The bacterial degradation of flavonoids. Hydroxylation of the A-ring of taxifolin by a soil pseudomonad.
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ABSTRACT:
SUBMITTER: Jeffrey AM
PROVIDER: S-EPMC1174416 | biostudies-other | 1972 Nov
REPOSITORIES: biostudies-other
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Project description:Cell-free extracts prepared from a Pseudomonas sp., grown on (+)-catechin, oxidized dihydrogossypetin (3',4',5,7,8-pentahydroxyflavanonol) by cleaving the A-ring to form oxaloacetic acid from C-5, C-6, C-7 and C-8 together with 5-(3,4-dihydroxyphenyl)-4-hydroxy-3-oxovalero-delta-lactone. The structure of this lactone was confirmed by synthesis of related phenylvalerolactones.
| S-EPMC1174417 | biostudies-other
Project description:1. A cell-free system, prepared from Pseudomonas N.C.I.B. 9340 grown on 4-chloro-2-methylphenoxyacetate (MCPA) was shown to catalyse the reaction sequence: 5-chloro-3-methylcatechol --> cis-cis-gamma-chloro-alpha-methylmuconate --> gamma-carboxymethylene-alpha-methyl-Delta(alphabeta)-butenolide --> gamma-hydroxy-alpha-methylmuconate. 2. The activity of the three enzymes involved in these reactions was completely resolved and the lactonizing and delactonizing enzymes were separated. 3. This part of the metabolic pathway of 4-chloro-2-methylphenoxyacetate is thus confirmed for this bacterium. 4. The ring-fission oxygenase required Fe(2+) or Fe(3+) and reduced glutathione for activity; the lactonizing enzyme is stimulated by Mn(2+), Mg(2+), Co(2+) and Fe(2+); no cofactor requirement could be demonstrated for the delactonizing enzyme. 5. cis-cis-gamma-Chloro-alpha-methylmuconic acid was isolated and found to be somewhat unstable, readily lactonizing to gamma-carboxymethylene-alpha-methyl-Delta(alphabeta)-butenolide. 6. Enzymically the lactonization appears to be a single-step dehydrochlorinase reaction.
| S-EPMC1176811 | biostudies-other
Project description:The s-triazine cyclopropylmelamine (N-cyclopropyl-1,3,5-triazine-2,4,6-triamine) was degraded to about 6 mol of NH4+/mol of substrate by a mixture of two bacteria (strains A and D, both Pseudomonas spp.) Only strain A grew with cyclopropylmelamine as sole and limiting source of nitrogen. The organism obtained 2 mol of nitrogen/mol of substrate and excreted a product that was identified as cyclopropylammelide [6-cyclopropylamino-1,3,5-triazine-2,4(1 H,3 H)-dione]. Proteins in extracts from strain A were separated on a Sephadex G-200 column. Cyclopropylmelamine was found to be deaminated in two separable steps to cyclopropylammelide via cyclopropylammeline [4-amino-6-cyclopropylamino-1,3,5-triazine-2(1 H)-one], which was identified. Strain D could not utilize cyclopropylmelamine or cyclopropylammeline, but could utilize cyclopropylammelide (or homologue) as sole and limiting source of nitrogen and obtain about 4 mol of nitrogen/mol of substrate. Proteins in cell extracts from strain D were separated on a DEAE-cellulose column. Alkylammelides were degraded quantitatively by one enzyme fraction to 1 mol of cyanuric acid plus 1 mol of alkylamine/mol of substrate. The specific activities of enzymes in extracts of the two strains were as high as the activities observed during growth. The three activities studied in the two strains were all active under aerobic and oxygen-free conditions. The reactions appear to be hydrolytic, yielding 2 mol of NH4+ plus 1 mol of cyclopropylamine and 1 mol of cyanuric acid/mol of substrate.
| S-EPMC1144181 | biostudies-other
Project description:Over half of the alpine meadows in the Qinghai-Tibet Plateau (QTP) are degraded due to human activities. Soil degradation from overgrazing is the most direct cause of grassland degradation. It is thus important to synthesize the effects of multiple soil degradation indicators on the belowground biomass of plants and soil microorganisms in the degraded QTP. We studied the diversities and structures of soil bacterial and fungal communities using soil bacterial 16S rRNA and the fungal ITS gene under four degradation gradients, D1: lightly degraded, D2: moderately degraded, D3: highly degraded, and a non-degraded control site (CK). The bacterial Shannon diversity in D3 was significantly lower than that in D1 (p < 0.001), and the bacterial richness index in D3 was significantly lower than that in D1 (p < 0.001). There was no difference in soil fungal diversity among the different degradation levels; however, soil fungal richness decreased significantly from CK to D3. The phyla Actinobacteria, Acidobacteria and the genus Mortierella were differed significantly under the four degradation gradients. Plant litter mass and root C/N ratio were important factors associated with bacterial and fungal diversity and richness. These results indicated that alpine meadow degradation can lead to variations in both microbial diversity and the potential functioning of micro-organisms in the QTP.
| S-EPMC8172827 | biostudies-literature
Project description:A large number of studies have reported the importance of bacterial communities in ecosystems and their responses to soil degradation, but the response mechanism in arid alpine wetlands is still unclear. Here, the non-degraded (ND), slightly degraded (SD), and heavily degraded (HD) regions of Bayinbuluk alpine wetland were used to analyzed the diversity, structure and function of bacterial communities in three degraded wetlands using 16S rRNA. The results showed that with the increase of degradation degree, the content of soil moisture (SM) and available nitrogen (AN) decreased significantly, plant species richness and total vegetation coverage decreased significantly, Cyperaceae (Cy) coverage decreased significantly, and Gramineae (Gr) coverage increased significantly. Degradation did not significantly affect the diversity of the bacterial community, but changed the relative abundance of the community structure. Degradation significantly increased the relative abundance of Actinobacteria (ND: 3.95%; SD: 7.27%; HD: 23.97%) and Gemmatimonadetes (ND: 0.39%; SD: 2.17%; HD: 10.78%), while significantly reducing the relative abundance of Chloroflexi (ND: 13.92%; SD: 8.68%; HD: 3.55%) and Nitrospirae (ND: 6.18%; SD: 0.45%; HD: 2.32%). Degradation significantly reduced some of the potential functions in the bacterial community associated with the carbon (C), nitrogen (N) and sulfur (S) cycles, such as hydrocarbon degradation (ND: 25.00%; SD: 1.74%; HD: 6.59%), such as aerobic ammonia oxidation (ND: 5.96%; SD: 22.82%; HD: 4.55%), and dark sulfide oxidation (ND: 32.68%; SD: 0.37%; HD: 0.28%). Distance-based redundancy analysis (db-RDA) results showed that the bacteria community was significantly related to the TC (total carbon) and Gr (P < 0.05). The results of linear discriminant analysis effect size (LEfSe) analysis indicate significant enrichments of Alphaproteobacteria and Sphingomonas in the HD area. The vegetation communities and soil nutrients changed significantly with increasing soil degradation levels, and Sphingomonas could be used as potential biomarker of degraded alpine wetlands.
| S-EPMC9848402 | biostudies-literature
Project description:Acyl-homoserine lactones (AHLs) are employed by several Proteobacteria as quorum-sensing signals. Past studies have established that these compounds are subject to biochemical decay and can be used as growth nutrients. Here we describe the isolation of a soil bacterium, Pseudomonas strain PAI-A, that degrades 3-oxododecanoyl-homoserine lactone (3OC12HSL) and other long-acyl, but not short-acyl, AHLs as sole energy sources for growth. The small-subunit rRNA gene from strain PAI-A was 98.4% identical to that of Pseudomonas aeruginosa, but the soil isolate did not produce obvious pigments or AHLs or grow under denitrifying conditions or at 42 degrees C. The quorum-sensing bacterium P. aeruginosa, which produces both 3OC12HSL and C4HSL, was examined for the ability to utilize AHLs for growth. It did so with a specificity similar to that of strain PAI-A, i.e., degrading long-acyl but not short-acyl AHLs. In contrast to the growth observed with strain PAI-A, P. aeruginosa strain PAO1 growth on AHLs commenced only after extremely long lag phases. Liquid-chromatography-atmospheric pressure chemical ionization-mass spectrometry analyses indicate that strain PAO1 degrades long-acyl AHLs via an AHL acylase and a homoserine-generating HSL lactonase. A P. aeruginosa gene, pvdQ (PA2385), has previously been identified as being a homologue of the AHL acylase described as occurring in a Ralstonia species. Escherichia coli expressing pvdQ catalyzed the rapid inactivation of long-acyl AHLs and the release of HSL. P. aeruginosa engineered to constitutively express pvdQ did not accumulate its 3OC12HSL quorum signal when grown in rich media. However, pvdQ knockout mutants of P. aeruginosa were still able to grow by utilizing 3OC12HSL. To our knowledge, this is the first report of the degradation of AHLs by pseudomonads or other gamma-Proteobacteria, of AHL acylase activity in a quorum-sensing bacterium, of HSL lactonase activity in any bacterium, and of AHL degradation with specificity only towards AHLs with long side chains.
| S-EPMC201243 | biostudies-literature
Project description:Despite the increasing application of biodegradable plastic mulches (BDMs) in agriculture, the colonization and succession of the attached microbial community on BDMs during their degradation processes remain poorly characterized. Here, we buried four types of commonly used BDMs, including pure polylactic acid (PLA), pure polybutylene adipate terephthalate (PBAT), and two mixtures of PLA and PBAT (85:15 and 15:85 w/w), and one classic polyethylene (PE) mulch in soil for 5 months. Both plastic components and incubation time significantly shaped the β-diversities of microbiota on the plastic mulches (p < 0.001). Meanwhile, the microbial compositions and community structures on BDMs were significantly different from PE mulch, and when excluding PE mulch, the microbiota varied more with time than by the composition of the four BDMs. The orders Burkholderiales and Pseudonocardiales were dominant on most BDMs across different time points. The genus Ramlibacter was revealed as a common biomarker for both PLA and PBAT by random-forest model, and all biomarkers for the BDMs belonged to the dominant order Burkholderiales. In addition, degradation-related and pathogen-related functional taxa were enriched in all mulches among all 40 functional groups, while surprisingly, potential pathogens were detected at higher levels on BDMs than PE. For community assembly on all mulches, the drift and dispersal processes played more important roles than selection, and in particular, the contribution of stochastic drift increased during the degradation process of BDMs while selection decreased, while the opposite trend was observed with PE mulch. Overall, our results demonstrated some degradation species and pathogens were specifically enriched on BDMs, though stochastic processes also had important impacts on the community assembly. It suggested that, similar to conventional plastic mulch, the increased usage of BDMs could lead to potential hazards to crops and human health.
| S-EPMC8762578 | biostudies-literature
Project description:Bacterial community dynamics and biodegradation processes were examined in a highly creosote-contaminated soil undergoing a range of laboratory-based bioremediation treatments. The dynamics of the eubacterial community, the number of heterotrophs and polycyclic aromatic hydrocarbon (PAH) degraders, and the total petroleum hydrocarbon (TPH) and PAH concentrations were monitored during the bioremediation process. TPH and PAHs were significantly degraded in all treatments (72 to 79% and 83 to 87%, respectively), and the biodegradation values were higher when nutrients were not added, especially for benzo(a)anthracene and chrysene. The moisture content and aeration were determined to be the key factors associated with PAH bioremediation. Neither biosurfactant addition, bioaugmentation, nor ferric octate addition led to differences in PAH or TPH biodegradation compared to biodegradation with nutrient treatment. All treatments resulted in a high first-order degradation rate during the first 45 days, which was markedly reduced after 90 days. A sharp increase in the size of the heterotrophic and PAH-degrading microbial populations was observed, which coincided with the highest rates of TPH and PAH biodegradation. At the end of the incubation period, PAH degraders were more prevalent in samples to which nutrients had not been added. Denaturing gradient gel electrophoresis analysis and principal-component analysis confirmed that there was a remarkable shift in the composition of the bacterial community due to both the biodegradation process and the addition of nutrients. At early stages of biodegradation, the alpha-Proteobacteria group (genera Sphingomonas and Azospirillum) was the dominant group in all treatments. At later stages, the gamma-Proteobacteria group (genus Xanthomonas), the alpha-Proteobacteria group (genus Sphingomonas), and the Cytophaga-Flexibacter-Bacteroides group (Bacteroidetes) were the dominant groups in the nonnutrient treatment, while the gamma-Proteobacteria group (genus Xathomonas), the beta-Proteobacteria group (genera Alcaligenes and Achromobacter), and the alpha-Proteobacteria group (genus Sphingomonas) were the dominant groups in the nutrient treatment. This study shows that specific bacterial phylotypes are associated both with different phases of PAH degradation and with nutrient addition in a preadapted PAH-contaminated soil. Our findings also suggest that there are complex interactions between bacterial species and medium conditions that influence the biodegradation capacity of the microbial communities involved in bioremediation processes.
| S-EPMC1287751 | biostudies-literature
Project description:Bioremediation as a method for removing polycyclic aromatic hydrocarbons (PAHs) from contaminated environments has been criticized for poor removal of potentially carcinogenic but less bioavailable high molecular weight (HMW) compounds. As a partial remedy to this constraint, we studied surfactant addition at sub-micellar concentrations to contaminated soil to enhance the biodegradation of PAHs remaining after conventional aerobic bioremediation. We demonstrated increased removal of four- and five-ring PAHs using two nonionic surfactants, polyoxyethylene(4)lauryl ether (Brij 30) and polyoxyethylene sorbitol hexaoleate (POESH), and analyzed bacterial community shifts associated with those conditions. Eight groups of abundant bacteria were implicated as potentially being involved in increased HMW PAH removal. A group of unclassified Alphaproteobacteria and members of the Phenylobacterium genus in particular showed significantly increased relative abundance in the two conditions exhibiting increased PAH removal. Other implicated groups included members of the Sediminibacterium, Terrimonas, Acidovorax, and Luteimonas genera, as well as uncharacterized organisms within the families Chitinophagaceae and Bradyrhizobiaceae. Targeted isolation identified a subset of the community likely using the surfactants as a growth substrate, but few of the isolates exhibited PAH-degradation capability. Isolates recovered from the Acidovorax and uncharacterized Bradyrhizobiaceae groups suggest the abundance of those groups may have been attributable to growth on surfactants. Understanding the specific bacteria responsible for HMW PAH removal in natural and engineered systems and their response to stimuli such as surfactant amendment may improve bioremediation efficacy during treatment of contaminated environmental media.
| S-EPMC5380000 | biostudies-literature
Project description:Several asco-, basidio-, and zygomycetes isolated from an agricultural field were shown to be able to hydroxylate the phenylurea herbicide isoproturon [N-(4-isopropylphenyl)-N',N'-dimethylurea] to N-(4-(2-hydroxy-1-methylethyl)phenyl)-N',N'-dimethylurea and N-(4-(1-hydroxy-1-methylethyl)phenyl)-N',N'-dimethylurea. Bacterial metabolism of isoproturon has previously been shown to proceed by an initial demethylation to N-(4-isopropylphenyl)-N'-methylurea. In soils, however, hydroxylated metabolites have also been detected. In this study we identified fungi as organisms that potentially play a major role in the formation of these hydroxylated metabolites in soils treated with isoproturon. Isolates of Mortierella sp. strain Gr4, Phoma cf. eupyrena Gr61, and Alternaria sp. strain Gr174 hydroxylated isoproturon at the first position of the isopropyl side chain, yielding N-(4-(2-hydroxy-1-methylethyl)phenyl)-N',N'-dimethylurea, while Mucor sp. strain Gr22 hydroxylated the molecule at the second position, yielding N-(4-(1-hydroxy-1-methylethyl)phenyl)-N',N'-dimethylurea. Hydroxylation was the dominant mode of isoproturon transformation in these fungi, although some cultures also produced traces of the N-demethylated metabolite N-(4-isopropylphenyl)-N'-methylurea. A basidiomycete isolate produced a mixture of the two hydroxylated and N-demethylated metabolites at low concentrations. Clonostachys sp. strain Gr141 and putative Tetracladium sp. strain Gr57 did not hydroxylate isoproturon but N demethylated the compound to a minor extent. Mortierella sp. strain Gr4 also produced N-(4-(2-hydroxy-1-methylethyl)phenyl)-N'-methylurea, which is the product resulting from combined N demethylation and hydroxylation.
| S-EPMC1317374 | biostudies-literature