Preparation of petroleum-degrading bacterial agent and its application in remediation of contaminated soil in Shengli Oil Field, China

Assembly and functional profile of rhizosphere microbial community during the Salix viminalis-AMF remediation of polycyclic aromatic hydrocarbon polluted soils

Arbuscular mycorrhizal fungi (AMF) are positive to the phytoremediation by improving plant biomass and soil properties. However, the role of AM plants to the remediation of polycyclic aromatic hydrocarbons (PAHs) is yet to be widely recognized, and the impact of AM plants to indigenous microbial communities during remediation remains unclear. In this work, a 90-day study was conducted to assess the effect of AMF-Salix viminalis on the removal of PAHs, and explore the impact to the microbial community composition, abundance, and function. Results showed that AMF-Salix viminalis effectively enhanced the removal of benzo[a]pyrene, and enriched more PAH-degrading bacteria, consisting of Actinobacteria, Chloroflexi, Sphingomonas, and Stenotrophobacter, as well as fungi including Basidiomycota, Pseudogymnoascus, and Tomentella. For gene function, AM willow enhanced the enrichment of genes involved in amino acid synthesis, aminoacyl-tRNA biosynthesis, and cysteine and methionine metabolism pathways. F. mosseae inoculation had a greater effect on alpha- and beta-diversity of microbial genes at 90 d. Additionally, AMF inoculation significantly increased the soil microbial biomass carbon and organic matter concentration. All together, the microbial community assembly and function shaped by AM willow promoted the dissipation of PAHs. Our results support the effectiveness of AM remediation and contribute to reveal the enhancing-remediation mechanism to PAHs using multi-omics data.

Chemodiversity of soil organic matters determines biodegradation of polychlorinated biphenyls by a graphene oxide-assisted bacterial agent

A promising strategy for degrading persistent organic pollutants (POPs) in soil is amendment with nanomaterial-assisted functional bacteria. However, the influence of soil organic matter chemodiversity on the performance of nanomaterial-assisted bacterial agents remains unclear. Herein, different types of soil (Mollisol soil, MS; Ultisol soil, US; and Inceptisol soil, IS) were inoculated with a graphene oxide (GO)-assisted bacterial agent (Bradyrhizobium diazoefficiens USDA 110, B. diazoefficiens USDA 110) to investigate the association between soil organic matter chemodiversity and stimulation of polychlorinated biphenyl (PCB) degradation. Results indicated that the high-aromatic solid organic matter (SOM) inhibited PCB bioavailability, and lignin-dominant dissolved organic matter (DOM) with high biotransformation potential was a favored substrate for all PCB degraders, which led to no stimulation of PCB degradation in MS. Differently, high-aliphatic SOM in US and IS promoted PCB bioavailability. The high/low biotransformation potential of multiple DOM components (e.g., lignin, condensed hydrocarbon, unsaturated hydrocarbon, etc.) in US/IS further resulted to the enhanced PCB degradation by B. diazoefficiens USDA 110 (up to 30.34%) /all PCB degraders (up to 17.65%), respectively. Overall, the category and biotransformation potential of DOM components and the aromaticity of SOM collaboratively determine the stimulation of GO-assisted bacterial agent on PCB degradation.

Comparative genomic analysis provides insight into the phylogeny and potential mechanisms of adaptive evolution of Sphingobacterium sp. CZ-2

Sphingobacterium is a class of Gram-negative, non-fermentative bacilli that have received widespread attention due to their broad ecological distribution and oil degradation ability, but are rarely involved in infections. In this manuscript, a novel Sphingobacterium strain isolated from wildfire-infected tobacco leaves was named Sphingobacterium sp. CZ-2. NGS and TGS sequencing results showed a whole genome of 3.92 Mb with 40.68 mol% GC content and containing 3,462 protein-coding genes, 9 rRNA-coding genes and 50 tRNA-coding genes. Phylogenetic analysis, ANI and dDDH calculations all supported that Sphingobacterium sp. CZ-2 represented a novel species of the genus Sphingobacterium. Analysis of the specific genes of Sphingobacterium sp. CZ-2 by comparative genomics revealed that metal transport proteins encoded by the troD and cusA genes could maintain the balance of heavy metal ion concentrations in the internal environment of bacteria and avoid heavy metal toxicity while meeting the needs of growth and reproduction, and transport proteins encoded by the malG gene could keep nutrients required for the survival of bacteria. Synteny and genome evolutionary analyses of Sphingobacterium strains implicated that the gene family contraction as a major process in genome evolution, with insertional sequences leading to mutations, deletions and reversals of genes that help bacteria to withstand complex environmental changes. Complete genome sequencing and systematic comparative genomic analysis will contribute new insights into the adaptive evolution of this novel species and the genus Sphingobacterium.

In situ bioremediation of petroleum hydrocarbon–contaminated soil: isolation and application of a Rhodococcus strain

Due to low consumption and high efficiency, in situ microbial remediation of petroleum hydrocarbons (PHs)-contaminated sites in in-service petrochemical enterprises has attracted more and more attention. In this study, a degrading strain was isolated from oil depot-contaminated soil with soil extract (PHs) as the sole carbon source, identified and named Rhodococcus sp. OBD-3. Strain OBD-3 exhibited wide adaptability and degradability over a wide range of temperatures (15-37 °C), pH (6.0-9.0), and salinities (1-7% NaCl) to degrade 60.6-86.6% of PHs. Under extreme conditions (15 °C and 3-7% salinity), PHs were degraded by 60.6 ± 8.2% and more than 82.1% respectively. In OBD-3, the alkane monooxygenase genes alkB1 and alkB2 (GenBank accession numbers: MZ688386 and MZ688387) were found, which belonged to Rhodococcus by sequence alignment. Moreover, strain OBD-3 was used in lab scale remediation in which the contaminated soil with OBD-3 was isolated as the remediation object. The PHs were removed at 2,809 ± 597 mg/kg within 2 months, and the relative abundances of Sphingobium and Pseudomonas in soil increased more than fivefold. This study not only established a system for the isolation and identification of indigenous degrading strains that could efficiently degrade pollutants in the isolated environment but also enabled the isolated degrading strains to have potential application prospects in the in situ bioremediation of PHs-contaminated soils.

Design of a Microbial Remediation Inoculation Program for Petroleum Hydrocarbon Contaminated Sites Based on Degradation Pathways

This paper analyzed the degradation pathways of petroleum hydrocarbon degradation bacteria, screened the main degradation pathways, and found the petroleum hydrocarbon degradation enzymes corresponding to each step of the degradation pathway. Through the Copeland method, the best inoculation program of petroleum hydrocarbon degradation bacteria in a polluted site was selected as follows: single oxygenation path was dominated by Streptomyces avermitilis, hydroxylation path was dominated by Methylosinus trichosporium OB3b, secondary oxygenation path was dominated by Pseudomonas aeruginosa, secondary hydroxylation path was dominated by Methylococcus capsulatus, double oxygenation path was dominated by Acinetobacter baylyi ADP1, hydrolysis path was dominated by Rhodococcus erythropolis, and CoA path was dominated by Geobacter metallireducens GS-15 to repair petroleum hydrocarbon contaminated sites. The Copeland method score for this solution is 22, which is the highest among the 375 solutions designed in this paper, indicating that it has the best degradation effect. Meanwhile, we verified its effect by the Cdocker method, and the Cdocker energy of this solution is −285.811 kcal/mol, which has the highest absolute value. Among the inoculation programs of the top 13 petroleum hydrocarbon degradation bacteria, the effect of the best inoculation program of petroleum hydrocarbon degradation bacteria was 18% higher than that of the 13th group, verifying that this solution has the best overall degradation effect. The inoculation program of petroleum hydrocarbon degradation bacteria designed in this paper considered the main pathways of petroleum hydrocarbon pollutant degradation, especially highlighting the degradability of petroleum hydrocarbon intermediate degradation products, and enriching the theoretical program of microbial remediation of petroleum hydrocarbon contaminated sites.

Study on the treatment of oily sludge in oil fields with lipopeptide/sophorolipid complex bio-surfactant

A systematic study had been carried out to get insight into the micellar behavior of anionic lipopeptide (LT) and nonionic sophorolipid (SL) in their different mass ratio mixed state using the technique of tensiometry. The models proposed by Clint, Rubingh and Gibbs et al. had been employed to interpret the formation of mixed micelles and found out synergism. The obtained experimental critical micelle concentrations (CMC) were lower than the ideal CMCs, indicating negative deviation from ideal behavior for all multi-component mixed micelles formation. A suited binary bio-surfactant mixing system was selected as the washing agents to treat the oily sludge produced from Huabei oilfield by the thermal bio-surfactant washing method. The results showed that in case of the mass ratios of 8:2 the CMC was dramatically decreased and synergism was the strongest in LT and SL bi mixed surfactant systems. The studied binary mixed bio-surfactant system showed higher washing efficiency for oily sludge than single surfactant system. In addition, the washing power of binary mixed bio-surfactants towards oily sludge was the best at below washing conditions: (a) the concentration of the mixed system (100 mg/L), (b) temperature (55 ℃), (c) ratio of sludge/liquid (1:3), (d) washing time (3 h), and (e) stirring speed (300 rpm). Certainly, the washing abilities of the selected surfactants not only depend on their mixing ratio and washing conditions but also associate with microstructure and mineral components of oily sludge.

Sphingomonas corticis sp. nov., and Sphingobacterium corticibacterium sp. nov., from bark canker

Two Gram-stain-negative, aerobic, non-motile bacterial strains, 36D10-4-7^T and 30C10-4-7^T, were isolated from bark canker tissue of Populus × euramericana, respectively. 16S rRNA gene sequence analysis revealed that strain 36D10-4-7^T shows 98.0 % sequence similarity to Sphingomonas adhaesiva DSM 7418^T, and strain 30C10-4-7^T shows highest sequence similarity to Sphingobacterium arenae H-12^T (95.6 %). Average nucleotide identity analysis indicates that strain 36D10-4-7^T is a novel member different from recognized species in the genus Sphingomonas. The main fatty acids and respiratory quinone detected in strain 36D10-4-7^T are C_18 : 1  ω7c and/or C_18 : 1  ω6c and Q-10, respectively. The polar lipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, aminolipid, phosphatidylethanolamine, sphingoglycolipid, two uncharacterized phospholipids and two uncharacterized lipids. For strain 30C10-4-7^T, the major fatty acids and menaquinone are iso-C_15 : 0, C_16 : 1  ω7c and/or C_16 : 1  ω6c and iso-C_17 : 0 3-OH and MK-7, respectively. The polar lipid profile includes phosphatidylethanolamine, phospholipids, two aminophospholipids and six unidentified lipids. Based on phenotypic and genotypic characteristics, these two strains represent two novel species within the genera Sphingomonas and Sphingobacterium. The name Sphingomonas corticis sp. nov. (type strain 36D10-4-7^T=CFCC 13112^T=KCTC 52799^T) and Sphingobacterium corticibacterium sp. nov. (type strain 30C10-4-7^T=CFCC 13069^T=KCTC 52797^T) are proposed.

Characterization of hexaconazole-degrading strain Sphingobacterium multivorum and analysis of transcriptome for biodegradation mechanism

Hexaconazole is a triazole fungicide, which is stable and difficult to degrade in the environment. The existence of hexaconazole could pose a certain risk to the environment and the health of living organisms. In this study, an efficient degradation strain B-3 (Sphingobacterium multivorum) of hexaconazole was isolated from sewage, activated sludge, and soil. The degradation efficiency of hexaconazole can reach 85.6% in 6 days at a temperature of 32.5 °C, pH of 6.31, initial inoculum of 0.4 g L^-1 and initial concentration of hexaconazole of 50 mg L^-1. During degradation, three metabolites (M1: 2-(2, 4-dichlorophenyl)-1-(1H-1, 2, 4-triazol-1-yl) hexane-2, 5-diol; M2: 2-(2, 4-dichlorophenyl) hexane-1, 2-diol; M3: 1H-1, 2, 4-triazole) were identified. Moreover, 45.6% hexaconazole can be degraded in 60 days in natural soil containing B-3. The results of the transcriptome sequencing indicated the presence of 864 differential genes, in which aldehyde dehydrogenase, monooxygenase, RND transporters, and ABC transporters were up-regulated. The generation of 2-(2, 4-dichlorophenyl)-1-(1H-1, 2, 4-triazol-1-yl) hexane-2, 5-diol may be due to the participation of monooxygenase.

Transcriptome profiling reveals the molecular processes for survival of Lysinibacillus fusiformis strain 15-4 in petroleum environments

A bacterial strain designated Lysinibacillus fusiformis 15-4 was isolated from oil-free soil on the Qinghai-Tibet Plateau, which can grow well utilizing petroleum hydrocarbons as a carbon source at a lower temperature. To deeply characterize the molecular adaptations and metabolic processes of this strain when grown in a petroleum-containing environment, transcriptome analysis was performed. A total of 4664 genes and the expression of 3969 genes were observed in strain 15-4. When the strain was grown in petroleum-containing medium, 2192 genes were significantly regulated, of which 1312 (60%) were upregulated and 880 (40%) were downregulated. This strain degraded and adapted to petroleum via modulation of diverse molecular processes, including improvements in transporter activity, oxidoreductase/dehydrogenase activity, two-component system/signal transduction, transcriptional regulation, fatty acid catabolism, amino acid metabolism, and environmental stress responses. Many strain-specific genes were involved in the oxidation of hydrocarbon compounds, such as several luciferase family alkane monooxygenase genes, flavin-utilizing monooxygenase family genes, and flavoprotein-like family alkanesulfonate monooxygenase genes. Several cold shock protein genes were also induced suggesting adaptation to cold environments and the potential for petroleum degradation at low temperatures. The results obtained in this study may broaden our understanding of molecular adaptation of bacteria to hydrocarbon-containing environments and may provide valuable data for further study of L. fusiformis.

Effect of immature and mature compost addition on petroleum contaminated soils composting: kinetics

PURPOSE

The kinetic studies and effect of amendment addition on the performance of the composting process in reduction of total petroleum hydrocarbons (TPH) from petroleum contaminated soils (PCS) were investigated in the present research.

METHODS

Seven composting experiments containing various mixing ratios of PCS to unfinished compost (UC) and finished compost (FC) were set up and operated for 14 weeks. The mixing rations consisted of 1:0 (as control experiment), 1:0.3, 1:0.6, and 1:1. The initial C/N/P and moisture contents of the composting piles were adjusted to 100/5/1 and 50-55%, respectively.

RESULTS

Results showed that 50.09-79.49% of TPH was removed in the composting experiments after 14 weeks. The highest and lowest removal rates were achieved in the ratios of 1:1 and 1:0.3, respectively. Moreover, application of UC as amendments and bulking agent is more efficient than FC. The biodecomposition of TPH was fitted to the first-order kinetic with the half lives and rate constants of 5.63-11.55 days and 0.060-0.123 d^-1, respectively. The bacteria detected from the composting treatments were Staphylococcus sp., Bacillus sp., and Pseudomonas sp.

CONCLUSIONS

The study confirmed the suitability of composting process for PCS bioremediation and superiority of UC than FC as bulking agent.

Study on the efficiency of phytoremediation of soils heavily polluted with PAHs in petroleum-contaminated sites by microorganism

The effects of Fire Phoenix (a mixture of Festuca L.) and Purple coneflower (Echinacea purpurea (L.) Moench) on the remediation of two different high concentrations of PAH-contaminated soils were studied under the effect of strain N12 (Mycobacterium sp.), and the changes in rhizosphere enzymatic activity were preliminarily studied. The results of three culture stages (60 d, 120 d, and 150 d) showed that N12 has a promotional effect on the biomass of Fire Phoenix and E. purpurea, and the effect of N12 on the biomass of Fire Phoenix is better. Under the strengthening of N12, the maximum removal rates of Fire Phoenix reached 86.77% and 67.82% at two high PAH concentrations (A and B, respectively). The activity of dehydrogenase (DHO) is positively correlated with the degradation rate of PAHs at the A concentration (P < 0.05). The activity of DHO in soil will continue to increase at a higher level of the B concentration, but the positive correlation between the activity of DHO and the degradation rate of PAH is weakened. In the rhizosphere soil of the two plants, the change in polyphenol oxidase (PPO) activity with time has a significant negative correlation with the degradation rate of PAHs (P < 0.05). The experiment proved that Fire Phoenix is more suitable for the remediation of heavy PAH-contaminated soil under the condition of microorganism-strengthening, and it can achieve a better degradation effect when the concentrations of PAHs are < 150 mg·kg^-1. Results provide a further scientific basis for the remediation of contaminated sites.

Comparison of metalworking fluids biodegradation efficiency by autochthonous and environmental communities

The aim of this study was to evaluate the biodegradation potential of microbiota isolated from different environmental niches towards different types of metalworking fluids (MWF). The first experimental stage was focused on the assessment of biochemical oxygen demand reduction efficiency of autochthonous and environmental microbial communities. Based on the obtained results, the following order describing the biodegradation potential of communities from the studied niches was established: petroleum contaminated soil > waste repository ≥ waste MWF tanks > pesticide-treated field > activated sludge > municipal sewage effluents. For comparative purposes, the most efficient community originating from petroleum contaminated soil (PCS1) was selected for further studies along with the most efficient community originating from a waste MWF tank (WMT1). The studied communities achieved 100% biodegradation efficiency of decanedioic and dodecanedioic acids as well as glycerine and polyethoxylated dodecanol. However, the PCS1 community was more versatile and displayed significantly higher biodegradation efficiency of mineral oil (80% compared to 50% in case of WMT1). Similarly, experiments using pristine and spent MWF solutions confirmed that the PCS1 community outperformed the WMT1 community during the biodegradation of MWF containing oil as the main component (COD reduction of 80, 60 and 30% in case of semi-synthetic MWF, soluble oil and spent MWF, respectively). Results of community dynamics assessment using quantitative real-time PCR after the biodegradation of different types of MWF confirmed that the PCS1 community was characterized by high genetic stability and allowed to indicate the potential 'key players'.

Rapid degradation of long-chain crude oil in soil by indigenous bacteria using fermented food waste supernatant

The objective of this study is to explore how to stimulate soil indigenous bacteria for the degradation of long-chain crude oil by adding fermented food waste supernatant (FS). Four concentrations of FS (0 mL, 0.1 mL, 1 mL, and 3 mL) were added to two oil-contaminated soils S1 and S2 for 30 days of bioremediation experiments. The results showed that the biodegradation of long-chain alkanes (C₂₉ - C₂₄) could reach up to 1756 mg/kg (49.3%, S1) and 3937 mg/kg (43.9%, S2), which were 3.1 and 3.2 times that of the non-nutrient system. In addition, the logarithmic growth rate of the indigenous hydrocarbon degraders (IHD) reached 41.5%. The long-chain crude oil can be rapidly degraded by indigenous bacteria with FS added in a short time. The glucose and acetic acid accelerated the consumption of ammonia nitrogen (NH₄⁺-N) in the prophase of bioremediation and the molar ratio of consumed carbon (contained in glucose and acetic acid) to consumed NH₄⁺-N (C/N) was high by adding FS. Thus, the IHD can multiply rapidly. The analysis of microbial diversity revealed that the IHD (genera Acinetobacter and Aquabacterium) became the dominant bacteria. Long-chain alkanes became the main carbon sources for IHD after 14 days in soil S1 and 16 days in soil S2. Thus, the rapid biodegradation of long-chain crude oil was achieved. The genus Aquabacterium which was uncultivable on crude oil medium became the dominant bacteria. This study provides an environment-friendly and sustainable remediation technology for bioremediation of oil-contaminated soils.

Effects of Phytoremediation Treatment on Bacterial Community Structure and Diversity in Different Petroleum-Contaminated Soils

Increased exploitation and use of petroleum resources is leading to increased risk of petroleum contamination of soil and groundwater. Although phytoremediation is a widely-used and cost-effective method for rehabilitating soils polluted by petroleum, bacterial community structure and diversity in soils undergoing phytoremediation is poorly understood. We investigate bacterial community response to phytoremediation in two distinct petroleum-contaminated soils (add prepared petroleum-contaminated soils) from northwest China, Weihe Terrace soil and silty loam from loess tableland. High-throughput sequencing technology was used to compare the bacterial communities in 24 different samples, yielding 18,670 operational taxonomic units (OTUs). The dominant bacterial groups, Proteobacteria (31.92%), Actinobacteria (16.67%), Acidobacteria (13.29%) and Bacteroidetes (6.58%), increased with increasing petroleum concentration from 3000 mg/kg–10,000 mg/kg, while Crenarchaeota (13.58%) and Chloroflexi (4.7%) decreased. At the order level, RB41, Actinomycetales, Cytophagales, envOPS12, Rhodospirillales, MND1 and Xanthomonadales, except Nitrososphaerales, were dominant in Weihe Terrace soil. Bacterial community structure and diversity in the two soils were significantly different at similar petroleum concentrations. In addition, the dominant genera were affected by available nitrogen, which is strongly associated with the plants used for remediation. Overall, the bacterial community structure and diversity were markedly different in the two soils, depending on the species of plants used and the petroleum concentration.

Optimization of combined in-vessel composting process and chemical oxidation for remediation of bottom sludge of crude oil storage tanks

In this research, removal of petroleum hydrocarbons from oily sludge of crude oil storage tanks was investigated under the optimized conditions of in-vessel composting process and chemical oxidation with H₂O₂ and Fenton. After determining the optimum conditions, the sludge was pre-treated with the optimum state of the oxidation process. Then, the determined optimum ratios of the sludge to immature compost were composted at a C:N:P ratio of 100:5:1 and moisture content of 55% for a period of 10 weeks. Finally, both pre-treated and composted mixtures were again oxidized with the optimum conditions of the oxidants. Results showed that total petroleum hydrocarbons (TPH) removal of the 1:8 and 1:10 composting reactors which were pre-treated with H₂O₂ were 88.34% and 90.4%, respectively. In addition, reduction of TPH in 1:8 and 1:10 composting reactors which were pre-treated with Fenton were 83.90% and 84.40%, respectively. Without applying the pre-treatment step, the composting reactors had a removal rate of about 80%. Therefore, pre-treatment of the reactors increased the TPH removal. However, post-oxidation of both pre-treated and composted mixtures reduced only 13-16% of TPH. Based on the results, remarkable overall removal of TPH (about 99%) was achieved by using chemical oxidation and subsequent composting process. The study showed that chemical oxidation with H₂O₂ followed by in-vessel composting is a viable choice for the remediation of the sludge.

Abundance and diversity of soil petroleum hydrocarbon-degrading microbial communities in oil exploring areas

Alkanes and polycyclic aromatic hydrocarbons (PAHs) are the commonly detected petroleum hydrocarbon contaminants in soils in oil exploring areas. Hydrocarbon-degrading genes are useful biomarks for estimation of the bioremediation potential of contaminated sites. However, the links between environmental factors and the distribution of alkane and PAH metabolic genes still remain largely unclear. The present study investigated the abundances and diversities of soil n-alkane and PAH-degrading bacterial communities targeting both alkB and nah genes in two oil exploring areas at different geographic regions. A large variation in the abundances and diversities of alkB and nah genes occurred in the studied soil samples. Various environmental variables regulated the spatial distribution of soil alkane and PAH metabolic genes, dependent on geographic location. The soil alkane-degrading bacterial communities in oil exploring areas mainly consisted of Pedobacter, Mycobacterium, and unknown alkB-harboring microorganisms. Moreover, the novel PAH-degraders predominated in nah gene clone libraries from soils of the two oil exploring areas. This work could provide some new insights towards the distribution of hydrocarbon-degrading microorganisms and their biodegradation potential in soil ecosystems.