably due to the low level of alkB transcripts. Moreover, the alkB gene expression of dominant OTUs has been observed in unoiled microcosms indicating that the expression of this gene cannot be directly related to the oil contamination. Although the dominant alkB genes and transcripts detected were closely related to the alkB of Marinobacter aquaeolei isolated from an oil-producing well, and to alkB genes related to the obligate alkanotroph Alcanivorax borkumensis, no clear relationship between the oil contamination and the expression of the alkB genes could be established. This finding suggests that in such coastal environments, alkB gene expression is not a function relevant enough to monitor bacterial response to oil contamination.