Structure and mechanism of the alkane-oxidizing enzyme AlkB

Metabolic characterization of alkane monooxygenases and the growth phenotypes of Pseudomonas aeruginosa ATCC 33988 on hydrocarbons

There is a demand and widespread interest in evaluating microbial community structures and metabolic processes in hydrocarbon environments. The current work aims to detect microbial subgroups (phenotypic subsets) and their metabolic processes, such as substrate specificity and expression of niche-associated genes. In this study, we were able to discriminate different cell types in real time from a complex sample matrix to allow the detection of live, dead, and injured cell populations in jet fuels. We found that the expression of alkB1 and alkB2 genes is induced in a growth-dependent manner and alkB2 induction started before alkB1. This indicates that as an early response of Pseudomonas aeruginosa cells' exposure to alkanes, cells activate alkB2 gene induction. Deletion of alkB1 and alkB2 genes completely inhibited P. aeruginosa ATCC 33988 growth in jet fuel, suggesting that two alkane monooxygenases are responsible for the degradation of alkanes and jet fuel. Interestingly, the AlkB2 has a broader (n-C8-n-C16) substrate range compared to AlkB1 (n-C12-n-C16). The data indicate that two alkane utilization pathways can coexist in P. aeruginosa ATCC 33988, and they are differentially expressed in response to n-C6-n-C16 alkanes found in jet fuel. This study provided additional information on the heterogeneity and phenotypic diversity within the same species after exposure to hydrocarbons. This work advances our understanding of microbial community structures and provides new insight into the alkane metabolism of P. aeruginosa.IMPORTANCEAlkane degradation allows for the natural breakdown of hydrocarbons found in crude oil, which can significantly contribute to environmental remediation. The metabolic process of microbes to hydrocarbons and the expression of niche-associated genes are not well understood. Pseudomonas aeruginosa ATCC 33988, originally isolated from a jet fuel tank, degrades hydrocarbons effectively and outcompetes the type strain Pseudomonas aeruginosa PAO1. In this study, we found differential expression of alkB1 and alkB2 alkane monooxygenase genes and the relative importance of these genes in alkane degradation. We found different phenotypic subsets within the same genotype, which are influenced by hydrocarbon stress. Overall, the research conducted in this study significantly contributes to our knowledge about microbial processes and community structure in hydrocarbon environments.

Biodegradation of polystyrene by Spodoptera litura and Spodoptera frugiperda larvae (Lepidoptera: Noctuidae): Insights into the frass characterization and responses of gut microbiomes

Polystyrene (PS) biodegradation by some lepidoptera larvae has been demonstrated, but little is known about the Spodoptera litura and Spodoptera frugiperda (Lepidoptera: Noctuidae). Here we confirmed that PS-fed larvae showed significantly higher survival rates than starvation and antibiotic groups, with S. frugiperda consuming PS more efficiently than S. litura (1.52 vs. 0.56 mg larva⁻¹ day⁻¹). PS-frass characterization revealed oxygen-containing groups (C-O, CO, -OH) with reduced thermal stability and a significant decrease in weight-average molecular weight (S. litura: -6.01 %; S. frugiperda: -8.93 %), evidencing oxidative depolymerization of PS by both species. The gut microbiota (Pedobacter, Achromobacter, Pseudomonas, Acinetobacter, etc.) and functional enzymes (e.g., monooxygenase, dioxygenase, chitinases) were upregulated in PS-fed larvae. Metabolome analysis revealed altered stress responses and reprogrammed metabolic pathways, particularly in lipid and carbohydrate metabolism, which correlated strongly with gut microbiota changes. Overall, we demonstrated the biodegradation of PS by S. litura and S. frugiperda for the first time, and proposed a plausible degradation mechanism mediated by gut microbiota, illustrating both the host and gut microbiomes contributed to PS biodegradation. These findings highlight the feasibility of developing insect-based plastic degradation systems through the isolation of key microbial-enzymatic consortia, offering a sustainable solution for plastic waste management.

The GntR/VanR transcription regulator AlkR represses AlkB2 monooxygenase expression and regulates n-alkane degradation in Pseudomonas aeruginosa SJTD-1

Transmembrane alkane monooxygenase (AlkB)-type monooxygenases, especially AlkB2 monooxygenases, are crucial for aerobic degradation of the medium-to-long-chain n-alkanes in hydrocarbon-utilizing microorganisms. In this study, we identified a GntR/VanR transcription regulator AlkR of Pseudomonas aeruginosa SJTD-1 involved in the negative regulation of AlkB2 and deciphered its nature of DNA binding and ligand release. The deletion of alkR enhanced the transcription levels of the alkB2 gene and the utilization efficiency of the medium-to-long-chain n-alkanes by strain SJTD-1. The dimer of AlkR recognizes and binds to a conserved palindromic motif in the promoter of the alkB2 gene, and structural symmetry is vital for DNA binding and transcription repression. The long-chain fatty acyl coenzyme A compounds can release AlkR and stimulate transcription of alkB2, reflecting the effect of alkane catabolic metabolites. Structural insights unveiled that the arginine residues and scaffold residues of AlkR are critical for DNA binding. Further bioinformatics analysis of AlkR revealed the widespread VanR-AlkB couples distributed in Pseudomonadaceae with high conservation in the sequences of functional genes and intergenic regions, highlighting a conserved regulatory pattern for n-alkane utilization across this family. These findings demonstrate the regulatory mechanism and structural basis of GntR/VanR transcription regulators in modulating n-alkane biodegradation and provide valuable insights in improving the bioremediation efficiency of hydrocarbon pollution.

Fontimonas thermophila Alkane Monooxygenase (FtAlkB) Is an Alkyl Fluoride Dehalogenase

Purified alkane monooxygenase (AlkB) from Fontimonas thermophila (FtAlkB) catalyzes the defluorination of 1-fluorooctane, producing octanal, which is partially reduced under the reaction conditions to generate 1-octanol. This reaction occurs preferentially at the monofluorinated methyl group, with only a minor amount of oxidation at the nonfluorinated end of the molecule. The dehalogenation chemistry is specific to 1-fluorooctane, as neither 1-chlorooctane or 1-bromooctane are dehalogenated to an appreciable extent. Furthermore, P. putida cells containing the structurally related AlkB (PpAlkB) along with the full set of genes required for alkane metabolism, utilize 1-fluorooctane as their sole source of carbon with growth rates comparable to those for cells grown with octane.

Generalization of Classification of AlkB Family Alkane Monooxygenases from Rhodococcus (sensu lato) Group Based on Phylogenetic Analysis and Genomic Context Comparison

Alkane-oxidizing bacteria play a crucial role in the global carbon cycle. Rhodococcus species are well-known hydrocarbon degraders, distinguished by the harboring of multiple homologs of AlkB family alkane monooxygenases. Although different types of rhodococcal AlkBs have been described, the overall picture of their diversity remains unclear, leaving gaps in the current classification. We conducted a phylogenetic analysis of all AlkBs identified in Rhodococcus (sensu lato) and examined the genomic context of the corresponding genes. The sequence clustering was well aligned with genomic neighborhoods, allowing both features to be used as criteria for proposing AlkB types that form distinct phylogenetic groups and have characteristic genomic contexts. Our approach allowed us to revise the classification of previously described AlkBs, identifying eight types on their basis, and to propose three new ones. Alkane monooxygenases whose genes are co-localized with rubredoxin genes can be considered a generalized AlkBR type, the most common among all Rhodococcus. In the AlkB0 type, which is a paralog of AlkBR, violations of conservativity in known alkane monooxygenase signature motifs were found. Our findings provide a more consistent classification framework for rhodococcal AlkB that prevents the over-reporting of "novel" types and contributes to a deeper understanding of alkane monooxygenase diversity.

Phylogenetic and Functional Diversity of Soluble Di-Iron Monooxygenases

Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in the carbon and nitrogen cycles, are important for the biodegradation of pollutants and can act as biocatalysts for chemical manufacture. The soluble di-iron monooxygenases (SDIMOs) are of interest due to their broad substrate range, high enantioselectivity and ability to oxidise inert substrates such as methane. Here, we re-examine the phylogeny and functions of these enzymes, using recent advances in the field and expansions in sequence diversity in databases to highlight relationships between SDIMOs and revisit their classification. We discuss the impact of horizontal gene transfer on SDIMO phylogeny, the potential of SDIMOs for the biodegradation of pollutants and the importance of heterologous expression as a tool for understanding SDIMO functions and enabling their use as biocatalysts. Our analysis highlights current knowledge gaps, most notably, the unknown substrate ranges and physiological roles of enzymes that have so far only been detected via genome or metagenome sequencing. Enhanced understanding of the diversity and functions of the SDIMO enzymes will enable better prediction and management of biogeochemical processes and also enable new applications of these enzymes for biocatalysis and bioremediation.

Recent Insights into the Reaction Mechanisms of Non-Heme Diiron Enzymes Containing Oxoiron(IV) Complexes

Oxoiron(IV) complexes are key intermediates in the catalytic reactions of some non-heme diiron enzymes. These enzymes, across various subfamilies, activate dioxygen to generate high-valent diiron-oxo species, which, in turn, drive the activation of substrates and mediate a variety of challenging oxidative transformations. In this review, we summarize the structures, formation mechanisms, and functions of high-valent diiron-oxo intermediates in eight representative diiron enzymes (sMMO, RNR, ToMO, MIOX, PhnZ, SCD1, AlkB, and SznF) spanning five subfamilies. We also categorize and analyze the structural and mechanistic differences among these enzymes.

Regulation mechanism of the long-chain n-alkane monooxygenase gene almA in Acinetobacter venetianus RAG-1

As toxic pollutants, n-alkanes are pervasively distributed in most environmental matrices. Although the alkane monooxygenase AlmA plays a critical role in the metabolic pathway of solid long-chain n-alkanes (≥C20) that are extremely difficult to degrade, the mechanism regulating this process remains unclear. Here, we characterized the function of AlmA in Acinetobacter venetianus RAG-1, which was mainly involved in the degradation of long-chain n-alkanes (C26-C38), among which, n-C32 induced the almA promoter activity most. APR1 (AlmA Positive Regulator) that it is an AraC/XylS-type transcription regulator, a potential transcriptional regulator of almA, was screened by DNA-pull down, which was determined by conserved domain analysis. The deletion of apR1 severely reduced the capacity of strain RAG-1 to utilize long-chain n-alkanes (C22-C38), indicating the involvement of APR1 in n-alkanes degradation. The results of the APR1-dependent reporter system, electrophoretic mobility shift assay, and microscale thermophoresis further proved that APR1 was able to directly bind to the almA promoter region, thus activating the almA transcription. Furthermore, APR1 could inhibit self-expression through autoregulation in the absence of long-chain n-alkanes. n-C32 acted as a ligand of APR1, and the amino acid residues Val10, Gln50, Ala99, and Ile106 at the N-terminus of APR1 were necessary for binding n-C32. In addition, the key amino acid residues of APR1 within the C-terminal helix-turn-helix motif that bound to the downstream promoter region were confirmed by multiple sequence alignment and site-directed mutagenesis. The homologs of AlmA and APR1 shared a similar evolutionary course in the Proteobacteria; thus, this mode of regulation might be relatively conserved.

IMPORTANCE

The extreme hydrophobicity of long-chain n-alkanes ({greater than or equal to}C20) presents a significant challenge to their degradation in natural environments. It is, therefore, imperative to elucidate the regulatory mechanisms of the metabolic pathways of long-chain n-alkanes, which will be of great significance for the future application of hydrocarbon-degrading bacteria to treat oil spills. However, the majority of current studies have focused on the regulatory mechanisms of short- and medium-chain n-alkanes, with long-chain n-alkanes receiving comparatively little attention. In this study, we identified APR1, a transcriptional regulator of the alkane monooxygenase AlmA in Acinetobacter venetianus RAG-1, and characterized its function and regulatory mechanism. In the presence of ligand n-C32, APR1 could directly activate the transcription of almA, which was involved in the n-C32 metabolism. The amino acid residue unique to the C-terminal DNA-binding domain of AraC/XylS type n-alkanes transcription regulators was also identified. These findings further improved our understanding of the long-chain n-alkanes degradation mechanism, which is important for the management of petroleum pollution.

No Bridge between Us: EXAFS and Computations Confirm Two Distant Iron Ions Comprise the Active Site of Alkane Monooxygenase (AlkB)

Alkane monooxygenase (AlkB) is the dominant enzyme that catalyzes the oxidation of liquid alkanes in the environment. Two recent structural models derived from cryo-electron microscopy (cryo-EM) reveal an unusual active site: a histidine-rich center that binds two iron ions without a bridging ligand. To ensure that potential photoreduction and radiation damage are not responsible for the absence of a bridging ligand in the cryo-EM structures, spectroscopic methods are needed. We present the results of extended X-ray absorption fine structure (EXAFS) experiments collected under conditions where photodamage was avoided. Careful data analysis reveals an active site structure consistent with the cryo-EM structures in which the two iron ions are ligated by nine histidines and separated by at least 5 Å. The EXAFS data were used to inform structural models for molecular dynamics (MD) simulations. The MD simulations corroborate EXAFS observations that neither of the two conserved carboxylate-containing residues (E281 and D190) near the active site are likely candidates for metal ion bridging. Mutagenesis experiments, spectroscopy, and additional MD simulations were used to further explore the role of these carboxylate residues. A variant in which a carboxylate containing residue (E281) was changed to a methyl residue (E281A) showed little change in pre-edge features, consistent with the observation that it is not essential for activity and hence unlikely to serve as a bridging ligand at any point in the catalytic cycle. D190 variants had substantially diminished activity, suggesting an important role in catalysis not yet fully understood.

Old but not ancient: Rock-leached organic carbon drives groundwater microbiomes

More than 90% of earth's microbial biomass resides in the continental subsurface, where sedimentary rocks provide the largest source of organic carbon (C). While many studies indicate microbial utilization of fossil C sources, the extent to which rock-organic C is driving microbial activities in aquifers remains largely unknown. Here we incubated oxic and anoxic groundwater with crushed carbonate rocks from the host aquifer and an outcrop rock of the unsaturated zone characterized by higher organic C content, and compared the natural abundance of radiocarbon (14C) of available C pools and microbial biomarkers. The ancient rocks surprisingly released organic substances with up to 72.6 ± 0.3% modern C into the groundwater, suggesting leachable fresh organic material from surface transport was preserved within rock fractures. Over half of the rock-leached compounds were also found in the original groundwater dissolved organic carbon (DOC), indicating in situ release of material stored in rock fractures through weathering processes. In addition to aliphatic and aromatic hydrocarbons, rock-leachates were rich in lipids, peptides, and carbohydrates. Radiocarbon analysis of phospholipid-derived fatty acids showed a rapid microbial response to this 'younger' organic material, comprising up to 31% (anoxic) and 51% (oxic) of their biomass C from the rock-leachate after 18 days of incubation. Predictive functional profiling of rock-enriched taxa, including species of Desulfosporosinus, Ferribacterium and Rhodoferax, also suggested metabolic potential for aliphatic and aromatic hydrocarbon degradation. PLFAs of the original groundwater were highly 14C-depleted, indicating utilization of a mixture of fossil and 'younger' C sources. Our findings suggest that carbonate rocks act as temporal sink for 'younger' organic matter, that leaches with fossil hydrocarbons from sedimentary rocks, driving microbial metabolism in subsurface ecosystems.

Genome-resolved analysis of Serratia marcescens strain SMTT infers niche specialization as a hydrocarbon-degrader

Bacteria that are chronically exposed to high levels of pollutants demonstrate genomic and corresponding metabolic diversity that complement their strategies for adaptation to hydrocarbon-rich environments. Whole genome sequencing was carried out to infer functional traits of Serratia marcescens strain SMTT recovered from soil contaminated with crude oil. The genome size (Mb) was 5,013,981 with a total gene count of 4,842. Comparative analyses with carefully selected S. marcescens strains, 2 of which are associated with contaminated soil, show conservation of central metabolic pathways in addition to intra-specific genetic diversity and metabolic flexibility. Genome comparisons also indicated an enrichment of genes associated with multidrug resistance and efflux pumps for SMTT. The SMTT genome contained genes that enable the catabolism of aromatic compounds via the protocatechuate para-degradation pathway, in addition to meta-cleavage of catechol (meta-cleavage pathway II); gene enrichment for aromatic compound degradation was markedly higher for SMTT compared to the other S. marcescens strains analysed. Our data presents a valuable genetic inventory for future studies on strains of S. marcescens and provides insights into those genomic features of SMTT with industrial potential.

Review of key issues and potential strategies in bio-degradation of polyolefins

Polyolefins are the most widely used plastic product and a major contributor to white pollution. Currently, studies on polyolefin degradation systems are mainly focused on microorganisms and some redox enzymes, and there is a serious black-box phenomenon. The use of polyolefin-degrading enzymes is limited because of the small number of enzymes; in addition, the catalytic efficiency of these enzymes is poor and their catalytic mechanism is unclear, which leads to the incomplete degradation of polyolefins to produce microplastics. In this review, three questions are addressed: the generation and degradation of action targets that promote the degradation of polyolefins, the different modes by which enzymes bind substrates and their application scenarios, and possible multienzyme systems in a unified system. This review will be valuable for mining or modifying polyolefin degradation enzymes and constructing polyolefins degradation systems and may provide novel ideas and opportunities for polyolefin degradation.

The biochemical mechanisms of plastic biodegradation

Since the invention of the first synthetic plastic, an estimated 12 billion metric tons of plastics have been manufactured, 70% of which was produced in the last 20 years. Plastic waste is placing new selective pressures on humans and the organisms we depend on, yet it also places new pressures on microorganisms as they compete to exploit this new and growing source of carbon. The limited efficacy of traditional recycling methods on plastic waste, which can leach into the environment at low purity and concentration, indicates the utility of this evolving metabolic activity. This review will categorize and discuss the probable metabolic routes for each industrially relevant plastic, rank the most effective biodegraders for each plastic by harmonizing and reinterpreting prior literature, and explain the experimental techniques most often used in plastic biodegradation research, thus providing a comprehensive resource for researchers investigating and engineering plastic biodegradation.

Arsenic Enhances the Degradation of Middle-Chain Petroleum Hydrocarbons by Rhodococcus sp. 2021 Under Their Combined Pollution

The efficient and green remediation of petroleum hydrocarbon (PH) contamination has emerged as a viable strategy for environmental management. Here, we investigated the interaction between arsenic and PH degradation by Rhodococcus sp. 2021 under their combined pollution. The strain exhibited disparate responses to varying concentrations and valences of arsenic. The elevated concentration of arsenic (>100 mg/L) facilitated the degradation of PHs, and there was a positive correlation between arsenic-promoted degradation of PHs and their carbon-chain length. The degradation of PHs changed with arsenic conditions as follows: trivalent arsenic groups > pentavalent arsenic groups > arsenic-free groups (control). Arsenite and arsenate significantly promoted the gene expression of arsenic metabolism and alkane degrading. But unlike arsenite, arsenate also significantly promoted the gene expression of phosphate metabolism. And arsenite promoted the up-regulation of the expression of genes involved in the process of PHs oxidation and fatty acid oxidation. These results highlight the potential of Rhodococcus sp. 2021 in the remediation of combined total petroleum hydrocarbon (TPH) and heavy metal pollution, providing new insights into the green and sustainable bioremediation of combined pollution of organic matters such as PHs and heavy metals/heavy metal-like elements such as arsenic.

Enterobacter cloacae-mediated polymer biodegradation: in-silico analysis predicts broad spectrum degradation potential by Alkane monooxygenase

Plastic pollution poses a significant environmental challenge. In this study, the strain Enterobacter cloacae O5-E, a bacterium displaying polyethylene-degrading capabilities was isolated. Over a span of 30 days, analytical techniques including x-ray diffractometry, scanning electron microscopy, optical profilometry, hardness testing and mass spectrometric analysis were employed to examine alterations in the polymer. Results revealed an 11.48% reduction in crystallinity, a 50% decrease in hardness, and a substantial 25-fold increase in surface roughness resulting from the pits and cracks introduced in the polymer by the isolate. Additionally, the presence of degradational by-products revealed via gas chromatography ascertains the steady progression of degradation. Further, recognizing the pivotal role of alkane monooxygenase in plastic degradation, the study expanded to detect this enzyme in the isolate molecularly. Molecular docking studies were conducted to assess the enzyme's affinity with various polymers, demonstrating notable binding capability with most polymers, especially with polyurethane (- 5.47 kcal/mol). These findings highlight the biodegradation potential of Enterobacter cloacae O5-E and the crucial involvement of alkane monooxygenase in the initial steps of the degradation process, offering a promising avenue to address the global plastic pollution crisis.

Computational Insights into the Non-Heme Diiron Alkane Monooxygenase Enzyme AlkB: Electronic Structures, Dioxygen Activation, and Hydroxylation Mechanism of Liquid Alkanes

Alkane monooxygenase (AlkB) is a membrane-spanning metalloenzyme that catalyzes the terminal hydroxylation of straight-chain alkanes involved in the microbially mediated degradation of liquid alkanes. According to the cryoEM structures, AlkB features a unique multihistidine ligand coordination environment with a long Fe-Fe distance in its active center. Up to now, how AlkB employs the diiron center to activate dioxygen and which species is responsible for triggering the hydroxylation are still elusive. In this work, we constructed computational models and performed quantum mechanics/molecular mechanics (QM/MM) calculations to illuminate the electronic characteristics of the diiron active center and how AlkB carries out the terminal hydroxylation. Our calculations revealed that the spin-spin interaction between two irons is rather weak. The dioxygen may ligate to either the Fe1 or Fe2 atom and prefers to act as a linker to increase the spin-spin interaction of two irons, facilitating the dioxygen cleavage to generate the highly reactive Fe(IV)═O. Thus, AlkB employs Fe(IV)═O to trigger the hydrogen abstraction. In addition, the previously suggested mechanism that AlkB uses both the dioxygen and Fe-coordinated water to perform hydroxylation was calculated to be unlikely. Besides, our results indicate that AlkB cannot use the Fe-coordinated dioxygen to directly trigger hydrogen abstraction.

Biotransformation of PFAA Precursors by Oxygenase-Expressing Bacteria in AFFF-Impacted Groundwater and in Pure-Compound Studies with 6:2 FTS and EtFOSE

Numerous US drinking water aquifers have been contaminated with per- and polyfluoroalkyl substances (PFAS) from fire-fighting and fire-training activities using aqueous film-forming foam (AFFF). These sites often contain other organic compounds, such as fuel hydrocarbons and methane, which may serve as primary substrates for cometabolic (i.e., nongrowth-linked) biotransformation reactions. This work investigates the abilities of AFFF site relevant bacteria (methanotrophs, propanotrophs, octane, pentane, isobutane, toluene, and ammonia oxidizers), known to express oxygenase enzymes when degrading their primary substrates, to biotransform perfluoroalkyl acid (PFAA) precursors to terminal PFAAs. Microcosms containing AFFF-impacted groundwater, 6:2 fluorotelomer sulfonate (6:2 FTS), or N-ethylperfluorooctane sulfonamidoethanol (EtFOSE) were inoculated with the aerobic cultures above and incubated for 4 and 8 weeks at 22 °C. Bottles were sacrificed, extracted, and subjected to target, nontarget, and suspect screening for PFAS. The PFAA precursors 6:2 FTS, N-sulfopropyldimethyl ammoniopropyl perfluorohexane sulfonamide (SPrAmPr-FHxSA), and EtFOSE transformed up to 99, 71, and 93%, respectively, and relevant daughter products, such as the 6:1 fluorotelomer ketone sulfonate (6:1 FTKS), were identified in quantities previously not observed, implicating oxygenase enzymes. This is the first report of a suite of site relevant PFAA precursors being transformed in AFFF-impacted groundwater by bacteria grown on substrates known to induce specific oxygenase enzymes. The data provide crucial insights into the microbial transformation of these compounds in the subsurface.

Regulation of intracellular process by two-component systems: Exploring the mechanism of plasmid-mediated conjugative transfer

Plasmid-mediated conjugative transfer facilitates the dissemination of antibiotic resistance, yet the comprehensive regulatory mechanisms governing this process remain elusive. Herein, we established pure bacteria and activated sludge conjugation system to investigate the regulatory mechanisms of conjugative transfer, leveraging metformin as an exogenous agent. Transcriptomic analysis unveiled that substantial upregulation of genes associated with the two-component system (e.g., AcrB/AcrA, EnvZ/Omp, and CpxA/CpxR) upon exposure to metformin. Furthermore, downstream regulators of the two-component system, including reactive oxygen species (ROS), cytoplasmic membrane permeability, and adenosine triphosphate (ATP) production, were enhanced by 1.7, 1.4 and 1.1 times, respectively, compared to the control group under 0.1 mg/L metformin exposure. Moreover, flow sorting and high-throughput sequencing revealed increased microbial community diversity among transconjugants in activated sludge systems. Notably, the antibacterial potential of human pathogenic bacteria (e.g., Bacteroides, Escherichia-Shigella, and Lactobacillus) was augmented, posing a potential threat to human health. Our findings shed light on the spread of antibiotic resistance bacteria and assess the ecological risks associated with plasmid-mediated conjugative transfer in wastewater treatment systems.

Synergistic functional activity of a landfill microbial consortium in a microplastic-enriched environment

Plastic pollution of the soil is a global issue of increasing concern, with far-reaching impact on the environment and human health. To fully understand the medium- and long-term impact of plastic dispersal in the environment, it is necessary to define its interaction with the residing microbial communities and the biochemical routes of its degradation and metabolization. However, despite recent attention on this problem, research has largely focussed on microbial functional potential, failing to clearly identify collective adaptation strategies of these communities. Our study combines genome-centric metagenomics and metatranscriptomics to characterise soil microbial communities adapting to high polyethylene and polyethylene terephthalate concentration. The microbiota were sampled from a landfill subject to decades-old plastic contamination and enriched through prolonged cultivation using these microplastics as the only carbon source. This approach aimed to select the microorganisms that best adapt to these specific substrates. As a result, we obtained simplified communities where multiple plastic metabolization pathways are widespread across abundant and rare microbial taxa. Major differences were found in terms of expression, which on average was higher in planktonic microbes than those firmly adhered to plastic, indicating complementary metabolic roles in potential microplastic assimilation. Moreover, metatranscriptomic patterns indicate a high transcriptional level of numerous genes in emerging taxa characterised by a marked accumulation of genomic variants, supporting the hypothesis that plastic metabolization requires an extensive rewiring in energy metabolism and thus provides a strong selective pressure. Altogether, our results provide an improved characterisation of the impact of microplastics derived from common plastics types on terrestrial microbial communities and suggest biotic responses investing contaminated sites as well as potential biotechnological targets for cooperative plastic upcycling.

N-alkane shape distinctive microbial patterns in Kuroshio Extension

Marine microorganisms are primary drivers of the elemental cycling. The interaction between heterotrophic prokaryotes and biomarker (n-alkane) in Kuroshio Extension (KE) remains unclear. Here, we categorize KE into three characteristic areas based on ocean temperatures and nutrient conditions: Cold Water Area (CWA), Mixed Area (MA), and Warm Water Area (WWA). A total of 49 samples were collected during two-year voyage to identify the source of n-alkane and associated degrading microorganisms. Total n-alkane concentrations (Σn-Alk) in surface water (SW) spanned from 1,308 ng L-1 to 1,890 ng L-1, it was significantly higher (Tukey-Kramer test, p < 0.05) in MA than CWA and WWA. The Σn-Alk in surface sediments (SS) gradually increased from north to south, ranging from 5,982 ng g-1 to 37,857 ng g-1. Bacteria and algae were the primary sources of n-alkane in both SW and SS. Proteobacteria was the most widely distributed among three areas. The presence of Rhodobacteraceae with alkB was the primary reason affecting n-alkane concentrations in SW. The Gammaproteobacteria with alkB and alkR chiefly affected n-alkane concentrations in SS. In summary, n-alkane s serve as an energy source for particular microorganisms, shaping the unique oceanographic patterns.

Genomic and transcriptomic analyses provide new insights into the allelochemical degradation preference of a novel Acinetobacter strain

A novel n-alkane- and phenolic acid-degrading Acinetobacter strain (designated C16S1T) was isolated from rhizosphere soil. The strain was identified as a novel species named Acinetobacter suaedae sp. nov. using a polyphasic taxonomic approach. Strain C16S1T showed preferential degradation of three compounds: p-hydroxybenzoate (PHBA) > ferulic acid (FA) > n-hexadecane. In a medium containing two or three of these allelochemicals, coexisting n-hexadecane and PHBA accelerated each other's degradation and that of FA. FA typically hindered the degradation of n-hexadecane but accelerated PHBA degradation. The upregulated expression of n-hexadecane- and PHBA-degrading genes induced, by their related substrates, was mutually enhanced by coexisting PHBA or n-hexadecane; in contrast, expression of both gene types was reduced by FA. Coexisting PHBA or n-hexadecane enhanced the upregulation of FA-degrading genes induced by FA. The expressions of degrading genes affected by coexisting chemicals coincided with the observed degradation efficiencies. Iron shortage limited the degradation efficiency of all three compounds and changed the degradation preference of Acinetobacter. The present study demonstrated that the biodegradability of the chemicals, the effects of coexisting chemicals on the expression of degrading genes and the strain's growth, the shortage of essential elements, and the toxicity of the chemicals were the four major factors affecting the removal rates of the coexisting allelochemicals.

Functional production and biochemical investigation of an integral membrane enzyme for olefin biosynthesis

Integral membrane enzymes play essential roles in a plethora of biochemical processes. The fatty acid desaturases (FADS)-like superfamily is an important group of integral membrane enzymes that catalyze a wide array of reactions, including hydroxylation, desaturation, and cyclization; however, due to the membrane-bound nature, the majority of these enzymes have remained poorly understood. UndB is a member of the FADS-like superfamily, which catalyzes fatty acid decarboxylation, a chemically challenging reaction at the membrane interface. UndB reaction produces terminal olefins that are prominent biofuel candidates and building blocks of polymers with widespread industrial applications. Despite the great importance of UndB for several biotechnological applications, the enzyme has eluded comprehensive investigation. Here, we report details of the expression, solubilization, and purification of several constructs of UndB to achieve the optimally functional enzyme. We gained important insights into the biochemical, biophysical, and catalytic properties of UndB, including the thermal stability and factors influencing the enzyme activity. Additionally, we established the ability and kinetics of UndB to produce dienes by performing di-decarboxylation of diacids. We found that the reaction proceeds by forming a mono-carboxylic acid intermediate. Our findings shed light on the unexplored biochemical properties of the UndB and extend opportunities for its rigorous mechanistic and structural characterization.

AlmA involved in the long-chain n-alkane degradation pathway in Acinetobacter baylyi ADP1 is a Baeyer-Villiger monooxygenase

Many Acinetobacter species can grow on n-alkanes of varying lengths (≤C40). AlmA, a unique flavoprotein in these Acinetobacter strains, is the only enzyme proven to be required for the degradation of long-chain (LC) n-alkanes, including C32 and C36 alkanes. Although it is commonly presumed to be a terminal hydroxylase, its role in n-alkane degradation remains elusive. In this study, we conducted physiological, biochemical, and bioinformatics analyses of AlmA to determine its role in n-alkane degradation by Acinetobacter baylyi ADP1. Consistent with previous reports, gene deletion analysis showed that almA was vital for the degradation of LC n-alkanes (C26-C36). Additionally, enzymatic analysis revealed that AlmA catalyzed the conversion of aliphatic 2-ketones (C10-C16) to their corresponding esters, but it did not conduct n-alkane hydroxylation under the same conditions, thus suggesting that AlmA in strain ADP1 possesses Baeyer-Villiger monooxygenase (BVMO) activity. These results were further confirmed by bioinformatics analysis, which revealed that AlmA was closer to functionally identified BVMOs than to hydroxylases. Altogether, the results of our study suggest that LC n-alkane degradation by strain ADP1 possibly follows a novel subterminal oxidation pathway that is distinct from the terminal oxidation pathway followed for short-chain n-alkane degradation. Furthermore, our findings suggest that AlmA catalyzes the third reaction in the LC n-alkane degradation pathway.IMPORTANCEMany microbial studies on n-alkane degradation are focused on the genes involved in short-chain n-alkane (≤C16) degradation; however, reports on the genes involved in long-chain (LC) n-alkane (>C20) degradation are limited. Thus far, only AlmA has been reported to be involved in LC n-alkane degradation by Acinetobacter spp.; however, its role in the n-alkane degradation pathway remains elusive. In this study, we conducted a detailed characterization of AlmA in A. baylyi ADP1 and found that AlmA exhibits Baeyer-Villiger monooxygenase activity, thus indicating the presence of a novel LC n-alkane biodegradation mechanism in strain ADP1.

Degradation of low-density polyethylene by the bacterium Rhodococcus sp. C-2 isolated from seawater

Low-density polyethylene (LDPE), which accounts for 20% of the global plastic production, is discharged in great quantities into the ocean, threatening marine life and ecosystems. Marine microorganisms have previously been reported to degrade LDPE plastics; however, the exploration of strains and enzymes that degrade LDPE is still limited. Here, an LDPE-degrading bacterium was isolated from seawater of the Changjiang Estuary, China and identified as Rhodococcus sp. C-2, the relative abundance of which was dramatically enhanced during PE-degrading microbial enrichment. The strain C-2 exhibited the degradation of LDPE films, leading to their morphological deterioration, reduced hydrophobicity and tensile strength, weight loss, as well as the formation of oxygen-containing functional groups in short-chain products. Sixteen bacterial enzymes potentially involved in LDPE degradation were screened using genomic, transcriptomic, and degradation product analyses. Thereinto, the glutathione peroxidase GPx with exposed active sites catalyzed the LDPE depolymerization with the cooperation of its dissociated superoxide anion radicals. Furthermore, an LDPE degradation model involving multiple enzymes was proposed. The present study identifies a novel PE-degrading enzyme (PEase) for polyethylene bioremediation and promotes the understanding of LDPE degradation.

Structure and Function of Alkane Monooxygenase (AlkB)

Every year, perhaps as much as 800 million tons of hydrocarbons enters the environment; alkanes make up a large percentage of it. Most are transformed by organisms that utilize these molecules as sources of energy and carbon. Both aerobic and anaerobic alkane transformation chemistries exist, capitalizing on the presence of alkanes in both oxic and anoxic environments. Over the past 40 years, tremendous progress has been made in understanding the structure and mechanism of enzymes that catalyze the transformation of methane. By contrast, progress involving enzymes that transform liquid alkanes has been slower with the first structures of AlkB, the predominant aerobic alkane hydroxylase in the environment, appearing in 2023. Because of the fundamental importance of C-H bond activation chemistries, interest in understanding how biology activates and transforms alkanes is high.In this Account, we focus on steps we have taken to understand the mechanism and structure of alkane monooxygenase (AlkB), the metalloenzyme that dominates the transformation of liquid alkanes in the environment (not to be confused with another AlkB that is an α-ketogluturate-dependent enzyme involved in DNA repair). First, we briefly describe what is known about the prevalence of AlkB in the environment and its role in the carbon cycle. Then we review the key findings from our recent high-resolution cryoEM structure of AlkB and highlight important similarities and differences in the structures of members of class III diiron enzymes. Functional studies, which we summarize, from a number of single residue variants enable us to say a great deal about how the structure of AlkB facilitates its function. Next, we overview work from our laboratories using mechanistically diagnostic radical clock substrates to characterize the mechanism of AlkB and contextualize the results we have obtained on AlkB with results we have obtained on other alkane-oxidizing enzymes and explain these results in light of the enzyme's structure. Finally, we integrate recent work in our laboratories with information from prior studies of AlkB, and relevant model systems, to create a holistic picture of the enzyme. We end by pointing to critical questions that still need to be answered, questions about the electronic structure of the active site of the enzyme throughout the reaction cycle and about whether and to what extent the enzyme plays functional roles in biology beyond simply initiating the degradation of alkanes.