Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era

Cohesive phycoremediation of pyrene by freshwater microalgae Selenastrum sp. and biodiesel production and its assessment

In this study, the freshwater microalgae Selenastrum sp. was assessed for the effective degradation of pyrene and simultaneous production of biodiesel from pyrene-tolerant biomass. The growth of algae was determined based on the cell dry weight, cell density, chlorophyll content, and biomass productivity under different pyrene concentrations. Further, lipids from pyrene tolerant culture were converted into biodiesel by acid-catalyzed transesterification, which was characterized for the total fatty acid profile by gas chromatography. Increased pyrene concentration revealed less biomass yield and productivity after 20 days of treatment, indicating potent pyrene biodegradation by Selenastrum sp. Biomass yield was unaffected till the 20 mg/L pyrene. A 95% of pyrene bioremediation was observed at 20 days of culturing. Lipid accumulation of 22.14%, as evident from the estimation of the total lipid content, indicated a marginal increase in corroborating pyrene stress in the culture. Fatty acid methyl esters yield of 63.06% (% per 100 g lipids) was noticed from the pyrene tolerant culture. Moreover, fatty acid profile analysis of biodiesel produced under 10 mg/L and 20 mg/L pyrene condition showed escalated levels of desirable fatty acids in Selenastrum sp., compared to the control. Further, Selenastrum sp. and other freshwater microalgae are catalogued for sustainable development goals attainment by 2030, as per the UNSDG (United Nations Sustainable Development Goals) agenda. Critical applications for the Selenastrum sp. in bioremediation of pyrene, along with biodiesel production, are enumerated for sustainable and renewable energy production and resource management.

Evaluation of surfactant-aided polycyclic aromatic hydrocarbon biodegradation by molecular docking and molecular dynamic simulation in the marine environment

Marine oil spills directly cause polycyclic aromatic hydrocarbons (PAHs) pollution and affect marine organisms due to their toxic property. Chemical and bio-based dispersants composed of surfactants and solvents are considered effective oil spill-treating agents. Dispersants enhance oil biodegradation in the marine environment by rapidly increasing their solubility in the water column. However, the effect of dispersants, especially surfactants, on PAHs degradation by enzymes produced by microorganisms has not been studied at the molecular level. The role of the cytochrome P450 (CYP) enzyme in converting contaminants into reactive metabolites during the biodegradation process has been evidenced, but the activity in the presence of surfactants is still ambiguous. Thus, this study focused on the evaluation of the impact of chemical and bio-surfactants (i.e., Tween 80 (TWE) and Surfactin (SUC)) on the biodegradation of naphthalene (NAP), chrysene (CHR), and pyrene (PYR), the representative components of PAHs, with CYP enzyme from microalgae Parachlorella kessleri using molecular docking and molecular dynamics (MD) simulation. The molecular docking analysis revealed that PAHs bound to residues at the CYP active site through hydrophobic interactions for biodegradation. The MD simulation showed that the surfactant addition changed the enzyme conformation in the CYP-PAH complexes to provide more interactions between the enzyme and PAHs. This led to an increase in the enzyme's capability to degrade PAHs. Binding free energy (ΔG‌‌Bind) calculations confirmed that surfactant treatment could enhance PAHs degradation by the enzyme. The SUC gave a better result on NAP and PYR biodegradation based on ΔG‌‌Bind, while TWE facilitated the biodegradation of CHR. The research outputs could greatly facilitate evaluating the behaviors of oil spill-treating agents and oil spill response operations in the marine environment.

Three strategy rules of filamentous fungi in hydrocarbon remediation: an overview

Remediation of hydrocarbon contaminations requires much attention nowadays since it causes detrimental effects on land and even worse impacts on aquatic environments. Tools of bioremediation especially filamentous fungi permissible for cleaning up as much as conceivable, at least they turn into non-toxic residues with less consumed periods. Inorganic chemicals, CO2, H2O, and cell biomass are produced as a result of the breakdown and mineralization of petroleum hydrocarbon pollutants. This paper presents a detailed overview of three strategic rules of filamentous fungi in remediating the various aliphatic, and aromatic hydrocarbon compounds: utilizing carbons from hydrocarbons as sole energy, Co-metabolism manners (Enzymatic and Non-enzymatic theories), and Biosorption approaches. Upliftment in the degradation rate of complex hydrocarbon by the Filamentous Fungi in consortia scenario we can say, "Fungal Talk", which includes a variety of cellular mechanisms, including biosurfactant production, biomineralization, and precipitation, etc., This review not only displays its efficiency but showcases the field applications - cost-effective, reliable, eco-friendly, easy to culture as biomass, applicable in both land and any water bodies in operational environment cleanups. Nevertheless, the potentiality of fungi-human interaction has not been fully understood, henceforth further studies are highly endorsed with spore pathogenicity of the fungal species capable of high remediation rate, and the gene knockout study, if the specific peptides cause toxicity to any living matters via Genomics and Proteomics approaches, before application of any in situ or ex situ environments.

Evaluating the productivity and bioremediation potential of two tropical marine algae in petroleum hydrocarbon polluted tropical marine water

Bioremediation using tropical marine algae provides cost effective and eco-friendly alternative mean of removing toxic and harmful substances from the environment. Bioremediation is an important tool in sustainable environmental management and protection. This study examined the productivity and bioremediation potential of Nannochloropsis oculata and Porphyridium cruentum in Water Soluble Fraction (WSF) of petroleum fuels by investigating the growth of Nannochloropsis oculata and Porphyridium cruentum at 0%, 10% 20% 30% 40% 50% 75% 100% of WSF of kerosene, diesel, and gasoline. Growth was monitored optically every two days for fourteen days using 721 Visible Spectrophotometer. Productivity was measured using prescribed procedure. Bioremediation potential of test algae were examined using standard method for the GC analysis of diesel range organics in 100% WSFs. The minimum growth for both species was recorded at 100% in all the fuels. The maximum growth of Porphyridium cruentum was obtained at 10% in all fuels, while the maximum growth of Nannochloropsis oculata was obtained at 30% in both kerosene and gasoline and at 50% in diesel. Whereas Porphyridium cruentum was greatly inhibited by all fuels, Nannochloropsis oculata was stimulated at lower concentration of the fuels. Nannochloropsis oculata proved more efficient for bioremediation of the petroleum fuels with 84.58%, 65.51% and 70.77% removal efficiency for kerosene, diesel and gasoline respectively, while Porphyridium cruentum was 58.94%, 46.64% and 56.67% respectively. Nannochloropsis oculata is a very strong and reliable candidate for bioremediation of petroleum hydrocarbons and should be subjected to further examination for sustainable and eco-friendly remediation of petroleum pollution.

Engineering green wall botanical biofiltration to abate indoor volatile organic compounds: A review on mechanisms, phyllosphere bioaugmentation, and modeling

Indoor air pollution affects the global population, especially in developed countries where people spend around 90% of their time indoors. The recent pandemic exacerbated the exposure by relying on indoor spaces and a teleworking lifestyle. VOCs are a group of indoor air pollutants with harmful effects on human health at low concentrations. It is widespread that plants can remove indoor VOCs. To this day, research has combined principles of phytoremediation, biofiltration, and bioremediation into a holistic and sustainable technology called botanical biofiltration. Overall, it is sustained that its main advantage is the capacity to break down and biodegrade pollutants using low energy input. This differs from traditional systems that transfer VOCs to another phase. Furthermore, it offers additional benefits like decreased indoor air health costs, enhanced work productivity, and well-being. However, many disparities exist within the field regarding the role of plants, substrate, and phyllosphere bacteria. Yet their role has been theorized; its stability is poorly known for an engineering approach. Previous research has not addressed the bioaugmentation of the phyllosphere to increase the performance, which could boost the system. Moreover, most experiments have studied passive potted plant systems at a lab scale using small chambers, making it difficult to extrapolate findings into tangible parameters to engineer the technology. Active systems are believed to be more efficient yet require more maintenance and knowledge expertize; besides, the impact of the active flow on the long term is not fully understood. Besides, modeling the system has been oversimplified, limiting the understanding and optimization. This review sheds light on the field's gains and gaps, like concepts, experiments, and modeling. We believe that embracing a multidisciplinary approach encompassing experiments, multiphysics modeling, microbial community analysis, and coworking with the indoor air sector will enable the optimization of the technology and facilitate its adoption.

Batch-mode degradation of high-strength phenolic pollutants by Pseudomonas aeruginosa strain STV1713 immobilized on single and hybrid matrices

Controlled environments are pivotal in all bioconversion processes, influencing the efficacy of biocatalysts. In this study, we designed a batch bioreactor system with a packed immobilization column and a decontamination chamber to enhance phenol and 2,4-dichlorophenol degradation using the hyper-tolerant bacterium Pseudomonas aeruginosa STV1713. When free cells were employed to degrade phenol and 2,4-DCP at a concentration of 1000 mg/L, the cells completely removed the pollutants within 28 h and 66 h, respectively. Simultaneous reductions in chemical oxygen demand and biological oxygen demand were observed (phenol: 30.21 mg/L/h and 16.92 mg/L/h, respectively; 2,4-dichlorophenol: 12.85 mg/L/h and 7.21 mg/L/h, respectively). After assessing the degradation capabilities, the bacterium was immobilized on various matrices (sodium alginate, alginate-chitosan-alginate and polyvinyl alcohol-alginate) to enhance pollutant removal. Hybrid immobilized cells exhibited greater tolerance and degradation capabilities than those immobilized in a single matrix. Among them, polyvinyl alcohol-alginate immobilized cells displayed the highest degradation capacities (up to 2000 mg/L for phenol and 2500 mg/L for 2,4-dichlorophenol). Morphological analysis of the immobilized cells revealed enhanced cell preservation in hybrid matrices. Furthermore, the elucidation of the metabolic pathway through the catechol dioxygenase enzyme assay indicated higher activity of the catechol 1,2-dioxygenase enzyme, suggesting that the bacterium employed an ortho-degradation mechanism for pollutant removal. Additionally, enzyme zymography confirmed the presence of catechol 1,2-dioxygenase, with the molecular weight of the enzyme determined as 245 kDa.

Effect of ultra-violet light radiation on Scenedesmus vacuolatus growth kinetics, metabolic performance, and preliminary biodegradation study

This study presents the effect of ultra-violet (UV) light radiation on the process kinetics, metabolic performance, and biodegradation capability of Scenedesmus vacuolatus. The impact of the UV radiation on S. vacuolatus morphology, chlorophyll, carotenoid, carbohydrates, proteins, lipid accumulation, growth rate, substrate affinity and substrate versatility were evaluated. Thereafter, a preliminary biodegradative potential of UV-exposed S. vacuolatus on spent coolant waste (SCW) was carried out based on dehydrogenase activity (DHA) and total petroleum hydrocarbon degradation (TPH). Pronounced structural changes were observed in S. vacuolatus exposed to UV radiation for 24 h compared to the 2, 4, 6, 12 and 48 h UV exposure. Exposure of S. vacuolatus to UV radiation improved cellular chlorophyll (chla = 1.89-fold, chlb = 2.02-fold), carotenoid (1.24-fold), carbohydrates (4.62-fold), proteins (1.44-fold) and lipid accumulations (1.40-fold). In addition, the 24 h UV exposed S. vacuolatus showed a significant increase in substrate affinity (1/Ks) (0.959), specific growth rate (µ) (0.024 h-1) and biomass accumulation (0.513 g/L) by 1.50, 2 and 1.9-fold respectively. Moreover, enhanced DHA (55%) and TPH (100%) degradation efficiency were observed in UV-exposed S. vacuolatus. These findings provided major insights into the use of UV radiation to enhance S. vacuolatus biodegradative performance towards sustainable green environment negating the use of expensive chemicals and other unfriendly environmental practices.

Biodegradation of benzo[a]pyrene by a marine Chlorella vulgaris LH-1 with heterotrophic ability

In this study, a microalga, Chlorella vulgaris LH-1, with heterotrophic ability to degrade BaP was explored. The effect of BaP concentration on microalga growth was investigated, and the possible biodegradation mechanism of BaP was proposed. Results showed that low BaP concentration (<5 mg/L) had less negative influence on the growth of this microalga under mixotrophic condition, but high BaP concentration (>5 mg/L) had a significant inhibitory effect on its growth. During heterotrophic cultivation, low BaP concentration (<20 mg/L) promoted the growth of C. vulgaris LH-1, whereas high BaP concentration (>20 mg/L) inhibited its growth significantly. The degradation rates of mixotrophic and heterotrophic C. vulgaris LH-1 were 62.56 %-74.13 % and 52.07 %-71.67 %, respectively, when the BaP concentration ranged from 0.5 mg/L to 2 mg/L. The expression of functional enzyme genes of C. vulgaris LH-1 such as phenol 2-monooxygenase activity, protocatechuate 3,4-dioxygenase activity, catechol 1,2-dioxygenase activity, styrene degradation, and benzoate degradation were upregulated in the process of BaP degradation. C. vulgaris LH-1 may degrade BaP by monooxygenase and dioxygenase simultaneously. The degradation of BaP by this microalga under mixotrophic condition goes through the degradation pathway of phthalic acid, whereas it goes through the degradation pathway of benzoic acid under heterotrophic condition.

Microalgae mediated bioremediation of polycyclic aromatic hydrocarbons: Strategies, advancement and regulations

Polycyclic aromatic hydrocarbons (PAHs) are pervasive in the atmosphere and are one of the emerging pollutants that cause harmful effects in living systems. There are some natural and anthropogenic sources that can produce PAHs in an uncontrolled way. Several health hazards associated with PAHs like abnormality in the reproductive system, endocrine system as well as immune system have been explained. The mutagenic or carcinogenic effects of hydrocarbons in living systems including algae, vertebrates and invertebrates have been discussed. For controlling PAHs, biodegradation has been suggested as an effective and eco-friendly process. Microalgae-based biosorption and biodegradation resulted in the removal of toxic contaminants. Microalgae both in unialgal form and in consortium (with bacteria or fungi) performed good results in bioaccumulation and biodegradation. In the present review, we highlighted the general information about the PAHs, conventional versus advanced technology for removal. In addition microalgae based removal and toxicity is discussed. Furthermore this work provides an idea on modern scientific applications like genetic and metabolic engineering, nanomaterials-based technologies, artificial neural network (ANN), machine learning (ML) etc. As rapid and effective methods for bioremediation of PAHs. With several pros and cons, biological treatments using microalgae are found to be better for PAH removal than any other conventional technologies.

Update on new trend and progress of the mechanism of polycyclic aromatic hydrocarbon biodegradation by Rhodococcus, based on the new understanding of relevant theories: a review

Rapid industrial and societal developments have led to substantial increases in the use and exploitation of petroleum, and petroleum hydrocarbon pollution has become a serious threat to human health and the environment. Polycyclic aromatic hydrocarbons (PAHs) are primary components of petroleum hydrocarbons. In recent years, microbial remediation of PAHs pollution has been regarded as the most promising and cost-effective treatment measure because of its low cost, robust efficacy, and lack of secondary pollution. Rhodococcus bacteria are regarded as one of main microorganisms that can effectively degrade PAHs because of their wide distribution, broad degradation spectrum, and network-like evolution of degradation gene clusters. In this review, we focus on the biological characteristics of Rhodococcus; current trends in PAHs degradation based on knowledge maps; and the cellular structural, biochemical, and enzymatic basis of degradation mechanisms, along with whole genome and transcriptional regulation. These research advances provide clues for the prospects of Rhodococcus-based applications in environmental protection.

Microbial genome (Illumina MiSeq) sequencing of drinking water treatment residuals to evaluate compatibility with environmental applications

The clarification of drinking water leads to the production of large quantities of water treatment residuals (WTRs). DNA was extracted from six WTR samples collected from water treatment plants within the UK to compare their bacterial communities and examine whether factors such as coagulant usage (aluminium versus iron salt), the type of water source (reservoir or river), or leachable chemical composition influence these communities. Bacterial 16S variable region 4 (V4) was amplified and sequenced using Illumina MiSeq sequencing. The most abundant phyla in WTR samples were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes, collectively representing 92.77-97.8% of the total bacterial sequences. Statistical analysis of microbial profiles indicated that water source played a significant role in microbial community structure, diversity, and richness, however coagulant type did not. PERMANOVA analysis showed that no single chemical variable (pH, organic matter, or extractable element concentration) influenced microbial composition significantly; however, canonical correspondence analysis of WTR microbiomes yielded a model using all these variables that could be used to explain variations in microbial community structures of WTRs (p < 0.05). No common, potentially toxic cyanobacteria, or related pathogens of concern were found. Analysis with PICRUSt showed that WTRs all had similar predicted microbial functional profiles. Overall, the results indicate that WTRs analysed in this study are unlikely to pose any threat to soil microbial community structure when applied to land as a soil conditioner or enhancer and may help to enhance the soil microbial community.

Microalgae biofilm system as an efficient tool for wastewater remediation and potential bioresources for pharmaceutical product production: an overview

The role of microalgae in wastewater remediation and metabolite production has been well documented, but the limitations of microalgae harvesting and low biomass production call for a more sustainable method of microalgae utilization. The current review gives an insight on how microalgae biofilms can be utilized as a more efficient system for wastewater remediation and as potential source of metabolite for pharmaceutical product production. The review affirms that the extracellular polymeric substance (EPS) is the vital component of the microalgae biofilm because it influences the spatial organization of the organisms forming microalgae biofilm. The EPS is also responsible for the ease interaction between organisms forming microalgae biofilm. This review restate the crucial role play by EPS in the removal of heavy metals from water to be due to the presence of binding sites on its surface. This review also attribute the ability of microalgae biofilm to bio-transform organic pollutant to be dependent on enzymatic activities and the production of reactive oxygen species (ROS). The review assert that during the treatment of wastewater, the wastewater pollutants induce oxidative stress on microalgae biofilms. The response of the microalgae biofilm toward counteracting the stress induced by ROS leads to production of metabolites. These metabolites are important tools that can be harness for the production of pharmaceutical products.

New insights into the bioremediation of petroleum contaminants: A systematic review

Petroleum product is an essential resource for energy, that has been exploited by wide range of industries and regular life. A carbonaceous contamination of marine and terrestrial environments caused by errant runoffs of consequential petroleum-derived contaminants. Additionally, petroleum hydrocarbons can have adverse effects on human health and global ecosystems and also have negative demographic consequences in petroleum industries. Key contaminants of petroleum products, primarily includes aliphatic hydrocarbons, benzene, toluene, ethylbenzene, and xylene (BTEX), polycyclic aromatic hydrocarbons (PAHs), resins, and asphaltenes. On environmental interaction, these pollutants result in ecotoxicity as well as human toxicity. Oxidative stress, mitochondrial damage, DNA mutations, and protein dysfunction are a few key causative mechanisms behind the toxic impacts. Henceforth, it becomes very evident to have certain remedial strategies which could help on eliminating these xenobiotics from the environment. This brings the efficacious application of bioremediation to remove or degrade pollutants from the ecosystems. In the recent scenario, extensive research and experimentation have been implemented towards bio-benign remediation of these petroleum-based pollutants, aiming to reduce the load of these toxic molecules in the environment. This review gives a detailed overview of petroleum pollutants, and their toxicity. Methods used for degrading them in the environment using microbes, periphytes, phyto-microbial interactions, genetically modified organisms, and nano-microbial remediation. All of these methods could have a significant impact on environmental management.

Halobacteria-Based Biofertilizers: A Promising Alternative for Enhancing Soil Fertility and Crop Productivity under Biotic and Abiotic Stresses-A Review

Abiotic and biotic stresses such as salt stress and fungal infections significantly affect plant growth and productivity, leading to reduced crop yield. Traditional methods of managing stress factors, such as developing resistant varieties, chemical fertilizers, and pesticides, have shown limited success in the presence of combined biotic and abiotic stress factors. Halotolerant bacteria found in saline environments have potential as plant promoters under stressful conditions. These microorganisms produce bioactive molecules and plant growth regulators, making them a promising agent for enhancing soil fertility, improving plant resistance to adversities, and increasing crop production. This review highlights the capability of plant-growth-promoting halobacteria (PGPH) to stimulate plant growth in non-saline conditions, strengthen plant tolerance and resistance to biotic and abiotic stressors, and sustain soil fertility. The major attempted points are: (i) the various abiotic and biotic challenges that limit agriculture sustainability and food safety, (ii) the mechanisms employed by PGPH to promote plant tolerance and resistance to both biotic and abiotic stressors, (iii) the important role played by PGPH in the recovery and remediation of agricultural affected soils, and (iv) the concerns and limitations of using PGHB as an innovative approach to boost crop production and food security.

Enhanced remediation of oil-contaminated intertidal sediment by bacterial consortium of petroleum degraders and biosurfactant producers

Oil pollution in intertidal zones is an important environmental issue that has serious adverse effects on coastal ecosystems. This study investigated the efficacy of a bacterial consortium constructed from petroleum degraders and biosurfactant producers in the bioremediation of oil-polluted sediment. Inoculation of the constructed consortium significantly enhanced the removal of C₈-C₄₀n-alkanes (80.2 ± 2.8% removal efficiency) and aromatic compounds (34.4 ± 10.8% removal efficiency) within 10 weeks. The consortium played dual functions of petroleum degradation and biosurfactant production, greatly improving microbial growth and metabolic activities. Real-time quantitative polymerase chain reaction (PCR) showed that the consortium markedly increased the proportions of indigenous alkane-degrading populations (up to 3.88-times higher than that of the control treatment). Microbial community analysis demonstrated that the exogenous consortium activated the degradation functions of indigenous microflora and promoted synergistic cooperation among microorganisms. Our findings indicated that supplementation of a bacterial consortium of petroleum degraders and biosurfactant producers is a promising bioremediation strategy for oil-polluted sediments.

Significance of microbial genome in environmental remediation

Environmental pollutants seriously threaten the ecosystem and health of various life forms, particularly with the rapid industrialization and emerging population. Conventionally physical and chemical strategies are being opted for the removal of these pollutants. Bioremediation, through several advancements, has been a boon to combat the existing threat faced today. Microbes with enzymes degrade various pollutants and utilize them as a carbon and energy source. With the existing demand and through several research explorations, Genetically Engineered Microorganisms (GEMs) have paved to be a successful approach to abate pollution through bioremediation. The genome of the microbe determines its biodegradative nature. Thus, methods including pure culture techniques and metagenomics are used for analyzing the genome of microbes, which provides information about catabolic genes. The information obtained along with the aid of biotechnology helps to construct GEMs that are cost-effective and safer thereby exhibiting higher degradation of pollutants. The present review focuses on the role of microbes in the degradation of environmental pollutants, role of evolution in habitat and adaptation of microbes, microbial degenerative genes, their pathways, and the efficacy of recombinant DNA (rDNA) technology for creating GEMs for bioremediation. The present review also provides a gist of existing GEMs for bioremediation and their limitations, thereby providing a future scope of implementation of these GEMs for a sustainable environment.

Filamentous fungi for sustainable remediation of pharmaceutical compounds, heavy metal and oil hydrocarbons

This review presents a comprehensive summary of the latest research in the field of bioremediation with filamentous fungi. The main focus is on the issue of recent progress in remediation of pharmaceutical compounds, heavy metal treatment and oil hydrocarbons mycoremediation that are usually insufficiently represented in other reviews. It encompasses a variety of cellular mechanisms involved in bioremediation used by filamentous fungi, including bio-adsorption, bio-surfactant production, bio-mineralization, bio-precipitation, as well as extracellular and intracellular enzymatic processes. Processes for wastewater treatment accomplished through physical, biological, and chemical processes are briefly described. The species diversity of filamentous fungi used in pollutant removal, including widely studied species of Aspergillus, Penicillium, Fusarium, Verticillium, Phanerochaete and other species of Basidiomycota and Zygomycota are summarized. The removal efficiency of filamentous fungi and time of elimination of a wide variety of pollutant compounds and their easy handling make them excellent tools for the bioremediation of emerging contaminants. Various types of beneficial byproducts made by filamentous fungi, such as raw material for feed and food production, chitosan, ethanol, lignocellulolytic enzymes, organic acids, as well as nanoparticles, are discussed. Finally, challenges faced, future prospects, and how innovative technologies can be used to further exploit and enhance the abilities of fungi in wastewater remediation, are mentioned.

Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation

Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.

Marine-derived fungi as biocatalysts

Marine microorganisms account for over 90% of ocean biomass and their diversity is believed to be the result of their ability to adapt to extreme conditions of the marine environment. Biotransformations are used to produce a wide range of high-added value materials, and marine-derived fungi have proven to be a source of new enzymes, even for activities not previously discovered. This review focuses on biotransformations by fungi from marine environments, including bioremediation, from the standpoint of the chemical structure of the substrate, and covers up to September 2022.

Fungal assisted bio-treatment of environmental pollutants with comprehensive emphasis on noxious heavy metals: Recent updates

In the present time of speedy developments and industrialization, heavy metals are being uncovered in aquatic environment and soil via refining, electroplating, processing, mining, metallurgical activities, dyeing and other several metallic and metal based industrial and synthetic activities. Heavy metals like lead (Pb), mercury (Hg), cadmium (Cd), arsenic (As), Zinc (Zn), Cobalt (Co), Iron (Fe), and many other are considered as seriously noxious and toxic for the aquatic environment, human, and other aquatic lives and have damaging influences. Such heavy metals, which are very tough to be degraded, can be managed by reducing their potential through various processes like removal, precipitation, oxidation-reduction, bio-sorption, recovery, bioaccumulation, bio-mineralization etc. Microbes are known as talented bio-agents for the heavy metals detoxification process and fungi are one of the cherished bio-sources that show noteworthy aptitude of heavy metal sorption and metal tolerance. Thus, the main objective of the authors was to come with a comprehensive review having methodological insights on the novel and recent results in the field of mycoremediation of heavy metals. This review significantly assesses the potential talent of fungi in heavy metal detoxification and thus, in environmental restoration. Many reported works, methodologies and mechanistic sights have been evaluated to explore the fungal-assisted heavy metal remediation. Herein, a compact and effectual discussion on the recent mycoremediation studies of organic pollutants like dyes, petroleum, pesticides, insecticides, herbicides, and pharmaceutical wastes have also been presented.

Synergy between microalgae and microbiome in polluted waters

Microalga-microbiome interactions are central to both health and disease of aquatic environments. Despite impressive advances in deciphering how microorganisms participate in and impact aquatic ecosystems, the evolution and ecological involvement of microalgae and the microbiome in polluted waters are typically studied independently. Here, the phycosphere (i.e., the consortia of microalgae and the related microbiome) is regarded as an independent and integrated life form, and we summarize the survival strategies exhibited by this symbiont when exposed to anthropogenic pollution. We highlight the cellular strategies and discuss the modulation at the transcriptional and population levels, which reciprocally alters community structure or genome composition for medium-term acclimation or long-term adaptation. We propose a 'PollutantBiome' concept to help the understanding of microalga-microbiome interactions and development of beneficial microbial synthetic communities for pollutant remediation.

Wide distribution of the sad gene cluster for sub-terminal oxidation in alkane utilizers

Alkane constitutes major fractions of crude oils, and its microbial aerobic degradation dominantly follows the terminal oxidation and the sub-terminal pathways. However, the latter one received much less attention, especially since the related genes were yet to be fully defined. Here, we isolated a bacterium designated Acinetobacter sp. strain NyZ410, capable of growing on alkanes with a range of chain lengths and derived sub-terminal oxidation products. From its genome, a secondary alcohol degradation gene cluster (sad) was identified to be likely involved in converting the aliphatic secondary alcohols (the sub-terminal oxidation products of alkanes) to the corresponding primary alcohols by removing two-carbon unit. On this cluster, sadC encoded an alcohol dehydrogenase converting the aliphatic secondary alcohols to the corresponding ketones; sadD encoded a Baeyer-Villiger monooxygenase catalysing the conversion of the aliphatic ketones to the corresponding esters; SadA and SadB are two esterases hydrolyzing aliphatic esters to the primary alcohols and acetic acids. Bioinformatics analyses indicated that the sad cluster was widely distributed in the genomes of probable alkane degraders, apparently coexisting (64%) with the signature enzymes AlkM and AlmA for alkane terminal oxidation in 350 bacterial genomes. It suggests that the alkane sub-terminal oxidation may be more ubiquitous than previously thought.

Bioremediation of Crude Oil by Haematococcus Pluvialis: A Preliminary Study

Nowadays, oil pollution is one of the main environmental problems. The current methods for recovering spills mainly involve chemical agents, but scientific research has focused on more natural and less harmful techniques for the environment, including a consortium of bacteria and microalgae to clean up water contaminated by hydrocarbons. The purpose of this preliminary study was to evaluate the ability of a microalga belonging to Chlorophyceae to grow in the presence of crude oil and remove the principal contaminants. H. pluvialis, which is usually used for nutraceutical purposes, thanks to the production of astaxanthin, was able to grow in anaerobic conditions, varying its metabolism from autotrophic to heterotrophic, exploiting the carbon present in the solution deriving from the presence of 1% of crude oil. Furthermore, the results of bioremediation showed a relevant reduction in chemical pollutants such as nitrate, fluoride, sulfate, and phosphate. The most important aspect of the study was the reduction after 160 days in the hydrocarbon concentration inside not only the culture medium (−32%) but also the algal biomass (−80.25%), demonstrating an optimized degradation rather than a simple absorption inside the alga.

Biodegradation of Petroleum Hydrocarbons by Drechsleraspicifera Isolated from Contaminated Soil in Riyadh, Saudi Arabia

Currently, the bioremediation of petroleum hydrocarbons employs microbial biosurfactants because of their public acceptability, biological safety, and low cost. These organisms can degrade or detoxify organic-contaminated areas, such as marine ecosystems. The current study aimed to test the oil-biodegradation ability of the fungus Drechslera spicifera, which was isolated from contaminated soil samples in Riyadh, Saudi Arabia. We used hydrocarbon tolerance, scanning electron microscopy, DCPIP, drop-collapse, emulsification activity, recovery of biosurfactants, and germination assays to assess the biodegradation characteristics of the D. spicifera against kerosene, crude, diesel, used, and mixed oils. The results of DCPIP show that the highest oxidation (0.736 a.u.) was induced by crude oil on the 15th day. In contrast, kerosene and used oil had the highest measurements in emulsification activity and drop-collapse assays, respectively. Meanwhile, crude and used oils produced the highest amounts of biosurfactants through acid precipitation and solvent extraction assays. Furthermore, the biosurfactants stimulated the germination of tomato seeds by more than 50% compared to the control. These findings highlight the biodegradation ability of D. spicifera, which has been proven in the use of petroleum oils as the sole source of carbon. That might encourage further research to demonstrate its application in the cleaning of large, contaminated areas.

A critical review of oil spills in the Niger Delta aquatic environment: causes, impacts, and bioremediation assessment

The Niger Delta region in South-South Nigeria, on Africa's West Coast, is densely populated. The region, which contains a substantial stock of crude oil and natural gas, has been nicknamed "the engine room" for Nigeria's economic development and progress. It is responsible for up to 90% of the country's economic growth (or gross domestic product/GDP). The region has multiple ecosystems, such as the aquatic environment, that are critical to the survival of the area's various habitats and living species. However, the same region has witnessed unjustifiable environmental pollution arising from oil activities over the years of exploration and production which has orchestrated negative consequences on the Niger Delta ecosystem. This has led to extended negative consequences on natural resources, which also have detrimental repercussions psychologically, ecologically, socially, economically, and physically which, in turn, impacts the overall health of the affected individuals. This write-up provides an overview of the major drivers of the oil leakage in Nigeria's Niger Delta ecosystem as well as the major impacts on the environment. It will also analyze numerous means of remediation in use and extend such for a more inclusive and productive option. Moreover, this review offers key measures that may help to maintain long-term policies for reducing adverse implications and increasing the living standard for the Niger Delta area's affected communities.

Potential Use of Deep-Sea Sediment Bacteria for Oil Spill Biodegradation: A Laboratory Simulation

Deep-sea sedimentary hydrocarbonoclastic bacteria are still not widely used in the bioremediation field, especially for crude oil spill biodegradation. This study utilized a mixed culture of Raoultella sp., Enterobacter sp., and Pseudomonas sp. isolated from deep-sea sediment to determine the abilities of bacteria to degrade petroleum hydrocarbons while incorporating environmental variations in a microcosm study. The oil biodegradation extent was determined by measuring the remaining oil and grease in the sample vials. The highest percentage of biodegradation was 88.6%, with a constant degradation rate of 0.399 day^–1. GC-MS analysis showed that the most degradable compound in the oil samples was paraffin. This study also observed that microbial degradation was optimized within three days of exposure and that degradation ability decreased at 35 °C. The salinity variation effects were insignificant. Based on all analyses, deep-sea sediment bacteria have great potential in oil spill biodegradation in a microcosm scale.

Sustainable strategies for combating hydrocarbon pollution: Special emphasis on mobil oil bioremediation

The global rise in industrialization and vehicularization has led to the increasing trend in the use of different crude oil types. Among these mobil oil has major application in automobiles and different machines. The combustion of mobil oil renders a non-usable form that ultimately enters the environment thereby causing problems to environmental health. The aliphatic and aromatic hydrocarbon fraction of mobil oil has serious human and environmental health hazards. These components upon interaction with soil affect its fertility and microbial diversity. The recent advancement in the omics approach viz. metagenomics, metatranscriptomics and metaproteomics has led to increased efficiency for the use of microbial based remediation strategy. Additionally, the use of biosurfactants further aids in increasing the bioavailability and thus biodegradation of crude oil constituents. The combination of more than one approach could serve as an effective tool for efficient reduction of oil contamination from diverse ecosystems. To the best of our knowledge only a few publications on mobil oil have been published in the last decade. This systematic review could be extremely useful in designing a micro-bioremediation strategy for aquatic and terrestrial ecosystems contaminated with mobil oil or petroleum hydrocarbons that is both efficient and feasible. The state-of-art information and future research directions have been discussed to address the issue efficiently.

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.

Fungi Can Be More Effective than Bacteria for the Bioremediation of Marine Sediments Highly Contaminated with Heavy Metals

The contamination of coastal marine sediments with heavy metals (HMs) is a widespread phenomenon that requires effective remediation actions. Bioremediation based on the use of bacteria is an economically and environmentally sustainable effective strategy for reducing HM contamination and/or toxicity in marine sediments. However, information on the efficiency of marine-derived fungi for HM decontamination of marine sediments is still largely lacking, despite evidence of the performance of terrestrial fungal strains on other contaminated matrixes (e.g., soils, freshwater sediments, industrial wastes). Here, we carried out for the first time an array of parallel laboratory experiments by using different combinations of chemical and microbial amendments (including acidophilic autotrophic and heterotrophic bacteria, as well as filamentous marine fungi) for the bioremediation of highly HM-contaminated sediments of the Portman Bay (NW Mediterranean Sea), an area largely affected by long-term historical discharges of mine tailings. Our results indicate that the bioleaching performance of metals from the sediment is based on the addition of fungi (Aspergillus niger and Trichoderma sp.), either alone or in combination with autotrophic bacteria, was higher when compared to other treatments. In particular, fungal addition allowed obtaining bioleaching yields for As eight times higher than those by chemical treatments and double compared with the addition of bacteria alone. Moreover, in our study, the fungal addition was the only treatment allowing effective bioleaching of otherwise not mobile fractions of Zn and Cd, thus overtaking bacterial treatments. We found that the lower the sediment pH reached by the experimental conditions, as in the case of fungal addition, the higher the solubilization yield of metals, suggesting that the specific metabolic features of A. niger and Trichoderma sp. enable lowering sediment pH and enhance HM bioleaching. Overall, our findings indicate that fungi can be more effective than acidophilic autotrophic and heterotrophic bacteria in HM bioleaching, and as such, their use can represent a promising and efficient strategy for the bioremediation of marine sediments highly contaminated with heavy metals.

How Do Fungi Survive in the Sea and Respond to Climate Change?

With the over 2000 marine fungi and fungal-like organisms documented so far, some have adapted fully to life in the sea, while some have the ability to tolerate environmental conditions in the marine milieu. These organisms have evolved various mechanisms for growth in the marine environment, especially against salinity gradients. This review highlights the response of marine fungi, fungal-like organisms and terrestrial fungi (for comparison) towards salinity variations in terms of their growth, spore germination, sporulation, physiology, and genetic adaptability. Marine, freshwater and terrestrial fungi and fungal-like organisms vary greatly in their response to salinity. Generally, terrestrial and freshwater fungi grow, germinate and sporulate better at lower salinities, while marine fungi do so over a wide range of salinities. Zoosporic fungal-like organisms are more sensitive to salinity than true fungi, especially Ascomycota and Basidiomycota. Labyrinthulomycota and marine Oomycota are more salinity tolerant than saprolegniaceous organisms in terms of growth and reproduction. Wide adaptability to saline conditions in marine or marine-related habitats requires mechanisms for maintaining accumulation of ions in the vacuoles, the exclusion of high levels of sodium chloride, the maintenance of turgor in the mycelium, optimal growth at alkaline pH, a broad temperature growth range from polar to tropical waters, and growth at depths and often under anoxic conditions, and these properties may allow marine fungi to positively respond to the challenges that climate change will bring. Other related topics will also be discussed in this article, such as the effect of salinity on secondary metabolite production by marine fungi, their evolution in the sea, and marine endophytes.

Oil Spill Governance: Evidence from Bintan Island, Indonesia

Issues of oil spills in various locations worldwide have been widely published in several studies. However, studies on policy management and strategies for handling cases related to oil spills are still limited. As one of the largest oil-producing countries with international shipping traffic, Indonesia is vulnerable to oil spills. Therefore, by drawing upon evidence from Bintan Island, this study aims to provide recommendations for stakeholders concerning governance and policy to address the oil spill case, which has had adverse social, economic, and environmental impacts. Data were collected from semi-structured interviews, focus group discussion, observation, actual online news, and official government reports using a case study approach. The result indicates that the local government is slow in responding to Bintan Island’s reoccurring yearly oil spillage. Policy responses are still focused on repressive and conventional methods. Hence, preventive and multi-stakeholder governance is required to handle oil spills. Furthermore, this study provides an overview of the oil spill problem and its management strategy in developing countries, especially Indonesia.

Transcriptomic analyses reveal increased expression of dioxygenases, monooxygenases, and other metabolizing enzymes involved in anthracene degradation in the marine alga Ulva lactuca

To analyze the mechanisms involved in anthracene (ANT) degradation in the marine alga Ulva lactuca, total RNA was obtained from the alga cultivated without ANT and with 5 μM of ANT for 24 h, and transcriptomic analyses were performed. A de novo transcriptome was assembled, transcripts differentially expressed were selected, and those overexpressed were identified. Overexpressed transcripts potentially involved in ANT degradation were: one aromatic ring dioxygenase, three 2-oxoglutarate Fe (II) dioxygenases (2-OGDOs), and three dienelactone hydrolases that may account for anthraquinone, phthalic anhydride, salicylic acid, and phthalic acid production (pathway 1). In addition, two flavin adenine dinucleotide (FAD)-dependent monooxygenases, four cytP450 monooxygenases, two epoxide hydrolase, one hydroxyphenylpyruvic acid dioxygenase (HPPDO), and two homogentisic acid dioxygenases (HGDOs) were identified that may also participate in ANT degradation (pathway 2). Moreover, an alkane monooxygenase (alkB), two alcohol dehydrogenases, and three aldehyde dehydrogenases were identified, which may participate in linear hydrocarbon degradation (pathway 3). Furthermore, the level of transcripts encoding some of mentioned enzymes were quantified by qRT-PCR are in the alga cultivated with 5 μM of ANT for 0-48 h, and those more increased were 2-OGDO, HGDO, and alkB monooxygenase. Thus, at least three pathways for ANT and linear hydrocarbons degradation may be existed in U. lactuca. In addition, ANT metabolites were analyzed by gas chromatography and mass spectrometry (GC-MS), allowing the identification of anthraquinone, phthalic anhydride, salicylic acid, and phthalic acid, thus validating the pathway 1.