Isolation and characterization of an estrogen-degrading Pseudomonas putida strain SJTE-1

A Novel Estrone Degradation Gene Cluster and Catabolic Mechanism in Microbacterium oxydans ML-6

Global-scale estrone (E1) contamination of soil and aquatic environments results from the widespread use of animal manure as fertilizer, threatening both human health and environmental security. A detailed understanding of the degradation of E1 by microorganisms and the associated catabolic mechanism remains a key challenge for the bioremediation of E1-contaminated soil. Here, Microbacterium oxydans ML-6, isolated from estrogen-contaminated soil, was shown to efficiently degrade E1. A complete catabolic pathway for E1 was proposed via liquid chromatography-tandem mass spectrometry (LC-MS/MS), genome sequencing, transcriptomic analysis, and quantitative reverse transcription-PCR (qRT-PCR). In particular, a novel gene cluster (moc) associated with E1 catabolism was predicted. The combination of heterologous expression, gene knockout, and complementation experiments demonstrated that the 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) encoded by the mocA gene was responsible for the initial hydroxylation of E1. Furthermore, to demonstrate the detoxification of E1 by strain ML-6, phytotoxicity tests were performed. Overall, our findings provide new insight into the molecular mechanism underlying the diversity of E1 catabolism in microorganisms and suggest that M. oxydans ML-6 and its enzymes have potential applications in E1 bioremediation to reduce or eliminate E1-related environmental pollution. IMPORTANCE Steroidal estrogens (SEs) are mainly produced by animals, while bacteria are major consumers of SEs in the biosphere. However, the understanding of the gene clusters that participate in E1 degradation is still limited, and the enzymes involved in the biodegradation of E1 have not been well characterized. The present study reports that M. oxydans ML-6 has effective SE degradation capacity, which facilitates the development of strain ML-6 as a broad-spectrum biocatalyst for the production of certain desired compounds. A novel gene cluster (moc) associated with E1 catabolism was predicted. The 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) identified in the moc cluster was found to be necessary and specific for the initial hydroxylation of E1 to generate 4-OHE1, providing new insight into the biological role of flavoprotein monooxygenase.

Distribution, ecological fate, and risks of steroid estrogens in environmental matrices

Over the past two decades, steroidal estrogens (SEs) such as 17α-ethylestradiol (EE2), 17β-estradiol (E2),17α-estradiol (17α-E2), estriol (E3) and estrone (E1) have elicited worldwide attention due to their potentially harmful effects on human health and aquatic organisms even at low concentration ng/L. Natural steroidal estrogens exhibit greater endocrine disruption potency due to their high binding effect on nuclear estrogen receptors (ER). However, less has been explored regarding their associated environmental risks and fate. A comprehensive bibliometric study of the current research status of SEs was conducted using the Web of Science to assess the development trends and current knowledge of SEs in the last two decades, from 2001 to 2021 October. The number of publications has tremendously increased from 2003 to 2021. We summarized the contamination status and the associated ecological risks of SEs in different environmental compartments. The results revealed that SEs are ubiquitous in surface waters and natural SEs are most studied. We further carried out an in-depth evaluation and synthesis of major research hotspots and the dominant SEs in the matrices were E1, 17β-E2, 17α-E2, E3 and EE2. Nonetheless, investigations of SEs in soils, groundwater, and sediments remain scarce. This study elucidates SEs distribution, toxicological risks, ecological fate and mitigation measures, which will be beneficial for future monitoring, management, and risk assessment. Further studies are recommended to assess the toxicological risks of different SEs in complex environmental matrices to pursue a more precise and holistic quantitative estimation of estrogenic risk.

Metabolism analysis of 17α-ethynylestradiol by Pseudomonas citronellolis SJTE-3 and identification of the functional genes

Synthetic estrogens are the most hazardous and persistent environmental estrogenic contaminants, with few reports on their biodegradation. Pseudomonas citronellolis SJTE-3 degraded natural steroids efficiently and metabolized 17α-ethynylestradiol (EE2) with the addition of different easily used energy sources (glucose, peptone, ethanol, yeast extract, fulvic acid and ammonia). Over 92% of EE2 (1 mg/L) and 55% of EE2 (10 mg/L) in culture were removed in seven days with the addition of 0.1% ethanol, and the EE2-biotransforming efficiency increased with the increasing ethanol concentrations. Two novel intermediate metabolites of EE2 (C₂₂H₂₂O and C₁₈H₃₄O₂) were identified with high-performance liquid chromatography (HPLC) and GC-Orbitrap/MS. Comparative analysis and genome mining revealed strain SJTE-3 contained a unique genetic basis for EE2 metabolism, and the putative EE2-degrading genes exhibited dispersed distribution. The EE2 metabolism of strain SJTE-3 was inducible and the transcription of eight genes were significantly induced by EE2. Three genes (sdr3, yjcH and cyp2) encoding a short-chain dehydrogenase, a membrane transporter and a cytochrome P450 hydroxylase, respectively, were vital for EE2 metabolism in strain SJTE-3; their over-expression accelerated EE2 metabolic processes and advanced the generation of intermediate metabolites. This work could promote the study of bacterial EE2 metabolism mechanisms and facilitate efficient bioremediation for EE2 pollution.

Isolation and identification of 17β-estradiol degrading bacteria and its degradation pathway

The widespread presence of 17β-estradiol (E2) in the environment is an emerging problem because it poses a potential threat to human health and aquatic organisms. In this study, a strain of E2 degrading bacteria was isolated from activated sludge. 16s rRNA analysis combined with physiological and biochemical detection confirmed that the bacterium was Ochrobactrum sp. strain FJ1. At an initial E2 concentration of 15 mg L^-1, strain FJ1 degraded 98 ± 1% of E2 after 10 days. Furthermore, when methanol was added as an additional carbon source, the biomass of strain FJ1 increased by 35 ± 1%, and E2 degradation efficiency was slightly inhibited. Compared with E2 alone when glucose, sodium acetate, and methanol were added as additional carbon sources, biomass decreased by 20 ± 1, 13 ± 1 and 35 ± 1%, respectively. Analysis of the degradation products of E2 by LC/Q-TOF-MS confirmed that the major degradation products of E2 were estrone (E1) and 4,16-OH-E1, which was further degraded by strain FJ1 to several other unknown compounds. Based on SEM and FTIR analysis, the morphology of the bacteria became thicker and the thickness of the cell walls decreased under initial E2 stress, and thereafter E2 was transported into the bacteria primarily via several proteins on the cell surface. Considering the ability and efficiency of Ochrobactrum sp. strain FJ1 to degrade high E2 content, the strain could provide a new bioremediation technology for the effective biodegradation of E2. Finally, a potential bioremediation pathway of E2 by Ochrobactrum sp. strain FJ1 was proposed.

Identification of the EdcR Estrogen-Dependent Repressor in Caenibius tardaugens NBRC 16725: Construction of a Cellular Estradiol Biosensor

In this work, Caenibius tardaugens NBRC 16725 (strain ARI-1) (formerly Novosphingobium tardaugens) was isolated due to its capacity to mineralize estrogenic endocrine disruptors. Its genome encodes the edc genes cluster responsible for the degradation of 17β-estradiol, consisting of two putative operons (OpA and OpB) encoding the enzymes of the upper degradation pathway. Inside the edc cluster, we identified the edcR gene encoding a TetR-like protein. Genetic studies carried out with C. tardaugens mutants demonstrated that EdcR represses the promoters that control the expression of the two operons. These genetic analyses have also shown that 17β-estradiol and estrone, the second intermediate of the degradation pathway, are the true effectors of EdcR. This regulatory system has been heterologously expressed in Escherichia coli, foreseeing its use to detect estrogens in environmental samples. Genome comparisons have identified a similar regulatory system in the edc cluster of Altererythrobacter estronivorus MHB5, suggesting that this regulatory arrangement has been horizontally transferred to other bacteria.

Degradation of 2,4,6-Trinitrotoluene (TNT): Involvement of Protocatechuate 3,4-Dioxygenase (P34O) in Buttiauxella sp. S19-1

Extensive use and disposal of 2,4,6-trinitrotoluene (TNT), a primary constituent of explosives, pollutes the environment and causes severe damage to human health. Complete mineralization of TNT via bacterial degradation has recently gained research interest as an effective method for the restoration of contaminated sites. Here, screening for TNT degradation by six selected bacteria revealed that Buttiauxella sp. S19-1, possesses the strongest degrading ability. Moreover, BuP34O (a gene encoding for protocatechuate 3,4-dioxygenase—P34O, a key enzyme in the β-ketoadipate pathway) was upregulated during TNT degradation. A knockout of BuP34O in S19-1 to generate S-M1 mutant strain caused a marked reduction in TNT degradation efficiency compared to S19-1. Additionally, the EM1 mutant strain (Escherichia coli DH5α transfected with BuP34O) showed higher degradation efficiency than DH5α. Gas chromatography mass spectrometry (GC-MS) analysis of TNT degradation by S19-1 revealed 4-amino-2,6-dinitrotolune (ADNT) as the intermediate metabolite of TNT. Furthermore, the recombinant protein P34O (rP34O) expressed the activity of 2.46 µmol/min·mg. Our findings present the first report on the involvement of P34O in bacterial degradation of TNT and its metabolites, suggesting that P34O could catalyze downstream reactions in the TNT degradation pathway. In addition, the TNT-degrading ability of S19-1, a Gram-negative marine-derived bacterium, presents enormous potential for restoration of TNT-contaminated seas.

Experimental and Genomic Evaluation of the Oestrogen Degrading Bacterium Rhodococcus equi ATCC13557

Rhodococcus equi ATCC13557 was selected as a model organism to study oestrogen degradation based on its previous ability to degrade 17α-ethinylestradiol (EE2). Biodegradation experiments revealed that R. equi ATCC13557 was unable to metabolise EE2. However, it was able to metabolise E2 with the major metabolite being E1 with no further degradation of E1. However, the conversion of E2 into E1 was incomplete, with 11.2 and 50.6% of E2 degraded in mixed (E1-E2-EE2) and E2-only conditions, respectively. Therefore, the metabolic pathway of E2 degradation by R. equi ATCC13557 may have two possible pathways. The genome of R. equi ATCC13557 was sequenced, assembled, and mapped for the first time. The genome analysis allowed the identification of genes possibly responsible for the observed biodegradation characteristics of R. equi ATCC13557. Several genes within R. equi ATCC13557 are similar, but not identical in sequence, to those identified within the genomes of other oestrogen degrading bacteria, including Pseudomonas putida strain SJTE-1 and Sphingomonas strain KC8. Homologous gene sequences coding for enzymes potentially involved in oestrogen degradation, most commonly a cytochrome P450 monooxygenase (oecB), extradiol dioxygenase (oecC), and 17β-hydroxysteroid dehydrogenase (oecA), were identified within the genome of R. equi ATCC13557. These searches also revealed a gene cluster potentially coding for enzymes involved in steroid/oestrogen degradation; 3-carboxyethylcatechol 2,3-dioxygenase, 2-hydroxymuconic semialdehyde hydrolase, 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase, 3-(3-hydroxy-phenyl)propionate hydroxylase, cytochrome P450 monooxygenase, and 3-oxosteroid 1-dehydrogenase. Further, the searches revealed steroid hormone metabolism gene clusters from the 9, 10-seco pathway, therefore R. equi ATCC13557 also has the potential to metabolise other steroid hormones such as cholesterol.

Sediments in the mangrove areas contribute to the removal of endocrine disrupting chemicals in coastal sediments of Macau SAR, China, and harbour microbial communities capable of degrading E2, EE2, BPA and BPS

The occurrence of endocrine disrupting chemicals (EDCs) is a major issue for marine and coastal environments in the proximity of urban areas. The occurrence of EDCs in the Pearl River Delta region is well documented but specific data related to Macao is unavailable. The levels of bisphenol-A (BPA), estrone (E1), 17α-estradiol (αE2), 17β-estradiol (E2), estriol (E3), and 17α-ethynylestradiol (EE2) were measured in sediment samples collected along the coastline of Macao. BPA was found in all 45 collected samples with lower BPA concentrations associated to the presence of mangrove trees. Biodegradation assays were performed to evaluate the capacity of the microbial communities of the surveyed ecosystems to degrade BPA and its analogue BPS. Using sediments collected at a WWTP discharge point as inoculum, at a concentration of 2 mg l^-1 complete removal of BPA was observed within 6 days, whereas for the same concentration BPS removal was of 95% after 10 days, which is particularly interesting since this compound is considered recalcitrant to biodegradation and likely to accumulate in the environment. Supplementation with BPA improved the degradation of bisphenol-S (BPS). Aiming at the isolation of EDCs-degrading bacteria, enrichments were established with sediments supplied with BPA, BPS, E2 and EE2, which led to the isolation of a bacterial strain, identified as Rhodoccoccus sp. ED55, able to degrade the four compounds at different extents. The isolated strain represents a valuable candidate for bioremediation of contaminated soils and waters.

Isolation and characterization of a new highly effective 17β-estradiol-degrading Gordonia sp. strain R9

In this report, Gordonia sp. strain R9 isolated from an enrichment culture of chicken leachate was confirmed to degrade 17β-estradiol (E2), which can also use other estrogens (estrone, estriol, and 17α-ethynylestradiol) and testosterone as sole carbon and energy sources. Optimization of growth conditions showed that Gordonia sp. strain R9 can tolerate a very wide range of temperature (4-40 °C) and pH (1.0-11.0), and is sensitive to antibiotics including kanamycin, ampicillin, chloramphenicol, and carbenicillin. Optimal culture conditions for E2 degradation were 30 °C and pH 7.0 with almost 100% degradation of E2 concentrations ranging from 50 µg/L to 5 mg/L within 24 h. The E2 intermediates so generated included estrone (E1), estratriol (E3), (3Z)-3-(3-hydroxy-3a-methyl-7-oxododecahydro-6H-cyclopenta[a]naphthalen-6-ylidene) propanoic acid and 3-hydroxy-3a-methyl-7-oxododecahydro-1H-cyclopenta[a]naphthalene-6-carboxylic acid. These results indicate that the highly effective E2-degradative ability of Gordonia sp. strain R9 merits further investigation as a candidate for large-scale estrogen biodegradation.