Conjugative Transfer of Dioxin-Catabolic Megaplasmids and Bioaugmentation Prospects of a Rhodococcus sp

LuxR solo regulates recalcitrant aromatic compound biodegradation: Repression and activation of dibenzofuran-catabolic genes expression in a Rhodococcus sp

Aromatic compounds contribute to the category of prevalent, toxic, and persistent pollutants in the environment. Microbial degradation of aromatic pollutants is eco-friendly, which depends on efficient manipulation of catabolic enzyme activity. As homologs of quorum sensing LuxR family regulators, LuxR solos play important roles in cell-cell interaction; however, there are few studies on its regulation of recalcitrant aromatic compounds degradation. In this study, the transcriptional regulatory mechanism of dibenzofuran catabolic genes controlled by LuxR solo was elucidated in the dioxin-degrader Rhodococcus sp. strain p52. LuxR solo encoded by catabolic plasmid pDF01 was detected to bind to the promoters of dfdA and dfdB and inhibit the genes expression, which are involved in dibenzofuran degradation. The repression of the LuxR on the catabolic genes expression was not affected by dibenzofuran, but could be alleviated by the intermediate of dibenzofuran degradation, salicylic acid. RNA-Seq analysis suggested that the LuxR solo related to regulating the expression of multiple key genes on the chromosome and catabolic plasmids pDF02. Phylogenetic analysis indicated that LuxR solos frequently distribute among aromatics-degrading bacteria. This study reveals the molecular regulatory network of dibenzofuran degradation mediated by LuxR solo and deepens the understanding of transcriptional regulatory mechanisms of aromatic compounds degradation.

Chlorine removal technologies for resource utilization of municipal solid waste incineration fly ash

The resource utilization of municipal solid waste incineration fly ash (MSWI FA) has been widely concerned at present. The chlorine removal from MSWI FA is of great significance for controlling environmental risk and improving materials properties in the process of its resource utilization. This work specifically proposes to divide the chlorine in MSWI FA into inorganic chloride and organic chloride. The removal rate, influencing factors, and removal mechanism of chlorine in MSWI FA using various technologies were systematically analyzed. In addition, the applicability, advantages and disadvantages of chlorine removal technology in different scenarios were highlighted. This work identifies the technical barriers that need to be solved urgently in the current research and proposes a key direction for future research on the regulation of chlorine removal technologies of MSWI FA.

Fitness and adaptive evolution of a Rhodococcus sp. harboring dioxin-catabolic plasmids

Catabolic plasmids are critical factors in the degradation of recalcitrant xenobiotics, such as dioxins. Understanding the persistence and evolution of native catabolic plasmids is pivotal for controlling their function in microbial remediation. Here, we track the fitness and evolution of Rhodococcus sp. strain p52 harboring dioxin-catabolic plasmids under nonselective conditions without contaminant. Growth curve analysis and competition experiments demonstrated that pDF01 imposed fitness costs, whereas pDF02 conferred fitness benefits. During stability tests, pDF01 tended to be lost from the population, while pDF02 maintained at least one copy in the cell until proliferation of the 400th generation. Genome-wide gene expression profiling combined with codon usage bias analysis revealed that the high expression of pDF01 genes involved in dibenzofuran catabolism and regulation caused metabolic burdens. In contrast, potential cooperation between the pDF02-encoded short-chain dehydrogenase/reductase family oxidoreductase and the redox cofactor mycofactocin, which synthetic genes are located on the chromosome, may explain the benefit of pDF02. The fitness cost imposed by pDF01 was alleviated during adaptive evolution and was associated with the transcriptional downregulation of the dibenzofuran degradation genes on pDF01, and the global regulation of genome-wide gene expression involving basic metabolism, transport, and signal transduction. This study broadens our understandings on the persistence and evolution of dioxin-catabolic mega-plasmids, thus paving the way for the bioremediation of recalcitrant xenobiotic pollution in the environment.

Metabolic cross-feeding between the competent degrader Rhodococcus sp. strain p52 and an incompetent partner during catabolism of dibenzofuran: Understanding the leading and supporting roles

Microbial interactions, particularly metabolic cross-feeding, play important roles in removing recalcitrant environmental pollutants; however, the underlying mechanisms involved in this process remain unclear. Thus, this study aimed to elucidate the mechanism by which metabolic cross-feeding occurs during synergistic dibenzofuran degradation between a highly efficient degrader, Rhodococcus sp. strain p52, and a partner incapable of utilizing dibenzofuran. A bottom-up approach combined with pairwise coculturing was used to examine metabolic cross-feeding between strain p52 and Arthrobacter sp. W06 or Achromobacter sp. D10. Pairwise coculture not only promoted bacterial pair growth but also facilitated dibenzofuran degradation. Specifically, strain p52, acting as a donor, released dibenzofuran metabolic intermediates, including salicylic acid and gentisic acid, for utilization and growth, respectively, by the partner strains W06 and D10. Both salicylic acid and gentisic acid exhibited biotoxicity, and their accumulation inhibited dibenzofuran degradation. The transcriptional activity of the genes responsible for the catabolism of dibenzofuran and its metabolic intermediates was coordinately regulated in strain p52 and its cocultivated partners, thus achieving synergistic dibenzofuran degradation. This study provides insights into microbial metabolic cross-feeding during recalcitrant environmental pollutant removal.

(Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation

The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.IMPORTANCERhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.

Analysis and discussion on formation and control of dioxins generated from municipal solid waste incineration process

Dioxins are a kind of persistent organic pollutants (POPs) with extremely toxic. Municipal solid waste incineration (MSWI) process has become one of the most dominant discharge sources of dioxins. A comprehensive discussion about dioxin formation mechanisms was reviewed in this paper, and the mechanisms of high-temperature gas-phase reaction and "de novo" synthesis were systematically illustrated in the form of diagrams. What's more, the effects of various influencing factors on the formation of PCDD/Fs were briefly analyzed in the form of a table. We believed that temperature, catalyst, chlorine source, carbon source, oxygen concentration and moisture were necessary factors for PCDD/Fs formation. Control technologies of dioxins in MSWI process were summarized subsequently from three stages: pre-combustion, in-combustion and post-combustion, and a device for synergistic removal of dioxins based on multi-field force coupling and technical routes for controlling dioxin emissions were proposed, so as to provide mechanisms and methods for effectively reducing the emission concentration of dioxins. An introduction was also conducted of dioxin control technologies in municipal solid waste incineration fly ash (MSWI-FA) in this paper, and their mechanisms, advantages, disadvantages and technical maturity were illustrated in the form of diagrams, which can provide theory and reference for in-depth research of follow-up scholars and industrial application of dioxin control technologies. Finally, current research hotspots, challenges and future research directions were proposed.Implications: In this paper, the main research contents and achievements are as follows: With the emphasis placed on the formation mechanism of dioxins and effects of various influencing factors on the formation of PCDD/Fs. The control technology of dioxins in MSWI process is summarized subsequently from three stages: pre-combustion, in-combustion and post-combustion.A device for synergistic removal of dioxins based on multi-field force coupling and technical routes for controlling dioxin emissions are proposed.A systematic review is conducted of the research progress on control technologies of dioxins in MSWI fly ash in the most recent years.The mechanisms, advantages, disadvantages and technical maturity of PCDD/Fs degradation technologies in MSWI fly ash are illustrated in the form of diagrams.Current research hotspots, challenges and future research directions are proposed.

The impact of pollutant as selection pressure on conjugative transfer of dioxin-catabolic plasmids harbored by Rhodococcus sp. strain p52

Plasmid-mediated bioaugmentation has potential application in the cleanup of recalcitrant environmental pollutants. In this study, we examined the influence of various contaminants (in different categories or different amounts) as a selection pressure on the spread of catabolic plasmids within an activated sludge bacteria community bioaugmented with Rhodococcus sp. strain p52 harboring pDF01 and pDF02. The distinguishable genera of transconjugants were isolated under the stresses of phenanthrene, dibenzothiophene, and dibenzo-p-dioxin. The three contaminants exerted different degrees of influence on the activated sludge bacteria bearing the catabolic plasmids. The relatively high ratios of transconjugant-bearing catabolic plasmids were detected in the reactor fed with dibenzo-p-dioxin. As dibenzo-p-dioxin from 10 to 80 mg/L was fed into the reactors, the ratios of transconjugant-bearing catabolic plasmids increased. Additionally, levels of ROS and extracellular LDH of activated sludge bacteria in the contaminants-fed reactors increased, comparing with that in the control reactor, indicating that the contaminants exerted toxicity which promoted the cell membrane permeability of the activated sludge bacteria. Our study provides a characterization of the recalcitrant contaminants as a selection pressure that can modulate catabolic plasmid transfer during genetic bioaugmentation for the removal of contaminants.

Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures

Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.

Horizontal Gene Transfer of Genes Encoding Copper-Containing Membrane-Bound Monooxygenase (CuMMO) and Soluble Di-iron Monooxygenase (SDIMO) in Ethane- and Propane-Oxidizing Rhodococcus Bacteria

The families of copper-containing membrane-bound monooxygenases (CuMMOs) and soluble di-iron monooxygenases (SDIMOs) are involved not only in methane oxidation but also in short-chain alkane oxidation. Here, we describe Rhodococcus sp. strain ZPP, a bacterium able to grow with ethane or propane as the sole carbon and energy source, and report on the horizontal gene transfer (HGT) of actinobacterial hydrocarbon monooxygenases (HMOs) of the CuMMO family and the sMMO (soluble methane monooxygenase)-like SDIMO in the genus Rhodococcus. The key function of HMO in strain ZPP for propane oxidation was verified by allylthiourea inhibition. The HMO genes (designated hmoCAB) and those encoding sMMO-like SDIMO (designated smoXYB1C1Z) are located on a linear megaplasmid (pRZP1) of strain ZPP. Comparative genomic analysis of similar plasmids indicated the mobility of these plasmids within the genus Rhodococcus. The plasmid pRZP1 in strain ZPP could be conjugatively transferred to a recipient Rhodococcus erythropolis strain in a mating experiment and showed similar ethane- and propane-consuming activities. Finally, our findings demonstrate that the horizontal transfer of plasmid-based CuMMO and SDIMO genes confers the ability to use ethane and propane on the recipient. IMPORTANCE CuMMOs and SDIMOs initiate the aerobic oxidation of alkanes in bacteria. Here, the supposition that horizontally transferred plasmid-based CuMMO and SDIMO genes confer on the recipient similar abilities to use ethane and propane was proposed and confirmed in Rhodococcus. This study is a living example of HGT of CuMMOs and SDIMOs and outlines the plasmid-borne properties responsible for gaseous alkane degradation. Our results indicate that plasmids can support the rapid evolution of enzyme-mediated biogeochemical processes.

Bioaugmentation of triclocarban and its dechlorinated congeners contaminated soil with functional degraders and the bacterial community response

Partial removal of haloaromatic antimicrobial triclocarban (TCC) during wastewater treatment caused the final introduction of residual TCC into soils. Bioaugmentation has been proposed for the biodegradation of TCC and its dechlorinated congeners 4,4'-dichlorocarbanilide (DCC) and carbanilide (NCC) in soil. The isolated TCC-degrading strain Ochrobactrum sp. TCC-2 and chloroanilines-degrading strain Diaphorobacter sp. LD72 were used to study the removal efficiency of TCC, DCC and NCC mixture and their chloroanilines intermediates, respectively. The potential degradation competition between TCC and its dechlorinated congeners, and the response of bacterial community during the bioremediation were also investigated. The biodegradation of DCC and TCC was significantly enhanced for soil with inoculums compared with sterilized and natural soils. Chloroanilines products could also be effectively removed. For the degradation of combined substrates in the aqueous medium, NCC had negative effect on the degradation of TCC and DCC, while TCC and DCC negatively influenced each other. The bioaugmentation with two degraders obviously changed the phylogenetic composition and function of indigenous soil microbiome. Importantly, the inoculated degraders could be maintained, suggesting their adaptability and potential application in bioaugmentation for such recalcitrant contaminants. This study offers new insights into the enhanced bioremediation of TCC and its dechlorinated congeners contaminated soils by the bioaugmentation of functional degraders and the structure and function response of the indigenous soil microbiome to the bioremediation process.

The effect and mechanism of urban fine particulate matter (PM2.5) on horizontal transfer of plasmid-mediated antimicrobial resistance genes

Fine particulate matter (PM_2.5) and antimicrobial resistance are two major threats to public health worldwide. Current air pollution studies rely heavily on the assessment of PM_2.5 chemistry and toxicity. However, whether and how PM_2.5 affects the proliferation and transfer of antimicrobial resistance genes (ARGs) in various environments has remained unanswered. This study investigated the effects and potential mechanisms of urban PM_2.5 on the horizontal transfer of ARGs between opportunistic Escherichia coli (E. coli) strains. The results showed that urban PM_2.5 samples collected from Xi'an (XA), Shanghai (SH), and Shijiazhuang (SJZ) in China induced location- and concentration-dependent promotion of conjugative transfer frequencies compared to the control group. The relevant mechanisms were also explored, including the formation of intracellular reactive oxygen species (ROS) and the subsequent induction of oxidative stress, SOS response, changes in membrane permeability, and alternations in mRNA expression of genes involved in horizontal transfer. This study highlights the effect of PM_2.5 on promoting the horizontal transfer of ARGs and elucidates the mechanism of the antimicrobial-resistance risks posed by urban PM_2.5. These findings are of great value in understanding the transmission of antimicrobial resistance in various environments and provide valuable information for re-evaluating air quality assessment practices.

Enhanced plasmid-mediated bioaugmentation of RDX-contaminated matrices in column studies using donor strain Gordonia sp. KTR9

Horizontal gene transfer (HGT) is the lateral movement of genetic material between organisms. The RDX explosive-degrading bacterium Gordonia sp. KTR9 has been shown previously to transfer the pGKT2 plasmid containing the RDX degradative genes (xplAB) by HGT. Overall, fitness costs to the transconjugants to maintain pGKT2 was determined through growth and survivability assessments. Rhodococcus jostii RHA1 transconjugants demonstrated a fitness cost while other strains showed minimal cost. Biogeochemical parameters that stimulate HGT of pGKT2 were evaluated in soil slurry mating experiments and the absence of nitrogen was found to increase HGT events three orders of magnitude. Experiments evaluating RDX degradation in flow-through soil columns containing mating pairs showed 20% greater degradation than columns with only the donor KTR9 strain. Understanding the factors governing HGT will benefit bioaugmentation efforts where beneficial bacteria with transferrable traits could be used to more efficiently degrade contaminants through gene transfer to native populations.

Genetic Bioaugmentation of Activated Sludge with Dioxin-Catabolic Plasmids Harbored by Rhodococcus sp. Strain p52

Horizontal transfer of catabolic plasmids is used in genetic bioaugmentation for environmental pollutant remediation. In this study, we examined the effectiveness of genetic bioaugmentation with dioxin-catabolic plasmids harbored by Rhodococcus sp. strain p52 in laboratory-scale sequencing batch reactors (SBRs). During 100 days of operation, bioaugmentation decreased the dibenzofuran content (120 mg L^-1) in the synthetic wastewater by 32.6%-100% of that in the nonbioaugmented SBR. Additionally, dibenzofuran was removed to undetectable levels in the bioaugmented SBR, in contrast, 46.8 ± 4.1% of that in the influent remained in the nonbioaugmented SBR after 96 days. Moreover, transconjugants harboring pDF01 and pDF02 were isolated from the bioaugmented SBR after 2 days, and their abilities to degrade dibenzofuran were confirmed. After 80 days, the copy numbers of strain p52 decreased by 3 orders of magnitude and accounted for 0.05 ± 0.01% of the total bacteria, while transconjugants were present at around 10⁶ copies mL^-1 sludge and accounted for 8.2 ± 0.3% of the total bacteria. Evaluation of the bacterial community profile of sludge by high-throughput 16S rRNA gene sequencing revealed that genetic bioaugmentation led to a bacterial community with an even distribution of genera in the SBR. This study demonstrates the promise of genetic bioaugmentation with catabolic plasmids for dioxins remediation.