Degradation of fluorobenzene by Rhizobiales strain F11 via ortho cleavage of 4-fluorocatechol and catechol

Short-term exposure to triclocarban alters microbial community composition and metabolite profiles in freshwater biofilms

Triclocarban (TCC), an emerging contaminant in water environments, its effects on freshwater biofilms remain insufficiently understood. This study investigates the effects of TCC exposure (at concentrations of 10 μg L-1 and 10 mg L-1) on mature freshwater biofilms. TCC was found to inhibit biofilm activity as evidenced by changes in surface morphology and the ratio of live/dead cells. Moreover, both concentrations of TCC were observed to modify the structure of the biofilm community. Metabolomics analysis revealed an overlap in the toxicity mechanisms and detoxification strategies triggered by various concentrations of TCC in biofilms. However, the higher toxicity induced by 10 mg L-1 TCC resulted from the downregulation of proline betaine, disrupting the homeostasis of cellular osmotic pressure regulation in biofilms. Notably, lipid and lipid-like molecules showed high sensitivity to different concentrations of TCC, indicating their potential as biomarkers for TCC exposure. Annotation of the differential metabolites by KEGG revealed that alterations in amino acid and carbon metabolism constituted the primary response mechanisms of biofilms to TCC. Moreover, the biofilm demonstrated enhanced nucleic acid metabolism, which bolstered resistance against TCC stress and heightened tolerance. Furthermore, elevated TCC concentrations prompted more robust detoxification processes for self-defense. Overall, short-term exposure to TCC induced acute toxicity in biofilms, yet they managed to regulate their community structure and metabolic levels to uphold oxidative homeostasis and activity. This research contributes to a deeper comprehension of TCC risk assessment and policy control in aquatic environments.

Influence of chemical structures on reduction rates and defluorination of fluoroarenes during catalytic reduction using a rhodium-based catalyst

Continuous growth in fluoroarene production has led to environmental pollution and health concerns owing to their persistence, which is attributed to the stable C-F bond in their structures. Herein, we investigated fluoroarene decomposition via hydrodefluorination using a rhodium-based catalyst, focusing on the effects of the chemical structure and functional group on the defluorination yield. Most compounds, except (pentafluoroethyl)benzene, exhibited full or partial reduction with pseudo-first-order rate constants in the range of 0.002-0.396 min-1 and defluorination yields of 0%-100%. Fluoroarenes with hydroxyl, methyl, and carboxylate groups were selected to elucidate how hydrocarbon and oxygen-containing functional groups influence the reaction rate and defluorination. Inhibition of the reaction rate and defluorination yield based on functional groups increased in the order of hydroxyl < methyl < carboxylate, which was identical to the order of the electron-withdrawing effect. Fluoroarenes with polyfluoro groups were also assessed; polyfluoro groups demonstrated a different influence on catalyst activity than non-fluorine functional groups because of fluorine atoms in the substituents undergoing defluorination. The reaction kinetics of (difluoromethyl)fluorobenzenes and their intermediates suggested that hydrogenation and defluorination occurred during degradation. Finally, the effects of the type and position of functional groups on the reaction rate and defluorination yield were investigated via multivariable linear regression analysis. Notably, the electron-withdrawing nature of functional groups appeared to have a greater impact on the defluorination yield of fluoroarenes than the calculated C-F bond dissociation energy.

Reasons why life on Earth rarely makes fluorine-containing compounds and their implications for the search for life beyond Earth

Life on Earth is known to rarely make fluorinated carbon compounds, as compared to other halocarbons. We quantify this rarity, based on our exhaustive natural products database curated from available literature. We build on explanations for the scarcity of fluorine chemistry in life on Earth, namely that the exclusion of the C-F bond stems from the unique physico-chemical properties of fluorine, predominantly its extreme electronegativity and strong hydration shell. We further show that the C-F bond is very hard to synthesize and when it is made by life its potential biological functions can be readily provided by alternative functional groups that are much less costly to incorporate into existing biochemistry. As a result, the overall evolutionary cost-to-benefit balance of incorporation of the C-F bond into the chemical repertoire of life is not favorable. We argue that the limitations of organofluorine chemistry are likely universal in that they do not exclusively apply to specifics of Earth's biochemistry. C-F bonds, therefore, will be rare in life beyond Earth no matter its chemical makeup.

Unveiling bacterial consortium for xenobiotic biodegradation from Pichavaram mangrove forest soil: a metagenomic approach

Pichavaram mangrove forest was established as a wetland of International Importance by Article 2.1 in April 2022 by the Ministry of Environment, Forest and Climate Change, India. Even though it is a conserved site, xenobiotic agrochemical leaching on the forest land during monsoon is inevitable. These threaten the microbial diversity in the environment. Xenobiotic degradation is achieved using bacterial consortia already acclimatised to this environment. This study aims to identify the indigenous microbial consortia able to degrade xenobiotic compounds such as fluorobenzoate, furfural, and steroids. Pichavaram mangrove metagenomic dataset was obtained by shotgun sequencing of soil DNA and processed using the automated tool SqueezeMeta. Further, the DIAMOND database provided the taxonomical classification of the microbes in each contig. With reference to the KEGG database, the selected xenobiotic degradation pathways were confirmed in the dataset. Of 1,253,029 total contigs, 1332, 72 and 1262 were involved in fluorobenzoate, furfural and steroid degradation, respectively. This study identified that microbial consortia comprising Marinobacter, Methyloceanibacter and Vibrio natriegens/Gramella sp. can degrade fluorobenzoate. While Afipia, Nitrosopumilus sp., and Phototrophicus methaneseepsis favour the degradation of furfural compound. The steroid degradation pathway possessed a plethora of bacteria belonging to the phylum Proteobacteria.

Biodegradation and Metabolic Pathway of the Neonicotinoid Insecticide Thiamethoxam by Labrys portucalensis F11

Thiamethoxam (TMX) is an effective neonicotinoid insecticide. However, its widespread use is detrimental to non-targeted organisms and water systems. This study investigates the biodegradation of this insecticide by Labrys portucalensis F11. After 30 days of incubation in mineral salt medium, L. portucalensis F11 was able to remove 41%, 35% and 100% of a supplied amount of TMX (10.8 mg L^-1) provided as the sole carbon and nitrogen source, the sole carbon and sulfur source and as the sole carbon source, respectively. Periodic feeding with sodium acetate as the supplementary carbon source resulted in faster degradation of TMX (10.8 mg L^-1); more than 90% was removed in 3 days. The detection and identification of biodegradation intermediates was performed by UPLC-QTOF/MS/MS. The chemical structure of 12 metabolites is proposed. Nitro reduction, oxadiazine ring cleavage and dechlorination are the main degradation pathways proposed. After biodegradation, toxicity was removed as indicated using Aliivibrio fischeri and by assessing the synthesis of an inducible β-galactosidase by an E. coli mutant (Toxi-Chromo test). L. portucalensis F11 was able to degrade TMX under different conditions and could be effective in bioremediation strategies.

Unravelling metabolism and microbial community of a phytobed co-planted with Typha angustifolia and Ipomoea aquatica for biodegradation of doxylamine from wastewater

Pharmaceutical contaminants in environment induce unexpected effects on ecological systems and human; thus, development of efficient technologies for their removal is immensely necessary. In this study, biodegradation and metabolic fate of a frequently found pharmaceutical contaminant, doxylamine by Typha angustifolia and Ipomoea aquatica was investigated. Microbial community of the plant rhizosphere has been identified to understand the important roles of the functional microbes. The plants reduced 48-80.5 % of doxylamine through hydrolysis/dehydroxylation and carbonylation/decarbonylation. A constructed phytobed co-planted with T. angustifolia and I. aquatica removed 77.3 %, 100 %, 83.67 %, and 61.13 % of chemical oxygen demand, total nitrogen, total phosphorus, and doxylamine respectively from real wastewater. High-throughput sequencing of soil and rhizosphere indicated that the phyla Proteobacteria, Bacteroidetes, Firmicutes, Planctomycetes, Actinobacteria, and Cyanobacteria dominated the microbial communities of the phytobed. Current study has demonstrated the applicability of the developed phytobeds for the treatment of doxylamine from municipal wastewater and provide a comprehensive understanding of its metabolism through plant and its rhizospheric microbial communities.

Biological Waste Air and Waste Gas Treatment: Overview, Challenges, Operational Efficiency, and Current Trends

International contracts to restrict emissions of climate-relevant gases, and thus global warming, also require a critical reconsideration of technologies for treating municipal, commercial, industrial, and agricultural waste gas emissions. A change from energy- and resource-intensive technologies, such as thermal post-combustion and adsorption, as well to low-emission technologies with high energy and resource efficiency, becomes mandatory. Biological processes already meet these requirements, but show restrictions in case of treatment of complex volatile organic compound (VOC) mixtures and space demand. Innovative approaches combining advanced oxidation and biofiltration processes seem to be a solution. In this review, biological processes, both as stand-alone technology and in combination with advanced oxidation processes, were critically evaluated in regard to technical, economical, and climate policy aspects, as well as present limitations and corresponding solutions to overcome these restrictions.

Carbon-fluorine bond cleavage mediated by metalloenzymes

Fluorochemicals are a widely distributed class of compounds and have been utilized across a wide range of industries for decades. Given the environmental toxicity and adverse health threats of some fluorochemicals, the development of new methods for their decomposition is significant to public health. However, the carbon-fluorine (C-F) bond is among the most chemically robust bonds; consequently, the degradation of fluorinated hydrocarbons is exceptionally difficult. Here, metalloenzymes that catalyze the cleavage of this chemically challenging bond are reviewed. These enzymes include histidine-ligated heme-dependent dehaloperoxidase and tyrosine hydroxylase, thiolate-ligated heme-dependent cytochrome P450, and four nonheme oxygenases, namely, tetrahydrobiopterin-dependent aromatic amino acid hydroxylase, 2-oxoglutarate-dependent hydroxylase, Rieske dioxygenase, and thiol dioxygenase. While much of the literature regarding the aforementioned enzymes highlights their ability to catalyze C-H bond activation and functionalization, in many cases, the C-F bond cleavage has been shown to occur on fluorinated substrates. A copper-dependent laccase-mediated system representing an unnatural radical defluorination approach is also described. Detailed discussions on the structure-function relationships and catalytic mechanisms provide insights into biocatalytic defluorination, which may inspire drug design considerations and environmental remediation of halogenated contaminants.

Bioengineered Graphene Oxide Microcomposites Containing Metabolically Versatile Paracoccus sp. MKU1 for Enhanced Catechol Degradation

Paracoccus sp. MKU1, a metabolically versatile bacterium that encompasses diverse metabolic pathways in its genome for the degradation of aromatic compounds, was investigated for catechol bioremediation here for the first time to our knowledge. Paracoccus sp. MKU1 degraded catechol at an optimal pH of 7.5 and a temperature of 37 °C, wherein 100 mg/L catechol was completely mineralized in 96 h but required 192 h for complete mineralization of 500 mg/L catechol. While investigating the molecular mechanisms of its degradation potential, it was unveiled that Paracoccus sp. MKU1 employed both the ortho and meta pathways by inducing the expression of catechol 1,2-dioxygenase (C12O) and catechol 2,3-dioxygenase (C23O), respectively. C23O expression at transcriptional levels was significantly more abundant than C12O, which indicated that catechol degradation was primarily mediated by extradiol cleavage by MKU1. Furthermore, poly(MAA-co-BMA)-GO (PGO) microcomposites containing Paracoccus sp. MKU1 were synthesized, which degraded catechol (100 mg/L) completely within 48 h with excellent recycling performance for three cycles. Thus, PGO@Paracoccus microcomposites proved to be efficient in catechol degradation at not only faster rates but also with excellent recycling performances than free cells. These findings accomplish that Paracoccus sp. MKU1 could serve as a potential tool for bioremediation of catechol-polluted industrial wastewater and soil.

Aerobic degradation of 2- and 3-fluoroaniline in mixed culture systems and microbial community analysis

Among three monofluoroanilines, 2-fluoroaniline (2-FA) and 3-fluoroaniline (3-FA) exhibit relatively poor biodegradability. This work examined their degradation characteristics in a mixed culture system and also analyzed the microorganism community. After acclimation for 58 d and 43 d, the high removal efficiency of 100% of 2-FA and 95.3% of 3-FA was obtained by adding 25 mg L^-1 of 2-FA or 3-FA to the two reactors, respectively. In addition, the high defluorination rates of 2-FA and 3-FA were observed to be 87.0% and 89.3%, respectively. The degradation kinetics showed that the maximum specific degradation rates of 2-FA and 3-FA were (21.23 ± 0.91) mg FA (g•VSS·h)^-1, and (11.75 ± 0.99) mg FA (g•VSS·h)^-1, respectively. PCR-DGGE analysis revealed that the unique bacteria degrading 2-FA were mainly composed of six genera (Novosphingobium, Bradyrhizobium, Aquaspirillum, Aminobacter, Ochrobactrum, and Labrys), and five genera that degraded 3-FA (Ochrobactrum, Aquaspirillum, Lachnobacterium, Bradyrhizobium, and Variovorax). Analysis of the key catabolic enzyme activities indicated that the simultaneous hydroxylation and dehalogenation were involved in monooxygenase elimination of 2-FA and conversion of 3-FA to 4-fluorocatechol by dioxygenase, indicating that enriched mixed cultures were effective to metabolize 2-FA or 3-FA by unconventional pathways to prevent the accumulation of toxic metabolites.

Degradation of 3-fluoroanilne by Rhizobium sp. JF-3

The interest of fluoroanilines in the environment is due to their extensive applications in industry and their low natural biodegradability. A pure bacterial strain capable of degrading 3-fluoroaniline (3-FA) as the sole source of carbon and energy was isolated from a sequencing batch reactor operating for the treatment of 3-FA. The strain (designated as JF-3) was identified by 16S rRNA gene analysis as a member of the genus Rhizobium. When grown in 3-FA medium at concentrations of 100-700 mg/L, strain JF-3 almost completely removed 3-FA within 72 h. However, the obvious cell growth inhibition was observed in cultures treated with 3-FA concentrations greater than 500 mg/L. The degradation kinetics of 3-FA were consistent with Haldane's model with the maximum degradation rate as 67.66 mg/(g dry cell h). The growth kinetics of strain JF-3 followed Andrew's model with the maximum growth rate as 30.87 h^-1. Also, strain JF-3 was able to degrade 4-fluoroaniline, aniline, and catechol, but hardly grew on 2-fluoroaniline, 2,4-dfluoroaniline, 2,3,4-trifluoroaniline, 3-fluorocatechol, and 4-fluorocatechol. Additionally, it was able to grow over a wide pH range (pH 6-10), and also showed tolerance to salinity with lower than 1.0%. This result, in combination with the enzyme assays and analysis of metabolite intermediates, indicated an unconventional pathway for 3-fluoroaniline metabolism that involved conversion to 3-aminophenol and resorcinol by monooxygenase, and which was subsequently metabolized via the ortho-cleavage pathway. To our knowledge, this is the first report on the utilization of 3-FA as a growth substrate by Rhizobium sp.

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol

The complex structural and functional responses of agricultural soil microbial communities to the addition of carbonaceous compounds such as biochar remain poorly understood. This severely limits the predictive ability for both the potential enhancement of soil fertility and greenhouse gas mitigation. In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with Napier grass. Our analyses revealed that biochar-amended soil microbiomes exhibited significant shifts in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification, were enriched under biochar amendment. These community shifts were in part associated with increased soil carbon, such as labile and aromatic carbon compounds, which was likely stimulated by the increased available nutrients associated with biochar amendment. These findings indicate that the soil microbiome response to the combination of biochar addition and to incubation conditions confers enhanced nutrient cycling and a small decrease in CO₂ emissions and potentially mitigates nitrous oxide emissions.IMPORTANCE The incorporation of biochar into soil is a promising management strategy for sustainable agriculture owing to its potential to sequester carbon and improve soil fertility. Expanding the addition of biochar to large-scale agriculture hinges on its lasting beneficial effects on the microbial community. However, there exists a significant knowledge gap regarding the specific role that biochar plays in altering the key biological soil processes that influence plant growth and carbon storage in soil. Previous studies that examined the soil microbiome under biochar amendment principally characterized only how the composition alters in response to biochar amendment. In the present study, we shed light on the functional alterations of the microbial community response 2 years after biochar amendment. Our results show that biochar increased the abundance of genes involved in denitrification and carbon turnover and that biochar-amended soil microcosms had a reduction in cumulative CO₂ production.

Bioremediation of bezafibrate and paroxetine by microorganisms from estuarine sediment and activated sludge of an associated wastewater treatment plant

The present work aimed to explore the potential of autochthonous microorganisms from an urban estuary and from activated sludge of an associated wastewater treatment plant (WWTP), for biodegradation of an antidepressant drug, paroxetine, and on a cholesterol-lowering agent, bezafibrate. These compounds were chosen as representatives of extensively used pharmaceuticals. Autochthonous microorganisms from the indicated sources were exposed to the target pharmaceuticals (1 mg/L) in co-metabolism with sodium acetate (500 mg/L) along a two-weeks period, for a total of 7 two-weeks periods (here referred as cycles). Exposures were carried out in batch mode, under different incubation conditions (agitation vs. static). Removal of pharmaceuticals was monitored at the end of each cycle, by analysing the culture medium. For paroxetine, fluoride ion release was also followed as an indicator of defluorination of the molecule. The structure of the bacterial communities was analysed by ARISA (Automated rRNA Intergenic Spacer Analysis), at the beginning of the experiment and at the end of the first and the last cycles to identify substantial changes associated with the time of exposure, the incubation conditions and the presence and type of pharmaceuticals. Incubation conditions affected not only the bacterial community structure, but also the biodegradation efficiency. At the beginning of the experiment, removal of target pharmaceuticals was found to be lower under agitation than under static conditions, but at the end of the experiment, results showed high removal of the pharmaceuticals from the culture medium (>97%) under both conditions, mainly by microbiological processes. For paroxetine, adsorption and abiotic processes also had an important influence on its removal, but defluorination only occurred in the presence of microorganisms. These results highlight that autochthonous microorganisms from estuarine sediments and WWTP sludge have high ability to remove the selected pharmaceuticals with relevant implications for the development of new bioremediation tools for environmental restoration.

Removal of veterinary antibiotics in constructed wetland microcosms - Response of bacterial communities

This study aimed to evaluate the response of bacteria, in terms of microbial community structure, from constructed wetland (CW) microcosms exposed to two veterinary antibiotics, enrofloxacin (ENR) and ceftiofur (CEF), alone or in a mixture, identifying which bacterial groups were dominant in CWs substrate during livestock wastewater treatment. Wastewater, not-doped or doped with ENR and/or CEF (100 µg/L each), was treated during 18 one-week cycles. Systems showed removal percentages > 85% for the added antibiotics, showing also high removal percentages for nutrients and organic matter and confirming CWs systems were working properly. However, both time of exposure and presence of antibiotics influenced significantly CWs substrate bacterial community structure. Pyrosequencing results showed bacterial communities were dominated by phyla Proteobacteria (38-48%), Firmicutes (20-27%), Bacteroidetes (12-15%) and Actinobacteria (4-9%), and that their relative abundance was clearly affected by the presence of the antibiotics. Results suggest the applicability of CWs for the removal of veterinary antibiotics from livestock wastewaters and provide new knowledge about the bacteria within the system, which can potentially be involved in removal processes. This information could in the future be used to improve CWs removal rates of pharmaceuticals from livestock wastewaters.

Biodegradation of Diclofenac by the bacterial strain Labrys portucalensis F11

Diclofenac (DCF) is a widely used non-steroidal anti-inflammatory pharmaceutical which is detected in the environment at concentrations which can pose a threat to living organisms. In this study, biodegradation of DCF was assessed using the bacterial strain Labrys portucalensis F11. Biotransformation of 70% of DCF (1.7-34 μM), supplied as the sole carbon source, was achieved in 30 days. Complete degradation was reached via co-metabolism with acetate, over a period of 6 days for 1.7 µM and 25 days for 34 μM of DCF. The detection and identification of biodegradation intermediates was performed by UPLC-QTOF/MS/MS. The chemical structure of 12 metabolites is proposed. DCF degradation by strain F11 proceeds mainly by hydroxylation reactions; the formation of benzoquinone imine species seems to be a central step in the degradation pathway. Moreover, this is the first report that identified conjugated metabolites, resulting from sulfation reactions of DCF by bacteria. Stoichiometric liberation of chlorine and no detection of metabolites at the end of the experiments are strong indications of complete degradation of DCF by strain F11. To the best of our knowledge this is the first report that points to complete degradation of DCF by a single bacterial strain isolated from the environment.

Genomic insights of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: a paradigm of soil isolate with elements of biodegradation

This research employs draft genome sequence data of Klebsiella pneumoniae AWD5 to explore genes that contribute to the degradation of polyaromatic hydrocarbon (PAH) and stimulate plant growth, for rhizosphere-mediated bioremediation. Annotation analysis suggests that the strain AWD5 not only possess gene clusters for PAH utilization, but also for utilization of benzoate, fluorobenzoate, phenylacetate (paa), hydroxyphenylacetic acid (hpa), 3-hydroxyphenyl propionate (mhp). A comparative genome analysis revealed that the genome of AWD5 was highly similar with genomes of environmental as well as clinical K. pneumoniae isolates. The artemis output confirmed that there are 139 different genes present in AWD5 which were absent in genome of clinical strain K. pneumoniae ATCC BAA-2146, and 25 genes were identified to be present in AWD5 genome but absent in genome of environmental strain K. pneumoniae KP-1. Pathway analyzed using Kyoto Encyclopedia of Genes and Genomes enzyme database revealed the presence of gene clusters that code for enzymes to initiate the opening of aromatic rings. The polyaromatic hydrocarbon and benzoate degradation were found to be metabolized through ortho-cleavage pathway, mineralizing the compounds to TCA cycle intermediates. Genes for plant growth promoting attributes such as Indole acetic acid (IAA) synthesis, siderophore production, and phosphate solubilization were detected in the genome. These attributes were verified in vitro, including IAA (14.75 µg/ml), siderophore production (13.56%), phosphate solubilization (198.28 ng/ml), and ACC deaminase (0.118 mM α-ketobutyrate/mg) in the presence of pyrene, and also compared with results obtained in glucose amended medium. K. pneumoniae AWD5 enhanced the growth of Jatropha curcas in the presence of pyrene-contaminated soil. Moreover, AWD5 harbors heavy metal resistance genes indicating adaptation to contaminants. The study revealed the genomic attributes of K. pneumoniae AWD5 for its catabolic characteristics for different aromatic compounds, which makes it suitable for rhizoremediation of PAH-contaminated soil.

Simultaneous partial nitrification and 2-fluorophenol biodegradation with aerobic granular biomass: Reactor performance and microbial communities

An aerobic granular bioreactor was operated for over 4months, treating a synthetic wastewater with a high ammonium content (100mgNL^-1). The inoculum was collected from a bioreactor performing simultaneous partial nitrification and aromatic compounds biodegradation. From day-56 onwards, 2-fluorophenol (2-FP) (12.4mgL^-1) was added to the feeding wastewater and the system was bioaugmented with a 2-FP degrading bacteria (Rhodococcus sp. FP1). By the end of operation, complete 2-FP biodegradation and partial nitrification were simultaneously achieved. Aerobic granules remained stable over time. During the 2-FP loading, a shift in the community structure occurred, coinciding with the improvement of 2-FP degradation. DGGE analysis did not allow to infer on the bioaugmented strain presence but pyrosequencing analysis detected Rhodococcus genus by the end of operation. Together with other potential phenolic-degraders within granules, these microorganisms were probably responsible for 2-FP degradation.

Phenol Is the Initial Product Formed during Growth and Degradation of Bromobenzene by Tropical Marine Yeast, Yarrowia lipolytica NCIM 3589 via an Early Dehalogenation Step

Bromobenzene (BrB), a hydrophobic, recalcitrant organic compound, is listed by the environmental protection agencies as an environmental and marine pollutant having hepatotoxic, mutagenic, teratogenic, and carcinogenic effects. The tropical marine yeast Yarrowia lipolytica 3589 was seen to grow aerobically on BrB and displayed a maximum growth rate (μmax) of 0.04 h-1. Furthermore, we also observed an increase in cell size and sedimentation velocity for the cells grown on BrB as compared to the glucose grown cells. The cells attached to the hydrophobic bromobenzene droplets through its hydrophobic and acid-base interactions. The BrB (0.5%, 47.6 mM) was utilized by the cells with the release of a corresponding amount of bromide (12.87 mM) and yielded a cell mass of 1.86 g/L after showing 34% degradation in 96 h. Maximum dehalogenase activity of 16.16 U/mL was seen in the cell free supernatant after 24 h of growth. Identification of metabolites formed as a result of BrB degradation, namely, phenol, catechol, cis, cis muconic acid, and carbon dioxide were determined by LC-MS and GC-MS. The initial attack on bromobenzene by Y. lipolytica cells lead to the transient accumulation of phenol as an early intermediate which is being reported for the first time. Degradation of phenol led to catechol which was degraded by the ortho- cleavage pathway forming cis, cis muconic acid and then to Krebs cycle intermediates eventually leading to CO2 production. The study shows that dehalogenation via an extracellular dehalogenase occurs prior to ring cleavage with phenol as the preliminary degradative compound being produced. The yeast was also able to grow on the degradative products, i.e., phenol and catechol, to varying degrees which would be of potential relevance in the degradation and remediation of xenobiotic environmental bromoaromatic pollutants such as bromobenzene.

Natural production of fluorinated compounds and biotechnological prospects of the fluorinase enzyme

Fluorinated compounds are finding increasing uses in several applications. They are employed in almost all areas of modern society. These compounds are all produced by chemical synthesis and their abundance highly contrasts with fluorinated molecules of natural origin. To date, only some plants and a handful of actinomycetes species are known to produce a small number of fluorinated compounds that include fluoroacetate (FA), some ω-fluorinated fatty acids, nucleocidin, 4-fluorothreonine (4-FT), and the more recently identified (2R3S4S)-5-fluoro-2,3,4-trihydroxypentanoic acid. This largely differs from other naturally produced halogenated compounds, which totals more than 5000. The mechanisms underlying biological fluorination have been uncovered after discovering the first actinomycete species, Streptomyces cattleya, that is capable of producing FA and 4-FT, and a fluorinase has been identified as the enzyme responsible for the formation of the C-F bond. The discovery of this enzyme has opened new perspectives for the biotechnological production of fluorinated compounds and many advancements have been achieved in its application mainly as a biocatalyst for the synthesis of [¹⁸F]-labeled radiotracers for medical imaging. Natural fluorinated compounds may also be derived from abiogenic sources, such as volcanoes and rocks, though their concentrations and production mechanisms are not well known. This review provides an outlook of what is currently known about fluorinated compounds with natural origin. The paucity of these compounds and the biological mechanisms responsible for their production are addressed. Due to its relevance, special emphasis is given to the discovery, characterization and biotechnological potential of the unique fluorinase enzyme.

Degradation of benzotrifluoride via the dioxygenase pathway in Rhodococcus sp. 065240

We previously isolated Rhodococcus sp. 065240, which catalyzes the defluorination of benzotrifluoride (BTF). In order to investigate the mechanism of this degradation of BTF, we performed proteomic analysis of cells grown with or without BTF. Three proteins, which resemble dioxygenase pathway enzymes responsible for isopropylbenzene degradation from Rhodococcus erythropolis BD2, were induced by BTF. Genomic PCR and DNA sequence analysis revealed that the Rhodococcus sp. 065240 carries the gene cluster, btf, which is highly homologous to the ipb gene cluster from R. erythropolis BD2. A mutant strain, which could not catalyze BTF defluorination, was isolated from 065240 strain by UV mutagenesis. The mutant strain had one mutation in the btfT gene, which encodes a response regulator of the two component system. The defluorinating ability of the mutant strain was recovered by complementation of btfT. These results suggest that the btf gene cluster is responsible for degradation of BTF.

Co-metabolic degradation of mono-fluorophenols by the ectomycorrhizal fungi Pisolithus tinctorius

The release of fluorinated organic compounds from fire retardants or agrochemical products may have a significant negative effect on soil ecosystems. In this study, the ability of Pisolithus tinctorius to tolerate and degrade mono-fluorophenols (FP) was assessed. In vitro studies showed fungal growth in the presence of 0.45mM of 2-FP and 3-FP, but not in the presence of 4-FP. P. tinctorius was able to degrade up to 79% and 92% of 1mM 2-FP and 3-FP, respectively, in glucose supplemented liquid medium, suggesting that 2- and 3-FP degradation occurred in co-metabolism with glucose consumption. 3-Fluorocatechol (FC) and 4-FC were identified as metabolic intermediates using HPLC and LC-MS. Liberation of fluoride was not detected suggesting that a fluorinated dead-end product was formed. In extracts of cells collected at the end of cultures supplemented with the mono-FPs, a metabolic intermediate compatible with a mass corresponding to a fluoromuconate compound, according to LC-MS data, was recovered. The results further suggest that ectomycorrhizal fungi may be able to degrade mono-FP in pure culture while using glucose as a carbon source, through a similar pathway as that found in bacteria. To our knowledge, this is the first time that degradation of mono-FPs by an ectomycorrhizal fungus is reported.

Degradation of toluene by ortho cleavage enzymes in Burkholderia fungorum FLU100

Burkholderia fungorum FLU100 simultaneously oxidized any mixture of toluene, benzene and mono-halogen benzenes to (3-substituted) catechols with a selectivity of nearly 100%. Further metabolism occurred via enzymes of ortho cleavage pathways with complete mineralization. During the transformation of 3-methylcatechol, 4-carboxymethyl-2-methylbut-2-en-4-olide (2-methyl-2-enelactone, 2-ML) accumulated transiently, being further mineralized only after a lag phase of 2 h in case of cells pre-grown on benzene or mono-halogen benzenes. No lag phase, however, occurred after growth on toluene. Cultures inhibited by chloramphenicol after growth on benzene or mono-halogen benzenes were unable to metabolize 2-ML supplied externally, even after prolonged incubation. A control culture grown with toluene did not show any lag phase and used 2-ML as a substrate. This means that 2-ML is an intermediate of toluene degradation and converted by specific enzymes. The conversion of 4-methylcatechol as a very minor by-product of toluene degradation in strain FLU100 resulted in the accumulation of 4-carboxymethyl-4-methylbut-2-en-4-olide (4-methyl-2-enelactone, 4-ML) as a dead-end product, excluding its nature as a possible intermediate. Thus, 3-methylcyclohexa-3,5-diene-1,2-diol, 3-methylcatechol, 2-methyl muconate and 2-ML were identified as central intermediates of productive ortho cleavage pathways for toluene metabolism in B. fungorum FLU100.

Microbiota associated with the migration and transformation of chlorinated aliphatic hydrocarbons in groundwater

Pollution of groundwater with chlorinated aliphatic hydrocarbons (CAHs) is a serious environmental problem which is threatening human health. Microorganisms are the major participants in degrading these contaminants. Here, groundwater contaminated for a decade with CAHs was investigated. Numerical simulation and field measurements were used to track and forecast the migration and transformation of the pollutants. The diversity, abundance, and possible activity of groundwater microbial communities at CAH-polluted sites were characterized by molecular approaches. The number of microorganisms was between 5.65E+05 and 1.49E+08 16S rRNA gene clone numbers per liter according to quantitative real-time PCR analysis. In 16S rRNA gene clone libraries constructed from samples along the groundwater flow, eight phyla were detected, and Proteobacteria were dominant (72.8 %). The microbial communities varied with the composition and concentration of pollutants. Meanwhile, toluene monooxygenases and methane monooxygenases capable of degradation of PCE and TCE were detected, demonstrating the major mechanism for PCE and TCE degradation and possibility for in situ remediation by addition of oxygen in this study.

Complete hydrodehalogenation of polyfluorinated and other polyhalogenated benzenes under mild catalytic conditions

Polyfluorinated arenes are increasingly used in industry and can be considered emerging contaminants. Environmentally applicable degradation methods leading to full defluorination are not reported in the literature. In this study, it is demonstrated that the heterogeneous catalyst Rh/Al2O3 is capable of fully defluorinating and hydrogenating polyfluorinated benzenes in water under mild conditions (1 atm H2, ambient temperature) with degradation half-lives between 11 and 42 min. Analysis of the degradation rates of the 12 fluorobenzene congeners showed two trends: slower degradation with increasing number of fluorine substituents and increasing degradation rates with increasing number of adjacent fluorine substituents. The observed fluorinated intermediates indicated that adjacent fluorine substituents are preferably removed. Besides defluorination and hydrogenation, the scope of the catalyst includes dehalogenation of polychlorinated benzenes, bromobenzene, iodobenzene, and selected mixed dihalobenzenes. Polychlorobenzene degradation rates, like their fluorinated counterparts, decreased with increasing halogen substitution. In contrast to the polyfluorobenzenes though, removal of chlorine substituents was sterically driven. All monohalobenzenes were degraded at similar rates; however, when two carbon-halogen bonds were in direct intramolecular competition, the weaker bond was broken first. Differences in sorption affinities of the substrates are suggested to play a major role in determining the relative rates of transformation of halobenzenes by Rh/Al2O3 and H2.

Isolation, identification and characterization of a novel Ralstonia sp. FD-1, capable of degrading 4-fluoroaniline

A gram-negative strain, designated as FD-1, isolated from aerobic activated sludge was capable of metabolizing 4-fluoroaniline (4-FA) as its sole carbon and nitrogen source and energy supply. According to the Biolog GNIII detection method 17 of 71 carbon substrates were easily utilized, while 12 of 23 substrates did not inhibit strain FD-1. The 16S rDNA sequence from strain FD-1 was 99 % similar to Ralstonia sp., suggesting that it belonged to the genus Ralstonia. The optimal conditions for growth and 4-FA degradation were pH 7 and 30 °C. The tolerance to 4-FA were 1,250 mg/L, while the tolerance to salinity was 15 g/L. Catechol 2,3-dioxygenase activity was detected and degradation intermediates were analyzed by liquid chromatography mass spectrometry leading to a proposed degradation pathway and suggesting that extradiol cleavage was involved in 4-FA degradation. This is the first report on the degradation of 4-FA by a bacterium from the Ralstonia genus.

Hydrodefluorination and hydrogenation of fluorobenzene under mild aqueous conditions

Fluorinated organic compounds are increasingly used in many applications, and their release to the environment is expected. It is therefore important to find suitable methods for degradation of fluorinated compounds under environmentally relevant conditions. In this study, a simple heterogeneous rhodium-based catalytic system (Rh/Al(2)O(3) and H(2)) for hydrodefluorination and hydrogenation of fluorobenzene under mild aqueous conditions (1 atm of H(2), ambient temperature) was developed and the underlying reaction mechanism was investigated. Fluorobenzene degraded rapidly (t(1/2) ≈ 0.2 h) to form cyclohexane and fluoride (F(-)) as the stable end products, with benzene and cyclohexene observed as intermediates. Cyclohexadiene intermediates were not observed but were expected to form during the hydrogenation of benzene. Three postulated but unobserved fluorinated intermediates were subjected to the catalytic reaction conditions, and it was concluded that they most likely do not form during the fluorobenzene degradation reaction. Isotope labeling experiments showed that the unsaturated intermediates undergo rapid and reversible hydrogenation/dehydrogenation under the reaction conditions and also that fully saturated compounds are unreactive in the catalytic system. Both molecular hydrogen and water were sources of hydrogen in the final cyclohexane product. Kinetic fitting indicated that sorption/desorption of fluorobenzene onto the catalyst surface plays an important role in the mechanism.

Effect of the metals iron, copper and silver on fluorobenzene biodegradation by Labrys portucalensis

Organic and metallic pollutants are ubiquitous in the environment. Many metals are reported to be toxic to microorganisms and to inhibit biodegradation. The effect of the metals iron, copper and silver on the metabolism of Labrys portucalensis F11 and on fluorobenzene (FB) biodegradation was examined. The results indicate that the addition of 1 mM of Fe(2+) to the culture medium has a positive effect on bacterial growth and has no impact in the biodegradation of 1 and 2 mM of FB. The presence of 1 mM of Cu(2+) was found to strongly inhibit the growth of F11 cultures and to reduce the biodegradation of 1 and 2 mM of FB to ca. 50 %, with 80 % of stoichiometrically expected fluoride released. In the experiments with resting cells, the FB degraded (from 2 mM supplied) was reduced ca. 20 % whereas the fluoride released was reduced to 45 % of that stoichiometrically expected. Ag(+) was the most potent inhibitor of FB degradation. In experiments with growing cells, the addition of 1 mM of Ag(+) to the culture medium containing 1 and 2 mM of FB resulted in no fluoride release, whereas FB degradation was only one third of that observed in control cultures. In the experiments with resting cells, the addition of Ag(+) resulted in 25 % reduction in substrate degradation and fluoride release was only 20 % of that stoichiometrically expected. The accumulation of catechol and 4-fluorocatechol in cultures supplemented with Cu(2+) or Ag(+) suggest inhibition of the key enzyme of FB metabolism-catechol 1,2-dioxygenase.

2-fluorophenol degradation by aerobic granular sludge in a sequencing batch reactor

Aerobic granular sludge is extremely promising for the treatment of effluents containing toxic compounds, and it can economically compete with conventional activated sludge systems. A laboratory scale granular sequencing batch reactor (SBR) was established and operated during 444 days for the treatment of an aqueous stream containing a toxic compound, 2-fluorophenol (2-FP), in successive phases. Initially during ca. 3 months, the SBR was intermittently fed with 0.22 mM of 2-FP added to an acetate containing medium. No biodegradation of the target compound was observed. Bioaugmentation with a specialized bacterial strain able to degrade 2-FP was subsequently performed. The reactor was thereafter continuously fed with 0.22 and 0.44 mM of 2-FP and with 5.9 mM of acetate (used as co-substrate), for 15 months. Full degradation of the compound was reached with a stoichiometric fluoride release. The 2-FP degrading strain was successfully retained by aerobic granules, as shown through the recovering of the strain from the granular sludge at the end of the experiment. Overall, the granular SBR has shown to be robust, exhibiting a high performance after bioaugmentation with the 2-FP degrading strain. This study corroborates the fact that bioaugmentation is often needed in cases where biodegradation of highly recalcitrant compounds is targeted.

Biology of fluoro-organic compounds

Investigations on diverse aspects of fluoro-organic compounds have rapidly increased during the past decades. Because natural sources of fluoro-organic compounds are extremely rare, the industrial synthesis of fluorinated organic compounds and production of fluorinated natural product derivatives have greatly expanded in recent years because of their increasing importance in the agrochemical and pharmaceutical industries. Due to structural complexity or instability, synthetic modification is often not possible, and various biofluorination strategies have been developed in recent years for applications in the anti-cancer, anti-viral and anti-infection fields. Despite the industrial importance of fluorinated compounds, there have been serious concerns worldwide over the levels and synthetic routes of certain fluorinated organic compounds, in particular perfluorinated chemicals (PFCs). PFCs are emerging and recalcitrant pollutants which are widely distributed in the environment and have been detected in humans and wildlife globally. PFCs have been demonstrated to be potentially carcinogenic, adversely affect the neuroendocrine and immune systems, and produce neurotoxicity, heptatotoxicity and endocrine disrupting effects in vertebrate animals. Here, we provide an overview of recent advances in our understanding of the biology of various fluoro-organic compounds and perspectives for new enzymes and metabolic pathways for bioremediation of these chemicals.

Biotransformation of fluorobiphenyl by Cunninghamella elegans

The fungus Cunninghamella elegans is a useful model of human catabolism of xenobiotics. In this paper, the biotransformation of fluorinated biphenyls by C. elegans was investigated by analysis of the culture supernatants with a variety of analytical techniques. 4-Fluorobiphenyl was principally transformed to 4-fluoro-4'-hydroxybiphenyl, but other mono- and dihydroxylated compounds were detected in organic extracts by gas chromatography-mass spectrometry. Additionally, fluorinated water-soluble products were detected by (19)F NMR and were identified as sulphate and beta-glucuronide conjugates. Other fluorobiphenyls (2-fluoro-, 4,4'-difluoro- and 2,3,4,5,6-pentafluoro-biphenyl) were catabolised by C. elegans, yielding mono- and dihydroxylated products, but phase II metabolites were detected from 4,4'-difluorobiphenyl only.

Analysis of two gene clusters involved in the degradation of 4-fluorophenol by Arthrobacter sp. strain IF1

Arthrobacter sp. strain IF1 is able to grow on 4-fluorophenol (4-FP) as a sole source of carbon and energy. To clone the 4-FP degradation genes, DNA libraries were constructed and screened with a probe obtained by PCR using primers designed on the basis of conserved regions of aromatic two-component monooxygenases. Sequencing of positive clones yielded two gene clusters, each harboring a gene encoding a monooxygenase with high sequence similarity to the oxygenase component of 4-nitrophenol and 4-chlorophenol monooxygenase systems. Both these monooxygenase genes were differentially expressed during growth on 4-FP, as revealed by Northern blotting and reverse transcription-PCR. One cluster also contained a gene for a flavin reductase. The monooxygenase and reductase were purified from Escherichia coli cells expressing the corresponding genes, and together they catalyzed NADH-dependent hydroxylation and dehalogenation of 4-halophenols. The results indicate that strain IF1 transforms 4-FP to hydroquinone by a two-component monooxygenase system of which one component provides reduced flavin adenine dinucleotide at the expense of NADH and the other catalyzes para-hydroxylation of 4-FP and other 4-substituted phenols.

Metabolism of fluoroorganic compounds in microorganisms: impacts for the environment and the production of fine chemicals

Incorporation of fluorine into an organic compound can favourably alter its physicochemical properties with respect to biological activity, stability and lipophilicity. Accordingly, this element is found in many pharmaceutical and industrial chemicals. Organofluorine compounds are accepted as substrates by many enzymes, and the interactions of microorganisms with these compounds are of relevance to the environment and the fine chemicals industry. On the one hand, the microbial transformation of organofluorines can lead to the generation of toxic compounds that are of environmental concern, yet similar biotransformations can yield difficult-to-synthesise products and intermediates, in particular derivatives of biologically active secondary metabolites. In this paper, we review the historical and recent developments of organofluorine biotransformation in microorganisms and highlight the possibility of using microbes as models of fluorinated drug metabolism in mammals.