Pathway for biodegrading coumarin by a newly isolated Pseudomonas sp. USTB-Z

Detoxification of coumarins by rumen anaerobic fungi: insights into microbial degradation pathways and agricultural applications

BACKGROUND

Coumarins are toxic phytochemicals found in a variety of plants and are known to limit microbial degradation and interfere with nutrient cycling. While the degradation of coumarins by fungi has been studied in an environmental context, little is known about their degradation in the gastrointestinal system of herbivores after ingestion.

RESULTS

In this study, we investigated in vitro fermentation by microbial enrichment, transcriptome sequencing, and high-resolution mass spectrometry to evaluate the ability of rumen anaerobic fungi to degrade coumarins. The results showed that despite the low abundance of anaerobic fungi in the rumen microbiota, they were able to effectively degrade coumarins. Specifically, Pecoramyces ruminantium F1 could tolerate coumarin concentrations up to 3 mmol/L and degrade it efficiently via metabolic pathways involving alpha/beta hydrolases and NAD(P)H oxidoreductases within the late growth phase. The fungus metabolized coumarin to less toxic compounds, including o-coumaric acid and melilotic acid, highlighting the detoxification potential of anaerobic fungi.

CONCLUSIONS

This study is the first to demonstrate the ability of rumen anaerobic fungi to degrade coumarin, providing new insights into the use of anaerobic fungi in sustainable agricultural practices and environmental detoxification strategies.

Elucidating the role of the genus Pseudomonas involved in coumarin degradation

Coumarin, a synthetic chemical and phytotoxin, exhibits hepatotoxicity and carcinogenicity, posing threats to both human health and environmental safety. Microbial degradation effectively mitigates environmental contamination. In this study, a coumarin-degrading bacterial consortium designated as XDS-7 with Pseudomonas as the key degrader was obtained. However, there is a lack of comprehensive perspective on the key role of the genus Pseudomonas involved in coumarin degradation. We employed the consortium XDS-7 as a model system to investigate the critical role of the genus Pseudomonas involved in coumarin degradation. Metagenomic binning analysis indicated that bin 14 (Pseudomonas sp.) contains the full complement of genes required for coumarin degradation. A coumarin-degrading bacterium, Pseudomonas sp. strain X4, was isolated from consortium XDS-7 using a traditional enrichment method supplemented with chloramphenicol. Genomic analysis demonstrated that strain X4 carries a suite of genes to completely degrade coumarin. Bioinformatics analysis revealed that putative coumarin-degrading bacteria are widely distributed across diverse bacteria of the genus Pseudomonas. In addition, strain X4 completely removed 100 mg kg-1 of coumarin from contaminated soil within 48 h and 100 mg L-1 of coumarin from contaminated wastewater within 4 h. This study will greatly enhance our understanding and utilization of these valuable bioresources.

Biochemical and molecular mechanisms of Rhodococcus rhodochrous IITR131 for polyethylene terephthalate degradation

AIMS

To isolate polyethylene terephthalate (PET)-degrading bacteria and elucidate the underlying mechanisms of PET biodegradation through biochemical and genome analysis.

METHODS AND RESULTS

Rhodococcus rhodochrous IITR131 was found to degrade PET. Strain IITR131 genome revealed metabolic versatility of the bacterium and had the ability to form biofilm on PET sheet, resulting in the cracks, abrasions, and degradation. IITR131 showed a reduction of 19.7%, exhibiting a half-life of 189.9 d of 0.1 mm PET film in 60 d and formed metabolites bis(2-hydroxyethyl) terephthalate (BHET), terephthalic acid (TPA), and benzoic acid (BA). The draft genome of 5.9 Mb of IITR131 revealed that this bacterium has plethora of genes such as terephthalate 1, 2 dioxygenase, carboxylesterase that together constituted a complete pathway for PET degradation. Moreover, strain IITR131 was found to have a variety of genes encoding for enzymes for the metabolism of several plastic polymers, xenobiotics including chloroalkanes, and polycyclic aromatic hydrocarbons.

CONCLUSIONS

Rhodococcus rhodochrous IITR131 demonstrated a significant potential in the biodegradation of PET. The comprehensive genomic and metabolic analyses further elucidated the molecular pathway involved in PET degradation, enhancing our understanding of the mechanisms underlying microbial PET biodegradation. These findings underscore the applicability of R. rhodochrous IITR131 in biotechnological approaches for mitigating plastic pollution.

Redundant and scattered genetic determinants for coumarin biodegradation in Pseudomonas sp. strain NyZ480

Coumarin (COU) is both a naturally derived phytotoxin and a synthetic pollutant which causes hepatotoxicity in susceptible humans. Microbes have potentials in COU biodegradation; however, its underlying genetic determinants remain unknown. Pseudomonas sp. strain NyZ480, a robust COU degrader, has been isolated and proven to grow on COU as its sole carbon source. In this study, five homologs of xenobiotic reductase A scattered throughout the chromosome of strain NyZ480 were identified, which catalyzed the conversion of COU to dihydrocoumarin (DHC) in vitro. Phylogenetic analysis indicated that these COU reductases belong to different subgroups of the old yellow enzyme family. Moreover, two hydrolases (CouB1 and CouB2) homologous to the 3,4-dihydrocoumarin hydrolase in the fluorene degradation were found to accelerate the generation of melilotic acid (MA) from DHC. CouC, a new member from the group A flavin monooxygenase, was heterologously expressed and purified, catalyzing the hydroxylation of MA to produce 3-(2,3-dihydroxyphenyl)propionate (DHPP). Gene deletion and complementation of couC indicated that couC played an essential role in the COU catabolism in strain NyZ480, considering that the genes involved in the downstream catabolism of DHPP have been characterized (Y. Xu and N. Y. Zhou, Appl Environ Microbiol 86:e02385-19, 2020) and homologous catabolic cluster exists in strain NyZ480. This study elucidated the genetic determinants for complete degradation of COU by Pseudomonas sp. strain NyZ480.IMPORTANCECoumarin (COU) is a phytochemical widely distributed in the plant kingdom and also artificially produced as an ingredient for personal care products. Hence, the environmental occurrence of COU has been reported in different places. Toxicologically, COU was proven hepatotoxic to individuals with mutations in the CYP2A6 gene and listed as a group 3 carcinogen by the International Agency for Research on Cancer and thus has raised increasing concerns. Until now, different physicochemical methods have been developed for the removal of COU, whereas their practical applications were hampered due to high cost and the risk of secondary contamination. In this study, genetic evidence and biochemical characterization of the COU degradation by Pseudomonas sp. strain NyZ480 are presented. With the gene and strain resources provided here, better managements of the hazards that humans face from COU could be achieved, and the possible microbiota-plant interaction mediated by the COU-utilizing rhizobacteria could also be investigated.

Elucidation of the coumarin degradation by Pseudomonas sp. strain NyZ480

As a phytotoxin and synthetic chemical, coumarin (COU) is known for its hepatotoxicity and carcinogenicity. However, no thorough characterization of its microbial degradation has been reported. Here, Pseudomonas sp. strain NyZ480 was isolated for its capability of utilizing COU as the sole carbon source. Studies on its growth and degradation efficiency of COU under various conditions suggested that strain NyZ480 performed the optimum degradation at 30 ℃, pH 7, and 0.5 mM COU was completely removed within 4 h with 1% inoculum. HPLC and LC-MS analyses indicated that dihydrocoumarin (DHC), melilotic acid (MA) and 3-(2,3-dihydroxyphenyl)propionate (DHPP) were the upstream biotransformation intermediates of COU. Enzyme assay established that the initial reaction transforming COU to DHC required an NAD(P)H-dependent reductase, followed by the hydrolysis of DHC to generate MA, and the third reaction catalyzing the monooxygenation of MA to DHPP utilized a strict NADH-dependent hydroxylase. Combining genomics and transcriptomics, we proposed that the COU downstream degradation (from DHPP) was catalyzed by enzymes encoded by a gene cluster homologous to the mhp cluster for 3(3-hydroxyphenyl)propionate degradation via DHPP in E. coli. This study thoroughly identified the intermediates from the COU catabolism, providing essential insights into the molecular evidences of its biodegradation pathway.

Isolation, Identification and Characterization of Growth Parameters of Pseudomonas putida HSM-C2 with Coumarin-Degrading Bacteria

Natural coumarins contribute to the aroma of licorice, and they are often used as a flavoring and stabilizing agents. However, coumarins usage in food has been banned by various countries due to its toxic effect. In this study, a strain of HSM-C2 that can biodegrade coumarin with high efficiency was isolated from soil and identified as Pseudomonas putida through performing 16S rDNA sequence analysis. The HSM-C2 catalyzed the biodegradation up to 99.83% of 1 mg/mL coumarin within 24 h under optimal culture conditions, such as 30 °C and pH 7, which highlights the strong coumarin biodegrading potential of this strain. The product, such as dihydrocoumarin, generated after the biodegradation of coumarin was identified by performing GC-MS analysis. The present study provides a theoretical basis and microbial resource for further research on coumarin biodegradation.

The combined effect of Diversispora versiformis and sodium bentonite contributes on the colonization of Phragmites in cadmium-contaminated soil

To promote the colonization of Phragmites in Cd polluted, nutrient deprived and structural damaged soil, the combined remediation using chemical and microbial modifiers were carried out in potting experiments. The co-application of Diversispora versiformis and sodium bentonite significantly improved the soil structure and phosphorus utilization of the plant, while decreasing the content of cadmium bound by diethylenetriaminepentaacetic acid by 77.72%. As a result, the Phragmites height, tillers, and photosynthetic capacity were increased by 71.60%, 38.37%, and 17.54%, respectively. Further analysis suggested the co-application increased the abundance of phosphorus-releasing microbial communities like Pseudomonassp. and Gemmatimonadetes. Results of rhizosphere metabolites also proved that the signal molecule of lysophosphatidylcholine regulated the phosphorus fixation and utilization by the plant. This work finds composite modifiers are effective in the colonization of Phragmites in Cd contaminated soil by decreasing the bioavailable Cd, increasing the abundance of functional microbial communities and regulating the phosphorus fixation.

Characterization and genomic analysis of an efficient dibutyl phthalate degrading bacterium Microbacterium sp. USTB-Y

A promising bacterial strain for biodegrading dibutyl phthalate (DBP) was successfully isolated from activated sludge and characterized as a potential novel Microbacterium sp. USTB-Y based on 16S rRNA sequence analysis and whole genome average nucleotide identity (ANI). Initial DBP of 50 mg/L could be completely biodegraded by USTB-Y both in mineral salt medium and in DBP artificially contaminated soil within 12 h at the optimal culture conditions of pH 7.5 and 30 ℃, which indicates that USTB-Y has a strong ability in DBP biodegradation. Phthalic acid (PA) was identified as the end-product of DBP biodegraded by USTB-Y using GC/MS. The draft genome of USTB-Y was sequenced by Illumina NovaSeq and 29 and 188 genes encoding for putative esterase/carboxylesterase and hydrolase/alpha/beta hydrolase were annotated based on NR (non redundant protein sequence database) analysis, respectively. Gene3781 and gene3780 from strain USTB-Y showed 100% identity with dpeH and mpeH from Microbacterium sp. PAE-1. But no phthalate catabolic gene (pht) cluster was found in the genome of strain USTB-Y. The results in the present study are valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs biodegrading Microbacterium sp. strains.