Assessment of the Degradation Potential and Genomic Insights towards Phenanthrene by Dietzia psychralcaliphila JI1D

Exploring di (2-ethylhexyl) phthalate degradation by a synthetic marine bacterial consortium: Genomic insights, pathway and interaction prediction, and application in sediment microcosms

Di (2-ethylhexyl) phthalate (DEHP), a toxic phthalate ester (PAE) plasticizer, is often detected in marine sediment and biota. Our understanding of DEHP-degrading marine bacteria and the associated genetic mechanisms is limited. This study established a synthetic bacterial consortium (A02) consisting of three marine bacteria (OR05, OR16, and OR21). Consortium A02 outperformed the individual strains in DEHP degradation. Investigations into the degradation of DEHP intermediates revealed that OR05 and OR16 likely contributed to enhanced DEHP degradation by Consortium A02 via the utilization of DEHP intermediates, such as protocatechuic acid and mono (ethylhexyl) phthalate, with OR21 as the key DEHP degrader. A pathway of DEHP degradation by Consortium A02 was predicted based on genome analysis and experimental degradation. Bioaugmentation with Consortium A02 led to 80% DEHP degradation in 26 days in saline sediment (100 mg/kg), surpassing the 53% degradation by indigenous microbes, indicating the potential of A02 for treating DEHP-contaminated sediments. Meanwhile, bioaugmentation notably changed the bacterial community, with the exclusive presence of certain bacterial genera in the A02 bioaugmented microcosms, and was predicted to result in a more dynamic and active sediment bacterial community. This study contributes to the limited literature on DEHP degradation by marine bacteria and their associated genes.

Genomic, Phylogenetic and Physiological Characterization of the PAH-Degrading Strain Gordonia polyisoprenivorans 135

The strain Gordonia polyisoprenivorans 135 is able to utilize a wide range of aromatic compounds. The aim of this work was to study the features of genetic organization and biotechnological potential of the strain G. polyisoprenivorans 135 as a degrader of aromatic compounds. The study of the genome of the strain 135 and the pangenome of the G. polyisoprenivorans species revealed that some genes, presumably involved in PAH catabolism, are atypical for Gordonia and belong to the pangenome of Actinobacteria. Analyzing the intergenic regions of strain 135 alongside the "panIGRome" of G. polyisoprenivorans showed that some intergenic regions in strain 135 also differ from those located between the same pairs of genes in related strains. The strain G. polyisoprenivorans 135 in our work utilized naphthalene (degradation degree 39.43%) and grew actively on salicylate. At present, this is the only known strain of G. polyisoprenivorans with experimentally confirmed ability to utilize these compounds.

Bioprospecting the potential of the microbial community associated to Antarctic marine sediments for hydrocarbon bioremediation

Microorganisms that inhabit the cold Antarctic environment can produce ligninolytic enzymes potentially useful in bioremediation. Our study focused on characterizing Antarctic bacteria and fungi from marine sediment samples of King George and Deception Islands, maritime Antarctica, potentially affected by hydrocarbon influence, able to produce enzymes for use in bioremediation processes in environments impacted with petroleum derivatives. A total of 168 microorganism isolates were obtained: 56 from sediments of King George Island and 112 from Deception Island. Among them, five bacterial isolates were tolerant to cell growth in the presence of diesel oil and gasoline and seven fungal were able to discolor RBBR dye. In addition, 16 isolates (15 bacterial and one fungal) displayed enzymatic emulsifying activities. Two isolates were characterized taxonomically by showing better biotechnological results. Psychrobacter sp. BAD17 and Cladosporium sp. FAR18 showed pyrene tolerance (cell growth of 0.03 g mL-1 and 0.2 g mL-1) and laccase enzymatic activity (0.006 UL-1 and 0.10 UL-1), respectively. Our results indicate that bacteria and fungi living in sediments under potential effect of hydrocarbon pollution may represent a promising alternative to bioremediate cold environments contaminated with polluting compounds derived from petroleum such as polycyclic aromatic hydrocarbons and dyes.

Bacterial crude oil and polyaromatic hydrocarbon degraders from Kazakh oil fields as barley growth support

Bacterial strains of the genera Arthrobacter, Bacillus, Dietzia, Kocuria, and Micrococcus were isolated from oil-contaminated soils of the Balgimbaev, Dossor, and Zaburunye oil fields in Kazakhstan. They were selected from 1376 isolated strains based on their unique ability to use crude oil and polyaromatic hydrocarbons (PAHs) as sole source of carbon and energy in growth experiments. The isolated strains degraded a wide range of aliphatic and aromatic components from crude oil to generate a total of 170 acid metabolites. Eight metabolites were detected during the degradation of anthracene and of phenanthrene, two of which led to the description of a new degradation pathway. The selected bacterial strains Arthrobacter bussei/agilis SBUG 2290, Bacillus atrophaeus SBUG 2291, Bacillus subtilis SBUG 2285, Dietzia kunjamensis SBUG 2289, Kocuria rosea SBUG 2287, Kocuria polaris SBUG 2288, and Micrococcus luteus SBUG 2286 promoted the growth of barley shoots and roots in oil-contaminated soil, demonstrating the enormous potential of isolatable and cultivable soil bacteria in soil remediation. KEY POINTS: • Special powerful bacterial strains as potential crude oil and PAH degraders. • Growth on crude oil or PAHs as sole source of carbon and energy. • Bacterial support of barley growth as resource for soil remediation.

Diverse hydrocarbon degradation genes, heavy metal resistome, and microbiome of a fluorene-enriched animal-charcoal polluted soil

Environmental compartments polluted with animal charcoal from the skin and hide cottage industries are rich in toxic heavy metals and diverse hydrocarbon classes, some of which are carcinogenic, mutagenic, and genotoxic, and thus require a bio-based eco-benign decommission strategies. A shotgun metagenomic approach was used to decipher the microbiome, hydrocarbon degradation genes, and heavy metal resistome of a microbial consortium (FN8) from an animal-charcoal polluted site enriched with fluorene. Structurally, the FN8 microbial consortium consists of 26 phyla, 53 classes, 119 orders, 245 families, 620 genera, and 1021 species. The dominant phylum, class, order, family, genus, and species in the consortium are Proteobacteria (51.37%), Gammaproteobacteria (39.01%), Bacillales (18.09%), Microbulbiferaceae (11.65%), Microbulbifer (12.21%), and Microbulbifer sp. A4B17 (19.65%), respectively. The microbial consortium degraded 57.56% (28.78 mg/L) and 87.14% (43.57 mg/L) of the initial fluorene concentration in 14 and 21 days. Functional annotation of the protein sequences (ORFs) of the FN8 metagenome using the KEGG GhostKOALA, KofamKOALA, NCBI's conserved domain database, and BacMet revealed the detection of hydrocarbon degradation genes for benzoate, aminobenzoate, polycyclic aromatic hydrocarbons (PAHs), chlorocyclohexane/chlorobenzene, chloroalkane/chloroalkene, toluene, xylene, styrene, naphthalene, nitrotoluene, and several others. The annotation also revealed putative genes for the transport, uptake, efflux, and regulation of heavy metals such as arsenic, cadmium, chromium, mercury, nickel, copper, zinc, and several others. Findings from this study have established that members of the FN8 consortium are well-adapted and imbued with requisite gene sets and could be a potential bioresource for on-site depuration of animal charcoal polluted sites.

Simultaneous immobilization enhances synergistic interactions and crude oil removal of bacterial consortium

Oil spillage has serious adverse effects on marine environments. The degradation of crude oil by microorganisms may be an effective and sustainable approach. In this study, the removal of crude oil from seawater by immobilized bacterial consortium was performed and the enhancement of crude oil degradation efficiency by varying immobilization methods and inoculum volume ratio was examined. The nonpathogenic and heavy metal-tolerant bacterial consortium of Sphingobium naphthae MO2-4 and Priestia aryabhattai TL01-2 was immobilized by biofilm formation on aquaporousgels. The simultaneous immobilization of strains MO2-4 and TL01-2 showed better crude oil removal efficiency than independent immobilization, which indicated positive interactions among consortium members in the mixed-culture immobilized systems. Moreover, the immobilized consortium at a 2:1 (MO2-4:TL01-2) inoculum volume ratio showed the best crude oil removal capacity. The immobilized consortium removed 77% of 2000 mg L-1 crude oil in seawater over 7 days. The immobilized consortium maintained crude oil removal efficacy in semicontinuous experiments. In addition, the immobilized consortium was used to remediate seawater contaminated with 1000 mg L-1 crude oil in a 20 L wave tank. After 28 days, the crude oil degradation efficiency of immobilized consortium was approximately 70%, and crude oil degradation through natural attenuation was not observed. Moreover, the genomic features of strains MO2-4 and TL01-2 are reported. Genomic analyses of both strains confirmed the presence of many genes involved in hydrocarbon degradation, heavy metal resistance, biosurfactant synthesis, and biofilm formation, supporting the biodegradation results and characterizing strain properties. The results of this work introduce the potential benefit of simultaneous immobilization of bacterial consortia to improve efficiency of crude oil biodegradation and has motivated further investigations into large-scale remediation of crude oil-contaminated seawater.

Insights into molecular mechanism of plasticizer biodegradation in Dietzia kunjamensis IITR165 and Brucella intermedia IITR166 isolated from a solid waste dumpsite

AIMS

Isolation of phthalate esters (PAEs) degrading bacteria from a solid waste dumpsite could degrade many plasticizers efficiently and to investigate their degrading kinetics, pathways, and genes.

METHODS AND RESULTS

Based on their 16S rRNA gene sequence the strains were identified as Dietzia kunjamensis IITR165 and Brucella intermedia IITR166, which showed a first-order degradation kinetic model under lab conditions. The quantification of phthalates and their intermediate metabolites identification were done by using ultra-high-performance liquid chromatography (UHPLC) and gas chromatography-tandem mass-spectrometry (GC-MS/MS), respectively. Both the bacteria utilized >99% dibutyl phthalate at a high concentration of 100-400 mg L-1 within 192 h as monitored by UHPLC. GC-MS/MS revealed the presence of metabolites dimethyl phthalate (DMP), phthalic acid (PA), and benzoic acid (BA) during DBP degradation by IITR165 while monobutyl phthalate (MBP) and PA were identified in IITR166. Phthalate esters degrading gene cluster in IITR165 comprised two novel genes coding for carboxylesterase (dkca1) and mono-alkyl phthalate hydrolase (maph), having only 37.47% and 47.74% homology, respectively, with reported phthalate degradation genes, along with the terephthalate dioxygenase system (tphA1, A2, A3, and B). However, IITR166 harbored different gene clusters comprising di-alkyl phthalate hydrolase (dph_bi), and phthalate dioxygenase (ophA, B, and C) genes.

CONCLUSIONS

Two novel bacterial strains, Dietzia kunjamensis IITR165 and Brucella intermedia IITR166, were isolated and found to efficiently degrade DBP at high concentrations. The degradation followed first-order kinetics, and both strains exhibited a removal efficiency of over 99%. Metabolite analysis revealed that both bacteria utilized de-methylation, de-esterification, and decarboxylation steps during degradation.

Genomic analysis of lignocellulolytic enzyme producing novel Streptomyces sp.MS2A for the bioethanol applications

The conversion of lignocellulosic waste to energy offers a cost-effective biofuel. The current study discusses the utilization of cellulose in rice husks by lichen-associated Streptomyces sp. MS2A via carbohydrate metabolism. Out of 39 actinobacteria, one actinobacterial strain MS2A, showed CMCase, FPase, and cellobiohydrolase activity. The whole genome analysis of Streptomyces sp. MS2A showed maximum similarity with Streptomyces sp. CCM_MD2014. The genome analysis confirmed the presence of cellulose-degrading genes along with xylan-degrading genes that code for GH3, GH6, GH9, GH11, GH43, GH51, and 15 other GH families with glycosyl transferase, carbohydrate-binding modules, and energy metabolism groups. Protein family analysis corroborates the enzyme family. Among the 19,402 genes of Streptomyces sp. MS2A, approximately 70 GH family codes for lignocellulose degradation enzymes. The structure of cellulase was modeled and validated. Scanning electron microscopy and gas chromatography-mass spectrometry (GCMS) was performed to analyze the lignocellulosic degradation of rice husk and the end product bioethanol.

Detoxification of fluoroglucocorticoid by Acinetobacter pittii C3 via a novel defluorination pathway with hydrolysis, oxidation and reduction: Performance, genomic characteristics, and mechanism

Biological dehalogenation degradation was an important detoxification method for the ecotoxicity and teratogenic toxicity of fluorocorticosteroids (FGCs). The functional strain Acinetobacter pittii C3 can effectively biodegrade and defluorinate to 1 mg/L Triamcinolone acetonide (TA), a representative FGCs, with 86 % and 79 % removal proportion in 168 h with the biodegradation and detoxification kinetic constant of 0.031/h and 0.016/h. The dehalogenation and degradation ability of strain C3 was related to its dehalogenation genomic characteristics, which manifested in the functional gene expression of dehalogenation, degradation, and toxicity tolerance. Three detoxification mechanisms were positively correlated with defluorination pathways through hydrolysis, oxidation, and reduction, which were regulated by the expression of the haloacid dehalogenase (HAD) gene (mupP, yrfG, and gph), oxygenase gene (dmpA and catA), and reductase gene (nrdAB and TgnAB). Hydrolysis defluorination was the most critical way for TA detoxification metabolism, which could rapidly generate low-toxicity metabolites and reduce toxic bioaccumulation due to hydrolytic dehalogenase-induced defluorination. The mechanism of hydrolytic defluorination was that the active pocket of hydrolytic dehalogenase was matched well with the spatial structure of TA under the adjustment of the hydrogen bond, and thus induced molecular recognition to promote the catalytic hydrolytic degradation of various amino acid residues. This work provided an effective bioremediation method and mechanism for improving defluorination and detoxification performance.

Determining the degradation mechanism and application potential of benzopyrene-degrading bacterium Acinetobacter XS-4 by screening

In industrial wastewater treatment, organic pollutants are usually removed by in-situ microorganisms and exogenous bactericides. Benzo [a] pyrene (BaP) is a typical persistent organic pollutant and difficult to be removed. In this study, a new strain of BaP degrading bacteria Acinetobacter XS-4 was obtained and the degradation rate was optimized by response surface method. The results showed that the degradation rate of BaP was 62.73% when pH= 8, substrate concentration was 10 mg/L, temperature was 25 °C, inoculation amount was 15% and culture rate was 180 r/min. Its degradation rate was better than that of the reported degrading bacteria. XS-4 is active in the degradation of BaP. BaP is degraded into phenanthrene by 3, 4-dioxygenase (α subunit and β subunit) in pathway Ⅰ and rapidly forms aldehydes, esters and alkanes. The pathway Ⅱ is realized by the action of salicylic acid hydroxylase. When sodium alginate and polyvinyl alcohol were added to the actual coking wastewater to immobilize XS-4, the degradation rate of BaP was 72.68% after 7 days, and the removal effect was better than that of single BaP wastewater (62.36%), which has the application potential. This study provides theoretical and technical support for microbial degradation of BaP in industrial wastewater.

Formulation of synthetic bacteria consortia for enzymatic biodegradation of polyaromatic hydrocarbons contaminated soil: soil column study

As an efficient method to remove contaminants from highly polluted sites, enzyme biodegradation addresses unresolved issues such as bioremediation inefficiency. In this study, the key enzymes involved in PAH degradation were brought together from different arctic strains for the biodegradation of highly contaminated soil. These enzymes were produced via a multi-culture of psychrophilic Pseudomonas and Rhodococcus strains. As a result of biosurfactant production, the removal of pyrene was sufficiently prompted by Alcanivorax borkumensis. The key enzymes (e.g., naphthalene dioxygenase, pyrene dioxygenase, catechol-2,3 dioxygenase, 1-hydroxy-2-naphthoate hydroxylase, protocatechuic acid 3,4-dioxygenase) obtained via multi-culture were characterized by tandem LC-MS/MS and kinetic studies. To simulate in situ application of produced enzyme solutions, pyrene- and dilbit-contaminated soil was bioremediated in soil columns and flask tests by injecting enzyme cocktails from the most promising consortia. The enzyme cocktail contained about 35.2 U/mg protein pyrene dioxygenase, 61.4 U/mg protein naphthalene dioxygenase, 56.5 U/mg protein catechol-2,3-dioxygenase, 6.1 U/mg protein 1-hydroxy-2-naphthoate hydroxylase, and 33.5 U/mg protein protocatechuic acid (P3,4D) 3,4-dioxygenase enzymes. It was found that after 6 weeks, the average pyrene removal values showed that the enzyme solution could be effective in the soil column system (80-85% degradation of pyrene).

Oil Biodegradation and Bioremediation in Cold Marine Environment

Petroleum hydrocarbons pose a substantial threat to marine ecosystems [...].

Unravelling the genetic potential for hydrocarbon degradation in the sediment microbiome of Antarctic islands

Hydrocarbons may have a natural or anthropogenic origin and serve as a source of carbon and energy for microorganisms in Antarctic soils. Herein, 16S rRNA gene and shotgun sequencing were employed to characterize taxonomic diversity and genetic potential for hydrocarbon degradation of the microbiome from sediments of sites located in two Antarctic islands subjected to different temperatures, geochemical compositions, and levels of presumed anthropogenic impact, named: Crater Lake/Deception Island (pristine area), Whalers Bay and Fumarole Bay/Deception Island (anthropogenic-impacted area), and Hannah Point/Livingston Island (anthropogenic-impacted area). Hydrocarbon concentrations were measured for further correlation analyses with biological data. The majority of the hydrocarbon-degrading genes were affiliated to the most abundant bacterial groups of the microbiome: Proteobacteria and Actinobacteria. KEGG annotation revealed 125 catabolic genes related to aromatic hydrocarbon (styrene, toluene, ethylbenzene, xylene, naphthalene, and polycyclic hydrocarbons) and aliphatic (alkanes and cycloalkanes) pathways. Only aliphatic hydrocarbons, in low concentrations, were detected in all areas, thus not characterizing the areas under study as anthropogenically impacted or nonimpacted. The high richness and abundance of hydrocarbon-degrading genes suggest that the genetic potential of the microbiome from Antarctic sediments for hydrocarbon degradation is driven by natural hydrocarbon occurrence.

Antimicrobial Biosynthetic Potential and Phylogenetic Analysis of Culturable Bacteria Associated with the Sponge Ophlitaspongia sp. from the Yellow Sea, China

Sponge-derived bacteria are considered to be a promising source of novel drugs, owing to their abundant secondary metabolites that have diverse biological activities. In this study, we explored the antimicrobial biosynthetic potential and phylogenetics of culturable bacteria associated with the sponge Ophlitaspongia sp. from the Yellow Sea, China. Using culture-dependent methods, we obtained 151 bacterial strains, which were then analysed for their antimicrobial activities against seven indicator strains. The results indicate that 94 (62.3%) of the 151 isolated strains exhibited antimicrobial activities and inhibited at least one of the indicator strains. Fifty-two strains were selected for further phylogenetic analysis using 16S rRNA gene sequencing, as well as for the presence of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes. These 52 strains belonged to 20 genera from 18 families in 4 phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Five strains with PKS genes and ten strains with NRPS genes were detected. Among them, two strains contained both PKS and NRPS genes. Notoacmeibacter sp. strain HMA008 (class Alphaproteobacteria) exhibited potent antimicrobial activity; thus, whole genome sequencing methods were used to analyse its secondary metabolite biosynthetic gene clusters. The genome of HMA008 contained 12 biosynthetic gene clusters that potentially encode secondary metabolites belonging to compound classes such as non-ribosomal peptides, prodigiosin, terpene, β-lactones, and siderophore, among others. This study indicates that the sponge Ophlitaspongia sp. harbours diverse bacterial strains with antimicrobial properties and may serve as a potential source of bioactive compounds.

Efficient biodegradation of phenanthrene using Pseudomonas stutzeri LSH-PAH1 with the addition of sophorolipids: Alleviation of biotoxicity and cometabolism studies

Phenanthrene (PHE) is widely distributed, and it can cause genotoxicity in humans by interacting with enzymes in the body. A current challenge for PHE bioremediation is the inhibitory effect of biotoxic intermediates on bacterial growth. Notably, the aerobic biotransformation processes for PHE in the presence of sophorolipids have been poorly studied. Here, a PHE-degrading strain was isolated from sediments and identified as Pseudomonas stutzeri and named LSH-PAH1. It was observed that 1-naphthol (a biotoxic substance that can inhibit strain growth) was produced during the PHE metabolism process of LSH-PAH1. The biodegradation ratio increased from 21.4% to 91.7% within 48 h after the addition of sophorolipids. Unexpectedly, this addition accelerated the metabolic process for 1-naphthol rather than causing its accumulation. The cometabolism of 1-naphthol and sophorolipids alleviated the biotoxic effects for the strain, which was verified by gene expression analysis. We identified a new PHE-degrading strain and provided a mechanism for PHE biodegradation using LSH-PAH1 with the addition of sophorolipids, which provides a reference for practical applications of the bioremediation of PHE and study of the cometabolism of biotoxic intermediates.

Bacterial communities of the Black Sea exhibit activity against persistent organic pollutants in the water column and sediments

The ability of bacteria to degrade organic pollutants influences their fate in the environment, impact on the other biota and accumulation in the food web. The aim of this study was to evaluate abundance and expression activity of the catabolic genes targeting widespread pollutants, such as polyaromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and hexachloro-cyclohexane (HCH) in the Black Sea water column and sediments. Concentrations of PAHs, PCBs and HCH were determined by gas chromatography (GC) coupled to mass spectrometry (MS) and electron capture (ECD) detectors. bphA1, PAH-RHDα, nahAc, linA and linB that encode biphenyl 2,3 dioxygenase, α-subunits of ring hydroxylating dioxygenases, naphthalene dioxygenase, dehydrochlorinase and halidohydrolase correspondently were quantified by quantitative PCR. More recalcitrant PAHs, PCBs and HCH tended to accumulate in the Black Sea environments. In water samples, 3- and 4-ringed PAHs outnumbered naphthalene, while PAHs with > 4 rings prevailed in the sediments. Congeners with 4-8 chlorines with ortho-position of the substituents were the most abundant among the PCBs. β-HCH was determined at highest concentration in water samples, and total amount of HCH exceeded its legacy Environmental Quality Standard value. bphA1, was the most numerous gene in water layers (105 copies/mL) and sediments (105 copies/mg), followed by linB and PAH-RHDα genes (103 copies/mL; 105 copies/mg). The least abundant genes were linA (103 copies/mL; 104 copies/mg) and nahAc (102 copies/mL; 104 copies/mg). The most widely distributed gene bphА1 was one of the least expressed (10-3-10-2 copies/mL; 10-1 copies/mg). The most actively expressed genes were linB (101-102 copies/mL; 103 copies/mg), PAH-RHDα (101 copies/mL; 102 copies/mg) and linA (10-1-100 copies/mL; 100 copies/mg). Interaction of bacteria with PAHs, PCBs and HCH is evidenced by high copy numbers of the catabolic genes that initiate their degradation. More persistent compounds, such as high-molecular weight PAHs or β-HCH are accumulating in the Black Sea water and sediments, albeit microbial activity is directed against them.