Novel PCB-degrading Rhodococcus strains able to promote plant growth for assisted rhizoremediation of historically polluted soils

Polychlorinated biphenyls modify Arabidopsis root exudation pattern to accommodate degrading bacteria, showing strain and functional trait specificity

Introduction

The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized.

Methods

Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms.

Results

Arabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-β-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation.

Discussion

These findings expand the knowledge on PCB-triggered "cry-for-help" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.

Potential of the plant growth-promoting rhizobacterium Rhodococcus qingshengii LMR356 in mitigating lead stress impact on Sulla spinosissima L

Mining-related lead (Pb) pollution of the soil poses serious hazards to ecosystems and living organisms, including humans. Improved heavy metal phytoremediation efficacy, achieved by using phytostabilizing plants assisted by plant-growth-promoting (PGP) microorganisms, has been presented as an effective strategy for remediating polluted soils. The objective of this research was to examine the response and potential of the plant-growth-promoting bacterium LMR356, a Rhodococcus qingshengii strain isolated from an abandoned mining soil, under lead stress conditions. Compared to non-contaminated culture media, the presence of lead induced a significant decrease in auxin production (from 21.17 to 2.65 μg mL-1) and phosphate solubilization (from 33.60 to 8.22 mg L-1), whereas other PGP traits increased drastically, such as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity (from 38.17 to 71.37 nmol mg-1 h-1 α-ketobutyrate), siderophore production (from 69 to 83%), exopolysaccharide production (from 1952.28 to 3637.72 mg mL-1), biofilm formation, and motility. We, therefore, investigated the behavior of Sulla spinosissima L. in the presence or absence of this strain under a variety of experimental conditions. Under hydroponic conditions, Sulla plants showed endurance to varying lead concentrations (500-1000 μM). Inoculation of plants with Rhodococcus qingshengii strain LMR356 enhanced plant tolerance, as demonstrated by the increase in plant biomass (ranging from 14.41 to 79.12%) compared to non-inoculated Pb-stressed and non-stressed control plants. Antioxidant enzyme activities (increasing by -42.71 to 126.8%) and chlorophyll (383.33%) and carotenoid (613.04%) content were also augmented. In addition to its impact on plant lead tolerance, strain LMR356 showed a growth-promoting effect on Sulla plants when cultivated in sterilized non-contaminated sand. Parameters such as plant biomass (16.57%), chlorophyll (24.14%), and carotenoid (30%) contents, as well as ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT) activities, were all elevated compared to non-inoculated plants. Furthermore, when the same plant species was cultivated in highly polluted soil, inoculation increased plant biomass and improved its physiological properties. These findings demonstrate that LMR356 is a phytobeneficial bacterial strain capable of enhancing Sulla growth under normal conditions and improving its heavy metal tolerance in multi-polluted soils. Thus, it can be considered a promising biofertilizer candidate for growing Sulla spinosissima L. or other selected plants intended for application in restoration and stabilization initiatives aimed at reviving and safeguarding environmentally compromised and polluted soils after mining activities.

Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase

Monohydroxylated PCBs (OH-PCBs) are an (eco)toxicologically significant group of compounds, as they arise from the oxidation of polychlorinated biphenyls (PCBs) and, at the same time, may exert even more severe toxic effects than their parent PCB molecules. Despite having been widely detected in environmental samples, plants, and animals, information on the fate of OH-PCBs in the environment is scarce, including on the enzymatic machinery behind their degradation. To date, only a few bacterial taxa capable of OH-PCB transformation have been reported. In this study, we aimed to obtain a deeper insight into the transformation of OH-PCBs in soil bacteria and isolated a Pseudomonas sp. strain P1B16 based on its ability to use o-phenylphenol (2-PP) which, when exposed to the Delor 103-derived OH-PCB mixture, depleted a wide spectrum of mono-, di, and trichlorinated OH-PCBs. In the P1B16 genome, a region designated as hbp was identified, which bears a set of putative genes involved in the transformation of OH-PCBs, namely hbpA encoding for a putative flavin-dependent 2-hydroxybiphenyl monooxygenase, hbpC (2,3-dihydroxybiphenyl-1,2-dioxygenase), hbpD (2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase), and the transcriptional activator-encoding gene hbpR. The hbpA coding sequence was heterologously expressed, purified, and its substrate specificity was investigated towards the Delor 103-derived OH-PCB mixture, individual OH-PCBs, and multiple (chlorinated) phenolics. Apart from 2-PP and 2-chlorophenol, HbpA was also demonstrated to transform a range of OH-PCBs, including a 3-hydroxy-2,2',4',5,5'-pentachlorobiphenyl. Importantly, this is the first direct evidence of HbpA homologs being involved in the degradation of OH-PCBs. Moreover, using a P1B16-based biosensor strain, the specific induction of hbp genes by 2-PP, 3-phenylphenol, 4-phenylphenol, and the OH-PCB mixture was demonstrated. This study provides direct evidence on the specific enzymatic machinery responsible for the transformation of OH-PCBs in bacteria, with many implications in ecotoxicology, environmental restoration, and microbial ecology in habitats burdened with PCB contamination.

Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil

Endogenous hydrogen (H₂) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H₂ leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H₂ from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H₂. Based on metagenomes of ¹³C-enriched DNA fractions, endogenous H₂ selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H₂ of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H₂ is a significant energy source for active PCB-degrading communities and suggests that elevated H₂ can influence the microbial ecology and biogeochemistry of the legume rhizosphere.

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.

Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future

Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.

Fate and Transformation of 6:2 Fluorotelomer Sulfonic Acid Affected by Plant, Nutrient, Bioaugmentation, and Soil Microbiome Interactions

6:2 Fluorotelomer sulfonic acid (6:2 FTSA) is a dominant per- and poly-fluoroalkyl substance (PFAS) in aqueous film-forming foam (AFFF)-impacted soil. While its biotransformation mechanisms have been studied, the complex effects from plants, nutrients, and soil microbiome interactions on the fate and removal of 6:2 FTSA are poorly understood. This study systematically investigated the potential of phytoremediation for 6:2 FTSA byArabidopsis thalianacoupled with bioaugmentation ofRhodococcus jostiiRHA1 (designated as RHA1 hereafter) under different nutrient and microbiome conditions. Hyperaccumulation of 6:2 FTSA, defined as tissue/soil concentration > 10 and high translocation factor > 3, was observed in plants. However, biotransformation of 6:2 FTSA only occurred under sulfur-limited conditions. Spiking RHA1 not only enhanced the biotransformation of 6:2 FTSA in soil but also promoted plant growth. Soil microbiome analysis uncovered Rhodococcus as one of the dominant species in all RHA1-spiked soil. Different nutrients such as sulfur and carbon, bioaugmentation, and amendment of 6:2 FTSA caused significant changes in - microbial community structure. This study revealed the synergistic effects of phytoremediation and bioaugmentation on 6:2 FTSA removal. and highlighted that the fate of 6:2 FTSA was highly influced by the complex interactions of plants, nutrients, and soil microbiome.

Biostimulation and Bioaugmentation of Soils Contaminated with Decachlorobiphenyl (PCB-209) Using Native Bacterial Strains Individually and in Consortia

Historically, microorganisms have proven to be efficient alternatives for the removal of PCBs, since these contaminants continue to be a major problem for human health and the environment. In this work, the removal of decachlorobiphenyl (PCB-209) was evaluated using native bacterial strains individually and in consortia through biostimulation and bioaugmentation processes. Bacillus sp. DCB13, Staphylococcus sp. DCB28, and Acinetobacter sp. DCB104 were biostimulated in a minimal medium that initially contained biphenyl and later PCB-209 for adaptation as a carbon source. The removal potential of PCB-209 by bacterial strains was evaluated in a bioaugmentation process under aerobic conditions. Using a completely randomized design, ten different treatments were evaluated. Finally, the bacterial growth (CFU/g of soil) and the chemical characteristics of the bioaugmented soil were determined, as was the content of PCB-209 removed by gas chromatography–mass spectrometry. Strains DCB13, DCB28, and DCB104 showed cell growth (>3.4 × 105 CFU/mL) during 120 h of biostimulation, with a marked difference between treatments with biphenyl compared with those where PCB-209 was added. Strains DCB13 and DCB104 (3.4 × 105 CFU/mL and 2.0 × 106 CFU/mL, respectively) grew better with PCB-209, while DCB28 grew better with biphenyl (4.5 × 106 CFU/mL). In bioaugmented soils contaminated with PCB-209, the strains showed maximum growth when inoculated in a consortium (>2.0 × 104 CFU/g). The results showe that the range of the bacterial elimination of PCB-209 in the treatments was from 9.58 to 17.33 mg/kg. The highest elimination potential of PCB-209 was obtained when the bacterial strains were inoculated in a consortium. These findings open a wide perspective for the use of native bacteria for the cleaning and restoration of soils contaminated by toxic chemicals.

Hyunsoonleella sp. HU1-3 Increased the Biomass of Ulva fasciata

Green algae are photosynthetic organisms and play an important role in coastal environment. The microbial community on the surface of green algae has an effect on the health and nutrition of the host. However, few species of epiphytic microbiota have been reported to play a role in promoting the growth of algae. In this study, 16S rDNA sequencing was used to study the changes of microbial composition on the surface of Ulva fasciata at different growth stages. Some growth promoting bacteria were identified. The possible growth-promoting behavior of the strains were verified by co-culture of pure bacteria obtained from the surface of U. fasciata with its sterile host. Among the identified species, a new bacterial species, Hyunsoonleella sp. HU1-3 (belonging to the family Flavobacteriaceae) significantly promoted the growth of U. fasciata. The results also showed that there were many genes involved in the synthesis of growth hormone and cytokinin in the genome of Hyunsoonleella sp. HU1-3. This study identified the bacterium Hyunsoonleella sp. HU1-3 for the first time, in which this bacterium has strong growth-promoting effects on U. fasciata. Our findings not only provide insights on the establishment of the surface microbiota of U. fasciata, but also indicate that Hyunsoonleella sp. HU1-3 is one of the important species to promote the growth of U. fasciata.

Predominant Biphenyl Dioxygenase From Legacy Polychlorinated Biphenyl (PCB)-Contaminated Soil Is a Part of Unusual Gene Cluster and Transforms Flavone and Flavanone

In this study, the diversity of bphA genes was assessed in a ¹³C-enriched metagenome upon stable isotope probing (SIP) of microbial populations in legacy PCB-contaminated soil with ¹³C-biphenyl (BP). In total, 13 bphA sequence variants (SVs) were identified in the final amplicon dataset. Of these, one SV comprised 59% of all sequences, and when it was translated into a protein sequence, it exhibited 87, 77.4, and 76.7% identity to its homologs from Pseudomonas furukawaii KF707, Cupriavidus sp. WS, and Pseudomonas alcaliphila B-367, respectively. This same BphA sequence also contained unusual amino acid residues, Alanine, Valine, and Serine in region III, which had been reported to be crucial for the substrate specificity of the corresponding biphenyl dioxygenase (BPDO), and was accordingly designated BphA_AVS. The DNA locus of 18 kbp containing the BphA_AVS-coding sequence retrieved from the metagenome was comprised of 16 ORFs and was most likely borne by Paraburkholderia sp. The BPDO corresponding to bphAE_AVS was cloned and heterologously expressed in E. coli, and its substrate specificity toward PCBs and a spectrum of flavonoids was assessed. Although depleting a rather narrow spectrum of PCB congeners, the efficient transformation of flavone and flavanone was demonstrated through dihydroxylation of the B-ring of the molecules. The homology-based functional assignment of the putative proteins encoded by the rest of ORFs in the AVS region suggests their potential involvement in the transformation of aromatic compounds, such as flavonoids. In conclusion, this study contributes to the body of information on the involvement of soil-borne BPDOs in the metabolism of flavonoid compounds, and our paper provides a more advanced context for understanding the interactions between plants, microbes and anthropogenic compounds in the soil.

An actinomycete strain of Nocardiopsis lucentensis reduces arsenic toxicity in barley and maize

Accumulation of arsenic in plant tissues poses a substantial threat to global crop yields. The use of plant growth-promoting bacterial strains to mitigate heavy metal toxicity has been illustrated before. However, its potential to reduce plant arsenic uptake and toxicity has not been investigated to date. Here, we describe the identification and characterization of a Nocardiopsis lucentensis strain isolated from heavy metal contaminated soil. Inoculation with this bioactive actinomycete strain decreased arsenic root and shoot bioaccumulation in both C3 and C4 crop species namely barley and maize. Upon arsenate treatment, N. lucentensis S5 stimulated root citric acid production and the plant's innate detoxification capacity in a species-specific manner. In addition, this specific strain promoted biomass gain, despite substantial tissue arsenic levels. Detoxification (metallothionein, phytochelatin, glutathione-S-transferase levels) was upregulated in arsenate-exposed shoot and roots, and this response was further enhanced upon S5 supplementation, particularly in barley and maize roots. Compared to barley, maize plants were more tolerant to arsenate-induced oxidative stress (less H₂O₂ and lipid peroxidation levels). However, barley plants invested more in antioxidative capacity induction (ascorbate-glutathione turnover) to mitigate arsenic oxidative stress, which was strongly enhanced by S5. We quantify and mechanistically discuss the physiological and biochemical basis of N. lucentensis-mediated plant biomass recovery on arsenate polluted soils. Our findings substantiate the potential applicability of a bactoremediation strategy to mitigate arsenic-induced yield loss in crops.

Clover Root Exudates Favor Novosphingobium sp. HR1a Establishment in the Rhizosphere and Promote Phenanthrene Rhizoremediation

Rhizoremediation is based on the ability of microorganisms to metabolize nutrients from plant root exudates and, thereby, to cometabolize or even mineralize toxic environmental contaminants. Novosphingobium sp. HR1a is a bacterial strain able to degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs). Here, we have demonstrated that the number of CFU in microcosms vegetated with clover was almost 2 orders of magnitude higher than that in nonvegetated microcosms or microcosms vegetated with rye-grass or grass. Strain HR1a was able to eliminate 92% of the phenanthrene in the microcosms with clover after 9 days. We have studied the molecular basis of the interaction between strain HR1a and clover by phenomic, metabolomic, and transcriptomic analyses. By measuring the relative concentrations of several metabolites exudated by clover both in the presence and in the absence of the bacteria, we identified some compounds that were probably consumed in the rhizosphere; the transcriptomic analyses confirmed the expression of genes involved in the catabolism of these compounds. By using a transcriptional fusion of the green fluorescent protein (GFP) to the promoter of the gene encoding the dioxygenase involved in the degradation of PAHs, we have demonstrated that this gene is induced at higher levels in clover microcosms than in nonvegetated microcosms. Therefore, the positive interaction between clover and Novosphingobium sp. HR1a during rhizoremediation is a result of the bacterial utilization of different carbon and nitrogen sources released during seedling development and the capacity of clover exudates to induce the PAH degradation pathway. IMPORTANCE The success of an eco-friendly and cost-effective strategy for soil decontamination is conditioned by the understanding of the ecology of plant-microorganism interactions. Although many studies have been published about the bacterial metabolic capacities in the rhizosphere and about rhizoremediation of contaminants, there are fewer studies dealing with the integration of bacterial metabolic capacities in the rhizosphere during PAH bioremediation, and some aspects still remain controversial. Some authors have postulated that the presence of easily metabolizable carbon sources in root exudates might repress the expression of genes required for contaminant degradation, while others found that specific rhizosphere compounds can induce such genes. Novosphingobium sp. HR1a, which is our model organism, has two characteristics desirable in bacteria for use in remediation: its ubiquity and the capacity to degrade a wide variety of contaminants. We have demonstrated that this bacterium consumes several rhizospheric compounds without repression of the genes required for the mineralization of PAHs. In fact, some compounds even induced their expression.

Microbiome Fingerprint as Biomarker for Geographical Origin and Heredity in Crocus sativus: A Feasibility Study

Host–microbiome interactions are specific and not random, making them defining entities for the host. The hypothesis proposed by various researchers earlier, that both plants and animals harbor specific inheritable core microbiome, is being augmented in the present study. Additionally, a case for using microbial fingerprint as a biomarker, not only for plant identification but also as a geographical indicator, has been investigated, taking Crocus sativus, saffron, as a study material. Crocus sativus, a monogenetic herb, on account of its male sterility and vegetative propagation, is reported to lack genome based molecular markers. Cormosphere microbiome (microbiome associated with corm) has been compared across three geographical locations, in two continents, to identify the core and unique microbiome, during the vegetative phase of its growth. Microbiome analysis done at phylum and genus level, using next generation sequencing technology, revealed that cormosphere at three locations harbored common phyla. At genus level, 24 genera were found common to all three geographical locations, indicating them to be part of the core microbiome of saffron. However, there were some bacterial genera unique to Kashmir, Kishtwar, and Morocco that can be used to develop microbial markers/geographical indicators for saffron grown in these regions. This is a preliminary study, indicating that the location specific bacterial community can be used to develop microbial barcodes but needs further augmentation with high coverage data from other saffron growing geographical regions.

Biphenyl 2,3-Dioxygenase in Pseudomonas alcaliphila JAB1 Is Both Induced by Phenolics and Monoterpenes and Involved in Their Transformation

The involvement of bacterial aromatic ring-hydroxylating dioxygenases (ARHDs) in the degradation of aromatic pollutants, such as polychlorinated biphenyls (PCBs), has been well studied. However, there is considerable speculation as to the origin of this ability. One hypothesis is centered on a connection between the ability to degrade aromatic pollutants and the necessity of soil bacteria to cope with and/or utilize secondary plant metabolites (SPMs). To investigate this connection, we researched the involvement of biphenyl 2,3-dioxygenase (BPDO), an ARHD essential for the degradation of PCBs, in the metabolism of SPMs in the soil bacterium Pseudomonas alcaliphila JAB1, a versatile degrader of PCBs. We demonstrated the ability of the strain JAB1 to transform a variety of SPMs, namely the flavonoids apigenin, flavone, flavanone, naringenin, fisetin, quercetin, morin, and catechin, caffeic acid, trans-cinnamic acid, and the monoterpenes (S)-limonene and (R)-carvone. Of those, the transformation of flavone, flavanone, and (S)-limonene was conditioned by the activity of JAB1-borne BPDO and thus was researched in more detail, and we found evidence for the limonene monooxygenase activity of the BPDO. Furthermore, the bphA gene in the strain JAB1 was demonstrated to be induced by a wide range of SPMs, with monoterpenes being the strongest inducers of the SPMs tested. Thus, our findings contribute to the growing body of evidence that ARHDs not only play a role in the catabolism of aromatic pollutants, but also of natural plant-derived aromatics, and this study supports the hypothesis that ARHDs participate in ecological processes mediated by SPMs.

Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility

Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.