Monitoring of microbial hydrocarbon remediation in the soil

Bioremediation of petroleum hydrocarbons polluted soil by spent mushroom substrates: Microbiological structure and functionality

Spent mushroom substrate (SMS) holds valuable microbiota that can be useful in remediating polluted soils with hydrocarbons. However, the microorganisms behind the bioremediation process remain uncertain. In this work, a bioremediation assay of total petroleum hydrocarbons (TPHs) polluted soil by SMS application was performed to elucidate the microorganisms and consortia involved in biodegradation by a metabarcoding analysis. Untreated polluted soil was compared to seven bioremediation treatments by adding SMS of Agaricus bisporus, Pleurotus eryngii, Pleurotus ostreatus, and combinations. Soil microbial activity, TPH biodegradation, taxonomic classification, and predictive functional analysis were evaluated in the microbiopiles at 60 days. Different metagenomics approaches were performed to understand the impact of each SMS on native soil microbiota and TPHs biodegradation. All SMSs enhanced the degradation of aliphatic and aromatic hydrocarbons, being A. bisporus the most effective, promoting an efficient consortium constituted by the bacterial families Alcanivoraceae, Alcaligenaceae, and Dietziaceae along with the fungal genera Scedosporium and Aspergillus. The predictive 16 S rRNA gene study partially explained the decontamination efficacy by observing changes in the taxonomic structure of bacteria and fungi, and changes in the potential profiles of estimated degradative genes across the different treatments. This work provides new insights into TPHs bioremediation.

Spatial distribution characteristics and degradation mechanism of microorganisms in n-hexadecane contaminated vadose zone

The damage caused by petroleum hydrocarbon pollution to soil and groundwater environment is becoming increasingly significant. The vadose zone is the only way for petroleum hydrocarbon pollutants to leak from surface into groundwater. The spatial distribution characteristics of indigenous microorganisms in vadose zone, considering presence of capillary zones, have rarely been reported. To explore the spatial distribution characteristics of indigenous microorganisms in vadose zone contaminated by petroleum hydrocarbons, a one-dimensional column migration experiment was conducted using n-hexadecane as characteristic pollutant. Soil samples were collected periodically from different heights during experiment. Corresponding environmental factors were monitored online. The microbial community structure and spatial distribution characteristics of the cumulative relative abundance were systematically analyzed using 16S rRNA sequencing. In addition, the microbial degradation mechanism of n-hexadecane was analyzed using metabolomics. The results showed that presence of capillary zone had a strong retarding effect on n-hexadecane infiltration. Leaked pollutants were mainly concentrated in areas with strong capillary action. Infiltration and displacement of NAPL-phase pollutants were major driving force for change in moisture content (θ) and electric conductivity (EC) in vadose zone. The degradation by microorganisms results in a downward trend in potential of hydrogen (pH) and oxidation-reduction potential (ORP). Five petroleum hydrocarbon-degrading bacterial phyla and 11 degradable straight-chain alkane bacterial genera were detected. Microbial degradation was strong in the area near edge of capillary zone and locations of pollutant accumulation. Mainly Sphingomonas and Nocardioides bacteria were involved in microbial degradation of n-hexadecane. Single-end oxidation involved microbial degradation of n-hexadecane (C16H34). The oxygen consumed, hexadecanoic acid (C16H32O2) produced during this process, and release of hydrogen ions (H+) were the driving factors for reduction of ORP and pH. The vadose zone in this study considered presence of capillary zone, which was more in line with actual contaminated site conditions compared with previous studies. This study systematically elucidated vertical distribution characteristics of petroleum hydrocarbon pollutants and spatiotemporal variation characteristics of indigenous microorganisms in vadose zone considered presence of capillary zone. In addition, the n-hexadecane degradation mechanism was elucidated using metabolomics. This study provides theoretical support for development of natural attenuation remediation measures for petroleum-hydrocarbon-contaminated soil and groundwater.

Microbial remediation of petroleum-contaminated soil focused on the mechanism and microbial response: a review

The environmental pollution caused by petroleum hydrocarbons has received considerable attention in recent years. Microbial remediation has emerged as the preferred method for the degradation of petroleum hydrocarbons, which is experiencing rapid development driven by advancements in molecular biology. Herein, the capacity of different microorganisms used for crude oil bioremediation was reviewed. Moreover, factors influencing the effectiveness of microbial remediation were discussed. Microbial remediation methods, such as bioaugmentation, biostimulation, and bioventilation, are summarized in this review. Aerobic and anaerobic degradation mechanisms were reviewed to elucidate the metabolic pathways involved. The impacts of petroleum hydrocarbons on microorganisms and the environment were also revealed. A brief overview of synthetic biology and a unique perspective of technique combinations were presented to provide insight into research trends. The challenges and future outlook were also presented to stimulate contemplation of the mechanisms involved and the development of innovative techniques.

High-performance diesel biodegradation using biogas digestate as microbial inoculum in lab-scale solid supported bioreactors

Industrial anaerobic digestion (AD) produces biogas and a digestate that is usually applied as a biofertilizer. However, the study and application of this by-product in terms of its rich microbial diversity and high metabolic activity have been barely investigated. In this work, the digestate regarded as an inoculum-without any further manipulation-was faced to a target hydrocarbon (i.e., diesel oil) to explore its biodegradation capability and potential application in bioaugmentation strategies. Lab-scale single batch bioreactors with solid support (i.e., sand or gravel) embedded with the inoculum and diesel were used to improve bioaccessibility and biofilm formation. In addition, different experimental conditions were assayed varying the initial diesel concentration, microbial load, type of solid support, inoculum aging time, and presence or absence of oxygen. Remaining diesel concentration, dehydrogenase activity and microbial community structure were periodically determined. Remarkably, this low-cost consortium was capable of a significant reduction (>90%) in the concentration of diesel, within 14 days and when the initial load was as high as 6950 mg/kg dry solid support. Furthermore, a 10-fold increment in dehydrogenase activity, alongside an increase in the abundance of hydrocarbon-degrading bacterial groups, and the enrichment of genes for alkane monooxygenase and aromatic ring-hydroxylating dioxygenases, encourage further study of this consortium for bioremediation purposes.

Metabolic capacity to alter polycyclic aromatic hydrocarbons and its microbe-mediated remediation

The elimination of contaminants caused by anthropogenic activities and rapid industrialization can be accomplished using the widely used technology of bioremediation. Recent years have seen significant advancement in our understanding of the bioremediation of coupled polycyclic aromatic hydrocarbon contamination caused by microbial communities including bacteria, algae, fungi, yeast, etc. One of the newest techniques is microbial-based bioremediation because of its greater productivity, high efficiency, and non-toxic approach. Microbes are appealing candidates for bioremediation because they have amazing metabolic capacity to alter most types of organic material and can endure harsh environmental conditions. Microbes have been characterized as extremophiles that can survive in a variety of environmental circumstances, making them the treasure troves for environmental cleanup and the recovery of contaminated soil. In this study, the mechanisms underlying the bioremediation process as well as the current situation of microbial bioremediation of polycyclic aromatic hydrocarbon are briefly described.

Isolation and characterization of fungi and bacteria able to grow on media containing gasoline and diesel fuel

Petroleum products are significant environmental pollutants. This study aimed to isolate microorganisms able to grow on media containing gasoline and diesel fuel. Microorganisms were isolated from soils sampled near gasoline and diesel pumps. Bacterial isolates were characterized and tested on media containing concentrations ranging from 10 to 100 % gasoline and diesel fuel and combinations of both 50/50 % and 25/25/50 % (gasoline/ diesel/ Mueller Hinton broth). Results showed that microbial isolates belong to the genera Pseudomonas, Bacillus, Staphylococcus, Micrococcus, Flavobacterium, Actinobacteria, Penicillium, Hansfordia and Alternaria. Pseudomonas spp. and Bacillus spp. showed the ability to grow on both products up to the concentration of 80 %. However, no growth was noticed above that concentration and on both mixtures. Throughout this study, it has been shown that using a selective screening method for microorganisms able to grow on pollutants can present a significant advantage for bioremediation. Keywords: Pollution; gasoline; diesel; microorganisms.

Role of Indigenous Bacteria in Corrosion of Two Types of Carbon Steel

This study aimed to investigate the presence of both aerobic and anaerobic bacteria in a water sample collected from a nuclear power plant and establish if the indigenous bacteria or the products of their metabolic activities could initiate the corrosion of two different types of carbon steel (i.e., A570, 1045). The aerobic (heterotrophic, iron-oxidizing) and anaerobic (sulfate-reducing) bacteria were detected in low numbers in the water sample. Three bacterial strains were isolated by the enrichment procedure from this sample. Based on phenotypic and genotypic characteristics, the isolated bacteria were identified as Stenotrophomonas maltophilia IBB_Cn1 (MT893712), Stenotrophomonas maltophilia IBB_Cn2 (MT893713), and Bacillus thuringiensis IBB_Cn3 (MT893714). The bacteria existing in the water sample were able to initiate the corrosion of carbon steel A570 and 1045. The sulfate-reducing bacteria were detected in higher numbers than the heterotrophic bacteria and iron-oxidizing bacteria at the end of the biocorrosion experiments. The carbon steel coupons revealed macroscopic and microscopic changes in the surface characteristics, and these changes could be due to biofilm formation on their surfaces and the accumulation of the corrosion products. The corrosion rate varied from one type of carbon steel to another, depending on the incubation conditions and the chemical composition of the coupons.

Isolation and identification of promising antibiotic-producing bacteria

Multiple stresses in waste dumpsite soils can drive antibiotic production as one of the strategies for survival. Bacteria are the most prolific producers of antibiotics. This study investigated the antibiotic production potential of bacteria isolated from Bahir Dar city municipal solid waste dumpsite (MSWDS). Bacteria were isolated from soil collected from the dumpsite on starch casein or nutrient agar. The isolates were carefully screened for antimicrobial activity against six pathogenic bacterial test strains. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were also determined from cell-free metabolites of the most promising isolates. Isolates showing antimicrobial activity were identified using cultural and biochemical methods. A total of 143 distinctive colonies were obtained and tentatively identified to 13 bacterial genera. Twenty-six (18.18%) of the isolates (six Bacillus and 20 actinobacteria related) demonstrated antimicrobial activities at least against one of the tested bacterial strains. These isolates were related to two actinobacterial and 11 other bacterial genera. Seven out of 26 isolates showed a broad-spectrum of antibiotic activities. Two isolates, which showed a wide spectrum, were selected for the MIC and MBC tests against Escherichia coli and Staphylococcus aureus. The MIC and MBC of the isolates were recorded to be 250–500 µg/mL against the test strains. Bahir Dar city MSWDS contained a high incidence of antibiotic-producing bacteria. Strain level identification of the isolates and detailed characterization of the metabolites will give a good insight into the antimicrobial production potential in the waste dumpsite.

Emerging bio-dispersant and bioremediation technologies as environmentally friendly management responses toward marine oil spill: A comprehensive review

Marine oil spills emanating from wells, pipelines, freighters, tankers, and storage facilities draw public attention and necessitate quick and environmentally friendly response measures. It is sometimes feasible to contain the oil with booms and collect it with skimmers or burn it, but this is impracticable in many circumstances, and all that can be done without causing further environmental damage is adopting natural attenuation, particularly through microbial biodegradation. Biodegradation can be aided by carefully supplying biologically accessible nitrogen and phosphorus to alleviate some of the microbial growth constraints at the shoreline. This review discussed the characteristics of oil spills, origin, ecotoxicology, health impact of marine oils spills, and responses, including the variety of remedies and responses to oil spills using biological techniques. The different bioremediation and bio-dispersant treatment technologies are then described, with a focus on the use of green surfactants and their advances, benefits/drawbacks. These technologies were thoroughly explained, with a timeline of research and recent studies. Finally, the hurdles that persist as a result of spills are explored, as well as the measures that must be taken and the potential for the development of existing treatment technologies, all of which must be linked to the application of integrated procedures.

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.

Ecotoxicity and bioremediation potential assessment of soil from oil refinery station area

PURPOSE

The aim of the present study was to evaluate the toxicity and biodegradation potential of oil hydrocarbons contaminated soil samples obtained from different depths at an oil refinery station area. An approach involving chemical, microbiological, respirometry and ecotoxicity assessment of soil polluted by oil hydrocarbons was adopted, in order to determine the biodegradability of pollutants and ecotoxicological effects of natural attenuation strategy.

METHODS

The ecotoxicity of soil samples was evaluated using an ostracod test kit and a seed germination test. The results of the phytotoxicity assay were expressed as a percentage of seedling emergence and as the relative yield of fresh and dry biomass compared to control plants. The intrinsic biodegradation potential of the contaminated soil was examined using a Micro-Oxymax respirometer. Intrinsic biodegradation rates were estimated from the slopes of linear regressions curves plotted for cumulative O₂ uptake. The obtained values were then entered in the mass balance equation for the stoichiometric reaction of hydrocarbon decomposition and converted per kg of soil per day.

RESULTS

Although the tested contaminants were biodegradable in the respirometric assay, they were slightly to moderately toxic to plants and extremely toxic to ostracods. The noxious effects raised with the increased concentration of contaminants. The monocotyledonous oat was more tolerant to higher concentrations of oil hydrocarbons than the other test plants, indicating its greater suitability for soil reclamation purposes.

CONCLUSION

By assessing phytotoxicity and effect on ostracod mortality and progress of soil self-decontamination process, proper approach of reclamation of demoted area can be provided.

From Surface Water to the Deep Sea: A Review on Factors Affecting the Biodegradation of Spilled Oil in Marine Environment

Over the past century, the demand for petroleum products has increased rapidly, leading to higher oil extraction, processing and transportation, which result in numerous oil spills in coastal-marine environments. As the spilled oil can negatively affect the coastal-marine ecosystems, its transport and fates captured a significant interest of the scientific community and regulatory agencies. Typically, the environment has natural mechanisms (e.g., photooxidation, biodegradation, evaporation) to weather/degrade and remove the spilled oil from the environment. Among various oil weathering mechanisms, biodegradation by naturally occurring bacterial populations removes a majority of spilled oil, thus the focus on bioremediation has increased significantly. Helping in the marginal recognition of this promising technique for oil-spill degradation, this paper reviews recently published articles that will help broaden the understanding of the factors affecting biodegradation of spilled oil in coastal-marine environments. The goal of this review is to examine the effects of various environmental variables that contribute to oil degradation in the coastal-marine environments, as well as the factors that influence these processes. Physico-chemical parameters such as temperature, oxygen level, pressure, shoreline energy, salinity, and pH are taken into account. In general, increase in temperature, exposure to sunlight (photooxidation), dissolved oxygen (DO), nutrients (nitrogen, phosphorous and potassium), shoreline energy (physical advection—waves) and diverse hydrocarbon-degrading microorganisms consortium were found to increase spilled oil degradation in marine environments. In contrast, higher initial oil concentration and seawater pressure can lower oil degradation rates. There is limited information on the influences of seawater pH and salinity on oil degradation, thus warranting additional research. This comprehensive review can be used as a guide for bioremediation modeling and mitigating future oil spill pollution in the marine environment by utilizing the bacteria adapted to certain conditions.

Depth-resolved microbial diversity and functional profiles of trichloroethylene-contaminated soils for Biolog EcoPlate-based biostimulation strategy

This study explores the toxic effect of TCE at different depths of sub-surface soil and underpins microbial community-level suitable carbon (C)-sources that provided directionality to the in situ biostimulation effort via augmentation strategy for effective TCE remediation in soil. The impacts on resident microbial communities and their functional profiles that govern the TCE biodegradation process were identified. Highly contaminated PW01 soil (9 m depth) had severely limited microbial diversity and was enriched in Proteobacteria and Firmicutes. The abundance of TCE degradation-associated genera was observed in all contaminated samples, and the abundance of TCE-degradation-related taxa were positively correlated with soil TCE contamination levels. Community-level metabolic activity associated with the utilization of diverse external C-sources was directly influenced by TCE concentration and soil depth. Multivariate data analysis revealed that the functional genus, TCE concentration, and selected available C substrate uptake capacity correlated in soil samples. Pearson's correlation tests revealed that C sources such as L-arginine, phenylethylamine and γ-hydroxybutyric acid utilization trait exhibited significant positive correlations with chloroalkane and chloroalkene degradation pathway abundance. Ultimately, depth and TCE contamination level-associated soil microbiota and their most preferred C-source understanding could add to facilitate effective biostimulation via external nutrient amendment for efficient in situ TCE degradation.

Diversity and Hydrocarbon-Degrading Potential of Deep-Sea Microbial Community from the Mid-Atlantic Ridge, South of the Azores (North Atlantic Ocean)

Deep-sea sediments (DSS) are one of the largest biotopes on Earth and host a surprisingly diverse microbial community. The harsh conditions of this cold environment lower the rate of natural attenuation, allowing the petroleum pollutants to persist for a long time in deep marine sediments raising problematic environmental concerns. The present work aims to contribute to the study of DSS microbial resources as biotechnological tools for bioremediation of petroleum hydrocarbon polluted environments. Four deep-sea sediment samples were collected in the Mid-Atlantic Ridge, south of the Azores (North Atlantic Ocean). Their autochthonous microbial diversity was investigated by 16S rRNA metabarcoding analysis. In addition, a total of 26 deep-sea bacteria strains with the ability to utilize crude oil as their sole carbon and energy source were isolated from the DSS samples. Eight of them were selected for a novel hydrocarbonoclastic-bacterial consortium and their potential to degrade petroleum hydrocarbons was tested in a bioremediation experiment. Bioaugmentation treatments (with inoculum pre-grown either in sodium acetate or petroleum) showed an increase in degradation of the hydrocarbons comparatively to natural attenuation. Our results provide new insights into deep-ocean oil spill bioremediation by applying DSS hydrocarbon-degrading consortium in lab-scale microcosm to simulate an oil spill in natural seawater.

Profiling of Indigenous Biosurfactant-Producing Bacillus Isolates in the Bioremediation of Soil Contaminated by Petroleum Products and Olive Oil

Petroleum is, up to this date, an inimitable nonrenewable energy resource. Petroleum leakage, which arises during transport, storage, and refining, is the most important contaminant in the environment, as it produces harm to the surrounding ecosystem. Bioremediation is an efficient method used to treat petroleum hydrocarbon-contaminated soil using indigenous microorganisms. The degradation characteristics for a variety of hydrocarbons (hexane, benzene, gasoline, and diesel) were qualitatively and quantitatively investigated using Bacillus isolates. Microbiological and biochemical methods have been used including isolation of oil-degrading bacteria, enzymatic activities, the determination of physicochemical parameters, biosurfactant production and extraction assay, oil displacement assay, antimicrobial assay of the biosurfactants, and bioremediation kinetics. Consequently, of the 60 isolates capable of degrading different hydrocarbons at fast rates, 34 were suspected to be Bacillus isolates capable of growing in 24 h or 48 h on BH medium supplemented with 2% of hexane, benzene, gasoline, diesel, and olive oil, respectively. Among the 34 isolates, 61% (21/34) are capable of producing biosurfactant-like molecules by using gasoline, 70% (24/34) with diesel oil, 85% (29/34) with hexane, and 82% (28/34) with benzene. It was found that biosurfactant-producing isolates are extractable with HCl (100%), ammonium sulphate (95%), chloroform (95%), and ethanol (100%). Biosurfactants showed stability at 20°C, 37°C, 40°C, and 60°C. Biosurfactant secreted by Bacillus strains has shown an antagonistic effect in Escherichia coli, Shigella flexneri 5a M90T, and Bacillus cereus. The selected isolates could therefore be safely used for biodegradation. Substrate biodegradation patterns by individual isolates were found to significantly differ. The study shows that benzene was degraded faster, followed by hexane, gasoline, and finally diesel. The Bacillus consortium used can decrease hydrocarbon content from 195 to 112 (g/kg) in 15 days.

Bioremediation of Polycyclic Aromatic Hydrocarbons from Industry Contaminated Soil Using Indigenous Bacillus spp

Polycyclic aromatic hydrocarbons (PAHs) are reportedly toxic, ubiquitous and organic compounds that can persist in the environment and are released largely due to the incomplete combustion of fossil fuel. There is a range of microorganisms that are capable of degrading low molecular weight PAHs, such as naphthalene; however, fewer were reported to degrade higher molecular weight PAHs. Bacillus spp. has shown to be effective in neutralizing polluted streams containing hydrocarbons. Following the growing regulatory requirement to meet the PAH specification upon disposal of contaminated soil, the following study aimed to identify potential Bacillus strains that could effectively remediate low and high molecular weight PAHs from the soil. Six potential hydrocarbon-degrading strains were formulated into two prototypes and tested for the ability to remove PAHs from industry-contaminated soil. Following the dosing of each respective soil system with prototypes 1 and 2, the samples were analyzed for PAH concentration over 11 weeks against an un-augmented control system. After 11 weeks, the control system indicated the presence of naphthalene (3.11 µg·kg−1), phenanthrene (24.47 µg·kg−1), fluoranthene (17.80 µg·kg−1) and pyrene (28.92 µg·kg−1), which illustrated the recalcitrant nature of aromatic hydrocarbons. The soil system dosed with prototype 2 was capable of completely degrading (100%) naphthalene, phenanthrene and pyrene over the experimental period. However, the accumulation of PAHs, namely phenanthrene, fluoranthene and pyrene, were observed using prototype 1. The results showed that prototype 2, consisting of a combination of Bacillus cereus and Bacillus subtilis strains, was more effective in the biodegradation of PAHs and intermediate products. Furthermore, the bio-augmented system dosed with prototype 2 showed an improvement in the overall degradation (10–50%) of PAHs, naphthalene, phenanthrene and pyrene, over the un-augmented control system. The following study demonstrates the potential of using Bacillus spp. in a bioremediation solution for sites contaminated with PAHs and informs the use of biological additives for large-scale environmental remediation.

Bioremediation of polycyclic aromatic hydrocarbons in contaminated mangroves: Understanding the historical and key parameter profiles

Sensitive biomes, such as coastal ecosystems, have become increasingly susceptible to environmental impacts caused by oil logistics and storing, which, although more efficient nowadays, still cause spills. Thus, bioremediation techniques attract attention owing to their low impact on the environment. Among petroleum-based compounds, polycyclic aromatic hydrocarbons (PAHs) are known for their potential impact and persistence in the environment. Therefore, PAH bioremediation is notably a technique capable of reducing these polluting compounds in the environment. However, there is a lack of understanding of microbial growth process conditions, leading to a less efficient choice of bioremediation methods. This article provides a review of the bioremediation processes in mangroves contaminated with oils and PAHs and an overview of some physicochemical and biological factors. Special attention was given to the lack of approach regarding experiments that have been conducted in situ and that considered the predominance of the anaerobic condition of mangroves.

Five-Year Enhanced Natural Attenuation of Historically Coal-Tar-Contaminated Soil: Analysis of Polycyclic Aromatic Hydrocarbon and Phenol Contents

The objective of this study was to assess the soil pollution on an industrial wasteland, where coal-tar was processed in the period between 1880 and 1997, and subsequent to assess the decline in the content of phenols and polycyclic aromatic hydrocarbons (PAHs) during enhanced natural attenuation. The soil of the investigated area was formed from a layer of uncompacted fill. Twelve sampling points were established in the investigated area for collecting soil samples. A study conducted in 2015 did not reveal any increase in the content of heavy metals, monoaromatic hydrocarbons (BTEX), and cyanides. However, the content of PAHs and phenols was higher than the content permitted by Polish norms in force until 2016. In the case of PAHs, it was observed for individual compounds and their total contents. Among the various methods, enhanced natural attenuation was chosen for the remediation of investigated area. Repeated analyses of the contents of phenols and PAHs were conducted in 2020. The results of the analyses showed that enhanced natural attenuation has led to efficient degradation of the simplest substances—phenol and naphthalene. The content of these compounds in 2020 was not elevated compared to the standards for industrial wastelands. The three- and four-ring hydrocarbons were degraded at a lower intensity. Based on the mean decrease in content after 5-year enhanced natural attenuation, the compounds can be arranged in the following order: phenols > naphthalene > phenanthrene > fluoranthene > benzo(a)anthracene > chrysene > anthracene.

An insight into the current oil spills and on-site bioremediation approaches to contaminated sites in Nigeria

Land oil spills in Nigeria have a long history of contaminating the soil, groundwater, vegetation, and streams with spill extension being the primary of numerous ordeals. These have left the host communities of oil fields and pipelines in crucial need of soil rehabilitation. Thus, this review provides insights into the current state of land oil spills and the effectiveness of on-site remediation approaches across communities. A total of 44 incidents of land oil spills of ≥ 500 bbl, amounting to 53,631 bbl between 2011 and 2019, was recorded by the Shell Petroleum Development Company, which primarily attributed to 83% of the total sabotage. Over 73% of the 53,631 bbl spills were unrecovered from the spill areas, which had deleterious impacts on farmlands, fishponds, rivers, and residential areas. Remediation by enhanced natural attenuation (RENA) is a feasible technique for restoring petroleum hydrocarbon-contaminated sites, but it might be ineffective when limited to tiling, windrows, and fertilizer applications due to the presence of non-biodegradable residues and contaminants beyond the aeration depth. However, bioremediation techniques ranging from non-supplemented in-situ and fertilizer supplemented in-situ to mixed in-situ and ex-situ bio-cells supplemented RENA are feasible approaches for spill sites. However, challenging limitations with regard to RENA application failures in the region include delayed responses to spill emergency, large amounts of un-recovered spilled oil, and un-implemented legislative guidelines for spill cleanup. Nevertheless, the temperature, moisture, nutrient, oxygen, and pH of the soil are essential parameters to be considered when implementing a landfarming remediation approach.

Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico

Background

Coastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites.

Methods

The potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation.

Results

We found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution.

Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment

Background

Soils polluted with animal charcoal from skin and hide cottage industries harbour extremely toxic and carcinogenic hydrocarbon pollutants and thus require a bio-based eco-friendly strategy for their depuration. The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal-polluted soil was monitored for 6 weeks in field moist microcosms consisting of CFMM-treated soil (FN4) and an untreated control (FN1). Hydrocarbon degradation was monitored using gas chromatography-flame ionization detector (GC-FID), and changes in microbial community structure were monitored using Kraken, while functional annotation of putative open reading frames (ORFs) was done using KEGG KofamKOALA and NCBI’s conserved domain database (CDD).

Results

Gas chromatographic analysis of hydrocarbon fractions revealed the removal of 84.02% and 82.38% aliphatic and 70.09% and 70.14% aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure. In the FN4 metagenome, 92.97% of the population belong to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%) and Firmicutes (11.20%), and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%), were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for aromatic hydrocarbons, benzoate, xylene, chlorocyclohexane/chlorobenzene, toluene and several others in FN1 metagenome. In the FN4 metagenome, only seven hydrocarbon degradation genes were detected.

Conclusion

This study revealed that though CFMM amendment slightly increases the rate of hydrocarbon degradation, it negatively impacts the structural and functional properties of the animal charcoal-polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-020-00089-9.

Enhanced biotreatability of petroleum hydrocarbon-contaminated mining waste coupled with the attenuation of acid drainage production

A biostimulation study was conducted on mining waste residue with nutrient (nitrogen and phosphorus) and/or liming agent (ash or CaCO₃ ) amendment to assess petroleum hydrocarbon (PHC) biodegradation efficiency by indigenous microorganisms. Compounds accumulated and/or released by treated samples were also monitored to determine the potential for acid mine drainage production during biostimulation. The potential for natural attenuation (i.e., the biodegradation of PHC contamination) was initially low but increased significantly upon nutrient addition. The best results were obtained when nutrient addition was coupled with the addition of a liming agent, notably CaCO₃ , which contributed to maintaining near-neutral pH values. In fact, during treatment without a liming agent, pH decreased due to the oxidation of sulfide minerals, resulting in acid mine drainage production with increased metals released into sample leachates. Sulfur- and iron-oxidizing bacteria were detected primarily in samples not amended with liming agents, and the predominant organisms were affiliated with Acidithiobacillus spp. and Acidiphilium spp. Overall, the results of the present study demonstrated that amendment with a liming agent when treating PHC-contaminated mining waste residue contributes to maintaining a pH close to neutrality, mitigates sulfate release, and reduces the release of metals without negatively affecting the activity of PHC degraders.

Performance enhancement of a biofilter with pH buffering and filter bed supporting material in removal of chlorobenzene

Acidic substances, which produced during chlorinated volatile organic compounds, will corrode the commonly used packing materials, and then affect the removal performance of biofiltration. In this study, three biofilters with different filter bed structure were established to treat gaseous chlorobenzene. CaCO₃ and 3D matrix material was added in filter bed as pH buffering material and filter bed supporting material, respectively. A comprehensive investigation of removal performance, biomass accumulation, microbial community, filter bed height, voidage, pressure drops, and specific surface area of the three biofilters was compared. The biofilter with CaCO₃ and 3D matrix material addition presented stable removal performance and microbial community, and greater biomass density (209.9 kg biomass/m³ filter bed) and growth rate (0.033 d^-1) were obtained by using logistic equation. After 200 days operation, the height, voidage, pressure drop, specific surface area of the filter bed consisted of perlite was 27.4 cm, 0.39, 32.8 Pa/m, 974,89 m²/m³, while those of the filter bed with CaCO₃ addition was 28.2 cm, 0.43, 21.3 Pa/m, and 1021.03 m²/m³, and those of the filter bed with CaCO₃ and 3D matrix material addition was 28.7 cm, 0.55, 17.4 Pa/m, and 1041.60 m²/m³. All the results verified the biofilter with CaCO₃ and 3D matrix material addition is capable of sustaining the long-term performance of biofilters. CaCO₃ could limit the changes of removal efficiency, microbial community and filter bed structure by buffering the pH variation. And 3D matrix material could maintain the filter bed structure by supporting the filter bed, regardless of the buffering effect.

Impact of Various Grass Species on Soil Bacteriobiome

Today, various grass species are important not only in animal feeding but, increasingly often, also in energetics and, due to esthetic and cultural values, in landscape architecture. Therefore, it is essential to establish the roles various grass species and their functional forms play in modifying soil bacteriobiome and enzymatic activity. To this end, a pot experiment was conducted to examine effects of various fodder grass and lawn grass species on the bacteriobiome and biochemical properties of soil. Nonsown soil served as the control for data interpretation. Analyses were carried out with standard and metagenomic methods. The intensity of effects elicited by grasses depended on both their species and functional form. More favorable living conditions promoting the development of soil bacteria and, thereby, enzymatic activity were offered by fodder than by lawn grass species. Among the fodder grasses, the greatest bacteriobiome diversity was caused by sowing the soil with Phleum pratense (Pp), whereas among lawn grasses in the soil sown with Poa pratensis (Pr). Among the fodder grasses, the highest enzymatic activity was determined in the soil sown with Lolium x hybridum Hausskn (Lh), and among the lawn grasses—in the soil sown with Lolium perenne. Sowing the soil with grasses caused the succession of a population of bacterial communities from r strategy to k strategy.

Gel-encapsulated microorganisms used as a strategy to rapidly recover biofilters after starvation interruption

Biosystems used for volatile organic compound (VOC) control have slow re-acclimation after extended starvation. In this study, a gel-encapsuled microorganism biofilter (GEBF) for the treatment of VOCs was used for rapid recovery after starvation interruption. Another conventional perlite biofilter (BF) was used as a control. Results showed that GEBF and BF needed 3 and 6 days for fully recovery after short-term (6 days) starvation. For long-term (20 days) starvation, GEBF fully recovered the removal performance after 9 days, whereas BF recovered only 70% within the same period. Flow cytometry analysis indicated that GEBF presented better viability state of microbial population than that in BF under starvation. The average metabolic activity of microorganisms in GEBF remained a relatively high during and after starvation (0.0049 h^-1). However, the average metabolic activity of microorganisms in BF decreased from 0.0042 h^-1 before starvation to 0.0033 h^-1 under starvation. Changes in the microbial community structure in GEBF and BF were investigated and compared by high-throughput sequencing and principal component analysis. Notably, the microbial community structure in the two biofilters showed different behavior. All these results demonstrated that the gel encapsulation of microorganisms is a promising strategy to resist starvation in biofiltration technologies.

Bacterial succession in oil-contaminated soil under phytoremediation with poplars

Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soil, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils experienced succession of bacteria over time, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.

Bioprospecting potential of microbial communities in solid waste landfills for novel enzymes through metagenomic approach

Landfills are repository for complex microbial diversity responsible for bio-degradation of solid waste. To elucidate this complexity, samples from three different landfill sites of North India (sample V: Bhalswa near Karnal byepass road, New Delhi, India; sample T: Chandigarh, India and sample S3: Una, H.P., India) were analyzed using metagenomic approach. Selected landfill sites had different geographical location, varied in waste composition, size of landfill and climate zone. For comparison, one sample from high altitude (sample J) having less human interference was taken in this study. The aim of this study was to explore microbial diversity of communities responsible for degradation of landfill. Samples were characterized by 16S rRNA gene sequencing. Data from three landfill sites showed abundance of phylum Proteobacteria while less contaminated sample from high altitude showed abundance of phylum Cholroflexi followed by phylum Proteobacteria. The most abundant genus was unknown suggesting that these landfills could be repository for various novel bacterial communities. Sample T was relatively more active in terms of microbial activity. It was relatively abundant in enzymes responsible for dioxin degradation, styrene degradation, steroid degradation, streptomycin biosynthesis, carbapenem biosynthesis, monobactam biosynthesis, furfural degradation pathways while sample J was predicted to be enriched in plant cell wall degrading enzymes. Co-occurrence analysis revealed presence of complex interaction networks between microbial assemblages responsible for bio-degradation of hydrocarbons. The data provides insights about synergetic interactions and functional interplay between bacterial communities in different landfill sites which could be further exploited to develop an effective bioremediation process.

Endophytic Bacteria in in planta Organopollutant Detoxification in Crops

Microbe-assisted organopollutant removal, or in planta crop decontamination, is based on an interactive system between organopollutant-degrading endophytic bacteria (DEB_OP) and crops in alleviating organic toxins in plants. This script focuses on the fast-growing body of literature that has recently bloomed in organopollutant control in agricultural plants. The various facets of DEB_OP under study include their colonization, distribution, plant growth-promoting mechanisms, and modes of action in the detoxification process in plants. Also, an assessment of the biotechnological advances, advantages, and bottlenecks in accelerating the implementation of this decontamination strategy will be undertaken. The highlighted key research directions from this review will shape the future of agro-environmental sustainability and preservation of human health.

Biodegradation of total petroleum hydrocarbons (TPH) in highly contaminated soils by natural attenuation and bioaugmentation

Bioremediation is an emerging and sustainable technique that can either occur naturally or be enhanced by introducing nutrients or bacteria able to degrade specific contaminants. In this study, the efficiencies of natural attenuation with nutrients, and bioaugmentation with nutrients and a consortium of five exogenous bacteria, were evaluated for total petroleum hydrocarbon (TPH) degradation in five highly contaminated soils from China, and Kuwait. The bioaugmentation treatment exhibited better efficiencies than the natural attenuation, and reached 48.10% of TPH degradation with a half-life of 41.76 d. The addition of exogenous bacteria also increased the removal of TPH in the highest contaminated soil sample. The concentration of TPH in that soil was reduced from 236, 500 mg kg^-1 of dry soil to 176, 566 mg kg^-1 of dry soil in 40 d, which was equivalent to 25.4% degradation of TPH. The degradation rate (1501.8 mg kg^-1d^-1 of TPH) was higher than those reported in previous studies with a lower concentration of TPH. The bioaugmented strains could withstand high concentrations of TPH and thrive in five different types of soils. Consequently, these strains can be used to remediate soils that are heavily contaminated with petroleum hydrocarbons.

Petroleum Hydrocarbon Contamination in Terrestrial Ecosystems-Fate and Microbial Responses

Petroleum hydrocarbons represent the most frequent environmental contaminant. The introduction of petroleum hydrocarbons into a pristine environment immediately changes the nature of that environment, resulting in reduced ecosystem functionality. Natural attenuation represents the single, most important biological process which removes petroleum hydrocarbons from the environment. It is a process where microorganisms present at the site degrade the organic contaminants without the input of external bioremediation enhancers (i.e., electron donors, electron acceptors, other microorganisms or nutrients). So successful is this natural attenuation process that in environmental biotechnology, bioremediation has developed steadily over the past 50 years based on this natural biodegradation process. Bioremediation is recognized as the most environmentally friendly remediation approach for the removal of petroleum hydrocarbons from an environment as it does not require intensive chemical, mechanical, and costly interventions. However, it is under-utilized as a commercial remediation strategy due to incomplete hydrocarbon catabolism and lengthy remediation times when compared with rival technologies. This review aims to describe the fate of petroleum hydrocarbons in the environment and discuss their interactions with abiotic and biotic components of the environment under both aerobic and anaerobic conditions. Furthermore, the mechanisms for dealing with petroleum hydrocarbon contamination in the environment will be examined. When petroleum hydrocarbons contaminate land, they start to interact with its surrounding, including physical (dispersion), physiochemical (evaporation, dissolution, sorption), chemical (photo-oxidation, auto-oxidation), and biological (plant and microbial catabolism of hydrocarbons) interactions. As microorganism (including bacteria and fungi) play an important role in the degradation of petroleum hydrocarbons, investigations into the microbial communities within contaminated soils is essential for any bioremediation project. This review highlights the fate of petroleum hydrocarbons in tertial environments, as well as the contributions of different microbial consortia for optimum petroleum hydrocarbon bioremediation potential. The impact of high-throughput metagenomic sequencing in determining the underlying degradation mechanisms is also discussed. This knowledge will aid the development of more efficient, cost-effective commercial bioremediation technologies.

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.

Effect of Organic Nutrient Addition to the Biodegradation of Hydrocarbon Contaminated Marine Sediment in Malaysia

The effect of organic nutrient on the biodegradation of hydrocarbon contaminated marine sediment in Malaysia was investigated. Biodegradation was assessed in microcosm experiments containing 10% (w/w) of crude oil amended with fertilizers in three ways, which were with inorganic nutrients (NP), organic matter in the form of plant-based (Elaeis guineensis) and fish-amendments (Scomber australasicus). It was observed that hydrocarbon degradation occurred in all treatments, with the highest biodegradation rates inS. australasicussupplemented sediment. The addition of S. australasicus managed to reduce the oil concentration to 48% while the addition ofE. guineensisand inorganic NP reduced the final oil concentration to 66% and 63% respectively. All three amendments show faster degradation rate compared to the control. Isolation of the soil sample on specific nutrient agar, centrimide, revealed the presence of Pseudomonas aeruginosa that are well known for its ability to degrade hydrocarbon in crude oil.

Toxicity assessment of fresh and weathered petroleum hydrocarbons in contaminated soil- a review

Soil contamination with total petroleum hydrocarbons (TPH) is widespread throughout the globe due to the massive production of TPH anthropogenically and its occurrence in the soil. TPH is toxic to beneficial soil organisms and humans and thus has become a serious concern among the public. Traditionally TPH toxicity in the soil is estimated based on chemical fractions and a range of bioassays including plants, invertebrates and microorganisms. There is a large inconsistency among ecotoxicology data using these assays due to the nature of TPH and their weathering. Therefore, in this article, we critically reviewed the weathered conditions of TPH, the potential fate in soil and the bioindicators for the assessment of the ecotoxicity. Based on the current research and the state-of-the-art problem, we also highlighted key recommendations for future research scope for the real-world solution of the ecotoxicological studies of hydrocarbons.

Bioprospecting for microbes with potential hydrocarbon remediation activity on the northwest coast of the Yucatan Peninsula, Mexico, using DNA sequencing

Coastal environments harbor diverse microbial communities, which can contain genera with potential bioremediation activity. Next-generation DNA sequencing was used to identify bacteria to the genus level in water and sediment samples collected from the open ocean, shoreline, wetlands and freshwater upwellings on the northwest coast of the Yucatan Peninsula. Supported by an extensive literature review, a phylogenetic investigation of the communities was done using reconstruction of unobserved states software (PICRUSt) to predict metagenome functional content from the sequenced 16S gene in all the samples. Bacterial genera were identified for their potential hydrocarbon bioremediation activity. These included generalist genera commonly reported in hydrocarbon-polluted areas and petroleum reservoirs, as well as specialists such as Alcanivorax and Cycloclasticus. The highest readings for bacteria with potential hydrocarbon bioremediation activity were for the genera Vibrio, Alteromonas, Pseudomonas, Acinetobacter, Burkholderia, Acidovorax and Pseudoalteromonas from different environments in the study area. Some genera were identified only in specific sites; for example, Aquabacterium and Polaromonas were found only in freshwater upwellings. Variation in genera distribution was probably due to differences in environmental conditions in the sampled zones. Bacterial diversity was high in the study area and included numerous genera with known bioremediation activity. Functional prediction of the metagenome indicated that the studied bacterial communities would most probably degrade toluene, naphthalene, chloroalkane and chloroalkene, with lower degradation proportions for aromatic hydrocarbons, fluorobenzoate and xylene. Differences in predicted degradation existed between sediments and water, and between different locations.

Catabolic Fingerprinting and Diversity of Bacteria in Mollic Gleysol Contaminated with Petroleum Substances

This study focused on the determination of both catabolic and genetic fingerprinting of bacteria inhabiting soil contaminated with car fuels. A surface layer (0–20 cm) of Mollic Gleysol was used for the experiment and was contaminated with car fuels—unleaded 95-octane petrol and diesel at a dose of 15 g per 10 g of soil. The experiment lasted 42 days and was performed at 20 °C. The metabolic potential of soil bacterial communities was evaluated using the Biolog EcoPlate system. The results demonstrated that petroleum substances influenced the structure of the microbial populations and their catabolic activity. The Arthrobacter, Paenibacillus, and Pseudomonas genera were found in diesel-contaminated soil, whilst Bacillus and Microbacterium were found in petrol-contaminated soil. Rhodococcus species were identified in both variants of impurities, suggesting the widest capability of car fuel degradation by this bacterial genus. The contamination with unleaded 95-octane petrol caused rapid inhibition of the metabolic activity of soil bacteria in contrast to the diesel treatment, where high metabolic activity of bacteria was observed until the end of the incubation period. Higher toxicity of petrol in comparison with diesel car fuel was evidenced.

Microbial functional responses to long-term anthropogenic impact in mangrove soils

Mangroves are coastal ecosystems of transition between terrestrial and marine environments, that have been particularly contaminated in the last decades. Organic compounds are part of these contaminants, which have increased in the environment due to industrial activities and accidental oil spills. These contaminants are toxic to higher organisms, but microorganisms can metabolize most of these compounds and thus offer a tool for bioremediation purposes. The aim of the present study was to characterize the microbial potential and activity for degradation of aromatic compounds in sediment samples from mangroves using metagenomic and metatranscriptomic approaches. Sediment samples were collected for DNA and RNA extraction from each of the mangrove sites: highly oil-impacted (Oil Mgv), anthropogenically impacted (Ant Mgv) and pristine (Prs Mgv) mangrove. Hydrocarbon concentrations in Oil Mgv sediments were higher than those observed in Ant Mgv and Prs Mgv. Genes and transcripts associated with aromatic compound degradation, particularly the meta and ortho-pathways, were more abundant in Oil Mgv and Ant Mgv suggesting that many of the aromatic compounds are being aerobically degraded by the microbiome in these sites. Functions involved in the degradation of aromatic compounds were also found in pristine site, although in lower abundance. Members of the genera Aromatoleum, Desulfococcus, Desulfatibacillum, Desulfitobacterium and Vibrio were actively involved in the detoxification of sediments affected by the oil spill. Results obtained from this study provided strong evidence that microbial degradation of aromatic compounds plays an active role in the biological response to mangrove sediment pollution and subsequent ecosystem recovery.

Role of hemoglobin in hemoglobin-based remediation of the crude oil-contaminated soil

This study investigated the changes in the indigenous microbial community structure with hemoglobin (Hb) application to determine the role of Hb in Hb-based remediation of crude oil-contaminated soil. The phylogenetic diversity of the bacterial community showed that the Hb addition selected surfactants-producing species, thereby, promoting TPH degradation. The significant increase in the CO₂ generation, which can be related to the increase in the bacterial abundance inferred from the 16S rRNA gene copy number, supports the enhanced TPH degradation with Hb application. The similar residual TPH concentrations in the presence of only hydrogen peroxide (H₂O₂) and both Hb and H₂O₂ suggested that the role of Hb as a catalyst was not as significant as the role of Hb as a nutrient. Also, in the presence of H₂O₂, a greater recovery of the microbial community structure was observed with the double Hb injection than the single Hb injection. Overall, this study shows that the Hb-based remediation strategies via microbial metabolism can be successfully applied to remediate the crude-oil contaminated Kuwaiti soil.

Potential of dissimilatory nitrate reduction pathways in polycyclic aromatic hydrocarbon degradation

This study investigates the potential of an indigenous estuarine microbial consortium to degrade two polycyclic aromatic hydrocarbons (PAHs), naphthalene and fluoranthene, under nitrate-reducing conditions. Two physicochemically diverse sediment samples from the Lima Estuary (Portugal) were spiked individually with 25 mg L^-1 of each PAH in laboratory designed microcosms. Sediments without PAHs and autoclaved sediments spiked with PAHs were run in parallel. Destructive sampling at the beginning and after 3, 6, 12, 30 and 63 weeks incubation was performed. Naphthalene and fluoranthene levels decreased over time with distinct degradation dynamics varying with sediment type. Next-generation sequencing (NGS) of 16 S rRNA gene amplicons revealed that the sediment type and incubation time were the main drivers influencing the microbial community structure rather than the impact of PAH amendments. Predicted microbial functional analyses revealed clear shifts and interrelationships between genes involved in anaerobic and aerobic degradation of PAHs and in the dissimilatory nitrate-reducing pathways (denitrification and dissimilatory nitrate reduction to ammonium - DNRA). These findings reinforced by clear biogeochemical denitrification signals (NO₃^- consumption, and NH₄⁺ increased during the incubation period), suggest that naphthalene and fluoranthene degradation may be coupled with denitrification and DNRA metabolism. The results of this study contribute to the understanding of the dissimilatory nitrate-reducing pathways and help uncover their involvement in degradation of PAHs, which will be crucial for directing remediation strategies of PAH-contaminated anoxic sediments.

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

BACKGROUND

One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life.

METHODS

Here, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed.

RESULTS

The 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation.

CONCLUSIONS

Fungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.

Metabolic Model Reconstruction and Analysis of an Artificial Microbial Ecosystem

Microbial communities are widespread in the environment, and to isolate and identify species or to determine relations among microorganisms, some 'omics methods like metagenomics, proteomics, and metabolomics have been used. When combined with various 'omics data, models known as artificial microbial ecosystems (AME) are powerful methods that can make functional predictions about microbial communities. Reconstruction of an AME model is the first step for model analysis. Many techniques have been applied to the construction of AME models, e.g., the compartmentalization approach, community objectives method, and dynamic analysis approach. Of these approaches, species compartmentalization is the most relevant to genetics. Besides, some algorithms have been developed for the analysis of AME models. In this chapter, we present a general protocol for the use of the species compartmentalization method to reconstruct a model of microbial communities. Then, the analysis of an AME is discussed.

Biosurfactant and enzyme mediated crude oil degradation by Pseudomonas stutzeri NA3 and Acinetobacter baumannii MN3

The present study focuses on the optimization of biosurfactant (BS) production using two potential biosurfactant producer Pseudomonas stutzeri NA3 and Acinetobacter baumannii MN3 and role of enzymes in the biodegradation of crude oil. The optimal conditions for P. stutzeri NA3 and A. baumannii MN3 for biodegradation were pH of 8 and 7; temperature of 30 and 40 °C, respectively. P. stutzeri NA3 and A. baumannii MN3 produced 3.81 and 4.68 g/L of BS, respectively. Gas chromatography mass spectrometry confirmed that BS was mainly composed of fatty acids. Furthermore, the role of the degradative enzymes, alkane hydroxylase, alcohol dehydrogenase and laccase on biodegradation of crude oil are explained. Maximum biodegradation efficiency (BE) was recorded for mixed consortia (86%) followed by strain P. stutzeri NA3 (84%). Both bacterial strains were found to be vigorous biodegraders of crude oil than other biosurfactant-producing bacteria due to their enzyme production capabilities and our results suggests that the bacterial isolates can be used for effective degradation of crude oil within short time periods.

Shift in microbial group during remediation by enhanced natural attenuation (RENA) of a crude oil-impacted soil: a case study of Ikarama Community, Bayelsa, Nigeria

Acute and chronic pollution of environments with crude oil does not bode well for biota living within the vicinity of polluted environments. This is due to environmental and public health concerns on the negative impact of crude oil pollution on living organisms. Enhancing microbial activities by adding nutrients and other amendments had proved effective in pollutant removal during bioremediation. This study was carried out to determine how microbial group respond during remediation by enhanced natural attenuation (RENA) during a field-scale bioremediation. Crude oil-polluted soil samples were collected (before, during, and after remediation) from a site undergoing remediation by enhanced natural attenuation (RENA) at Ikarama Community, Bayelsa State, Nigeria, and were analyzed for total petroleum hydrocarbon (TPH), polyaromatic hydrocarbon (PAH), and a shift in microbial community. The gas chromatography-flame ionization detector (GC-FID) results showed that the pollutant concentrations (TPH and PAH) reduced by 98 and 85%, respectively, after the remediation. Culturable hydrocarbon utilizing bacteria (CHUB) was highest (8.3 × 10⁴ cfu/g) for sample collected during the remediation studies, whilst sample collected after remediation had low CHUB (6.1 × 10⁴ cfu/g) compared to that collected before remediation (7.7 × 10⁴ cfu/g). Analysis of 16S rRNA of the isolated CHUB showed they belonged to eight bacterial genera namely: Achromobacter, Alcaligenes, Azospirillus, Bacillus, Lysinibacillus, Ochrobactrum, Proteus, and Pusillimonas, with Alcaligenes as the dominant genus. In this study, it was observed that the bacterial community shifted from mixed group (Gram-positive and -negative) before and during the remediation, to only the latter group after the remediation studies. The betaproteobacteria groups were the dominant isolated bacterial phylotype. This study showed that RENA is an effective method of reducing pollutant concentration in crude oil-polluted sites, and could be applied to other polluted sites in the Niger Delta region of Nigeria to mitigate the devastating effects of crude oil pollution.

Phytoremediation: State-of-the-art and a key role for the plant microbiome in future trends and research prospects

Phytoremediation is increasingly adopted as a more sustainable approach for soil remediation. However, significant advances in efficiency are still necessary to attain higher levels of environmental and economic sustainability. Current interventions do not always give the expected outcomes in field settings due to an incomplete understanding of the multicomponent biological interactions. New advances in -omics are gradually implemented for studying microbial communities of polluted land in situ. This opens new perspectives for the discovery of biodegradative strains and provides us new ways of interfering with microbial communities to enhance bioremediation rates. This review presents retrospectives and future perspectives for plant microbiome studies relevant to phytoremediation, as well as some knowledge gaps in this promising research field. The implementation of phytoremediation in soil clean-up management systems is discussed, and an overview of the promoting factors that determine the growth of the phytoremediation market is given. Continuous growth is expected since elimination of contaminants from the environment is demanded. The evolution of scientific thought from a reductionist view to a more holistic approach will boost phytoremediation as an efficient and reliable phytotechnology. It is anticipated that phytoremediation will prove the most promising for organic contaminant degradation and bioenergy crop production on marginal land.

Bioremediation of Heavy Crude Oil Contamination

Crude oil contamination is one of the major environmental concerns and it has drawn interest from researchers and industries. Heavy oils contain 24-64% saturates and aromatics, 14-39% resins and 11-45% asphaltene. Resins and asphaltenes mainly consist of naphthenic aromatic hydrocarbons with alicyclic chains which are the hardest to degrade. Crude oil biodegradation process, with its minimal energy need and environmentally friendly approach, presents an opportunity for bioremediation and as well for enhanced oil recovery to utilize heavy oil resources in an efficient manner. Biodegradation entails crude oil utilization as a carbon source for microorganisms that in turn change the physical properties of heavy crude oil by oxidizing aromatic rings, chelating metals and severing internal bonds/chains between molecules. Biodegradation does not necessarily lower quality of crude oil as there are cases where quality was improved. This paper provides information on heavy crude oil chemistry, bioremediation concept, biodegradation enzymes, cases of Microbial Enhanced heavy crude Oil Recovery (MEOR) and screening criteria towards a better understanding of the biodegradation application. Through the utilization of single microorganisms and consortia, researchers were able to biodegrade single pure hydrocarbon components, transform heavy crude oil fractions to lighter fractions, remove heavy metals and reduce viscosity of crude oil.

Isolation and characterisation of crude oil sludge degrading bacteria

Background

The use of microorganisms in remediating environmental contaminants such as crude oil sludge has become a promising technique owing to its economy and the fact it is environmentally friendly. Polycyclic aromatic hydrocarbons (PAHs), as the major components of oil sludge, are hydrophobic and recalcitrant. An important way of enhancing the rate of PAH desorption is to compost crude oil sludge by incorporating commercial surfactants, thereby making them available for microbial degradation. In this study, crude oil sludge was composted for 16 weeks during which surfactants were added in the form of a solution.

Results

Molecular characterisation of the 16S rRNA genes indicated that the isolates obtained on a mineral salts medium belonged to different genera, including Stenotrophmonas, Pseudomonas, Bordetella, Brucella, Bacillus, Achromobacter, Ochrobactrum, Advenella, Mycobacterium, Mesorhizobium, Klebsiella, Pusillimonas and Raoultella. The percentage degradation rates of these isolates were estimated by measuring the absorbance of the 2,6-dichlorophenol indophenol medium. Pseudomonas emerged as the top degrader with an estimated percentage degradation rate of 73.7% after 7 days of incubation at 28 °C. In addition, the presence of the catabolic gene, catechol-2,3-dioxygenase was detected in the bacteria isolates as well as in evolutionary classifications based on phylogeny.

Conclusions

The bacteria isolated in this study are potential agents for the bioremediation of crude oil sludge.