Development of an Efficient Bacterial Consortium for the Potential Remediation of Hydrocarbons from Contaminated Sites

Ecological and human health risk associated with heavy metals (HMs) contaminant sourced from petroleum refinery oily sludge

The environmental and human health risk of heavy metals (HMs) in petroleum based oily sludge (OS) varies depending upon the source of origin of the crude oil and treatment processes practiced at the refineries. Consequently, the present study explores the potential risk associated with HMs of OS obtained from different refinery sites to the environment and human health. The results showed that HMs (Cu, Ni, Zn, Mn) present in OS surpasses the permissible limit of WHO guidelines except for Cr. Additionally, the Igeo value (grade 3-6), Ef (2.48-121.4), PLI (5.12-22.65), Cd (32.48-204.76) and PERI (grade 1-5) confirmed the high level of HMs contamination into the OS and its risk to the environment. Besides, the hazard index (HI) and the total carcinogenic risk (TCR) for HMs show substantial risk to both adult and children health. Likewise, the G-mean enzyme index and potential soil enzyme risk index (PSERI) of the OS showed a high risk to soil biological properties. Furthermore, statistical analysis confirmed the heterogeneity in properties of the OS and its potential impact on the soil ecosystem arising from different sites. Finally, the study unveils a novel perspective on the environmental and human health consequences associated with the OS.

Characterization of Diesel Degrading Indigenous Bacterial Strains, Acinetobacter pittii and Pseudomonas aeruginosa, Isolated from Oil Contaminated Soils

In this study, 13 diesel degrading bacteria were isolated from the oil contaminated soils and the promising strains identified as Acinetobacter pittii ED1 and Pseudomonas aeruginosa BN were evaluated for their diesel degrading capabilities. These strains degraded the diesel optimally at 30 °C, pH 7.0 and 1% diesel concentration. Both the strains produced biofilm at 1% diesel concentration indicating their ability to tolerate diesel induced abiotic stress. Gravimetric analysis of the spent medium after 7 days of incubation showed that A. pittii ED1 and P. aeruginosa BN degraded 68.61% and 76% diesel, respectively, while biodegradation reached more than 90% after 21 days. Fourier Transform Infrared (FTIR) analysis of the degraded diesel showed 1636.67 cm-1 (C=C stretch, N-H bond) peak corresponding to alkenes and primary amines, while GC-TOF-MS analysis showed decline in hydrocarbon intensities after 7 days of incubation. The present study revealed that newly isolated A. pittii ED1 and P. aeruginosa BN were able to degrade diesel hydrocarbons (C11-C18, and C19-C24) efficiently and have potential for bioremediation of the oil-contaminated sites.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-024-01317-3.

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

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

Soil Microbiome in Conditions of Oil Pollution of Subarctic Ecosystems

The present study aimed to investigate the recovery of soil quality and the bacterial and fungal communities following various recultivation methods in areas contaminated with oil. Oil spills are known to have severe impacts on ecosystems; thus, the restoration of contaminated soils has become a significant challenge nowadays. The study was conducted in the forest-tundra zone of the European North-East, where 39 soil samples from five oil-contaminated sites and reference sites were subjected to metagenomic analyses. The contaminated sites were treated with different biopreparations, and the recovery of soil quality and microbial communities were analyzed. The analysis of bacteria and fungi communities was carried out using 16S rDNA and ITS metabarcoding. It was found that 68% of bacterial OTUs and 64% of fungal OTUs were unique to the reference plot and not registered in any of the recultivated plots. However, the species diversity of recultivated sites was similar, with 50-80% of bacterial OTUs and 44-60% of fungal OTUs being common to all sites. New data obtained through soil metabarcoding confirm our earlier conclusions about the effectiveness of using biopreparations with indigenous oil-oxidizing micro-organisms also with mineral fertilizers, and herbaceous plant seeds for soil remediation. It is possible that the characteristics of microbial communities will be informative in the bioindication of soils reclaimed after oil pollution.

Mitigation of hydrocarbon toxicity using bacterial consortium in microcosm environment for agrarian fecundity

Petroleum contamination in the soil has been well emphasized as a toxic and hazardous soil pollution contributing to a significant portion of soil infertility worldwide. In the present study, bacterial consortium CHM1 composed of 5 strains belonging to genera Klebsiella, Pantoea, and Enterobacter was evaluated for hydrocarbon degradation ability in the soil environment, as well as their performance in remediating ecotoxicity and phytotoxicity. Initially, the degradation efficiency (1.98%/day) in the soil environment was evaluated. Scanning Electron Microscopy combined with Energy Dispersive X-ray spectroscopy revealed an increase in nitrogen content by 24.98% and a decrease in carbon content by 22.76% implying an improvement in soil fertility. The Fourier Transform InfraRed spectroscopy and Gas Chromatographic analysis revealed significant depletion of aromatic, cyclic, long aliphatic, and complex acid and ester content of the test soil. Moreover, the quantitative PCR analysis exhibited the non-competitive coexistence of each component of the CHM1 consortium. Different enzymatic assays revealed elevated dehydrogenase and superoxide dismutase activity in the degradation system due to the introduction of CHM1 in the soil microcosm. Vibrio fischeri-assisted ecotoxicity analysis had established the potential of CHM1 to efficiently minimize the ecotoxicity of hydrocarbon contamination. The phytotoxicity analysis was performed using four different plant models viz. Chickpeas (Cicer arientinum), Coriander (Coriandrum sativum), Fenugreek (Trigonella foenum-graecum), and Spinach (Spinacia oleracea) exhibiting CHM1 amendment helped to restore plant germination and growth in hydrocarbon-contaminated soil system efficiently. The promising results from this study indicated the possible application of the bacterial consortium in hydrocarbon-contaminated land management and soil restoration for cultivation or other plantation purposes.

Impacts of rhizoremediation and biostimulation on soil microbial community, for enhanced degradation of petroleum hydrocarbons in crude oil-contaminated agricultural soils

Hydrocarbonoclastic bacterial strains were isolated from rhizosphere of plants growing in crude oil-contaminated sites of Assam, India. These bacteria showed plant growth-promoting attributes, even when exposed to crude oil. Two independent pot trials were conducted to test the rhizodegradation ability of the bacterial consortium in combination of plants Azadirchta indica or Delonix regia in crude oil-contaminated soil. Field experiments were conducted at two crude oil-contaminated agricultural field at Assam (India), where plants (A. indica or D. regia) were grown with the selected bacterial consortium consisting of five hydrocarbonoclastic bacterial isolates (Gordonia amicalis BB-DAC, Pseudomonas aeruginosa BB-BE3, P. citronellolis BB-NA1, Rhodococcus ruber BB-VND, and Ochrobactrum anthropi BB-NM2), and NPK was added to the soil for biostimulation. The bacterial consortium-NPK biostimulation led to change in rhizosphere microbiome with enhanced degradation of petroleum hydrocarbons (PHs) in soils contaminated with crude oil. After 120 days of planting A. indica + consortium + NPK treatment, degradation of PHs was found to be up to 67%, which was 55% with D. regia with the same treatment. Significant changes in the activities of plant and soil enzymes were also noted. The shift is bacterial community was also apparent as with A. indica, the relative abundance of Proteobacteria, Actinobacteria, and Acidobacteria increased by 35.35%, 26.59%, and 20.98%, respectively. In the case of D. regia, the relative abundance of Proteobacteria, Actinobacteria, and Acidobacteria were increased by 39.28%, 35.79%, and 9.60%, respectively. The predicted gene functions shifted in favor of the breakdown of xenobiotic compounds. This study suggests that a combination of plant-bacterial consortium and NPK biostimulation could be a productive approach to bioengineering the rhizosphere microbiome for the purpose of commercial bioremediation of crude oil-contaminated sites, which is a major environmental issue faced globally.

High-throughput bioamphiphile production by ethyl methane sulphonate induced mutant of hydrocarbonoclastic Enterobacter xiangfangensis STP-3: In depth structural elucidation and application to petroleum refinery oil sludge bioremediation

The environmental release of noxious petroleum hydrocarbons (PHCs) from the petroleum refining industries is an intractable global challenge. Indigenous PHCs degrading microbes produce insufficient yield of amphiphilic biomolecules with trivial efficiency makes the bioremediation process ineffective. In this concern, the present study is focused on the production of high yield multi-functional amphiphilic biomolecule through the genetic modification of Enterobacter xiangfangensis STP-3 strain using Ethyl methane sulphonate (EMS) induced mutagenesis. Mutant M9_{E.xiangfangensis} showed 2.32-fold increased yield of bioamphiphile than wild-type strain. Novel bioamphiphile produced by M9_{E.xiangfangensis} exhibited improved surface and emulsification activities which ensure the maximum degradation of petroleum oil sludge (POS) by 86% than wild-type (72%). SARA, FT-IR, and GC-MS analyses confirmed the expedited degradation of POS and ICP-MS analysis indicated the enhanced removal of heavy metals in connection with the ample production of functionally improved bioamphiphile. FT-IR NMR, MALDI-TOF, GC-MS and LC-MS/MS analyses portrayed the lipoprotein nature of bioamphiphile comprising pentameric fatty acid moiety conjugated with the catalytic esterase moiety. Further, homology modelling and molecular docking revealed the stronger interaction of hydrophobic amino acids, leucine and isoleucine with the PHCs in the case of wild-type esterase moiety, whereas in the mutant, aromatic amino acids were majorly interacted with the long chain and branched chain alkanes, thereby exhibited better efficiency. This is the first report on the adoption of EMS induced mutagenesis strategy to ameliorate the amphiphilic biomolecules for their sustainable applications in diverse biotechnological, environmental and industrial arenas.

Bioaccumulation and Bioremediation of Heavy Metals in Fishes-A Review

Heavy metals, the most potent contaminants of the environment, are discharged into the aquatic ecosystems through the effluents of several industries, resulting in serious aquatic pollution. This type of severe heavy metal contamination in aquaculture systems has attracted great attention throughout the world. These toxic heavy metals are transmitted into the food chain through their bioaccumulation in different tissues of aquatic species and have aroused serious public health concerns. Heavy metal toxicity negatively affects the growth, reproduction, and physiology of fish, which is threatening the sustainable development of the aquaculture sector. Recently, several techniques, such as adsorption, physio-biochemical, molecular, and phytoremediation mechanisms have been successfully applied to reduce the toxicants in the environment. Microorganisms, especially several bacterial species, play a key role in this bioremediation process. In this context, the present review summarizes the bioaccumulation of different heavy metals into fishes, their toxic effects, and possible bioremediation techniques to protect the fishes from heavy metal contamination. Additionally, this paper discusses existing strategies to bioremediate heavy metals from aquatic ecosystems and the scope of genetic and molecular approaches for the effective bioremediation of heavy metals.

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.

Soil contamination by diesel fuel destabilizes the soil microbial pools: Insights from permafrost soil incubations

Arctic contamination by diesel fuel (DF) is of great concern because of the uncertain feedback of permafrost carbon (C) and soil microbiota to DF in the context of climate change in high latitudes. We conducted a laboratory incubation experiment with a gradient of DF addition ratios to examine the responses of the soil microbiota of the typical permafrost soils in the tundra ecosystems of the Norilsk region (Siberia). The study revealed initial heterogeneity in the microbial activity of the studied soils (Histic Gleyic Cryosols (CR-hi,gl), Turbic Cryosols (CR-tu), Turbic Spodic Folic Cryosols (CR-tu,sd,fo), Gleyic Fluvisols (FL-gl)). We applied the two-pool model for evaluation of the effect of DF on the proportions of C pools and revealed significant differences between soil types in the fast and slow C pools in response to DF addition. The results showed that DF addition treatments had varying effects on the fast and slow C pools, microbial activity, and microbial community structure in the studied soils. For minor exceptions, DF dramatically accelerated C loss from the slow C pool in all soil types. We assume that differences in C pool and microbiota responses to DF addition were caused by soil texture and changes in microbial community structure. We isolated Serratia proteamaculans, S. liquefaciens, S. plymuthica, Rhodococcus erythropolis, Pseudomonas antarctica, P. libanensis, P. brassicacearum, and P. chlororaphis from the DF-polluted soils. These species are recommended for bioremediation to mitigate the DF contamination of permafrost soils, especially regarding climate change and the sustainable well-being of Arctic ecosystems.

Reconstruction of microbiome and functionality accelerated crude oil biodegradation of 2,4-DCP-oil-contaminated soil systems using composite microbial agent B-Cl

Biodegradation is one of the safest and most economical methods for the elimination of toxic chlorophenols and crude oil from the environment. In this study, aerobic degradation of the aforementioned compounds by composite microbial agent B-Cl, which consisted of Bacillus B1 and B2 in a 3:2 ratio, was analyzed. The biodegradation mechanism of B-Cl was assessed based on whole genome sequencing, Fourier transform infrared spectroscopy and gas chromatographic analyses. B-Cl was most effective at reducing Cl^- concentrations (65.17%) and crude oil biodegradation (59.18%) at 7 d, which was when the content of alkanes ≤ C₃₀ showed the greatest decrease. Furthermore, adding B-Cl solution to soil significantly decreased the 2,4-DCP and oil content to below the detection limit and by 80.68%, respectively, and reconstructed of the soil microbial into a system containing more CPs-degrading (exaA, frmA, L-2-HAD, dehH, ALDH, catABE), aromatic compounds-degrading (pcaGH, catAE, benA-xylX, paaHF) and alkane- and fatty acid-degrading (alkB, atoB, fadANJ) microorganisms. Moreover, the presence of 2,4-DCP was the main hinder of the observed effects. This study demonstrates the importance of adding B-Cl solution to determine the interplay of CPs with microbes and accelerating oil degradation, which can be used for in-situ bioremediation of CPs and oil-contaminated soil.

Environmental microbiome engineering for the mitigation of climate change

Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the long-term stabilization of carbon in ecosystems. In this review, we outline the process of environmental engineering and synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community and modify an ecosystem function target. Recent work, enabled by high-throughput technologies and modeling approaches, indicate that microbial inocula designed from the top-down, particularly through directed evolution, may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering. We address outstanding questions about the determinants of inocula establishment and provide suggestions for further research about the possibilities and challenges of environmental microbiome engineering as a tool to combat climate change.

Soil treatment using a biosurfactant producing bacterial consortium in rice fields contaminated with oily sludge- a sustainable approach

A consortium of two biosurfactant-producing bacteria (Bacillus pumilus KS2 and Bacillus cereus R2) was developed to remediate petroleum hydrocarbon-contaminated paddy soil. Soil samples from a heavily contaminated rice field near Assam's Lakwa oilfield were collected and placed in earthen pots for treatment. After each month of incubation, 50 g of soil from each earthen pot was collected, and the soil TPH (ppm) in each sample was determined. The extracted TPH samples were analysed by Gas chromatography-mass spectrometry (GC-MS) to confirm microbial degradation. The soil samples were examined for changes in pH, conductivity, total organic content (TOC), water holding capacity, and total nitrogen content in addition to TPH degradation. An increasing trend in TPH degradation was observed with each passing month. After six months of treatment, the sample with the lowest initial TPH concentration (1735 ppm) had the highest degradation (91.24%), while the soil with the highest amount of TPH (5780 ppm) had the lowest degradation (74.35%). A wide range of aliphatic hydrocarbons found in soil samples was degraded by the bacterial consortium. The soil samples contained eight different low- and high-molecular-weight PAHs. Some were fully mineralized, while others were significantly reduced. With the decrease in the TPH level in the polluted soil, a significant improvement in the soil's physicochemical qualities (such as pH, electrical conductivity, total organic content, and water-holding capacity) was observed.

Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments

Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.

Enhancing plant growth promoting rhizobacterial activities through consortium exposure: A review

Plant Growth Promoting Rhizobacteria (PGPR) has gained immense importance in the last decade due to its in-depth study and the role of the rhizosphere as an ecological unit in the biosphere. A putative PGPR is considered PGPR only when it may have a positive impact on the plant after inoculation. From the various pieces of literature, it has been found that these bacteria improve the growth of plants and their products through their plant growth-promoting activities. A microbial consortium has a positive effect on plant growth-promoting (PGP) activities evident by the literature. In the natural ecosystem, rhizobacteria interact synergistically and antagonistically with each other in the form of a consortium, but in a natural consortium, there are various oscillating environmental conditions that affect the potential mechanism of the consortium. For the sustainable development of our ecological environment, it is our utmost necessity to maintain the stability of the rhizobacterial consortium in fluctuating environmental conditions. In the last decade, various studies have been conducted to design synthetic rhizobacterial consortium that helps to integrate cross-feeding over microbial strains and reveal their social interactions. In this review, the authors have emphasized covering all the studies on designing synthetic rhizobacterial consortiums, their strategies, mechanism, and their application in the field of environmental ecology and biotechnology.

Supramolecular bioamphiphile facilitated bioemulsification and concomitant treatment of recalcitrant hydrocarbons in petroleum refining industry oily waste

Bioremediation of real-time petroleum refining industry oily waste (PRIOW) is a major challenge due to the poor emulsification potential and oil sludge disintegration efficiency of conventional bioamphiphile molecules. The present study was focused on the design of a covalently engineered supramolecular bioamphiphile complex (SUBC) rich in hydrophobic amino acids for proficient emulsification of hydrocarbons followed by the concomitant degradation of total petroleum hydrocarbons (TPH) in PRIOW using the hydrocarbonoclastic microbial bio-formulation system. The synthesis of SUBC was carried out by pH regulated microbial biosynthesis process and the yield was obtained to be 450.8 mg/g of petroleum oil sludge. The FT-IR and XPS analyses of SUBC revealed the anchoring of hydrophilic moieties of monomeric bioamphiphilic molecules, resulting in the formation of SUBC via covalent interaction. The SUBC was found to be lipoprotein in nature. The maximum loading capacity of SUBC onto surface modified rice hull (SMRH) was achieved to be 45.25 mg/g SMRH at the optimized conditions using RSM-CCD design. The SUBC anchored SMRH was confirmed using SEM, FT-IR, XRD and TGA analyses. The adsorption isotherm models of SUBC onto SMRH were performed. The integrated approach of SUBC-SMRH and hydrocarbonoclastic microbial bio-formulation system, emulsified oil from PRIOW by 92.86 ± 2.26% within 24 h and degraded TPH by 89.25 ± 1.75% within 4 days at the optimum dosage ratio of SUBC-SMRH (0.25 g): PRIOW (1 g): mass of microbial-assisted biocarrier material (0.05 g). The TPH degradation was confirmed by SARA fractional analysis, FT-IR, ¹H NMR and GC-MS analyses. The study suggested that the application of covalently engineered SUBC has resulted in the accelerated degradation of real-time PRIOW in a very short duration without any secondary sludge generation. Thus, the SUBC integrated approach can be considered to effectively manage the hydrocarbon contaminants from petroleum refining industries under optimal conditions.

Identification of hydrocarbon-degrading bacterial consortium isolated from the oil-contaminated muddy soil in Hanoi, Vietnam

Bioremediation is a promising approach for treating oil-contaminated environments. The main objective of this study was to isolate bacteria capable of degrading hydrocarbons for application in oily wastewater treatment from oil-contaminated sites in Hanoi, Vietnam. The bacterial consortium studied was obtained from an oil-contaminated muddy soil sample enriched with crude oil mixed with diesel oil as a carbon source. The reconstituted consortium was able to degrade 93% of the oil content after 7 days of testing. A total of five pure bacterial strains were isolated on TSA agar from the complex microbial communities and were selected as potential candidates for oily sludge biodegradation processes. These isolates were identified based on their morphological and biochemical characteristics. By using molecular biology techniques, five hydrocarbons degrading bacteria were investigated and identified as Pseudomonas mendocina strain MD1 (OL687411.1), Pseudomonas hydrolytica strain MD2 (OL771695.1), Brucella intermedia strain MD3 (OL687412.1), Pseudomonas stutzeri strain MD4 (OL687413.1), and Stenotrophomonas nitritireducens strain MD5 (OL687414.1). The morphological and biochemical characterization of these bacteria showed that five of them were Gram-negative, rod-shaped, catalase positive, the ideal pH was neutral, and the optimum growth temperature was 30ºC in a culture medium with a salinity of 0.5%. These strains are capable of producing extracellular enzymes, such as lipase, amylase, cellulase, and protease.

Integration of green economy concepts for sustainable biosurfactant production - A review

The link between increasing global population, food demand, industrialization, and agricultural waste is strong. Decomposing by-products from food cycles can introduce harmful toxic heavy metals, active degrading microbes, and enzymes to the environment. Additionally, high greenhouse gas emissions from the decomposing wastes contribute to global change and a high carbon economy. The bioeconomy and circular economy of biosurfactant production utilize these cheap feedstocks and promote waste to valuable product initiatives. Waste reduction, reuse, and recycling in an integrating green economy bioprocess ensure the sustainability of novel, cost-effective, safe, and renewable health-grade biosurfactants. This work reviews green economy concepts integration with sustainable biosurfactant production and its application in health-related industries. Benefits from recent advances in the production, characterization, and health-wise classification of biosurfactants were further discussed, including its limitations, techno-economic assessment, market evaluations, possible roadblocks, and future directions.

Ecological risk assessment of priority PAHs pollutants in crude oil contaminated soil and its impacts on soil biological properties

Polycyclic aromatic hydrocarbons (PAHs) are one of the major toxic constituents of crude oil and therefore, an understanding on PAHs associated risks and their relationship with soil biological parameters are necessary for adopting effective risk-based and site specific remediation strategies in the contaminated soil. Here, risks evaluation of eight detected PAHs in terms of toxic equivalent concentration (TEQ_C), benzo(a)pyrene equivalent (BaPeq), contamination factor (CF), pollution load index (PLI), hazard quotient (HQ), hazard index (HI), toxic unit for individual PAHs (TU) and PAHs mixture (TU_m) have been evaluated. Besides, the effect of PAHs contamination on soil biological properties has also been investigated and correlated with PAHs concentrations. The TEQc of eight PAHs was recorded in the range of 0.06-5.0 mg kg^-1 soil_, whereas the BaPeq value was 25.3 mg kg^-1 soil which exceed the permissible limit. Similarly, CF (85.5-1668.2), PLI (322.8), HQ (311.7-8340.9), HI (26,443.8), TU (227.9-3821.6) and TU_m(7916.2) also exceed the permissible values for non-toxic conditions indicating carcinogenic risk for humans. Besides, activities of soil dehydrogenase, urease, alkaline-phosphatase, catalase, amylase and cellulase were decreased by 1.5-2.3 folds in the contaminated soil than control. The results of Pearson's correlation matrix also established negative impact of PAHs on the soil's biological properties.

Biotechnology of Microorganisms from Coal Environments: From Environmental Remediation to Energy Production

Simple Summary

Despite the wide perception that coal environments are extreme habitats, they harbor resident microbial communities. Coal-associated habitats, such as coal mine areas/drainages, spoil heaps, and coalbeds, are defined as complex ecosystems with indigenous microbial groups and native microecological networks. Resident microorganisms possess rich functional potentials and profoundly shape a range of biotechnological processes in the coal industry, from production to remediation.

Abstract

It was generally believed that coal sources are not favorable as live-in habitats for microorganisms due to their recalcitrant chemical nature and negligible decomposition. However, accumulating evidence has revealed the presence of diverse microbial groups in coal environments and their significant metabolic role in coal biogeochemical dynamics and ecosystem functioning. The high oxygen content, organic fractions, and lignin-like structures of lower-rank coals may provide effective means for microbial attack, still representing a greatly unexplored frontier in microbiology. Coal degradation/conversion technology by native bacterial and fungal species has great potential in agricultural development, chemical industry production, and environmental rehabilitation. Furthermore, native microalgal species can offer a sustainable energy source and an excellent bioremediation strategy applicable to coal spill/seam waters. Additionally, the measures of the fate of the microbial community would serve as an indicator of restoration progress on post-coal-mining sites. This review puts forward a comprehensive vision of coal biodegradation and bioprocessing by microorganisms native to coal environments for determining their biotechnological potential and possible applications.

Understanding biochemical defense and phytoremediation potential of Leucas aspera in crude oil polluted soil

The phytoremediation potential and enzymatic defense of a medicinal herb Leucas aspera was studied in the crude oil contaminated soil. The productivity, antioxidants, and phytochemical and functional group profiles of the plant species in stress conditions were investigated. Besides, changes in enzymes, beneficial bacterial population, and physico-chemical and total oil and grease (TOG) profiles in the contaminated soil were also studied. The results showed improvement in physico-chemical conditions, increase in beneficial bacterial population (4.1-5.4 folds), and decrease in TOG (31.3%) level of the contaminated soil by end of the experimental trials. The L. aspera treated contaminated soil showed enhancement in dehydrogenase (32.3%), urease (102.8%), alkaline phosphatase (174.4%), catalase (68.5%), amylase (76.16%), and cellulase (23.6%) activities by end of the experimental trials. Furthermore, there were significant variations in leaf area index, chlorophyll, and biomass contents of the experimental plant as against the initial level and control. Besides, the significant reduction in IC₅₀ values (24-27.4%) of L. aspera samples grown in contaminated soil confirms the strong antioxidant enzymatic defense of the plant species against the crude oil associated abiotic stress. The Fourier-transform infrared (FT-IR) analysis confirmed the uptake and metabolism of aliphatic hydrocarbons, aldehydes, alkyl halides, and nitro compounds by the experimental plant from the contaminated soil.

Great Abilities of Shinella zoogloeoides Strain from a Landfarming Soil for Crude Oil Degradation and a Synergy Model for Alginate-Bead-Entrapped Consortium Efficiency

Oil contamination is of great concern worldwide and needs to be properly addressed. The present work aimed to contribute to the development of bacterial consortia for oil recovery. We investigated the community structure of a landfarming-treated soil (LF2) by metagenomics to unravel the presence of hydrocarbon degraders. Moreover, we isolated Shinella zoogloeoides LFG9 and Bacillus swezeyi LFS15 from LF2 and combined them with Pseudomonas guguanensis SGPP2 isolated from an auto mechanic workshop soil to form the mixed consortium COG1. Bacterial isolates were tested for biosurfactant production. Additionally, the bioremediation potential of COG1 was studied as free and entrapped consortia by gas chromatography-mass spectrometry, in comparison to the single strains. Results revealed the presence of Actinobacteria (66.11%), Proteobacteria (32.21%), Gammaproteobacteria (5.39%), Actinomycetales (65.15%), Burkholderiales (13.92%), and Mycobacterium (32.22%) taxa, indicating the presence of hydrocarbon degraders in soil LF2. All three isolated strains were biosurfactant producers capable of degrading crude oil components within 14 days. However, Shinella zoogloeoides LFG9 performed best and was retained as candidate for further bioremediation investigation. In addition, COG1 performed better when immobilized, with entrapment effectiveness manifested by increased fatty acids and aromatic compound degradation. Attempt to improve crude oil biodegradation by adding surfactants failed as sodium dodecyl sulfate restrained the immobilized consortium performance.

Characterization and biodegradability assessment of water-soluble fraction of oily sludge using stir bar sorptive extraction and GCxGC-TOF MS

Percolation of water through oily sludge during storage and handling of the sludge can cause soil and groundwater contamination. In this study, oily sludge from a refinery was equilibrated with water to obtain the water-soluble fraction (WSF) of oily sludge. The WSF had dissolved organic carbon (DOC) of 166 mg/L. Human cell line-based toxicity assay revealed IC₅₀ of 41 mg/L indicating its toxic nature. The predominant compounds in WSF of oily sludge included isomers of methyl, dimethyl and trimethyl quinolines and naphthalenes along with phenol derivatives and other polynuclear aromatic hydrocarbons (PAHs). Biodegradation of WSF of oily sludge was studied using a consortium of Rhodococcus ruber, Bacillus sp. and Bacillus cereus isolated from the refinery sludge. The consortium of the three strains resulted in 70% degradation over 15 days with a first-order degradation rate of 0.161 day^-1. Further analysis of the WSF was performed using the stir-bar sorptive extraction (SBSE) followed by GCxGC-TOF MS employing a PDMS Twister. The GCxGC analysis showed that Bacillus cereus was capable of degrading the quinoline, phenol and naphthalene derivatives in WSF of oily sludge at a faster rate compared to pyridine and benzoquinoline derivatives. Quinoline, phenol, biphenyl, naphthalene, pyridine and benzoquinolines derivatives in the WSF of oily sludge were reduced by 87%, 92%, 88%, 77%, 40% and 62%, respectively with respect to the controls. The WSF of oily sludge contained, n-alkanes, ranging from n-C12 to n-C18 which were removed within 2 days of biodegradation.

Hydrocarbon exposure effect on energetic metabolism and immune response in Crassostrea virginica

Crassostrea virginica was exposed to different light crude oil levels to assess the effect on transcriptomic response and metabolic rate. The exposure time was 21 days, and levels of 100 and 200 μg/L were used, including a control. The most significant difference among treatments was the overexpression of several genes associated with energy production, reactive oxygen species (ROS) regulation, immune system response, and inflammatory response. Also, a hydrocarbon concentration-related pattern was identified in ROS regulation, with a gene expression ratio near 1.8:1 between 200 and 100 μg/L treatments. Statistical analysis showed no interaction effect for metabolic rate; however, significant differences were found for oil concentration and time factors, with a higher oxygen consumption at 200 μg/L. Our findings provide novel information about the metabolic response of C. virginica during hydrocarbons exposure. In addition, our results point out which biological processes should be investigated as targets for searching bioindicators.

Investigating the effect of nanoparticle on phenanthrene biodegradation by Labedella gwakjiensis strain KDI

Polycyclic aromatic hydrocarbons (PAHs), as persistent organic contaminants, are a major source of concern due to their toxic effect on ecosystems and human health. This study attempted to isolate halotolerant PAHs degrading bacteria from saline oil-contaminated soils. Among the isolates, strain KDI with the highest 16S rRNA gene sequence similarity to Labedella gwakjiensis was able to reduce surface tension (ST) from 65.42 to 26.60 mN m^-1 and increase the emulsification index to 81.04%, as a result of significant biosurfactant production. Response Surface Methodology (RSM) analysis was applied to optimize the factors, i.e. PAHs concentration and NaCl concentration as well as to determine the effect of these important variables on PAHs biodegradation. The Carbon Quantum Dots. Iron Oxide (CQDs.Fe₃O₄) nanoparticles were characterized by several popular analytical techniques, after which the effect of CQD.Fe₃O₄ nanoparticles on biodegradation was examined. PAHs biodegradation rate and efficiency of strain KDI to degrade PHE in the presence of CQD.Fe₃O₄ nanoparticles was analyzed by GC. According to the results during biodegradation both the concentration of PAHs and the amount of NaCl were effective. The biodegradation rate significantly increased in the presence of CQD.Fe₃O₄. The highest biodegradation of PHE occurred in the presence of 0.5 g/L of CQD.Fe₃O₄ which was 63.63% and 81.77% after 48 and 72 h of incubation. To the best of our knowledge, this is the first report on optimization of PAHs concentration and salinity by RSM and nanobioremediation of PHE using a bacterial strain in the presence of CQD.Fe₃O₄ nanoparticles.

Are Wetlands as an Integrated Bioremediation System Applicable for the Treatment of Wastewater from Underground Coal Gasification Processes?

Underground coal gasification (UCG) can be considered as one of the clean coal technologies. During the process, the gas of industrial value is produced, which can be used to produce heat and electricity, liquid fuels or can replace natural gas in chemistry. However, UCG does carry some environmental risks, mainly related to potential negative impacts on surface and groundwater. Wastewater and sludge from UCG contain significant amounts of aliphatic and aromatic hydrocarbons, phenols, ammonia, cyanides and hazardous metals such as arsenic. This complicated matrix containing high concentrations of hazardous pollutants is similar to wastewater from the coke industry and, similarly to them, requires complex mechanical, chemical and biological treatment. The focus of the review is to explain how the wetlands systems, described as one of bioremediation methods, work and whether these systems are suitable for removing organic and inorganic contaminants from heavily contaminated industrial wastewater, of which underground coal gasification wastewater is a particularly challenging example. Wetlands appear to be suitable systems for the treatment of UCG wastewater and can provide the benefits of nature-based solutions. This review explains the principles of constructed wetlands (CWs) and provides examples of industrial wastewater treated by various wetland systems along with their operating principles. In addition, the physicochemical characteristics of the wastewater from different coal gasifications under various conditions, obtained from UCG’s own experiments, are presented.

Surface treated Phoenix sylvestris for bioadsorption of oil from aqueous solution: Isotherms and kinetic studies

Biosorption is a versatile technique of removing the oil spill - one of the major toxicants that causes water pollution, which threatens the ecological balance of the aquatic ecosystem. The proposed research aims in developing a viable adsorbent from discarded agricultural waste, Phoenix sylvestris, which was surface altered, assessed and utilised as a biosorbent for the effective removal of diesel from aqueous solution in batch adsorption trials. Waste palm leaves, Phoenix sylvestris (RPS)was physically (PMPS) and chemically modified (CMPS) to adsorb diesel in the emulsion. The synthesised materials were characterised by FTIR, SEM, and EDS, confirming a well-defined microporous structure consisting of ionisable groups. The studies indicated optimised conditions of 10 g, 4.5 g and 2 g of RPS, PMPS and CMPS respectively at 303K for an optimised adsorption time of 60 min. Freundlich isotherm agreed well with experimental data, and the kinetic mechanism claimed better results with RPS, PMPS and CMPS for Pseudo first-order model. The adsorbents could be reused five times without much loss of efficiency. From the performed studies, it can be inferred that good adsorption capacities at optimised conditions followed the order of CMPS > PMPS > RPS. Thermodynamic analysis proved the feasibility of such biosorption with exothermic nature predicting spontaneous attraction of oil components to the surface of PMPS and CMPS. Moreover, the density of the CMPS layer rendered proven results for such biosorption displaying a hyperbolic dependency assuring its efficacy. Hence, it can be concluded that the prepared adsorbent from Phoenix sylvestris, an agricultural waste, possess good adsorptive properties.

Biosurfactants and chemotaxis interplay in microbial consortium-based hydrocarbons degradation

Hydrocarbons are routinely detected at low concentrations, despite the degrading metabolic potential of ubiquitous microorganisms. The potential drivers of hydrocarbons persistence are lower bioavailability and mass transfer limitation. Recently, bioremediation strategies have developed rapidly, but still, the solution is not resilient. Biosurfactants, known to increase bioavailability and augment biodegradation, are tightly linked to bacterial surface motility and chemotaxis, while chemotaxis help bacteria to locate aromatic compounds and increase the mass transfer. Harassing the biosurfactant production and chemotaxis properties of degrading microorganisms could be a possible approach for the complete degradation of hydrocarbons. This review provides an overview of interplay between biosurfactants and chemotaxis in bioremediation. Besides, we discuss the chemical surfactants and biosurfactant-mediated biodegradation by microbial consortium.

Comparative Analysis of Microbial Consortiums and Nanoparticles for Rehabilitating Petroleum Waste Contaminated Soils

Nano-bioremediation application is an ecologically and environmentally friendly technique to overcome the catastrophic situation in soil because of petroleum waste contamination. We evaluated the efficiency of oil-degrading bacterial consortium and silver nanoparticles (AgNPs) with or without fertilizer to remediate soils collected from petroleum waste contaminated oil fields. Physicochemical characteristics of control soil and petroleum contaminated soils were assessed. Four oil-degrading strains, namely Bacillus pumilus (KY010576), Exiguobacteriaum aurantiacum (KY010578), Lysinibacillus fusiformis (KY010586), and Pseudomonas putida (KX580766), were selected based on their in vitrohydrocarbon-degrading efficiency. In a lab experiment, contaminated soils were treated alone and with combined amendments of the bacterial consortium, AgNPs, and fertilizers (ammonium nitrate and diammonium phosphate). We detected the degradation rate of total petroleum hydrocarbons (TPHs) of the soil samples with GC-FID at different intervals of the incubation period (0, 5, 20, 60, 240 days). The bacterial population (CFU/g) was also monitored during the entire period of incubation. The results showed that 70% more TPH was degraded with a consortium with their sole application in 20 days of incubation. There was a positive correlation between TPH degradation and the 100-fold increase in bacterial population in contaminated soils. This study revealed that bacterial consortiums alone showed the maximum increase in the degradation of TPHs at 20 days. The application of nanoparticles and fertilizer has non-significant effects on the consortium degradation potential. Moreover, fertilizer alone or in combination with AgNPs and consortium slows the rate of degradation of TPHs over a short period. Still, it subsequently accelerates the rate of degradation of TPHs, and a negligible amount remains at the end of the incubation period.

Microbial associations for bioremediation. What does "microbial consortia" mean?

Microbial associations arise as useful tools in several biotechnological processes. Among them, bioremediation of contaminated environments usually takes advantage of these microbial associations. Despite being frequently used, these associations are indicated using a variety of expressions, showing a lack of consensus by specialists in the field. The main idea of this work is to analyze the variety of microbial associations referred to as "microbial consortia" (MC) in the context of pollutants biodegradation and bioremediation. To do that, we summarize the origin of the term pointing out the features that an MC is expected to meet, according to the opinion of several authors. An analysis of related bibliography was done seeking criteria to rationalize and classify MC in the context of bioremediation. We identify that the microbe's origin and the level of human intervention are usually considered as a category to classify them as natural microbial consortia (NMC), artificial microbial consortia (AMC), and synthetic microbial consortia (SMC). In this sense, NMC are those associations composed by microorganisms obtained from a single source while AMC members come from different sources. SMC are a class of AMC in which microbial composition is defined to accomplish a certain specific task. We propose that the effective or potential existence of the interaction among MC members in the source material should be considered as a category in the classification as well, in combination with the origin of the source and level of intervention. Cross-kingdom MC and new developments were also considered. Finally, the existence of grey zones in the limits between each proposed microbial consortia category is addressed. KEY POINTS: • Microbial consortia for bioremediation can be obtained through different methods. • The use of the term "microbial consortia" is unclear in the specialized literature. • We propose a simplified classification for microbial consortia for bioremediation.

Structural and functional characterization of a novel biosurfactant from Bacillus sp. IITD106

Plant saponins are attractive biosurfactants and have been used to enhance phytoremediation. There are only limited reports on saponins produced by bacteria. Here, we report structural and functional characterization of a novel saponin produced by Bacillus sp. IITD106. Biosurfactant production was determined by emulsion index, drop collapse, oil displacement and hemolytic assays. The biosurfactant was stable over a range of temperature (30 °C to 70 °C), salinity (0-150 g liter^-1) and pH (4-10). The surface tension of the medium reduced from 58.89 mN/m to 27.29 mN/m using the isolated biosurfactant. Chromatographic analysis revealed the biosurfactant to be a glycolipid. LCMS, FT-IR and NMR analysis identified the biosurfactant to be a saponin containing two sugar groups and a 5 ringed triterpene sapogenin unit. Genome sequencing of the strain revealed the presence of genes responsible for biosynthesis of saponin. Statistical optimization of culture medium resulted in 9.3-fold increase in biosurfactant production. Kinetics study of biosurfactant production performed in a stirred tank batch bioreactor resulted in 6.04 g liter^-1 and 6.9 g liter^-1 biomass and biosurfactant concentration, respectively. The biosurfactant was found to solubilize polycyclic aromatic hydrocarbons. The potential of cell free biosurfactant containing broth to enhance oil recovery was tested in a sand pack column and recovery of 63% of residual oil was observed. To our knowledge this is the first report of saponin production by any of the strains of Bacillus.

Mathematical Modelling of Canola Oil Biodegradation and Optimisation of Biosurfactant Production by an Antarctic Bacterial Consortium Using Response Surface Methodology

An Antarctic soil bacterial consortium (reference BS14) was confirmed to biodegrade canola oil, and kinetic studies on this biodegradation were carried out. The purpose of this study was to examine the ability of BS14 to produce biosurfactants during the biodegradation of canola oil. Secondary mathematical equations were chosen for kinetic analyses (Monod, Haldane, Teissier-Edwards, Aiba and Yano models). At the same time, biosurfactant production was confirmed through a preliminary screening test and further optimised using response surface methodology (RSM). Mathematical modelling demonstrated that the best-fitting model was the Haldane model for both waste (WCO) and pure canola oil (PCO) degradation. Kinetic parameters including the maximum degradation rate (μmax) and maximum concentration of substrate tolerated (Sm) were obtained. For WCO degradation these were 0.365 min-1 and 0.308%, respectively, while for PCO they were 0.307 min-1 and 0.591%, respectively. The results of all preliminary screenings for biosurfactants were positive. BS14 was able to produce biosurfactant concentrations of up to 13.44 and 14.06 mg/mL in the presence of WCO and PCO, respectively, after optimisation. The optimum values for each factor were determined using a three-dimensional contour plot generated in a central composite design, where a combination of 0.06% salinity, pH 7.30 and 1.55% initial substrate concentration led to the highest biosurfactant production when using WCO. Using PCO, the highest biosurfactant yield was obtained at 0.13% salinity, pH 7.30 and 1.25% initial substrate concentration. This study could help inform the development of large-scale bioremediation applications, not only for the degradation of canola oil but also of other hydrocarbons in the Antarctic by utilising the biosurfactants produced by BS14.

Bioballs carrying a syntrophic Rhodococcus and Mycolicibacterium consortium for simultaneous sorption and biodegradation of fuel oil in contaminated freshwater

Nonpathogenic effective bacterial hydrocarbon degraders, Rhodococcus ruber S103, Mycolicibacterium parafortuitum J101 and Mycolicibacterium austroafricanum Y502, were isolated from mixed polycyclic aromatic hydrocarbon (PAH)-enriched river sediments. They possessed broad substrate specificities toward various PAHs and aliphatic compounds as sole carbon sources. These strains exhibited promising characteristics, including biosurfactant production, high cell hydrophobicity, biofilm formation and no antagonistic interactions, and contained genes encoding hydrocarbon-degrading enzymes. The mixed bacterial consortium combining S103, J101 and Y502, showed more effective syntrophic degradation of two types of refined petroleum products, diesel and fuel oils, than monocultures. The defined consortium immobilized on plastic balls achieved over 50% removal efficiency of high fuel oil concentration (3000 mg L^-1) in a synthetic medium and contaminated freshwater. Furthermore, the immobilized cells simultaneously degraded more than 46% of total fuel oil adsorbed on plastic balls in both culture systems. SEM imaging confirmed that the immobilized consortium exhibited biofilm formation with the bacterial community covering most of the bioball surface, resulting in high bacterial survival against toxic contaminants. The results of this study showed the potential use of the cooperative interaction between Rhodococcus and Mycolicibacterium as immobilized bioballs for the bioremediation of fuel oil-contaminated environments. Additionally, this research has motivated further investigations into the development of bioremediation products for fuel oil degradation.

Genomic characterization of Enterobacter xiangfangensis STP-3: Application to real time petroleum oil sludge bioremediation

Sustainable treatment of petroleum oil sludge still remains as a major challenge to petroleum refineries. Bioremediation is the promising technology involving bacteria for simultaneous production of biosurfactant and followed by degradation of petroleum compounds. Complete genomic knowledge on such potential microbes could accentuate its successful exploitation. The present study discusses the genomic characteristics of novel biosurfactant producing petrophilic/ petroleum hydrocarbon degrading strain, Enterobacter xiangfangensis STP-3, isolated from petroleum refinery oil sludge contaminated soil. The genome has 4,584,462 bp and 4372 protein coding sequences. Functional analysis using the RAST and KEGG databases revealed the presence of biosynthetic gene clusters linked to glycolipid and lipopeptide production and multiple key candidate genes linked with the degradation pathway of petroleum hydrocarbons. Orthology study revealed diversity in gene clusters associated to membrane transport, carbohydrate, amino acid metabolism, virulence and defence mechanisms, and nucleoside and nucleotide synthesis. The comparative analysis with 27 other genomes predicted that the core genome contributes to its inherent bioremediation potential, whereas the accessory genome influences its environmental adaptability in unconventional environmental conditions. Further, experimental results showed that E. xiangfangensis STP-3 was able to degrade PHCs by 82 % in 14 days during the bioremediation of real time petroleum oil sludge with the concomitant production of biosurfactant and metabolic enzymes, To the best of our knowledge, no comprehensive genomic study has been previously reported on the biotechnological prospective of this species.

The remediation potential for PAHs of Verbascum sinuatum L. combined with an enhanced rhizosphere landscape: A full-scale mesocosm experiment

A full-scale mesocosm study was conducted to depict how integrated biological systems interact to adapt to contaminant stress and improve remediation of polycyclic aromatic hydrocarbons (PAHs)contaminated soils. The combination of Verbascum sinuatum L. and microbial consortium (fungi and bacteria) was employed along with three differently contaminated soils. After 240 days the highest PAHs removal (up to 68 %) and 6-rings compounds decrease was found in soil with lower pollution and cation exchange capacity. V. sinuatum showed a significant adaptability over time in terms of redox biology. Soil enzyme activities and microscopic evidences proved a rising plant-microorganisms association and a successful mycorrhization, arising from the inoculation of our consortia. In addition, an enhanced richness of PAHs degrading genes was achieved. Microbial co-metabolism, helped by the establishment of complex relationships with hosting plant, demonstrated to be suitable for the degradation of high molecular weight PAHs and represents a biotechnology with great prospects.

Characterization of lipopeptide biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis: The role of biosurfactant in carbazole solubilisation

AIM

Characterization of biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis and proteomic analysis of intracellular proteins of bacterium while growing on glucose and carbazole medium.

METHODS AND RESULTS

The bacterium R. cervicalis was isolated from a soil sample contaminated with crude petroleum oil. PCR amplification ascertained the existence of some hydrocarbon-degrading catabolic genes (alkB and PAH-RHDα, C12O, and C23O) in the bacterial genome. GC-MS and RP-HPLC analyses demonstrated 62% and 60% carbazole degradation, respectively, by R. cervicalis 144 h post-incubation at 37℃ and pH 6.5. Due to the paucity of protein databases, expressions of only 29 and 14 intracellular proteins were explicitly recognized and quantitated by mass spectrometry analysis when R. cervicalis was grown in carbazole and glucose medium, respectively. FTIR, NMR and HR-MS/MS analyses demonstrated the lipopeptide nature of the purified biosurfactant produced by R. cervicalis. The biosurfactant is also presumed to assist in the solubilization of carbazole.

CONCLUSION

The isolated R. cervicalis strain is a potential candidate for the bioremediation of carbazole in petroleum-oil-contaminated sites.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of the promising R. cervicalis strain proficient in carbazole biodegradation.

Genomic and functional potential of the immobilized microbial consortium MCSt-1 for wastewater treatment

Treatment of wastewater prior to release in water bodies is an imperative need of the current time to address the global water crises. Thus, consortium MCSt-1 was designed for an effective wastewater treatment based on its cellulolytic, proteolytic, lipolytic, phenol and sodium dodecyl sulfate degrading activities along with effective nutrient removal capacity. Performance of the designed consortium was assayed using two differently configured lab-scale bioreactors as subjected to immobilization on two different matrices (pebbles and nylon mesh). Consortium MCSt-1 proficiently removes soluble chemical oxygen demand, nitrate, ammonia and phosphorus with 83%, 67%, 76%, and 62% removal efficiency, respectively. The immobilization on a mesh is recommended as it exhibited better biofilm formation, hence results in significant organic load and nutrient removal. The functional potential of the consortium MCSt-1 explored through genome characterization and reveal the presence of genes responsible for phosphorus metabolism and removal (pst operon and ppk), ammonia assimilation (amt), and nitrate; nitrite reductase (nar, nir, nor). Additionally, consortium members also annotated with the phenol, catechol and benzoate degradation, stress response, heavy metal and antibiotics resistance genes. Hence, the designed consortium MCSt-1 can withstand the harsh condition of treatment plants and serves as the best solution for enhancing wastewater treatment efficiency.

Biocatalytic remediation of industrial pollutants for environmental sustainability: Research needs and opportunities

An increasing quantum of pollutants from various industrial sector activities represents a severe menace to environmental & ecological balance. Bioremediation is gaining flow globally due to its cost-effective and environment-friendly nature. Understanding biodegradation mechanisms is of high ecological significance. Application of microbial enzymes has been reported as sustainable approach to mitigate the pollution. Immobilized enzyme catalyzed transformations are getting accelerated attention as potential alternatives to physical and chemical methods. The attention is now also focused on developing novel protein engineering strategies and bioreactor design systems to ameliorate overall biocatalysis and waste treatment further. This paper presents and discusses the most advanced and state of the art scientific & technical developments about biocatalytic remediation of industrial pollutants. It also covers various biocatalysts and the associated sustainable technologies to remediate various pollutants from waste streams. Enzyme production and immobilization in bioreactors have also been discussed. This paper also covers challenges and future research directions in this field.

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.

The Use of Response Surface Methodology as a Statistical Tool for the Optimisation of Waste and Pure Canola Oil Biodegradation by Antarctic Soil Bacteria

Hydrocarbons can cause pollution to Antarctic terrestrial and aquatic ecosystems, both through accidental release and the discharge of waste cooking oil in grey water. Such pollutants can persist for long periods in cold environments. The native microbial community may play a role in their biodegradation. In this study, using mixed native Antarctic bacterial communities, several environmental factors influencing biodegradation of waste canola oil (WCO) and pure canola oil (PCO) were optimised using established one-factor-at-a-time (OFAT) and response surface methodology (RSM) approaches. The factors include salinity, pH, type of nitrogen and concentration, temperature, yeast extract and initial substrate concentration in OFAT and only the significant factors proceeded for the statistical optimisation through RSM. High concentration of substrate targeted for degradation activity through RSM compared to OFAT method. As for the result, all factors were significant in PBD, while only 4 factors were significant in biodegradation of PCO (pH, nitrogen concentration, yeast extract and initial substrate concentration). Using OFAT, the most effective microbial community examined was able to degrade 94.42% and 86.83% (from an initial concentration of 0.5% (v/v)) of WCO and PCO, respectively, within 7 days. Using RSM, 94.99% and 79.77% degradation of WCO and PCO was achieved in 6 days. The significant interaction for the RSM in biodegradation activity between temperature and WCO concentration in WCO media were exhibited. Meanwhile, in biodegradation of PCO the significant factors were between (1) pH and PCO concentration, (2) nitrogen concentration and yeast extract, (3) nitrogen concentration and PCO concentration. The models for the RSM were validated for both WCO and PCO media and it showed no significant difference between experimental and predicted values. The efficiency of canola oil biodegradation achieved in this study provides support for the development of practical strategies for efficient bioremediation in the Antarctic environment.

The effects of biostimulation and bioaugmentation on crude oil biodegradation in two adjacent terrestrial oil spills of different age, in a hyper-arid region

This study deals with two adjacent terrestrial oil spills, with similar properties, located in a hyper-arid region in Israel, one from 1975 and the other from 2014. It tests the effect of biostimulation on crude oil degradation in both spills and whether biostimulated sediments from the 1975 spill can bioaugment crude oil degradation in the 2014 spill. Soil hydrophobicity, expressed as Water Drop Penetration Time (WDPT), and Gasoline Range Organics (GRO) and Diesel Range Organics (DRO) content in sediments were measured in one-month ex-situ experiments. No significant reduction in hydrophobicity and GRO + DRO content was observed in non-biostimulated controls. A combined treatment of mineral fertilization at t₀ and maintaining 50% water saturation, significantly accelerated the decrease in hydrophobicity and GRO + DRO content in sediments of both spills. The addition of biostimulated sediments from the 1975 spill failed to accelerate the reduction of GRO + DRO content and hydrophobicity in the 2014 spill. Surprisingly, the GRO + DRO degradation rate in biostimulated sediments from the 2014 spill was 36% higher than in biostimulated sediments from the 1975 spill. Crude oil composition in both spills changes during its degradation and is characterized by an increase in the GRO fraction. To a certain range, WDPT was found to serve as a reliable indicator for oil content in the soil. We conclude that even in a hyper-arid region, oil bio-degradation capabilities develop in a relatively short time. Moreover, while biostimulation was effective in accelerating biodegradation, bioaugmentation with biostimulated sediments from a nearby older spill was found ineffective.

Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics

Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.

Research Trends of Biodegradation of Cooking Oil in Antarctica from 2001 to 2021: A Bibliometric Analysis Based on the Scopus Database

In the present age, environmental pollution is multiplying due to various anthropogenic activities. Pollution from waste cooking oil is one of the main issues facing the current human population. Scientists and researchers are seriously concerned about the oils released from various activities, including the blockage of the urban drainage system and odor issues. In addition, cooking oil is known to be harmful and may have a carcinogenic effect. It was found that current research studies and publications are growing on these topics due to environmental problems. A bibliometric analysis of studies published from 2001 to 2021 on cooking oil degradation was carried out using the Scopus database. Primarily, this analysis identified the reliability of the topic for the present-day and explored the past and present progresses of publications on various aspects, including the contributing countries, journals and keywords co-occurrence. The links and interactions between the selected subjects (journals and keywords) were further visualised using the VOSviewer software. The analysis showed that the productivity of the publications is still developing, with the most contributing country being the United States, followed by China and India with 635, 359 and 320 publications, respectively. From a total of 1915 publications, 85 publications were published in the Journal of Agricultural and Food Chemistry. Meanwhile, the second and third of the most influential journals were Bioresource Technology and Industrial Crops and Products with 76 and 70 total publications, respectively. Most importantly, the co-occurrence of the author’s keywords revealed “biodegradation”, “bioremediation”, “vegetable oil” and “Antarctic” as the popular topics in this study area, especially from 2011 to 2015. In conclusion, this bibliometric analysis on the degradation of cooking oil may serve as guide for future avenues of research in this area of research.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.

Effect of consortium bioaugmentation and biostimulation on remediation efficiency and bacterial diversity of diesel-contaminated aged soil

This study aimed to evaluate the effects of consortium bioaugmentation (CB) and various biostimulation options on the remediation efficiency and bacterial diversity of diesel-contaminated aged soil. The bacterial consortium was prepared using strains D-46, D-99, D134-1, MSM-2-10-13, and Oil-4, isolated from oil-contaminated soil. The effects of CB and biostimulation were evaluated in various soil microcosms: CT (water), T1 (CB only), T2 (CB + NH₄NO₃ and KH₂PO_4, nutrients), T3 (CB + activated charcoal, AC), T4 (CB + nutrients + AC), T5 (AC + water), T6 (CB + nutrients + zero-valent iron nanoparticles, nZVI), T7 (CB + nutrients + AC + nZVI), T8 (CB + activated peroxidase, oxidant), T9 (AC + nZVI), and T10 (CB + nZVI + AC + oxidant). Preliminary evaluation of the bacterial consortium revealed 81.9% diesel degradation in liquid media. After 60 days of treatment, T6 demonstrated the highest total petroleum hydrocarbon (TPH) degradation (99.0%), followed by T1 (97.4%), T2 (97.9%), T4 (96.0%), T7 (96.0%), T8 (94.8%), T3 (93.6%), and T10 (86.2%). The lowest TPH degradation was found in T5 (24.2%), T9 (17.2%), and CT (11.7%). Application of CB and biostimulation to the soil microcosms decreased bacterial diversity, leading to selective enrichment of bacterial communities. T2, T6, and T10 contained Firmicutes (50.06%), Proteobacteria (64.69%), and Actinobacteria (54.36%) as the predominant phyla, respectively. The initial soil exhibited the lowest metabolic activity, which improved after treatment. The study results indicated that biostimulation alone is inadequate for remediation of contaminated soil that lacks indigenous oil degraders, suggesting the need for a holistic approach that includes both CB and biostimulation. Graphical Abstract.