Degradation Of Polychlorinated Biphenyls Research Articles

Unveiling the distribution characteristics of rpf-like genes and indigenous resuscitation promoting factor production in PCB-contaminated soils

Resuscitation promoting factors (Rpfs), known for their anti-dormancy cytokine properties, have been extensively investigated in the medical field. Although the Rpf from Micrococcus luteus has been successfully utilized to resuscitate and stimulate microbial populations for the degradation of polychlorinated biphenyls (PCBs), the presence of indigenous Rpf homologs in PCB-contaminated soils has not been established. In this study, the distribution characteristics of rpf-like genes and indigenous strain capable of producing Rpf in PCB-contaminated soils were explored. The results revealed the widespread presence of Rpf-like domains and their associated genes, particularly in close association with heavy metals and PCBs. The rpf-like genes were predominantly found in Proteobacteria and displayed a positive correlation with genes involved in PCB degradation and viable but non-culturable (VBNC) formation. Notably, the recombinant Rpf-Ac protein derived from the indigenous strain Achromobacter sp. HR2 exhibited muralytic activity and demonstrated significant efficacy in resuscitating the growth of VBNC cells, while also stimulating the growth of normal cells. These findings shed light on the prevalent presence of Rpf homologs in PCB-contaminated soils and their potential to resuscitate functional populations in the VBNC state, thereby enhancing in situ bioremediation.

Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400.

Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress. By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400. Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern. This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.

Whole-cell biosensor engineering based on the transcription factor XylS/Pm for sensitive detection of PCB intermediate chlorobenzoic acid

Chlorobenzoic acids (Cba) are toxic chloride pollutants commonly released by chemical industries or formed during the degradation pathway of organic chlorides, such as polychlorinated biphenyls (PCBs). Here, we successfully developed a highly sensitive Escherichia coli whole-cell Cba biosensor, named XyF10 (MG1655(DE3)-Ps-XylS (Step13)-Pm1-EGFP), by comprehensive engineering the elements of Cba sensing genetic circuit from Pseudomonas putida. Compared to the native sensing system, XyF10 exhibited a significantly reduced detection limit (<1 μM vs. 50 μM) and an increased signal-to-noise ratio (11.7-fold vs. 4.4-fold), making it a highly efficient whole-cell sensor with the lowest detection limit for Cba reported to date. Structural analysis and molecular dynamics simulations of XylS and its variants revealed that the increased flexibility of a ring structure in XylS (Step13) variant promoted the sensing efficiency of XyF10 system by fascinating the formation of active dimers and enabled more stable binding with inducer. Furthermore, the XyF10 system displayed an obvious preference for meta-substituted Cba (3-Cba) as substrates, which was attributed by the stronger interaction between 3-Cba and the active site of XylS. Overall, our research not only advanced the Cba detection techniques for large-scale detection of Cba in the environment, but also provided potential tools for high-throughput screening of PCB degradation pathways and enzymes.

A novel mechanism of enhanced PCBs degradation associated with nitrogen in the rhizosphere of the wetland plant Myriophyllum aquaticum

Co-contamination of polychlorinated biphenyls (PCBs) and nitrogen (N) is widespread. Here, N removal and PCBs degradation were investigated in constructed wetlands populated with Myriophyllum aquaticum, and the role of N in PCBs degradation was explored as well. Nearly 97% of N was removed in the planted system, whereas less than 40% was removed in the plant-free system. Compared to the treatment with plants and no N amendment, N addition enhanced plant growth by 31.9% and PCBs removal by 9.90%. PCBs attenuation was mainly attributed to microbial degradation rather than plant uptake. Using DNA stable-isotope probing, 26 operational taxonomic units were identified across all treatments, of which 25 were linked to PCBs degradation for the first time. Some PCB-degraders were associated with nitrification/denitrification and were significantly enriched in the treatment that included both plants and N application, indicating that PCBs degradation was promoted by recruiting ammonia-oxidising and denitrifying microbes with PCBs metabolic ability. This was confirmed by the higher A13/A12 ratios for the bphC, amoA, and nirK genes and their significant positive correlations. Overall, the findings clarify the novel mechanism by which N promotes PCBs degradation in constructed wetlands and offers a theoretical basis for efficiently removing inorganic elements and persistent organic pollutants.

Promoted Photocatalytic Activity of Green Titanium Oxide-Clay Nanocomposite Toward Polychlorinated Biphenyl Degradation in Actual Samples

Promoted Photocatalytic Activity of Green Titanium Oxide-Clay Nanocomposite Toward Polychlorinated Biphenyl Degradation in Actual Samples

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.

Removal of cadmium and polychlorinated biphenyls by clover and the associated microbial community in a long-term co-contaminated soil

Legumes such as clover are cost-effective and environmentally friendly components of strategies for remediating soils contaminated with heavy metals or organic pollutants. However, the mechanisms by which clover remediates co-contaminated soils are unclear. The present study explored the effects of phytoremediation by clover on pollutant removal and the microbial community in soil co-contaminated with cadmium (Cd) and polychlorinated biphenyls (PCBs). After 18 months of phytoremediation, Cd removal increased from 20.25 % in the control to 40.65 % in soil planted with clover, while PCB removal increased from 29.81 % to 60.02 %. High-throughput sequencing analysis showed that the relative abundances of the bacterial phylum Proteobacteria and the diazotrophic genus Rhizobium increased significantly after phytoremediation. Random forest analysis showed that bacterial and diazotrophic diversity significantly influenced Cd and PCB removal. Furthermore, co-occurrence network and correlation analyses revealed that Rhizobiales and Micromonosporales were the main bacteria associated with Cd removal, while Rhizobiales, Burkholderiales, and Xanthomonadales were identified as the main degraders of PCBs. PICRUSt functional prediction demonstrated that the gene bphC, which is related to PCB degradation, was significantly increased in the rhizosphere soil in the presence of clover. These results provide a better understanding for further studies of remediation efficiency by clover, rhizosphere microbial response and remediation mechanisms of co-contaminated soils under in situ conditions in the field.

Remediation of polychlorinated biphenyls (PCBs) polluted soil using dielectric barrier discharge (DBD) plasma: Reactive nitrogen species (RNS) and produced dioxins

Soil contaminated by PCBs from the electronic processing industries has attracted global concern because of their potentially persistent risks to human and ecological health. In this study, remediation of PCBs polluted soil using dielectric barrier discharge plasma (DBD) focused on 3,3′,4,4′-tetrachlorobiphenyl (PCB77) and 2,2′-dichlorobiphenyl (PCB4). About 90 % of PCB77 and PCB4 were degraded under input power of 120 W within 30 min. The carbon dioxide mineralization of PCB77 achieved at 18.2 % in 10 min treatment. Greater PCBs degradation was obtained with higher input power, lower moisture content, weaker acidity and presence of oxygenated gas. Increasing initial concentration of PCBs had no significant effect on PCB77 degradation, but contributed to PCB4 removal. PCBs degradation reactions were initiated by high-energy electrons. Reactive oxygen species (ROS) played major roles in PCBs degradation, which was also promoted by reactive nitrogen species (RNS) such as peroxynitrous radicals (HOONO). Multiple spectroscopies showed that chlorine radicals participated in PCBs degradation reactions. Chlorine substitution, ring-opening and bridge cleavage reactions were the main degradation pathways for PCB77. The production and re-degradation of trace dioxin-like substances ensured the safety of DBD use in the remediation of PCBs-contaminated soils.

Simultaneous adsorption and biodegradation of polychlorinated biphenyls using resuscitated strain Streptococcus sp. SPC0 immobilized in polyvinyl alcohol‑sodium alginate

Enhanced bioremediation of polychlorinated biphenyls (PCBs) is a promising and effective strategy for eliminating the risks posed by PCBs. In the present study, the feasibility of utilizing an immobilization approach to enhance the PCBs degradation performance of a resuscitated strain Streptococcus sp. SPC0 was evaluated. The results indicated that a mixed matrix containing polyvinyl alcohol (PVA) and sodium alginate (SA) used as immobilized carriers provided a porous microstructure space for SPC0 colonization and proliferation. The enhanced removal of PCBs by immobilized SPC0 was attributed to simultaneous adsorption and biodegradation performances of PVA-SA-SPC0 beads. The relative equilibrium adsorption capacity of immobilized beads increased with elevated initial concentration, and the maximum theoretical value calculated was 1.64 mg/g. The adsorption process of PCBs by immobilized beads was well fitted to the quasi-second-order kinetic model, and most suitable for Langmuir isotherm model. Immobilized SPC0 enhanced PCB removal with 1.0–7.1 times higher than free cells. Especially, more effective removal of PCBs at higher concentrations could be achieved, in which 73.9 % of 20 mg/L PCBs was removed at 12 h by immobilized SPC0, whereas only 12.0 % by free cells. Moreover, the immobilized SPC0 with excellent stability and reusability retained almost 100 % of the original PCBs removal activity after reusing four times. These results revealed the application potential of immobilizing resuscitated strains for enhanced bioremediation of PCBs.

Bacterial Degradation of PCB 70 and its Hydroxy Derivatives is an Environmentally Friendly Way to Destroy Pops

One of the problems of our time is the environmentally safe destruction of polychlorinated biphenyls (PCBs) and their hydroxylated derivatives. The aim of the study was to investigate the features and prospects of the decomposition of PCB 70 (2,5,3’,4’-tetrachlorobiphenyl) and hydroxylated chlorobiphenyls derived from it by Rhodococcus wratislaviensis strain CH628. As a result of the application of methods of periodic cultivation, gas chromatography and light spectrometry, it was found that the efficiency of destruction of PCB 70 1 g of cells of strain CH628 was 90 mg PCB/day, and the same indicator for a mixture consisting of hydroxy derivatives obtained from PCB 70 was 56 mg PCB/day. It was shown that the strain uses all components of the mixture of hydroxy-PCB 70 as a growth substrate, but with different degradation rates. When cultivated in a mineral medium with PCB 70 or a mixture of hydroxy-PCB 70, strain CH628 forms biofilms. The analysis of the obtained results shows that the use of the Rhodococcus wratislaviensis CH628 strain will make it possible to develop a technology for the environmentally safe destruction of PCB 70 and hydroxy-PCBs derived from it.

Flower-like and nanorods ZnO deposited on rGO as efficient photocatalysts for removal of polychlorinated biphenyls (PCBs)

PCBs were used for several decades as coolants, lubricants in transformers, plasticizers, and dielectric fluids, being highly carcinogenic and representing a severe environmental problem in soil and water. Pure and modified TiO2 has been the most studied photocatalyst looking to degrade PCBs into less toxic products. Lately, ZnO-graphene composites have played an essential role in the photocatalytic degradation of various toxic organic compounds. In this work, ZnO nanostructures were coupled with reduced graphene oxide (ZnO-rGO) via a one-pot microwave-assisted hydrothermal route. As a result, the composites exhibited improved photocatalytic performance for PCBs degradation compared to ZnO nanoparticles. Thus, this research provides an in-situ method to grow different morphologies of ZnO on rGO.

DNA stable isotope probing on soil treated by plant biostimulation and flooding revealed the bacterial communities involved in PCB degradation

Polychlorinated biphenyl (PCB)-contaminated soils represent a major treat for ecosystems health. Plant biostimulation of autochthonous microbial PCB degraders is a way to restore polluted sites where traditional remediation techniques are not sustainable, though its success requires the understanding of site-specific plant–microbe interactions. In an historical PCB contaminated soil, we applied DNA stable isotope probing (SIP) using 13C-labeled 4-chlorobiphenyl (4-CB) and 16S rRNA MiSeq amplicon sequencing to determine how the structure of total and PCB-degrading bacterial populations were affected by different treatments: biostimulation with Phalaris arundinacea subjected (PhalRed) or not (Phal) to a redox cycle and the non-planted controls (Bulk and BulkRed). Phal soils hosted the most diverse community and plant biostimulation induced an enrichment of Actinobacteria. Mineralization of 4-CB in SIP microcosms varied between 10% in Bulk and 39% in PhalRed soil. The most abundant taxa deriving carbon from PCB were Betaproteobacteria and Actinobacteria. Comamonadaceae was the family most represented in Phal soils, Rhodocyclaceae and Nocardiaceae in non-planted soils. Planted soils subjected to redox cycle enriched PCB degraders affiliated to Pseudonocardiaceae, Micromonosporaceae and Nocardioidaceae. Overall, we demonstrated different responses of soil bacterial taxa to specific rhizoremediation treatments and we provided new insights into the populations active in PCB biodegradation.

Biotechnology methods for succession of bacterial communities in polychlorinated biphenyls (PCBs) contaminated soils and isolation novel PCBs-degrading bacteria

Polychlorinated Biphenyls (PCBs) are persistence in the contaminated sites as a result of lacking PCBs-degrading microorganisms. Cultivation-independent technique called single-strand-conformation polymorphism (SSCP) based on 16SrRNA genes was chosen to characterize the diversity of bacterial communities in PCBs polluted soil samples. The bacterial communities showed an increasing diversity from the genetic profiles using SSCP technique. 51 single products were identified from the profiles using PCR reamplification and cloning. DNA sequencing of the 51 products, it showed similarities to Acidobacteria, Actinobacteria, Betaproteobateria, Gammaproteobacteria and Alphaproteobacteria, the range of similarities were 92.3 to 100%. Pure 23 isolates were identified from PCBs contaminated sites. The identified isolates belonged to genus Bacillus, Brevibacillus, Burkholderia, Pandoraea, Pseudomonas, and Rhodococcus. The new strains have the capability to use PCBs as a source of sole carbon and harbor 2,3-dihydroxybiphenyl dioxygenase (DHBDO) which could be used as molecular marker for detection PCBs-degrading bacteria in the PCBs contaminated sites. This finding may enhance the PCBs bioremediation by monitoring and characterization of the PCBs degraders using DHBDO in PCBs contaminated sites.

Technological Developments and Remediation Mechanisms for Phytoremediation of PCB-Contaminated Soils

Polychlorinated biphenyls (PCBs) have been detected in a variety of environmental media, and they have been continuously introduced into the environment for industrial reasons, despite their harmful impact upon ecological health. Considering the adverse effects of PCBs, many researchers have begun to analyze remediation technologies for PCB-contaminated soil. In this study, the rise and fall of PCBs, as well as their physical and chemical properties and environmental impact, were reviewed. The pollution status of PCBs in soil was summarized. Based on the analysis and comparison of various remediation technologies, the limitations of several phytoremediation technologies in PCB-contaminated soils were analyzed. The influencing factors and transformation mechanisms of the phytoremediation of PCB-contaminated soil were investigated, and the research direction of enhancing the degradation of PCBs through the use of plants was also discussed.

Enhanced rhizoremediation of polychlorinated biphenyls by resuscitation-promoting factor stimulation linked to plant growth promotion and response of functional microbial populations

Rhizoremediation is acknowledged as a green technology for removing polychlorinated biphenyls (PCBs) in soil. However, rhizoremediation is limited because most soil microorganisms enter into a viable but non-culturable (VBNC) state under PCBs stress. This work was to study the effect of resuscitation-promoting factor (Rpf) on rhizoremediation efficiency of PCBs in alfalfa and rhizosphere microbiological communities. Results suggested that Rpf promoted alfalfa growth in PCB-contaminated soil by improving antioxidant enzymes and detoxification metabolites in alfalfa. After 40 d Rpf treatment, removal rate for five selected PCBs significantly increased by 0.5–2.2 times. Rpf enhanced relative abundances of bphA and bphC responsible for degrading PCBs, and enzymatic activities of metabolizing exogenous compounds in rhizosphere soil. High-throughput sequencing showed that Rpf did not change the dominant microbial population at phyla and genera levels, but caused variation of the bacterial community structures. The promoting function of Rpf was linked to the shift of various key populations having different functions depending on Rpf concentrations. Pseudomonas and Rhizobium spp. enrichment might stimulate PCB degradation and Streptomyces and Bacillus spp. primarily contributed to alfalfa growth. Predicted functions in rhizosphere soil bacterial community indicated Rpf facilitated soil nutrient cycling and environmental adaptation. This study indicated that Rpf was an active additive for strengthening rhizoremediation efficiency of PCB-contaminated soil and enhancing their in-situ remediation.

Pollution and edaphic factors shape bacterial community structure and functionality in historically contaminated soils

Studies about biodegradation potential in soils often refer to artificially contaminated and simplified systems, overlooking the complexity associated with contaminated sites in a real context. This work aims to provide a holistic view on microbiome assembly and functional diversity in the model site SIN Brescia-Caffaro (Italy), characterized by historical and uneven contamination by organic and inorganic compounds. Here, physical and chemical analyses and microbiota characterization were applied on one-hundred-twenty-seven soil samples to unravel the environmental factors driving bacterial community assembly and biodegradation potential in three former agricultural fields. Chemical analyses showed a patchy distribution of metals, metalloids and polychlorinated biphenyls (PCB) and allowed soil categorization according to depth and area of collections. Likewise, the bacterial community structure, described by molecular fingerprinting and 16S rRNA gene analyses, was significantly different according to collection site and depth. Pollutant concentrations (i.e., hexachloro-biphenyls, arsenic and mercury), nitrogen content and parameters related to soil texture were identified as main drivers of microbiota assembly, being significantly correlated to bacterial community composition. Moreover, bacteria putatively involved in the aerobic degradation of PCBs were enriched over the total bacterial community in topsoils, where the highest activity was recorded using fluorescein hydrolysis as proxy. Metataxonomic analyses revealed the presence of bacteria having metabolic pathways related to PCB degradation and tolerance to heavy metals and metalloids in the topsoil samples collected in all areas. Overall, the provided dissection of soil microbiota structure and its degradation potential in the SIN Brescia-Caffaro can contribute to target specific areas for rhizoremediation implementation. Metagenomics studies could be implemented in the future to understand if specific degradative pathways are present in historically polluted sites characterized by the co-occurrence of multiple classes of contaminants.

The influence of anaerobic dechlorination on the aerobic degradation of PCBs in e-waste-contaminated soils in an anaerobic-aerobic two-stage treatment

The combination of microbial reductive dechlorination and aerobic oxidation (RD-AO) process was proposed to be a promising strategy for extensive bioremediation of highly chlorinated polychlorinated biphenyls (PCBs). Nonetheless, experimental evidence on the impact of the RD on subsequent AO in anaerobic-aerobic two-stage treatment remains scarce. The present study applied stable-isotope probing (SIP) to explore the RD-AO mediated degradation of PCBs in an e-waste-contaminated soil. The RD-AO treatment resulted in 37.1 % and 48.2 % degradation of PCB180 and PCB9, respectively, while the PCB9 degradation efficiency decreased compared to the sole AO (81.2 %). The inhibition of PCB aerobic degradation might be caused by the alteration of aerobic bacterial community, which was proved by a higher abundance of anaerobic bacteria and a lower abundance of aerobic bacteria being observed in the aerobic stage of RD-AO. Further evidence was obtained using DNA-SIP that the anaerobic stage altered the PCB degraders' community structures and changed three of the five degraders. There were four lineages (Arenimonas, Steroidobacter, Sulfurifustis, and Thermoanaerobacterales) identified as PCB degraders for the first time. Interestingly, three of them were found in RD-AO microcosm, suggesting that anaerobic-aerobic two-stage treatment can recruit novel bacteria involved in PCBs aerobic degradation. The present study provided novel insight into the synergistic integration of anaerobic and aerobic processes for extensive degradation of highly chlorinated PCBs.

Elsholtzia splendens promotes phenanthrene and polychlorinated biphenyl degradation under Cu stress through enrichment of microbial degraders

Co-contamination of heavy metals and organic pollutants is widespread in the environment. Metal-tolerant/hyperaccumulating plants have the advantage of enhancing co-operation between plants and rhizospheric microbes under heavy metal stress, but the underlying mechanism remains unclear. In the present study, the effects of Elsholtzia splendens and Lolium perenne on the rhizospheric microbial community and degraders of phenanthrene (PHE) and polychlorinated biphenyls (PCBs) were investigated. The results showed E. splendens could tolerate high Cu concentrations, while L. perenne was sensitive to Cu toxicity. Although Cu played the most important role in microbial community construction, both E. splendens and L. perenne caused shifts in the rhizospheric microbial community. For PHE and PCB degradation, L. perenne was more efficient under low Cu concentrations, whereas E. splendens performed better under high Cu concentrations. This difference can be attributed to shifts in the degrader community and key degradation genes identified by stable isotope probing. Moreover, higher abundances of various genes for organic pollutant degradation were observed in the rhizosphere of E. splendens than L. perenne based on gene prediction under high Cu stress. Our study reveals underlying mechanism of the advantages of heavy metal-tolerant plants for organic pollutant removal in soils co-contaminated with heavy metals.

The positive role of root decomposition on the bioremediation of organic pollutants contaminated soil: A case study using PCB-9 as a model compound

Root decomposition keeps occurring widely in soils, particularly after plant harvest and death, and drives critical microbial ecological functions. However, its role in the destiny of soil organic pollutants and underlying mechanisms remain unclear. In this study, DNA stable isotope probing (DNA-SIP) was combined with metabolomics to investigate the mechanisms of soil polychlorinated biphenyls (PCBs) degradation in the root decomposition process by identifying the active PCBs degraders in situ and corresponding metabolites. The 2,5-dichlorobiphenyl (PCB-9) degradation was improved by 7.4% in the root decomposition treatment relative to the rhizosphere treatment, and the degradation was faster in both treatments than the control after 6-week cultivation. Both root decomposition and rhizosphere treatments altered soil microbial community, changing the active PCB-9 degraders to different extents. The root decomposition treatment had the highest “average phylogenetic distance index” (ADI) value, indicating a competition reduction effect of root decomposition on microbial survival, and the lowest corrected average phylogenetic distance index (ADIC) value, suggesting a preference toward aerobic PCBs degraders during root decomposition. Metabolites associated with the root decomposition process critically affected both the whole microbial community and active PCB-9 degraders. Compounds related to carbohydrate and lipid metabolisms were enriched during the root decomposition process and might be important to the active PCB-9-degrading community assembly. Our results confirmed that root decomposition improved the biodegradation of organic pollutants in soil and reminded us of its importance in soil quality.

Micro-synteny conservation analysis revealed the evolutionary history of bacterial biphenyl degradation pathway.

Phenolic compounds have been enlisted by the United States Environmental Protection Agency (USEPA) and the European Union (EU) as pollutants of priority concern. The biphenyl degradation pathway plays an essential role in prokaryote polychlorinated biphenyls degradation. Our understanding of prokaryotic pathways and their evolution has dramatically increased in recent years with the advancements in prokaryotic genome sequencing and analysis tools. In this work, we applied bioinformatics tools to study the evolution of the biphenyl degradation pathway focusing on the phylogeny and initiation of four representative species (Burkholderia xenovorans LB400, Polaromonas naphthalenivorans CJ2, Pseudomonas putida F1 and Rhodococcus jostii RHA1). These species contained partial or full concatenated genes from bph gene cluster (i.e. bphRbphA1A2A3A4BCKHJID). The aim was to establish this pathway's origin and development mode in the prokaryotic world. Genomic screening revealed that many bacterial species possess genes for the biphenyl degradation pathway. However, the micro-synteny conservation analysis indicated that massive gene recruitment events might have occurred during the evolution of the biphenyl degradation pathway. Combining with the phylogenetic positions, this work points to the evolutionary process of acquiring the biphenyl degradation pathway by different fragments through horizontal gene transfer in these bacterial groups. This study reports the first-ever evidence of the birth of this pathway in the represented species.