Bioremediation of soils saturated with spilled crude oil

Eco-friendly and safe alternatives for the valorization of shrimp farming waste

The seafood industry generates waste, including shells, bones, intestines, and wastewater. The discards are nutrient-rich, containing varying concentrations of carotenoids, proteins, chitin, and other minerals. Thus, it is imperative to subject seafood waste, including shrimp waste (SW), to secondary processing and valorization for demineralization and deproteination to retrieve industrially essential compounds. Although several chemical processes are available for SW processing, most of them are inherently ecotoxic. Bioconversion of SW is cost-effective, ecofriendly, and safe. Microbial fermentation and the action of exogenous enzymes are among the significant SW bioconversion processes that transform seafood waste into valuable products. SW is a potential raw material for agrochemicals, microbial culture media, adsorbents, therapeutics, nutraceuticals, and bio-nanomaterials. This review comprehensively elucidates the valorization approaches of SW, addressing the drawbacks of chemically mediated methods for SW treatments. It is a broad overview of the applications associated with nutrient-rich SW, besides highlighting the role of major shrimp-producing countries in exploring SW to achieve safe, ecofriendly, and efficient bio-products.

Complete genome sequence of phi29-like Microbacterium foliorum podovirus phage PineapplePizza

Bacteriophage PineapplePizza is a podovirus infecting Microbacterium foliorum NRRL B-24224. The genome is 16,662 bp long and contains 23 predicted protein-coding genes. Interestingly, PineapplePizza shows amino acid similarities to well-studied Bacillus subtilis phage phi29.

Advanced bioremediation by an amalgamation of nanotechnology and modern artificial intelligence for efficient restoration of crude petroleum oil-contaminated sites: a prospective study

Crude petroleum oil spillage is becoming a global concern for environmental pollution and poses a severe threat to flora and fauna. Bioremediation is considered a clean, eco-friendly, and cost-effective process to achieve success among the several technologies adopted to mitigate fossil fuel pollution. However, due to the hydrophobic and recalcitrant nature of the oily components, they are not readily bioavailable to the biological components for the remediation process. In the last decade, nanoparticle-based restoration of oil-contaminated, owing to several attractive properties, has gained significant momentum. Thus, intertwining nano- and bioremediation can lead to a suitable technology termed 'nanobioremediation' expected to nullify bioremediation's drawbacks. Furthermore, artificial intelligence (AI), an advanced and sophisticated technique that utilizes digital brains or software to perform different tasks, may radically transfer the bioremediation process to develop an efficient, faster, robust, and more accurate method for rehabilitating oil-contaminated systems. The present review outlines the critical issues associated with the conventional bioremediation process. It analyses the significance of the nanobioremediation process in combination with AI to overcome such drawbacks of a traditional approach for efficiently remedying crude petroleum oil-contaminated sites.

Oxidative damage in the Vesper mouse (Calomys laucha) exposed to a simulated oil spill-a multi-organ study

Small wild mammals have been used to measure the damage caused by exposure to oil-contaminated soil, including deer mice. However, the study of toxic effects of crude oil using oxidative damage biomarkers in the wild rodent Calomys laucha (Vesper mouse) is absent. This investigation aimed to evaluate the effects of acute exposure to contaminated soil with different concentrations of crude oil (0, 1, 2, 4 and 8% w/w), simulating an accidental spill, using oxidative stress biomarkers in the liver, kidneys, lungs, testes, paw muscle, and lymphocytes of C. laucha. Animals exposed to the contaminated soil showed increases in lipid peroxidation and protein carbonylation at the highest exposure concentrations in most organ homogenates analyzed and also in blood cells, but responses to total antioxidant capacity were tissue-dependent. These results showed that acute exposure to oil-contaminated soil caused oxidative damage in C. laucha and indicate these small mammals may be susceptible to suffer the impacts of such contamination in its occurrence region, threatening the species' survival.

Preliminary investigation of polycyclic aromatic hydrocarbons (PAHs) concentration, compositional pattern, and ecological risk in crude oil-impacted soil from Niger delta, Nigeria

Crude oil contamination could serve as an important source of polycyclic aromatic hydrocarbons (PAHs) in the environment. Determining the concentration and distribution of PAHs and their ecological risk could provide clues for appropriate remediation. The present study investigated the concentrations, composition pattern, and ecological risk of PAHs in crude oil-contaminated soil collected from the Niger Delta, Nigeria. The concentrations of Σ₂₉PAHs and 16 priority US-EPA PAHs (Σ₁₆PAHs) in the soil ranged from 24230.68 to 40845.32 ng/g (average: 29953.47 ng/g) and 7361.66-14141.49 ng/g (average: 9819.96 ng/g), respectively. The concentrations of Σ₁₆PAHs US-EPA in all the studied locations far exceeded the safety value of 1000 ng/g set by the soil quality guidelines of Switzerland and above which is regarded as being highly contaminated for Agricultural soils of Poland. The percentage composition of 2-, 3-,4-, 5-, and 6-ring in the soils were 33.69%, 56.31%, 9.47%, 0.52%, and 0.02% of the total PAHs, respectively, indicating the predominance of low molecular weight PAHs typical of petrogenic origin. Ecological risk assessment indicated a high risk to the soil biota and ecosystem in the studied soil samples as presented by individual PAH and total PAHs. 2-, 3- and 4-ring PAHs in the soil contributed significantly to the ecological risk burden in the soils. This research work provides useful information on the ecological risk associated with crude oil contamination and consequently would assist the government in formulating precise, targeted, and effective remediation measures for soil contaminated with crude oil.

Robust Superhydrophobic PDMS@SiO2@UiO66-OSiR Sponge for Efficient Water-in-Oil Emulsion Separation

A major challenge in oil/water separation is the processing of surfactant-stabilized emulsions from the water medium. One of the feasible schemes of emulsion separation is the porous melamine sponge coupled with functional particles. Here, we proposed a novel superhydrophobic metal-organic framework (MOF)-based sponge for water-in-oil emulsion separation. The porous melamine sponge was combined with poly(dimethylsiloxane) (PDMS)-coated hydrophobic SiO₂ and UiO66-OSiR particles were prepared for demulsification via the one-step dipping method for the first time. The PDMS@SiO₂@UiO66-OSiR sponge revealed excellent superhydrophobicity at a water contact angle of 160.7° and superlipophilicity at an oil contact angle of 0°. Compared with the pristine melamine sponge, the size-controllable PDMS@SiO₂@UiO66-OSiR sponge could separate stabilized water-in-oil emulsions with ultrahigh separation efficiency (>98.64%) and high flux (e.g., 970 L·m^-2·h^-1). Meanwhile, the PDMS@SiO₂@UiO66-OSiR sponge exhibited superior durability and mechanical reusability. Under harsh conditions such as strong acid and alkali, organic solvent corrosion, etc., all water contact angles of the PDMS@SiO₂@UiO66-OSiR sponge were over 152°. Furthermore, the stress decreased by 5% when the sponge was subjected to 10 loading/unloading compression cycles at a constant strain of 60%. These results demonstrate that the PDMS@SiO₂@UiO66-OSiR sponge can efficiently separate water-in-oil emulsions through its adjustable porous structure coupled with demulsification and hydrophobic particles. This study provides a step forward in developing a feasible strategy for the MOF-based sponge for emulsion separation.

Acidophilic microorganisms in remediation of contaminants present in extremely acidic conditions

Acidophiles are a group of microorganisms that thrive in acidic environments where pH level is far below the neutral value 7.0. They belong to a larger family called extremophiles, which is a group that thrives in various extreme environmental conditions which are normally inhospitable to other organisms. Several human activities such as mining, construction and other industrial processes release highly acidic effluents and wastes into the environment. Those acidic wastes and wastewaters contain different types of pollutants such as heavy metals, radioactive, and organic, whose have adverse effects on human being as well as on other living organisms. To protect the whole ecosystem, those pollutants containing effluents or wastes must be clean properly before releasing into environment. Physicochemical cleanup processes under extremely acidic conditions are not always successful due to high cost and release of toxic byproducts. While in case of biological methods, except acidophiles, no other microorganisms cannot survive in highly acidic conditions. Therefore, acidophiles can be a good choice for remediation of different types of contaminants present in acidic conditions. In this review article, various roles of acidophilic microorganisms responsible for removing heavy metals and radioactive pollutants from acidic environments were discussed. Bioremediation of various acidic organic pollutants by using acidophiles was also studied. Overall, this review could be helpful to extend our knowledge as well as to do further relevant novel studies in the field of acidic pollutants remediation by applying acidophilic microorganisms.

Bioremediation of petroleum hydrocarbon contaminated soil by microorganisms immobilized on sludge modified by non-ionic surfactant

The immobilization of microorganisms on high-quality and inexpensive carriers to remediate oil-contaminated soil is an effective strategy for contaminated soil remediation. Due to the abundance in nutrients, large specific surface area, and fewer pathogens, the composting sludge is considered a high-quality immobilized material. Herein, two non-ionic surfactants, TW-80 and sophorolipid, were used to modify composted sludge. High-efficiency petroleum hydrocarbon-degrading bacteria groups selected in the laboratory were fixed on the modified composting sludge under optimal conditions. The immobilized material was placed in the soil contaminated by petroleum hydrocarbons at an additive amount of 2wt/%, and a simulated remediation experiment was performed for 90 days. Both soil properties and microbial structure were characterized. Surfactant-modified compost sludge enhances the adsorption capacity to petroleum hydrocarbon. The immobilized microorganisms in the modified compost sludge showed a good effect on the remediation of soil contaminated by petroleum hydrocarbons. In addition, immobilized materials also increase the diversity of the microbial community structure in the soil. High-efficiency petroleum hydrocarbon-degrading bacteria immobilized on surfactant-modified compost can effectively promote the degradation of petroleum hydrocarbons in the soil and increase the abundance of microorganisms in the soil. It shows the feasibility of eco-friendly remediation of hydrocarbon-contaminated soil.

Biostimulation of Petroleum-Contaminated Soil Using Organic and Inorganic Amendments

The most common approaches for the in-situ bioremediation of contaminated sites worldwide are bioaugmentation and biostimulation. Biostimulation has often proved more effective for chronically contaminated sites. This study examined the effectiveness of optimized water hyacinth compost in comparison with other organic and inorganic amendments for the remediation of crude oil-polluted soils. Water hyacinth was found to be rich in nutrients necessary to stimulate microbial growth and activity. An organic geochemical analysis revealed that all amendments in this study increased total petroleum hydrocarbon (TPH) biodegradation by ≥75% within 56 days, with the greatest biodegradation (93%) occurring in sterilized soil inoculated with optimized water hyacinth compost. This was followed by polluted soil amended with a combination of spent mushroom and water hyacinth composts (SMC + WH), which recorded a TPH biodegradation of 89%. Soil amendment using the inorganic fertilizer NPK (20:10:10) resulted in 86% TPH biodegradation. On the other hand, control samples (natural attenuation) recorded only 4% degradation. A molecular analysis of residual polycyclic aromatic hydrocarbons (PAHs) showed that the 16 PAHs designated by the US EPA as priority pollutants were either completely or highly degraded in the combined treatment (SMC + WH), indicating the potential of this amendment for the environmental remediation of soils contaminated with recalcitrant organic pollutants.

Bacterial Communities Associated with Crude Oil Bioremediation through Composting Approaches with Indigenous Bacterial Isolate

In this study, we aim to investigate the efficiency of crude oil bioremediation through composting and culture-assisted composting. First, forty-eight bacteria were isolated from a crude oil-contaminated soil, and the isolate with the highest crude oil degradation activity, identified as Pseudomonas aeruginosa, was selected. The bioremediation was then investigated and compared between crude oil-contaminated soil (S), the contaminated soil composted with fruit-based waste (SW), and the contaminated soil composted with the same waste with the addition of the selected bacterium (SWB). Both compost-based methods showed high efficiencies of crude oil bioremediation (78.1% and 83.84% for SW and SWB, respectively). However, only a slight difference between the treatments without and with the addition of P. aeruginosa was observed. To make a clear understanding of this point, bacterial communities throughout the 4-week bioremediation period were analyzed. It was found that the community dynamics between both composted treatments were similar, which corresponds with their similar bioremediation efficiencies. Interestingly, Pseudomonas disappeared from the system after one week, which suggests that this genus was not the key degrader or only involved in the early stage of the process. Altogether, our results elaborate that fruit-based composting is an effective approach for crude oil bioremediation.

Distribution and Relationships of Polycyclic Aromatic Hydrocarbons (PAHs) in Soils and Plants near Major Lakes in Eastern China

The distributions and correlations among polycyclic aromatic hydrocarbons (PAHs) in soils and plants were analyzed. In this study, 9 soil samples and 44 plant samples were collected near major lakes (Hongze Lake, Luoma Lake, Chaohu, Changhu, Danjiangkou Reservoir, Wuhan East Lake, Longgan Lake, Qiandao Lake and Liangzi Lake) in eastern China. The following results were obtained: The total contents of PAHs in soil varied from 99.17 to 552.10 ng/g with an average of 190.35 ng/g, and the total contents of PAHs in plants varied from 122.93 to 743.44 ng/g, with an average of 274.66 ng/g. The PAHs in soil were dominated by medium- and low-molecular-weight PAHs, while the PAHs in plants were dominated by low-molecular-weight PAHs. The proportion of high-molecular-weight PAHs was the lowest in both soil and plants. Diagnostic ratios and principal component analysis (PCA) identified combustion as the main source of PAHs in soil and plants. The plant PAH monomer content was negatively correlated with Koa. Acenaphthylene, anthracene, benzo[k]fluoranthene, benzo[b]fluoranthene and dibenzo[a,h]anthracene were significantly correlated in plants and soil. In addition, no significant correlation between the total contents of the 16 PAHs and the content of high-, medium-, and low-molecular-weight PAHs in plants and soil was found. Bidens pilosa L. and Gaillardia pulchella Foug in the Compositae family and cron in the Poaceae family showed relatively stronger accumulation of PAHs, indicating their potential for phytoremediation.

Microbial Journey: Mount Everest to Mars

A rigorous exploration of microbial diversity has revealed its presence on Earth, deep oceans, and vast space. The presence of microbial life in diverse environmental conditions, ranging from moderate to extreme temperature, pH, salinity, oxygen, radiations, and altitudes, has provided the necessary impetus to search for them by extending the limits of their habitats. Microbiology started as a distinct science in the mid-nineteenth century and has provided inputs for the betterment of mankind during the last 150 years. As beneficial microbes are assets and pathogens are detrimental, studying both have its own merits. Scientists are nowadays working on illustrating the microbial dynamics in Earth's subsurface, deep sea, and polar regions. In addition to studying the role of microbes in the environment, the microbe-host interactions in humans, animals and plants are also unearthing newer insights that can help us to improve the health of the host by modulating the microbiota. Microbes have the potential to remediate persistent organic pollutants. Antimicrobial resistance which is a serious concern can also be tackled only after monitoring the spread of resistant microbes using disciplines of genomics and metagenomics The cognizance of microbiology has reached the top of the world. Space Missions are now looking for signs of life on the planets (specifically Mars), the Moon and beyond them. Among the most potent pieces of evidence to support the existence of life is to look for microbial, plant, and animal fossils. There is also an urgent need to deliberate and communicate these findings to layman and policymakers that would help them to take an adequate decision for better health and the environment around us. Here, we present a glimpse of recent advancements by scientists from around the world, exploring and exploiting microbial diversity.

Indigenous oil-degrading bacteria more efficient in soil bioremediation than microbial consortium and active even in super oil-saturated soils

A microbial consortium of the hydrocarbonoclastic bacterial species, comprising Actinotalea ferrariae, Arthrobacter ginsengisoli, Dietzia cinnamea, Dietzia papillomatosis, and Pseudomonas songnenensis, isolated from oil-saturated desert soil did not consume more oil in batch cultures than the individual species with the maximum oil consumption. In oil-polluted desert soil microcosms, the rate of oil removal in the soil samples bioaugmented with the microbial consortium was similar to the rate of oil removal in the unbioaugmented ones through a 6-month bioremediation experiment. Although the composition of hydrocarbonoclastic bacterial communities in the unbioaugmented and bioaugmented soil samples was different, the predominant bacterial species during most of the months were the same. Toward the end of the bioremediation experiment, Ar. ginsengisoli prevailed in both soil samples, suggesting its important role in oil removal. Self-cleaning proceeded in desert soil samples artificially polluted with 1, 10, 20, and 30% of crude oil and incubated at 30 °C for 6 months. Oil was removed effectively at rates reaching 73.6 and 69.3% in the soils polluted with 1 and 10% oil concentrations, respectively, and reached 50% in desert soils polluted with 20 and 30% oil concentrations. The bacterial numbers increased in all soil samples from hundreds of thousands per gram of soil samples at time zero to millions and tens of millions per gram of soil samples after 6 months. It was concluded that bioaugmenting oil-polluted soil samples with microbial consortium of hydrocarbonoclastic bacterial species with high oil removal potential did not drastically enhance oil bioremediation and that even in super oil-saturated soils, indigenous oil-degrading bacteria will prevail and effectively contribute to oil removal from the surrounding environment.

Characterization of Phages YuuY, KaiHaiDragon, and OneinaGillian Isolated from Microbacterium foliorum

Microbacterium foliorum is a Gram-positive bacteria found in organic matter. Three lytic bacteriophages, KaiHaiDragon, OneinaGillian, and YuuY, were isolated from M. foliorum strain NRRL B-24224. Phage YuuY in particular expresses a broad host range as it possesses the ability to infect closely related bacterial species Microbacterium aerolatum at a high plating efficiency. Characterization tests were performed on all three Microbacterium phage to assess morphology, genomic characteristics, pH and thermal stabilities, life cycle, and the type of receptor used for infection. All three phages showed similar pH stability, ranging from pH 5-11, except for KaiHaiDragon, which had a reduced infection effectiveness at a pH of 11. YuuY possessed a significantly higher temperature tolerance compared to the other Microbacterium phages as some phage particles remained viable after incubation temperatures of up to 80 °C. Based on the one-step growth curve assay, all three Microbacterium phages possessed a relatively short latent period of 90 min and an approximately two-fold burst size factor. Moreover, all three phages utilize a carbohydrate receptor to initiate infection. Based on bioinformatics analysis, YuuY, KaiHaiDragon and OneinaGillian were assigned to clusters EA10, EC, and EG, respectively.

Efficient removal of heavily oil-contaminated soil using a combination of fenton pre-oxidation with biostimulated iron and bioremediation

Crude oil contamination severely deteriorates soils quality. Bioremediation utilizing soil indigenous organisms could be employed to decompose petroleum hydrocarbons thanks to its low cost and minor environmental disturbance. However, slow kinetics limit the successful application of this biotechnique. Pretreating oil-contaminated soils with Fenton pre-oxidation could accelerate the subsequent bioremediation process. This study was to explore the mechanisms behind the rapid propagation of indigenous petroleum-degrading bacteria (IPDB) and the efficient degradation of total petroleum hydrocarbons (TPH) in soil after Fenton pre-oxidation with biostimulated iron. Biostimulated iron and non-biostimulated iron were used in the experiments, where Fenton pre-oxidation was combined with the bioremediation of oil-contaminated soil (TPH = 13221 mg/kg). Although the amount of Fenton pre-oxidized TPH (3331-3775 mg/kg) was similar with biostimulated and non-biostimulated irons, the biodegradation of TPH after Fenton pre-oxidation with biostimulated iron (5840 mg/kg) was much higher than that with non-biostimulated iron (3034-4034 mg/kg). Moreover, abundant nutrients and a high population of residual IPDB were found after Fenton pre-oxidation with biostimulated iron, which benefited stable consumption of NH₃-N and dissolved organic carbon (DOC) by IPDB during the subsequent bioremediation. However, Fenton pre-oxidation with non-biostimulated iron either resulted in greater damage to IPDB or produced fewer nutrients, thereby failing to ensure the continuous propagation of IPDB during the subsequent bioremediation. Therefore, we propose that Fenton pre-oxidation with biostimulated iron should be applied to heavily oil-contaminated soils prior to bioremediation.

Computational analyses of bacterial strains from shotgun reads

Shotgun sequencing is routinely employed to study bacteria in microbial communities. With the vast amount of shotgun sequencing reads generated in a metagenomic project, it is crucial to determine the microbial composition at the strain level. This study investigated 20 computational tools that attempt to infer bacterial strain genomes from shotgun reads. For the first time, we discussed the methodology behind these tools. We also systematically evaluated six novel-strain-targeting tools on the same datasets and found that BHap, mixtureS and StrainFinder performed better than other tools. Because the performance of the best tools is still suboptimal, we discussed future directions that may address the limitations.

Innovative Culturomic Approaches and Predictive Functional Metagenomic Analysis: The Isolation of Hydrocarbonoclastic Bacteria with Plant Growth Promoting Capacity

Innovative culturomic approaches were adopted to isolate hydrocarbonoclastic bacteria capable of degrading diesel oil, bitumen and a selection of polycyclic aromatic hydrocarbons (PAH), e.g., pyrene, anthracene, and dibenzothiophene, from a soil historically contaminated by total petroleum hydrocarbons (TPH) (10,347 ± 98 mg TPH/kg). The culturomic approach focussed on the isolation of saprophytic microorganisms and specialist bacteria utilising the contaminants as sole carbon sources. Bacterial isolates belonging to Pseudomonas, Arthrobacter, Achromobacter, Bacillus, Lysinibacillus, Microbacterium sps. were isolated for their capacity to utilise diesel oil, bitumen, pyrene, anthracene, dibenzothiphene, and their mixture as sole carbon sources. Pseudomonas, Arthrobacter, Achromobacter and Microbacterium sps. showed plant growth promoting activity, producing indole-3-acetic acid and expressing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. In parallel to the culturomic approach, in the microbial community of interest, bacterial community metabarcoding and predictive functional metagenomic analysis were adopted to confirm the potentiality of the isolates in terms of their functional representativeness. The combination of isolation and molecular approaches for the characterisation of a TPH contaminated soil microbial community is proposed as an instrument for the construction of an artificial hydrocarbonoclastic microbiota for environmental restoration.

Beneficial biofilms: A mini-review of strategies to enhance biofilm formation for biotechnological applications

The capacity of bacteria to form biofilms is an important trait for their survival and persistence. Biofilms occur naturally in soil and aquatic environments, are associated with animals ranging from insects to humans and are also found in built environments. They are typically encountered as a challenge in healthcare, food industry, and water supply ecosystems. In contrast, they are known to play a key role in the industrial production of commercially valuable products, environmental remediation processes, and in microbe-catalysed electrochemical systems for energy and resource recovery from wastewater. While there are many recent articles on biofilm control and removal, review articles on promoting biofilm growth for biotechnological applications are unavailable. Biofilm formation is a tightly regulated response to perturbations in the external environment. The multi-stage process, mediated by an assortment of proteins and signaling systems, involves the attachment of bacterial cells to a surface followed by their aggregation in a matrix of extracellular polymeric substances. Biofilms can be promoted by altering the external environment in a controlled manner, supplying molecules that trigger the aggregation of cells and engineering genes associated with biofilm development. This mini-review synthesizes findings from studies that have described such strategies and highlights areas needing research attention.

Molecular signatures of Janthinobacterium lividum from Trinidad support high potential for crude oil metabolism

Background

Janthinobacterium lividum is considered to be a psychrotrophic bacterial species. For the first time in the literature, J. lividum strains were isolated from Trinidad presenting with atypical features - hydrocarbonoclastic and able to survive in a tropical environment.

Methods

Identification of the Trinidad strains was carried out through 16S rRNA phylogenetic analysis. Gene-specific primers were designed to target the VioA which encodes violacein pigment and the EstA/B gene which encodes secreted extracellular lipase. Bioinformatics analyses were carried out on the nucleotide and amino acid sequences of VioA and EstA/B genes of the Trinidad Janthinobacterium strains to assess functionality and phylogenetic relatedness to other Janthinobacterium sequences specifically and more broadly, to other members of the Oxalobacteraceae family of betaproteobacteria.

Results

16S rRNA confirmed the identity of the Trinidad strains as J. lividum and resolved three of the Trinidad strains at the intra-specific level. Typical motility patterns of this species were recorded. VioAp sequences were highly conserved, however, synonymous substitutions located outside of the critical sites for enzyme function were detected for the Trinidad strains. Comparisons with PDB 6g2p model from aa231 to aa406 further indicated no functional disruption of the VioA gene of the Trinidad strains. Phylogeny of the VioA protein sequences inferred placement of all J. lividum taxa into a highly supported species-specific clade (bs = 98%). EstA/Bp sequences were highly conserved, however, synonymous substitutions were detected that were unique to the Trinidad strains. Phylogenetic inference positioned the Trinidad consensus VioA and EstA protein sequences in a clearly distinct branch.

Conclusions

The findings showed that the primary sequence of VioAp and EstA/Bp were unique to the Trinidad strains and these molecular signatures were reflected in phylogenetic inference. Our results supported chemotaxis, possible elective inactivation of VioA gene expression and secreted lipase activity as survival mechanisms of the Trinidad strains in petrogenic conditions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02346-4.

Biodiversity and biocatalyst activity of culturable hydrocarbonoclastic fungi isolated from Marac-Moruga mud volcano in South Trinidad

Mud volcanoes (MVs) are visible signs of oil and gas reserves present deep beneath land and sea. The Marac MV in Trinidad is the only MV associated with natural hydrocarbon seeps. Petrogenic polyaromatic hydrocarbons (PAHs) in its sediments must undergo biogeochemical cycles of detoxification as they can enter the water table and aquifers threatening ecosystems and biota. Recurrent hydrocarbon seep activity of MVs consolidates the growth of hydrocarbonoclastic fungal communities. Fungi possess advantageous metabolic and ecophysiological features for remediation but are underexplored compared to bacteria. Additionally, indigenous fungi are more efficient at PAH detoxification than commercial/foreign counterparts and remediation strategies remain site-specific. Few studies have focused on hydrocarbonoclastic fungal incidence and potential in MVs, an aspect that has not been explored in Trinidad. This study determined the unique biodiversity of culturable fungi from the Marac MV capable of metabolizing PAHs in vitro and investigated their extracellular peroxidase activity to utilize different substrates ergo their extracellular oxidoreductase activity (> 50% of the strains decolourized of methylene blue dye). Dothideomycetes and Eurotiomycetes (89% combined incidence) were predominantly isolated. ITS rDNA sequence cluster analysis confirmed strain identities. 18 indigenous hydrocarbonoclastic strains not previously reported in the literature and some of which were biosurfactant-producing, were identified. Intra-strain variability was apparent for PAH utilization, oil-tolerance and hydroxylase substrate specificity. Comparatively high levels of extracellular protein were detected for strains that demonstrated low substrate specificity. Halotolerant strains were also recovered which indicated marine-mixed substrata of the MV as a result of deep sea conduits. This work highlighted novel MV fungal strains as potential bioremediators and biocatalysts with a broad industrial applications.

Investigating the potential of bioremediation in aged oil-polluted hypersaline soils in the south oilfields of Iran

To date, studies for bioremediation of oil-polluted hypersaline soils have been neglected or limited to specific spots. Hence, in this study, ten samples of oil field soils in the Khuzestan province of Iran were collected to evaluate bioremediation's feasibility. These samples were analyzed for their physicochemical properties as well as the most probable number of total and hydrocarbon-degrading bacteria. Thirty-nine hydrocarbon-degrading bacteria were isolated from these soils over a 1-month incubation in an MSM medium enriched with diesel oil as the sole source of carbon. As revealed by 16S-rRNA analysis, the identified strains belonged to the genera Ochrobactrum, Microbacterium, and Bacillus with a high frequency of Ochrobactrum species. Additionally, by using degenerate primers, the third group of alkB gene was detected in Ochrobactrum and Microbacterium isolates through the touchdown nested PCR method for the first time. Ochrobactrum species possessing the alkB gene showed the highest population, and therefore, the highest adaptation to harsh environmental conditions. Most isolates showed outstanding results in the ability to grow with crude and diesel oil and tolerate high salt percentages, biosurfactant production, and emulsification activity, which are considered the most effective factors in bioremediation of such environments. Considering the soil analysis, limiting factors in bioremediation like available phosphorous, and the abundance of bacteria with remediation traits in these soils, these extremely polluted environments can be refined.

Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment

Soil contamination by hydrocarbons due to oil spills has become a global concern and it has more implications in oil producing regions. Biostimulation is considered as one of the promising remediation techniques that can be adopted to enhance the rate of degradation of crude oil. The soil microbial consortia play a critical role in governing the biodegradation of total petroleum hydrocarbons (TPHs), in particular polycyclic aromatic hydrocarbons (PAHs). In this study, the degradation pattern of TPHs and PAHs of Kuwait soil biopiles was measured at three-month intervals. Then, the microbial consortium associated with oil degradation at each interval was revealed through 16S rRNA based next generation sequencing. Rapid degradation of TPHs and most of the PAHs was noticed at the first 3 months of biostimulation with a degradation rate of pyrene significantly higher compared to other PAHs counterparts. The taxonomic profiling of individual stages of remediation revealed that, biostimulation of the investigated soil favored the growth of Proteobacteria, Alphaprotobacteria, Chloroflexi, Chlorobi, and Acidobacteria groups. These findings provide a key step towards the restoration of oil-contaminated lands in the arid environment.

Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad

Trinidad and Tobago is the largest producer of oil and natural gas in Central America and the Caribbean. Natural crude oil seeps, in addition to leaking petroleum pipelines, have resulted in chronic contamination of the surrounding terrestrial environments since the time of petroleum discovery, production, and refinement in Trinidad. In this study, we isolated microbes from soils chronically contaminated with crude oil using a culture-dependent approach with enrichment. The sampling of eight such sites located in the southern peninsula of Trinidad revealed a diverse microbial composition and novel oil-degrading filamentous fungi and yeast as single-isolate degraders and naturally occurring consortia, with specific bacterial species not previously reported in the literature. Multiple sequence comparisons and phylogenetic analyses confirmed the identity of the top degraders. The filamentous fungal community based on culturable species was dominated by Ascomycota, and the recovered yeast isolates were affiliated with Basidiomycota (65.23%) and Ascomycota (34.78%) phyla. Enhanced biodegradation of petroleum hydrocarbons is maintained by biocatalysts such as lipases. Five out of seven species demonstrated extracellular lipase activity in vitro. Our findings could provide new insights into microbial resources from chronically contaminated terrestrial environments, and this information will be beneficial to the bioremediation of petroleum contamination and other industrial applications.

Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli

Burkholderia gladioli has high versatility and adaptability to various ecological niches. Here, we constructed a pan-genome using 14 genome sequences of B. gladioli, which originate from different niches, including gladiolus, rice, humans, and nature. Functional roles of core and niche-associated genomes were investigated by pathway enrichment analyses. Consequently, we inferred the uniquely important role of niche-associated genomes in (1) selenium availability during competition with gladiolus host; (2) aromatic compound degradation in seed-borne and crude oil-accumulated environments, and (3) stress-induced DNA repair system/recombination in the cystic fibrosis-niche. We also identified the conservation of the rhizomide biosynthetic gene cluster in all the B. gladioli strains and the concentrated distribution of this cluster in human isolates. It was confirmed the absence of complete CRISPR/Cas system in both plant and human pathogenic B. gladioli and the presence of the system in B. gladioli living in nature, possibly reflecting the inverse relationship between CRISPR/Cas system and virulence.

Microbiological Study in Petrol-Spiked Soil

The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 unleaded petrol with Active technology. A pot experiment was carried out in which Eutric Cambisol soil was polluted with petrol to determine its effect on the microbiological and biochemical properties of this soil. Analyses were carried out to determine soil microbiome composition-with the incubation and metagenomic methods, the activity of seven enzymes, and cocksfoot effect on hydrocarbon degradation. The following indices were determined: colony development index (CD); ecophysiological diversity index (EP); index of cocksfoot effect on soil microorganisms and enzymes (IFG); index of petrol effect on soil microorganisms and enzymes (IFP); index of the resistance of microorganisms, enzymes, and cocksfoot to soil pollution with petrol (RS); Shannon-Weaver's index of bacterial taxa diversity (H); and Shannon-Weaver's index of hydrocarbon degradation (IDH). The soil pollution with petrol was found to increase population numbers of bacteria and fungi, and Protebacteria phylum abundance as well as to decrease the abundance of Actinobacteria and Acidobacteria phyla. The cultivation of cocksfoot on the petrol-polluted soil had an especially beneficial effect mainly on the bacteria belonging to the Ramlibacter, Pseudoxanthomonas, Mycoplana, and Sphingobium genera. The least susceptible to the soil pollution with petrol and cocksfoot cultivation were the bacteria of the following genera: Kaistobacter, Rhodoplanes, Bacillus, Streptomyces, Paenibacillus, Phenylobacterium, and Terracoccus. Cocksfoot proved effective in the phytoremediation of petrol-polluted soil, as it accelerated hydrocarbon degradation and increased the genetic diversity of bacteria. It additionally enhanced the activities of soil enzymes.

Isolation Chip Increases Culturable Bacterial Diversity and Reduces Cultivation Bias

Conventional cultivation methods, including petri dish plating, are selective and biased to enrich specific microorganisms, such as big population and fast-growing bacteria. In this study, we evaluated the ability of isolation chip (ichip) to reduce cultivation bias. We used the ichip and petri dish plating methods to cultivate bacteria from soil contaminated with (contaminated soil) or without (natural soil) crude oil. Ichip improved the richness and evenness of bacterial isolates in both the natural and contaminated soil samples. Using the petri dish plating method, Pseudomonas and Lysinibacillus isolates were found to be the most abundant, with over 50% of the relative abundance in the natural and oil-polluted soil-cultured communities, respectively. In comparison, using the ichip method, the isolates with the highest relative abundances were from Bacillus and Aeromonas in natural and contaminated soil-cultured communities, which only accounted for 20% and 28% of the total isolates, respectively. Interestingly, the evenness and richness of the bacteria varied slightly between the natural and oil-polluted soil samples, indicating that ichip had the ability to reduce the cultivation bias. In addition, oil selective pressure enriched the functional bacteria isolated using the petri dish plating method. In summary, ichip allows bacteria to grow evenly, as well as allowing for substance exchange between the environment and single cells. As such, it is a very good method for increasing culturable bacterial diversity and reducing cultivation bias.

Isolation and characterization of a halophilic Modicisalibacter sp. strain Wilcox from produced water

We report the isolation a halophilic bacterium that degrades both aromatic and aliphatic hydrocarbons as the sole sources of carbon at high salinity from produced water. Phylogenetic analysis of 16S rRNA-gene sequences shows the isolate is a close relative of Modicisalibacter tunisiensis isolated from an oil-field water in Tunisia. We designate our isolate as Modicisalibacter sp. strain Wilcox. Genome analysis of strain Wilcox revealed the presence of a repertoire of genes involved in the metabolism of aliphatic and aromatic hydrocarbons. Laboratory culture studies corroborated the predicted hydrocarbon degradation potential. The strain degraded benzene, toluene, ethylbenzene, and xylenes at salinities ranging from 0.016 to 4.0 M NaCl, with optimal degradation at 1 M NaCl. Also, the strain degraded phenol, benzoate, biphenyl and phenylacetate as the sole sources of carbon at 2.5 M NaCl. Among aliphatic compounds, the strain degraded n-decane and n-hexadecane as the sole sources of carbon at 2.5 M NaCl. Genome analysis also predicted the presence of many heavy metal resistance genes including genes for metal efflux pumps, transport proteins, and enzymatic detoxification. Overall, due to its ability to degrade many hydrocarbons and withstand high salt and heavy metals, strain Wilcox may prove useful for remediation of produced waters.

The potential association of Echinochloa polystachya (Kunth) Hitchc. with bacterial consortium for petroleum degradation in contaminated soil

In recent years, environmental impacts related to the contamination of ecosystems by petroleum have become frequent. In contact with the environment, petroleum can cause toxic effects in the biodiversity and on human health and compromise both water and land resources. Among the strategies to overcome this issue, bioremediation stands out as viable and promising alternative for environmental decontamination. To bioremediate petroleum-contaminated sites, phytoremediation and bioaugmentation techniques can be used. Thus, this research aimed to evaluate through a pot experiment four bioremediation strategies: (1) natural attenuation, (2) phytoremediation with Echinochloa polystachya, (3) bioaugmentation with bacterial consortium and (4) bioaugmentation-assisted phytoremediation, for the treatment of a co-contaminated soil presenting 100 g kg−1 of petroleum. In addition, two control treatments were carried out with substrates not contaminated with petroleum: (5) control with E. polystachya and (6) control treatment with bacterial consortium and E. polystachya. The experiment lasted 60 days in a greenhouse. The survival rate of E. polystachya was 100% in the contaminant tolerance aspect, resulting in increased stomatal density and aerenchyma, affecting few parameters of the plant, which demonstrate its phytoremediation capacity. In all treatments, petroleum degradation occurred. The highest degree of total petroleum hydrocarbon removal was obtained for contaminated soil cultivated with E. polystachya (phytoremediation), followed by contaminated soil cultivated with E. polystachya and bacterial (bioaugmentation-assisted phytoremediation treatment) and contaminated soil treated with bacterial consortium (bioaugmentation). Natural attenuation was less effective, proving the efficiency of the phytoremediation by E. polystachya and bacterial consortium, that responded positively to the stresses generated by contamination. However, further studies should direct to aim understanding the metabolic processes involved in the degradation and that these approaches to assist in environmental decontamination.

Extremophilic Microorganisms for the Treatment of Toxic Pollutants in the Environment

As concerns about the substantial effect of various hazardous toxic pollutants on the environment and public health are increasing, the development of effective and sustainable treatment methods is urgently needed. In particular, the remediation of toxic components such as radioactive waste, toxic heavy metals, and other harmful substances under extreme conditions is quite difficult due to their restricted accessibility. Thus, novel treatment methods for the removal of toxic pollutants using extremophilic microorganisms that can thrive under extreme conditions have been investigated during the past several decades. In this review, recent trends in bioremediation using extremophilic microorganisms and related approaches to develop them are reviewed, with relevant examples and perspectives.

Bacterial Community Composition in Produced Water of Diyarbakır Oil Fields in Turkey : Bacterial communities in produced waters of south-eastern Turkey reported in detail for the first time

Oil fields harbour a wide variety of microorganisms with different metabolic capabilities. To examine the microbial ecology of petroleum reservoirs, a molecular-based approach was used to assess the composition of bacterial communities in produced water of Diyarbakır oil fields in Turkey. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments was performed to characterise the bacterial community structure of produced water samples and to identify predominant community members after sequencing of separated DGGE bands. The majority of bacterial sequences retrieved from DGGE analysis of produced water samples belonged to unclassified bacteria (50%). Among the classified bacteria, Proteobacteria (29.2%), Firmicutes (8.3%), Bacteroidetes (8.3%) and Actinobacteria (4.2%) groups were identified. Pseudomonas was the dominant genus detected in the produced water samples. The results of this research provide, for the first time, insight into the complexity of microbial communities in the Diyarbakır oil reservoirs and their dominant constituents.

Genomic diversity of bacteriophages infecting Microbacterium spp

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.

The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity

The global demand for petroleum contributes to a significant increase in soil pollution with petroleum-based products that pose a severe risk not only to humans but also to plants and the soil microbiome. The increasing pollution of the natural environment urges the search for effective remediation methods. Considering the above, the objective of this study was to determine the usability of Dactylis glomerata for the degradation of hydrocarbons contained in diesel oil (DO), as well as the effects of both the plant tested and DO on the biochemical functionality and changes in the soil microbiome. The experiment was conducted in a greenhouse with non-polluted soil as well as soil polluted with DO and phytoremediated with Dactylis glomerata. Soil pollution with DO increased the numbers of microorganisms and soil enzymes and decreased the value of the ecophysiological diversity index of microorganisms. Besides, it contributed to changes in the bacterial structure at all taxonomic levels. DO was found to increase the abundance of Proteobacteria and to decrease that of Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes and Firmicutes. In the non-polluted soil, the core microbiome was represented by Kaistobacter and Rhodoplanes, whereas in the DO-polluted soil, it was represented by Parvibaculum and Rhodococcus. In soil sown with Dactylis glomerata, gasoline fraction (C₆–C₁₂) degradation was higher by 17%; mineral oil (C₁₂–C₃₅), by 9%; benzene, by 31%; anthracene, by 12%; chrysene, by 38%; benzo(a)anthracene, by 19%; benzo(a)pyrene, by 17%; benzo(b)fluoranthene, by 15%; and benzo(k)fluoranthene, by 18% than in non-sowed soil. To conclude, Dactylis glomerata proved useful in degrading DO hydrocarbons and, therefore, may be recommended for the phytoremediation of soils polluted with petroleum-based products. It has been shown that the microbiological, biochemical and chemical tests are fast and sensitive in the diagnosis of soil contamination with petroleum products, and a combination of all these tests gives a reliable assessment of the state of soils.