Acinetobacter sp. as the key player in diesel oil degrading community exposed to PAHs and heavy metals

Response of antioxidant activity, active constituent and rhizosphere microorganisms of Salvia miltiorrhiza to combined application of microbial inoculant, microalgae and biochar under Cu stress

Salvia miltiorrhiza, a widely used medicinal herb renowned for its properties in promoting blood circulation, removing blood stasis and alleviating pain, is currently facing quality degradation due to excessive heavy metal levels, posing a threat to medication safety. In order to investigate the effects of microbial inoculant, microalgae and biochar on the growth of Salvia miltiorrhiza under copper (Cu) stress, as well as its Cu absorption, antioxidant activity, active component contents and rhizosphere microbial community, a pot experiment was conducted. Salvia miltiorrhiza plants were cultivated in the soil containing 400 mg/kg of Cu for six months and treated with microbial inoculant, microalgae and biochar, either individually or in combination. Almost all soil amendment treatments led to an increase in root biomass. Notably, co-application of microbial inoculant and microalgae had the optimal effect with a 63.07 % increase compared to the group treated solely with Cu. Moreover, when microbial inoculant was applied alone or in combination with microalgae, the Cu content in plant roots was reduced by 19.29 % and 25.37 %, respectively, whereas other treatments failed to show a decreasing trend. Intriguingly, Cu stress increased the active component contents in plant roots, and they could also be enhanced beyond non-stress levels when microbial inoculant and microalgae were applied together or in combination with biochar. Analyses of plant antioxidant activity, soil properties and rhizosphere microorganisms indicated that these amendments may alleviate Cu stress by enhancing peroxidase activity, facilitating plant nutrient absorption, and enriching beneficial microorganisms capable of promoting plant growth and mitigating heavy metal-induced damage. This study suggests that the combined application of microbial inoculant and microalgae can reduce Cu levels in Salvia miltiorrhiza while enhancing its quality under Cu stress.

AI-assisted systematic review on remediation of contaminated soils with PAHs and heavy metals

This systematic review addresses soil contamination by crude oil, a pressing global environmental issue, by exploring effective treatment strategies for sites co-contaminated with heavy metals and polycyclic aromatic hydrocarbons (PAHs). Our study aims to answer pivotal research questions: (1) What are the interaction mechanisms between heavy metals and PAHs in contaminated soils, and how do these affect the efficacy of different remediation methods? (2) What are the challenges and limitations of combined remediation techniques for co-contaminated soils compared to single-treatment methods in terms of efficiency, stability, and specificity? (3) How do various factors influence the effectiveness of biological, chemical, and physical remediation methods, both individually and combined, in co-contaminated soils, and what role do specific agents play in the degradation, immobilization, or removal of heavy metals and PAHs under diverse environmental conditions? (4) Do AI-powered search tools offer a superior alternative to conventional search methodologies for executing an exhaustive systematic review? Utilizing big-data analytics and AI tools such as Litmaps.co, ResearchRabbit, and MAXQDA, this study conducts a thorough analysis of remediation techniques for soils co-contaminated with heavy metals and PAHs. It emphasizes the significance of cation-π interactions and soil composition in dictating the solubility and behavior of these pollutants. The study pays particular attention to the interplay between heavy metals and PAH solubility, as well as the impact of soil properties like clay type and organic matter on heavy metal adsorption, which results in nonlinear sorption patterns. The research identifies a growing trend towards employing combined remediation techniques, especially biological strategies like biostimulation-bioaugmentation, noting their effectiveness in laboratory settings, albeit with potentially higher costs in field applications. Plants such as Medicago sativa L. and Solanum nigrum L. are highlighted for their effectiveness in phytoremediation, working synergistically with beneficial microbes to decompose contaminants. Furthermore, the study illustrates that the incorporation of biochar and surfactants, along with chelating agents like EDTA, can significantly enhance treatment efficiency. However, the research acknowledges that varying environmental conditions necessitate site-specific adaptations in remediation strategies. Life Cycle Assessment (LCA) findings indicate that while high-energy methods like Steam Enhanced Extraction and Thermal Resistivity - ERH are effective, they also entail substantial environmental and financial costs. Conversely, Natural Attenuation, despite being a low-impact and cost-effective option, may require prolonged monitoring. The study advocates for an integrative approach to soil remediation, one that harmoniously balances environmental sustainability, cost-effectiveness, and the specific requirements of contaminated sites. It underscores the necessity of a holistic strategy that combines various remediation methods, tailored to meet both regulatory compliance and the long-term sustainability of decontamination efforts.

Enhancement of benzo[a]pyrene mineralization: symbiotic biodegradation by Acinetobacter sp. strain HAP1 in Association with Cyanobacteriota sp. S66

The ability of Acinetobacter sp. strain HAP1, isolated from petroleum refinery effluent, to eliminate different concentrations (20, 40, 60, 80 and 100 mg/L) of Benzo[a]Pyrene degradation (BaP) was studied. A test to improve this degradation capacity was carried out by culturing the bacterial strain in association with a cyanobacteria. The results show a highly significant effect of the concentration of (BaP) and a very highly significant effect of the symbiosis between the bacterial strain and the cyanobacteria. This combination was able to significantly improve the (BaP) degradation rate by up to 18%. This degradation and especially in association leads to a complete mineralization of (BaP) and there is a difference in yield that can go up to 15%. Through molecular identification based on 16S rRNA gene sequence analysis, strains HAP1 and S66 were recognized as Acinetobacter sp. strain HAP1 and Cyanobacteriota sp. S66, respectively. Comparison of the retrieved sequences with the NCBI GenBank database was done, and the closest matches were found to be Acinetobacter pittii strain JD-10 for bacteria and Pseudochroococcus couteii strain PMC 885.14 for cyanobacteria.

Simultaneous removal of crude oil and heavy metals by highly adapted bacterial strain Cutibacterium sp. NL2 isolated from Algerian oilfield

Investigating the ability of bacteria to simultaneously enhance hydrocarbon removal and reduce heavy metals' toxicity is necessary to design more effective bioremediation strategies. A bacterium (NL2 strain) isolated from an Algerian oilfield was cultivated on crude oil as sole carbon and energy sources. Molecular analyses of the 16S rRNA gene sequence placed the strain within the Cutibacterium genera. This isolate was able to tolerate up to 60% of crude oil as sole carbon source. Chemical analyses (GC-MS) evidenced that strain NL2 was able to degrade 92.22% of crude oil (at optimal growing conditions: pH 10, 44 °C, 50 g L-1 NaCl, and 20% of crude oil (v/v) as sole carbon source) in only 7 days. NL2 isolate was also able to produce biosurfactants with reduction of surface tension of growing media (29.4 mN m-1). On the other hand, NL2 strain was able to tolerate high lead (Pb) and copper (Cu) concentrations (up to 60 mM). In fact, NL2 cultivated in the presence of 20% of crude oil, and 0.48 mM of Pb was able to reduce Pb concentration by a 41.36%. In turn, when cultivated on high Pb concentration (15 mM), the strain was able to remove 35.19% of it and 86.25% of crude oil, both in a time frame of 7 days. Our findings suggest that Cutibacterium strain NL2 is able to efficiently use and remove a wide range of crude oil substrates in presence of high Pb concentration. Accordingly, NL2 strain is of extreme interest from a biotechnological standpoint.

Effect of the Application of Ochrobactrum sp.-Immobilised Biochar on the Remediation of Diesel-Contaminated Soil

The immobilisation of bacteria on biochar has shown potential for enhanced remediation of petroleum hydrocarbon-contaminated soil. However, there is a lack of knowledge regarding the effect of bacterial immobilisation on biosolids-derived biochar for the remediation of diesel-contaminated soil. This current study aimed to assess the impact of the immobilisation of an autochthonous hydrocarbonoclastic bacteria, Ochrobacterium sp. (BIB) on biosolids-derived biochar for the remediation of diesel-contaminated soil. Additionally, the effect of fertiliser application on the efficacy of the BIB treatment was investigated. Biochar (BC) application alone led to significantly higher hydrocarbon removal than the control treatment at all sampling times (4887-11,589 mg/kg higher). When Ochrobacterium sp. was immobilised on biochar (BIB), the hydrocarbon removal was greater than BC by 5533 mg/kg and 1607 mg/kg at weeks 10 and 22, respectively. However, when BIB was co-applied with fertiliser (BIBF), hydrocarbon removal was lower than BIB alone by 6987-11,767 mg/kg. Quantitative PCR (q-PCR) analysis revealed that the gene related to Ochrobacterium sp. was higher in BIB than in the BC treatment, which likely contributed to higher hydrocarbon removal in the BIB treatment. The results of the q-PCR analysis for the presence of alkB genes and FTIR analysis suggest that the degradation of alkane contributed to hydrocarbon removal. The findings of this study demonstrate that bacterial immobilisation on biosolids-derived biochar is a promising technique for the remediation of diesel-contaminated soil. Future studies should focus on optimising the immobilisation process for enhanced hydrocarbon removal.

Adaptation strategies and functional transitions of microbial community in pyrene-contaminated soils promoted by lead with Pseudomonas veronii and its extracellular polymeric substances

Pyrene was designated as a remediation target in this study, and low contamination of lead (Pb) was set to induce heavy metal stress. Pseudomonas veronii and its extracellular polymeric substances (EPSs) were chosen for biofortification, with the aim of elucidating the structural, metabolic, and functional responses of soil microbial communities. Community analysis of soil microorganisms using high-throughput sequencing showed that the co-addition of P. veronii and EPSs resulted in an increase in relative abundance of phyla associated with pyrene degradation, and formed a symbiotic system dominated by Firmicutes and Proteobacteria, which involved in pyrene metabolism. Co-occurrence network analysis revealed that the module containing P. veronii was the only one exhibiting a positive correlation between bacterial abundance and pyrene removal, indicating the potential of bioaugmentation in enriching functional taxa. Biofortification also enhanced the abundance of functional gene linked to EPS production (biofilm formation-Pseudomonas aeruginosa) and pyrene degradation. Furthermore, 17 potential functional bacteria were screened out using random forest algorithm. Lead contamination further promoted the growth of Proteobacteria, intensified cooperative associations among bacteria, and increased the abundance of bacteria with positive correlation with pyrene degradation. The results offer novel perspectives on alterations in microbial communities resulting from the synergistic impact of heavy metal stress and biofortification.

Differences in soil bacterial community structure during the remediation of Cd-polluted cotton fields by biochar and biofertilizer in Xinjiang, China

Introduction

Heavy metal pollution is a major worldwide environmental problem. Many remediation techniques have been developed, these techniques have different performance in different environments.

Methods

In this study, soil sampling was conducted in multiple cotton fields in Xinjiang, China, and found that cadmium (Cd) was the most abundant soil heavy metal. Then, to find the most suitable technique for the remediation of Cd pollution in cotton fields, a two-year study was conducted to explore the effects of cotton straw-derived biochar (BC, 3%) and Bacillus-based biofertilizer (BF, 1.5%) on cotton Cd uptake and transport and soil microbial community structure under Cd exposure conditions (soil Cd contents: 1, 2, and 4 mg·kg-1).

Results

The results showed that the bioaccumulation coefficients (Cd content of cotton organs / soil available Cd content) of cotton roots, stems, leaves, and buds/bolls reduced by 15.93%, 14.41%, 23.53%, and 20.68%, respectively after the application of BC, and reduced by 16.83%, 17.15%, 22.21%, and 26.25%, respectively after the application of BF, compared with the control (no BC and BF). Besides, the application of BC and BF reduced the transport of Cd from soil to root system, and enhanced the diversity of soil bacterial communities (dominant species: Alphaproteobacteria and Actinobacteria) and the metabolic functions related to amino acid synthesis. It was worth noting that the differential species for BF group vs BC group including Alphaproteobacteria, Gemmatimonadetes, Bacilli, and Vicinamibacteria were associated with the enrichment and transport of Cd, especially the transport of Cd from cotton roots to stems.

Discussion

Therefore, the application of BC and BF changed the soil bacterial diversity in Cd-polluted cotton field, and then promoted the transport of Cd in cotton, ultimately improving soil quality. This study will provide a reference for the selection of soil heavy metal pollution remediation techniques in Xinjiang, China.

Application of bacterial agent YH for remediation of pyrene-heavy metal co-pollution system: Efficiency, mechanism, and microbial response

The combination of organic and heavy metal pollutants can be effectively and sustainably remediated using bioremediation, which is acknowledged as an environmentally friendly and economical approach. In this study, bacterial agent YH was used as the research object to explore its potential and mechanism for bioremediation of pyrene-heavy metal co-contaminated system. Under the optimal conditions (pH 7.0, temperature 35°C), it was observed that pyrene (PYR), Pb(II), and Cu(II) were effectively eliminated in liquid medium, with removal rates of 43.46%, 97.73% and 81.60%, respectively. The microscopic characterization (SEM/TEM-EDS, XPS, XRD and FTIR) results showed that Pb(II) and Cu(II) were eliminated by extracellular adsorption and intracellular accumulation of YH. Furthermore, the presence of resistance gene clusters (cop, pco, cus and pbr) plays an important role in the detoxification of Pb(II) and Cu(II) by strains YH. The degradation rate of PYR reached 72.51% in composite contaminated soil, which was 4.33 times that of the control group, suggesting that YH promoted the dissipation of pyrene. Simultaneously, the content of Cu, Pb and Cr in the form of F4 (residual state) increased by 25.17%, 6.34% and 36.88%, respectively, indicating a decrease in the bioavailability of heavy metals. Furthermore, YH reorganized the microbial community structure and enriched the abundance of hydrocarbon degradation pathways and enzyme-related functions. This study would provide an effective microbial agent and new insights for the remediation of soil and water contaminated with organic pollutants and heavy metals.

Limited impact of weathered residues from the Deepwater Horizon oil spill on the gut-microbiome and foraging behavior of sheepshead minnows (Cyprinodon variegatus)

The Deepwater Horizon disaster of April 2010 was the largest oil spill in U.S. history and exerted catastrophic effects on several ecologically important fish species in the Gulf of Mexico (GoM). Within fish, the microbiome plays a key symbiotic role in maintaining host health and aids in acquiring nutrients, supporting immune function, and modulating behavior. The aim of this study was to examine if exposure to weathered oil might produce significant shifts in fish gut-associated microbial communities as determined from taxa and genes known for hydrocarbon degradation, and whether foraging behavior was affected. The gut microbiome (16S rRNA and shotgun metagenomics) of sheepshead minnow (Cyprinodon variegatus) was characterized after fish were exposed to oil in High Energy Water Accommodated Fractions (HEWAF; tPAH = 81.1 ± 12.4 µg/L) for 7 days. A foraging behavioral assay was used to determine feeding efficiency before and after oil exposure. The fish gut microbiome was not significantly altered in alpha or beta diversity. None of the most abundant taxa produced any significant shifts as a result of oil exposure, with only rare taxa showing significant shifts in abundance between treatments. However, several bioindicator taxa known for hydrocarbon degradation were detected in the oil treatment, primarily Sphingomonas and Acinetobacter. Notably, the genus Stenotrophomonas was detected in high abundance in 16S data, which previously was not described as a core member of fish gut microbiomes. Data also demonstrated that behavior was not significantly affected by oil exposure. Potential low bioavailability of the oil may have been a factor in our observation of minor shifts in taxa and no behavioral effects. This study lays a foundation for understanding the microbiome of captive sheepshead minnows and indicates the need for further research to elucidate the responses of the fish gut-microbiome under oil spill conditions.

Main Factors Determining the Scale-Up Effectiveness of Mycoremediation for the Decontamination of Aliphatic Hydrocarbons in Soil

Soil contamination constitutes a significant threat to the health of soil ecosystems in terms of complexity, toxicity, and recalcitrance. Among all contaminants, aliphatic petroleum hydrocarbons (APH) are of particular concern due to their abundance and persistence in the environment and the need of remediation technologies to ensure their removal in an environmentally, socially, and economically sustainable way. Soil remediation technologies presently available on the market to tackle soil contamination by petroleum hydrocarbons (PH) include landfilling, physical treatments (e.g., thermal desorption), chemical treatments (e.g., oxidation), and conventional bioremediation. The first two solutions are costly and energy-intensive approaches. Conversely, bioremediation of on-site excavated soil arranged in biopiles is a more sustainable procedure. Biopiles are engineered heaps able to stimulate microbial activity and enhance biodegradation, thus ensuring the removal of organic pollutants. This soil remediation technology is currently the most environmentally friendly solution available on the market, as it is less energy-intensive and has no detrimental impact on biological soil functions. However, its major limitation is its low removal efficiency, especially for long-chain hydrocarbons (LCH), compared to thermal desorption. Nevertheless, the use of fungi for remediation of environmental contaminants retains the benefits of bioremediation treatments, including low economic, social, and environmental costs, while attaining removal efficiencies similar to thermal desorption. Mycoremediation is a widely studied technology at lab scale, but there are few experiences at pilot scale. Several factors may reduce the overall efficiency of on-site mycoremediation biopiles (mycopiles), and the efficiency detected in the bench scale. These factors include the bioavailability of hydrocarbons, the selection of fungal species and bulking agents and their application rate, the interaction between the inoculated fungi and the indigenous microbiota, soil properties and nutrients, and other environmental factors (e.g., humidity, oxygen, and temperature). The identification of these factors at an early stage of biotreatability experiments would allow the application of this on-site technology to be refined and fine-tuned. This review brings together all mycoremediation work applied to aliphatic petroleum hydrocarbons (APH) and identifies the key factors in making mycoremediation effective. It also includes technological advances that reduce the effect of these factors, such as the structure of mycopiles, the application of surfactants, and the control of environmental factors.

Effects of single and combined contamination of total petroleum hydrocarbons and heavy metals on soil microecosystems: Insights into bacterial diversity, assembly, and ecological function

Deciphering the impact of single and combined contamination of total petroleum hydrocarbons (TPH) and heavy metals on soil microecosystems is essential for the remediation of contaminated habitats, yet it remains incompletely understood. In this study, we employed high-throughput sequencing to investigate the impact of single TPH contamination, single metal contamination, and their co-contamination on soil microbial diversity, assembly mechanisms, composition, ecological function, and resistome. Our results revealed that contamination led to a reduction in alpha diversity, with single contamination displaying lower diversity compared to co-contamination, depending on the concentration of pollutants. Community beta diversity was primarily driven by turnover rather than nestedness, and narrower ecological niches were detected under pollution conditions. The neutral community model suggested that homogenizing dispersal played a significant role in the community assembly process under single TPH or co-contamination, while homogeneous selection dominated under heavy metals pollution. Procrustes analysis demonstrated a correlation between community composition and functional divergence, while Mantel tests linked this divergence to concentrations of Cr, Cr6+, Pb, and TPH. Interestingly, soils co-polluted with TPH and heavy metals exhibited similar genera, community functions, and resistomes as soils contaminated with only metals, highlighting the significant impact of heavy metals. Ecological functions related to carbon (C), nitrogen (N), and sulfur (S) cycles were enhanced under TPH pollution but impaired under heavy metals stress. These findings enhance our understanding of soil microecosystems subjected to TPH, heavy metals, and their co-contamination, and carry significant implications for environmental microecology and pollutant risk assessment.

Remediation of hydrocarbons and metals by hydrocarbon utilizing Pseudomonas taiwanensis YSA-17 isolated from soil contaminated with petroleum

Careless handling of petroleum in petrochemical industries releases toxic hydrocarbons and metals to soil and water. The aim of the present study was to isolate hydrocarbon-utilizing and metal-tolerant bacteria. Hydrocarbon-utilizing bacteria from petroleum-contaminated soils were isolated on the Bushnell Hass medium. Hydrocarbon degradation by Pseudomonas taiwanensis strain YSA-17 was observed by gas chromatography-mass spectrometry. Bioaccumulation of metals by strain YSA-17 was assessed in nutrient broth. Among different strains, YSA-17 showed the highest potential for hydrocarbon utilization. After 20 days of incubation, YSA-17 completely degraded one compound and during its degradation, there was the formation of 13 new compounds which were absent in uninoculated control. Results of scanning electron microscope and Fourier transmission infrared (FTIR) indicated degradation of hydrocarbons. FTIR showed the formation of new functional groups in YSA-17 inoculated medium. Expression of the total quantity of hydrocarbon-degrading gene (AlkB and NehAc) in petroleum-amended nutrient broth inoculated with strain YSA-17 enhanced significantly during 20 days of incubation compared to control. YSA-17 also significantly removed metals. This study concluded that bioinoculant can be utilized for the bioremediation of pollutants cocontaminated with hydrocarbons and metals. Petroleum-contaminated soil will be remediated for pollutants.

Mechanism of synergistic remediation of soil phenanthrene contamination in paddy fields by rice-crab coculture and bioaugmentation with Pseudomonas sp

Polycyclic aromatic hydrocarbons (PAHs) are persistent and harmful pollutants with high priority concern in agricultural fields. This work constructed a rice-crab coculture and bioaugmentation (RCM) system to remediate phenanthrene (a model PAH) contamination in rice fields. The results showed that RCM had a higher remediation performance of phenanthrene in rice paddy compared with rice cultivation alone, microbial addition alone, and crab-rice coculture, reaching a remediation efficiency of 88.92 % in 42 d. The concentration of phenanthrene in the rice plants decreased to 6.58 mg/kg, and its bioconcentration effect was efficiently inhibited in the RCM system. In addition, some low molecular weight organic acids of rice root increased by 12.87 %∼73.87 %, and some amino acids increased by 140 %∼1150 % in RCM. Bioturbation of crabs improves soil aeration structure and microbial migration, and adding Pseudomonas promoted the proliferation of some plant growth-promoting rhizobacteria (PGPRs), which facilitated the degradation of phenanthrene. This coupling rice-crab coculture with bioaugmentation had favorable effects on soil enzyme activity, microbial community structure, and PAH degradation genes in paddy fields, enhancing the removal of and resistance to PAH contamination in paddy fields and providing new strategies for achieving a balance between production and remediation in contaminated paddy fields.

Unraveling the Positive Effect of Soil Moisture on the Bioaugmentation of Petroleum-Contaminated Soil Using Bioinformatics

Petroleum contamination is a severe threat to the soil environment. Previous studies have demonstrated that petroleum degradation efficiency is promoted by enhancing soil moisture content (MC). However, the effects of MC on soil microbial ecological functions during bioremediation remain unclear. Here, we investigated the impacts of 5% and 15% of moisture contents on petroleum degradation, soil microbial structures and functions, and the related genes using high-throughput sequencing and gene function prediction. Results indicated that petroleum biodegradation efficiency was increased by 8.06% in the soils with 15% MC when compared to that with 5% of MC. The complexity and stability of soil microbial community structures with 15% MC were higher than those in the soils with 5% MC when hydrocarbon-degrading bacterial flora (HDBF) were inoculated into the soils. Fifteen percent of moisture content strengthened the interaction of the bacterial community network and reduced the loss of some key bacteria species including Mycobacterium, Sphingomonas, and Gemmatimonas. Some downregulated gene pathways relating to bioaugmentation were enhanced in the soils with 15% MC. The results suggested that the dynamic balances of microbial communities and the metabolic interactions by 15% MC treatment are the driving forces for the enhancement of bioremediation in petroleum-contaminated soil.

Improved efficiency of Sedum lineare (Crassulaceae) in remediation of arsenic-contaminated soil by phosphate-dissolving strain P-1 in association with phosphate rock

The selection of appropriate plants and growth strategies is a key factor in improving the efficiency and universal applicability of phytoremediation. Sedum lineare grows rapidly and tolerates multiple adversities. The effects of inoculation of Acinetobacter sp. phosphate solubilizing bacteria P-1 and application of phosphate rock (PR) as additives on the remediation efficiency of As-contaminated soil by S. lineare were investigated. Compared with the control, both the single treatment and the combination of inoculation with strain P-1 and application of PR improved the biomass by 30.7-395.5%, chlorophyll content by 48.1-134.8%, total protein content by 12.5-92.4% and total As accumulation by 45.1-177.5%, and reduced the As-induced oxidative damage. Inoculation with strain P-1 increased the activities of superoxide dismutases and catalases of S. lineare under As stress, decreased the accumulation of reactive oxygen species in plant tissues and promoted the accumulation of As in roots. In contrast, simultaneous application of PR decreased As concentration in S. lineare tissues, attenuated As-induced lipid peroxidation and improved As transport to shoots. In addition, the combined application showed the best performance in improving resistance and biomass, which significantly increased root length by 149.1%, shoot length by 33%, fresh weight by 395.5% and total arsenic accumulation by 159.2%, but decreased the malondialdehyde content by 89.1%. Our results indicate that the combined application of strain P-1 and PR with S. lineare is a promising bioremediation strategy to accelerate phytoremediation of As-contaminated soils.

Insights into relationships between polycyclic aromatic hydrocarbon concentration, bacterial communities and organic matter composition in coal gangue site

Coal mining usually brought polycyclic aromatic hydrocarbons (PAHs) contamination. Relationships between the concentration of PAHs, bacterial communities and soil environmental factors were important for bioremediation of PAHs in soil. Total 4 kinds of soil samples with different concentrations of PAHs were selected from 7 typical coal gangue（CG） sites in Huainan, Anhui Province. The relationships between microorganisms, dissolved organic matter (DOM) composition and PAHs concentration were systematically analyzed in this work. Total 11 kinds of PAHs were enriched in the soil surface layer. That was attributed to the strong binding of soil organic matter (SOM) to PAHs. PAHs contamination reduced the diversity of soil microbial. The abundance of PAHs-degrading genera such as Arthrobacter decreased with the increasing concentration of PAHs. Mycobacterium increased with the increasing concentration of PAHs in all samples. The microbial activities decreased with increasing concentration of PAHs. The increasing contents of LWM-PAHs and DOM were beneficial to improve the activities of soil microbial. The increasing DOM aromaticity was beneficial to improve the bioavailability of PAHs according to the correlation analysis between PAHs content and DOM structural parameters. The obtained results provide a basis for better understanding the contamination characteristics and microbial communities of coal gangue PAH-contaminated sites.

The microbial removal of bisphenols in aquatic microcosms and associated alteration in bacterial community

The concept of the study resulted from numerous concerns around bisphenol A (BPA) and bisphenol S (BPS) in aquatic environments. In this study, river water and sediment microcosms highly polluted with bisphenols and bioaugmented with two BPs-removing bacterial strains were constructed. The study aimed to determine the rate of high-concentrated BPA and BPS (BPs) removal from river water and sediment microniches, and the effect of water bioaugmentation with bacterial consortium on the removal rates of these pollutants. Moreover, the impact of introduced strains and exposure to BPs on the structural and functional composition of the autochthonous bacterial communities was elucidated. Our findings indicate that the removal activity of autochthonous bacteria was sufficient for effectively BPA elimination and reducing BPS content in the microcosms. The number of introduced bacterial cells decreased continuously until day 40, and on consecutive sampling days, no bioaugmented cells were detected. Sequencing analysis of the total 16S rRNA genes revealed that the community composition in bioaugmented microcosms amended with BPs differed significantly from those treated either with bacteria or BPs. A metagenomic analysis found an increase in the abundance of proteins responsible for xenobiotics removal in BPs-amended microcosms. This study provides new insights into the effects of bioaugmentation with a bacterial consortium on bacterial diversity and BPs removal in aquatic environments.

Effect of Heavy-Metal-Resistant PGPR Inoculants on Growth, Rhizosphere Microbiome and Remediation Potential of Miscanthus × giganteus in Zinc-Contaminated Soil

Microbial-assisted phytoremediation is considered a more effective approach to soil rehabilitation than the sole use of plants. Mycolicibacterium sp. Pb113 and Chitinophaga sp. Zn19, heavy-metal-resistant PGPR strains originally isolated from the rhizosphere of Miscanthus × giganteus, were used as inoculants of the host plant grown in control and zinc-contaminated (1650 mg/kg) soil in a 4-month pot experiment. The diversity and taxonomic structure of the rhizosphere microbiomes, assessed with metagenomic analysis of rhizosphere samples for the 16S rRNA gene, were studied. Principal coordinate analysis showed differences in the formation of the microbiomes, which was affected by zinc rather than by the inoculants. Bacterial taxa affected by zinc and the inoculants, and the taxa potentially involved in the promotion of plant growth as well as in assisted phytoremediation, were identified. Both inoculants promoted miscanthus growth, but only Chitinophaga sp. Zn19 contributed to significant Zn accumulation in the aboveground part of the plant. In this study, the positive effect of miscanthus inoculation with Mycolicibacterium spp. and Chitinophaga spp. was demonstrated for the first time. On the basis of our data, the bacterial strains studied may be recommended to improve the efficiency of M. × giganteus phytoremediation of zinc-contaminated soil.

The characteristics and metabolic potentials of the soil bacterial community of two typical military demolition ranges in China

The response mechanism of soil microbiota in military polluted sites can effectively indicate the biotoxicity of ammunition. In this study, two military demolition ranges polluted soils of grenades and bullet were collected. According to high-throughput sequencing, after grenade explosion, the dominant bacteria in Site 1 (S1) are Proteobacteria (97.29 %) and Actinobacteria (1.05 %). The dominant bacterium in Site 2 (S2) is Proteobacteria (32.95 %), followed by Actinobacteria (31.17 %). After the military exercise, the soil bacterial diversity index declined significantly, and the bacterial communities interacted more closely. The indigenous bacteria in S1 were influenced more compared to those in S2. According to the environmental factor analysis, the bacteria composition can easily be influenced by heavy metals and organic pollutants, including Cu, Pb, Cr and Trinitrotoluene (TNT). About 269 metabolic pathways annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were detected in bacterial communities, including nutrition metabolism (C, 4.09 %; N, 1.14 %; S, 0.82 %), external pollutant metabolism (2.52 %) and heavy metal detoxication (2.12 %), respectively. The explosion of ammunition changes the basic metabolism of indigenous bacteria, and heavy metal stress inhibits the TNT degradation ability of bacterial communities. The pollution degree and community structure influence the metal detoxication strategy at the contaminated sites together. Heavy metal ions in S1 are mainly discharged through membrane transporters, while heavy metal ions in S2 are mainly degraded through lipid metabolism and biosynthesis of secondary metabolites. The results obtained in this study can provide deep insight into the response mechanism of the soil bacterial community in military demolition ranges with composite pollutions of heavy metals and organic substances. CAPSULE: Heavy metal stress changed the composition, interaction and metabolism of indigenous communities in military demolition ranges, especially the TNT degradation process.

Microbial communities and their roles in the Cenozoic sulfurous oil reservoirs in the Southwestern Qaidam Basin, Western China

The latest discovery of sulfurous natural gas marked a breakthrough in the Cenozoic natural gas exploration in the southwestern margin of Qaidam Basin. The 16S rRNA analyses were performed on the crude oil samples from H₂S-rich reservoirs in the Yuejin, Shizigou and Huatugou profiles, to understand the sulfurous gas origin, which was also integrated with carbon and hydrogen isotopes of alkane and sulfur isotopes of H₂S collected from the Yingxiongling Area. Results show that the microorganisms in samples can survive in the hypersaline reservoirs, and can be classified into multiple phyla, including Proteobacteria, Planctomycetes, Firmicutes, Bacteroidetes, and Haloanaerobiaeota. Methanogens are abundant in all of the three profiles, while sulfate-reducing bacteria are abundant in Yuejin and Huatugou profiles, contributing to the methane and H₂S components in the natural gas. The carbon, hydrogen and sulfur isotopes of sulfurous natural gas in the Yingxiongling Area show that the natural gas is a mixture of coal-type gas and oil-type gas, which was primarily derived from thermal degradation, and natural gas from the Yuejin and Huatugou profiles also originated from biodegradation. The isotopic analysis agrees well with the 16S rRNA results, i.e., H₂S-rich natural gas from the Cenozoic reservoirs in the southwest margin of the Qaidam Basin was primarily of thermal genesis, with microbial genesis of secondary importance.

Isolation of a polyethylene-degrading bacterium, Acinetobacter guillouiae, using a novel screening method based on a redox indicator

Plastic, a polymer synthesized from petrochemicals, is used worldwide. However, natural degradation of plastic is difficult, causing environmental pollution, with microplastics posing a serious threat to human health. In this study, we aimed to use a new screening method based on the oxidation-reduction indicator, 2,6-dichlorophenolindophenol, to isolate a polyethylene-degrading bacterium, Acinetobacter guillouiae, from insect larvae. Plastic-degrading strains are identified by the color change in the redox indicator from blue to colorless as plastic metabolism occurs. Polyethylene biodegradation by A. guillouiae was verified through weight loss, surface erosion, physiological evidence, and chemical changes on the plastic surface. In addition, we analyzed the characteristics of hydrocarbon metabolism in polyethylene-degrading bacteria. Results suggested that alkane hydroxylation and alcohol dehydrogenation were key steps in polyethylene degradation. This novel screening method will pave the way for high-throughput screening of polyethylene-degrading microorganisms and extending its application to other types of plastics may potentially address plastic pollution.

Biodegradation of petroleum hydrocarbons based pollutants in contaminated soil by exogenous effective microorganisms and indigenous microbiome

Microbial remediation is an eco-friendly and promising approach for the restoration of sites contaminated by petroleum hydrocarbons (PHCs). The degradation of total petroleum hydrocarbons (TPHs), semi volatile organic compounds (SVOCs) and volatile organic compounds (VOCs) of the soil samples collected from a petrochemical site by indigenous microbiome and exogenous microbes (Saccharomyces cerevisiae ATCC 204508/S288c, Candida utilis AS2.281, Rhodotorula benthica CBS9124, Lactobacillus plantarum S1L6, Bacillus thuringiensis GDMCC1.817) was evaluated. Community structure and function of soil microbiome and the mechanism involved in degradation were also revealed. After bioremediation for two weeks, the concentration of TPHs in soil samples was reduced from 17,800 to 13,100 mg/kg. The biodegradation efficiencies of naphthalene, benzo[a]anthracene, benzo[b]fluoranthene, benzo[a]pyrene, indeno[1,2,3-cd]pyrene, dibenzo[a,h]anthracene, 1,2,3-trichloropropane, 1,2-dichloropropane, ethylbenzene and benzene in soil samples with the addition of S. cerevisiae were 38.0%, 35.7%, 36.2%, 40.4%, 33.6%, 36.2%, 12.0%, 43.9%, 43.3% and 43.0%, respectively. The microbial diversity and community structure were improved during the biodegradation process. S. cerevisiae supplemented soil samples exhibited the highest relative abundance of the genus Acinetobacter for bacteria and Saccharomyces for yeast. The findings offer insight into the correlation between microbes and the degradation of PHC-based pollutants during the bioremediation process.

Microbial Removal of Petroleum Hydrocarbons from Contaminated Soil under Arsenic Stress

The contamination of soils with petroleum and its derivatives is a longstanding, widespread, and worsening environmental issue. However, efforts to remediate petroleum hydrocarbon-polluted soils often neglect or overlook the interference of heavy metals that often co-contaminate these soils and occur in petroleum itself. Here, we identified Acinetobacter baumannii strain JYZ-03 according to its Gram staining, oxidase reaction, biochemical tests, and FAME and 16S rDNA gene sequence analyses and determined that it has the ability to degrade petroleum hydrocarbons. It was isolated from soil contaminated by both heavy metals and petroleum hydrocarbons. Strain JYZ-03 utilized diesel oil, long-chain n-alkanes, branched alkanes, and polycyclic aromatic hydrocarbons (PAHs) as its sole carbon sources. It degraded 93.29% of the diesel oil burden in 7 days. It also had a high tolerance to heavy metal stress caused by arsenic (As). Its petroleum hydrocarbon degradation efficiency remained constant over the 0-300 mg/L As(V) range. Its optimal growth conditions were pH 7.0 and 25-30 °C, respectively, and its growth was not inhibited even by 3.0% (w/v) NaCl. Strain JYZ-03 effectively bioremediates petroleum hydrocarbon-contaminated soil in the presence of As stress. Therefore, strain JYZ-03 may be of high value in petroleum- and heavy-metal-contaminated site bioremediation.

Application of biochar-immobilized Bacillus sp. KSB7 to enhance the phytoremediation of PAHs and heavy metals in a coking plant

The co-existence of heavy metals and polycyclic aromatic hydrocarbons (PAHs) challenges the remediation of polluted soil. This study aimed to investigate whether a combined amendment of biochar-immobilized bacterium (BM) could enhance the phytoremediation of heavy metals and PAHs in co-contaminated soil. The Bacillus sp. KSB7 with the capabilities of plant-growth promotion, metal tolerance, and PAH degradation was immobilized on the peanut shell biochar prepared at 400 °C and 600 °C (PBM4 and PBM6, respectively). After 90 days, PBM4 treatment increased the removal of PAHs by 94.17% and decreased the amounts of diethylenetriamine pentaacetic acid-extractable Zn, Pb, Cr, and Cu by 58.46%, 53.42%, 84.94%, and 83.15%, respectively, compared with Kochia scoparia-alone treatment. Meanwhile, PBM4 was more effective in promoting K. scoparia growth and reducing the uptake of co-contaminants. The abundance of Gram-negative PAH-degrader and 1-aminocyclopropane-1-carboxylic deaminase-producing bacteria within rhizosphere soil was significantly improved after PBM4 treatment. Moreover, the relative abundance of the Bacillus genus increased by 0.66 and 2.05 times under PBM4 treatment compared with biochar alone and KSB7, indicating that KSB7 could colonize in the rhizosphere soil of K. scoparia. However, the removal of PAHs and heavy metals after PBM6 and 600 °C biochar-alone treatments caused no obvious difference. This study suggested that low-temperature BM-amended plant cultivation would be an effective approach to remove PAHs and heavy metals in co-contaminated soil.

Construction of bifunctional bacterial community for co-contamination remediation: Pyrene biodegradation and cadmium biomineralization

Polycyclic aromatic hydrocarbons and heavy metals are typical pollutants in the non-ferrous metal smelting industry. The combination of biodegradation and biomineralization has great development potential for co-contamination removal as an environmentally friendly method. Pyrene (Pyr) and cadmium (Cd) were regarded as model pollutants of co-contamination in this study. A bifunctional bacterial community named Ycp was screened from a non-ferrous smelting slag field soil. The 16S rRNA gene high throughput sequencing analysis showed that Enterobacter was the dominant genus (99.1%). Ycp had adaptability under a wide range of environmental conditions (pH 3-9, salinity 0-10 g L^-1 NaCl, Pyr concentration 0-50 mg L^-1, Cd concentration 0-100 mg L^-1), and the removal rate of Pyr and Cd reached 41.8%-76.9%, 82.8%-98.8%, respectively. It was found that compound carbon sources had promoting effect on the removal of Pyr and Cd, with the maximum removal rate of 88.3% and 98.0%. According to the degradation products of Pyr by LC-MS analysis and the mineralized products of Cd²⁺ by XRD and SEM-EDS analysis, the mechanism of Ycp for co-contamination remediation was: Ycp biodegraded Pyr through salicylic acid and phthalic acid metabolic pathways, and biomineralized Cd²⁺ into CdCO₃ through microbially induced carbonate precipitation. This study provided a basis for microbial remediation of co-contamination.

Response to Cold Adaption in Acinetobacter johnsonii XY27 from Spoiled Bigeye Tuna (Thunnus obesus): Membrane Protein Composition and Protein Biomarker Identification by Proteomics

Acinetobacter johnsonii is one of the major food-spoilage bacteria and can survive under cold stress. In this study, the membrane composition, membrane permeability, and energy transduction of A. johnsonii XY27 cultured at 4 and 30 °C were examined comparatively by flow cytometry combined with liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. The Na⁺/K⁺ATPase activity, alkaline phosphatase and ATPase activity, fluorescence intensity, and cell viability in A. johnsonii XY27 increased with the decrease in cultivation temperature. The polyunsaturated fatty acid and monounsaturated fatty acids have a higher content in A. johnsonii XY27 cultured at 4 °C compared to that cultured at 30 °C, in which the contents of methyl palmitoleate, methyl myristoleate, and methyl oleate increased dramatically with decreasing temperature. Comparative proteomics analysis revealed that 31 proteins were downregulated and 4 proteins were upregulated, in which catalase-peroxidase 1 and cold shock proteins as biomarker proteins could effectively control A. johnsonii during cold adaptation.

Biodegradation Pathway and Detoxification of β-cyfluthrin by the Bacterial Consortium and Its Bacterial Community Structure

In the process of microbial degradation of pyrethroid pesticides, the synergistic effect of the microbial community is more conducive to the complete degradation of toxic compounds than a single strain. At present, the degradation pathway of pyrethroids in a single strain has been well revealed, but the synergistic metabolism at the community level has not been well explained. This study elucidated the bacterial community succession, metabolic pathway, and phytotoxicity assessment during β-cyfluthrin biodegradation by a novel bacterial consortium enriched from contaminated soil. The results showed that the half-life of β-cyfluthrin at different initial concentrations of 0.25, 0.5, 0.75, and 1.0 mg mL^-1 were 4.16, 7.34, 12.81, and 22.73 days, respectively. Enterobacter was involved in β-cyfluthrin degradation metabolism in the initial stage, and other bacterial genera (Microbacterium, Ochrobactrum, Pseudomonas, Hyphomicrobiaceae, Achromobacter, etc.) significantly contribute to the degradation of intermediate metabolites in the later stages. Functional gene prediction and metabolite analysis showed that xenobiotic biodegradation and metabolism, especially benzoate degradation and metabolism by cytochrome P450 were the major means of β-cyfluthrin degradation. Further, two degradation pathways of β-cyfluthrin were proposed, which were mainly ester hydrolysis and oxidation to degrade β-cyfluthrin through the production of carboxylesterase and oxidoreductase. In addition, the inoculated bacterial consortium could degrade β-cyfluthrin residues in water and soil and reduce its phytotoxicity in Medicago sativa. Hence, this novel bacterial consortium has important application in the remediation environments polluted by β-cyfluthrin.

Dose–Response Effect of Nitrogen on Microbial Community during Hydrocarbon Biodegradation in Simplified Model System

Knowledge about the influence of C:N ratio on the biodegradation process of hydrocarbon compounds is of significant importance in the development of biostimulation techniques. The purpose of this study was to assess the impact of nitrogen compounds on the environmental consortium during the process of biological decomposition of hydrocarbons. The experimental variants represented low, moderate, and excessive biostimulation with nitrogen compounds. The metabolic activity of the consortium was tested using the flow cytometry technique. The efficiency of the biodegradation of hydrocarbons of the consortium, based on the gas chromatography method, and metapopulation changes, based on the analysis of V4 16srRNA sequencing data, were assessed. The results of the research confirm the positive effect of properly optimized biostimulation with nitrogen compounds on the biological decomposition of polycyclic aromatic hydrocarbons. The negative impact of excessive biostimulation on the biodegradation efficiency and metabolic activity of microorganisms is also proven. Low resistance to changes in the supply of nitrogen compounds is demonstrated among the orders Xanthomonadales, Burkholderiales, Sphingomonadales, Flavobacteriales, and Sphingobacteriales. It is proven that quantitative analysis of the order of Rhizobiales, characterized by a high-predicted potential for the decomposition of polycyclic aromatic hydrocarbons, may be helpful during biostimulation optimization processes in areas with a high nitrogen deficiency.

Petroleum-contaminated soil: environmental occurrence and remediation strategies

Soil is an environmental matrix that carries life for all living things. With the rise of human activities and the acceleration of population, the soil has been exposed in part to pollution by the discharge of various xenobiotics and persistent pollutants into it. The disposal of toxic substances such as polycyclic aromatic hydrocarbons (PAHs) alters soil properties, affects microbial biodiversity, and damages objects. Considering the mutagenicity, carcinogenicity, and toxicity of petroleum hydrocarbons, the restoration and clean-up of PAH-polluted sites represents an important technological and environmental challenge for sustainable growth and development. Though several treatment methods to remediate PAH-polluted soils exist, interesting bacteria, fungi, and their enzymes receive considerable attention. The aim of the present review is to discuss PAHs' impact on soil properties. Also, this review illustrates physicochemical and biological remediation strategies for treating PAH-contaminated soil. The degradation pathways and contributing factors of microbial PAH-degradation are elucidated. This review also assesses the use of conventional microbial remediation compared to the application of genetically engineered microorganisms (GEM) that can provide a cost-effective and eco-friendly PAH-bioremediation strategy.

Synergetic effects of microbial-phytoremediation reshape microbial communities and improve degradation of petroleum contaminants

Microbial-phytoremediation is an effective bioremediation technology that introduces petroleum-degrading bacteria and oil-tolerant plants into oil-contaminated soils in order to achieve effective degradation of total petroleum hydrocarbons (TPH). In this work, natural attenuation (NA), microbial remediation (MR, using Acinetobacter sp. Tust-DM21), phytoremediation (PR, using Suaeda glauca), and microbial-phytoremediation (MPR, using both species) were utilized to degrade petroleum hydrocarbons. We evaluated four different biological treatments, assessing TPH degradation rates, soil enzyme activities, and the structure of microbial community in the petroleum-contaminated soil. This finding revealed that the roots of Suaeda glauca adsorbed small amounts of polycyclic aromatic hydrocarbons, causing the structure of soil microbiota community to reshape. The abundance of petroleum-degrading bacteria and plant growth-promoting rhizobacteria (PGPR) has increased, as has microbial diversity. According to correlation research, these genera increased soil enzyme activity, boosted the number of degradation-functional genes in the petroleum hydrocarbon degradation pathway, and accelerated the dissipation and degradation of TPH in petroleum-contaminated soil. This evidence contributes to a better understanding of the mechanisms involved in the combined microbial-phytoremediation strategies for contaminated soil, specifically the interaction between microflora and plants in co-remediation and the effects on the structural reshaping of rhizosphere microbial communities.

Spatial clustering and source-specific risk of combined pollutants in soils from an industrial area in Shanxi Province, China

Heavy metal (loid)s (HMs) and polycyclic aromatic hydrocarbons (PAHs) in soils from a typical industrial county of Shanxi were synchronously measured to determine the spatial clustering of combined HMs and PAHs pollution, and the resulting source-specific health risks. The spatial interaction of HMs and PAHs was determined by the Moran's I index, and a bivariate local indicators of spatial association (LISA) analysis showed that the high HMs-high PAHs clusters were mainly distributed in Fencheng and Xijia towns, as well as the main urban areas of Xiangfen County. The spatial clusters of high naphthalene (Nap)-high HMs were more obvious than those of high benzo(a)pyrene (Bap)-high HMs. Based on positive matrix factorization (PMF), four sources were identified for both HMs and PAHs, with coal consumption and industrial emission identified as common sources of both pollutants. The source-oriented health risk was determined using an improved health risk assessment model. The cancer risk from the combined pollution industrial emissions was relatively serious for both adults and children, with the risk value exceeding 10^-6. Therefore, special attention should be paid to emission control. Based on spatial clustering and source-specific health risk assessment, the largest risk areas and pollutant sources were in the main urban areas of Fencheng and Xijia towns. The spatial interaction patterns and source-specific HMs and PAHs pollution concentrations provide a basis for effective pollution management and control. Finally, a systematic framework for reference was proposed for risk area identification and analysis of the source-oriented health risks of combined HMs and PAHs pollution.

Bioremediation of PAHs and heavy metals co-contaminated soils: Challenges and enhancement strategies

Systemic studies on the bioremediation of co-contaminated PAHs and heavy metals are lacking, and this paper provides an in-depth review on the topic. The released sources and transport of co-contaminated PAHs and heavy metals, including their co-occurrence through formation of cation-π interactions and their adsorption in soil are examined. Moreover, it is investigated that co-contamination of PAHs and heavy metals can drive a synergistic positive influence on bioremediation through enhanced secretion of extracellular polymeric substances (EPSs), production of biosynthetic genes, organic acid and enzymatic proliferation. However, PAHs molecular structure, PAHs-heavy metals bioavailability and their interactive cytotoxic effects on microorganisms can exert a challenging influence on the bioremediation under co-contaminated conditions. The fluctuations in bioavailability for microorganisms are associated with soil properties, chemical coordinative interactions, and biological activities under the co-contaminated PAHs-heavy metals conditions. The interactive cytotoxicity caused by the emergence of co-contaminants includes microbial cell disruption, denaturation of DNA and protein structure, and deregulation of antioxidant biological molecules. Finally, this paper presents the emerging strategies to overcome the bioavailability problems and recommends the use of biostimulation and bioaugmentation along with the microbial immobilization for enhanced bioremediation of PAHs-heavy metals co-contaminated sites. Better knowledge of the bioremediation potential is imperative to improve the use of these approaches for the sustainable and cost-effective remediation of PAHs and heavy metals co-contamination in the near future.

Structural Selectivity of PAH Removal Processes in Soil, and the Effect of Metal Co-Contaminants

Polycyclic aromatic hydrocarbons (PAHs) form a convenient structural series of molecules with which to examine the selectivity exerted on their removal by soil microbiota. It is known that there is an inverse relationship between PAH molecular size and degradation rates in soil. In this paper, we look at how the magnitude of the slope for this relationship, m, can be used as an indicator of the effect of metal co-contaminants on degradation rates across a range of PAH molecular weights. The analysis utilises data collected from our previous microcosm study (Deary, M.E.; Ekumankama, C.C.; Cummings, S.P. Development of a novel kinetic model for the analysis of PAH biodegradation in the presence of lead and cadmium co-contaminants. Journal of Hazard Materials 2016, 307, 240–252) in which we followed the degradation of the 16 US EPA PAHs over 40 weeks in soil microcosms taken from a high organic matter content woodland soil. The soil was amended with a PAH mixture (total concentration of 2166 mg kg−1) and with a range of metal co-contaminant concentrations (lead, up to 782 mg kg−1; cadmium up to 620 mg kg−1; and mercury up to 1150 mg kg−1). It was found that the magnitude of m increases in relation to the applied concentration of metal co-contaminant, indicating a more adverse effect on microbial communities that participate in the removal of higher molecular weight PAHs. We conclude that m is a useful parameter by which we might measure the differential effects of environmental contaminants on the PAH removal. Such information will be useful in planning and implementing remediation strategies.

Effects of Salinity on the Biodegradation of Polycyclic Aromatic Hydrocarbons in Oilfield Soils Emphasizing Degradation Genes and Soil Enzymes

The biodegradation of organic pollutants is the main pathway for the natural dissipation and anthropogenic remediation of polycyclic aromatic hydrocarbons (PAHs) in the environment. However, in the saline soils, the PAH biodegradation could be influenced by soil salts through altering the structures of microbial communities and physiological metabolism of degradation bacteria. In the worldwide, soils from oilfields are commonly threated by both soil salinity and PAH contamination, while the influence mechanism of soil salinity on PAH biodegradation were still unclear, especially the shifts of degradation genes and soil enzyme activities. In order to explain the responses of soils and bacterial communities, analysis was conducted including soil properties, structures of bacterial community, PAH degradation genes and soil enzyme activities during a biodegradation process of PAHs in oilfield soils. The results showed that, though low soil salinity (1% NaCl, w/w) could slightly increase PAH degradation rate, the biodegradation in high salt condition (3% NaCl, w/w) were restrained significantly. The higher the soil salinity, the lower the bacterial community diversity, copy number of degradation gene and soil enzyme activity, which could be the reason for reductions of degradation rates in saline soils. Analysis of bacterial community structure showed that, the additions of NaCl increase the abundance of salt-tolerant and halophilic genera, especially in high salt treatments where the halophilic genera dominant, such as Acinetobacter and Halomonas. Picrust2 and redundancy analysis (RDA) both revealed suppression of PAH degradation genes by soil salts, which meant the decrease of degradation microbes and should be the primary cause of reduction of PAH removal. The soil enzyme activities could be indicators for microorganisms when they are facing adverse environmental conditions.

Enhanced degradation of petroleum hydrocarbons by immobilizing multiple bacteria on wheat bran biochar and its effect on greenhouse gas emission in saline-alkali soil

In this study, an immobilization method for forming and keeping dominant petroleum degradation bacteria was successfully developed by immobilizing Pseudomonas, Acinetobacter, and Sphingobacterium genus bacteria on wheat bran biochar pyrolyzed at 300, 500, and 700 °C. The removal efficiency indicated that the highest TPHs (total petroleum hydrocarbons) removal rate of BC500-4 B (biochar pyrolyzed at 500 °C with four kinds of petroleum bacteria) was 58.31%, which was higher than that of BC500 (36.91%) and 4 B (43.98%) used alone. The soil properties revealed that the application of biochar increased the content of organic matter, available phosphorus, and available potassium, but decreased pH and ammonium nitrogen content in soil. Bacterial community analysis suggested that the formation of dominant degrading community represented by Acinetobacter played key roles in TPHs removal. The removal rate of alkanes was similar to that of TPHs. Besides, biochar and immobilized material can also mediate greenhouse gas emission while removing petroleum, biochar used alone and immobilized all could improve CO₂ emission, but decrease N₂O emission and had no significant impact on CH₄ emission. Furthermore, it was the first time to found the addition of Acinetobacter genus bacteria can accelerate the process of forming a dominant degrading community in wheat bran biochar consortium. This study focused on controlling greenhouse gas emission which provides a wider application of combining biochar and bacteria in petroleum soil remediation.

Genomic insights into Pseudoalteromonas sp. JSTW coping with petroleum-heavy metals combined pollution

Worldwide marine compound contamination by petroleum products and heavy metals is a burgeoning environmental concern. Pseudoalteromonas, prevalently distributed in marine environment, has been proven to degrade petroleum and plays an essential role in the fate of oil pollution under the combined pollution. Nevertheless, the research on the reference genes is still incomplete. Therefore, this study aims to thoroughly investigate the reference genes represented by Pseudoalteromonas sp. JSTW via whole-genome sequencing. Next-generation sequencing technology unfolded a genome of 4,026,258 bp, database including Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were utilized to annotate the genes and metabolic pathways conferring to petroleum hydrocarbon degradation. The results show that common alkane and aromatic hydrocarbon degradation genes (alkB, ligB, yqhD, and ladA), chemotaxis gene (MCP, cheA, cheB, pcaY, and pcaR), heavy-metal resistance, and biofilm genes (σ54, merC, pcoA, copB, etc.) were observed in whole-genome sequence (WGS) of JSTW, which indicated that strain JSTW could potentially cope with combined pollution. The degradation efficiency of naphthalene in 60 h by JSTW was 99% without Cu²⁺ and 67% with 400 mg L^-1 Cu²⁺ . Comparative genome analysis revealed that genomes of Pseudoalteromonas lipolytica strain LEMB 39 and Pseudoalteromonas donghaensis strain HJ51 shared similarity with strain JSTW, suggesting they are also the potential degradater of petroleum hydrocarbons under combined pollution. Therefore, this study provides a WGS annotation and reveals the mechanism of response to combined pollution of Pseudoalteromonas sp. JSTW.

Aerobic and Anaerobic Bacterial and Fungal Degradation of Pyrene: Mechanism Pathway Including Biochemical Reaction and Catabolic Genes

Microbial biodegradation is one of the acceptable technologies to remediate and control the pollution by polycyclic aromatic hydrocarbon (PAH). Several bacteria, fungi, and cyanobacteria strains have been isolated and used for bioremediation purpose. This review paper is intended to provide key information on the various steps and actors involved in the bacterial and fungal aerobic and anaerobic degradation of pyrene, a high molecular weight PAH, including catabolic genes and enzymes, in order to expand our understanding on pyrene degradation. The aerobic degradation pathway by Mycobacterium vanbaalenii PRY-1 and Mycobactetrium sp. KMS and the anaerobic one, by the facultative bacteria anaerobe Pseudomonas sp. JP1 and Klebsiella sp. LZ6 are reviewed and presented, to describe the complete and integrated degradation mechanism pathway of pyrene. The different microbial strains with the ability to degrade pyrene are listed, and the degradation of pyrene by consortium is also discussed. The future studies on the anaerobic degradation of pyrene would be a great initiative to understand and address the degradation mechanism pathway, since, although some strains are identified to degrade pyrene in reduced or total absence of oxygen, the degradation pathway of more than 90% remains unclear and incomplete. Additionally, the present review recommends the use of the combination of various strains of anaerobic fungi and a fungi consortium and anaerobic bacteria to achieve maximum efficiency of the pyrene biodegradation mechanism.

Effect of biostimulation and bioaugmentation on hydrocarbon degradation and detoxification of diesel-contaminated soil: a microcosm study

Soil contamination with diesel oil is quite common during processes of transport and storage. Bioremediation is considered a safe, economical, and environmentally friendly approach for contaminated soil treatment. In this context, studies using hydrocarbon bioremediation have focused on total petroleum hydrocarbon (TPH) analysis to assess process effectiveness, while ecotoxicity has been neglected. Thus, this study aimed to select a microbial consortium capable of detoxifying diesel oil and apply this consortium to the bioremediation of soil contaminated with this environmental pollutant through different bioremediation approaches. Gas chromatography (GC-FID) was used to analyze diesel oil degradation, while ecotoxicological bioassays with the bioindicators Artemia sp., Aliivibrio fischeri (Microtox), and Cucumis sativus were used to assess detoxification. After 90 days of bioremediation, we found that the biostimulation and biostimulation/bioaugmentation approaches showed higher rates of diesel oil degradation in relation to natural attenuation (41.9 and 26.7%, respectively). Phytotoxicity increased in the biostimulation and biostimulation/bioaugmentation treatments during the degradation process, whereas in the Microtox test, the toxicity was the same in these treatments as that in the natural attenuation treatment. In both the phytotoxicity and Microtox tests, bioaugmentation treatment showed lower toxicity. However, compared with natural attenuation, this approach did not show satisfactory hydrocarbon degradation. Based on the microcosm experiments results, we conclude that a broader analysis of the success of bioremediation requires the performance of toxicity bioassays.

Response of soil bacterial communities to high petroleum content in the absence of remediation procedures

Oil spills are events that frequently lead to petroleum pollution. This pollution may cause stress to microbial communities, which require long adaption periods. Soil petroleum pollution is currently considered one of the most serious environmental problems. In the present work, processes occurring in the bacterial communities of three soil samples with different physicochemical characteristics, artificially polluted with 12% of crude oil, were investigated in 120-day laboratory experiment. It was found that the total petroleum hydrocarbon content did not decrease during this time; however, the proportion of petroleum fractions was altered. Petroleum pollution led to a short-term decrease in the bacterial 16S rRNA gene copy number. On the basis of amplicon sequencing analysis, it was concluded that bacterial community successions were similar in the three soils investigated. Thus, the phyla Actinobacteria and Proteobacteria and candidate TM7 phylum (Saccaribacteria) were predominant with relative abundances ranging from 35 to 58%, 25 to 30%, and 15 to 35% in different samples, respectively. The predominant operational taxonomic units (OTUs) after pollution belonged to the genera Rhodococcus and Mycobacterium, families Nocardioidaceae and Sinobacteraceae, and candidate class ТМ7-3. Genes from the alkIII group encoding monoxygenases were the most abundant compared with other catabolic genes from the alkI, alkII, GN-PAH, and GP-PAH groups, and their copy number significantly increased after pollution. The copy numbers of expressed genes involved in the horizontal transfer of catabolic genes, FlgC, TraG, and OmpF, also increased after pollution by 11-33, 16-63, and 11-71 times, respectively. The bacterial community structure after a high level of petroleum pollution changed because of proliferation of the cells that initially were able to decompose hydrocarbons, and in the second place, because proliferation of the cells that received these catabolic genes through horizontal transfer.

Bacterial community response to petroleum contamination in brackish tidal marsh sediments in the Yangtze River Estuary, China

The brackish tidal marsh in the Baimaosha area of the Yangtze River Estuary was severely contaminated by 400 tons of heavy crude petroleum from a tanker that sank in December 2012. The spill accident led to severe environmental damage owing to its high toxicity, persistence and wide distribution. Microbial communities play vital roles in petroleum degradation in marsh sediments. Therefore, taxonomic analysis, high-throughput sequencing and 16S rRNA functional prediction were used to analyze the structure and function of microbial communities among uncontaminated (CK), lightly polluted (LP), heavily polluted (HP), and treated (TD) sediments. The bacterial communities responded with increased richness and decreased diversity when exposed to petroleum contamination. The dominant class changed from Deltaproteobacteria to Gammaproteobacteria after petroleum contamination. The phylum Firmicutes increased dramatically in oil-enriched sediment by 75.78%, 346.19% and 267.26% in LP, HP and TD, respectively. One of the suspected oil-degrading genera, Dechloromonas, increased the most in oil-contaminated sediment, by 540.54%, 711.27% and 656.78% in LP, HP and TD, respectively. Spore protease, quinate dehydrogenase (quinone) and glutathione-independent formaldehyde dehydrogenase, three types of identified enzymes, increased enormously with the increasing petroleum concentration. In conclusion, petroleum contamination altered the community composition and microorganism structure, and promoted some bacteria to produce the corresponding degrading enzymes. Additionally, the suspected petroleum-degrading genera should be considered when restoring oil-contaminated sediment.

The relationship between culturable doxycycline-resistant bacterial communities and antibiotic resistance gene hosts in pig farm wastewater treatment plants

Pig farm wastewater treatment plants (WWTPs) are an important repository for resistant bacterial communities (RBCs) and antibiotic resistance genes (ARGs). However, the relationship between RBCs and ARG hosts has not been well characterized. In this study, water samples from influent and effluent from five pig farm WWTPs were collected. Gradient concentrations of doxycycline (DOX) were used to screen the culturable RBCs. The abundance of 21 subtypes of ARGs and the bacterial community were investigated. This study detected a large number of culturable DOX-RBCs and ARGs in the influent and effluent of pig farm WWTPs. The abundances of ARGs and RBCs in all effluent samples was significantly lower than that in the influent samples (P < 0.05), which indicated that the WWTPs can effectively remove most ARGs and RBCs in pig farm wastewater. The main potential culturable RBCs in pig farm wastewater were the dominant bacteria Proteobacteria, Actinobacteria, Pseudomonas, and Rheinheimera. However, most of the ARGs were mainly present in Bacteroidetes, Actinobacteria, Corynebacteriaceae, Macellibacteroides, Acinetobacter, and Enterobacteriaceae, which are considered potential ARG hosts. The results presented here showed that there were obvious differences between the species of culturable DOX-RBCs and ARG hosts in the pig farm WWTPs, which may be due to various environmental factors. This highlights the urgent need for further research on the relationship between RBCs and ARG hosts.

Alterations in the Gut Microbiota of Zebrafish (Danio rerio) in Response to Water-Soluble Crude Oil Components and Its Mixture With a Chemical Dispersant

Crude oil spills have caused substantial impacts to aquatic ecosystems. Chemical dispersants are used to palliate the impact of oil spillages, but their use is polemic due to their additional potential toxic effect when mixed with oil-derived components. In this work, we used a 16S-based metagenomic approach to analyze the changes of the gut microbiota of adult zebrafish (Danio rerio) exposed to the water accommodated fraction (WAF) of a light crude oil (35° API gravity), and the chemically enhanced WAF (CEWAF), prepared with Nokomis 3-F4® dispersant. After 96 h of exposure, WAF induced an increase in the alpha and beta diversity, altering the relative abundance of Vibrio, Flavobacterium, and Novosphingobium. In contrast, CEWAF only caused an increase in the beta diversity, and an enrichment of the genus Pseudomona. Both treatments diminished the abundances of Aeromonas, Cetobacterium, Coxiella, Dinghuibacter, and Paucibacter. Moreover, the co-occurrence network among genera was more complex in WAF than in CEWAF, indicating a greater bacterial interaction in response to WAF. Our results indicate that short-term exposure to WAF and CEWAF can induce a dysbiosis in the gut microbiota of D. rerio, but these changes are specific in each treatment.

Effects of chronic exposure to water accommodated fraction (WAF) of light crude oil on gut microbiota composition of the lined sole (Achirus lineatus)

Exposure of marine fish to hydrocarbon compounds from crude oil can cause physiological and ecological alterations that can result in several cytotoxic, genotoxic, and teratogenic damages. One consequence of this exposure is the dysbiosis of the gut microbiota, where the normal bacterial composition is modified. Herein, we assessed the effect of the exposure to water accommodated fraction (WAF) of a light crude oil into the gut microbiota of a native species, the lined sole Achirus lineatus, a benthonic fish widely distributed in the Gulf of Mexico (GoM). We performed a chronic bioassay using two WAF concentrations (5 and 10% v/v), collecting lined sole entire gastrointestinal tracts for microbiota analyses at two timepoints, 14 and 28 days. Changes in the gut microbiota composition were determined by high throughput amplicon sequencing of the gene 16S rRNA. Diversity analyses showed that WAF exposure produced similar changes in the microbiota composition at both concentrations. Metagenomic functional prediction showed that these alterations could result in a shift in the gut redox status, towards a more anoxygenic environment. Enrichment of bacteria capable of use hydrocarbon as carbon source seems to be fast regardless time of exposure or WAF concentrations. Our results suggest that chronic WAF exposure can cause a dysbiosis in this benthic native species from the GoM.

Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil

Our objective was to study the bacterial community changes that determine enhanced removal of petroleum hydrocarbons from soils subjected to bioaugmentation with the hydrocarbon-degrading strains Rhodococcus erythropolis CD 130, CD 167, and their combination. To achieve this, a high-throughput sequencing of the 16S rRNA gene was performed. The changes in the bacterial community composition were most apparent the day after bacterial inoculation. These changes represented an increase in the percentage abundance of Rhodococcus and Pseudomonas genera. Surprisingly, members of the Rhodococcus genus were not present after day 91. At the end of the experiment, the bacterial communities from the CD 130, CD 167, and control soils had a similar structure. Nevertheless, the composition of the bacteria in the CD 130 + CD 167 soil was still distinct from the control. Metagenomic predictions from the 16S rRNA gene sequences showed that the introduction of bacteria had a significant influence on the predicted pathways (metabolism of xenobiotics, lipids, terpenoids, polyketides, and amino acids) on day one. On day 182, differences in the abundance of functional pathways were also detected in the CD 130 and CD 130 + CD 167 soils. Additionally, we observed that on day one, in all bioaugmented soils, the alkH gene was mainly contributed by the Rhodococcus and Mycobacterium genera, whereas in non-treated soil, this gene was contributed only by the Mycobacterium genus. Interestingly, from day 91, the Mycobacterium genus was the main contributor for the tested genes in all studied soils. Our results showed that hydrocarbon depletion from the analyzed soils resulted from the activity of the autochthonous bacteria. However, these changes in the composition and function of the indigenous bacterial community occurred under the influence of the introduced bacteria.

Fungal bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals

Abstract

Much research has been carried out on the bacterial bioremediation of soil contaminated with petroleum hydrocarbons and toxic metals but much less is known about the potential of fungi in sites that are co-contaminated with both classes of pollutants. This article documents the roles of fungi in soil polluted with both petroleum hydrocarbons and toxic metals as well as the mechanisms involved in the biotransformation of such substances. Soil characteristics (e.g., structural components, pH, and temperature) and intracellular or excreted extracellular enzymes and metabolites are crucial factors which affect the efficiency of combined pollutant transformations. At present, bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals is mostly focused on the removal, detoxification, or degradation efficiency of single or composite pollutants of each type. Little research has been carried out on the metabolism of fungi in response to complex pollutant stress. To overcome current bottlenecks in understanding fungal bioremediation, the potential of new approaches, e.g., gradient diffusion film technology (DGT) and metabolomics, is also discussed.

Key points

• Fungi play important roles in soil co-contaminated with TPH and toxic metals.

• Soil characteristics, enzymes, and metabolites are major factors in bioremediation.

• DGT and metabolomics can be applied to overcome current bottlenecks.

Biodegradation of Total Petroleum Hydrocarbons in Soil: Isolation and Characterization of Bacterial Strains from Oil Contaminated Soil

In this study, we isolated seven strains (termed BY1–7) from polluted soil at an oil station and evaluated their abilities to degrade total petroleum hydrocarbons (TPHs). Following 16 rRNA sequence analysis, the strains were identified as belonging to the genera Bacillus, Acinetobacter, Sphingobium, Rhodococcus, and Pseudomonas, respectively. Growth characterization studies indicated that the optimal growth conditions for the majority of the strains was at 30 °C, with a pH value of approximately 7. Under these conditions, the strains showed a high TPH removal efficiency (50%) after incubation in beef extract peptone medium for seven days. Additionally, we investigated the effect of different growth media on growth impact factors that could potentially affect the strains’ biodegradation rates. Our results suggest a potential application for these strains to facilitate the biodegradation of TPH-contaminated soil.

A Rapid and High Throughput MIC Determination Method to Screen Uranium Resistant Microorganisms

The assessment of minimum inhibitory concentration (MIC) is a conventional technique used for the screening of microbial resistance against antibiotics, biocides, and contaminants such as heavy metals. However, as part of our ongoing work, we have observed biases associated with using traditional liquid MIC method to screen microbial heavy metal resistance, including both bacterial and fungal strains. Specifically, the addition of uranium into synthetic media causes immediate precipitation prior to the initiation of microbial growth, thus hampering the optical density measurements, and the obtained MIC values are thus flawed and inaccurate. To address this discrepancy, we report the optimization and development of a serial-dilution-based MIC method conducted on solid growth media supplemented with uranium, which is more accurate, relative to the testing of MICs performed in liquid cultures. Notably, we report on the efficacy of this method to screen not only bacteria that are resistant to uranium but also demonstrate the successful application to yeast and fungal isolates, for their ability to resist uranium, is more accurate and sensitive relative to the liquid method. We believe that this newly developed method to screen heavy metal resistance, such as uranium, is far superior to the existing liquid MIC method and propose replacing the liquid assay with the solid plate MIC reported herein.

Heavy Metals as a Factor Increasing the Functional Genetic Potential of Bacterial Community for Polycyclic Aromatic Hydrocarbon Biodegradation

The bioremediation of areas contaminated with hydrocarbon compounds and heavy metals is challenging due to the synergistic toxic effects of these contaminants. On the other hand, the phenomenon of the induction of microbial secretion of exopolysaccharides (EPS) under the influence of heavy metals may contribute to affect the interaction between hydrophobic hydrocarbons and microbial cells, thus increasing the bioavailability of hydrophobic organic pollutants. The purpose of this study was to analyze the impact of heavy metals on the changes in the metapopulation structure of an environmental consortium, with particular emphasis on the number of copies of orthologous genes involved in exopolysaccharide synthesis pathways and the biodegradation of hydrocarbons. The results of the experiment confirmed that the presence of heavy metals at concentrations of 50 mg·L^-1 and 150 mg·L^-1 resulted in a decrease in the metabolic activity of the microbial consortium and its biodiversity. Despite this, an increase in the biological degradation rate of polycyclic aromatic hydrocarbons was noted of 17.9% and 16.9%, respectively. An assessment of the estimated number of genes crucial for EPS synthesis and biodegradation of polycyclic aromatic hydrocarbons confirmed the relationship between the activation of EPS synthesis pathways and polyaromatic hydrocarbon biodegradation pathways. It was established that microorganisms that belong to the Burkholderiales order are characterized by a high representation of the analyzed orthologs and high application potential in areas contaminated with heavy metals and hydrocarbons.

Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures

The aim of the present study was to reveal how different microbial communities evolve in diesel fuel/crude oil-contaminated environments under aerobic and microaerobic conditions. To investigate this question, aerobic and microaerobic bacterial enrichments amended with a diesel fuel/crude oil mixture were established and analysed. The representative aerobic enrichment community was dominated by Gammaproteobacteria (64.5%) with high an abundance of Betaproteobacteriales (36.5%), followed by Alphaproteobacteria (8.7%), Actinobacteria (5.6%), and Candidatus Saccharibacteria (4.5%). The most abundant alkane monooxygenase (alkB) genotypes in this enrichment could be linked to members of the genus Rhodococcus and to a novel Gammaproteobacterium, for which we generated a high-quality draft genome using genome-resolved metagenomics of the enrichment culture. Contrarily, in the microaerobic enrichment, Gammaproteobacteria (99%) overwhelmingly dominated the microbial community with a high abundance of the genera Acinetobacter (66.3%), Pseudomonas (11%) and Acidovorax (11%). Under microaerobic conditions, the vast majority of alkB gene sequences could be linked to Pseudomonas veronii. Consequently, results shed light on the fact that the excellent aliphatic hydrocarbon degrading Rhodococcus species favour clear aerobic conditions, while oxygen-limited conditions can facilitate the high abundance of Acinetobacter species in aliphatic hydrocarbon-contaminated subsurface environments.