Evaluation of rhizoremediation and methane emission in diesel-contaminated soil cultivated with tall fescue (Festuca arundinacea)

Exploring the bioremediation capability of petroleum-contaminated soils for enhanced environmental sustainability and minimization of ecotoxicological concerns

The bioremediation of soils contaminated with petroleum hydrocarbons (PHCs) has emerged as a promising approach, with its effectiveness contingent upon various types of PHCs, i.e., crude oil, diesel, gasoline, and other petroleum products. Strategies like genetically modified microorganisms, nanotechnology, and bioaugmentation hold potential for enhancing remediation of polycyclic aromatic hydrocarbon (PAH) contamination. The effectiveness of bioremediation relies on factors such as metabolite toxicity, microbial competition, and environmental conditions. Aerobic degradation involves enzymatic oxidative reactions, while bacterial anaerobic degradation employs reductive reactions with alternative electron acceptors. Algae employ monooxygenase and dioxygenase enzymes, breaking down PAHs through biodegradation and bioaccumulation, yielding hydroxylated and dihydroxylated intermediates. Fungi contribute via mycoremediation, using co-metabolism and monooxygenase enzymes to produce CO2 and oxidized products. Ligninolytic fungi transform PAHs into water-soluble compounds, while non-ligninolytic fungi oxidize PAHs into arene oxides and phenols. Certain fungi produce biosurfactants enhancing degradation of less soluble, high molecular-weight PAHs. Successful bioremediation offers sustainable solutions to mitigate petroleum spills and environmental impacts. Monitoring and assessing strategy effectiveness are vital for optimizing biodegradation in petroleum-contaminated soils. This review presents insights and challenges in bioremediation, focusing on arable land safety and ecotoxicological concerns.

Identifying local associations in biological time series: algorithms, statistical significance, and applications

Local associations refer to spatial-temporal correlations that emerge from the biological realm, such as time-dependent gene co-expression or seasonal interactions between microbes. One can reveal the intricate dynamics and inherent interactions of biological systems by examining the biological time series data for these associations. To accomplish this goal, local similarity analysis algorithms and statistical methods that facilitate the local alignment of time series and assess the significance of the resulting alignments have been developed. Although these algorithms were initially devised for gene expression analysis from microarrays, they have been adapted and accelerated for multi-omics next generation sequencing datasets, achieving high scientific impact. In this review, we present an overview of the historical developments and recent advances for local similarity analysis algorithms, their statistical properties, and real applications in analyzing biological time series data. The benchmark data and analysis scripts used in this review are freely available at http://github.com/labxscut/lsareview.

The combined rhizoremediation by a triad: plant-microorganism-functional materials

The article describes new strategies for the remediation of soils contaminated with organic and inorganic pollutants. The aim of this study is to investigate the synergistic effects of combining plant-microorganism-functional materials for a more effective reduction of soil contamination with toxic chemicals. The innovative triad involves functional materials as a habitat for microorganisms, which helps to control the release of pollutants into the soil solution from the adsorbed form. This, in turn, reduces the toxic effect on microorganisms and plants. Microorganisms play a complex role, consisting of partial biodegradation of pollutants, stimulation of plant growth, and support for nutrient supply. Plants synthesize root exudates that facilitate microorganisms in biodegrading organic pollutants and stimulate their growth. The plant takes up pollutants through the root system, which can be further supported by endophytic microorganisms. The cooperation of the three players produces a synergistic effect that enhances the effectiveness of rhizodegradation supported by functional materials, which is more effective than using microorganisms, phytoremediation, or functional materials alone. The combination of physicochemical methods (functional materials) and microbiological methods (bacteria and fungi, rhizosphere, symbiotic and non-symbiotic) supported by plants (hyperaccumulators) is a promising approach for reducing chemicals from soil. Key examples of the synergistic effects of combining plant-microorganism-functional materials have been provided in this article.

Long-term comparison of the performance of biostimulation and phytoextraction in soil contaminated with diesel and heavy metals

The long-term remediation performance under the natural conditions is required to establish the appropriate remediation strategy for contaminated soil. The objective of this study was to compare the long-term remediation efficiency of biostimulation and phytoextraction in contaminated soil containing petroleum hydrocarbons (PHs) and heavy metals. Two types of contaminated soil (soil contaminated with diesel only and co-contaminated with diesel and heavy metals) were prepared. For the biostimulation treatments, the soil was amended with compost, whereas maize, a representative phytoremediation plant, was cultivated for the phytoextraction treatments. There was no significant difference in remediation performance of biostimulation and phytoextraction in the diesel-contaminated soil, in which the maximum total petroleum hydrocarbon (TPH) removability was 94-96% (p < 0.05). However, phytoextraction exhibited the higher removability for TPH and heavy metals than biostimulation in the co-contaminated soil. There was no considerable change in the TPH removal in biostimulation (16-25%), while phytoextraction showed a 75% of TPH removal rate in the co-contaminated soil. Additionally, no significant changes were observed in heavy metals concentration of biostimulation, whereas the removability of heavy metals was 33-63% in phytoextraction. Meanwhile, maize, which is a suitable plant for phytoextraction, showed a translocation factor (translocating efficiency from roots to shoots) value of >1. Correlation analysis revealed that soil properties (pH, water content, and organic content) negatively correlated with pollutants removal. Additionally, the soil bacterial communities were changed over the investigated period, and the types of pollutants exerted a significant influence on the bacterial community dynamics. This study performed a pilot-scale comparison of two types of biological remediation technologies under natural environmental conditions and provided information on changes in the bacterial community structures. This study can be useful for establishing appropriate biological remediation methods to restore soil contaminated with PHs and heavy metals.

Effect of Novosphingobium sp. CuT1 inoculation on the rhizoremediation of heavy metal- and diesel-contaminated soil planted with tall fescue

Rhizoremediation is a promising method based on the synergism between plant and rhizobacteria to remediate soil co-contaminated with heavy metals and total petroleum hydrocarbons (TPHs). A plant growth-promoting (PGP) rhizobacterium with diesel-degrading capacity and heavy metal tolerance was isolated from the rhizosphere of tall fescue (Festuca arundinacea L.), after which the effects of its inoculation on rhizoremediation performance were evaluated in heavy metal- and diesel-contaminated soil planted with tall fescue. The bacterial isolate (Novosphingobium sp. CuT1) was characterized by its indole-3-acetic acid (IAA) production, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, and siderophore productivity as PGP traits. CuT1 was able to grow on 1/10 LB-agar plates containing 5 mM of Cu or 5 mM of Pb. To evaluate the remediation effect of heavy metal- and diesel-contaminated soil by CuT1 inoculation, the experimental conditions were prepared as follows. The soil was artificially contaminated with heavy metals (Cu and Pb) at a final concentration of 500 ppm. The soil was then further contaminated with diesel at final concentrations of 0, 10,000, and 30,000 ppm. Finally, all plots were planted with tall fescue, a representative hyperaccumulating plant. Compared to the rhizoremediation performance of the co-contaminated soil (Cu + Pb + diesel) without inoculation, the bioavailable Cu concentrations in the soil and the tall fescue biomass were significantly increased in CuT1 inoculation. Additionally, the root growth of tall fescue was also promoted in CuT1 inoculation. Correlation analysis showed that Cu bioavailability and bioconcentration factor were positively correlated with CuT1 inoculation. The diesel removal efficiency showed a positive correlation with CuT1 inoculation, although the diesel removal was below 30%. CuT1 inoculation was positively correlated with IAA and dehydrogenase activity in the soil. Moreover, the dry biomass of the tall fescue's roots was highly associated with CuT1 inoculation. Collectively, our findings suggest that Novosphingobium sp. CuT1 can be utilized as an applicable bioresource to enhance rhizoremediation performance in heavy metal- and TPH-contaminated soils.

Short-term microbial effects on n-alkane during the early phase degradation and consequential modification of biomarkers in a lowland subtropical rainforest in southern Taiwan: A litterbag experiment

Accurate reconstructions of past environments are critical and urgent because they can help understand how modern environments might respond to current climatic and land-use changes. However, the effect of microbial degradation and consequential modification in plant-derived-biomarkers during the early degradation phase is not yet apparent, that might bias the paleoenvironmental investigation. In this regard, a litterbag experiment was conducted to reveal the microbial effects on n-alkane-associated biomarker changes associated with three habitats (ravine, windward, and leeward) in a lowland subtropical rainforest in southern Taiwan. Freshly collected leaves of plant species Iles rotunda, Ficus benjamina, and Castanopsis carlesii were distributed in the habitat leaf litterbag experiment for 15 and 75 days incubation, respectively. The results revealed that the average leaf decomposition rate was 19.4% ± 6.4% during the first 15 days and 39% ± 11% within 75 days incubation for all leaves. The overall leaf mass degradation of I. rotunda, F. benjamina and C. carlesii in the ravine after 75 days was 58%, 51% and 41%, respectively, which were higher than those in the windward (28%, 36% and 38%) and leeward habitats (35%, 26% and 42%, respectively) indicating higher decomposition rate in the ravine habitat than the others. The predominant n-alkanes in I. rotunda were C₃₁ and C₂₉, whereas in F. benjamina these were C₃₁, C₂₉, and C₃₃, and in C. carlesii it was C₃₁. After 75 days, the ravine habitat showed a 60% decrease in the total n-alkane concentration compared to windward and leeward habitats, suggesting the microbial community associated with the ravine habitat has a higher efficiency of degrading n-alkanes. However, the biomarkers such as carbon preference index (CPI), average carbon length (ACL) and the C₃₁/C₂₉ ratio did not show statistical difference in all habitats from 15 to 75 days incubation. The next-generation sequencing revealed that microbial communities changed significantly from 15 to 75 days in all habitats. The alkB gene-containing bacteria and their family lineages increased substantially during the first 15 days incubation in all habitats. Furthermore, several bacterial genera were exclusively present in the ravine habitat, whereas some were only in the leeward and windward habitats. Despite the heterogeneity of microbial proliferation, difference in biomass and n-alkane degradation among the three habitats, most of the n-alkane-associated biomarkers remained the same. Therefore, we concluded that the microbial effects on n-alkane degradation during the early phase in plant leaves had little influence on the results of most n-alkane biomarkers.

Inoculation effect of Pseudomonas sp. TF716 on N2O emissions during rhizoremediation of diesel-contaminated soil

The demand for rhizoremediation technology that can minimize greenhouse gas emissions while effectively removing pollutants in order to mitigate climate change has increased. The inoculation effect of N₂O-reducing Pseudomonas sp. TF716 on N₂O emissions and on remediation performance during the rhizoremediation of diesel-contaminated soil planted with tall fescue (Festuca arundinacea) or maize (Zea mays) was investigated. Pseudomonas sp. TF716 was isolated from the rhizosphere soil of tall fescue. The maximum N₂O reduction rate of TF716 was 18.9 mmol N₂O g dry cells⁻¹ h⁻¹, which is superior to the rates for previously reported Pseudomonas spp. When Pseudomonas sp. TF716 was added to diesel-contaminated soil planted with tall fescue, the soil N₂O-reduction potential was 2.88 times higher than that of soil with no inoculation during the initial period (0–19 d), and 1.08–1.13 times higher thereafter. However, there was no enhancement in the N₂O-reduction potential for the soil planted with maize following inoculation with strain TF716. In addition, TF716 inoculation did not significantly affect diesel degradation during rhizoremediation, suggesting that the activity of those microorganisms involved in diesel degradation was unaffected by TF716 treatment. Analysis of the dynamics of the bacterial genera associated with N₂O reduction showed that Pseudomonas had the highest relative abundance during the rhizoremediation of diesel-contaminated soil planted with tall fescue and treated with strain TF716. Overall, these results suggest that N₂O emissions during the rhizoremediation of diesel-contaminated soil using tall fescue can be reduced with the addition of Pseudomonas sp. TF716.

Study on the Enhanced Remediation of Petroleum-Contaminated Soil by Biochar/g-C3N4 Composites

This work developed an environmentally-friendly soil remediation method based on BC and g-C3N4, and demonstrated the technical feasibility of remediating petroleum-contaminated soil with biochar/graphite carbon nitride (BC/g-C3N4). The synthesis of BC/g-C3N4 composites was used for the removal of TPH in soil via adsorption and photocatalysis. BC, g-C3N4, and BC/g-C3N4 have been characterized by scanning electron microscopy (SEM), Brunauer–Emmett–Teller surface area analyzer (BET), FT-IR, and X-ray diffraction (XRD). BC/g-C3N4 facilitates the degradation due to reducing recombination and better electron-hole pair separation. BC, g-C3N4, and BC/g-C3N4 were tested for their adsorption and photocatalytic degradation capacities. Excellent and promising results are brought out by an apparent synergism between adsorption and photocatalysis. The optimum doping ratio of 1:3 between BC and g-C3N4 was determined by single-factor experiments. The removal rate of total petroleum hydrocarbons (TPH) by BC/g-C3N4 reached 54.5% by adding BC/g-C3N4 at a dosing rate of 0.08 g/g in a neutral soil with 10% moisture content, which was 2.12 and 1.95 times of BC and g-C3N4, respectively. The removal process of TPH by BC/g-C3N4 conformed to the pseudo-second-order kinetic model. In addition, the removal rates of different petroleum components in soil were analyzed in terms of gas chromatography–mass spectrometry (GC-MS), and the removal rates of nC13-nC35 were above 90% with the contaminated soil treated by BC/g-C3N4. The radical scavenger experiments indicated that superoxide radical played the major role in the photocatalytic degradation of TPH. This work definitely demonstrates that the BC/g-C3N4 composites have great potential for application in the remediation of organic pollutant contaminated soil.

Variation of bacterial community and alkane monooxygenase gene abundance in diesel n-alkane contaminated subsurface environment under seasonal water table fluctuation

n-Alkanes, the main component of diesel fuel, are common light non-aqueous phase liquids (LNAPLs) that threaten ecological security. The subsurface from vadose zone, through fluctuating zone, to saturated zone, is a critical multi-interface earth layer which significantly affects the biodegradation processes of n-alkanes. A pilot-scale diesel contaminated aquifer column experiment has been undertaken to investigate the variations of bacterial community and alkane monooxygenase (alkB) gene abundance in these zones due to water-table fluctuations. The n-alkanes formed a layer immediately above the water table, and when this was raised, they were carried upwards through the fluctuating zone into the vadose zone. Water content and n-alkanes component C10-C12 are main factors influencing bacterial community variation in the vadose zone, while C10-C12 is a key driving factor shaping bacterial community in the fluctuating zone. The most abundant bacterial phyla at all three zones were Proteobacteria, Firmicutes and Actinobacteria, but moisture-niche selection determined their relative abundance. The intermittent wetting cycle resulted in higher abundance of Proteobacteria, and lower abundance of Actinobacteria in the vadose and fluctuating zones in comparison to the control column with a static water-table. The abundances of the alkB gene variants were relatively uniform in different zones, probably because the bacterial populations harboring alkB gene are habituated to biogenic n-alkanes rather than responding to diesel fuel contamination. The variation in the bacterial populations with height due to moisture-niche selection had very little effect on the alkB gene abundance, possibly because numerous species in both phyla (Proteobacteria and Actinobacteria) carry an alkB gene variant. Nevertheless, the drop in the water table caused a short-term spike in alkB gene abundance in the saturated zone, which is most likely associated with transport of solutes or colloids from the fluctuating zone to bacteria species in the saturated zone, so a fluctuating water table could potentially increase n-alkane biodegradation function.

Seasonal Dynamics of Bacterial Community Structure in Diesel Oil-Contaminated Soil Cultivated with Tall Fescue (Festuca arundinacea)

The objective of this study was to explore the seasonal characteristics of rhizoremediation and the bacterial community structure over the course of a year in soil contaminated with diesel oil. The soil was contaminated with diesel oil at a total petroleum hydrocarbon (TPH) concentration of 30,000 mg-TPH·kg-soil⁻¹. Tall fescue seedlings were planted in the contaminated soil and rhizoremediation performance was monitored for 317 days. The TPH concentration gradually declined, reaching 75.6% after day 61. However, the TPH removability decreased by up to 30% after re-contamination in the fall and winter. The bacterial community structure exhibited distinct seasonal dynamics. Genus Pseudomonas significantly increased up to 55.7% in the winter, while the genera Immundisolibacter and Lysobacter, well-known petroleum hydrocarbon (PH)-degrading bacteria, were found to be positively linked to the TPH removal rate. Consequently, knowledge of this seasonal variation in rhizoremediation performance and the bacterial community structure is useful for the improvement of rhizoremediation in PH-contaminated environments.

Dynamics of bacterial functional genes and community structures during rhizoremediation of diesel-contaminated compost-amended soil

The objective of this study was to characterize the effects of organic soil amendment (compost) on bacterial populations associated with petroleum hydrocarbon (PH) degradation and nitrous oxide (N₂O) dynamics via pot experiments. Soil was artificially contaminated with diesel oil at total petroleum hydrocarbon (TPH) concentration of 30,000 mg·kg-soil^-1 and compost was mixed with the contaminated soil at a 1:9 ratio (w/w). Maize seedlings were planted in each pot and a total of ten pots with two treatments (compost-amended and unamended) were prepared. The pot experiment was conducted for 85 days. The compost-amended soil had a significantly higher TPH removal efficiency (51.1%) than unamended soil (21.4%). Additionally, the relative abundance of the alkB gene, which is associated with PH degradation, was higher in the compost-amended soil than in the unamended soil. Similarly, cnorB and nosZ (which are associated with nitric oxide (NO) and N₂O reduction, respectively) were also highly upregulated in the compost-amended soil. Moreover, the compost-amended soil exhibited higher richness and evenness indices, indicating that bacterial diversity was higher in the amended soil than in the unamended soil. Therefore, our findings may contribute to the development of strategies to enhance remediation efficiency and greenhouse gas mitigation during the rhizoremediation of diesel-contaminated soils.