Molecular response mechanism in Escherichia coli under hexabromocyclododecane stress

Global responses to tris(1-chloro-2-propyl) phosphate and tris(2-butoxyethyl) phosphate in Escherichia coli: Evidences from biomarkers, and metabolic disturbance using GC-MS and LC-MS metabolomics analyses

Tris(1-chloro-2-propyl) phosphate (TCPP) and tris(2-butoxyethyl) phosphate (TBEP) as pollutants of emerging concern have aroused the rising attention due to their potential risks on aquatic ecosystem and public health. Nevertheless, there is a lack of toxicological mechanisms exploration of TCPP and TBEP at molecular levels. Herein, the toxicity effects and molecular mechanism of them were fully researched and summarized on Escherichia coli (E.coli). Acute exposure to them significantly activated antioxidant defense system and caused lipid peroxidation, as proved by the changes of antioxidant enzymes and MDA. The ROS overload resulted in the drop of membrane potential as well as the downregulated synthesis of ATPase, endorsing that E. coli cytotoxicity was ascribed to oxidative stress damage induced by TCPP and TBEP. The combination of GC-MS and LC-MS based metabolomics validated that TCPP and TBEP induced metabolic reprogramming in E.coli. More specifically, the responsive metabolites in carbohydrate metabolism, lipids metabolism, nucleotide metabolism, amino acid metabolism, and organic acids metabolism were significantly disturbed by TCPP and TBEP, confirming the negative effects on metabolic functions and key bioprocesses. Additionally, several biomarkers including PE(16:1(5Z)/15:0), PA(17:1(9Z)/18:2(9Z,12Z)), PE(19:1(9Z)/0:0), and LysoPE(0:0/18:1(11Z)) were remarkably upregulated, verifying that the protection of cellular membrane was conducted by regulating the expression of lipids-associated metabolites. Collectively, this work sheds new light on the potential molecular toxicity mechanism of TCPP and TBEP on aquatic organisms, and these findings using GC-MS and LC-MS metabolomics generate a fresh insight into assessing the effects of OPFRs on target and non-target aquatic organisms.

Effects of polystyrene microplastics on the metabolic level of Pseudomonas aeruginosa

Given the widespread presence of Pseudomonas aeruginosa in water and its threat to human health, the metabolic changes in Pseudomonas aeruginosa when exposed to polystyrene microplastics (PS-MPs) exposure were studied, focusing on molecular level. Through non-targeted metabolomics, a total of 64 differential metabolites were screened out under positive ion mode and 44 under negative ion mode. The content of bacterial metabolites changed significantly, primarily involving lipids, nucleotides, amino acids, and organic acids. Heightened intracellular oxidative damage led to a decrease in lipid molecules and nucleotide-related metabolites. The down-regulation of amino acid metabolites, such as L-Glutamic and L-Proline, highlighted disruptions in cellular energy metabolism and the impaired ability to synthesize proteins as a defense against oxidation. The impact of PS-MPs on organic acid metabolism was evident in the inhibition of pyruvate and citrate, thereby disrupting the cells' normal participation in energy cycles. The integration of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that PS-MPs mainly caused changes in metabolic pathways, including ABC transporters, Aminoacyl-tRNA biosynthesis, Purine metabolism, Glycerophospholipid metabolism and TCA cycle in Pseudomonas aeruginosa. Most of the differential metabolites enriched in these pathways were down-regulated, demonstrating that PS-MPs hindered the expression of metabolic pathways, ultimately impairing the ability of cells to synthesize proteins, DNA, and RNA. This disruption affected cell proliferation and information transduction, thus hampering energy circulation and inhibiting cell growth. Findings of this study supplemented the toxic effects of microplastics and the defense mechanisms of microorganisms, in turn safeguarding drinking water safety and human health.

Enhanced bacterial adhesion force by rifampicin resistance promotes microbial colonization on PE plastic compared to non-resistant biofilm formation

The microbial biofilm formed on plastics, is ubiquitous in the environment. However, the effects of antibiotic resistance on the development of the biofilm on plastics, especially with regard to initial cell attachment, remain unclear. In this study, we investigated the initial bacterial adhesion and subsequent biofilm growth of a rifampin (Rif) resistant E. coli (RRE) and a normal gram-positive B. subtilis on a typical plastic (polyethylene, PE). The experiments were conducted in different antibiotic solutions, including Rif, sulfamethoxazole (SMX), and kanamycin (KM), with concentrations ranging from 1 to 1000 μg/L to simulate different aquatic environments. The AFM-based single-cell adhesion force determination revealed that Rif resistance strengthened the adhesion force of RRE to PE in the environment rich in Rif rather than SMX and KM. The enhanced adhesion force may be due to the higher secretion of extracellular polymeric substances (EPS), particularly proteins, by RRE in the presence of Rif compared to the other two antibiotics. In addition, the higher ATP level of RRE would facilitate the initial adhesion and subsequent biofilm growth. Transcriptome analysis of RRE separately cultured in Rif and SMX environments demonstrated a clear correlation between the expression of Rif resistance and the augmented bacterial adhesion and cellular activity. Biofilm biomass analysis confirmed the promotion effect of Rif resistance on biofilm growth when compared to non-resistant biofilms, establishing a novel association with the augmentation of microbial adhesion force. Our study highlights concerns related to the dissemination of antibiotic resistance during microbial colonization on plastic that may arise from antibiotic resistance.

The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms

The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.

Mechanism and security of UV driven sodium percarbonate for sulfamethoxazole degradation using DFT and metabolomic analysis

Recently, sodium percarbonate (SPC) as a solid substitute for H₂O₂ has aroused extensive attention in advanced oxidation processes. In current work, the degradation kinetics and mechanisms of antibiotic sulfamethoxazole (SMX) by ultraviolet (UV) driven SPC system were explored. The removal efficiency of SMX was enhanced as the increasing dosage of SPC. Moreover, hydroxyl radical (•OH), carbonate radical (CO₃^•-) and superoxide radical (O₂^•-) were verified to be presented by scavenger experiments and •OH, CO₃^•- exhibited a significant role in SMX degradation. Reactions mediated by these radicals were affected by anions and natural organic matters, implying that an incomplete mineralization of SMX would be ubiquitous. The screening four intermediates and transformation patterns of SMX were verified by DFT analysis. Metabolomic analysis demonstrated that a decreasing negative effect in E. coli after 24 h exposure was induced by intermediates products. In detail, SMX interfered in some key functional metabolic pathways including carbohydrate metabolism, pentose and glucuronate metabolism, nucleotide metabolism, arginine and proline metabolism, sphingolipid metabolism, which were mitigated after UV/SPC oxidation treatment, suggesting a declining environmental risk of SMX. This work provided new insights into biological impacts of SMX and its transformation products and vital guidance for SMX pollution control using UV/SPC technology.

Photocatalysis of carbamazepine via activating bisulfite by ultraviolet: Performance, transformation mechanism, and residual toxicity assessment of intermediates products

Carbamazepine (CBZ) as an extensively distributed emerging pollutant has menaced ecological security. The degradation performance of CBZ by UV driven bisulfite process was investigated in this work. The kinetics results indicated that CBZ was high-efficiently degraded by UV/bisulfite following a pseudo first-order kinetic model (K_obs = 0.0925 min^-1). SO₄^•- and •OH were verified as the reactive oxidants by EPR test and the radicals scavenging experiment using MeOH and TBA. SO₄^•- played a dominant role for CBZ degradation. The Density functional theory (DFT) and LC-qTOF-MS/MS clarified that hydroxylation, ketonation, ring opening reaction, and ring contraction were main transformation patterns of CBZ. As to influence factors, CBZ degradation was significantly hindered in presence of CO₃^2-, HPO₄^2- and NOM. Toxicological analysis derived from metabonomics suggested that the remarkable alteration of metabolic profile was triggered by exposure to intermediates mixture. CBZ intermediates interfered in several key metabolic pathways, including pentose phosphate, amino acids, lysine degradation, glycerophospholipid, glutathione, nucleotides and carbohydrate, which was alleviated after UV/bisulfite treatment. This work provided a meaningful support to potential risk of CBZ intermediates products, which shed light on the future application in eliminating drugs using UV /bisulfite.

Enhanced degradation of atrazine through UV/bisulfite: Mechanism, reaction pathways and toxicological analysis

Atrazine residue in the environment continues to threaten aquatic ecosystem and human health owing to its adverse effect. However, limited researches focused on degradation mechanism of atrazine by UV/bisulfite, especially risk of intermediates at cellular and molecular level has not been seriously elaborated. In current work, transformation patterns and residual toxicity of intermediates of atrazine by UV/bisulfite were systematically investigated. The atrazine degradation was described by a pseudo first-order kinetic model (K_obs = 0.1053 min^-1). The presence of H₂PO₄^-, HCO₃^- and HA had a powerful inhibition. Scavenging test of radicals illustrated that SO₄^•-, •OH and O₂^•- existed in UV/bisulfite system, SO₄^•- and •OH were mainly responsible for atrazine degradation. Eight degradation intermediates were identified, which were involved in dealkylation, alkyl oxidation, dechlorination-hydroxylation, and alkylic-hydroxylation. E. coli as a model microorganism was selected to assess the risk of degradation intermediates. The levels of reactive oxygen species, MDA and Na⁺/K⁺-ATPase were declined, suggesting that oxidative damage induced by these intermediates was weakened. According to differential metabolites expression analysis, several key metabolites including aspartate, L-tryptophan, L-asparagine, cytidine, cytosin, stearic acid, behenic acid, were up-regulated, and glutathione, cadaverin, L-2-hydroxyglutaric acid and phytosphingosine were downregulated, clarifying that effective detoxification of atrazine can be performed by UV/bisulfite.

Dimethyl phthalate destroys the cell membrane structural integrity of Pseudomonas fluorescens

A Gram-negative bacteria (Pseudomonas fluorescens) was exposed to different concentrations (0, 20, and 40 mg/L) of dimethyl phthalate (DMP) for 8 h, and then Fourier transform infrared spectroscopy (FTIR) analysis, lipopolysaccharide content detection, analysis of fatty acids, calcein release test, proteomics, non-targeted metabolomics, and enzyme activity assays were used to evaluate the toxicological effect of DMP on P. fluorescens. The results showed that DMP exposure caused an increase in the unsaturated fatty acid/saturated fatty acid (UFA/SFA) ratio and in the release of lipopolysaccharides (LPSs) from the cell outer membrane (OM) of P. fluorescens. Moreover, DMP regulated the abundances of phosphatidyl ethanolamine (PE) and phosphatidyl glycerol (PG) of P. fluorescens and induced dye leakage from an artificial membrane. Additionally, excessive reactive oxygen species (ROS), malondialdehyde (MDA), and changes in antioxidant enzymes (i.e., catalase [CAT] and superoxide dismutase [SOD]) activities, as well as the inhibition of Ca²⁺-Mg²⁺-ATPase and Na⁺/K⁺-ATPase activities in P. fluorescens, which were induced by the DMP. In summary, DMP could disrupt the lipid asymmetry of the outer membrane, increase the fluidity of the cell membrane, and destroy the integrity of the cell membrane of P. fluorescens through lipid peroxidation, oxidative stress, and ion imbalance.

Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms

The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.

Mechanochemical destruction and mineralization of solid-phase hexabromocyclododecane assisted by microscale zero-valent aluminum

Hexabromocyclododecane (HBCD) has been listed in Annex A of the Stockholm Convention as a persistent and bio-accumulative chemical. While HBCD is often present in the solid form for its low solubility, cost-effective technologies have been lacking for the degradation of solid-phase HBCD. In this work, mechanochemical (MC) destruction of high-energy ball milling was employed for direct destruction of solid-phase HBCD, where a strong reducer, microscale zero-valent aluminum (mZVAl), was used as the co-milling agent. The new mZVAl-assisted MC process achieved complete debromination and mineralization of HBCD within 3 h milling. The optimal operating parameters were determined, including the milling atmosphere, the milling speed, the mZVAl-to-HBCD molar ratio, and the ball-to-mZVAl mass ratio. Fourier transform infrared spectrometry and Raman analyses revealed that the organic structures of HBCD were destroyed and organic bromine was completely converted into inorganic bromide, accompanied by the generation of amorphous and graphite carbon. Analysis of the milled samples by GC-MS demonstrated the absence of obvious organic matter after MC treatment, also indicating the complete degradation and conversion of HBCD to inorganic compounds. Further X-ray photoelectron spectroscopic analysis indicates that the fresh surface of mZVAl was generated upon the MC treatment, and Al(0) served as a strong reducing agent (e-donor) for reductive debromination and destruction of the carbon skeleton. The mZVAl-assisted MC milling appears promising as a non-combustion approach for effective destruction and carbonization/mineralization of solid-phase HBCD or potentially other persistent organic pollutants.

A metagenomics study of hexabromocyclododecane degradation with a soil microbial community

Hexabromocyclododecanes (HBCDs) are globally prevalent and persistent organic pollutants (POPs) listed by the Stockholm Convention in 2013. They have been detected in many environmental media from waterbodies to Plantae and even in the human body. Due to their highly bioaccumulative characterization, they pose an urgent public health issue. Here, we demonstrate that the indigenous microbial community in the agricultural soil in Taiwan could decompose HBCDs with no additional carbon source incentive. The degradation kinetics reached 0.173 day^-1 after the first treatment and 0.104 day^-1 after second exposure. With additional C-sources, the rate constants decreased to 0.054-0.097 day^-1. The hydroxylic debromination metabolites and ring cleavage long-chain alkane metabolites were identified to support the potential metabolic pathways utilized by the soil microbial communities. The metagenome established by Nanopore sequencing showed significant compositional alteration in the soil microbial community after the HBCD treatment. After ranking, comparing relative abundances, and performing network analyses, several novel bacterial taxa were identified to contribute to HBCD biotransformation, including Herbaspirillum, Sphingomonas, Brevundimonas, Azospirillum, Caulobacter, and Microvirga, through halogenated / aromatic compound degradation, glutathione-S-transferase, and hydrolase activity. We present a compelling and applicable approach combining metagenomics research, degradation kinetics, and metabolomics strategies, which allowed us to decipher the natural attenuation and remediation mechanisms of HBCDs.

Transformation of sulfamethoxazole by sulfidated nanoscale zerovalent iron activated persulfate: Mechanism and risk assessment using environmental metabolomics

The threat caused by the misuse of antibiotics to ecology and human health has been aroused an extensive attention. Developing cost-effective techniques for removing antibiotics needs to put on the agenda. In current research, the degradation mechanism of sulfamethoxazole (SMX) by sulfidated nanoscale zerovalent iron (S-nZVI) driven persulfate, together with the potential risk of intermediates were studied. The degradation of SMX followed a pseudo-first order kinetics reaction with k_obs at 0.1176 min^-1. Both SO₄^•- and •OH were responsible for the degradation of SMX, and SO₄^•- was the predominant free radical. XPS analysis demonstrated that reduced sulfide species promoted the conversion of Fe (III) to Fe (II), resulting in the higher transformation rate of SMX. Six intermediates products were generated through hydroxylation, dehydration condensation, nucleophilic reaction, and hydrolysis. The risk of intermediates products is subsequently assessed using E. coli as a model microorganism. After E.coli exposure to intermediates for 24 h, the upmetabolism of carbohydrate, nucleotide, citrate acid cycle and downmetabolism of glutathione, sphingolipid, galactose by metabolomics analysis identified that SMX was effectively detoxified by oxidation treatment. These findings not only clarified the superiority of S-nZVI/persulfate, but also generated a novel insight into the security of advanced oxidation processes.

Metabolomic analysis and oxidative stress response reveals the toxicity in Escherichia coli induced by organophosphate flame retardants tris(2-chloroethyl) phosphate and triphenyl phosphate

Organophosphate flame retardants (OPFRs) are emerging environmental pollutants that are increasingly being used in consumer commodities. The adverse effects on biota induced by tris(2-chloroethyl) phosphate (TCEP) and triphenyl phosphate (TPHP) have become a growing concern. Unfortunately, toxic mechanisms at the molecular level for OPFRs in organisms are still lacking. Herein, Escherichia coli (E.coli) was exposed to TCEP and TPHP for 24 and 48 h to reveal oxidative stress response and molecular toxicity mechanisms. The results indicated that promotion of ROS overload occurred at higher dosages groups. The levels of SOD and CAT were significantly elevated along with the increase of MDA attributed to lipid peroxidation. Additionally, apoptosis rates increased, accompanied by a decline in membrane potential and Na⁺/K⁺-ATPase and Ca²⁺/Mg²⁺-ATPase contents, signifying that E. coli cytotoxicity induced by TCEP and TPHP was mediated by oxidative stress. Based on metabolomic analysis, different metabolic pathways were disrupted, including glycolysis/gluconeogenesis, pentose phosphate metabolism, purine metabolism, glutathione metabolism, amino acid biosynthesis, butanoate metabolism, alanine and aspartate metabolism. Most differentially expressed metabolites were downregulated, indicating an inhibitory effect on metabolic functions and key metabolic pathways. These findings generated new insights into the potential environmental risks of OPFRs in aquatic organisms.

Comparative toxicity reduction potential of UV/sodium percarbonate and UV/hydrogen peroxide treatments for bisphenol A in water: An integrated analysis using chemical, computational, biological, and metabolomic approaches

Bisphenol A (BPA) is a common industrial chemical with significant adverse impacts on biological systems as an environmental contaminant. UV/hydrogen peroxide (UV/H₂O₂) is a well-established technology for BPA treatment in water while UV/sodium percarbonate (UV/SPC) is an emerging technology with unclear biological impacts of treated effluent. Therefore, in this study, the toxicity evaluation of BPA solution treated with UV/H₂O₂ and UV/SPC was preformed and compared based on transformation products (TPs) profile, quantitative structure-activity relationship (QSAR), Escherichia coli (E. coli) toxicity assays, and metabolomic analysis. TPs with hydroxylation, double-ring split, and single-ring cleavage were generated from BPA during the treatments with both technologies, but TPs with quinonation were specifically detected in UV/H₂O₂ treated solution at the UV dose of 1470 mJ cm^-2. QSAR prediction based on TPs profile (excluding benzoquinone TPs) suggested that UV/H₂O₂ and UV/SPC treatments of BPA may increase matrix toxicity due to the formation of multi-hydroxylated TPs; however decreased bioaccumulation potential of all TPs may mitigate the increase of toxicity by reducing the chance of TPs to reach the concentration of toxicity threshold. In vivo assays with E. coli showed inhibited cell growth, arrested cell cycle, and increased cell death in BPA solution treated with UV/H₂O₂ at the UV dose of 1470 mJ cm^-2. Metabolomic analysis indicated that BPA solution treated with UV/H₂O₂ at UV dose of 1470 mJ cm^-2 impacted E. coli metabolism differently than other solutions with unique inhibition on glycerolipid metabolism. Moreover, BPA interfered in various metabolic pathways including alanine, aspartate and glutamate metabolism, starch and sucrose metabolism, pentose phosphate pathway, and lysine degradation, which were mitigated after the treatments. UV/SPC showed advantage over UV/H₂O₂ of attenuated impact on butanoate metabolism with UV irradiation. This study has generated valuable data for better understanding of biological impacts of BPA and its solutions treated with UV/H₂O₂ or UV/SPC, thus providing insights for their application prospect for water and wastewater treatment.

Differential regulation and the underlying mechanisms of clay minerals to Escherichia coli under the stress of polymyxin B: Comparing halloysite with kaolinite

The reuse of polymyxin B (PMB) has attracted extensive attention. Although the resistance mechanism to PMB is clear, there are few reports on the regulation mechanisms and effects of clay minerals on bacteria induced by PMB. The focus of this study is to investigate the multidrug resistance, cell morphology and physiological modification of Escherichia coli (E. coli) exposed to PMB in the presence and absence of clay minerals. To be specific, E. coli was cultured serially for 15 days in the increasing concentration of PMB, with or without halloysite or kaolinite. The potential influence mechanisms of halloysite and kaolinite on E. coli was analyzed by proteomics, antibiotic resistance testing, confocal laser scanning microscopy, scanning electron microscopy and Fourier transform infrared. The results showed that kaolinite could obviously promote the growth of bacteria. Moreover, compared with halloysite, kaolinite could stimulate the overexpression of PMB resistance-related proteins ArnA, ArnB and EptA in E. coli exposed to PMB, and promote the synthesis of peptidoglycan and activate glycolysis pathway to produce energy. In contrast, halloysite was able to regulate the production of low molecular weight thiols by E. coli to prevent bacteria from producing excessive reactive oxygen species, activate the oxidative phosphorylation pathway to supply energy for bacterial life activities, and reduce multidrug resistance of E. coli in a variety of ways. These findings are essential for exploring the impacts of clay minerals on the emergence and spread of multi-drug resistant strains in the environment.

Differential study of the Parabramis pekinensis intestinal microbiota according to different habitats and different parts of the intestine

Purpose

To identify the differences in gut bacterial community of Parabramis pekinensis under different growth conditions, and the effect of the diet in a controlled habitat on the community structure, aiming to provide a comprehensive survey of how the gut microbiota in P. pekinensis varies depending on habitat.

Methods

A total of 73 P. pekinensis from Yangtze River (W), rivers in the outskirts of Jingjiang (Jiangsu province, China, R), and farms (C) were collected to analyze the intestinal microbiota using high-throughput sequencing of the V3-V4 16S ribosomal RNA gene. We also subdivided the gut into the foregut (F), midgut (M), and hindgut (B) to analyze the differences between them.

Results

The dominant bacterial phyla in P. pekinensis were Fusobacteria, Firmicutes, Proteobacteria, and Actinobacteria; meanwhile, Cyanobacteria, Bacteroidetes, Chloroflexi, and Verrucomicrobia were also highly abundant. It is worth noting that the abundance of Fusobacteria Cetobacterium was also very high. The abundance and diversity of the intestinal microbiota structure of fish taken from breeding farm were significantly lower than those taken from Yangtze river and Suburban river, and the abundance of Aeromonas in the gut of fish taken from Yangtze river was much higher than that of fish taken from Suburban river. Compared to midgut, foregut and hindgut have similar microbiota structures, but did not differ significantly in them.

Conclusions

The core intestinal microbiota of P. pekinensis is the same to other herbivorous and partially omnivorous fish. There were significant differences in the intestinal microbiota structure of P. pekinensis from different habitats, but no significant differences in the microbiota abundance and diversity between the different parts of the intestine.

Time-course transcriptome analysis reveals the mechanisms of Burkholderia sp. adaptation to high phenol concentrations

Microbial tolerance to phenolic pollutants is the key to their efficient biodegradation. However, the metabolic mechanisms that allow some microorganisms to adapt to high phenol concentrations remain unclear. In this study, to reveal the underlying mechanisms of how Burkholderia sp. adapt to high phenol concentrations, the strain's tolerance ability and time-course transcriptome in combination with cell phenotype were evaluated. Surprisingly, Burkholderia sp. still grew normally after a long adaptation to a relatively high phenol concentration (1500 mg/L) and exhibited some time-dependent changes compared to unstressed cells prior to the phenol addition. Time-course transcriptome analysis results revealed that the mechanism of adaptations to phenol was an evolutionary process that transitioned from tolerance to positive degradation through precise gene regulation at appropriate times. Specifically, basal stress gene expression was upregulated and contributed to phenol tolerance, which involved stress, DNA repair, membrane, efflux pump and antioxidant protein-coding genes, while a phenol degradation gene cluster was specifically induced. Interestingly, both the catechol and protocatechuate branches of the β-ketoadipate pathway contributed to the early stage of phenol degradation, but only the catechol branch was used in the late stage. In addition, pathways involving flagella, chemotaxis, ATP-binding cassette transporters and two-component systems were positively associated with strain survival under phenolic stress. This study provides the first insights into the specific response of Burkholderia sp. to high phenol stress and shows potential for application in remediation of polluted environments. KEY POINTS: • Shock, DNA repair and antioxidant-related genes contributed to phenol tolerance. • β-Ketoadipate pathway branches differed at different stages of phenol degradation. • Adaptation mechanisms transitioned from negative tolerance to positive degradation.