Isolation, plant colonization potential, and phenanthrene degradation performance of the endophytic bacterium Pseudomonas sp. Ph6-gfp

Physiological, transcriptomic, and metabolomic analyses reveal that Pantoea sp. YSD J2 inoculation improves the accumulation of flavonoids in Cyperus esculentus L. var. sativus

Plant growth-promoting microorganisms (PGPMs), such as Pantoea sp. YSD J2, promote plant development and stress resistance, while their role in flavonoids accumulation still needs to be further understood. To investigate the complex flavonoid biosynthesis pathway of Cyperus esculentus L. var. sativus (tigernut), we compared Pantoea sp. YSD J2 inoculation (YSD J2) and water inoculation (CK) groups. YSD J2 significantly elevated the content of indole-3-acetic acid (IAA) and orientin. Furthermore, when analyzing flavonoid metabolome, YSD J2 caused increased levels of uralenol, petunidin-3-O-glucoside-5-O-arabinoside, luteolin-7-O-glucuronide-(2 → 1)-glucuronide, kaempferol-3-O-neohesperidoside, cyanidin-3-O-(2″-O-glucosyl)glucoside, kaempferol-3-O-glucuronide-7-O-glucoside, quercetin-3-O-glucoside, luteolin-7-O-glucuronide-(2 → 1)-(2″-sinapoyl)glucuronide, and quercetin-4'-O-glucoside, which further enhanced antioxidant activity. We then performed RNA-seq and LC-MS/MS, aiming to validate key genes and related flavonoid metabolites under YSD J2 inoculation, and rebuild the gene-metabolites regulatory subnetworks. Furthermore, the expression patterns of the trans cinnamate 4-monooxygenase (CYP73A), flavonol-3-O-L-rhamnoside-7-O-glucosyltransferase (UGT73C6), shikimate O-hydroxycinnamoyltransferase (HCT), chalcone isomerase (CHI), flavonol synthase (FLS), and anthocyanidin synthase (ANS) genes were confirmed by qRT-PCR. Additionally, 4 transcription factors (TF) (especially bHLH34, Cluster-37505.3) under YSD J2 inoculation are also engaged in regulating flavonoid accumulation. Moreover, the current work sheds new light on studying the regulatory effect of Pantoea sp. YSD J2 on tigernut development and flavonoid biosynthesis.

Effects and mechanisms of chlormequat on horizontal transfer of antibiotic resistance genes through plasmid-mediated conjugation in agro-ecosystems

Chlormequat (CCC) is widely used in agricultural production to increase the crop yield. However, the effects of CCC on transfer of ARGs in agricultural system are still unclear. In this study, using E.coli DH5α (carrying RP4 plasmid with AmpR, TetR, KanR) as the donor bacterium, E.coli HB101, endophytic Pseudomonas sp. Ph6 or rhizosphere Pseudomonas putida KT2440 as the recipient strain, three conjugative systems were designed to investigate the effects of CCC on ARG transfer. Meanwhile, hydroponics experiments were designed to study the ARG spread in the rice-nutrient solution system after CCC application. The results showed that CCC significantly promoted the RP4 conjugation by expanding cell membrane permeability and improving the relative transcription levels of trfAp, trbBp, traA and traL genes in RP4. Furthermore, the conjugation frequency between E. coli and Pseudomonas was much higher than that between E. coli cells. Compared with spraying foliage with 2500 mg·L-1 of CCC, soaking seeds with 250 mg·L-1 of CCC was more beneficial to the colonization of ARB in rice, and also increased the abundance of ARGs in rice cultivation system. These results remind that the use of CCC in agricultural production might promote the ARG transmission in agro-ecosystems; however, foliage spraying with 2500 mg·L-1 of CCC could control its spread.

Plants and endophytes interaction: a "secret wedlock" for sustainable biosynthesis of pharmaceutically important secondary metabolites

Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future.

Microbial-assisted phytodegradation for the amelioration of pyrene-contaminated soil using Pseudomonas aeruginosa and Aspergillus oryzae with alfalfa and sunflower

Environmental pollution caused by polycyclic aromatic hydrocarbons (PAHs) jeopardizes nature. PAHs are the most toxic, mutagenic, and carcinogenic pollutants and their cleanup is important for the environment. In the current research, to assess and evaluate three remediation strategies for pyrene removal from the soil, a pot experiment was performed: (a) bioremediation with Pseudomonas aeruginosa and Aspergillus oryzae, (b) phytoremediation with sunflower (Helianthus annuus) and alfalfa (Medicago sativa L.) and (c) microbial-assisted phytoremediation for the treatment of pyrene (700 mg kg-1). Results depict that P. aeruginosa significantly promoted the growth and tolerance of taken plants and reduced pyrene concentration in soil. Compared with those planted in pyrene-contaminated soil without inoculation. The highest percentage of pyrene removal was observed in P. aeruginosa inoculated alfalfa (91%), alfalfa inoculated with A. oryzae (83.96%), and without inoculation (78.20%). Moreover, alfalfa planted in P. aeruginosa augmented soil had the highest dehydrogenase activity (37.83 μg TPF g-1 soil h-1), and fluorescein diacetate hydrolysis (91.67 μg fluorescein g-1 dry soil). DHA and FDA are the indicators of bioaugmentation influence on the indigenous microbial activity of contaminated soil. As a result of the findings, the rhizospheric association of plants and microbes is beneficial for pyrene removal. Therefore, P. aeruginosa-assisted phytodegradation might be a more successful remediation technique for pyrene-contaminated soil than bioremediation and phytodegradation solely.

In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1

A metal-resistant bacterium Pseudomonas parafulva OS-1 was isolated from waste-contaminated soil in Ranchi City, India. The isolated strain OS-1 showed its growth at 25-45°C, pH 5.0-9.0, and in the presence of ZnSO₄ (upto 5 mM). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OS-1 belonged to the genus Pseudomonas and was most closely related to parafulva species. To unravel the genomic features, we sequenced the complete genome of P. parafulva OS-1 using Illumina HiSeq 4,000 sequencing platform. The results of average nucleotide identity (ANI) analysis indicated the closest similarity of OS-1 to P. parafulva PRS09-11288 and P. parafulva DTSP2. The metabolic potential of P. parafulva OS-1 based on Clusters of Othologous Genes (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux, etc., which is relatively rare in P. parafulva strains. Compared with other parafulva strains, P. parafulva OS-1 was found to have the unique β-lactam resistance and type VI secretion system (T6SS) gene. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain OS-1 have strong biomass degradation potential. The presence of genomic complexity in the OS-1 genome indicates that horizontal gene transfer (HGT) might happen during evolution. Therefore, genomic and comparative genome analysis of parafulva strains is valuable for further understanding the mechanism of resistance to metal stress and opens a perspective to exploit a newly isolated bacterium for biotechnological applications.

Metal oxide nanoparticles inhibit nitrogen fixation and rhizosphere colonization by inducing ROS in associative nitrogen-fixing bacteria Pseudomonas stutzeri A1501

The potential effects of engineered metal oxide nanoparticles (MONPs) on bacterial nitrogen fixation are of great concern. Herein, the impact and mechanism of the increasing-used MONPs, including TiO₂, Al₂O₃, and ZnO nanoparticles (TiO₂NP, Al₂O₃NP, and ZnONP, respectively), on nitrogenase activity was studied at the concentrations ranging from 0 to 10 mg L^-1 using associative rhizosphere nitrogen-fixing bacteria Pseudomonas stutzeri A1501. Nitrogen fixation capacity was inhibited by MONPs in an increasing degree of TiO₂NP < Al₂O₃NP < ZnONP. Realtime qPCR analysis showed that the expressions of nitrogenase synthesis-related genes, including nifA and nifH, were inhibited significantly when MONPs were added. MONPs could cause the explosion of intracellular ROS, and ROS not only changed the permeability of the membrane but also inhibited the expression of nifA and biofilm formation on the root surface. The repressed nifA gene could inhibit transcriptional activation of nif-specific genes, and ROS reduced the biofilm formation on the root surface which had a negative effect on resisting environmental stress. This study demonstrated that MONPs, including TiO₂NP, Al₂O₃NP, and ZnONP, inhibited bacterial biofilm formation and nitrogen fixation in the rice rhizosphere, which might have a negative effect on the nitrogen cycle in bacteria-rice system.

Evaluation of aerobic biodegradation of phenanthrene using Pseudomonas turukhanskensis: an optimized study

The ability of Pseudomonas turukhanskensis GEEL-01 to degrade the phenanthrene (PHE) was optimized by response surface methodology (RSM). Three factors as independent variables (including temperature, pH, and inoculum) were studied at 600 mg/L PHE where the highest growth of P. turukhanskensis GEEL-01 was observed. The optimum operating conditions were evaluated through the fit summary analysis, model summary statistics, fit statistics, ANOVA analysis, and model graphs. The degradation of PHE was monitored by high-performance liquid chromatography (HPLC) and the metabolites were identified by gas chromatography-mass spectrometry (GC-MS). The results showed that the correlation among independent variables with experimental and predicted responses was significant (p < 0.0001). The optimal temperature, pH, and inoculum were 30 ℃, 8, and 6 mL respectively. The HPLC peaks exhibited a reduction in PHE concentration from 600 mg/L to 4.97 mg/L with 99% degradation efficiency. The GC-MS peaks indicated that the major end products of PHE degradation were 1-Hydroxy-2-naphthoic acid, salicylic acid, phthalic acid, and catechol. This study demonstrated that the optimized parameters by RSM for P. turukhanskensis GEEL-01 could degrade PHE by phthalic and salicylic acid pathways.

Isolation, characterization and application of the epoxiconazole-degrading strain Pseudomonas sp. F1 in a soil-vegetable system

Epoxiconazole (EPX) has a long half-life in soil and causes various toxicological effects in both the ecosystem and mammals. In this study, eight strains of bacteria capable of degrading EPX were isolated from pesticide-contaminated soil, with strain F1 showing the best effect. This strain was identified as Pseudomonas sp. by 16S rRNA gene sequencing and physiological-biochemical analyses. Our results indicated that strain F1 has a high capacity to degrade EPX, removing 92.1% of EPX within 6 days. The temperature and pH were the two most important environmental factors affecting EPX degradation, followed by substrate concentration and inoculum dose. In addition, strain F1 has a high capacity to promote EPX degradation in soils, with a lower t_1/2 value (2.64 d) in F1-inoculated soil compared to the control (t_1/2 = 96.3 d) without strain F1. The strain could efficiently colonize rhizosphere soil and enhance degradation of EPX, leading to a significant decrease in the accumulation and translocation of EPX in vegetables, thereby alleviating the effects of EPX-induced stress on plants. Moreover, we observed that strain F1-gfp was able to colonize the roots, stems and leaves of Brassica rapa var. chinensis. Such colonization may play a role in the efficient degradation of EPX within plants. To our knowledge, this is the first study to demonstrate biodegradation of EPX in a soil-vegetable system using an EPX-degrading bacterium. This study indicates that strain F1 is a promising candidate for simultaneous bioremediation of soil contaminated with EPX and safe food production.

Evaluation of existing guidelines for their adequacy for the food and feed risk assessment of microorganisms obtained through synthetic biology

EFSA was asked by the European Commission to evaluate synthetic biology (SynBio) developments for agri-food use in the near future and to determine whether or not they are expected to constitute potential new hazards/risks. Moreover, EFSA was requested to evaluate the adequacy of existing guidelines for risk assessment of SynBio and if updated guidance is needed. The scope of this Opinion covers food and feed risk assessment, the variety of microorganisms that can be used in the food/feed chain and the whole spectrum of techniques used in SynBio. This Opinion complements a previously adopted Opinion with the evaluation of existing guidelines for the microbial characterisation and environmental risk assessment of microorganisms obtained through SynBio. The present Opinion confirms that microbial SynBio applications for food and feed use, with the exception of xenobionts, could be ready in the European Union in the next decade. New hazards were identified related to the use or production of unusual and/or new-to-nature components. Fifteen cases were selected for evaluating the adequacy of existing guidelines. These were generally adequate for assessing the product, the production process, nutritional and toxicological safety, allergenicity, exposure and post-market monitoring. The comparative approach and a safety assessment per se could be applied depending on the degree of familiarity of the SynBio organism/product with the non-genetically modified counterparts. Updated guidance is recommended for: (i) bacteriophages, protists/microalgae, (ii) exposure to plant protection products and biostimulants, (iii) xenobionts and (iv) feed additives for insects as target species. Development of risk assessment tools is recommended for assessing nutritional value of biomasses, influence of microorganisms on the gut microbiome and the gut function, allergenic potential of new-to-nature proteins, impact of horizontal gene transfer and potential risks of living cell intake. A further development towards a strain-driven risk assessment approach is recommended.

Response of Poplar and Associated Fungal Endophytic Communities to a PAH Contamination Gradient

Microbial populations associated to poplar are well described in non-contaminated and metal-contaminated environments but more poorly in the context of polycyclic aromatic hydrocarbon (PAH) contamination. This study aimed to understand how a gradient of phenanthrene (PHE) contamination affects poplar growth and the fungal microbiome in both soil and plant endosphere (roots, stems and leaves). Plant growth and fitness parameters indicated that the growth of Populus canadensis was impaired when PHE concentration increased above 400 mg kg^-1. Values of alpha-diversity indicators of fungal diversity and richness were not affected by the PHE gradient. The PHE contamination had a stronger impact on the fungal community composition in the soil and root compartments compared to that of the aboveground organs. Most of the indicator species whose relative abundance was correlated with PHE contamination decreased along the gradient indicating a toxic effect of PHE on these fungal OTUs (Operational Taxonomic Units). However, the relative abundance of some OTUs such as Cadophora, Alternaria and Aspergillus, potentially linked to PHE degradation or being plant-beneficial taxa, increased along the gradient. Finally, this study allowed a deeper understanding of the dual response of plant and fungal communities in the case of a soil PAH contamination gradient leading to new perspectives on fungal assisted phytoremediation.

Remediation of phenanthrene phytotoxicity by the interaction of rice and endophytic fungus P. liquidambaris in practice

Phenanthrene cannot be effectively degraded in the agricultural production systems and it is greatly hazardous for food safety and human health. In our study, the remediation ability and mechanism of rice and endophytic fungus Phomopsis liquidambaris interaction on phenanthrene in the rice-growing environment were explored using laboratory and pot experiments. The results showed that plant-endophyte interaction had the potential to enhance remediation on phenanthrene contamination in the rice-growing environment. The content of phenanthrene in soil and rice (including leaves, roots, and grains) of the plant-endophyte interaction system was about 42% and 27% lower than of the non-inoculated treatment under 100 mg kg^-1 treatment. The mechanism may be related to the improvement of plant growth, root activity, chlorophyll content, ATP energy supply, and antagonistic ability of rice to promote the absorption of phenanthrene in the rice-growing environment, and then the phenanthrene absorbed into the rice was degraded by improving the phenanthrene degrading enzyme activities and gene relative expression levels of P. liquidambaris during plant-endophyte interaction. Moreover, the plant-endophyte interaction system could also promote rice growth and increase rice yield by over 20% more than the control under 50 mg kg^-1 treatment. This study indicated a promising potential of the plant-endophyte interaction system for pollution remediation in agriculture.

Analysis of the Genome of the Heavy Metal Resistant and Hydrocarbon-Degrading Rhizospheric Pseudomonas qingdaonensis ZCR6 Strain and Assessment of Its Plant-Growth-Promoting Traits

The Pseudomonas qingdaonensis ZCR6 strain, isolated from the rhizosphere of Zea mays growing in soil co-contaminated with hydrocarbons and heavy metals, was investigated for its plant growth promotion, hydrocarbon degradation, and heavy metal resistance. In vitro bioassays confirmed all of the abovementioned properties. ZCR6 was able to produce indole acetic acid (IAA), siderophores, and ammonia, solubilized Ca₃(PO₄)₂, and showed surface active properties and activity of cellulase and very high activity of 1-aminocyclopropane-1-carboxylic acid deaminase (297 nmol α-ketobutyrate mg⁻¹ h⁻¹). The strain degraded petroleum hydrocarbons (76.52% of the initial hydrocarbon content was degraded) and was resistant to Cd, Zn, and Cu (minimal inhibitory concentrations reached 5, 15, and 10 mM metal, respectively). The genome of the ZCR6 strain consisted of 5,507,067 bp, and a total of 5055 genes were annotated, of which 4943 were protein-coding sequences. Annotation revealed the presence of genes associated with nitrogen fixation, phosphate solubilization, sulfur metabolism, siderophore biosynthesis and uptake, synthesis of IAA, ethylene modulation, heavy metal resistance, exopolysaccharide biosynthesis, and organic compound degradation. Complete characteristics of the ZCR6 strain showed its potential multiway properties for enhancing the phytoremediation of co-contaminated soils. To our knowledge, this is the first analysis of the biotechnological potential of the species P. qingdaonensis.

Reducing Phenanthrene Contamination in Trifolium repens L. With Root-Associated Phenanthrene-Degrading Bacterium Diaphorobacter sp. Phe15

Some root-associated bacteria could degrade polycyclic aromatic hydrocarbons (PAHs) in contaminated soil; however, their dynamic distribution and performance on root surface and in inner plant tissues are still unclear. In this study, greenhouse container experiments were conducted by inoculating the phenanthrene-degrading bacterium Diaphorobacter sp. Phe15, which was isolated from root surfaces of healthy plants contaminated with PAHs, with the white clover (Trifolium repens L.) via root irrigation or seed soaking. The dynamic colonization, distribution, and performance of Phe15 in white clover were investigated. Strain Phe15 could efficiently degrade phenanthrene in shaking flasks and produce IAA and siderophore. After cultivation for 30, 40, and 50 days, it could colonize the root surface of white clover by forming aggregates and enter its inner tissues via root irrigation or seed soaking. The number of strain Phe15 colonized on the white clover root surfaces was the highest, reaching 6.03 Log CFU⋅g^–1 FW, followed by that in the roots and the least in the shoots. Colonization of Phe15 significantly reduced the contents of phenanthrene in white clover; the contents of phenanthrene in Phe15-inoculated plants roots and shoots were reduced by 29.92–43.16 and 41.36–51.29%, respectively, compared with the Phe15-free treatment. The Phe15 colonization also significantly enhanced the phenanthrene removal from rhizosphere soil. The colonization and performance of strain Phe15 in white clove inoculated via root inoculation were better than seed soaking. This study provides the technical support and the resource of strains for reducing the plant PAH pollution in PAH-contaminated areas.

Selection of Endophytic Strains for Enhanced Bacteria-Assisted Phytoremediation of Organic Pollutants Posing a Public Health Hazard

Anthropogenic activities generate a high quantity of organic pollutants, which have an impact on human health and cause adverse environmental effects. Monitoring of many hazardous contaminations is subject to legal regulations, but some substances such as therapeutic agents, personal care products, hormones, and derivatives of common organic compounds are currently not included in these regulations. Classical methods of removal of organic pollutants involve economically challenging processes. In this regard, remediation with biological agents can be an alternative. For in situ decontamination, the plant-based approach called phytoremediation can be used. However, the main disadvantages of this method are the limited accumulation capacity of plants, sensitivity to the action of high concentrations of hazardous pollutants, and no possibility of using pollutants for growth. To overcome these drawbacks and additionally increase the efficiency of the process, an integrated technology of bacteria-assisted phytoremediation is being used recently. For the system to work, it is necessary to properly select partners, especially endophytes for specific plants, based on the knowledge of their metabolic abilities and plant colonization capacity. The best approach that allows broad recognition of all relationships occurring in a complex community of endophytic bacteria and its variability under the influence of various factors can be obtained using culture-independent techniques. However, for practical application, culture-based techniques have priority.

Removal Performance and Mechanism of Benzo(b)Fluorathene Using MnO2 Nanoflower/Graphene Oxide Composites

High-ring polycyclic aromatic hydrocarbons (PAHs, Benzo[b]fluorathene (BbFA), etc.) are difficult to biodegrade in the water environment. To address this issue, an innovative method for the preparation of MnO₂ nanoflower/graphene oxide composite (MnO₂ NF/GO) was proposed for adsorption removal of BbFA. The physicochemical properties of MnO₂ NF/GO were characterized by SEM, TEM, XRD, and N₂ adsorption/desorption and XPS techniques. Results show that the MnO₂ NF/GO had well-developed specific surface area and functional groups. Batch adsorption experiment results showed that adsorption capacity for BbFA was 74.07 mg/g. The pseudo-second-order kinetic model and Freundlich isotherm model are fitted well to the adsorption data. These show electron-donor-acceptor interaction; especially π-π interaction and π complexation played vital roles in BbFA removal onto MnO₂ NF/GO. The study highlights the promising potential adsorbent for removal of PAHs.

Rhizosphere assisted bioengineering approaches for the mitigation of petroleum hydrocarbons contamination in soil

The high demand for petroleum oil has led to hydrocarbon contamination in soil, including agricultural lands, and many other ecosystems across the globe. Physical and chemical treatments are effective strategies for the removal of high contamination levels and are useful for small areas, although with concerns of cost-effectiveness. Alternatively, several bacteria belonging to the Phylum: Proteobacteria, Bacteroidetes, Actinobacteria, Nocardioides, or Firmicutes are used for biodegradation of different hydrocarbons - aliphatic, polyaromatic hydrocarbons (PAH), and asphaltenes in the oil-contaminated soil. The rhizoremediation strategy with plant-microbe interactions has prospects to achieve the desired result in the field conditions. However, adequate biostimulation, and bioaugmentation with the suitable plant-microbe combination, and efficiency under a toxic environment needs to be evaluated. Modifying the microbiomes to achieve better biodegradation of contaminants is an upcoming strategy popularly known as microbiome engineering. In this review, rhizoremediation for the successful removal of the hydrocarbons have been critically discussed, with challenges for making it a feasible technology.HIGHLIGHTSPetroleum hydrocarbon contamination has increased around the globe.Rhizoremediation has the potential for the mitigation of pollutants from the contaminated sites.An accurate and detailed analysis of the physio-chemical and climatic conditions of the contaminated sites must be focused on.The suitable plant and bacteria, with other major considerations, may be employed for in-situ remediation.The appropriate data should be obtained using the omics approach to help toward the success of the rhizoremediation strategy.

Colonization and performance of a pyrene-degrading bacterium Mycolicibacterium sp. Pyr9 on root surfaces of white clover

Some rhizosphere bacteria could colonize on the root surface of plants, or even form biofilm to promote plant growth, enhance plant resistance to harsh external environments and block the soil contamination. In this study, to explore the effects of pyrene-degrading bacterium on root surface on plant uptake of pyrene, a pyrene-degrading bacterium Mycolicibacterium sp. Pyr9 was isolated from the root surface of Eleusine indica L. Gaertn. in PAH-contaminated fields; after antibiotic labeling, it was colonized onto the root surface of white clover (Trifolium repens L.), and its distribution and performance were monitored under different levels of pyrene contamination. Strain Pyr9 could degrade 98% of pyrene (with an initial concentration of 50 mg L^-1) in culture solution within 8 d; it also owns a variety of plant growth promoting characteristics and appreciable tolerance to harsh environments. The transcription of pyrene catabolic genes in Pyr9 enhanced obviously when induced by pyrene. Pyr9 colonized and grew well on the root surface of white clover via root inoculation; some cells could even enter into the root tissues and move to the shoots. Compared with the Pyr9-free treatment, the pyrene contents in the roots and shoots of Pyr9-inoculated white clover decreased by 25%-30% and 33%-42%, respectively. Correspondingly, the pyrene accumulation and translocation factors in white clover decreased as well. These results indicate that Pyr9 would be a good potential to circumvent plant pyrene pollution. This research may provide a theoretical basis and technical support for the safety of agricultural products and human health in PAH-contaminated sites.

Statement on the translocation potential by Pseudomonas chlororaphis MA342 in plants after seed treatment of cereals and peas and assessment of the risk to humans

The European Commission requested EFSA to provide scientific advice on the translocation potential by Pseudomonas chlororaphis MA342 in plants after seed treatment of cereals and peas and, if applicable, for a revision of the assessment of the risk to humans by its metabolite 2,3-deepoxy-2,3-didehydro-rhizoxin (DDR) and this based on the evidence available in the dossier for renewal of the approval. The information from other P. chlororaphis strains than MA342 was taken into account with care, because the studies available in the dossier did not confirm the identity of the strain MA342 as belonging to the species P. chlororaphis. It has been concluded that there is a potential for translocation of P. chlororaphis MA342 to edible plant parts following seed treatment till an estimated concentration up to about 105 cfu/g and some exposure can be assumed by consumption of fresh commodities. Also, production of the metabolite DDR in the plant cannot be excluded. Regarding levels of DDR in the raw agricultural commodities, exposure estimates based on the limit of quantification (LOQ) for DDR in cereals cannot be further refined while there is no information on the levels of DDR in peas in the dossier. As regards genotoxicity, DDR induced chromosomal damage; however, it was not possible to conclude whether it is through an aneugenic or clastogenic mechanism. Hence, it is not possible to draw a reliable conclusion that DDR is producing an aneugenic effect nor to determine a threshold dose for aneugenicity. Thus, it is not possible to revise the human risk assessment as regards exposure to DDR. The concerns identified in the EFSA conclusion of 2017 remain.

Occurrence, loadings and removal of EU-priority polycyclic aromatic hydrocarbons (PAHs) in wastewater and sludge by advanced biological treatment, stabilization pond and constructed wetland

Eight polycyclic aromatic hydrocarbon (PAH) compounds which have been accepted as priority micropollutants by European Union (EU) were analyzed both in wastewater and sludge lines throughout three full scale (located in city, sub-province and village) WWTPs during 12-month sampling period. Investigated WWTPs have different treatment types including advanced biological treatment, stabilization pond (SP) and constructed wetland (CW). Removal efficiencies for total PAH compounds varied from 48% in CW to 85% in advanced biological treatment plant. The maximum concentrations of 360-2282 ng/L observed for naphthalene in raw wastewater were decreased to 103-370 ng/L by treatment processes. Minimum concentration were detected for benzo(k)fluoranthene (B[k]F) and benzo(g,h,i)perylene (B[g,h,i]P) ranged between 8 and 12 ng/L and 19-33 ng/L, respectively. While minimum removal efficiencies were obtained for B[k]F and B[g,h,i]P maximum removal efficiencies were obtained for naphthalene in all WWTPs. PAHs present in minimum and maximum levels in the sludge samples were detected as 54 and 6826 ng/g for the B[g,h,I]P and naphthalene, respectively. Considering the removal mechanisms, PAHs have been determined to be removed by biodegradation or vaporization up to 84% and by settling (adsorption onto sludge) up to 2%. The greatest portion (99%) of naphthalene and anthracene were determined to be biodegraded or vaporized in biological treatment due to their low molecular weights. On the other hand, mechanism of adsorption onto sludge was determined as negligible for these two compounds. In addition, approximately 14% of PAHs were discharged to the receiving environment. Among the different WWTP types investigated, advanced biological treatment was found to be the most efficient plant for the removal of PAH compounds.

Comparison of Two Inoculation Methods of Endophytic Bacteria to Enhance Phytodegradation Efficacy of an Aged Petroleum Hydrocarbons Polluted Soil

Endophyte-enhanced phytodegradation is a promising technology to clean up polluted soils. To improve the success rate of this nature-based remediation approach, it is important to advance the inoculation method as this has been shown to strongly affect the final outcome. However, studies evaluating inoculation strategies and their effect on hydrocarbon degradation are limited. This study aims to investigate two different manners of endophyte inoculation in Lolium perenne growing in an aged petroleum hydrocarbon polluted soil: (1) direct soil inoculation (SI), and (2) pre-inoculation of the caryopses followed by soil inoculation (PI). Different endophytic bacterial strains, Rhodococcus erythropolis 5WK and Rhizobium sp. 10WK, were applied individually as well as in combination. Depending on the method of inoculation, the petroleum hydrocarbon (PHC) degradation potential was significantly different. The highest PHC removal was achieved after pre-inoculation of ryegrass caryopses with a consortium of both bacterial strains. Moreover, both strains established in the aged-polluted soil and could also colonize the roots and shoots of L. perenne. Importantly, used endophytes showed the selective colonization of the environment compartments. Our findings show that the method of inoculation determines the efficiency of the phytodegradation process, especially the rate of PHC degradation. This study provides valuable information for choosing the most cost-effective and beneficial means to optimize phytodegradation.

Bioelectrochemical remediation of phenanthrene in a microbial fuel cell using an anaerobic consortium enriched from a hydrocarbon-contaminated site

Polycyclic aromatic hydrocarbons (PAH) are organic pollutants that require remediation due to their detrimental impact on human and environmental health. In this study, we used a novel approach of sequestering a model PAH, phenanthrene, onto a solid carbon matrix bioanode in a microbial fuel cell (MFC) to assess its biodegradation coupled with power generation. Here, the bioanode serves as a site for enrichment of electroactive and hydrocarbon-degrading microorganisms, which can simultaneously act to biodegrade a pollutant and generate power. Carbon cloth electrodes loaded with two rates of phenanthrene (2 and 20 mg cm^-2) were compared using dual chamber MFCs that were operated for 50 days. The lower loading rate of 2 mg cm^-2 was most efficient in the degradation of phenanthrene and had higher power production capacities (37 mW m^-2) as compared to the higher loading rate of 20 mg cm^-2 (power production of 19.2 mW m^-2). FTIR (Fourier-Transform Infrared Spectroscopy) analyses showed a depletion in absorbance peak signals associated with phenanthrene. Microbes known to have electroactive properties or phenanthrene biodegradation abilities like Pseudomonas, Rhodococcus, Thauera and Ralstonia were enriched over time in the MFCs, substantiating the electrochemical and FTIR analyses. The MFC approach taken here thus offers great promise towards PAH bioelectroremediation.

Evaluation of two transformation protocols and screening of positive plasmid introduction into Bacillus cereus EB2, a gram-positive bacterium using qualitative analyses

Both Gram-positive and Gram-negative bacteria can take up exogenous DNA when they are in a competent state either naturally or artificially. However, the thick peptidoglycan layer in Gram-positive bacteria's cell wall is considered as a possible barrier to DNA uptake. In the present work, two transformation techniques have been evaluated in assessing the protocol's ability to introduce foreign DNA, pBBRGFP-45 plasmid which harbors kanamycin resistance and green fluorescent protein (GFP) genes into a Gram-positive bacterium, Bacillus cereus EB2. B. cereus EB2 is an endophytic bacterium, isolated from oil palm roots. A Gram-negative bacterium, Pseudomonas aeruginosa EB35 was used as a control sample for both transformation protocols. The cells were made competent using respective chemical treatment to Gram-positive and Gram-negative bacteria, and kanamycin concentration in the selective medium was also optimized. Preliminary findings using qualitative analysis of colony polymerase chain reaction (PCR)-GFP indicated that the putative positive transformants for B. cereus EB2 were acquired using the second transformation protocol. The positive transformants were then verified using molecular techniques such as observation of putative colonies on specific media under UV light, plasmid extraction, and validation analyses, followed by fluorescence microscopy. Conversely, both transformation protocols were relatively effective for introduction of plasmid DNA into P. aeruginosa EB35. Therefore, this finding demonstrated the potential of chemically prepared competent cells and the crucial step of heat-shock in foreign DNA transformation process of Gram-positive bacterium namely B. cereus was required for successful transformation.

Endophytic Bacteria in in planta Organopollutant Detoxification in Crops

Microbe-assisted organopollutant removal, or in planta crop decontamination, is based on an interactive system between organopollutant-degrading endophytic bacteria (DEB_OP) and crops in alleviating organic toxins in plants. This script focuses on the fast-growing body of literature that has recently bloomed in organopollutant control in agricultural plants. The various facets of DEB_OP under study include their colonization, distribution, plant growth-promoting mechanisms, and modes of action in the detoxification process in plants. Also, an assessment of the biotechnological advances, advantages, and bottlenecks in accelerating the implementation of this decontamination strategy will be undertaken. The highlighted key research directions from this review will shape the future of agro-environmental sustainability and preservation of human health.

Characterization of Biofilm Formed by Phenanthrene-Degrading Bacteria on Rice Root Surfaces for Reduction of PAH Contamination in Rice

One effective method in to reduce the uptake of organic contaminants by plants is the development of a root barrier. In this study, the characterization of biofilm structure and function by phenanthrene-degrading Pseudomonas sp. JM2-gfp on rice root surfaces were carried out. Our results showed that root surfaces from three rice species, namely Liaojing401, Koshihikari, and Zhenzhuhong all present hydrophobicity and a high initial adhesion of strain JM2-gfp. Matured robust biofilm formation occurred at 48 h on the root surfaces. The biofilm exhibited cell dense aggregates and biomass embedded in the extracellular polymeric substance (EPS) matrix. EPS composition results showed that the proteins, carbohydrates, lipids and nucleic acids are produced in the biofilm, while the content varied with rice species. Under the initial concentration of phenanthrene 50 mg·L-1, the residual phenanthrene in plant roots from 'Zhengzhuhong', 'Koshihikari' and 'Liaojing401' with biofilm mediated were significantly decreased by 71.9%, 69.3% and 58.7%, respectively, compared to those without biofilm groups after 10 days of exposure. Thus, the biofilm colonized on roots plays an important role of degradation in order to reduce the level of phenanthrene uptake of plants. Thereby, the present work provides significant new insights into lowering the environmental risks of polycyclic aromatic hydrocarbons (PAHs) in crop products from contaminated agriculture soils.

Indole-3-acetic-acid and ACC deaminase producing Leclercia adecarboxylata MO1 improves Solanum lycopersicum L. growth and salinity stress tolerance by endogenous secondary metabolites regulation

BACKGROUND

The utilization of plant growth-promoting microbes is an environment friendly strategy to counteract stressful condition and encourage plants tolerance. In this regards, the current study was designed to isolate ACC deaminase and indole-3-acetic acid (IAA) producing halotolerant bacteria to promote tomato (Solanum lycopersicum L.) growth and tolerance against salinity stress.

RESULTS

The selected bacterial isolate MO1 was identified as Leclercia adecarboxylata and IAA quantification results revealed that MO1 produced significant amount of IAA (9.815 ± 0.6293 μg mL- 1). The MO1 showed the presence of ACC (1-Aminocyclopropane-1-Carboxylate) deaminase responsible acdS gene and tolerance against salinity stress. A plant microbe interaction experiment using tomato (Solanum lycopersicum L.) with glycine betaine (GB) as a positive control was carried out to investigate the positive role MO1 in improving plant growth and stress tolerance. The results indicated that MO1 inoculation and GB application significantly increased growth attributes under normal as well as saline condition (120 mM NaCl). The MO1 inoculation and GB treatment approach conferred good protection against salinity stress by significantly improving glucose by 17.57 and 18.76%, sucrose by 34.2 and 12.49%, fructose by 19.9 and 10.9%, citric acid by 47.48 and 34.57%, malic acid by 52.19 and 28.38%, serine by 43.78 and 69.42%, glycine by 14.48 and 22.76%, methionine by 100 and 124.99%, threonine by 70 and 63.08%, and proline by 36.92 and 48.38%, respectively, while under normal conditions MO1 inoculation and GB treatment also enhanced glucose by 19.83 and 13.19%, sucrose by 23.43 and 15.75%, fructose by 15.79 and 8.18%, citric acid by 43.26 and 33.14%, malic acid by 36.18 and 14.48%, serine by 46.5 and 48.55%, glycine by 19.85 and 29.77%, methionine by 22.22 and 38.89%, threonine by 21.95 and 17.07%, and proline by 29.61 and 34.68% compared to levels in non-treated plants, respectively. In addition, the endogenous abscisic acid (ABA) level was noticeably lower in MO1-inoculated (30.28 and 30.04%) and GB-treated plants (45 and 35.35%) compared to their corresponding control plants under normal condition as well as salinity stress, respectively.

CONCLUSION

The current findings suggest that the IAA- and ACC-deaminase-producing abilities MO1 can improve plants tolerance to salinity stress.

Biodegradation of phenanthrene by endophytic fungus Phomopsis liquidambari in vitro and in vivo

Phenanthrene, as a widespread polycyclic aromatic hydrocarbons (PAHs) contaminant in vitro and in vivo of plant, has the characteristics of carcinogenicity, teratogenicity and mutagenicity. This work aimed to explore the phenanthrene metabolic mechanism by Phomopsis liquidambari in vitro, as well as the bioremediation ability through P. liquidambari-rice combination. This strain was able to use phenanthrene as source of carbon and energy to grow, more than 77% of added 50 mg L^-1 phenanthrene was removed after 10 d in MSM. We identified the metabolic products via HPLC-MS and proposed two possible degradation pathways. Phenanthrene was firstly combined with oxygen to become phenanthrene 9,10-oxide, and then degraded to 9-phenanthrol, followed by oxidization to 9,10-dihydroxyphenanthrene. In addition, that epoxide (phenanthrene 9,10-oxide) was also hydrolyzed to phenanthrene trans-9,10-dihydrodiol, and then dehydrogenized to 9,10-dihydroxyphenanthrene, which was further degraded to 9,10-phenanthrenequinone; during this metabolic pathway, the changes of P450 monooxygenase, epoxide hydrolase, dehydrogenase and catechol 2,3-dioxygenase activities and their corresponding gene transcription levels were closely related. What's more, P. liquidambari could combine with rice to eliminate phenanthrene accumulated in vivo of rice seedlings, and the removal rate in inoculation treatment represented a significant difference (increased 25.68%) compared with uninoculation treatment after cultivation 30 d. Therefore, we concluded that P. liquidambari could not only respond to phenanthrene pollution stress in vitro but also exert a mitigation effect on plants accumulated phenanthrene. This work provides a foundation for applying endophytic fungi to PAHs bioremediation in vitro and in vivo.

Biodegradation of di-n-butyl phthalate (DBP) by a novel endophytic Bacillus megaterium strain YJB3

Phthalic acid esters (PAEs) are a group of recalcitrant and hazardous organic compounds that pose a great threat to both ecosystem and human beings. A novel endophytic strain YJB3 that could utilize a wide range of PAEs as the sole carbon and energy sources for cell growth was isolated from Canna indica root tissue. It was identified as Bacillus megaterium based on morphological characteristics and 16S rDNA sequence homology analysis. The degradation capability of the strain YJB3 was investigated by incubation in mineral salt medium containing di-n-butyl-phthalate (DBP), one of important PAEs under different environmental conditions, showing 82.5% of the DBP removal in 5days of incubation under the optimum conditions (acetate 1.2g·L^-1, inocula 1.8%, and temperature 34.2°C) achieved by two-step sequential optimization technologies. The DBP metabolites including mono-butyl phthalate (MBP), phthalic acid (PA), protocatechuic acid (PCA), etc. were determined by GC-MS. The PCA catabolic genes responsible for the aromatic ring cleavage of PCA in the strain YJB3 were excavated by whole-genome sequencing. Thus, a degradation pathway of DBP by the strain YJB3 was proposed that MBP was formed, followed by PA, and then the intermediates were further utilized till complete degradation. To our knowledge, this is the first study to show the biodegradation of PAEs using endophyte. The results in the present study suggest that the strain YJB3 is greatly promising to act as a competent inoculum in removal of PAEs in both soils and crops.

Adsorptive removal of aromatic hydrocarbons from water over metal azolate framework-6-derived carbons

Metal azolate framework-6 (MAF-6) was pyrolyzed at 1000°C to yield MOF-derived carbons (MCs). The obtained MCs were used to eliminate aromatic hydrocarbons, including polyaromatic hydrocarbons (PAHs; e.g., naphthalene (NAP), anthracene (ATC), and pyrene (PRN)) and benzene (BZ) from water via adsorption. The adsorption results over the MCs were compared with that of pristine MAF-6 and commercial activated carbon (AC). MC obtained after 24h (MC-24) exhibited a remarkable adsorption efficiency compared to that of the other MCs (obtained after different durations), MAF-6, and AC. For example, MC-24 led to adsorptions of NAP around 17 and 2.5 times those of pristine MAF-6 and AC, respectively. Or, the maximum adsorption capacities (Q₀) of MAF-6, AC and MC-24 for NAP were 14, 104 and 237mg/g, respectively. Moreover, Q₀ values of MC-24 for ATC and PRN were also very high of 284 and 307mg/g, respectively. Based on the properties of PAHs and the hydrophobicity of MC-24, hydrophobic interaction was suggested as the main mechanism for the adsorption of PAHs and BZ. In addition, MC-24 can be recycled by washing with acetone with little loss in performance. Therefore, MC-24 is recommended as a competitive adsorbent for aromatic hydrocarbon removal from water.

Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities

Phytoremediation is a promising in situ green technology based on the use of plants to cleanup soils from organic and inorganic pollutants. Microbes, particularly bacteria and fungi, that closely interact with plant roots play key roles in phytoremediation processes. In polluted soils, the root-associated microbes contribute to alleviation of plant stress, improve nutrient uptake and may either degrade or sequester a large range of soil pollutants. Therefore, improving the efficiency of phytoremediation requires a thorough knowledge of the microbial diversity living in the rhizosphere and in close association with plant roots in both the surface and the endosphere. This study aims to assess fungal ITS and bacterial 16S rRNA gene diversity using high-throughput sequencing in rhizospheric soils and roots of three plant species (Solidago canadensis, Populus balsamifera, and Lycopus europaeus) growing spontaneously in three petroleum hydrocarbon polluted sedimentation basins. Microbial community structures of rhizospheric soils and roots were compared with those of microbes associated with arbuscular mycorrhizal fungal (AMF) spores to determine the links between the root and rhizosphere communities and those associated with AMF. Our results showed a difference in OTU richness and community structure composition between soils and roots for both bacteria and fungi. We found that petroleum hydrocarbon pollutant (PHP) concentrations have a significant effect on fungal and bacterial community structures in both soils and roots, whereas plant species identity showed a significant effect only on the roots for bacteria and fungi. Our results also showed that the community composition of bacteria and fungi in soil and roots varied from those associated with AMF spores harvested from the same plants. This let us to speculate that in petroleum hydrocarbon contaminated soils, AMF may release chemical compounds by which they recruit beneficial microbes to tolerate or degrade the PHPs present in the soil.

Hydrocarbon degradation potential and plant growth-promoting activity of culturable endophytic bacteria of Lotus corniculatus and Oenothera biennis from a long-term polluted site

Many endophytic bacteria exert beneficial effects on their host, but still little is known about the bacteria associated with plants growing in areas heavily polluted by hydrocarbons. The aim of the study was characterization of culturable hydrocarbon-degrading endophytic bacteria associated with Lotus corniculatus L. and Oenothera biennis L. collected in long-term petroleum hydrocarbon-polluted site using culture-dependent and molecular approaches. A total of 26 hydrocarbon-degrading endophytes from these plants were isolated. Phylogenetic analyses classified the isolates into the phyla Proteobacteria and Actinobacteria. The majority of strains belonged to the genera Rhizobium, Pseudomonas, Stenotrophomonas, and Rhodococcus. More than 90% of the isolates could grow on medium with diesel oil, approximately 20% could use n-hexadecane as a sole carbon and energy source. PCR analysis revealed that 40% of the isolates possessed the P450 gene encoding for cytochrome P450-type alkane hydroxylase (CYP153). In in vitro tests, all endophytic strains demonstrated a wide range of plant growth-promoting traits such as production of indole-3-acetic acid, hydrogen cyanide, siderophores, and phosphate solubilization. More than 40% of the bacteria carried the gene encoding for the 1-aminocyclopropane-1-carboxylic acid deaminase (acdS). Our study shows that the diversity of endophytic bacterial communities in tested plants was different. The results revealed also that the investigated plants were colonized by endophytic bacteria possessing plant growth-promoting features and a clear potential to degrade hydrocarbons. The properties of isolated endophytes indicate that they have the high potential to improve phytoremediation of petroleum hydrocarbon-polluted soils.

Phylloremediation of Air Pollutants: Exploiting the Potential of Plant Leaves and Leaf-Associated Microbes

Air pollution is air contaminated by anthropogenic or naturally occurring substances in high concentrations for a prolonged time, resulting in adverse effects on human comfort and health as well as on ecosystems. Major air pollutants include particulate matters (PMs), ground-level ozone (O3), sulfur dioxide (SO2), nitrogen dioxides (NO2), and volatile organic compounds (VOCs). During the last three decades, air has become increasingly polluted in countries like China and India due to rapid economic growth accompanied by increased energy consumption. Various policies, regulations, and technologies have been brought together for remediation of air pollution, but the air still remains polluted. In this review, we direct attention to bioremediation of air pollutants by exploiting the potentials of plant leaves and leaf-associated microbes. The aerial surfaces of plants, particularly leaves, are estimated to sum up to 4 × 108 km2 on the earth and are also home for up to 1026 bacterial cells. Plant leaves are able to adsorb or absorb air pollutants, and habituated microbes on leaf surface and in leaves (endophytes) are reported to be able to biodegrade or transform pollutants into less or nontoxic molecules, but their potentials for air remediation has been largely unexplored. With advances in omics technologies, molecular mechanisms underlying plant leaves and leaf associated microbes in reduction of air pollutants will be deeply examined, which will provide theoretical bases for developing leaf-based remediation technologies or phylloremediation for mitigating pollutants in the air.

Isolation, Characterization, and Degradation Performance of the 17β-Estradiol-Degrading Bacterium Novosphingobium sp. E2S

A 17β-estradiol (E2)-degrading bacterium E2S was isolated from the activated sludge in a sewage treatment plant (STP). The morphology, biological characteristics, and 16S ribosomal RNA (rRNA) gene sequence of strain E2S indicated that it belonged to the genus Novosphingobium. The optimal degrading conditions were 30 °C and pH 7.0. The ideal inoculum volume was 5% (v/v), and a 20-mL degradation system was sufficient to support the removal ability of strain E2S. The addition of extra NaCl to the system did not benefit the E2 degradation in batch culture by this strain. Strain E2S exhibited high degradation efficiency with initial substrate concentrations of 10-50 mg·L-1. For example, in mineral salt medium containing 50 mg·L-1 of E2, the degradation efficiency was 63.29% after seven days. In cow manure samples supplemented with 50 mg·L-1 of E2, strain E2S exhibited 66.40% degradation efficiency after seven days. The finding of the E2-degrading strain E2S provided a promising method for removing E2 from livestock manure in order to reduce the potential environmental risks of E2.

Comparative Investigation of Bacterial, Fungal, and Archaeal Community Structures in Soils in a Typical Oilfield in Jianghan, China

Agricultural soils in oilfields have high risk for polycyclic aromatic hydrocarbon (PAH) pollution. In this study, from the Jianghan Oilfield (Hubei Province, China) with a history of >50 years, 7 soil samples (OS-1 to OS-7) were collected. Subsequently, the bacterial, archaeal, and fungal community structures were investigated by Illumina MiSeq sequencing, and the relationship between microbial community structure and soil PAH content was analyzed. The results indicated that bacterial and archaeal Chao 1 indices showed a significantly negative relationship with soil PAH content, and only the bacterial Shannon index had a significantly negative relationship with soil PAH content. Moreover, the community structure of bacteria (r ² = 0.9001, p = 0.013) showed a stronger correlation with PAH content than that of fungi (r ² = 0.7357, p = 0.045), and no significant relationship was found between archaeal community structure (r ² = 0.4553, p = 0.262) and soil PAH content. In addition, the relative greater abundances of some bacterial genus belonging to Actinobacteria (Mycobacterium and Micromonospora) and Proteobacteria (Pseudomonas, Lysobacter, Idiomarina, Oxalobacteraceae, and Massilia), fungal genus belonging to Ascomycota (Sordariales and Pleosporales), and archaeal phylum (Euryarchaeota) were detected in the soil samples (OS-3 and OS-5) with greater PAH content. In summary, soil PAHs showed an obvious influence and selectivity on the soil microbiota. Furthermore, compared with fungi and archaea, bacteria was more sensitive to soil PAH pollution, and the diversity indices and community structure of bacteria both might be suitable indicators for assessment of soil PAH stress on the soil ecosystem.

Biodegradation of Mixed PAHs by PAH-Degrading Endophytic Bacteria

Endophytic bacteria can promote plant growth, induce plant defence mechanisms, and increase plant resistance to organic contaminants. The aims of the present study were to isolate highly PAH-degrading endophytic bacteria from plants growing at PAH-contaminated sites and to evaluate the capabilities of these bacteria to degrade polycyclic aromatic hydrocarbons (PAHs) in vitro, which will be beneficial for re-colonizing target plants and reducing plant PAH residues through the inoculation of plants with endophytic bacteria. Two endophytic bacterial strains P₁ (Stenotrophomonas sp.) and P₃ (Pseudomonas sp.), which degraded more than 90% of phenanthrene (PHE) within 7 days, were isolated from Conyza canadensis and Trifolium pretense L., respectively. Both strains could use naphthalene (NAP), PHE, fluorene (FLR), pyrene (PYR), and benzo(a)pyrene (B(a)P) as the sole sources of carbon and energy. Moreover, these bacteria reduced the contamination of mixed PAHs at high levels after inoculation for 7 days; strain P₁ degraded 98.0% NAP, 83.1% FLR, 87.8% PHE, 14.4% PYR, and 1.6% B(a)P, and strain P₃ degraded 95.3% NAP, 87.9% FLR, 90.4% PHE, 6.9% PYR, and negligible B(a)P. Notably, the biodegradation of PAHs could be promoted through additional carbon and nitrogen nutrients; therein, beef extract was suggested as the optimal co-substrate for the degradation of PAHs by these two strains (99.1% PHE was degraded within 7 days). Compared with strain P₁, strain P₃ has more potential for the use in the removal of PAHs from plant tissues. These results provide a novel perspective in the reduction of plant PAH residues in PAH-contaminated sites through inoculating plants with highly PAH-degrading endophytic bacteria.

Novel Biochar-Plant Tandem Approach for Remediating Hexachlorobenzene Contaminated Soils: Proof-of-Concept and New Insight into the Rhizosphere

Volatilization of semi/volatile persistent organic pollutants (POPs) from soils is a major source of global POPs emission. This proof-of-concept study investigated a novel biochar-plant tandem approach to effectively immobilize and then degrade POPs in soils using hexachlorobenzene (HCB) as a model POP and ryegrass (Lolium perenne L.) as a model plant growing in soils amended with wheat straw biochar. HCB dissipation was significantly enhanced in the rhizosphere and near rhizosphere soils, with the greatest dissipation in the 2 mm near rhizosphere. This enhanced HCB dissipation likely resulted from (i) increased bioavailability of immobilized HCB and (ii) enhanced microbial activities, both of which were induced by ryegrass root exudates. As a major component of ryegrass root exudates, oxalic acid suppressed HCB sorption to biochar and stimulated HCB desorption from biochar and biochar-amended soils, thus increasing the bioavailability of HCB. High-throughput sequencing results revealed that the 2 mm near rhizosphere soil showed the lowest bacterial diversity due to the increased abundance of some genera (e.g., Azohydromonas, Pseudomonas, Fluviicola, and Sporocytophaga). These bacteria were likely responsible for the enhanced degradation of HCB as their abundance was exponentially correlated with HCB dissipation. The results from this study suggest that the biochar-plant tandem approach could be an effective strategy for remediating soils contaminated with semi/volatile organic contaminants.

Potential of Endophytic Bacterium Paenibacillus sp. PHE-3 Isolated from Plantago asiatica L. for Reduction of PAH Contamination in Plant Tissues

Endophytes are ubiquitous in plants, and they may have a natural capacity to biodegrade polycyclic aromatic hydrocarbons (PAHs). In our study, a phenanthrene-degrading endophytic Paenibacillus sp. PHE-3 was isolated from P. asiatica L. grown in a PAH-contaminated site. The effects of environmental variables on phenanthrene biodegradation by strain PHE-3 were studied, and the ability of strain PHE-3 to use high molecular weight PAH (HMW-PAH) as a sole carbon source was also evaluated. Our results indicated that pH value of 4.0–8.0, temperature of 30 °C–42 °C, initial phenanthrene concentration less than 100 mg·L⁻¹, and some additional nutrients are favorable for the biodegradation of phenanthrene by strain PHE-3. The maximum biodegradation efficiency of phenanthrene was achieved at 99.9% after 84 h cultivation with additional glutamate. Moreover, the phenanthrene biodegradation by strain PHE-3 was positively correlated with the catechol 2,3-dioxygenase activity (ρ = 0.981, p < 0.05), suggesting that strain PHE-3 had the capability of degrading HMW-PAHs. In the presence of other 2-, 3-ringed PAHs, strain PHE-3 effectively degraded HMW-PAHs through co-metabolism. The results of this study are beneficial in that the re-colonization potential and PAH degradation performance of endophytic Paenibacillus sp. PHE-3 may be applied towards reducing PAH contamination in plants.

Biological Control of Lettuce Drop and Host Plant Colonization by Rhizospheric and Endophytic Streptomycetes

Lettuce drop, caused by the soil borne pathogen Sclerotinia sclerotiorum, is one of the most common and serious diseases of lettuce worldwide. Increased concerns about the side effects of chemical pesticides have resulted in greater interest in developing biocontrol strategies against S. sclerotiorum. However, relatively little is known about the mechanisms of Streptomyces spp. as biological control agents against S. sclerotiorum on lettuce. Two Streptomyces isolates, S. exfoliatus FT05W and S. cyaneus ZEA17I, inhibit mycelial growth of Sclerotinia sclerotiorum by more than 75% in vitro. We evaluated their biocontrol activity against S. sclerotiorum in vivo, and compared them to Streptomyces lydicus WYEC 108, isolated from Actinovate®. When Streptomyces spp. (10(6) CFU/mL) were applied to S. sclerotiorum inoculated substrate in a growth chamber 1 week prior lettuce sowing, they significantly reduced the risk of lettuce drop disease, compared to the inoculated control. Interestingly, under field conditions, S. exfoliatus FT05W and S. cyaneus ZEA17I protected lettuce from drop by 40 and 10% respectively, whereas S. lydicus WYEC 108 did not show any protection. We further labeled S. exfoliatus FT05W and S. cyaneus ZEA17I with the enhanced GFP (EGFP) marker to investigate their rhizosphere competence and ability to colonize lettuce roots using confocal laser scanning microscopy (CLSM). The abundant colonization of young lettuce seedlings by both strains demonstrated Streptomyces' capability to interact with the host from early stages of seed germination and root development. Moreover, the two strains were detected also on 2-week-old roots, indicating their potential of long-term interactions with lettuce. Additionally, scanning electron microscopy (SEM) observations showed EGFP-S. exfoliatus FT05W endophytic colonization of lettuce root cortex tissues. Finally, we determined its viability and persistence in the rhizosphere and endorhiza up to 3 weeks by quantifying its concentration in these compartments. Based on these results we conclude that S. exfoliatus FT05W has high potential to be exploited in agriculture for managing soil borne diseases barely controlled by available plant protection products.

Plant species affect colonization patterns and metabolic activity of associated endophytes during phytoremediation of crude oil-contaminated soil

Plants coupled with endophytic bacteria hold great potential for the remediation of polluted environment. The colonization patterns and activity of inoculated endophytes in rhizosphere and endosphere of host plant are among the primary factors that may influence the phytoremediation process. However, these colonization patterns and metabolic activity of the inoculated endophytes are in turn controlled by none other than the host plant itself. The present study aims to determine such an interaction specifically for plant-endophyte systems remediating crude oil-contaminated soil. A consortium (AP) of two oil-degrading endophytic bacteria (Acinetobacter sp. strain BRSI56 and Pseudomonas aeruginosa strain BRRI54) was inoculated to two grasses, Brachiaria mutica and Leptochloa fusca, vegetated in crude oil-contaminated soil. Colonization patterns and metabolic activity of the endophytes were monitored in the rhizosphere and endosphere of the plants. Bacterial augmentation enhanced plant growth and crude oil degradation. Maximum crude oil degradation (78%) was achieved with B. mutica plants inoculated with AP consortium. This degradation was significantly higher than those treatments, where plants and bacteria were used individually or L. fusca and endophytes were used in combination. Moreover, colonization and metabolic activity of the endophytes were higher in the rhizosphere and endosphere of B. mutica than L. fusca. The plant species affected not only colonization pattern and biofilm formation of the inoculated bacteria in the rhizosphere and endosphere of the host plant but also affected the expression of alkane hydroxylase gene, alkB. Hence, the investigation revealed that plant species can affect colonization patterns and metabolic activity of inoculated endophytic bacteria and ultimately the phytoremediation process.

Polycyclic aromatic hydrocarbons (PAHs) removal by sorption: A review

Polycyclic aromatic hydrocarbons (PAHs) are organic micro pollutants which are persistent compounds in the environment due to their hydrophobic nature. Concerns over their adverse effects in human health and environment have resulted in extensive studies on various types of PAHs removal methods. Sorption is one of the widely used methods as PAHs possess a great sorptive ability into the solid media and their low aqueous solubility property. Several adsorbent media such as activated carbon, biochar, modified clay minerals have been largely used to remove PAHs from aqueous solution and to immobilise PAHs in the contaminated soils. According to the past studies, very high removal efficiency could be achieved using the adsorbents such as removal efficiency of activated carbon, biochar and modified clay mineral were 100%, 98.6% and >99%, respectively. PAHs removal efficiency or adsorption/absorption capacity largely depends on several parameters such as particle size of the adsorbent, pH, temperature, solubility, salinity including the production process of adsorbents. Although many studies have been carried out to remove PAHs using the sorption process, the findings have not been consolidated which potentially hinder to get the correct information for future study and to design the sorption method to remove PAHs. Therefore, this paper summarized the adsorbent media which have been used to remove PAHs especially from aqueous solutions including the factor affecting the sorption process reported in 142 literature published between 1934 and 2015.

Pseudomonas sp. LZ-Q continuously degrades phenanthrene under hypersaline and hyperalkaline condition in a membrane bioreactor system

Graphical Abstract

Abstract

Phenanthrene is one of the most recalcitrant components of crude oil-contaminated wastewater. An efficient phenanthrene-degrading bacterium Pseudomonas sp. strain named LZ-Q was isolated from oil-contaminated soil near the sewage outlet of a petrochemical company. Pseudomonas sp. LZ-Q is able to degrade 1000 mg/L phenanthrene in Bushnell-Hass mineral salt medium. It also degrades other polycyclic aromatic hydrocarbons such as naphthalene, anthracene, pyrene, petrol, and diesel at broad ranges of salinities of 5 g/L to 75 g/L, pHs of 5.0–10.0, and temperatures of 10–42 °C. Therefore, Pseudomonas sp. LZ-Q could be a good candidate for remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated wastewater. A membrane bioreactor (MBR) was applied to investigate the remediation ability of the strain LZ-Q. Wastewater containing phenanthrene with pH of 8, salinity of 35 g/L, and COD of 500 mg/L was continuously added to the system (HRT = 3 h). Results showed that Pseudomonas sp. LZ-Q is capable of degrading 96% of 20 mg/L phenanthrene and 94% of 500 mg/L COD for 60 days in a continuous mode. These results showed that the MBR system with strain LZ-Q might be a good approach for PAHs’ remediation in industrial wastewaters.

Inoculating plants with the endophytic bacterium Pseudomonas sp. Ph6-gfp to reduce phenanthrene contamination

Plant organic contamination poses a serious threat to the safety of agricultural products and human health worldwide, and the association of endophytic bacteria with host plants may decrease organic pollutants in planta. In this study, we firstly determined the growth response and biofilm formation of endophytic Pseudomonas sp. Ph6-gfp, and then systematically evaluated the performance of different plant colonization methods (seed soaking (SS), root soaking (RS), leaf painting (LP)) for circumventing the risk of plant phenanthrene (PHE) contamination. After inoculation for 48 h, strain Ph6-gfp grew efficiently with PHE, oxalic acid, or malic acid as the sole sources of carbon and energy. Moreover, strain Ph6-gfp could form robust biofilms in LB medium. In greenhouse hydroponic experiments, strain Ph6-gfp could actively colonize inoculated plants internally, and plants colonized with Ph6-gfp showed a higher capacity for PHE removal. Compared with the Ph6-gfp-free treatment, the accumulations of PHE in Ph6-gfp-colonized plants via SS, RS, and LP were 20.1, 33.1, and 7.1 %, respectively, lower. Our results indicate that inoculating plants with Ph6-gfp could lower the risk of plant PHE contamination. RS was most efficient for improving PHE removal in whole plant bodies by increasing the cell numbers of Ph6-gfp in plant roots. The findings in this study provide an optimized method to strain Ph6-gfp reduce plant PAH residues, which may be applied to agricultural production in PAH-contaminated soil.

Conjugative transfer of a derivative of the IncP-1α plasmid RP4 and establishment of transconjugants in the indigenous bacterial community of poplar plants

The persistence of traits introduced into the indigenous bacterial community of poplar plants was investigated using bioluminescence mediated by the luc gene. Three endophytic bacterial strains provided with the IncP-1α plasmid RP4-Tn-luc were used to inoculate poplar cuttings at different phenological stages. Screening of isolates by bioluminescence and real-time PCR detection of the luc gene revealed stable persistence for at least 10 weeks. Although the inoculated strains became established with a high population density after inoculation at leaf development (April) and senescence (October), the strains were suppressed by the indigenous bacteria at stem elongation (June). Transconjugants could be detected only at this phenological stage. Indigenous bacteria harbouring RP4-Tn-luc became established with densities ranging from 2 × 10(5) to 9 × 10(6) CFU g(-1) fresh weight 3 and 10 weeks after inoculation. The increased colonization of the cuttings by indigenous bacteria at stem elongation seemed to strongly compete with the introduced strains. Otherwise, the phenological stage of the plants as well as the density of the indigenous recipients could serve as the driver for a more frequent conjugative plasmid transfer. A phylogenetic assignment of transconjugants indicated the transfer of RP4-Tn-luc into six genera of Proteobacteria, mainly Sphingomonas, Stenotrophomonas and Xanthomonas.

Complex Interactions Between the Macrophyte Acorus Calamus and Microbial Fuel Cells During Pyrene and Benzo[a]Pyrene Degradation in Sediments

This study investigated the interaction of the macrophyte Acorus calamus and sediment microbial fuel cells (SMFC) during the degradation of high molecular weight-polycyclic aromatic hydrocarbons (HMW-PAHs) in sediments. Over 367-days, the combination of macrophyte and SMFC led to an increase in pyrene and benzo[a]pyrene degradation rates by at least 70% compared to SMFC or macrophyte alone. While either the macrophyte or SMFC increased redox potential in sediments, redox potentials near the anode (approximately 6 cm depth) in the macrophyte-SMFC combination were markedly lower than that in the only macrophyte treatment. Moreover, rhizospheric bacterial communities in macrophyte-SMFC and macrophyte treatments were distinctly different. Aerobic genera (Vogesella, Pseudomonas, Flavobacterium and Rhizobium) and anaerobic genera (Longilinea, Bellilinea, Desulfobacca and Anaeromyxobacter) became dominant in the rhizosphere in macrophyte and macrophyte-SMFC treatments, respectively. In addition, the macrophyte-SMFC combination improved the numbers of not only aerobic but anaerobic PAHs degraders in sediments. So, the SMFC employment facilitated the formation of anoxic zones in sediments with oxygen loss and exudates from the roots. As a result, cooperation of anaerobic/aerobic microbial metabolism for accelerating HMW-PAHs removal occurred within sediments after combining macrophytes with SMFC.