Potential biodegradation of crude petroleum oil by newly isolated halotolerant microbial strains from polluted Red Sea area

Crude oil degrading efficiency of formulated consortium of bacterial strains isolated from petroleum-contaminated sludge

Crude oil contamination has been widely recognized as a major environmental issue due to its various adverse effects. The use of inhabitant microorganisms (native to the contaminated sites) to detoxify/remove pollutants owing to their diverse metabolic capabilities is an evolving method for the removal/degradation of petroleum industry contaminants. The present study deals with the exploitation of native resident bacteria from crude oil contaminated site (oil exploration field) for bioremediation procedures. Fifteen (out of forty-four) bioremediation-relevant aerobic bacterial strains, belonging to the genera of Bacillus, Stenotrophomonas, Pseudomonas, Paenibacillus, Rhizobium, Burkholderia, and Franconibacter, isolated from crude oil containing sludge, have been selected for the present bioremediation study. Crude oil bioremediation performance of the selected bacterial consortium was assessed using microcosm-based studies. Stimulation of the microbial consortium with nitrogen or phosphorous led to the degradation of 60-70% of total petroleum hydrocarbon (TPH) in 0.25% and 0.5% crude oil experimental sets. CO2 evolution, indicative of crude oil mineralization, was evident with the highest evolution being 28.6 mg mL-1. Ecotoxicity of treated crude oil-containing media was assessed using plant seed germination assay, in which most of the 0.25% and 0.5% treated crude oil sets gave positive results thereby suggesting a reduction in crude oil toxicity.

High temperature and solar radiation in the Red Sea enhance the dissolution of crude oil from surface films

The Red Sea is a hotspot of biodiversity susceptible to oil pollution. Besides, it is one of the warmest seas on the Earth with highly transparent waters. In this study, we estimated the oil dissolution rates under natural sunlight spectra and temperature conditions using coastal oil slicks collected after the 2019 Sabiti oil spill in the Red Sea. Optical analyses revealed the significant interactive effect of sunlight and temperature in enhancing the dissolution of oil into dissolved organic matter (DOM). The highest oil dissolution rate (38.68 g C m-3 d-1) was observed in full-spectrum sunlight. Oil dissolution significantly enhanced total organic carbon (TOC) and polycyclic aromatic hydrocarbons (PAHs) in seawater. High nucleic acid (HNA) bacteria, likely the oil degraders, proliferated from 30 to 70 - 90% after 4 days. The heavier stable carbon isotopic composition of methane (δ13C-CH4) and lighter stable carbon isotopic composition of carbon dioxide (δ13C-CO2) indicate the putative role of bacterial processes in the natural degradation of crude oil. The results indicated that the combined effect of temperature and solar radiation enhanced the biological and photochemical dissolution of oil on the Red Sea surface.

Levels, spatial distributions, and provision of petroleum hydrocarbons and phthalates in sediments from Obhur lagoon, Red Sea coast of Saudi Arabia

The levels, spatial distribution, and sources of petroleum hydrocarbons and phthalates were assessed in surface sediment samples from the urban lagoon of Obhur near Jeddah, the largest city on the Red Sea coast of Saudi Arabia. The lagoon was divided into the inner zone, middle zone, and outer zone based on its geomorphological features and developmental activities. n-Alkanes, hopane and sterane biomarkers, and unresolved complex mixture were the major petroleum hydrocarbon compounds of the total extractable organic matter. Phthalates were also measured in the sediment samples. In the three zones, n-alkanes ranged from 89.3 ± 88.5 to 103.2 ± 114.9 ng/g, whereas the hopane and sterane biomarkers varied from 69.4 ± 75.3 to 77.7 ± 69.9 ng/g and 72.5 ± 77.9-89.5 ± 82.2 ng/g, respectively. The UCM concentrations ranged from 821 ± 1119 to 1297 ± 1684 ng/g and phthalates from 37.4 ± 34.5 65 ± 68 ng/g. The primary origins of these anthropogenic hydrocarbons in the lagoon sediments were petroleum products (boat engine discharges, boat washing, lubricants, and wastewater flows) and plasticizers (plastic waste and litter). The proportions of anthropogenic hydrocarbons derived from petroleum products in the sediment's TEOM ranged from 43 ± 33 to 62 ± 15%, while the percentages for plasticizers varied from 2.9 ± 1.2 to 4.0 ± 1.6%. The presence and inputs of these contaminants from petroleum and plastic wastes in the lagoon's sediments will eventually have an impact on its habitats, including the benthic nursery and spawning areas.

Fungal bioproducts for petroleum hydrocarbons and toxic metals remediation: recent advances and emerging technologies

Petroleum hydrocarbons and toxic metals are sources of environmental contamination and are harmful to all ecosystems. Fungi have metabolic and morphological plasticity that turn them into potential prototypes for technological development in biological remediation of these contaminants due to their ability to interact with a specific contaminant and/or produced metabolites. Although fungal bioinoculants producing enzymes, biosurfactants, polymers, pigments and organic acids have potential to be protagonists in mycoremediation of hydrocarbons and toxic metals, they can still be only adjuvants together with bacteria, microalgae, plants or animals in such processes. However, the sudden accelerated development of emerging technologies related to the use of potential fungal bioproducts such as bioinoculants, enzymes and biosurfactants in the remediation of these contaminants, has boosted fungal bioprocesses to achieve higher performance and possible real application. In this review, we explore scientific and technological advances in bioprocesses related to the production and/or application of these potential fungal bioproducts when used in remediation of hydrocarbons and toxic metals from an integral perspective of biotechnological process development. In turn, it sheds light to overcome existing technological limitations or enable new experimental designs in the remediation of these and other emerging contaminants.

Transcontinental Dispersal of Nonendemic Fungal Pathogens through Wooden Handicraft Imports

This study examined the viability and diversity of fungi harbored in imported wooden handicraft products sold in six retail stores in Florida, United States. Despite being subjected to trade regulations that require various sterilization/fumigation protocols, our study demonstrates high survival and diversity of fungi in wood products originating from at least seven countries on three continents. Among these fungi were nonendemic plant and human pathogens, as well as mycotoxin producers. Several products that are sold for use in food preparation and consumption harbored a novel (to North America) plant and human pathogen, Paecilomyces formosus. In addition, a high number of species isolated were thermophilic and included halophilic species, suggesting adaptability and selection through current wood treatment protocols that utilize heat and/or fumigation with methyl-bromide. This research suggests that current federal guidelines for imports of wooden goods are not sufficient to avoid the transit of potential live pathogens and demonstrates the need to increase safeguards at both points of origin and entry for biosecurity against introduction from invasive fungal species in wood products. Future import regulations should consider living fungi, their tolerance to extreme conditions, and their potential survival in solid substrates. Mitigation efforts may require additional steps such as more stringent fumigation and/or sterilization strategies and limiting use of wood that has not been processed to remove bark and decay. IMPORTANCE This study, the first of its kind, demonstrates the risk of importation of nonendemic foreign fungi on wooden handicrafts into the United States despite the application of sanitation protocols. Previous risk assessments of imported wood products have focused on potential for introduction of invasive arthropods (and their fungal symbionts) or have focused on other classes of wood products (timber, wooden furniture, garden products, etc.). Little to no attention has been paid to wooden handicrafts and the fungal pathogens (of plants and humans) they may carry. Due to the large size and diversity of this market, the risk for introduction of potentially dangerous pathogens is significant as illustrated by the results of this study.

Prospects in the bioremediation of petroleum hydrocarbon contaminants from hypersaline environments: A review

Hypersaline environments are underappreciated and are frequently exposed to pollution from petroleum hydrocarbons. Unlike other environs, the high salinity conditions present are a deterrent to various remediation techniques. There is also production of hypersaline waters from oil-polluted ecosystems which contain toxic hydrophobic pollutants that are threat to public health, environmental protection, and sustainability. Currently, innovative advances are being proposed for the remediation of oil-contaminated hypersaline regions. Such advancements include the exploration and stimulation of native microbial communities capable of utilizing and degrading petroleum hydrocarbons. However, prevailing salinity in these environments is unfavourable for the growth of non-halophylic microorganisms, thus limiting effective bioremediation options. An in-depth understanding of the potentials of various remediation technologies of hydrocarbon-polluted hypersaline environments is lacking. Thus, we present an overview of petroleum hydrocarbon pollution in hypersaline ecosystems and discuss the challenges and prospects associated with several technologies that may be employed in remediation of hydrocarbon pollution in the presence of delimiting high salinities. The application of biological remediation technologies including the utilization of halophilic and halotolerant microorganisms is also discussed.

Di-n-octyl phthalate degradation by a halotolerant bacterial consortium LF and its application in soil

Di-n-octyl phthalate (DOP), a plasticizer used in many different industrial products, is a frequently observed pollutant in the environment. Biodegradation by microorganisms is considered to be a realistic choice for the remediation of DOP contamination. In the present research, the halotolerant bacterial consortium (LF) enriched in our previous research was used to degrade DOP. It was found that the optimal conditions for LF to degrade DOP was temperature 30^oC, pH 6.0, inoculum size >5%, and salt content <3%. LF could degrade a high concentration of DOP (2000 mg/L) with the removal efficiency of 96.33%. Substrate inhibition analyses indicated that the inhibition constant, maximum specific degradation rate and half-saturation constant were 2544.6 mg/L, 0.7 d^-1 and 59.1 mg/L, respectively. Based on the analysis of the gas chromatography-mass spectrometry (GC-MS), the biodegradation pathway for DOP by LF was proposed. Furthermore, LF could degrade DOP in soil (100 mg/kg) with the highest removal efficiency of 89.3%. This study is the first report on DOP biodegradation by bacterial consortium. These results suggest that LF can be used to remediate DOP-contaminated environment.

Rapid capturing of oil-degrading bacteria by engineered attapulgite and their synergistic remediation for oil spill

HYPOTHESIS

High-efficiency dispersion and enhanced biodegradation play important roles in the treatment of oily wastewater. Due to the flaws of chemical surfactants, it is necessary to study the alternative dispersants that are eco-friendly and sustainable. Therefore, applying natural attapulgite (ATP) to coat Brevibacillus parabrevis for dispersion and biodegradation was studied.

EXPERIMENTS

To capture negatively charged bacteria in water, ATP was modified by positively charged Poly (allylamine hydrochloride) (PAH). The capturing capability of Poly (allylamine hydrochloride)-attapulgite (PAH-ATP) particles for bacterial cells, emulsification of PAH-ATP particles and bacteria on oil, toxicity of PAH-ATP to bacteria, biodegradation of oil, etc., were comprehensively investigated.

FINDINGS

PAH-ATP modified bacteria show a highly effective emulsification for oil due to the synergism of PAH-ATP and bacteria. The emulsion stabilized by (PAH-ATP)@bacteria presents small and stable oil droplets in one month, which is benefit for the following biodegradation. Compared with bare bacteria and PAH-ATP, PAH-ATP can capture bacteria to the surface of the oil droplets which can greatly improve the degradation of oil pollution. Importantly, the presence of PAH-ATP does not inhibit the reproduction and activity of bacteria. Treatment of oily wastewater by combining natural nanoparticles and oil-degrading bacteria has the advantages of economy, environmental protection, and sustainability.

Optimization of an Autochthonous Bacterial Consortium Obtained from Beach Sediments for Bioremediation of Petroleum Hydrocarbons

Oil spill pollution remains a serious concern in marine environments and the development of effective oil bioremediation techniques are vital. This work is aimed at developing an autochthonous hydrocarbon-degrading consortium with bacterial strains with high potential for hydrocarbons degradation, optimizing first the growth conditions for the consortium, and then testing its hydrocarbon-degrading performance in microcosm bioremediation experiments. Bacterial strains, previously isolated from a sediment and cryopreserved in a georeferenced microbial bank, belonged to the genera Pseudomonas, Rhodococcus and Acinetobacter. Microcosms were assembled with natural seawater and petroleum, for testing: natural attenuation (NA); biostimulation (BS) (nutrients addition); bioaugmentation with inoculum pre-grown in petroleum (BA/P) and bioaugmentation with inoculum pre-grown in acetate (BA/A). After 15 days, a clear blending of petroleum with seawater was observed in BS, BA/P and BA/A but not in NA. Acetate was the best substrate for consortium growth. BA/A showed the highest hydrocarbons degradation (66%). All bacterial strains added as inoculum were recovered at the end of the experiment. This study provides an insight into the capacity of autochthonous communities to degrade hydrocarbons and on the use of alternative carbon sources for bacterial biomass growth for the development of bioremediation products to respond to oil spills.

Petroleum Contaminated Seawater Detoxification in Microcosm by Halotolerant Consortium Isolated from Persian Gulf

Bioremediation of a petroleum contaminated seawater from Persian Gulf was investigated and efficiency of natural attenuation by native halotolerant bacterial consortium, biostimulation by addition of macro nutrients (nitrogen and phosphorus) and surfactant and bioaugmentation by application of halotolerant hydrocarbon degrading strains were evaluated. Biodegradation rates in defined conditions were studied for 30 days. Four pure isolates including Bacillus sp. PG-1, Pseudomonas aeruginosa PG-2, Paenibacillus lautus PG-3, and Pseudomonas putida PG-4 were used to preparation of bacterial consortium. Results indicated that the bioaugmentation yielded the best TPH removal efficiency of 56.24%, followed by biostimulation with surfactant addition (removal of 31.52%). The most bacterial density was also observed for bioaugmentation bioreactor. Toxicity of reaction medium was evaluated by oxygen consumption rate inhibition, dehydrogenase activity inhibition and growth rate inhibition methods in which, the least toxicity rates of 27%, 25% and 31% were observed for bioaugmentation based bioreactor, respectively. Simultaneous bioaugmentation and biostimulation can efficiently reduce the crude oil content in the surface of seawater using halotolerant strains.

Dehalogenase-producing halophiles and their potential role in bioremediation

This review aims to briefly describe the potential role of dehalogenase-producing halophilic bacteria in decontamination of organohalide pollutants. Hypersaline habitats pose challenges to life because of low water activity (water content) and is considered as the largest and ultimate sink for pollutants due to naturally and anthropogenic activities in which a substantial amount of ecological contaminants are organohalides. Several such environments appear to host and support substantial diversity of extremely halophilic and halotolerant bacteria as well as halophilic archaea. Biodegradation of several toxic inorganic and organic compounds in both aerobic and anaerobic conditions are carried out by halophilic microbes. Therefore, remediation of polluted marine/hypersaline environments are the main scorching issues in the field of biotechnology. Although many microbial species are reported as effective pollutants degrader, but little has been isolated from marine/hypersaline environments. Therefore, more novel microbial species with dehalogenase-producing ability are still desired.

Microbial eco-physiological strategies for salinity-mediated crude oil biodegradation

Salinity variability strongly affects the behaviors of oil degrading bacteria for spilled oil biodegradation in the marine environment. However, limited studies explored the strategies of microbes on salinity-mediated crude oil biodegradation. In this study, a halotolerant bio-emulsifier producer, Exiguobacterium sp. N41P, was examined as a model strain for Alaska North Slope (ANS) crude oil (0.5%, v/v) biodegradation. Results indicated that Exiguobacterium sp. N41P could tolerant a wide range of salinity (0-120 g/L NaCl) and achieve the highest degradation efficiency under the salinity of 15 g/L NaCl due to the highest biofilm formation ability. Moreover, increased salinity induced decreased cell surface hydrophobicity and a migration of microbial growth from oil phase to aqueous phase, leading to limited bio-emulsifier productivity and depressed degradation of insoluble long-chain n-alkanes while enhancing the degradation of relative soluble naphthalene. Research findings illustrated the microbial eco-physiological mechanism for spilled oil biodegradation under diverse salinities and advanced the understanding of sophisticated marine crude oil biodegradation process.

Effect of Various Isolated Microbial Consortiums on the Biodegradation Process of Precipitated Asphaltenes from Crude Oil

One of the serious problems in the oil industry is precipitation and deposition of asphaltenes in the different oil production stages including formation, wellbore, production tubing, flow lines, and separation units. This phenomenon causes a dramatic increase in the cost of oil production, processing, and transferring. Thus, it seems to be very necessary to use the removing methods for precipitated asphaltenes in different crude oil production and transferring stages. In this study, the ability of microorganisms for biodegradation of precipitated asphaltenes was investigated. For this purpose, four bacterial consortiums were isolated from oil-contaminated soil, crude oil, reservoir water, and oil sludge samples of an oil field located in the southwest of Iran. Based on the results of the designed experiments, by using response surface methodology (RSM) and central composite design, the bacterial consortiums were cultured in the flasks. Three levels of temperatures, salinity, pH, and initial asphaltene concentration as the substrate were considered as the parameters of culture medium and incubated growth mediums for 60 days. The maximum asphaltene biodegradation was 46.41% caused by the crude oil consortium including Staphylococcus saprophyticus sp. and Bacillus cereus sp. at 45 °C, salinity 160 g·L^-1, pH 6.5, and 25 g·L^-1 initial asphaltene concentration. Also, it was observed that the negative or positive impacts of culture media conditions such as temperature and salinity on asphaltene degradation depended on the type of the available bacterial consortium. The carbon-hydrogen-nitrogen-sulfur analysis showed that carbon, hydrogen, nitrogen, and in some cases, the sulfur in biodegraded samples are less than in control samples. Moreover, Fourier transform infrared analysis indicated that the alkyne groups were less resistant to biodegradation and were eliminated thoroughly after 2 months of incubation. In addition, alkane components were partially removed in treated asphaltene fraction. The parameters of culture medium were optimized by RSM, and besides, their effects on the performance of bacteria in the asphaltene biodegradation process were discussed. The validity of some available kinetic models to describe the behavior of the studied bacteria consortium was investigated, and it was observed that Tessier, Moser, and Contois models accurately predict the values of asphaltenes and biomass concentration at 30, 45, and 60 °C, respectively.

Candida pseudoglaebosa and Kodamaea ohmeri are capable of degrading alkanes in the presence of heavy metals

The aim of this study was to examine four strains of two yeast species in relation to their capability for assimilating alkanes in the presence of heavy metals (HMs). The four strains tested were Candida pseudoglaebosa ENCB-7 and Kodamaea ohmeri ENCB-8R, ENCB-23, and ENCB-VIK. Determination was made of the expression of CYP52 genes involved in alkane hydroxylation. When exposed to Cu²⁺ , Zn²⁺ , Pb²⁺ , Cd²⁺ , and As³⁺ at pH 3 and 5, all four strains could assimilate several n-alkanes having at least six carbon atoms. The three K. ohmeri strains could also utilize branched alkanes, cycloalkanes, and n-octanol as sole carbon sources. Kinetic assays demonstrated greater biomass production and specific growth of the yeasts exposed to long-chain n-alkanes. Fragments of paralogous CYP52 genes of C. pseudoglaebosa ENCB-7 and K. ohmeri ENCB-23 were amplified, sequenced, and phylogenetically evaluated. Reverse-transcription polymerase chain reaction revealed that n-nonane and n-decane induced to CpCYP52-G3, CpCYP52-G9, and CpCYP52-G10. KoCYP52-G3 was induced with n-decane and n-octanol. Also, CpCYP52-G3 and CpCYP52-G9 were induced by glucose. In conclusion, C. pseudoglaebosa and K. ohmeri were able to degrade several alkanes in the presence of HMs and under acidic conditions. These yeasts harbor paralogous alkane-induced CYP52 genes, which display different profiles of transcriptional expression.

Candida pseudoglaebosa and Kodamaea ohmeri are capable of degrading alkanes in the presence of heavy metals

The aim of this study was to examine four strains of two yeast species in relation to their capability for assimilating alkanes in the presence of heavy metals (HMs). The four strains tested were Candida pseudoglaebosa ENCB-7 and Kodamaea ohmeri ENCB-8R, ENCB-23, and ENCB-VIK. Determination was made of the expression of CYP52 genes involved in alkane hydroxylation. When exposed to Cu2+ , Zn2+ , Pb2+ , Cd2+ , and As3+ at pH 3 and 5, all four strains could assimilate several n-alkanes having at least six carbon atoms. The three K. ohmeri strains could also utilize branched alkanes, cycloalkanes, and n-octanol as sole carbon sources. Kinetic assays demonstrated greater biomass production and specific growth of the yeasts exposed to long-chain n-alkanes. Fragments of paralogous CYP52 genes of C. pseudoglaebosa ENCB-7 and K. ohmeri ENCB-23 were amplified, sequenced, and phylogenetically evaluated. Reverse-transcription polymerase chain reaction revealed that n-nonane and n-decane induced to CpCYP52-G3, CpCYP52-G9, and CpCYP52-G10. KoCYP52-G3 was induced with n-decane and n-octanol. Also, CpCYP52-G3 and CpCYP52-G9 were induced by glucose. In conclusion, C. pseudoglaebosa and K. ohmeri were able to degrade several alkanes in the presence of HMs and under acidic conditions. These yeasts harbor paralogous alkane-induced CYP52 genes, which display different profiles of transcriptional expression.

Semi-industrial Scale Production of a New Yeast with Probiotic Traits, Cryptococcus sp. YMHS, Isolated from the Red Sea

A new yeast strain with promising probiotic traits was isolated from the Red Sea water samples. The isolate (YMHS) was subjected to genetic characterization and identified as Cryptococcus sp. Nucleotide sequence analysis of the rRNA gene internal transcribed spacer regions showed 95% sequence similarity between the isolate and Cryptococcus albidus. Cryptococcus sp. YMHS exhibited desirable characteristics of probiotic microorganisms; it has tolerance to low pH in simulated gastric juice, resistance to bile salts, hydrophobic characteristics, broad antimicrobial activity, and in vitro ability to degrade cholesterol. The isolate grew well in a semi-defined medium composed of yeast extract, glucose, KH₂PO₄, (NH₄)₂SO₄, and MgSO₄, yielding cell mass of 2.32 and 5.82 g/l in shake flask and in bioreactor cultures, respectively. Fed-batch cultivation, with controlled pH, increased the biomass gradually in culture, reaching 28.5 g/l after 32 h cultivation. Beside the feasible use as a probiotic, the new strain also could be beneficial in the development of functional foods or novel food preservatives. To our knowledge, this is the first report of yeast with probiotic properties isolated from the Red Sea.

Assessing the biodegradation of polycyclic aromatic hydrocarbons and laccase production by new fungus Trematophoma sp. UTMC 5003

Environmental pollution caused by petroleum compounds has become a global concern. The aim of this study was to evaluate the indigenous fungal isolates in Iran for biodegradation of crude oil pollutants. In order to isolate fungal strains, the soil samples were enriched in minimal salts medium (MSM) with 1% crude oil and then the crude oil degradation was measured by total petroleum hydrocarbon (TPH) assay. The degradation of hydrocarbons compounds was also analysed by FT-IR and HPLC, and the activity of peroxidase enzyme and biosurfactant production were also measured. We isolated 40 fungal strains and selected the isolate G-05 with 70% degradation ability of petroleum hydrocarbons as a premium isolate after 15 days. Residual crude oil analysis with FT-IR spectrophotometry and HPLC showed that G-05 is able to degrade 90 and 100% of aliphatic compounds and some polycyclic aromatic hydrocarbons (PAH), respectively. Evaluation of enzymatic activity showed that this isolate can produce 4 U L^-1 of Laccase enzyme for oil removal; it is capable of producing biosurfactant and reducing the surface tension of the medium to 25.95 ± 0.1 m Nm^-1. This strain was identified as a member of Trematophoma genus and the obtained results showed that this strain is a highly potent strain in bioremediation of soils contaminated by crude oil.