Reductive dehalogenation of 3,5-dibromo-4-hydroxybenzoate by an aerobic strain of Delftia sp. EOB-17

Elucidation of 4-Hydroxybenzoic Acid Catabolic Pathways in Pseudarthrobacter phenanthrenivorans Sphe3

4-hydroxybenzoic acid (4-HBA) is an aromatic compound with high chemical stability, being extensively used in food, pharmaceutical and cosmetic industries and therefore widely distributed in various environments. Bioremediation constitutes the most sustainable approach for the removal of 4-hydroxybenzoate and its derivatives (parabens) from polluted environments. Pseudarthrobacter phenanthrenivorans Sphe3, a strain capable of degrading several aromatic compounds, is able to grow on 4-HBA as the sole carbon and energy source. Here, an attempt is made to clarify the catabolic pathways that are involved in the biodegradation of 4-hydroxybenzoate by Sphe3, applying a metabolomic and transcriptomic analysis of cells grown on 4-HBA. It seems that in Sphe3, 4-hydroxybenzoate is hydroxylated to form protocatechuate, which subsequently is either cleaved in ortho- and/or meta-positions or decarboxylated to form catechol. Protocatechuate and catechol are funneled into the TCA cycle following either the β-ketoadipate or protocatechuate meta-cleavage branches. Our results also suggest the involvement of the oxidative decarboxylation of the protocatechuate peripheral pathway to form hydroxyquinol. As a conclusion, P. phenanthrenivorans Sphe3 seems to be a rather versatile strain considering the 4-hydroxybenzoate biodegradation, as it has the advantage to carry it out effectively following different catabolic pathways concurrently.

Antimicrobial Transformation Products in the Aquatic Environment: Global Occurrence, Ecotoxicological Risks, and Potential of Antibiotic Resistance

The global spread of antimicrobial resistance (AMR) is concerning for the health of humans, animals, and the environment in a One Health perspective. Assessments of AMR and associated environmental hazards mostly focus on antimicrobial parent compounds, while largely overlooking their transformation products (TPs). This review lists antimicrobial TPs identified in surface water environments and examines their potential for AMR promotion, ecological risk, as well as human health and environmental hazards using in silico models. Our review also summarizes the key transformation compartments of TPs, related pathways for TPs reaching surface waters and methodologies for studying the fate of TPs. The 56 antimicrobial TPs covered by the review were prioritized via scoring and ranking of various risk and hazard parameters. Most data on occurrences to date have been reported in Europe, while little is known about antibiotic TPs in Africa, Central and South America, Asia, and Oceania. Occurrence data on antiviral TPs and other antibacterial TPs are even scarcer. We propose evaluation of structural similarity between parent compounds and TPs for TP risk assessment. We predicted a risk of AMR for 13 TPs, especially TPs of tetracyclines and macrolides. We estimated the ecotoxicological effect concentrations of TPs from the experimental effect data of the parent chemical for bacteria, algae and water fleas, scaled by potency differences predicted by quantitative structure-activity relationships (QSARs) for baseline toxicity and a scaling factor for structural similarity. Inclusion of TPs in mixtures with their parent increased the ecological risk quotient over the threshold of one for 7 of the 24 antimicrobials included in this analysis, while only one parent had a risk quotient above one. Thirteen TPs, from which 6 were macrolide TPs, posed a risk to at least one of the three tested species. There were 12/21 TPs identified that are likely to exhibit a similar or higher level of mutagenicity/carcinogenicity, respectively, than their parent compound, with tetracycline TPs often showing increased mutagenicity. Most TPs with increased carcinogenicity belonged to sulfonamides. Most of the TPs were predicted to be mobile but not bioaccumulative, and 14 were predicted to be persistent. The six highest-priority TPs originated from the tetracycline antibiotic family and antivirals. This review, and in particular our ranking of antimicrobial TPs of concern, can support authorities in planning related intervention strategies and source mitigation of antimicrobials toward a sustainable future.

Microbial detoxification of 2,4,6-tribromophenol via a novel process with consecutive oxidative and hydrolytic debromination: Biochemical, genetic and evolutionary characterization

As a typical brominated flame retardants (BFRs), 2,4,6-tribromophenol (TBP) has serious hazard to the environmental health and its environmental fate has attracted considerable attention. Dehalogenation reaction plays key role in microbial TBP degradation and detoxification. So far, several halophenols-degrading enzymes have been reported to transform their substrate by oxidative dehalogenation; however, the molecular and biochemistry characterization of microbial hydrolytic dehalogenation is limited. In this study, Cupriavidus sp. CNP-8 with high TBP degradation activity was found to degrade TBP via an obviously differnet pathway as compared to other reported TBP-degraders. The transcription of hnp genes were significantly upregulated with TBP stimulation, indicating their involvment in TBP degradation. Enzymatic assays with ¹⁸O-labeling experiments showed that HnpAB, a two-component FAD-dependent monooxygenase, transformed TBP via consecutive oxidative and hydrolytic debromination reactions with the formation of 6-bromo-1,2,4-benzenetriol (BBT) as the ring-cleavage substrate. The function of the BBT ring-cleavage enzyme (HnpC) was also characterized both in vitro and in vivo. This finding provides new molecular mechanism of microbial detoxification of TBP and novel information of the environmental fate of this BFRs. Furthermore, to investigate the frequency of this novel dehalogenation mechanism in microbes, we also analyzed the distribution as well as the genetic structure of the hnpABC cluster by comparative genomics. Although hnpA homolog is distributed in several bacterial genera including Cupriavidus, Paraburkholderia, Variovorax and Streptomyces, the complete hnpABC cluster is only retrieved from Cupriavidus and strictly conservative in the genomes. This indicated that Cupriavidus have unique evolutionary pattern in acquiring the hnpABC to degrade TBP and its analogs, enhancing our understanding of the microbial adaptive evolution in halophenols-contaminated environment.

Enhanced bio-reductive degradation of fluoroglucocorticoids in the groundwater fluctuation zone by external electron donors: Performance, microbial community, and functional genes

This study evaluated the effectiveness of external electron donors on the bio-reductive degradation enhancement of fluoroglucocorticoids (FGCs) in the groundwater fluctuation zone during the wet season when reverse upward fluctuation of the groundwater table occurs and the dry season after the groundwater table declines. The results showed that the external electron donors, provided by the addition of nano zero-valent iron-modified biochar (nZVI@BC), inhibited the migration and enhanced the reductive defluorination of triamcinolone acetonide (TA), a representative FGC. The accumulation rate constant with temporal fluctuation depth and the attenuation rate constant with vertical fluctuation depth were -2.55 × 10^-3 and 4.20 × 10^-2, respectively, in the groundwater of the natural groundwater fluctuation zone (N-FZ). In contrast, the accumulation and attenuation rate constants were, respectively, 35.6% and 2.64 times higher in the groundwater fluctuation zone amended with nZVI@BC (nZVI@BC-FZ) as compared with those observed in the N-FZ. Furthermore, the decay rate constant of the TA residue in the dry season was 0.843 × 10^-2 μg/d in N-FZ and was 2.19 times higher in nZVI@BC-FZ. This enhancement effect, caused by the addition of external electrons, was positively correlated with the evolution of the microbial community and the expression of functional genes. The microbes evolved into functional genera with reductive dehalogenation (Xylophilus and Hydrogenophaga) and iron-oxidizing (Lysobacter, Pseudoxanthomonas, and Sphingomonas) abilities in the nZVI@BC-FZ system, which increased dehalogenation and iron oxide genes by a 4-5 order of magnitude. The utilization proportion of external electrons for TA metabolism was 50.04%, of which 30.82%, 10.26%, and 8.96% were utilized for defluorination, hydrogenation, and ring-opening, respectively. This study provides an effective method to reduce pollutant diffusion and enhance the bio-reductive degradation caused by groundwater table fluctuation.

Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions

Halogenated aromatics are used widely in various industrial, agricultural and household applications. However, due to their stability, most of these compounds persist for a long time, leading to accumulation in the environment. Biological degradation of halogenated aromatics provides sustainable, low-cost and environmentally friendly technologies for removing these toxicants from the environment. This minireview discusses the molecular mechanisms of the enzymatic reactions for degrading halogenated aromatics which naturally occur in various microorganisms. In general, the biodegradation process (especially for aerobic degradation) can be divided into three main steps: upper, middle and lower metabolic pathways which successively convert the toxic halogenated aromatics to common metabolites in cells. The most difficult step in the degradation of halogenated aromatics is the dehalogenation step in the middle pathway. Although a variety of enzymes are involved in the degradation of halogenated aromatics, these various pathways all share the common feature of eventually generating metabolites for utilizing in the energy-producing metabolic pathways in cells. An in-depth understanding of how microbes employ various enzymes in biodegradation can lead to the development of new biotechnologies via enzyme/cell/metabolic engineering or synthetic biology for sustainable biodegradation processes.

NanoFe3O4 accelerates anoxic biodegradation of 3, 5, 6-trichloro-2-pyridinol

3, 5, 6-trichloro-2-pyridinol (TCP) is a widespread organic pollutant with persistent, mobile and high antimicrobial effects. Here, nanoFe₃O₄ was firstly introduced into the anoxic biodegradation of TCP. It was found that nanoFe₃O₄ significantly accelerated TCP biodegradation. The removal rate of TCP (100 mg L^-1) increased from 83.03% to 98.74% within 12 h in the presence of nanoFe₃O₄, and the addition of nanoFe₃O₄ also promoted the accumulation of CO₂. Reductive dechlorination mechanism was involved in anoxic biodegradation of TCP. Molecular approaches further revealed that nanoFe₃O₄ distinctly induced the shifts of bacterial community. The dominant genus Ochrobactrum was converted to genus Delftia in nanoFe₃O₄ treatment, and the relative abundance of Delftia increased from 10.26% to 44.62%. Meanwhile, the total relative abundance of bacteria related to TCP dechlorination and degradation significantly increased in the presence of nanoFe₃O₄. These results indicated that nanoFe₃O₄ induced the enrichment of TCP-degrading bacteria to promote the anoxic biodegradation of TCP.

Degradation of Phenylurea Herbicides by a Novel Bacterial Consortium Containing Synergistically Catabolic Species and Functionally Complementary Hydrolases

Phenylurea herbicides (PHs) are frequently detected as major water contaminants in areas where there is extensive use. In this study, Diaphorobacter sp. strain LR2014-1, which initially hydrolyzes linuron to 3,4-dichloroanaline, and Achromobacter sp. strain ANB-1, which further mineralizes the produced aniline derivatives, were isolated from a linuron-mineralizing consortium despite being present at low abundance in the community. The synergistic catabolism of linuron by the consortium containing these two strains resulted in more efficient catabolism of linuron and growth of both strains. Strain LR2014-1 harbors two evolutionary divergent hydrolases from the amidohydrolase superfamily Phh and the amidase superfamily TccA2, which functioned complementarily in the hydrolysis of various types of PHs, including linuron ( N-methoxy- N-methyl-substituted), diuron, chlorotoluron, fluomethuron ( N, N-dimethyl-substituted), and siduron. These findings show that a bacterial consortium can contain catabolically synergistic species for PH mineralization, and one strain could harbor functionally complementary hydrolases for a broadened substrate range.

Comparative Transcriptome Analysis Reveals the Mechanism Underlying 3,5-Dibromo-4-Hydroxybenzoate Catabolism via a New Oxidative Decarboxylation Pathway

The compound 3,5-dibromo-4-hydroxybenzoate (DBHB) is both anthropogenically released into and naturally produced in the environment, and its environmental fate is of great concern. Aerobic and anaerobic reductive dehalogenations are the only two reported pathways for DBHB catabolism. In this study, a new oxidative decarboxylation pathway for DBHB catabolism was identified in a DBHB-utilizing strain, Pigmentiphaga sp. strain H8. The genetic determinants underlying this pathway were elucidated based on comparative transcriptome analysis and subsequent experimental validation. A gene cluster comprising orf420 to orf426, with transcripts that were about 33- to 4,400-fold upregulated in DBHB-induced cells compared with those in uninduced cells, was suspected to be involved in DBHB catabolism. The gene odcA (orf420), which is essential for the initial catabolism of DBHB, encodes a novel NAD(P)H-dependent flavin monooxygenase that mediates the oxidative decarboxylation of DBHB to 2,6-dibromohydroquinone (2,6-DBHQ). The substrate specificity of the purified OdcA indicated that the 4-hydroxyl group and its ortho-halogen(s) are important for hydroxylation of the C-1 site carboxyl group by OdcA. 2,6-DBHQ is then ring cleaved by the dioxygenase OdcB (Orf425) to 2-bromomaleylacetate, which is finally transformed to β-ketoadipate by the maleylacetate reductase OdcC (Orf426). These results provide a better understanding of the molecular mechanism underlying the catabolic diversity of halogenated para-hydroxybenzoates.IMPORTANCE Halogenated hydroxybenzoates (HBs), which are widely used synthetic precursors for chemical products and common metabolic intermediates from halogenated aromatics, exert considerable adverse effects on human health and ecological security. Microbial catabolism plays key roles in the dissipation of halogenated HBs in the environment. In this study, the discovery of a new catabolic pathway for 3,5-dibromo-4-hydroxybenzoate (DBHB) and clarification of the genetic determinants underlying the pathway broaden our knowledge of the catabolic diversity of halogenated HBs in microorganisms. Furthermore, the NAD(P)H-dependent flavin monooxygenase OdcA identified in Pigmentiphaga sp. strain H8 represents a novel 1-monooxygenase for halogenated para-HBs found in prokaryotes and enhances our knowledge of the decarboxylative hydroxylation of (halogenated) para-HBs.