Characterization of Hydrocarbon-Degrading Bacteria in Constructed Wetland Microcosms Used to Treat Crude Oil Polluted Water

Biochar-bacteria-plant combined potential for remediation of oil-contaminated soil

Oil pollution is a common type of soil organic pollution that is harmful to the ecosystem. Bioremediation, particularly microbe-assisted phytoremediation of oil-contaminated soil, has become a research hotspot in recent years. In order to explore more appropriate bioremediation strategies for soil oil contamination and the mechanism of remediation, we compared the remediation effects of three plants when applied in combination with a microbial agent and biochar. The combined remediation approach of Tagetes erecta, microbial agent, and biochar exhibited the best plant growth and the highest total petroleum hydrocarbons degradation efficiency (76.60%). In addition, all of the remediation methods provided varying degrees of restoration of carbon and nitrogen contents of soils. High-throughput sequencing found that microbial community diversity and richness were enhanced in most restored soils. Some soil microorganisms associated with oil degradation and plant growth promotion such as Cavicella, C1_B045, Sphingomonas, MND1, Bacillus and Ramlibacter were identified in this study, among which Bacillus was the major component in the microbial agent. Bacillus was positively correlated with all soil remediation indicators tested and was substantially enriched in the rhizosphere of T. erecta. Functional gene prediction of the soil bacterial community based on the KEGG database revealed that pathways of carbohydrate metabolism and amino acid metabolism were up-regulated during remediation of oil-contaminated soils. This study provides a potential method for efficient remediation of oil-contaminated soils and thoroughly examines the biochar-bacteria-plant combined remediation mechanisms of oil-contaminated soil, as well as the combined effects from the perspective of soil bacterial communities.

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.

Phytoremediation of DEHP and heavy metals co-contaminated soil by rice assisted with a PGPR consortium: Insights into the regulation of ion homeostasis, improvement of photosynthesis and enrichment of beneficial bacteria in rhizosphere soil

The coexistence of di (2-ethylhexyl) phthalate (DEHP), Cd, and Zn poses a serious challenge to soil ecosystems. This study aimed to evaluate the phytoremediation potential of rice assisted with a plant growth promoting rhizobacteria (PGPR) consortium for the remediation of DEHP, Cd, and Zn co-contaminated soil. The consortium consisted of four bacterial strains, all of which exhibited Cd-Zn resistance and DEHP degradability. The results showed that the rice assisted by the bacterial consortium dissipated 86.1% DEHP while removing 76.0% Cd²⁺ and 92.2% Zn²⁺ from soil within 30 d. The presence of the PGPR consortium promoted plant growth and improved soil enzymatic activity, which may have helped enhance the removal of DEHP and heavy metals from the soil. Moreover, the application of the consortium modified the bacterial community and increased the relative abundance of bacteria related to DEHP degradation (Sphingomonas, Xanthobacteraceae), heavy metal immobilization (Massilia), and soil nutrient cycling (Nitrospira, Vicinamibacterales), which promoted plant growth and the removal of DEHP and heavy metals from soil. Notably, the DEHP and heavy metal contents in rice decreased substantially during the phytoremediation process. Therefore, the PGPR consortium could be beneficial for enhancing the removal of DEHP and heavy metals from the soil, without inducing the accumulation of these pollutants in rice. In general, this study confirmed that the combined use of rice and the PGPR consortium could remedy DEHP and heavy metal co-contaminated soil economically and ecologically without simultaneously posing risks for rice consumption.

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Background

Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. 

Results

Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.

Conclusion

Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08906-w.

Tobacco-associated with Methylophilus sp. FP-6 enhances phytoremediation of benzophenone-3 through regulating soil microbial community, increasing photosynthetic capacity and maintaining redox homeostasis of plant

Benzophenone-3 (BP-3) has attracted widespread attention due to its large accumulation in the environment and its potential toxicity effects to human. This study aimed to investigate the effects of the combined application of tobacco and Methylophilus sp. strain FP-6 with both plant growth promoting (PGP) traits and BP-3 degradation function on BP-3 remediation in soil. The results showed that about 79.18% of BP-3 was removed from the soil after 30 days of plant culture inoculated with the FP-6 strain, which was significantly higher than the plant-alone treatment. Simultaneously, inoculation with strain FP-6 significantly improved growth performance, biomass production, antioxidant levels, osmoregulation substance, photosynthetic capacity and chlorophyll accumulation in tobacco. Moreover, the application of FP-6 shifted the bacterial community, and enhanced the abundance of BP-3-degrading or soil nutrient cycling-affecting bacteria (e.g., Chloroflexi, Bryobacter, MND1 and Myxococcales), which might be valuable for the promotion of plant growth and degradation of BP-3 in the soil. The results from this study gave first insights into the enhancement of BP-3 removal efficiency from soil by phytoremediation assisted with bacteria possessing both PGP properties and BP-3 degradation function. The role of soil bacterial community in this remediation process was also discussed.

Operational parameters optimization for remediation of crude oil-polluted water in floating treatment wetlands using response surface methodology

The application of floating treatment wetlands (FTWs) is an innovative nature-based solution for the remediation of polluted water. The rational improvement of water treatment via FTWs is typically based on multifactorial experiments which are labor-intensive and time-consuming. Here, we used the response surface methodology (RSM) for the optimization of FTW's operational parameters for the remediation of water polluted by crude oil. The central composite design (CCD) of RSM was used to generate the experimental layout for testing the effect of the variables hydrocarbon, nutrient, and surfactant concentrations, aeration, and retention time on the hydrocarbon removal in 50 different FTW test systems planted with the common reed, Phragmites australis. The results from these FTW were used to formulate a mathematical model in which the computational data strongly correlated with the experimental results. The operational parameters were further optimized via modeling prediction plus experimental validation in test FTW systems. In the FTW with optimized parameters, there was a 95% attenuation of the hydrocarbon concentration, which was very close to the 98% attenuation predicted by the model. The cost-effectiveness ratio showed a reduction of the treatment cost up to $0.048/liter of wastewater. The approach showed that RSM is a useful strategy for designing FTW experiments and optimizing operational parameters.

Enhanced degradation of hydrocarbons in constructed wetlands aided with nutrients, surfactant, and aeration

The use of constructed wetlands (CWs) is a promising approach for the remediation of hydrocarbon-polluted wastewater. The amendments of CWs with nutrients, surfactants, and aeration enhances the removal of pollutants from wastewater. The objective of the present study was to explore the effect of external stimulants, i.e., nutrients, surfactant, and aeration on hydrocarbons degradation potential of CWs. The CWs mesocosms were developed by the vegetation of Phragmites australis and amendments with nutrients (20 mg l^-1 N, 2.6 mg l^-1 P, and 16.4 mg l^-1 K), surfactant Tween 20 (0.2%, v/v), and aeration (7 mg l^-1) for the remediation of diesel-spiked water (2%, w/v). The comparative analysis showed that the addition of nutrients, surfactant, and aeration individually enhanced total petroleum hydrocarbons (TPHs) reduction, and maximum TPHs reduction (88.4%) was achieved after 60 days in the mesocosms amended with the combination of nutrients, surfactant, and aeration. Among different individual treatments, the aeration (alone) also played a pivotal role in TPHs reduction (61%). The least (12%) reduction in TPHs was achieved in the mesocosms supplied with surfactant only. This study revealed that the combined application of nutrients, surfactant, and aeration in CWs enhanced its hydrocarbons degradation performance.

Recent developments and applications of floating treatment wetlands for treating different source waters: a review

Most water bodies around the world suffer from pollution to varying degrees. Floating treatment wetlands (FTWs) are a simple and efficient ecological treatment technology and have been widely studied and applied as a sustainable solution for different source waters. Based on the analysis of abundant literature in the last ten years, this paper systematically reviews the history and the latest development of FTWs. Meanwhile, the treatment performance and pollutant removal mechanisms of FTWs on the natural water, stormwater, domestic wastewater, industrial wastewater, and agricultural runoff are analyzed. In particular, very interesting information is provided, such as water depth, water surface coverage, the ratio of dissolved to total phosphorous (DRP/TP), the ratio of nitrogen to phosphorous (N/P), BOD/COD ratio, and its effects on the efficiency and removal mechanisms of FTWs. This information will provide useful references and guidance for optimizing the design of FTW and pollutant treatment efficiency of different source waters. This paper also provides an objective review of the limitations of FTWs. Subsequently, the enhancements of FTW technology which are recognized to be effective, including aeration, adding functional fillers or obligate degrading bacteria, and construction of hybrid FTWs, are summarized and recommendations are made for further research.

An Overview: The Toxicity of Ageratina adenophora on Animals and Its Possible Interventions

Ageratina adenophora is one of the major invasive weeds that causes instability of the ecosystem. Research has reported that A. adenophora produces allelochemicals that inhibit the growth and development of food crops, and also contain some toxic compounds that cause toxicity to animals that consume it. Over the past decades, studies on the identification of major toxic compounds of A. adenophora and their toxic molecular mechanisms have been reported. In addition, weed control interventions, such as herbicides application, was employed to reduce the spread of A. adenophora. However, the development of therapeutic and prophylactic measures to treat the various A. adenophora-induced toxicities, such as hepatotoxicity, splenotoxicity and other related disorders, have not been established to date. The main toxic pathogenesis of A. adenophora is oxidative stress and inflammation. However, numerous studies have verified that some extracts and secondary metabolites isolated from A. adenophora possess anti-oxidation and anti-inflammation activities, which implies that these extracts can relieve toxicity and aid in the development of drug or feed supplements to treat poisoning-related disorders caused by A. adenophora. Furthermore, beneficial bacteria isolated from rumen microbes and A. adenophora can degrade major toxic compounds in A. adenophora so as to be developed into microbial feed additives to help ameliorate toxicity mediated by A. adenophora. This review presents an overview of the toxic mechanisms of A. adenophora, provides possible therapeutic strategies that are available to mitigate the toxicity of A. adenophora and introduces relevant information on identifying novel prophylactic and therapeutic measures against A. adenophora-induced toxicity.

Long-term dynamics of plant communities after biological remediation of oil-contaminated soils in far north

We studied the long-term dynamics of plant communities after bio and phytoremediation of oil-polluted soils. Nine plots located in European Northeast and treated using various bioremediation methods were monitored from 2002 to 2014. Geobotanical descriptions (relevés) of each plot were performed in 2006 and 2014, and Grime’s theoretical CSR (competition–stress–ruderality) framework was used to assess the vegetation state and dynamics. We observed a clear shift of communities from pioneer (where ruderal species were prevalent) to stable (where competitor species were dominant) states. However, the remediation type did not significantly impact the vegetation recovery rate. After 12 years, all methods led to a 55–90% decrease in the oil content of the soil and a recovery of the vegetation cover. The plant communities contained mainly cereals and sedges which significantly differed from the original tundra communities before the oil spill. The control plot, treated only by mechanical cleaning, had minimum oil degradation rate (50%) and vegetation recovery rates, although, in CSR terms, its vegetation assemblage resembled the background community. Cereals (Agrostis gigantea, Deschampsia cespitosa, Phalaris arundinacea, and Poa pratensis), sedges (Carex canescens, Carex limosa, and Eriophorum vaginatum), and shrubs (Salix) were found to be the most effective species for phytoremediation, exhibiting high community productivity under the harsh northern conditions.

Effects of salinity on the treatment of synthetic petroleum-industry wastewater in pilot vertical flow constructed wetlands under simulated hot arid climatic conditions

Petroleum-industry wastewater (PI-WW) is a potential source of water that can be reused in areas suffering from water stress. This water contains various fractions that need to be removed before reuse, such as light hydrocarbons, heavy metals and conditioning chemicals. Constructed wetlands (CWs) can remove these fractions, but the range of PI-WW salinities that can be treated in CWs and the influence of an increasing salinity on the CW removal efficiency for abovementioned fractions is unknown. Therefore, the impact of an increasing salinity on the removal of conditioning chemicals benzotriazole, aromatic hydrocarbon benzoic acid, and heavy metal zinc in lab-scale unplanted and Phragmites australis and Typha latifolia planted vertical-flow CWs was tested in the present study. P. australis was less sensitive than T. latifolia to increasing salinities and survived with a NaCl concentration of 12 g/L. The decay of T. latifolia was accompanied by a decrease in the removal efficiency for benzotriazole and benzoic acid, indicating that living vegetation enhanced the removal of these chemicals. Increased salinities resulted in the leaching of zinc from the planted CWs, probably as a result of active plant defence mechanisms against salt shocks that solubilized zinc. Plant growth also resulted in substantial evapotranspiration, leading to an increased salinity of the CW treated effluent. A too high salinity limits the reuse of the CW treated water. Therefore, CW treatment should be followed by desalination technologies to obtain salinities suitable for reuse. In this technology train, CWs enhance the efficiency of physicochemical desalination technologies by removing organics that induce membrane fouling. Hence, P. australis planted CWs are a suitable option for the treatment of water with a salinity below 12 g/L before further treatment or direct reuse in water scarce areas worldwide, where CWs may also boost the local biodiversity. Graphical abstract.

Hydrocarbon-degrading genes in root endophytic communities on oil sands reclamation covers

In response to environmental regulations, the Canadian oil sands industry aims to reclaim all disturbed areas to equivalent land capability prior to mining operations. However, tailing sands used in reclamation contain residual hydrocarbons and plants growing in these areas may rely on hydrocarbon-degrading endophytic bacteria to survive. This study assessed the hydrocarbon-degrading potential (genes: CYP153, alkB and nah) of culturable and unculturable endophytic bacteria associated with annual barley (Hordeum vulgare) and sweet clover (Melilotus albus) plants in an oil sands reclamation area. Our results suggest higher CYP153 gene copy numbers in sweet clover when compared to barley. Yet, no significant differences were detected in 16S rRNA, alkB and nah genes. In addition, total hydrocarbons, pH, total soil carbon, organic carbon and total nitrogen play an important role in determining hydrocarbon-degrading potential in these communities. The assessment of culturable hydrocarbon-degrading bacteria revealed 42 isolates (total of 316) that were positive for at least one hydrocarbon-degrading gene. Most of these isolates were positive for alkB, and closely match the database for Pantoea, Pseudomonas and Enterobacter spp. Thus, to improve oil sands reclamation strategies, plant inoculation with select hydrocarbon-degrading endophytes could be used to increase plant tolerance and hydrocarbon degradation in these areas.