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Frontiers in Plant Science 2022The integration of phytoremediation and biostimulation can improve pollutant removal from the environment. Plant secondary metabolites (PSMs), which are structurally...
The integration of phytoremediation and biostimulation can improve pollutant removal from the environment. Plant secondary metabolites (PSMs), which are structurally related to xenobiotics, can stimulate the presence of microbial community members, exhibiting specialized functions toward detoxifying, and thus mitigating soil toxicity. In this study, we evaluated the effects of enrichment of 4-chloro-2-methylphenoxyacetic acid (MCPA) contaminated soil (unplanted and zucchini-planted) with syringic acid (SA) on the bacterial community structure in soil, the rhizosphere, and zucchini endosphere. Additionally, we measured the concentration of MCPA in soil and fresh biomass of zucchini. The diversity of bacterial communities differed significantly between the studied compartments (i.e., unplanted soil, rhizospheric soil, and plant endosphere: roots or leaves) and between used treatments (MCPA or/and SA application). The highest diversity indices were observed for unplanted soil and rhizosphere. Although the lowest diversity was observed among leaf endophytes, this community was significantly affected by MCPA or SA: the compounds applied separately favored the growth of (especially ), while their simultaneous addition promoted the growth of (especially ). The application of MCPA + SA together lead also to enhanced growth of , , , and in the rhizosphere, while SA increased the occurrence of in leaves. In addition, SA appeared to have a positive influence on the degradative potential of the bacterial communities against MCPA: its addition, followed by zucchini planting, significantly increased the removal of the herbicide (50%) from the soil without affecting, neither positively nor negatively, the plant growth.
PubMed: 35712561
DOI: 10.3389/fpls.2022.882228 -
Huan Jing Ke Xue= Huanjing Kexue Mar 2024The removal mechanisms of phthalic acid esters (PAEs) have attracted much attention because of their endocrine-disrupting properties and persistence in environmental...
The removal mechanisms of phthalic acid esters (PAEs) have attracted much attention because of their endocrine-disrupting properties and persistence in environmental media. In order to reveal the removal mechanism of PAEs and involved keystone taxa and functional genes, purple soils were polluted by di--butyl phthalate (DBP) and di-2-ethylhexyl phthalate (DEHP), respectively, along a gradient of 0, 5, 10, and 20 mg·kg and cultured for 90 days in the dark. The results showed that the degradation dynamics of DBP and DEHP were well-fitted by the first-order kinetic model, and the half-life of DBP and DEHP ranged from 17.0 to 38.2 days. The degradation rate of DBP (5 mg·kg) was the fastest, and that of DEHP (20 mg·kg) was the slowest. The soil samples of the seventh day and the fifteenth day were analyzed using metagenomic sequencing. NMDS and cluster analysis showed that there was a significant difference between the bacterial community structure of soil samples from the seventh day and the fifteenth day. The relative abundance of increased from the seventh day to the fifteenth day. The smaller the half-life of DBP or DEHP, the higher the relative abundance of in the different treatments. In addition, was the dominant genus in all polluted soils. Co-occurrence network analysis elucidated that was a keystone genus of the soil bacterial communities, which could be used to indicate the pollution levels of DBP and DEHP. The results of KEGG annotation demonstrated that was responsible for benzoate degradation, quorum sensing, ABC transporters, and the two-component system and could promote the intercellular communications and the microbial growth and proliferation and maintain the stability of the community structure. Therefore, the degradation rate of DBP and DEHP in purple soils depended on their initial content and their own properties. played an important role in the PAEs degradation, and played a major part in promoting PAEs degradation and regulating the stability of the structure and function of degrading bacterial communities.
Topics: Soil; Diethylhexyl Phthalate; Phthalic Acids; Dibutyl Phthalate; Esters
PubMed: 38471894
DOI: 10.13227/j.hjkx.202303127 -
Fish & Shellfish Immunology Feb 2023Cryptocaryon irritans is a parasitic ciliate of marine fish, causing serious mortality and economic loss of grouper. In this study, the orange-spotted grouper...
Effects of Cryptocaryon irritans infection on the histopathology, oxidative stress, immune response, and intestinal microbiota in the orange-spotted grouper Epinephelus coioides.
Cryptocaryon irritans is a parasitic ciliate of marine fish, causing serious mortality and economic loss of grouper. In this study, the orange-spotted grouper (Epinephelus coioides) were separately exposed to C. irritans infection for 72 h at a dose of 5000 or 10000 active theronts per fish, and we evaluated the changes in histopathology, oxidative stress, immune response, and intestinal microbiota composition. The results showed that C. irritans infection caused pathological alteration on the skin, gills, and liver of E. coioides. Oxidative stress responses occurred in the liver and gills, reflected in the corresponding antioxidant enzyme and gene indexes. The mRNA expression levels of inflammation-related genes (IL-1β, IL-6, and IL-8) and the mediators of apoptosis (casp3, casp9, and cytc) were increased in the liver and gills of the fish. C. irritans infection also affected the diversity and composition of intestinal microbiota. Specifically, the relative abundance of Firmicutes was increased, whereas that of Proteobacteria was decreased. Several potentially beneficial bacteria (Pandoraea, Clostridium sensu stricto 1, Christensenellaceae R-7 group, and Weissella) were decreased, whereas pathogenic bacteria (Streptococcus and Acinetobacter) were increased. In conclusion, this study reveals that C. irritans infection caused histopathology, immune disorders, and intestinal microbial community variation in E. coioides.
Topics: Animals; Bass; Ciliophora Infections; Gastrointestinal Microbiome; Phylogeny; Ciliophora; Hymenostomatida; Immunity; Oxidative Stress; Fish Diseases; Fish Proteins
PubMed: 36682479
DOI: 10.1016/j.fsi.2023.108562 -
Frontiers in Microbiology 2023Pathogenic invasion of profoundly altered microflora in the crop production system, impacting diversity and composition in both artificial bed-log and fruiting bodies....
Pathogenic invasion of profoundly altered microflora in the crop production system, impacting diversity and composition in both artificial bed-log and fruiting bodies. A more complex ecological network between the diseased and healthy bodies. Researchers still have poor knowledge about how the important agricultural relationship between the composition of the microbiome of the artificial bed-log and the fruiting bodies is infected by the pathogenic invasive microbes , but this knowledge is crucial if we want to use or improve it. Here, we investigated 8 groups (48 biological samples) across 5 growth stages of the production system using metagenomic technology. Diseased and healthy fruiting bodies exhibited distinct microbial compositions, while core members in artificial bed-logs remained stable. Core microbiota analysis highlighted and bacterial genera, as well as , , , and fungal genera as biomarker species after the bodies were treated with the pathogenic invasive microbes . In diseased bodies, these core members upregulated pathways including polymyxin resistance, L-arginine degradation II, superpathway of L-arginine and L-ornithine degradation, glucose degradation (oxidative), glucose and glucose-1-phosphate degradation, promoting fruit spoilage. Our data confirm that plays an important role in the early stages of disease development in the crop generation system. The exposed volatile core microbiome may play an important role in accelerating -induced decay of fruiting bodies.
PubMed: 38029184
DOI: 10.3389/fmicb.2023.1263982 -
British Journal of Haematology Feb 2023
Topics: Humans; Neutrophils; Burkholderiaceae; Bacteremia
PubMed: 36377533
DOI: 10.1111/bjh.18556 -
Scientific Reports Nov 2022Polychlorinated Biphenyls (PCBs) are persistence in the contaminated sites as a result of lacking PCBs-degrading microorganisms. Cultivation-independent technique called...
Polychlorinated Biphenyls (PCBs) are persistence in the contaminated sites as a result of lacking PCBs-degrading microorganisms. Cultivation-independent technique called single-strand-conformation polymorphism (SSCP) based on 16SrRNA genes was chosen to characterize the diversity of bacterial communities in PCBs polluted soil samples. The bacterial communities showed an increasing diversity from the genetic profiles using SSCP technique. 51 single products were identified from the profiles using PCR reamplification and cloning. DNA sequencing of the 51 products, it showed similarities to Acidobacteria, Actinobacteria, Betaproteobateria, Gammaproteobacteria and Alphaproteobacteria, the range of similarities were 92.3 to 100%. Pure 23 isolates were identified from PCBs contaminated sites. The identified isolates belonged to genus Bacillus, Brevibacillus, Burkholderia, Pandoraea, Pseudomonas, and Rhodococcus. The new strains have the capability to use PCBs as a source of sole carbon and harbor 2,3-dihydroxybiphenyl dioxygenase (DHBDO) which could be used as molecular marker for detection PCBs-degrading bacteria in the PCBs contaminated sites. This finding may enhance the PCBs bioremediation by monitoring and characterization of the PCBs degraders using DHBDO in PCBs contaminated sites.
Topics: Polychlorinated Biphenyls; Soil; Soil Microbiology; Soil Pollutants; Biodegradation, Environmental; Bacteria; Biotechnology; Dioxygenases
PubMed: 36357504
DOI: 10.1038/s41598-022-23886-3 -
Journal of the Association of Medical... Oct 2020Diagnosis and clinical management of pulmonary infections in lung transplant patients are challenging. The increased diversity of bacterial species identified from...
Diagnosis and clinical management of pulmonary infections in lung transplant patients are challenging. The increased diversity of bacterial species identified from clinical samples with novel proteomics-based systems can further complicate clinical decision making in this highly vulnerable population. Whether newly recognized organisms are colonizers or true pathogens often remains controversial since symptoms causality and impact on lung function is often unknown. We present the case of a 48-year-old female lung transplant patient with sp infection. We review and discuss the role of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for accurate bacterial identification. We report on therapeutic management and clinical outcome.
PubMed: 36341313
DOI: 10.3138/jammi-2020-0001 -
Chemosphere Sep 2019Our understanding of the tetrahydrofuran (THF) degradation in complex environment is limited. The majority of THF degrading genes reported are group V soluble diiron...
Our understanding of the tetrahydrofuran (THF) degradation in complex environment is limited. The majority of THF degrading genes reported are group V soluble diiron monooxygenases and share greater than 95% homology with one another. In this study, we used sole-carbon-source incubation combined with high-throughput metagenomic sequencing to investigate this contaminant's degradation in environmental samples. We identified as-yet-uncultivated microbe from the genera Pseudonocardia and fungi Scedosporium sp. (Scedosporium sp. was successfully isolated) as THF degraders as containing THF degradation genes, while microbes from the genera Bordetella, Pandoraea and Rhodanobacter functioned as main cooperators by utilizing acidic intermediates and providing anti-acid mechanisms. Furthermore, a 9387-bp THF degradation cluster designated thmX from the as-yet-uncultivated Pseudonocardia (with 6 main ORFs and with 79-93% amino acid sequence identity with previously reported clusters) was discovered. We also found a THF-degrading related cytochrome P450 monooxygenase from the genus Scedosporium and predicted its cognate reductase for the first time. All the genes and clusters mentioned above were successfully amplified from samples and cloned into the suitable expression vectors. This study will provide novel insights for understanding of THF degradation mechanisms under acid stress conditions and mining new THF degradation genes.
Topics: Actinomycetales; Furans; Metagenome; Metagenomics; Microbiota; Mixed Function Oxygenases; Open Reading Frames
PubMed: 31129398
DOI: 10.1016/j.chemosphere.2019.05.137 -
Journal of Hazardous Materials Jun 2023Methomyl is a widely used carbamate pesticide, which has adverse biological effects and poses a serious threat to ecological environments and human health. Several...
Methomyl is a widely used carbamate pesticide, which has adverse biological effects and poses a serious threat to ecological environments and human health. Several bacterial isolates have been investigated for removing methomyl from environment. However, low degradation efficiency and poor environmental adaptability of pure cultures severely limits their potential for bioremediation of methomyl-contaminated environment. Here, a novel microbial consortium, MF0904, can degrade 100% of 25 mg/L methomyl within 96 h, an efficiency higher than that of any other consortia or pure microbes reported so far. The sequencing analysis revealed that Pandoraea, Stenotrophomonas and Paracoccus were the predominant members of MF0904 in the degradation process, suggesting that these genera might play pivotal roles in methomyl biodegradation. Moreover, five new metabolites including ethanamine, 1,2-dimethyldisulfane, 2-hydroxyacetonitrile, N-hydroxyacetamide, and acetaldehyde were identified using gas chromatography-mass spectrometry, indicating that methomyl could be degraded firstly by hydrolysis of its ester bond, followed by cleavage of the C-S ring and subsequent metabolism. Furthermore, MF0904 can successfully colonize and substantially enhance methomyl degradation in different soils, with complete degradation of 25 mg/L methomyl within 96 and 72 h in sterile and nonsterile soil, respectively. Together, the discovery of microbial consortium MF0904 fills a gap in the synergistic metabolism of methomyl at the community level and provides a potential candidate for bioremediation applications.
Topics: Humans; Methomyl; Biodegradation, Environmental; Pesticides; Bacteria; Soil; Metabolic Networks and Pathways; Microbial Consortia
PubMed: 37003005
DOI: 10.1016/j.jhazmat.2023.131287 -
International Microbiology : the... Jun 2024Chlorobenzene (CB), extensively used in industrial processes, has emerged as a significant contaminant in soil and groundwater. The eco-friendly and cost-effective...
Chlorobenzene (CB), extensively used in industrial processes, has emerged as a significant contaminant in soil and groundwater. The eco-friendly and cost-effective microbial remediation has been increasingly favored to address this environmental challenge. In this study, a degrading bacterium was isolated from CB-contaminated soil at a pesticide plant, identified as Pandoraea sp. XJJ-1 (CCTCC M 2021057). This strain completely degraded 100 mg·L CB and showed extensive degradability across a range of pH (5.0-9.0), temperature (10-37 °C), and CB concentrations (100-600 mg·L). Notably, the degradation efficiency was 85.2% at 15 °C, and the strain could also degrade six other aromatic hydrocarbons, including benzene, toluene, ethylbenzene, and xylene (o-, m-, p-). The metabolic pathway of CB was inferred using ultraperformance liquid chromatography, gas chromatography-mass spectrometry, and genomic analysis. In strain XJJ-1, CB was metabolized to o-chlorophenol and 3-chloroxychol by CB monooxygenase, followed by ortho-cleavage by the action of 3-chlorocatechol 1,2-dioxygenase. Moreover, the presence of the chlorobenzene monooxygenation pathway metabolism in strain XJJ-1 is reported for the first time in Pandoraea. As a bacterium with low-temperature resistance and composite pollutant degradation capacity, strain XJJ-1 has the potential application prospects in the in-situ bioremediation of CB-contaminated sites.
PubMed: 38900217
DOI: 10.1007/s10123-024-00544-4