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Biodegradation Apr 2024Pretilachlor and safener fenclorim are the main components of herbicides widely applied to control weeds. Although some pure cultures of bacteria and fungi which...
Pretilachlor and safener fenclorim are the main components of herbicides widely applied to control weeds. Although some pure cultures of bacteria and fungi which degraded these compounds under aerobic conditions were isolated, no isolated pretilachlor- and fenclorim-degrading bacterial strains under anaerobic condition had been available. In this study, the degradation of these compounds and the effects of them on bacterial community structures were investigated under anaerobic conditions. The dissipation rates of pretilachlor and fenclorim in slurries were in the order: soil from paddy field ≈ sediment from river > sediment from mangrove. Moreover, three pretilachlor-degrading bacterial strains (Pseudomonas sp. Pr1, Proteiniclasticum sp. Pr2 and Paracoccus denitrificans Pr3) and two fenclorim-degrading strains (Dechloromonas sp. Fe1 and Ralstonia pickettii Fe2) isolated from a slurry of paddy soil utilized the substrates as sole carbon and energy sources under anaerobic conditions. The degradation of pure pretilachlor and fenclorim at various concentrations by corresponding mixed pure cultures followed the Michaelis-Menten model, with the maximum degradation was 3.10 ± 0.31 µM/day for pretilachlor, and 2.08 ± 0.18 µM/day for fenclorim. During the degradation, 2-chloro-N-(2,6-diethylphenyl) acetamide and 2,6-dimethylaniline were produced in pretilachlor degradation, and benzene was a product of fenclorim degradation. The synergistic degradation of both substrates by all isolated bacteria reduced the metabolites concentrations accumulated in media. This study provides valuable information on effects of pretilachlor and fenclorim on bacterial communities in soil and sediments, and degradation of these substrates by isolated bacteria under anaerobic condition.
PubMed: 38662140
DOI: 10.1007/s10532-024-10078-1 -
Aquatic Toxicology (Amsterdam,... Dec 2023The red swamp crayfish (Procambarus clarkii) is an important farming species in China and there is a high degree of overlap between the main crayfish production areas...
The red swamp crayfish (Procambarus clarkii) is an important farming species in China and there is a high degree of overlap between the main crayfish production areas and areas contaminated with the heavy metal lead (Pb), thus putting crayfish farming at potential risk of Pb contamination. To assess the toxic effects of Pb on crayfish, in this study they were exposed to different concentrations of Pb (0, 0.1, 1, 10, 50 mg/L) for 72 h, and 0.1 mg/L represents the level of Pb in the contaminated water. Histomorphology and activities of antioxidant or immune-related enzymes suggest that the damage of Pb to the hepatopancreas and intestine was dose- and time-dependent, with the intestine being more sensitive to Pb than the hepatopancreas. Notably, after a short period (24 h) of stress at low concentrations (0.1 mg/L) of Pb, the malondialdehyde (MDA) content and antioxidant enzymes such as catalase (CAT) and glutathione peroxidase (GSH-Px) in the intestine of crayfish showed significant changes, indicating that low concentrations of Pb were also highly detrimental to crayfish. High-throughput sequencing of the intestinal microbial community indicated that Pb exposure led to a disturbance in the relative abundance of intestinal bacteria, increasing the abundance of pathogenic bacteria (Bosea, Cloacibacterium, Legionella spp.) and decreasing the abundance of potentially beneficial bacteria (Chitinibacter, Chitinilyticum, Paracoccus, Microbacterium, Demequina, and Acinetobacter spp.). In conclusion, Pb damages the hepatopancreas and intestinal barrier of crayfish, leading to the destruction of their anti-stress ability and immune response, and at the same time disrupts the homeostasis of intestinal microbes, resulting in adverse effects on the gut. This study contributed to the assessment of the ecotoxicity of the heavy metal Pb to the crustacean aquatic animals.
Topics: Animals; Antioxidants; Astacoidea; Gastrointestinal Microbiome; Lead; Water Pollutants, Chemical; Metals, Heavy; Fresh Water
PubMed: 38041968
DOI: 10.1016/j.aquatox.2023.106768 -
Journal of Environmental Management Dec 2023Microbial driven coupled processes between denitrification and methane/sulfur metabolism play a very substantial role in accelerating nitrogen removal in river...
Microbial driven coupled processes between denitrification and methane/sulfur metabolism play a very substantial role in accelerating nitrogen removal in river sediments. Until now, little is known about how element coupling processes alter nitrogen metabolism by the microbial functional communities. The primary objective of this research was to clarify the contributory role of microbial-mediated coupled processes in controlling denitrification. Specifically, the study sought to identify the key bioindicators (or metabolic pathway) for preferably regulating and predicting potential denitrification rate (PDR). Here, a total of 40 sediment samples were collected from the inflow rivers of Chaohu Lake under nitrogen stress. The results revealed the ecological importance of methanogens and sulfate reducing bacteria in the microbial interaction network. Correlations between quantitative or predicted genes showed that the methanogenic gene (mcrA) was synergistic with denitrifying genes, further unraveling that the key role of methanogenesis in denitrification process for facilitating nitrogen removal. The PDR of sediments ranged from 0.03 to 133.21 μg N·g·h. The study uncovered specific environmental factors (NH and OM) and microbial indicators (nosZ, mcrA, Paracoccus, Thauera, Methanobrevibacter and Desulfomicrobium) as potential contributors to the variations in PDR. Structural Equation Model (SEM) analysis revealed a significant direct effect of NH on PDR, evidenced by a standardized coefficient (λ) of 0.77 (P < 0.001). Additionally, the findings also emphasized the salient role of methanogens (Methanobrevibacter) and methanogenic gene (mcrA) in indicating PDR. The research's aforementioned findings shed light on the substantial consequences of methanogenesis on nitrogen metabolism in coupled processes, enabling improved control of nitrogen pollution in river sediments. This study provided fresh perspectives on the effects of multiple functional taxa on denitrification, and reinforces the significance of coupling processes for nitrogen removal.
Topics: Denitrification; Rivers; Lakes; Nitrogen; Geologic Sediments
PubMed: 37839205
DOI: 10.1016/j.jenvman.2023.119320 -
Journal of Bacteriology Apr 2024is a facultative methylotroph that can grow on methanol and methylamine as sole sources of carbon and energy. Both are oxidized to formaldehyde and then to formate, so...
is a facultative methylotroph that can grow on methanol and methylamine as sole sources of carbon and energy. Both are oxidized to formaldehyde and then to formate, so growth on C1 substrates induces the expression of genes encoding enzymes required for the oxidation of formaldehyde and formate. This induction involves a histidine kinase response regulator pair (FlhSR) that is likely triggered by formaldehyde. Catabolism of some complex organic substrates (e.g., choline and L-proline betaine) also generates formaldehyde. Thus, and mutants that fail to induce expression of the formaldehyde catabolic enzymes cannot grow on methanol, methylamine, and choline. Choline is oxidized to glycine via glycine betaine, dimethylglycine, and sarcosine. By exploring growth phenotypes and the activities of a promoter and enzyme known to be upregulated by formaldehyde, we identify the oxidative demethylations of glycine betaine, dimethylglycine, and sarcosine as sources of formaldehyde. Growth on glycine betaine, dimethylglycine, and sarcosine is accompanied by the production of up to three, two, and one equivalents of formaldehyde, respectively. Genetic evidence implicates two orthologous monooxygenases in the oxidation of glycine betaine. Interestingly, one of these appears to be a bifunctional enzyme that also oxidizes L-proline betaine (stachydrine). We present preliminary evidence to suggest that growth on L-proline betaine induces expression of a formaldehyde dehydrogenase distinct from the enzyme induced during growth on other formaldehyde-generating substrates.IMPORTANCEThe bacterial degradation of one-carbon compounds (methanol and methylamine) and some complex multi-carbon compounds (e.g., choline) generates formaldehyde. Formaldehyde is toxic and must be removed, which can be done by oxidation to formate and then to carbon dioxide. These oxidations provide a source of energy; in some species, the CO thus generated can be assimilated into biomass. Using the Gram-negative bacterium as the experimental model, we infer that oxidation of choline to glycine generates up to three equivalents of formaldehyde, and we identify the three steps in the catabolic pathway that are responsible. Our work sheds further light on metabolic pathways that are likely important in a variety of environmental contexts.
Topics: Betaine; Sarcosine; Paracoccus denitrificans; Methanol; Choline; Glycine; Formaldehyde; Formates; Methylamines
PubMed: 38501746
DOI: 10.1128/jb.00081-24 -
MSystems Mar 2024Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for...
Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for treatment by identifying microbial and molecular biomarkers. This study investigates the skin microbiome and metabolome of healthy adult subjects and lesion (ADL) and non-lesion (ADNL) of AD patients by 16S rRNA gene sequencing and mass spectrometry, respectively. Samples from AD patients showed alterations in the diversity and composition of the skin microbiome, with ADL skin having the greatest divergence. species, especially , were significantly increased in AD patients. Metabolomic profiles were also different between the groups. Dipeptide derivatives are more abundant in ADL, which may be related to skin inflammation. Co-occurrence network analysis of the microbiome and metabolomics data revealed higher co-occurrence of metabolites and bacteria in healthy ADNL compared to ADL. co-occurred with dipeptide derivatives in ADL, while phytosphingosine-derived compounds showed co-occurrences with commensal bacteria, for example sp., sp., , , sp., sp., , , , and , in healthy and ADNL groups. Therefore, these findings provide valuable insights into how AD affects the human skin metabolome and microbiome.IMPORTANCEThis study provides valuable insight into changes in the skin microbiome and associated metabolomic profiles in an adult population with mild to moderate atopic dermatitis. It also identifies new therapeutic targets that may be useful for developing personalized treatments for individuals with atopic dermatitis based on their unique skin microbiome and metabolic profiles.
Topics: Adult; Humans; Dermatitis, Atopic; Staphylococcus aureus; RNA, Ribosomal, 16S; Microbiota; Metabolome; Bacteria; Dipeptides
PubMed: 38319107
DOI: 10.1128/msystems.01119-23 -
Applied and Environmental Microbiology Jul 2023Metabolic degeneracy describes the phenomenon that cells can use one substrate through different metabolic routes, while metabolic plasticity, refers to the ability of...
Functional Degeneracy in Paracoccus denitrificans Pd1222 Is Coordinated via RamB, Which Links Expression of the Glyoxylate Cycle to Activity of the Ethylmalonyl-CoA Pathway.
Metabolic degeneracy describes the phenomenon that cells can use one substrate through different metabolic routes, while metabolic plasticity, refers to the ability of an organism to dynamically rewire its metabolism in response to changing physiological needs. A prime example for both phenomena is the dynamic switch between two alternative and seemingly degenerate acetyl-CoA assimilation routes in the alphaproteobacterium Paracoccus denitrificans Pd1222: the ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). The EMCP and the GC each tightly control the balance between catabolism and anabolism by shifting flux away from the oxidation of acetyl-CoA in the tricarboxylic acid (TCA) cycle toward biomass formation. However, the simultaneous presence of both the EMCP and GC in P. denitrificans Pd1222 raises the question of how this apparent functional degeneracy is globally coordinated during growth. Here, we show that RamB, a transcription factor of the ScfR family, controls expression of the GC in P. denitrificans Pd1222. Combining genetic, molecular biological and biochemical approaches, we identify the binding motif of RamB and demonstrate that CoA-thioester intermediates of the EMCP directly bind to the protein. Overall, our study shows that the EMCP and the GC are metabolically and genetically linked with each other, demonstrating a thus far undescribed bacterial strategy to achieve metabolic plasticity, in which one seemingly degenerate metabolic pathway directly drives expression of the other. Carbon metabolism provides organisms with energy and building blocks for cellular functions and growth. The tight regulation between degradation and assimilation of carbon substrates is central for optimal growth. Understanding the underlying mechanisms of metabolic control in bacteria is of importance for applications in health (e.g., targeting of metabolic pathways with new antibiotics, development of resistances) and biotechnology (e.g., metabolic engineering, introduction of new-to-nature pathways). In this study, we use the alphaproteobacterium P. denitrificans as model organism to study functional degeneracy, a well-known phenomenon of bacteria to use the same carbon source through two different (competing) metabolic routes. We demonstrate that two seemingly degenerate central carbon metabolic pathways are metabolically and genetically linked with each other, which allows the organism to control the switch between them in a coordinated manner during growth. Our study elucidates the molecular basis of metabolic plasticity in central carbon metabolism, which improves our understanding of how bacterial metabolism is able to partition fluxes between anabolism and catabolism.
Topics: Acetyl Coenzyme A; Paracoccus denitrificans; Bacterial Proteins; Carbon; Glyoxylates
PubMed: 37318336
DOI: 10.1128/aem.00238-23 -
Journal of Environmental Management Feb 2024Insufficient carbon source has become the main limiting factor for efficient nitrogen removal in wastewater treatment. In this study, an intermittently-aerated activated...
Insufficient carbon source has become the main limiting factor for efficient nitrogen removal in wastewater treatment. In this study, an intermittently-aerated activated sludge system with iron-chitosan (Fe-CS) beads addition was proposed for nitrogen removal from low C/N wastewater. By adding Fe-CS beads, partial nitrification-denitrification (PND) process and significant enrichment of Paracoccus (with ability of iron reduction/ammonium oxidation/aerobic denitrification) were observed in the reactor. The accumulation rate of NO-N reached 81.9 %, and the total nitrogen removal efficiency was improved to 93.9 % by shortening the aeration time. The higher activity of ammonium oxidizing bacteria and inhibited activity of nitrite-oxidizing bacteria in Fe-CS assisted system mediated the occurrence of PND. In contrast, the traditional nitrification and denitrification process occurred in the control group. The high-throughput sequencing analysis and metagenomic results confirmed that the addition of Fe-CS induced 77.8 % and 54.9 % enrichment of Paracoccus in sludge and Fe-CS beads, respectively, while almost no enrichment was observed in control group. Furthermore, with the addition of Fe-CS beads, the expression of genes related to outer membrane porin, cytochrome c, and TCA was strengthened, thereby enhancing the electron transport of Fe(Ⅱ) (electron donor) and Fe(Ⅲ) (electron acceptor) with pollutants in the periplasm. This study provides new insights into the direct enrichment of iron-reducing bacteria and its PND performance induced by the Fe-CS bead addition. It therefore offers an appealing strategy for low C/N wastewater treatment.
Topics: Nitrification; Sewage; Denitrification; Chitosan; Iron; Paracoccus; Bioreactors; Bacteria; Ammonium Compounds; Oxidation-Reduction; Nitrogen
PubMed: 38295644
DOI: 10.1016/j.jenvman.2024.120189 -
Journal of Invertebrate Pathology Sep 2023The gut microflora plays an important role in insect development and physiology. The gut bacterial microbiome of the fall armyworm (FAW), Spodoptera frugiperda, in both...
The gut microflora plays an important role in insect development and physiology. The gut bacterial microbiome of the fall armyworm (FAW), Spodoptera frugiperda, in both cornfield and laboratory-reared populations was investigated using a 16S metagenomic approach. The alpha- and beta-diversity of the cornfield FAW populations varied among sampling sites and were higher than those of the laboratory-reared FAW population, indicating that different diets and environments influence the gut bacterial composition. To better understand the interaction between the microbiome and entomopathogenic fungi (EPF), FAWs from organic and conventionally managed corn fields and from the laboratory-reared colony were inoculated with Beauveria bassiana NCHU-153 (Bb-NCHU-153). A longer median lethal time (LT) was observed in the Bb-NCHU-153-infected cornfield FAW population than in the laboratory-reared FAWs. In terms of the microbiome, three Bb-NCHU-153-infected FAW groups showed different gut bacterial compositions compared to noninfected FAW. Further investigation of the cooccurrence network and linear discriminant analysis (LDA) of effect size (LEfSe) revealed that the enriched bacterial genera, such as Enterococcus, Serratia, Achromobacter, and Tsukamurella, in the gut might play the role of opportunistic pathogens after fungal infection; in contrast, some gut bacteria of Methylobacterium, Marinomonas, Paenochrobactrum, Pseudomonas, Acinetobacter, Delftia, Dietzia, Gordonia, Leucobacter, Paracoccus, and Stenotrophomonas might be probiotics against EPF infection. These results indicated that EPF infection can change the gut bacterial composition and lead to a pathobiome in the FAW and that some bacterial species might protect the FAW from EPF infection. These findings could be applied to the design of pathobiome-inducing biocontrol strategies.
Topics: Animals; Spodoptera; Gastrointestinal Microbiome; Zea mays; Beauveria; Larva
PubMed: 37541570
DOI: 10.1016/j.jip.2023.107976 -
Microbiome Oct 2023Shrimp cultured in a biofloc system (BFS) have a lower disease incidence than those farmed in a water exchange system (WES). Although a number of studies have reported...
BACKGROUND
Shrimp cultured in a biofloc system (BFS) have a lower disease incidence than those farmed in a water exchange system (WES). Although a number of studies have reported that the gut bacterial community induced by BFS is highly associated with shrimp disease resistance, the causal relationship remains unknown. Here, the promotive roles of gut bacterial community induced by BFS in pathogenic Vibrio infection resistance and its potential micro-ecological and physiological mechanisms were investigated by gut bacterial consortium transplantation and synthetic community (SynCom) construction.
RESULTS
The BFS induced a more stable and resistant gut bacterial community, and significantly enriched some beneficial bacterial taxa, such as Paracoccus, Ruegeria, Microbacterium, Demequina, and Tenacibaculum. Transplantation of a gut bacterial consortium from BFS shrimp (Enrich) greatly enhanced the stability of the bacterial community and resistance against pathogenic V. parahaemolyticus infection in WES shrimp, while transplantation of a gut bacterial consortium from WES shrimp significantly disrupted the bacterial community and increased pathogen susceptibility in both WES and BFS shrimp. The addition of Enrich in shrimp postlarvae also improved the pathogen resistance through increasing the relative abundances of beneficial bacterial taxa and stability of bacterial community. The corresponding strains of five beneficial bacterial taxa enriched in BFS shrimp were isolated to construct a SynCom. The addition of SynCom could not only suppress disease development, but also improve shrimp growth, boost the digestive and immune activities, and restore health in diseased shrimp. Furthermore, the strains of SynCom well colonized shrimp gut to maintain a high stability of bacterial community.
CONCLUSIONS
Our study reveals an important role for native microbiota in protecting shrimp from bacterial pathogens and provides a micro-ecological regulation strategy towards the development of probiotics to ameliorate aquatic animal diseases. Video Abstract.
Topics: Animals; Vibrio parahaemolyticus; Gastrointestinal Microbiome; Penaeidae; Bacteria; Vibrio Infections; Aquaculture
PubMed: 37858205
DOI: 10.1186/s40168-023-01663-2 -
Frontiers in Microbiology 2024Hydrocarbon pollution is a widespread issue in both groundwater and surface-water systems; however, research on remediation at the interface of these two systems is...
Hydrocarbon pollution is a widespread issue in both groundwater and surface-water systems; however, research on remediation at the interface of these two systems is limited. This interface is the oxic-anoxic boundary, where hydrocarbon pollutant from contaminated groundwaters flows into surface waters and iron mats are formed by microaerophilic iron-oxidizing bacteria. Iron mats are highly chemically adsorptive and host a diverse community of microbes. To elucidate the effect of hydrocarbon exposure on iron mat geochemistry and microbial community structure and function, we sampled iron mats both upstream and downstream from a leaking underground storage tank. Hydrocarbon-exposed iron mats had significantly higher concentrations of oxidized iron and significantly lower dissolved organic carbon and total dissolved phosphate than unexposed iron mats. A strong negative correlation between dissolved phosphate and benzene was observed in the hydrocarbon-exposed iron mats and water samples. There were positive correlations between iron and other hydrocarbons with benzene in the hydrocarbon-exposed iron mats, which was unique from water samples. The hydrocarbon-exposed iron mats represented two types, flocculent and seep, which had significantly different concentrations of iron, hydrocarbons, and phosphate, indicating that iron mat is also an important context in studies of freshwater mats. Using constrained ordination, we found the best predictors for community structure to be dissolved oxygen, pH, and benzene. Alpha diversity and evenness were significantly lower in hydrocarbon-exposed iron mats than unexposed mats. Using 16S rDNA amplicon sequences, we found evidence of three putative nitrate-reducing iron-oxidizing taxa in microaerophile-dominated iron mats (, and ). 16S rDNA amplicons also indicated the presence of taxa that are associated with hydrocarbon degradation. Benzene remediation-associated genes were found using metagenomic analysis both in exposed and unexposed iron mats. Furthermore, the results indicated that season (summer vs. spring) exacerbates the negative effect of hydrocarbon exposure on community diversity and evenness and led to the increased abundance of numerous OTUs. This study represents the first of its kind to attempt to understand how contaminant exposure, specifically hydrocarbons, influences the geochemistry and microbial community of freshwater iron mats and further develops our understanding of hydrocarbon remediation at the land-water interface.
PubMed: 38800754
DOI: 10.3389/fmicb.2024.1388973