Characterization of hexaconazole-degrading strain Sphingobacterium multivorum and analysis of transcriptome for biodegradation mechanism

Bacterial community structure analysis of sludge from Taozi lake and isolation of an efficient 17β-Estradiol (E2) degrading strain Sphingobacterium sp. GEMB-CSS-01

Environmental challenges arising from organic pollutants pose a significant problem for modern societies. Efficient microbial resources for the degradation of these pollutants are highly valuable. In this study, the bacterial community structure of sludge samples from Taozi Lake (polluted by urban sewage) was studied using 16S rRNA sequencing. The bacterial phyla Proteobacteria, Bacteroidetes, and Chloroflexi, which are potentially important in organic matter degradation by previous studies, were identified as the predominant phyla in our samples, with relative abundances of 48.5%, 8.3%, and 6.6%, respectively. Additionally, the FAPROTAX and co-occurrence network analysis suggested that the core microbial populations in the samples may be closely associated with organic matter metabolism. Subsequently, sludge samples from Taozi Lake were subjected to enrichment cultivation to isolate organic pollutant-degrading microorganisms. The strain Sphingobacterium sp. GEMB-CSS-01, tolerant to sulfanilamide, was successfully isolated. Subsequent investigations demonstrated that Sphingobacterium sp. GEMB-CSS-01 efficiently degraded the endocrine-disrupting compound 17β-Estradiol (E2). It achieved degradation efficiencies of 80.0% and 53.5% for E2 concentrations of 10 mg/L and 20 mg/L, respectively, within 10 days. Notably, despite a reduction in degradation efficiency, Sphingobacterium sp. GEMB-CSS-01 retained its ability to degrade E2 even in the presence of sulfanilamide concentrations ranging from 50 to 200 mg/L. The findings of this research identify potential microbial resources for environmental bioremediation, and concurrently provide valuable information about the microbial community structure and patterns within Taozi Lake.

Integrated transcriptomics and metabolomics analyses reveal the aerobic biodegradation and molecular mechanisms of 2,3',4,4',5-pentachlorodiphenyl (PCB 118) in Methylorubrum sp. ZY-1

2,3',4,4',5-pentachlorodiphenyl (PCB 118), a highly representative PCB congener, has been frequently detected in various environments, garnering much attention across the scientific community. The degradation of highly chlorinated PCBs by aerobic microorganisms is challenging due to their hydrophobicity and persistence. Herein, the biodegradation and adaptation mechanisms of Methylorubrum sp. ZY-1 to PCB 118 were comprehensively investigated using an integrative approach that combined degradation performance, product identification, metabolomic and transcriptomic analyses. The results indicated that the highest degradation efficiency of 0.5 mg L-1 PCB 118 reached 75.66% after seven days of inoculation when the bacteria dosage was 1.0 g L-1 at pH 7.0. A total of eleven products were identified during the degradation process, including low chlorinated PCBs, hydroxylated PCBs, and ring-opening products, suggesting that strain ZY-1 degraded PCB 118 through dechlorination, hydroxylation, and ring-opening pathways. Metabolomic analysis demonstrated that the energy supply and redox metabolism of strain ZY-1 was disturbed with exposure to PCB 118. To counteract this environmental stress, strain ZY-1 adjusted both the fatty acid synthesis and purine metabolism. The analysis of transcriptomics disclosed that multiple intracellular and extracellular oxidoreductases (e.g., monooxygenase, alpha/beta hydrolase and cytochrome P450) participated in the degradation of PCB 118. Besides, active efflux of PCB 118 and its degradation intermediates mediated by multiple transporters (e.g., MFS transporter and ABC transporter ATP-binding protein) might enhance bacterial resistance against these substances. These discoveries provided the inaugural insights into the biotransformation of strain ZY-1 to PCB 118 stress, illustrating its potential in the remediation of contaminated environments.

Isolation, identification, degradation mechanism and exploration of active enzymes in the ochratoxin A degrading strain Acinetobacter pittii AP19

Ochratoxin A (OTA) is a polyketide mycotoxin that commonly contaminates agricultural products and causes significant economic losses. In this study, the efficient OTA-degrading strain AP19 was isolated from vineyard soil and was identified as Acinetobacter pittii. Compared with growth in nutrient broth supplemented with OTA (OTA-NB), strain AP19 grew faster in nutrient broth (NB), but the ability of the resulting cell lysates to remove OTA was weaker. After cultivation in NB, the cell lysate of strain AP19 was able to remove 100% of 1 mg/L OTA within 18 h. The cell lysate fraction > 30 kDa degraded 100% of OTA within 12 h, while the fractions < 30 kDa were practically unable to degrade OTA. Further anion exchange chromatography of the > 30 kDa fraction yielded two peaks exhibiting significant OTA degradation activity. The degradation product was identified as OTα. Amino acid metabolism exhibited major transcriptional trends in the response of AP19 to OTA. The dacC gene encoding carboxypeptidase was identified as one of the contributors to OTA degradation. Soil samples inoculated with strain AP19 showed significant OTA degradation. These results provide significant insights into the discovery of novel functions in A. pittii, as well as its potential as an OTA decomposer.

Unlocking a Sustainable Future for Plastics: A Chemical-Enzymatic Pathway for Efficient Conversion of Mixed Waste to MHET and Energy-Saving PET Recycling

The heterogeneous monomers obtained from plastic waste degradation are unfavorable for PET recondensation and high-value derivative synthesis. Herein, we developed an efficient chemical-enzymatic approach to convert mixed plastic wastes into homogeneous mono-2-hydroxyethyl terephthalate (MHET) without downstream purification, benefiting from three discovered BHETases (KbEst, KbHyd, and BrevEst) in nature. Towards the mixed plastic waste, integrating the chemical K2 CO3 -driven glycolysis process with the BHETase depolymerization technique resulted in an MHET yield of up to 98.26 % in 40 h. Remarkably, BrevEst accomplished the highest BHET hydrolysis (~87 % efficiency in 12 h) for yielding analytical-grade MHET compared to seven state-of-the-art PET hydrolases (18 %-40 %). In an investigation combining quantum theoretical computations and experimental validations, we established a MHET-initiated PET repolymerization pathway. This shortcut approach with MHET promises to strengthen the valorization of mixed plastics, offering a substantially more efficient and energy-saving route for PET recycling.

Degradation of Triazole Fungicides by Plant Growth-Promoting Bacteria from Contaminated Agricultural Soil

The widespread application of triazole fungicides (TFs) in agricultural practices can result in the considerable accumulation of active compound residues in the soil and a subsequent negative impact on the soil microbiota and crop health. In this study, we isolated three TF-degrading bacterial strains from contaminated agricultural soils and identified them as Klebsiella sp., Pseudomonas sp., and Citrobacter sp. based on analysis of morphological characteristics and 16S rRNA gene sequences. The strains used three common TFs, namely hexaconazole, difenoconazole, and propiconazole, as their only sources of carbon and energy for growth in a liquid mineral salt medium, with high concentrations (~ 500 mg/l) of each TF. In addition to the ability to degrade fungicides, the isolates also exhibited plant growth-promoting characteristics, such as nitrogen fixation, indole acetic acid production, phosphate dissolution, and cellulose degradation. The synergistic combination of three bacterial isolates significantly improved plant growth and development with an increased survival rate (57%), and achieved TF degradation ranging from 85.83 to 96.59% at a concentration of approximately 50 mg/kg of each TF within 45 days in the soil-plant system. Based on these findings, the three strains and their microbial consortium show promise for application in biofertilizers, to improve soil health and facilitate optimal plant growth.

Mechanism analysis and improved molecular modification: Design of high efficiency and environmentally friendly triazole fungicide substitutes

The adverse effects of triazole fungicides (TFs) on the soil and the environmental damage caused by their residues have attracted the attention of the international community. To effectively prevent and control the above problems, this paper designed 72 substitutes of TFs with significantly better molecular functionality (>40%) using Paclobutrazol (PBZ) as the template molecule. Then, the comprehensive scores for environmental effects calculated after normalization by "extreme value method-entropy weight method-weighted average method" was the dependent variable, the structural parameters of TFs molecules was the independent variable (PBZ-214 was the template molecule) to construct the 3D-QSAR model of integrated environmental effects of TFs with high degradability, low bioenrichment, low endocrine disruption effects, and low hepatotoxicity and designed 46 substitutes of TFs with significantly better comprehensive environmental effects (>20%). After confirming the above effects of TFs and assessing human health risk and the universality of biodegradation and endocrine disruption, we screened PBZ-319-175 as the eco-friendly substitute of TF, which had high efficiency (improved functionality) and better environmental effects than those of the target molecule by 51.63% and 36.09%, respectively. Finally, the results of the molecular docking analysis showed that non-bonding interactions (hydrogen bonding, electrostatic, or polar force) predominantly affected the association between PBZ-319-175 and its biodegradable protein, and the hydrophobic effect of the amino acids distributed around PBZ-319-175 played a significant role. Additionally, we determined the microbial degradation path of PBZ-319-175 and found that the steric hindrance of the substituent group after molecular modification promoted its biodegradability. In this study, we enhanced molecular functionality twice and also reduce the major damage of TFs to the environment by performing iterative modifications. This paper provided theoretical support for the development and application of high-performance, eco-friendly substitutes of TFs.

Whole genome sequencing and transcriptomics-based characterization of a novel β-cypermethrin-degrading Gordonia alkanivorans GH-1 isolated from fermented foods

Beta-cypermethrin (β-CY) is an organic compound that is widely used as a synthetic pesticide in agriculture and family. Excessive accumulation of β-CY inevitably causes environmental pollution, which has led to food safety and human health concerns. Identification of microorganisms from food sources that are capable of β-CY biodegradation may help prevent pollution due to β-CY accumulation. Here, Gordonia alkanivorans GH-1, which was isolated from the traditional Sichuan fermented food, Pixian Doubanjiang, could not only degrade 82.76% of 50 mg/L β-CY at 96 h, but also degraded the intermediate degradation products including dibutyl phthalate (DBP), benzoic acid (BA) and phenol (Ph). This bacterial strain, thus, effectively improved the efficiency of removal of β-CY and its related metabolites, without being limited by toxic intermediates. Whole genome sequencing and transcriptomics analyses have demonstrated that the bacteria affected the transcription of genes related to cell response and material transport under the stress induced by β-CY, and thereby promoted degradation and transformation of β-CY. Moreover, a complete pathway of β-CY degradation is proposed based on the key genes involved in degradation. This study provides important theoretical significance and reference value for eliminating pesticide residues in agricultural products and food to ensure food safety.

Distribution, horizontal transfer and influencing factors of antibiotic resistance genes and antimicrobial mechanism of compost tea

Compost tea was alternatives of chemical pesticide for green agriculture, but there were no reports about antibiotic resistance genes (ARGs) in compost tea. This study investigated the effect of livestock manures, sewage sludge, their composting products and liquid fermentation on ARGs, mobile genetic elements (MGEs), metal resistance genes (MRGs) and antimicrobial properties of various compost tea. The results showed aerobic liquid fermentation reduced ARGs by 65.93 % and 45.20 % in the compost tea of chicken manure and sludge, enriched ARGs by 8.57 % and 37.41 % in the compost tea of pig manure and bovine manure, and increased MGEs and MRGs by 1.25 × 10^-5-5.53 × 10^-3 and 2.03 × 10^-5-2.03 × 10^-3 in the four compost tea. The correlation coefficient of tetracycline and sulfonamide resistance genes between compost product and compost tea were 0.98 and 0.91. aadA2-02, sul2 and tetX abundant in the compost tea were positively correlated with MGEs and MRGs. Furthermore, liquid fermentation enriched the potential host of tetracycline and vancomycin resistance genes. Tetracycline resistance genes occupied 62.7 % of total ARGs in the compost tea. Alcaligenes and Bacillus enriched by 0.78-39.31 % in the four compost tea, which metabolites had high antimicrobial activity. The potential host of ARGs accounted for 42.1 % bacteria abundance in the four compost tea.

Analysis of the functional gene of degrading BDE-47 by Acinetobacter pittii GB-2 based on transcriptome sequencing

2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) is one of the most widely distributed PBDEs. BDE-47 is also the most abundant in organisms and the most toxic to humans and animals. Herein, we have studied the pathway of BDE-47 degradation and gene involvement in Acinetobacter pittii GB-2. This degradation is dominated by hydroxylation, resulting in hydroxylated products 6-OH-BDE-47, 5-OH-BDE-47 and 2'-OH-BDE-28, and bromophenol products 2,4-DBP and 4-BP. Transcriptome sequencing results showed 359 differentially expressed genes (DEGs) induced by BDE-47, of which 159 were up-regulated and 200 were down-regulated. The up-regulated ones were mainly related to substance transport, degradation and cell stress. From these results, we suggest that 1,2-dioxygenase, phenol hydroxylase and monooxygenase are involved in BDE-47 degradation. The function of AntA gene was identified by constructing a prokaryotic expression vector. Our study contributes to understanding how the metabolism of strain GB-2 changes under BDE-47 stress conditions, and sheds light on the mechanism of BDE-47 degradation.

Residue, dissipation and dietary intake risk assessment of tolfenpyrad in four leafy green vegetables under greenhouse conditions

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A QuEChERS-GC–MS/MS method was used to detect tolfenpyrad in leafy green vegetables.

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Half-lives of tolfenpyrad were 2.0–6.8 d in greenhouse-grown leafy green vegetables.

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PHI of tolfenpyrad was suggested as 21 d in BCL and 28 d in BBL, SOL and LSL.

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The potential health risk of tolfenpyrad was acceptable in leafy green vegetables.

A novel and accurate analytical method for the determination of tolfenpyrad in four leafy green vegetables, Brassica bara L., Spinacia oleracea L., Lactuca sativa L. and Brassica chinensis L., was developed and applied to investigate the residue distribution and dietary risk under greenhouse conditions. The established approach was determined to be adequate, with recoveries of 79.2%–92.9% and relative standard deviations < 8%. Tolfenpyrad dissipated relatively rapidly in four leafy green vegetables. Terminal residues of tolfenpyrad were below 0.5 mg/kg (maximum residue limit for Brassica bara L. set by China) in leafy green vegetables collected 28 d after the last application. Due to risk quotient values < 100%, the residue levels of tolfenpyrad in leafy green vegetables collected 21 days after the last application were deemed safe for consumers. The results provide field data for the reasonable use and dietary risk assessment of tolfenpyrad in leafy green vegetables.

Considerations on the Identity and Diversity of Organisms Affiliated with Sphingobacterium multivorum-Proposal for a New Species, Sphingobacterium paramultivorum

Plant biomass offers great potential as a sustainable resource, and microbial consortia are primordial in its bioconversion. The wheat-straw-biodegradative bacterial strain w15 has drawn much attention as a result of its biodegradative potential and superior degradation performance in bacterial-fungal consortia. Strain w15 was originally assigned to the species Sphingobacterium multivorum based on its 16S ribosomal RNA (rRNA) gene sequence. A closer examination of this taxonomic placement revealed that the sequence used has 98.9% identity with the ‘divergent’ 16S rRNA gene sequence of S. multivorum NCTC 11343^T, yet lower relatedness with the canonical 16S rRNA sequence. A specific region of the gene, located between positions 186 and 210, was found to be highly variable and determinative for the divergence. To solve the identity of strain w15, genome metrics and analyses of ecophysiological niches were undertaken on a selection of strains assigned to S. multivorum and related species. These analyses separated all strains into three clusters, with strain w15, together with strain BIGb0170, constituting a separate radiation, next to S. multivorum and S. siyangense. Moreover, the strains denoted FDAARGOS 1141 and 1142 were placed inside S. siyangense. We propose the renaming of strains w15 and BIGb0170 as members of the novel species, coined Sphingobacterium paramultivorum.

Occurrence and risk assessment of herbicides and fungicides in atmospheric particulate matter in Hanoi, Vietnam

Vietnam is a Southeast Asian developing country with rapidly increasing air pollution, especially in large cities. Over 350,000 chemicals and chemical mixtures are produced and used in Vietnam; however, the country has only implemented air quality standards for 44 substances, which are primarily focused on inorganic and volatile organic compounds. Although numerous pesticides are frequently applied across large cities in Vietnam, information on their concentrations in atmospheric particulate matter (APM) is limited. Therefore, to investigate their occurrence and health effects, 187 pesticides in APM were screened using the liquid chromatography-mass spectrometry-quadrupole time of flight- Sequential Window Acquisition of All Theoretical Fragment Ion Spectra method (LC-QTOF-MS-SWATH). A total of 22 pesticides (16 fungicides and 6 herbicides) were quantified in the dry and rainy seasons. Among them, 19 substances were quantified in APM for the first time in Vietnam. Their median total concentrations in the dry season were higher than those in the rainy season, and the concentrations in the daytime were one-third of the night-time concentrations in both seasons. Their total levels ranged from 0.82 to 21.1 ng m^-3 (median, 3.63 ng m^-3), the detection frequencies of 9 pesticides were higher than 70%, and 7-14 pesticides were detected per sample (median, 10). Some of the detected pesticides were likely sourced from their prevalent use in amenity turf protection (e.g., in parks and public roads) and weed control (e.g., in gardens, floriculture, and agriculture). The total daily intake (DI_air) values for adults, children, and infants were 8.17E-06, 2.06E-05, and 2.45E-05 mg kg^-1 d^-1, respectively, and the highest Hazard Quotients (HQs) were 4.81E-04, 1.22E-03, and 1.44E-03, respectively. All HQs and HIs of the pesticides were < 1 for all population groups (adults, children, and infants), indicating negligible exposure risks.

Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis

Many studies have shown that the space environment plays a pivotal role in changing the characteristics of conditional pathogens, especially their pathogenicity and virulence. However, Stenotrophomonas maltophilia, a type of conditional pathogen that has shown to a gradual increase in clinical morbidity in recent years, has rarely been reported for its impact in space. In this study, S. maltophilia was exposed to a simulated microgravity (SMG) environment in high-aspect ratio rotating-wall vessel bioreactors for 14days, while the control group was exposed to the same bioreactors in a normal gravity (NG) environment. Then, combined phenotypic, genomic, transcriptomic, and proteomic analyses were conducted to compare the influence of the SMG and NG on S. maltophilia. The results showed that S. maltophilia in simulated microgravity displayed an increased growth rate, enhanced biofilm formation ability, increased swimming motility, and metabolic alterations compared with those of S. maltophilia in normal gravity and the original strain of S. maltophilia. Clusters of Orthologous Groups (COG) annotation analysis indicated that the increased growth rate might be related to the upregulation of differentially expressed genes (DEGs) involved in energy metabolism and conversion, secondary metabolite biosynthesis, transport and catabolism, intracellular trafficking, secretion, and vesicular transport. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the increased motility might be associated the upregulation of differentially expressed proteins (DEPs) involved in locomotion, localization, biological adhesion, and binding, in accordance with the upregulated DEGs in cell motility according to COG classification, including pilP, pilM, flgE, flgG, and ronN. Additionally, the increased biofilm formation ability might be associated with the upregulation of DEPs involved in biofilm formation, the bacterial secretion system, biological adhesion, and cell adhesion, which were shown to be regulated by the differentially expressed genes (chpB, chpC, rpoN, pilA, pilG, pilH, and pilJ) through the integration of transcriptomic and proteomic analyses. These results suggested that simulated microgravity might increase the level of corresponding functional proteins by upregulating related genes to alter physiological characteristics and modulate growth rate, motility, biofilm formation, and metabolism. In conclusion, this study is the first general analysis of the phenotypic, genomic, transcriptomic, and proteomic changes in S. maltophilia under simulated microgravity and provides some suggestions for future studies of space microbiology.

Potential Role of Rhizobacteria Isolated from Citrus Rhizosphere for Biological Control of Citrus Dry Root Rot

Citrus trees face threats from several diseases that affect its production, in particular dry root rot (DRR). DRR is a multifactorial disease mainly attributed to Neocosmospora (Fusarium) solani and other several species of Neocosmospora and Fusarium spp. Nowadays, biological control holds a promising control strategy that showed its great potential as a reliable eco-friendly method for managing DRR disease. In the present study, antagonist rhizobacteria isolates were screened based on in vitro dual culture bioassay with N. solani. Out of 210 bacterial isolates collected from citrus rhizosphere, twenty isolates were selected and identified to the species level based on the 16S rRNA gene. Molecular identification based on 16S rRNA gene revealed nine species belonging to Bacillus, Stenotrophomonas, and Sphingobacterium genus. In addition, their possible mechanisms involved in biocontrol and plant growth promoting traits were also investigated. Results showed that pectinase, cellulose, and chitinase were produced by eighteen, sixteen, and eight bacterial isolates, respectively. All twenty isolates were able to produce amylase and protease, only four isolates produced hydrogen cyanide, fourteen isolates have solubilized tricalcium phosphate, and ten had the ability to produce indole-3-acetic acid (IAA). Surprisingly, antagonist bacteria differed substantially in their ability to produce antimicrobial substances such as bacillomycin (five isolates), iturin (ten isolates), fengycin (six isolates), surfactin (fourteen isolates), and bacteriocin (subtilosin A (six isolates)). Regarding the PGPR capabilities, an increase in the growth of the bacterial treated canola plants, used as a model plant, was observed. Interestingly, both bacterial isolates Bacillus subtilis K4-4 and GH3-8 appear to be more promising as biocontrol agents, since they completely suppressed the disease in greenhouse trials. Moreover, these antagonist bacteria could be used as bio-fertilizer for sustainable agriculture.

Comparison the dissipation behaviors and exposure risk of carbendazim and procymidone in greenhouse strawberries under different application method: Individual and joint applications

The dissipation behaviors and exposure risks of individual and joint application of procymidone and carbendazim in greenhouse strawberries were studied. The initial concentrations were similar after individual or joint applications, while the dissipation half-lives and finial concentrations were significantly different. After joint application, the dissipation half-lives of procymidone and carbendazim were 12.9 and 16.0 days, respectively, which were about 1.8 times higher than those after individual application. Furthermore, the final residues under joint application condition were 1.8-3.5 times higher than those under individual application condition. The joint application decreased the dissipation rates of procymidone or carbendazim in strawberries, and increased the final residue concentrations. The dietary intake risks of procymidone and carbendazim (whether applied individually or jointly) were no higher than 0.12, which were acceptable for human health. This work would shed a light for the guidance of the joint application and risk assessment of the typical fungicides in strawberry.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.