{"type": "FeatureCollection", "features": [{"id": "10.1016/j.scitotenv.2019.03.176", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:16:35Z", "type": "Journal Article", "created": "2019-03-13", "title": "Effect of digestate application on microbial respiration and bacterial communities' diversity during bioremediation of weathered petroleum hydrocarbons contaminated soils", "description": "Digestate is an organic by-product of biogas production via anaerobic digestion processes and has a great potential as soil fertilizer due to concentrated nutrients. In this study, we examined digestate as a potential nutrient and microbial seeding for bioremediation of weathered (aged) petroleum hydrocarbon contaminated soils. We analysed 6 different treatments in microcosm using two industrial soils having different textures: a clay rich soil and a sandy soil. After 30\u202fdays of incubation, the highest total petroleum hydrocarbons (TPH) removal was observed in microcosms containing digestate together with bulking agent (17.8% and 12.7% higher than control in clay rich soil and sandy soil, respectively) or digestate together with immobilized bacteria (13.4% and 9% higher than control in clay rich soil and sandy soil, respectively). After digestate application microbial respiration was enhanced in sandy soil and inhibited in clay rich soil due to aggregates formation. After bulking agent addition to clay rich soil aggregates size was reduced and oxygen uptake was improved. Application of digestate to soil resulted in the development of distinct microbial groups in amended and non-amended soils. Genera containing species able to degrade TPH like Acinetobacter and Mycobacterium were abundant in digestate and in soil amended with digestate. Quantification of alkB genes, encoding alkane monoxygenase, revealed high concentration of these genes in digestate bacterial community. After application of digestate, the level of alkB genes significantly increased in soils and remained high until the end of the treatment. The study revealed great potential of digestate as a nutrient and bacteria source for soil bioremediation.", "keywords": ["[SDE] Environmental Sciences", "TPH removal", "550", "Soil remediation", "0211 other engineering and technologies", "alkB genes; Organic fertilizers; qPCR; Soil remediation; TPH removal; Biodegradation", " Environmental; Environmental Restoration and Remediation; Hydrocarbons; Petroleum; Petroleum Pollution; Soil; Soil Pollutants; Soil Microbiology", "02 engineering and technology", "01 natural sciences", "7. Clean energy", "630", "Organic fertilizers", "Environmental", "Soil", "alkB genes", "Soil Pollutants", "Petroleum Pollution", "Environmental Restoration and Remediation", "Soil Microbiology", "0105 earth and related environmental sciences", "2. Zero hunger", "[SDE.IE]Environmental Sciences/Environmental Engineering", "15. Life on land", "Hydrocarbons", "6. Clean water", "qPCR", "Biodegradation", " Environmental", "Petroleum", "[SDE]Environmental Sciences", "Biodegradation", "[SDE.IE] Environmental Sciences/Environmental Engineering"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2019.03.176"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2019.03.176", "name": "item", "description": "10.1016/j.scitotenv.2019.03.176", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2019.03.176"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-01T00:00:00Z"}}, {"id": "10.1016/j.electacta.2021.138636", "type": "Feature", "geometry": null, "properties": {"license": "Restricted", "updated": "2026-07-26T16:15:47Z", "type": "Journal Article", "created": "2021-05-22", "title": "Simultaneous removal of hydrocarbons and sulfate from groundwater using a \u201cbioelectric well\u201d", "description": "Abstract Petroleum hydrocarbons (PHs) are often found in groundwater due to human activities like accidental spills, causing health and environmental risks, and requiring remediation. Microbial Electrochemical Technologies (METs) have emerged as a promising alternative to conventional bioremediation techniques for the treatment of PH-contaminated groundwater. However, the field-application of these promising sustainable as well as cost-effective technologies is still scarce. One major reason is the lack of scalable reactor configurations. Herein, an upgraded version of the \u201cbioelectric well\u201d, a novel tubular bioelectrochemical reactor that can be installed directly within a groundwater well, was tested for the simultaneous removal of oxidableoxidizable (i.e., toluene and other PH) and reducible (i.e., sulfate) compounds from a real contaminated groundwater. After a proof-of-concept study in batch mode, the system was operated in continuous-flow mode for 48 days with the anode polarized at 0.2\u00a0V vs. SHE and a hydraulic retention time of 11\u00a0h. In these conditions, a steady-state removal rate of toluene as high as 31\u00a0\u00b1\u00a02\u00a0mg L\u22121 d\u22121 was achieved, which was more than double the value observed with the open circuit potential (OCP) control and one of the highest reported in literature. The electrode polarization went along with a higher abundance of key-functional genes involved in toluene degradation. This was not only showing its clear functional connection to the microbial metabolism, but further allowed to identify the involved electrogenic biodegradation pathway. In addition, the system simultaneously removed sulfate (30\u00a0\u00b1\u00a01\u00a0mg L\u22121 d\u22121), with bacteria likely using the H2 generated at the cathode as electron donor. Nevertheless, the apparent sulfate removal rate in the polarized and in the OCP runs was similar. The analysis of the microbial communities evidenced a high abundance of the genus Chlorobium in the effluent of the polarized run. These microorganisms were probably responsible for the continuous oxidative regeneration of sulfate from the sulfide produced at the cathode by sulfate-reducing bacteria. This phenomenon probably hindered the overall removal of sulfate by the bioelectrochemical system.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Microbial electrochemical technologies", "Groundwater remediation", "bioremediation; groundwater remediation; microbial electrochemical technologies; petroleum hydrocarbons; toluene", "Petroleum hydrocarbons", "Bioremediation", "6. Clean water", "Toluene"]}, "links": [{"href": "https://doi.org/10.1016/j.electacta.2021.138636"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Electrochimica%20Acta", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.electacta.2021.138636", "name": "item", "description": "10.1016/j.electacta.2021.138636", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.electacta.2021.138636"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-01T00:00:00Z"}}, {"id": "10.1016/j.envres.2024.118880", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:15:52Z", "type": "Journal Article", "created": "2024-04-04", "title": "Unveiling the capacity of bioaugmentation application, in comparison with biochar and rhamnolipid for TPHs degradation in aged hydrocarbons polluted soil", "description": "Persistent, aged hydrocarbons in soil hinder remediation, posing a significant environmental threat. While bioremediation offers an environmentally friendly and cost-effective approach, its efficacy for complex contaminants relies on enhancing pollutant bioavailability. This study explores the potential of immobilized bacterial consortia combined with biochar and rhamnolipids to accelerate bioremediation of aged total petroleum hydrocarbon (TPH)-contaminated soil. Previous research indicates that biochar and biosurfactants can increase bioremediation rates, while mixed consortia offer sequential degradation and higher hydrocarbon mineralization. The present investigation aimed to assess whether combining these strategies could further enhance degradation in aged, complex soil matrices. The bioaugmentation (BA) with bacterial consortium increased the TPHs degradation in aged soil (over 20% compared to natural attenuation - NA). However, co-application of BA with biochar and rhamnolipid higher did not show a statistically prominent synergistic effect. While biochar application facilitated the maintenance of hydrocarbon degrading bacterial consortium in soil, the present study did not identify a direct influence in TPHs degradation. The biochar application in contaminated soil contributed to TPHs adsorption. Rhamnolipid alone slightly increased the TPHs biodegradation with NA, while the combined bioaugmentation treatment with rhamnolipid and biochar increased the degradation between 27.5 and 29.8%. These findings encourage further exploration of combining bioaugmentation with amendment, like biochar and rhamnolipid, for remediating diverse environmental matrices contaminated with complex and aged hydrocarbons.", "keywords": ["Qu\u00edmica agr\u00edcola", "Bioqu\u00edmica", "Biolog\u00eda molecular", "Rhamnolipids", "Molecular biology", "Chemistry", " Inorganic", "Biochemistry", "Qu\u00edmica inorg\u00e1nica", "Hydrocarbons", "Inorganic", "Chemistry", "Biochar", "Soil", "Bioaugmentation", "Agricultural chemistry", "Biodegradation", " Environmental", "Petroleum", "Recalcitrant hydrocarbons", "Charcoal", "Biodegradation", "Soil Pollutants", "TPHs polluted soils", "Glycolipids", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.envres.2024.118880"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envres.2024.118880", "name": "item", "description": "10.1016/j.envres.2024.118880", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envres.2024.118880"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-01-01T00:00:00Z"}}, {"id": "10.1016/j.jece.2022.107799", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:16:19Z", "type": "Journal Article", "created": "2022-04-27", "title": "\"Syntrophy drives the microbial electrochemical oxidation of toluene in a continuous-flow \"\"bioelectric well\"\"\"", "description": "Microbial electrochemical technologies (MET) are promising for the remediation of groundwater pollutants such as petroleum hydrocarbons (PH). Indeed, MET can provide virtually inexhaustible electron donors or acceptors directly in the subsurface environment. However, the degradation mechanisms linking contaminants removal to electric current flow are still largely unknown, hindering the development of robust design criteria. Here, we analysed the degradation of toluene, a model PH, in a bioelectrochemical reactor known as 'bioelectric well'operated in continuous-flow mode at various influent toluene concentrations. With increasing concentration of toluene, the removal rate increased while the current tended to a plateau, hence the columbic efficiency decreased. Operation at open circuit confirmed that the bioelectrochemical degradation of toluene proceeded via a syntrophic pathway involving cooperation between different microbial populations. First of all, hydrocarbon degraders quickly converted toluene into metabolic intermediates probably by breaking the aromatic ring upon fumarate addition. Subsequently, fermentative bacteria converted these intermediates into volatile fatty acids (VFA) and likely also H2, which were then used as substrates by electroactive microorganisms forming the anodic biofilm. As toluene degradation is faster than subsequent conversion steps, the increase in intermediate concentration could not result in a current increase. This work provides valuable insights on the syntrophic degradation of BTEX, which are essential for the application of microbial electrochemical system to groundwater remediation of petroleum hydrocarbons.", "keywords": ["Microbial electrochemical technologies", "13. Climate action", "Groundwater remediation", "bioremediation; groundwater remediation; microbial electrochemical technologies; petroleum hydrocarbons; toluene", "Petroleum hydrocarbons", "01 natural sciences", "Bioremediation", "6. Clean water", "Toluene", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/475025/1/Syntrophy%20drives%20the%20microbial%20electrochemical%20oxidation%20of%20toluene%20in%20a%20continuous-flow%20%e2%80%9cbioelectric%20well%e2%80%9d.pdf"}, {"href": "https://iris.uniroma1.it/bitstream/11573/1661830/2/Tucci_Syntrophy-drives-microbial_2022.pdf"}, {"href": "https://doi.org/10.1016/j.jece.2022.107799"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Environmental%20Chemical%20Engineering", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jece.2022.107799", "name": "item", "description": "10.1016/j.jece.2022.107799", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jece.2022.107799"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-06-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2022.157325", "type": "Feature", "geometry": null, "properties": {"license": "Restricted", "updated": "2026-07-26T16:16:36Z", "type": "Journal Article", "created": "2022-07-14", "title": "Passive electrobioremediation approaches for enhancing hydrocarbons biodegradation in contaminated soils,", "description": "Electrobioremediation technologies hold considerable potential for the treatment of soils contaminated by petroleum hydrocarbons (PH), since they allow stimulating biodegradation processes with no need for subsurface chemicals injection and with little to no energy consumption. Here, a microbial electrochemical snorkel (MES) was applied for the treatment of a soil contaminated by hydrocarbons. The MES consists of direct coupling of a microbial anode with a cathode, being a single conductive, non-polarized material positioned suitably to create an electrochemical connection between the anoxic zone (the contaminated soil) and the oxic zone (the overlying oxygenated water). Soil was also supplemented with electrically conductive particles of biochar as a strategy to construct a conductive network with microbes in the soil matrix, thus extending the radius of influence of the snorkel. The results of a comprehensive suite of chemical, microbiological and ecotoxicological analyses evidenced that biochar addition, rather than the presence of a snorkel, was the determining factor in accelerating PH removal from contaminated soils, possibly accelerating syntrophic and/or cooperative metabolisms involved in the degradation of PH. The enhancement of biodegradation was mirrored by an increased abundance of anaerobic and aerobic microorganisms known to be involved in the degradation of PH and related functional genes. Plant ecotoxicity assays confirmed a reduction of soils toxicity in treatments receiving electrically conductive biochar.", "keywords": ["02 engineering and technology", "01 natural sciences", "Hydrocarbons", "6. Clean water", "Biochar", "Soil", "Biodegradation", " Environmental", "Petroleum", "Soil Pollutants", "Contaminated soil", "Microbial electrochemical snorkel", "biochar; bioelectrochemical system; bioremediation; contaminated soil; microbial electrochemical snorkel; petroleum hydrocarbons", "0210 nano-technology", "Petroleum hydrocarbons", "Bioremediation", "Soil Microbiology", "Bioelectrochemical system", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2022.157325"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.scitotenv.2022.157325", "name": "item", "description": "10.1016/j.scitotenv.2022.157325", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2022.157325"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-11-01T00:00:00Z"}}, {"id": "10.1021/es102597f", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:17:14Z", "type": "Journal Article", "created": "2011-04-22", "title": "Quantifying Variability In Life Cycle Greenhouse Gas Inventories Of Alternative Middle Distillate Transportation Fuels", "description": "The presence of variability in life cycle analysis (LCA) is inherent due to both inexact LCA procedures and variation of numerical inputs. Variability in LCA needs to be clearly distinguished from uncertainty. This paper uses specific examples from the production of diesel and jet fuels from 14 different feedstocks to demonstrate general trends in the types and magnitudes of variability present in life cycle greenhouse gas (LC-GHG) inventories of middle distillate fuels. Sources of variability have been categorized as pathway specific, coproduct usage and allocation, and land use change. The results of this research demonstrate that subjective choices such as coproduct usage and allocation methodology can be more important sources of variability in the LC-GHG inventory of a fuel option than the process and energy use of fuel production. Through the application of a consistent analysis methodology across all fuel options, the influence of these subjective biases is minimized, and the LC-GHG inventories for each feedstock-to-fuel option can be effectively compared and discussed. By considering the types and magnitudes of variability across multiple fuel pathways, it is evident that LCA results should be presented as a range instead of a point value. The policy implications of this are discussed.", "keywords": ["Greenhouse Effect", "Air Pollutants", "Conservation of Natural Resources", "0211 other engineering and technologies", "Transportation", "02 engineering and technology", "7. Clean energy", "12. Responsible consumption", "Petroleum", "13. Climate action", "Air Pollution", "0202 electrical engineering", " electronic engineering", " information engineering", "Gasoline", "Carbon Footprint", "Vehicle Emissions"], "contacts": [{"organization": "Stratton, Russell William, Wong, Hsin Min, Hileman, James I.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1021/es102597f"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/es102597f", "name": "item", "description": "10.1021/es102597f", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/es102597f"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-04-22T00:00:00Z"}}, {"id": "10.1021/es404130v", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-07-26T16:17:14Z", "type": "Journal Article", "created": "2013-09-18", "title": "Regional Water Implications Of Reducing Oil Imports With Liquid Transportation Fuel Alternatives In The United States", "description": "The Renewable Fuel Standard (RFS) is among the cornerstone policies created to increase U.S. energy independence by using biofuels. Although greenhouse gas emissions have played a role in shaping the RFS, water implications are less understood. We demonstrate a spatial, life cycle approach to estimate water consumption of transportation fuel scenarios, including a comparison to current water withdrawals and drought incidence by state. The water consumption and land footprint of six scenarios are compared to the RFS, including shale oil, coal-to-liquids, shale gas-to-liquids, corn ethanol, and cellulosic ethanol from switchgrass. The corn scenario is the most water and land intense option and is weighted toward drought-prone states. Fossil options and cellulosic ethanol require significantly less water and are weighted toward less drought-prone states. Coal-to-liquids is an exception, where water consumption is partially weighted toward drought-prone states. Results suggest that there may be considerable water and land impacts associated with meeting energy security goals through using only biofuels. Ultimately, water and land requirements may constrain energy security goals without careful planning, indicating that there is a need to better balance trade-offs. Our approach provides policymakers with a method to integrate federal policies with regional planning over various temporal and spatial scales.", "keywords": ["Greenhouse Effect", "Marketing", "Conservation of Natural Resources", "Ethanol", "Transportation", "02 engineering and technology", "15. Life on land", "Zea mays", "7. Clean energy", "United States", "6. Clean water", "Coal", "Petroleum", "Water Supply", "13. Climate action", "Biofuels", "11. Sustainability", "0202 electrical engineering", " electronic engineering", " information engineering", "Biomass", "Policy Making"]}, "links": [{"href": "https://doi.org/10.1021/es404130v"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/es404130v", "name": "item", "description": "10.1021/es404130v", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/es404130v"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-10-09T00:00:00Z"}}, {"id": "10.1080/15226514.2024.2427925", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:18:06Z", "type": "Journal Article", "created": "2024-11-25", "title": "Application of herbaceous plant mixtures for remediation of TPH-contaminated soil", "description": "Soil pollution with petroleum products is an urgent public health and environmental problem. Therefore, innovative solutions for cleaning soils contaminated with petroleum products are needed. One such solution is rhizodegradation, which is recognized as a sustainable and effective method of in situ soil remediation. Much of the previous research was done with monocultures, therefore the effects of different combinations of plants on the removal of petroleum products remain ambiguous. These studies evaluated three different herbaceous plant mixtures for the removal of total petroleum hydrocarbons (TPHs) from contaminated soil. Promising results were obtained. Selected herbaceous plant species and their mixtures can be successfully grown in contaminated soil at a contamination level of 6,817\u2009mg/kg TPH DW according to the selected cultivation strategy. After applying a complex of biotechnology and agronomic solutions, the morphological and morphometric indicators revealed the good adaptability and tolerance of the selected herbaceous plants to growing in contaminated soil. After two years of pot testing application of different mixtures of herbaceous plants, the TPH (C6-C40) removal potential reached 85-90%.", "keywords": ["Soil", "Biodegradation", " Environmental", "Petroleum", "Soil Pollutants", "Plants", "Hydrocarbons"], "contacts": [{"organization": "Mantas, Rube\u017eius, \u017dygimantas, Kidikas, Alfreda, Kasiulien\u0117, Vilma, Keme\u0161yt\u0117, Vaclovas, Stukonis,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1080/15226514.2024.2427925"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Phytoremediation", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1080/15226514.2024.2427925", "name": "item", "description": "10.1080/15226514.2024.2427925", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1080/15226514.2024.2427925"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-11-25T00:00:00Z"}}, {"id": "10.1111/1751-7915.13654", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:18:27Z", "type": "Journal Article", "created": "2020-08-31", "title": "An underappreciated DIET for anaerobic petroleum hydrocarbon\u2010degrading microbial communities", "description": "Direct interspecies electron transfer (DIET) via electrically conductive minerals can play a role in the anaerobic oxidation of petroleum hydrocarbons in contaminated sites and can be exploited for the development of new, more effective bioremediation approaches.", "keywords": ["0301 basic medicine", "H100", "0303 health sciences", "petroleum hydrocarbon", "anaerobic degradation", "Microbiota", "H800", "Hydrocarbons", "6. Clean water", "DIET", "03 medical and health sciences", "Biodegradation", " Environmental", "Petroleum", "Soil Pollutants", "Anaerobiosis", "Crystal Ball", "TP248.13-248.65", "Biotechnology"]}, "links": [{"href": "https://nrl.northumbria.ac.uk/id/eprint/44983/8/1751-7915.13654.pdf"}, {"href": "https://iris.cnr.it/bitstream/20.500.14243/394172/1/An%20underappreciated%20DIET%20for%20anaerobic%20petroleum.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1751-7915.13654"}, {"href": "https://eprints.ncl.ac.uk/fulltext.aspx?url=270998/E5D81B02-CB5D-4798-8D73-9D54E5057C34.pdf&pub_id=270998"}, {"href": "https://doi.org/10.1111/1751-7915.13654"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1751-7915.13654", "name": "item", "description": "10.1111/1751-7915.13654", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1751-7915.13654"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-30T00:00:00Z"}}, {"id": "10.1186/s13568-024-01764-7", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:19:12Z", "type": "Journal Article", "created": "2024-09-28", "title": "Metagenomic analyses of a consortium for the bioremediation of hydrocarbons polluted soils", "description": "Abstract

A bacterial consortium was isolated from a soil in Noblejas (Toledo, Spain) with a long history of mixed hydrocarbons pollution, by enrichment cultivation. Serial cultures of hydrocarbons polluted soil samples were grown in a minimal medium using diesel (1\uffc2\uffa0mL/L) as the sole carbon and energy source. The bacterial composition of the Noblejas Consortium (NC) was determined by sequencing 16S rRNA gene amplicon libraries. The consortium contained around 50 amplicon sequence variants (ASVs) and the major populations belonged to the genera Pseudomonas, Enterobacter, Delftia, Stenotrophomonas, Achromobacter, Acinetobacter, Novosphingobium, Allorhizobium-Neorhizobium-Rhizobium, Ochrobactrum and Luteibacter. All other genera were below 1%. Metagenomic analysis of NC has shown a high abundance of genes encoding enzymes implicated in aliphatic and (poly) aromatic hydrocarbons degradation, and almost all pathways for hydrocarbon degradation are represented. Metagenomic analysis has also allowed the construction of metagenome assembled genomes (MAGs) for the major players of NC. Metatranscriptomic analysis has shown that several of the ASVs are implicated in hydrocarbon degradation, being Pseudomonas, Acinetobacter and Delftia the most active populations.Introduction: Bioremediation has been shown to be an effective strategy for removing toxic pollutants from the environment, particularly organic chemicals such as petroleum hydrocarbons. This paper investigates the changes in toxicity of petroleum-contaminated soil as a result of microbial remediation processes.

Methods: Changes in the ecotoxicity of the contaminated soil were examined using a plant, earthworm, enzyme activity and luminescent bacteria toxicity tests.

Results: The results showed that bioremediation could effectively degrade petroleum hydrocarbon (C10\uffe2\uff80\uff93C40) pollutants. After 42\uffc2\uffa0days of remediation, the petroleum hydrocarbon (C10\uffe2\uff80\uff93C40) content of Group A (bioaugmented polluted wetland soil) decreased from 1.66\uffc2\uffa0g/kg to 1.00\uffc2\uffa0g/kg, and the degradation rate was 40.6%. The petroleum hydrocarbon (C10\uffe2\uff80\uff93C40) content of Group B (bioaugmented polluted farmland soil decreased from 4.00\uffc2\uffa0g/kg to 1.94\uffc2\uffa0g/kg, and the degradation rate was 51.6%. During the microbial remediation progress, the ecological toxicity of petroleum-contaminated soil first increased and then decreased. The photosynthetic pigment content index in the higher plant toxicity test, the earthworm survival index and the soil catalase activity all showed good agreement with the relative luminescence index of extracted DCM/DMSO in the luminescent bacterial toxicity test. The soil toxicity decreased significantly after remediation. Specifically, the photosynthetic pigment content of wheat were inhibited in the soil during the whole process (remediation for 42\uffc2\uffa0days), and decreased to the minimum on remediation day 21. The 7-day and 14-day survival rate of earthworms in Group A and Group B gradually decreased in the soil remediation process, and then gradually increased, survival rate at the end of remediation was higher than at the beginning. Soil catalase activity was significantly negatively correlated with petroleum hydrocarbon (C10\uffe2\uff80\uff93C40) content (\uffe2\uff88\uff920.988, \uffe2\uff88\uff920.989). The ecological toxicity of contaminated soil reached to the maximum on the 21st day of remediation, relative luminosity of luminescent bacteria in dichloromethane/dimethyl sulfoxide extracts from Group A and Group B were 26.3% and 16.3%, respectively.

Conclusion: Bioremediation could effectively degrade petroleum hydrocarbon (C10\uffe2\uff80\uff93C40) pollutants. Wheat photosynthetic pigment content, earthworm survival rate, soil catalase activity and relative luminescence of luminescent bacteria can better indicate the ecological toxicity of petroleum-contaminated soil in bioremediation process.

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

", "keywords": ["0301 basic medicine", "TPH", "consortium", "Article", "diesel", "03 medical and health sciences", "PAHs", "rhizoremediation", "Pseudomonas", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Pollutants", "Polycyclic Aromatic Hydrocarbons", "bacteria", "Phylogeny", "Soil Microbiology", "Chryseobacterium", "2. Zero hunger", "metagenomics", "rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH", "0303 health sciences", "Microbiota", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "Rhizoremediation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://doi.org/10.3390/genes10060456"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes10060456", "name": "item", "description": "10.3390/genes10060456", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10060456"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-14T00:00:00Z"}}, {"id": "10.3390/metabo15020097", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:20:50Z", "type": "Journal Article", "created": "2025-02-05", "title": "Metabolomic-Based Assessment of Earthworm (Eisenia fetida) Exposure to Different Petroleum Fractions in Soils", "description": "

Background/Objectives: Petroleum contamination in soil exerts toxic effects on earthworms (Eisenia fetida) through non-polar narcotic mechanisms. However, the specific toxicities of individual petroleum components remain insufficiently understood. Methods: This study investigates the effects of four petroleum components\u2014saturated hydrocarbons, aromatic hydrocarbons, resins, and asphaltenes\u2014on earthworms in artificially contaminated soil, utilizing a combination of biochemical biomarker analysis and metabolomics to uncover the underlying molecular mechanisms. Results: The results revealed that aromatic hydrocarbons are the most toxic fraction, with EC50 concentrations significantly lower than those of other petroleum fractions. All tested fractions triggered notable metabolic disturbances and immune responses in earthworms after 7 days of exposure, as evidenced by significant changes in metabolite abundance within critical pathways such as arginine synthesis, a-linolenic acid metabolism, and the pentose phosphate pathway. According to the KEGG pathway analysis, saturated hydrocarbon fractions induced marked changes in glycerophospholipid metabolism, and arginine and proline metabolism pathways, contributing to the stabilization of the protein structure and membrane integrity. Aromatic hydrocarbon fractions disrupted the arachidonic acid metabolic pathway, leading to increased myotube production and enhanced immune defense mechanisms. The TCA cycle and riboflavin metabolic pathway were significantly altered during exposure to the colloidal fraction, affecting energy production and cellular respiration. The asphaltene fraction significantly impacted glycolysis, accelerating energy cycling to meet stress-induced increases in energy demands. Conclusions: Aromatic hydrocarbons accounted for the highest level of toxicity among the four components in petroleum-contaminated soils. However, the contributions of other fractions to overall toxicity should not be ignored, as each fraction uniquely affects key metabolic pathways and biological functions. These findings emphasize the importance of monitoring metabolic perturbations caused by petroleum components in non-target organisms such as earthworms. They also reveal the specificity of the toxic metabolic effects of different petroleum components on earthworms.

", "keywords": ["hydrocarbon series of petroleum", "ecotoxicity", "assessment", "earthworms", "metabolism", "Microbiology", "QR1-502", "Article", "soil"], "contacts": [{"organization": "Meiyu Liu, Mutian Wang, Xiaowen Fu, Fanyong Song, Fangyuan Zhou, Tianyuan Li, Jianing Wang,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3390/metabo15020097"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Metabolites", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/metabo15020097", "name": "item", "description": "10.3390/metabo15020097", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/metabo15020097"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-02-05T00:00:00Z"}}, {"id": "10.3390/microorganisms13040848", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:20:51Z", "type": "Journal Article", "created": "2025-04-10", "title": "Assessing Microbial Activity and Rhizoremediation in Hydrocarbon and Heavy Metal-Impacted Soil", "description": "

Rhizodegradation enhances pollutant degradation through plant\u2013microbe interactions in the rhizosphere. Plant roots provide a colonisation surface and root exudates that promote microbial abundance and activity, facilitating organic pollutant breakdown via direct microbial degradation and co-metabolism. This study assessed the rhizodegradation of weathered petroleum hydrocarbons (PHCs) in heavy metal co-contaminated soil in a microcosm-scale pot trial. Treatments included Sinapis alba, Lolium perenne, a L. perenne + Trifolium repens mix, and Cichorium intybus, alongside a non-planted control. After 14 weeks, PHC concentrations were analysed via gas chromatography, and rhizosphere microbial communities were characterised through sequencing. Sinapis alba achieved the highest PHC degradation (68%), significantly exceeding the non-planted control (p < 0.05, Kruskal\u2013Wallis test). Hydrocarbon-degrading bacteria, including KCM-B-112, C1-B045, Hydrogenophaga, unclassified Saccharimonadales sp., and Pedobacter, were enriched in the rhizosphere, with the uncultured clade mle1-27 potentially contributing indirectly. Metals analysis of plant tissues showed that mustard could accumulate copper more than lead and zinc, despite higher concentrations of zinc and lead in the soil. These results highlight the potential of S. alba for rhizoremediation in PHC\u2013heavy metal co-contaminated soils.

", "keywords": ["petroleum hydrocarbons", "bioremediation", "QH301-705.5", "microbial communities", "phytoremediation", "Biology (General)", "heavy metals", "rhizodegradation", "Article"], "contacts": [{"organization": "Robert Conlon, David N. Dowling, Kieran J. Germaine,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3390/microorganisms13040848"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms13040848", "name": "item", "description": "10.3390/microorganisms13040848", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms13040848"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-04-08T00:00:00Z"}}, {"id": "2950940967", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:25:54Z", "type": "Journal Article", "created": "2019-06-14", "title": "Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil", "description": "

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

", "keywords": ["0301 basic medicine", "TPH", "consortium", "Article", "diesel", "03 medical and health sciences", "PAHs", "rhizoremediation", "Pseudomonas", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Pollutants", "Polycyclic Aromatic Hydrocarbons", "bacteria", "Phylogeny", "Soil Microbiology", "Chryseobacterium", "2. Zero hunger", "metagenomics", "rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH", "0303 health sciences", "Microbiota", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "Rhizoremediation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://doi.org/2950940967"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2950940967", "name": "item", "description": "2950940967", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2950940967"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-14T00:00:00Z"}}, {"id": "10259/7423", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-26T16:24:34Z", "type": "Journal Article", "created": "2022-05-28", "title": "Evaluation of Biostimulation, Bioaugmentation, and Organic Amendments Application on the Bioremediation of Recalcitrant Hydrocarbons of Soil", "description": "In the present work, the operational conditions for improving the degradation rates of Total Petroleum Hydrocarbons (TPHs) in contaminated soil from a machinery park were optimized at a microcosms scale along a 90- days incubation period. In this study, bioremediation strategies and an organic amendment have been tested to verify the remediation of soil contaminated with different hydrocarbons, mineral oils, and heavy metals. Specifically, designed biostimulation and bioaugmentation strategies were compared with and without adding vermicompost. The polluted soil harboring multiple contaminants, partially attenuated for years, was used. The initial profile showed enrichment in heavy linear alkanes, suggesting a previous moderate weathering. The application of vermicompost increased five and two times the amounts of available phosphorus (P) and exchangeable potassium (K), respectively, as a direct consequence of the organic amendment addition. The microbial activity increased due to soil acidification, which influenced the solubility of P and other micronutrients. It also impacted the predominance and variability of the different microbial groups and the incubation, as reflected by phospholipid fatty acid (PLFA) results. An increase in the alkaline phosphatases and proteases linked to bacterial growth was displayed. This stimulation of microbial metabolism correlated with the degradation rates since TPHs degradation\u2019 efficiency after vermicompost addition reached 32.5% and 34.4% of the initial hydrocarbon levels for biostimulation and bioaugmentation, respectively. Although Polycyclic Aromatic", "keywords": ["Soil enzymes", "01 natural sciences", "Total petroleum hydrocarbons polluted soils", "Soil", "Bioaugmentation", "Alkanes", "Soil Pollutants", "Micronutrients", "Polycyclic Aromatic Hydrocarbons", "Materials", "Phospholipids", "Soil Microbiology", "0105 earth and related environmental sciences", "2. Zero hunger", "Minerals", "Materiales", "Fatty Acids", "Phosphorus", "Phenanthrenes", "Hydrocarbons", "Phosphoric Monoester Hydrolases", "6. Clean water", "Biostimulation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Phospholipid fatty acids", "Potassium", "Oils", "Biostimulation Bioaugmentation Phospholipid fatty acids Total petroleum hydrocarbons polluted soils Soil enzymes", "Peptide Hydrolases"]}, "links": [{"href": "https://doi.org/10259/7423"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/SSRN%20Electronic%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10259/7423", "name": "item", "description": "10259/7423", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10259/7423"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10486/713957", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:24:47Z", "type": "Journal Article", "created": "2019-06-14", "title": "Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil", "description": "

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

", "keywords": ["0301 basic medicine", "TPH", "consortium", "Article", "diesel", "03 medical and health sciences", "PAHs", "rhizoremediation", "Pseudomonas", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Pollutants", "Polycyclic Aromatic Hydrocarbons", "bacteria", "Phylogeny", "Soil Microbiology", "Chryseobacterium", "2. Zero hunger", "metagenomics", "rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH", "0303 health sciences", "Microbiota", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "Rhizoremediation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://doi.org/10486/713957"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10486/713957", "name": "item", "description": "10486/713957", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10486/713957"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-14T00:00:00Z"}}, {"id": "10486/717838", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:24:47Z", "type": "Journal Article", "created": "2024-09-28", "title": "Metagenomic analyses of a consortium for the bioremediation of hydrocarbons polluted soils", "description": "Abstract

A bacterial consortium was isolated from a soil in Noblejas (Toledo, Spain) with a long history of mixed hydrocarbons pollution, by enrichment cultivation. Serial cultures of hydrocarbons polluted soil samples were grown in a minimal medium using diesel (1\uffc2\uffa0mL/L) as the sole carbon and energy source. The bacterial composition of the Noblejas Consortium (NC) was determined by sequencing 16S rRNA gene amplicon libraries. The consortium contained around 50 amplicon sequence variants (ASVs) and the major populations belonged to the genera Pseudomonas, Enterobacter, Delftia, Stenotrophomonas, Achromobacter, Acinetobacter, Novosphingobium, Allorhizobium-Neorhizobium-Rhizobium, Ochrobactrum and Luteibacter. All other genera were below 1%. Metagenomic analysis of NC has shown a high abundance of genes encoding enzymes implicated in aliphatic and (poly) aromatic hydrocarbons degradation, and almost all pathways for hydrocarbon degradation are represented. Metagenomic analysis has also allowed the construction of metagenome assembled genomes (MAGs) for the major players of NC. Metatranscriptomic analysis has shown that several of the ASVs are implicated in hydrocarbon degradation, being Pseudomonas, Acinetobacter and Delftia the most active populations.

Background/Objectives: Petroleum contamination in soil exerts toxic effects on earthworms (Eisenia fetida) through non-polar narcotic mechanisms. However, the specific toxicities of individual petroleum components remain insufficiently understood. Methods: This study investigates the effects of four petroleum components\u2014saturated hydrocarbons, aromatic hydrocarbons, resins, and asphaltenes\u2014on earthworms in artificially contaminated soil, utilizing a combination of biochemical biomarker analysis and metabolomics to uncover the underlying molecular mechanisms. Results: The results revealed that aromatic hydrocarbons are the most toxic fraction, with EC50 concentrations significantly lower than those of other petroleum fractions. All tested fractions triggered notable metabolic disturbances and immune responses in earthworms after 7 days of exposure, as evidenced by significant changes in metabolite abundance within critical pathways such as arginine synthesis, a-linolenic acid metabolism, and the pentose phosphate pathway. According to the KEGG pathway analysis, saturated hydrocarbon fractions induced marked changes in glycerophospholipid metabolism, and arginine and proline metabolism pathways, contributing to the stabilization of the protein structure and membrane integrity. Aromatic hydrocarbon fractions disrupted the arachidonic acid metabolic pathway, leading to increased myotube production and enhanced immune defense mechanisms. The TCA cycle and riboflavin metabolic pathway were significantly altered during exposure to the colloidal fraction, affecting energy production and cellular respiration. The asphaltene fraction significantly impacted glycolysis, accelerating energy cycling to meet stress-induced increases in energy demands. Conclusions: Aromatic hydrocarbons accounted for the highest level of toxicity among the four components in petroleum-contaminated soils. However, the contributions of other fractions to overall toxicity should not be ignored, as each fraction uniquely affects key metabolic pathways and biological functions. These findings emphasize the importance of monitoring metabolic perturbations caused by petroleum components in non-target organisms such as earthworms. They also reveal the specificity of the toxic metabolic effects of different petroleum components on earthworms.

", "keywords": ["hydrocarbon series of petroleum", "ecotoxicity", "assessment", "earthworms", "metabolism", "Microbiology", "QR1-502", "Article", "soil"], "contacts": [{"organization": "Meiyu Liu, Mutian Wang, Xiaowen Fu, Fanyong Song, Fangyuan Zhou, Tianyuan Li, Jianing Wang,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/PMC11857538"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Metabolites", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC11857538", "name": "item", "description": "PMC11857538", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11857538"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-02-05T00:00:00Z"}}, {"id": "PMC12029208", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:28:19Z", "type": "Journal Article", "created": "2025-04-10", "title": "Assessing Microbial Activity and Rhizoremediation in Hydrocarbon and Heavy Metal-Impacted Soil", "description": "

Rhizodegradation enhances pollutant degradation through plant\u2013microbe interactions in the rhizosphere. Plant roots provide a colonisation surface and root exudates that promote microbial abundance and activity, facilitating organic pollutant breakdown via direct microbial degradation and co-metabolism. This study assessed the rhizodegradation of weathered petroleum hydrocarbons (PHCs) in heavy metal co-contaminated soil in a microcosm-scale pot trial. Treatments included Sinapis alba, Lolium perenne, a L. perenne + Trifolium repens mix, and Cichorium intybus, alongside a non-planted control. After 14 weeks, PHC concentrations were analysed via gas chromatography, and rhizosphere microbial communities were characterised through sequencing. Sinapis alba achieved the highest PHC degradation (68%), significantly exceeding the non-planted control (p < 0.05, Kruskal\u2013Wallis test). Hydrocarbon-degrading bacteria, including KCM-B-112, C1-B045, Hydrogenophaga, unclassified Saccharimonadales sp., and Pedobacter, were enriched in the rhizosphere, with the uncultured clade mle1-27 potentially contributing indirectly. Metals analysis of plant tissues showed that mustard could accumulate copper more than lead and zinc, despite higher concentrations of zinc and lead in the soil. These results highlight the potential of S. alba for rhizoremediation in PHC\u2013heavy metal co-contaminated soils.

", "keywords": ["petroleum hydrocarbons", "bioremediation", "QH301-705.5", "microbial communities", "phytoremediation", "Biology (General)", "heavy metals", "rhizodegradation", "Article"]}, "links": [{"href": "https://doi.org/PMC12029208"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC12029208", "name": "item", "description": "PMC12029208", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC12029208"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-04-08T00:00:00Z"}}, {"id": "ea11ab672a24dcb0c7e3fec4aaaa3527", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-26T16:30:17Z", "type": "Journal Article", "title": "Application of a microbial consortium immobilized onto a biochar for the remediation of a polluted soil with hydrocarbons", "description": "Open AccessThe contamination of soils by hydrocarbons is a serious environmental problem both due to the persistence of this pollution and by its effects on even the most pristine areas of the planet. Hydrocarbon decontamination techniques entail a high cost, imply in many cases their off-site treatment, and entail environmental risks. In contrast, the use of microbiological techniques through the addition of microbial consortia with the capacity to degrade these contaminants, are alternatives for soil biorecovery that are gathering growing interest in the construction of biopiles or ecopiles. However, for an effective application of these biotechnological techniques, it is necessary to guarantee an effectiveness in the action of these microbial consortia, whose persistence in soil is generally low. In this work, the stabilization of a microbial consortium specialized in the degradation of hydrocarbons and isolated from the own soil, has been studied through its immobilization on two classes biochars obtained form apricot stones at pyrolysis temperatures of 450\u00b0 and 650\u00b0C, respectively, as well as the increase of its efficiency rate through the addition of rhamnolipids. The introduced microbial consortium achieved a degradation of 17% of the highest molecular weight hydrocarbons, an efficiency that was increased with the application of biochar and rhamnolipids up to 25% of their initial content.", "keywords": ["total petroleum hydrocarbons", "bioremediation", "biochar", "polluted soils", "rhamnolipids"], "contacts": [{"organization": "Curiel Alegre, Sandra, Velasco-Arroyo, Blanca, Mart\u00ednez, Andrea, Rumbo, Carlos, Tamayo-Ramos, Juan Antonio, Khan, Aqib A.H., Rad, Carlos, Barros, Roc\u00edo,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/ea11ab672a24dcb0c7e3fec4aaaa3527"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Revista%20de%20Ci%C3%AAncias%20Agr%C3%A1rias", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "ea11ab672a24dcb0c7e3fec4aaaa3527", "name": "item", "description": "ea11ab672a24dcb0c7e3fec4aaaa3527", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/ea11ab672a24dcb0c7e3fec4aaaa3527"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-12-01T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Petroleum&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Petroleum&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Petroleum&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=Petroleum&offset=29", "hreflang": "en-US"}], "numberMatched": 29, "numberReturned": 29, "distributedFeatures": [], "timeStamp": "2026-07-26T17:12:15.753953Z"}