Prospect, isolation, and characterization of microorganisms for potential use in cases of oil bioremediation along the coast of Trindade Island, Brazil

Combined influence of the nanoplastics and polycyclic aromatic hydrocarbons exposure on microbial community in seawater environment

Nanoplastics (NPs) and polycyclic aromatic hydrocarbons (PAHs) are recognized as persistent organic pollutant (POPs) with demonstrated physiological toxicity. When present in aquatic environments, the two pollutants could combine with each other, resulting in cumulative toxicity to organisms. However, the combined impact of NPs and PAHs on microorganisms in seawater is not well understood. In this study, we conducted an exposure experiment to investigate the individual and synergistic effects of NPs and PAHs on the composition, biodiversity, co-occurrence networks of microbial communities in seawater. Exposure of individuals to PAHs led to a reduction in microbial community richness, but an increase in the relative abundance of species linked to PAHs degradation. These PAHs-degradation bacteria acting as keystone species, maintained a microbial network complexity similar to that of the control treatment. Exposure to individual NPs resulted in a reduction in the complexity of microbial networks. Furthermore, when PAHs and NPs were simultaneously present, the toxic effect of NPs hindered the presence of keystone species involved in PAHs degradation, subsequently limiting the degradation of PAHs by marine microorganisms, resulting in a decrease in community diversity and symbiotic network complexity. This situation potentially poses a heightened threat to the ecological stability of marine ecosystems. Our work strengthened the understanding of the combined impact of NPs and PAHs on microorganisms in seawater.

Tween-80 enhanced biodegradation of naphthalene by Klebsiella quasipneumoniae

Accidental spillage of petroleum products and industrial activities result in various hydrocarbons in the environment. While the n-hydrocarbons are readily degraded, the polycyclic aromatic hydrocarbons (PAHs) are recalcitrant to natural degradation, toxic to aquatic life and are responsible for diverse health challenges in terrestrial animals; suggesting the need for faster and more eco-friendly ways of removing PAHs from the environment. In this study, the surfactant tween-80 was used to enhance a bacterium's intrinsic naphthalene biodegradation activity. Eight bacteria isolated from oil-contaminated soils were characterised using morphological and biochemical methods. The most effective strain was identified as Klebsiella quasipneumoniae using 16S rRNA gene analysis. High-Performance Liquid Chromatography (HPLC) analyses showed that the detectable concentration of naphthalene was decreased from 500 to 157.18 μg/mL (67.4%) after 7 d in the absence of tween-80, while 99.4% removal was achieved in 3 d in the presence of tween-80 at 60 μg/mL concentration. The peaks observed in the Fourier Transform Infra-Red Spectroscopy (FTIR) spectrum of control (naphthalene), which were absent in that of the metabolites, further established naphthalene degradation. Furthermore, Gas Chromatography-Mass Spectrometer (GCMS) revealed metabolites of single aromatic ring, such as 3,4-dihydroxybenzoic acid 4-hydroxylmethylphenol, which confirmed that the removal of naphthalene is by biodegradation. Tyrosinase induction and laccase activities suggested the involvement of these enzymes in naphthalene biodegradation by the bacterium. Conclusively, a strain of K. quasipneumoniae that can effectively remove naphthalene from contaminated environments has been isolated, and its biodegradation rate was doubled in the presence of non-ionic surfactant, tween-80.

A novel dehydrocoenzyme activator combined with a composite microbial agent TY for enhanced bioremediation of crude oil-contaminated soil

Bioaugmentation (BA) and biostimulation (BS) synergistic remediation is an effective remediation strategy for oil-contaminated soil. In this study, the optimal combination system of composite microbial agent TY (Achromobacter: Pseudomona = 2:1) and dehydrocoenzyme activator (NaNO₃ (7.0 g/L), (NH₄)₂HPO₄ (1.0 g/L), riboflavin (6.0 mg/L)) was screened. Under the best combination system, the degradation rate of crude oil in oil-contaminated soil reached 79.44% after 60 d, which was 1.74 times and 1.23 times higher than that of compound microbial agent TY treatment and dehydrogenase activator treatment, respectively. In addition, a highly efficient combination system was found to target the degradation of oil C₁₀-C₂₈ fractions by gas chromatography (GC). The increased abundance of dehydrogenase coenzymes such as flavin nucleotides (FAD and FMN), coenzyme I (NAD⁺, Co I) and coenzyme II (NADP⁺, Co II) as well as dioxygenases and monooxygenases promote the degradation of crude oil. Furthermore, the dominant genera at the genus level in soil were analyzed by high-throughput sequencing, which were Nocardioides (46.48%-56.07%), Gordonia (11.40%-14.61%), Intrasporangiaceae (5.05%-10.58%), Pseudomonas (1.39%-1.92%) and Dietzia (0.64%-2.77%). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis showed that the abundance of genes associated with crude oil degradation such as ABC transporters (2.89%), fatty acid (1.04%), carbon metabolism (4.5%) and aromatic compound (0.92%) was assigned enhanced after 60 d of remediation. These results indicated that the combination system of the compound bacterium TY and the dehydrocoenzyme activator is a propective option for the bioremediation of oil-contaminated soil.

Degradation of long-chain n-alkanes by a novel thermal-tolerant Rhodococcus strain

A novel bacterial strain, CH91, was isolated from a high-temperature oil reservoir. Morphological characterization, phylogenetic analyses of 16S rRNA gene sequence and genome relatedness indicated that the strain is a potential new species in the genus Rhodococcus. Strain CH91 could grow in the temperature range of 25-50 °C (optimally at 37 °C) and utilize a broad range of long-chain n-alkanes from hexadecane to hexatriacontane. The utilization of the n-alkanes mixture of strain CH91 revealed that the degradation rate was correlated to the length of the carbon chain. Two novel alkB genes encoding alkane 1-monooxygenase were found in the genome of this strain. The protein sequences of both alkane 1-monooxygenases showed a remarkable phylogenetic distance to other reported AlkB protein sequences. These results would help broaden our knowledge about alkane degradation by Rhodocuccus and its potential ecological role. The ability of the strain in the long-chain alkane degradation and thermal tolerance could also be further exploited for bioremediation of oil contaminations and microbial enhanced oil recovery.

Bioaugmentation as a green technology for hydrocarbon pollution remediation. Problems and prospects

Environmental pollution mitigation measure involving bioremediation technology is a sustainable intervention for a greener ecosystem biorecovery, especially the obnoxious hydrocarbons, xenobiotics, and other environmental pollutants induced by anthropogenic stressors. Several successful case studies have provided evidence to this paradigm including the putative adoption that the technology is eco-friendly, cost-effective, and shows a high tendency for total contaminants mineralization into innocuous bye-products. The present review reports advances in bioremediation, types, and strategies conventionally adopted in contaminant clean-up. It identified that natural attenuation and biostimulation are faced with notable limitations including the poor remedial outcome under the natural attenuation system and the residual contamination occasion following a biostimulation operation. It remarks that the use of genetically engineered microorganisms shows a potentially promising insight as a prudent remedial approach but is currently challenged by few ethical restrictions and the rural unavailability of the technology. It underscores that bioaugmentation, particularly the use of high cell density assemblages referred to as microbial consortia possess promising remedial prospects thus offers a more sustainable environmental security. The authors, therefore, recommend bioaugmentation for large scale contaminated sites in regions where environmental degradation is commonplace.

Characterization and genomic analysis of Exiguobacterium alkaliphilum B-3531D, an efficient crude oil degrading strain

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B-3531D is the first E. alkaliphilum strain with fully assembled genome.

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It is the first E. alkaliphilum strain with the ability to utilize crude oil.

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Strain utilized 34.5% of crude oil for 14 days at 28 °C and a salinity of 11%.

The aim of the work was to carry out the physiological, biochemical and genetic characterization of the Exiguobacterium alkaliphilum B-3531D strain. This strain is promising for use in the field of environmental biotechnology, since it has a pronounced ability to utilize crude oil and individual hydrocarbons in a wide temperature range. The genome of the strain was sequenced and completely assembled, it consists of a 2,903,369 bp circular chromosome and two circular plasmids, namely, pE73 (73,590 bp) and pE52 (52,125 bp). When cultivated in a mineral medium containing 2% of crude oil, the strain utilized 50% within 30 days of the experiment. In simulated seawater with the same oil content, the loss of hydrocarbons was 45% over the same period. For the first time we observed in an E. alkaliphilum strain the ability to efficiently utilize crude oil, including with an increased content of sodium chloride in the cultivation medium.

Prokaryotic community diversity during bioremediation of crude oil contaminated oilfield soil: effects of hydrocarbon concentration and salinity

Crude oil extracted from oilfield reservoirs brings together hypersaline produced water. Failure in pipelines transporting this mixture causes contamination of the soil with oil and hypersaline water. Soil salinization is harmful to biological populations, impairing the biodegradation of contaminants. We simulated the contamination of a soil from an oilfield with produced water containing different concentrations of NaCl and crude oil, in order to evaluate the effect of salinity and hydrocarbon concentration on prokaryote community structure and biodegradation activity. Microcosms were incubated in CO₂-measuring respirometer. After the incubation, residual aliphatic hydrocarbons were quantified and were performed 16S rRNA gene sequencing. An increase in CO₂ emission and hydrocarbon biodegradation was observed with increasing oil concentration up to 100 g kg^-1. Alpha diversity decreased in oil-contaminated soils with an increase in the relative abundance of Actinobacteria and reduction of Bacteroidetes with increasing oil concentration. In the NaCl-contaminated soils, alpha diversity, CO₂ emission, and hydrocarbon biodegradation decreased with increasing NaCl concentration. There was an increase in the relative abundance of Firmicutes and Proteobacteria and a reduction of Actinobacteria with increasing salt concentration. Our results highlight the need to adopt specific bioremediation strategies in soils impacted by mixtures of crude oil and hypersaline produced water.

New benzo(a)pyrene-degrading strains of the Burkholderia cepacia complex prospected from activated sludge in a petrochemical wastewater treatment plant

The prospection of bacteria that are resistant to polyaromatic hydrocarbons (PAH) of activated sludge from a Petrochemical Wastewater Treatment Plant (WWTP) allows investigating potential biodegraders of PAH. For this purpose, sludge samples were cultured with benzo(a)pyrene and/or naphthalene as carbon sources. The recovered isolates were characterized by biochemical methods and identified based on the analysis of the sequence of three genes: 16S, recA and gyrB. The isolated strains were shown to be capable of producing surfactants, which are important for compound degradation. The ability to reduce benzo(a)pyrene in vitro was tested by gas chromatography. After 20 days of experiment, the consortium that was enriched with 1 mg/L of benzo(a)pyrene was able to reduce 30% of the compound when compared to a control without bacteria. The four isolated strains that significantly reduced benzo(a)pyrene belong to the Burkholderia cepacia complex and were identified within the consortium as the species B. cenocepacia IIIa, B. vietnamiensis, B. cepacia, and B. multivorans. This finding demonstrates the biotechnological potential of the B. cepacia complex strains for use in wastewater treatment and bioremediation. Previous studies on hydrocarbon-degrading strains focused mainly on contaminated soil or marine areas. In this work, the strains were prospected from activated sludge in a WWTP and showed the potential of indigenous samples to be used in both improving treatment systems and bioremediation of areas contaminated with petrochemical waste.

Strategy to improve crude oil biodegradation in oligotrophic aquatic environments: W/O/W fertilized emulsions and hydrocarbonoclastic bacteria

We studied petroleum biodegradation by biostimulation by using water in oil in water (W/O/W) double emulsions. These emulsions were developed using seawater, canola oil, surfactants, and mineral salts as sources of NPK. The emulsions were used in the simulation of hydrocarbon bioremediation in oligotrophic sea water. Hydrocarbon biodegradation was evaluated by CO2 emissions from microcosms. We also evaluated the release of inorganic nutrients and the stability of the emulsion's droplets. The double emulsions improved CO2 emission from the microcosms, suggesting the increase in the hydrocarbon biodegradation. Mineral nutrients were gradually released from the emulsions supporting the hydrocarbon biodegradation. This was attributed to the formation of different diameters of droplets and therefore, varying stabilities of the droplets. Addition of the selected hydrocarbonoclastic isolates simulating bioaugmentation improved the hydrocarbon biodegradation. We conclude that the nutrient-rich W/O/W emulsion developed in this study is an effective biostimulation agent for bioremediation in oligotrophic aquatic environments.

Leading edges in bioremediation technologies for removal of petroleum hydrocarbons

There is a worldwide concern regarding soil pollution caused by contamination of petroleum hydrocarbon, released during oil processing or production. Once a spill occurs, it disturbs the marine and freshwater ecosystem and greatly threatens human health. It usually requires complex technologies to remove it from soil. Petroleum hydrocarbons contain a range of chemicals which are extremely toxic and carcinogenic in nature. Although physical or chemical methods are widely employed for remediation, numerous studies revealed that bioremediation is a sustainable approach. Bioremediation is often preferred as clean and carbon-neutral solution. This review aims to provide series of sustainable solution for petroleum hydrocarbon degradation without exploiting the environment as well as opportunity to reuse treated media. Integrated and enhanced bioremediation technologies are more effective than natural degradation of petroleum hydrocarbons in terms of shorter time period and percent removal efficiency. It comprehensively illustrates bioremediation assisted with bacteria, fungi, and algae either by integrated technologies or by enhancing the process. Most recent application methods of petroleum hydrocarbon bioremediation (in situ and ex situ) are also reported. There is dire need to explore different cost-effective biotechnological resources for degradation of petroleum hydrocarbon by the screening of novel microbial strains or by the creation of genetically engineered bacteria to survive in harsh environment.

Phenanthrene removal and response of bacterial community in the combined system of photocatalysis and PAH-degrading microbial consortium in laboratory system

This work aimed to study the removal of phenanthrene, change of bacterial community and microbial functions through combined photocatalysis and biodegradation under ultraviolet (UV) and visible light illumination. Results showed that phenanthrene removal was enhanced in combined system irradiated by UV and visible light. High-throughput sequencing of 16S rRNA gene manifested that alpha diversity (richness, evenness and diversity) got promoted and data of relative abundance reported that Planococcaceae as the dominant bacteriawas replaced by Pseudomonadaceae, with some other functional bacteria quickly acclimatizing. Difference analysis indicated that top fifteen genera were generally different significantly (p < 0.001) among two distinct samples, particularly for Pseudomonas on relative abundance. Functional features' regulation suggested that the bacterial community not only protected itself well but also participated in degrading phenanthrene. Selecting suitable degrading microbial consortium from natural environment and understanding deeply on performance of bacterial community contribute to assemble effective and directional combined system.

Microbial diversity and bioremediation of rhizospheric soils from Trindade Island - Brazil

Pristine environments may harbor complex microbial communities with metabolic potential for use in bioremediation of organic pollutants. This study aimed to evaluate crude oil biodegradation by microbial communities present in rhizospheric soils of Bulbostylis nesiotis and Cyperus atlanticus on Trindade Island and the compositional structure of these communities. After 60 days under aerobic conditions, Total Petroleum Hydrocarbon biodegradation ranged from 66 to 75%, depending on the plant species and the origin of the soil samples. There was no response of petroleum biodegradation to fertilization with N:P:K (80:160:80 mg dm^-3). Soil contamination with crude oil did not necessarily reduce microbial diversity. The richness and diversity increased in contaminated soils in some specific situations. We conclude that microbial communities from pristine soils have the ability to remove hydrocarbons through biodegradation and that Bulbostylis nesiotis and Cyperus atlanticus inhabiting Trindade Island harbor rhizospheric microbial communities with potential for application in rhizoremediation.

Degradation of crude oil by mixed cultures of bacteria isolated from the Qinghai-Tibet plateau and comparative analysis of metabolic mechanisms

This study investigates the biodegradation of crude oil by a mixed culture of bacteria isolated from the Qinghai-Tibet plateau using gas chromatography-mass spectrometer (GC-MS) and the gravimetric method. The results showed that a mixed culture has a stronger ability to degrade hydrocarbon than pure cultures. Once both Nocardia soli Y48 and Rhodococcus erythropolis YF28-1 (8) were present in a culture, the culture demonstrated the highest crude oil removal efficiency of almost 100% after 10 days of incubation at 20 °C. Moreover, further analysis of the degradation mechanisms used by the above strains, which revealed utilization of different n-alkane substrates, indicated the diversity of evolution and variations in different strains, as well as the importance of multiple metabolic mechanisms for alkane degradation. Therefore, it is concluded that a mixed culture of Y48 and YF28-1 (8) strains can provide a more effective method for bioremediation of hydrocarbon-contaminated soil in permafrost regions.

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.

Aliphatic Hydrocarbon Enhances Phenanthrene Degradation by Autochthonous Prokaryotic Communities from a Pristine Seawater

The microbial diversity and functioning around oceanic islands is poorly described, despite its importance for ecosystem homeostasis. Here, we aimed to verify the occurrence of microbe-driven phenanthrene co-oxidation in the seawater surrounding the Trindade Island (Brazil). We also used Next-Generation Sequencing to evaluate the effects of aliphatic and polycyclic aromatic hydrocarbons (PAHs) on these microbial community assemblies. Microcosms containing seawater from the island enriched with either labelled (9-¹⁴C) or non-labelled phenanthrene together with hexadecane, weathered oil, fluoranthene or pyrene, and combinations of these compounds were incubated. Biodegradation of phenanthrene-9-¹⁴C was negatively affected in the presence of weathered oil and PAHs but increased in the presence of hexadecane. PAH contamination caused shifts in the seawater microbial community-from a highly diverse one dominated by Alphaproteobacteria to less diverse communities dominated by Gammaproteobacteria. Furthermore, the combination of PAHs exerted a compounded negative influence on the microbial community, reducing its diversity and thus functional capacity of the ecosystem. These results advance our understanding of bacterial community dynamics in response to contrasting qualities of hydrocarbon contamination. This understanding is fundamental in the application and monitoring of bioremediation strategies if accidents involving oil spillages occur near Trindade Island and similar ecosystems.

Draft genome of Nocardia farcinica TRH1, a linear and polycyclic aromatic hydrocarbon-degrading bacterium isolated from the coast of Trindade Island, Brazil

Here, we report the draft genome sequence and annotation of Nocardia farcinica TRH1, a petroleum hydrocarbons degrading Actinobacteria isolated from the coastal water of Trindade Island, Brazil.

Enhanced biodegradation of PAHs by microbial consortium with different amendment and their fate in in-situ condition

Microbial degradation is a useful tool to prevent chemical pollution in soil. In the present study, in-situ bioremediation of polyaromatic hydrocarbons (PAHs) by microbial consortium consisting of Serratia marcescens L-11, Streptomyces rochei PAH-13 and Phanerochaete chrysosporium VV-18 has been reported. In preliminary studies, the consortium degraded nearly 60-70% of PAHs in broth within 7 days under controlled conditions. The same consortium was evaluated for its competence under natural conditions by amending the soil with ammonium sulphate, paddy straw and compost. Highest microbial activity in terms of dehydrogenase, FDA hydrolase and aryl esterase was recorded on the 5(th) day. The degradation rate of PAHs significantly increased up to 56-98% within 7 days under in-situ however almost complete dissipation (83.50-100%) was observed on the 30(th) day. Among all the co-substrates evaluated, faster degradation of PAHs was observed in compost amended soil wherein fluorene, anthracene, phenanthrene and pyrene degraded with half-life of 1.71, 4.70, 2.04 and 6.14 days respectively. Different degradation products formed were also identified by GC-MS. Besides traces of parent PAHs eleven non-polar and five polar products were identified by direct and silylation reaction respectively. Various products formed indicated that consortium was capable to degrade PAHs by oxidation to mineralization.

Is the increase in oil pollution a possibility of the presence of diverse microorganisms? An experimental dataset on oil prevalent areas of Goa, India

Survey data and wet lab reports presented in this paper were collected from Western coastlines of India from Goan beaches. Oil polluted areas were captured on camera as evidence for oil and tar pollution. Several microorganisms showing diverse characteristics such as pigment producers, salt tolerant and hydrocarbon resistance were isolated and cultured in the laboratory. The dataset presented in this paper supports “A case study on effects of oil spills and tar-ball pollution on beaches of Goa (India)” (Rekadwad and Khobragade, 2015) [1] and “Microbial diversity of oil spills and tar resistant bacteria isolated from beaches of Goa (India)” (Rekadwad and Khobragade, 2016) [2].

Draft Genome of Rhodococcus rhodochrous TRN7, Isolated from the Coast of Trindade Island, Brazil

Here, we present a draft genome and annotation of Rhodococcus rhodochrous TRN7, isolated from Trindade Island, Brazil, which will provide genetic data to benefit the understanding of its metabolism.

Bioremediation strategies of hydrocarbons and microbial diversity in the Trindade Island shoreline--Brazil

This study analyzed the microbial diversity colonizing the surface of an oil sample during its contact with water, off the Trindade Island coast and simulated the efficiency of eight different bioremediation strategies for this environment. The diversity analysis was performed using acrylic coupons that served as the support for an oil inclusion at sea. The coupons were sampled over 30 days, and T-RFLP multiplex was employed to access the diversity of fungi, Bacteria and Archaea present on the oil surface. The bioremediation strategies were simulated in a respirometer. The results showed that the bacterial domain was the most dominant in oil colonization and that the richness of the species attached to the oil gradually increases with the exposure time of the coupons. The combination of biostimulation and bioaugmentation with a native population was proven to be an effective strategy for the remediation of oil off the Trindade Island shoreline.