-
Chemosphere Sep 2023The potential effects of engineered metal oxide nanoparticles (MONPs) on bacterial nitrogen fixation are of great concern. Herein, the impact and mechanism of the...
The potential effects of engineered metal oxide nanoparticles (MONPs) on bacterial nitrogen fixation are of great concern. Herein, the impact and mechanism of the increasing-used MONPs, including TiO, AlO, and ZnO nanoparticles (TiONP, AlONP, and ZnONP, respectively), on nitrogenase activity was studied at the concentrations ranging from 0 to 10 mg L using associative rhizosphere nitrogen-fixing bacteria Pseudomonas stutzeri A1501. Nitrogen fixation capacity was inhibited by MONPs in an increasing degree of TiONP < AlONP < ZnONP. Realtime qPCR analysis showed that the expressions of nitrogenase synthesis-related genes, including nifA and nifH, were inhibited significantly when MONPs were added. MONPs could cause the explosion of intracellular ROS, and ROS not only changed the permeability of the membrane but also inhibited the expression of nifA and biofilm formation on the root surface. The repressed nifA gene could inhibit transcriptional activation of nif-specific genes, and ROS reduced the biofilm formation on the root surface which had a negative effect on resisting environmental stress. This study demonstrated that MONPs, including TiONP, AlONP, and ZnONP, inhibited bacterial biofilm formation and nitrogen fixation in the rice rhizosphere, which might have a negative effect on the nitrogen cycle in bacteria-rice system.
Topics: Nitrogen Fixation; Pseudomonas stutzeri; Reactive Oxygen Species; Nitrogen-Fixing Bacteria; Rhizosphere; Oxides; Nitrogenase; Nanoparticles; Bacterial Proteins; Nitrogen
PubMed: 37327828
DOI: 10.1016/j.chemosphere.2023.139223 -
Applied and Environmental Microbiology Aug 2023Several microbial taxa have been associated with food processing facilities, and they might resist by attaching on tools and equipment even after sanitation procedures,...
Several microbial taxa have been associated with food processing facilities, and they might resist by attaching on tools and equipment even after sanitation procedures, producing biofilms that adhere to the surfaces and might embed other microorganisms, including spoilers and pathogens. There is increasing evidence that these communities can be transferred to the final product. To explore the microbial contamination routes in a facility producing ice creams, we collected foods and environmental swabs from industrial surfaces of equipment and tools and performed taxonomic and functional analyses of the microbial DNA extracted from the environmental samples. Our results suggest that complex communities dominated by psychrotrophic bacteria (e.g., Pseudomonas and Acinetobacter spp.) inhabit the food processing environment, and we demonstrate that these communities might be transferred from the surfaces to the products. Functional analysis performed on environmental samples highlighted the presence of several genes linked to antimicrobial resistance and adherence on abiotic surfaces; such genes were more abundant on food contact (FC) than on other surfaces. Metagenome-assembled genomes (MAGs) of Pseudomonas stutzeri showed genes linked with biofilm formation and motility, which are surely linked to colonizing capabilities in the processing lines. The study highlights clear potential advantages of applying microbiome mapping in the food industry for source tracking of microbial contamination and for planning appropriate sanitization strategies. Several microbial species might permanently establish in food processing facilities, thus contributing to food loss. In fact, food contact surfaces might transfer microorganisms to intermediates and products, potentially representing a hazard to human health. In this work, we provide evidence of the existence of complex microbial communities overcoming sanitation in an ice cream-producing facility. These communities harbored several genes that could potentially lead to attachment to surfaces and antimicrobial resistance. Also, prediction of routes of contamination showed that several potential spoilage taxa might end up in the final product. Importantly, in this work, we show that mapping the environmental microbiome is a high-resolution technique that might help food business operators ensure food quality and safety through detection of potentially hazardous microorganisms.
Topics: Humans; Ice Cream; Virulence; Bacteria; Food Handling; Biofilms; Anti-Infective Agents; Food Microbiology
PubMed: 37432121
DOI: 10.1128/aem.00765-23 -
Journal of Hazardous Materials Sep 2023In the study, we investigated the different compositions of biochar-derived dissolved organic matter (BDOM) that play a key role in the biodegradation of...
In the study, we investigated the different compositions of biochar-derived dissolved organic matter (BDOM) that play a key role in the biodegradation of sulfamethoxazole (SMX) and chloramphenicol (CAP) by P. stutzeri and S. putrefaciens, and found that aliphatic compounds in Group 4, fulvic acid like in Region III, and solid microbial byproduct like in region IV are key common factors. The growth and antibiotic degradation efficiency of P. stutzeri and S. putrefaciens are positively correlated with the content of Group 4 and Region III, and negatively correlated with Region IV. This is consistent with the optimal biodegradation results of BDOM700 with the highest content of Group 4 and Region III. Additionally, the degradation efficiency of SMX by Pseudomonas stutzeri is negatively correlated with the percentage of polycyclic aromatics in Group 1, but not with CAP. Similarly, the percentage of fatty acids in S. putrefaciens was positively correlated with Group 1, whereas P. stutzeri did not. This indicates that some components of BDOM have varying effects on different bacteria or types of antibiotics. This study provides new insights into enhancing antibiotic biodegradation by controlling the composition of BDOM.
Topics: Sulfamethoxazole; Chloramphenicol; Biodegradation, Environmental; Anti-Bacterial Agents
PubMed: 37423136
DOI: 10.1016/j.jhazmat.2023.131979 -
Microorganisms Jun 2024Enhanced denitrification has been reported under weak electric fields. However, it is difficult to investigate the mechanism of enhanced denitrification due to the...
Enhanced denitrification has been reported under weak electric fields. However, it is difficult to investigate the mechanism of enhanced denitrification due to the complex interspecific interactions of mixed-culture systems. In this study, , capable of denitrification under anaerobic conditions, was selected for treating low COD/N (2.0, ratio between concentration of chemical oxygen demand and NO-N) artificial wastewater under constant external voltages of 0.2, 0.4, and 0.6 V. The results revealed that exhibited the highest efficiency in nitrate reduction at 0.2 V. Moreover, the maximum nitrate removal rate was 15.96 mg/(L·h) among the closed-circuit groups, 19.39% higher than that under the open-circuit group. Additionally, a notable reduction in nitrite accumulation was observed under weak electric fields. Enzyme activity analysis showed that the nitrate reductase activities were significantly increased among the closed-circuit groups, while nitrite reductase activities were inhibited. Transcriptomic analysis indicated that amino acid metabolism, carbohydrate metabolism, and energy metabolism were increased, enhancing the resistance of to environmental stress and the efficiency of carbon source utilization for denitrification. The current study examined the impacts of weak electric fields on enzyme activities and microbial metabolic pathways and offers valuable insights into the mechanism by which denitrification is enhanced by weak electric fields.
PubMed: 38930600
DOI: 10.3390/microorganisms12061218 -
Frontiers in Medicine 2023Although pre/pro/postbiotics have become more prevalent in dermatologic and cosmetic fields, the mode of action when topically applied is largely unknown. A multi-omic...
INTRODUCTION
Although pre/pro/postbiotics have become more prevalent in dermatologic and cosmetic fields, the mode of action when topically applied is largely unknown. A multi-omic approach was applied to decipher the impact of the skincare products with pre/postbiotics on skin microbiome and metabolome.
METHODS
Subjects with dry skin applied a body wash and body lotion with or without pre/postbiotics for 6 weeks. Skin hydration was measured at baseline, 3 and 6 weeks. Skin swabs were collected for 16S rRNA gene sequencing, metagenomics and metabolomics analysis.
RESULTS
Skin hydration significantly increased in both groups. The prebiotic group significantly reduced opportunistic pathogens, e.g., and , and increased the commensals, e.g., , . Bacterial sugar degradation pathways were enriched in the prebiotic group, while fatty acid biosynthesis pathways were reduced in control. The changes on skin metabolome profiles by the products were more prominent. The prebiotic group performed greater modulation on many clinically-relevant metabolites compared to control. Correlation analysis showed and positively correlated with skin hydration, and negatively correlated with the metabolites that are positively associated with skin hydration improvement.
CONCLUSION
This holistic study supported a hypothesis that the pre/postbiotics increased skin hydration through the modulation of skin microbiome, metabolic pathways and metabolome.
PubMed: 37534320
DOI: 10.3389/fmed.2023.1165980 -
Biofilm Dec 2023Biofilms are complex microbial communities embedded in extracellular matrix. Pathogens within the biofilm become more resistant to the antibiotics than planktonic...
Biofilms are complex microbial communities embedded in extracellular matrix. Pathogens within the biofilm become more resistant to the antibiotics than planktonic counterparts. Novel strategies are required to encounter biofilms. Exopolysaccharides are one of the major components of biofilm matrix and play a vital role in biofilm architecture. In previous studies, a glycosyl hydrolase, PslG, from was found to be able to inhibit biofilm formation by disintegrating exopolysaccharide in biofilms. Here, we investigate the potential spectrum of PslG homologous protein with anti-biofilm activity. One glycosyl hydrolase from , PslG, exhibits anti-biofilm activities and the key catalytic residues of PslG are conserved with those of PslG. PslG at concentrations as low as 50 nM efficiently inhibits the biofilm formation of and disassemble its preformed biofilm. Furthermore, PslG exhibits anti-biofilm activity on a series of , including and pv. . PslG stays active under various temperatures. Our findings suggest that glycosyl hydrolase PslG has potential to be a broad spectrum inhibitor on biofilm formation of a wide range of .
PubMed: 37928620
DOI: 10.1016/j.bioflm.2023.100155 -
MSphere Jun 2024The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated...
UNLABELLED
The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated diazotrophs; however, its target RNAs and the mechanisms underlying nitrogen fixation remain largely unknown. Here, we used enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing to identify hundreds of Hfq-binding RNAs probably involved in nitrogen fixation, carbon substrate utilization, biofilm formation, and other functions. Collectively, these processes endow strain A1501 with the requisite capabilities to thrive in the highly competitive rhizosphere. Our findings revealed a previously uncharted landscape of Hfq target genes. Notable among these is , encoding an isomerase necessary for nitrogenase reductase solubility; , encoding an ammonium transporter; , encoding a carbohydrate porin; and , encoding a chemotaxis protein. Furthermore, we identified more than 100 genes of unknown function, which expands the potential direct regulatory targets of Hfq in diazotrophs. Our data showed that Hfq directly interacts with the mRNA of regulatory proteins (RsmA, AlgU, and NifA), regulatory ncRNA RsmY, and other potential targets, thus revealing the mechanistic links in nitrogen fixation and other metabolic pathways.
IMPORTANCE
Numerous experimental approaches often face challenges in distinguishing between direct and indirect effects of Hfq-mediated regulation. New technologies based on high-throughput sequencing are increasingly providing insight into the global regulation of Hfq in gene expression. Here, enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing was employed to identify the Hfq-binding sites and potential targets in the root-associated A1501 and identify hundreds of novel Hfq-binding RNAs that are predicted to be involved in metabolism, environmental adaptation, and nitrogen fixation. In particular, we have shown Hfq interactions with various regulatory proteins' mRNA and their potential targets at the posttranscriptional level. This study not only enhances our understanding of Hfq regulation but, importantly, also provides a framework for addressing integrated regulatory network underlying root-associated nitrogen fixation.
Topics: Pseudomonas stutzeri; Host Factor 1 Protein; Nitrogen Fixation; Gene Expression Regulation, Bacterial; Plant Roots; RNA, Bacterial; Gene Expression Profiling; Gene Regulatory Networks; Bacterial Proteins; High-Throughput Nucleotide Sequencing; Transcriptome; Rhizosphere
PubMed: 38747590
DOI: 10.1128/msphere.00762-23 -
IScience Oct 2023Emergence of new SARS-CoV-2 VOCs jeopardize global vaccine and herd immunity safeguards. VOCs interactions with host microbiota might affect clinical course and outcome....
Emergence of new SARS-CoV-2 VOCs jeopardize global vaccine and herd immunity safeguards. VOCs interactions with host microbiota might affect clinical course and outcome. This longitudinal investigation involving Pre-VOC and VOCs (Delta & Omicron) holo-transcriptome based nasopharyngeal microbiome at taxonomic levels followed by metabolic pathway analysis and integrative host-microbiome interaction. VOCs showed enrichment of with dominance of . Interestingly with superiority of and , were highlights of Delta VOC rather than Omicron. Common species comprising the core microbiome across all variants, reiterated the significance of in Delta, and its association with metabolic pathways enhancing inflammation in patients. Microbe-host gene correlation network revealed , , and modulating immune pathways, which might augment clinical severity in Delta. Importantly, opportunistic species of , , , and were abundant in Delta-mortality. The study establishes a functional association between elevated nasal pathobionts and dysregulated host response, particularly for Delta.
PubMed: 37701571
DOI: 10.1016/j.isci.2023.107779 -
Enrichment of native plastic-associated biofilm communities to enhance polyester degrading activity.Environmental Microbiology Dec 2023Plastic pollution is an increasing worldwide problem urgently requiring a solution. While recycling rates are increasing globally, only 9% of all plastic waste has been...
Plastic pollution is an increasing worldwide problem urgently requiring a solution. While recycling rates are increasing globally, only 9% of all plastic waste has been recycled, and with the cost and limited downstream uses of recycled plastic, an alternative is needed. Here, we found that expanded polystyrene (EPS) promoted high levels of bacterial biofilm formation and sought out environmental EPS waste to characterize these native communities. We demonstrated that the EPS attached communities had limited plastic degrading activity. We then performed a long-term enrichment experiment where we placed a robust selection pressure on these communities by limiting carbon availability such that the waste plastic was the only carbon source. Seven of the resulting enriched bacterial communities had increased plastic degrading activity compared to the starting bacterial communities. Pseudomonas stutzeri was predominantly identified in six of the seven enriched communities as the strongest polyester degrader. Sequencing of one isolate of P. stutzeri revealed two putative polyesterases and one putative MHETase. This indicates that waste plastic-associated biofilms are a source for bacteria that have plastic-degrading potential, and that this potential can be unlocked through selective pressure and further in vitro enrichment experiments, resulting in biodegradative communities that are better than nature.
Topics: Polyesters; Bacteria; Polystyrenes; Biofilms; Carbon
PubMed: 37515381
DOI: 10.1111/1462-2920.16466 -
Contact Lens & Anterior Eye : the... Dec 2023This study aimed to investigate the bacterial contamination of multi-use tear drops, gels, and ointments that patients use at home.
PURPOSE
This study aimed to investigate the bacterial contamination of multi-use tear drops, gels, and ointments that patients use at home.
METHOD
A total of 271 multi-use containers used by 168 patients were examined. Conjunctival culture samples were obtained from patients who used tear drops, gels, and ointments that were found to be contaminated.
RESULTS
Bacterial contamination was detected in 33 (12.2 %) out of the 271 containers. The contamination rate was 7.9 % in tear drops, 11.7 % in gels, and 32 % in ointments. A statistically significant difference was found between the drops, gels, and ointment groups (P = 0.04). Bacterial contamination was detected in 25 (18.9 %) out of 132 collapsible tubes and 8 (5.8 %) out of 139 plastic bottles (P = 0.01). Important bacteria, including Pseudomonas stutzeri, Pseudomonas aeruginosa, Bacillus licheniformis, Paenibacillus pabuli, Proteus mirabilis, Pantoea agglomerans, Morganella morganii, Serratia marcescens, and Serratia liquefaciens, were detected. Mucorales spp. fungus was seen in a gel. Staphylococcus epidermidis, methicillin-resistant Staphylococcus aureus, and M. morganii were found in the conjunctival microbiota of three patients.
CONCLUSION
The overall contamination rate of ocular lubricants was low (12.2%); however, a significant difference was found between the drops, gels, and ointments. The contamination rate was higher in gels and ointments than that in drops. The contamination rate was found to be increased in the collapsible tube. The use of ocular lubricants is safe; however, patients must be cautious when using multi-use tear drops, gels, and ointments to avoid contamination. Whenever possible, bottles should be preferred instead of collapsible tubes.
Topics: Humans; Ointments; Methicillin-Resistant Staphylococcus aureus; Bacteria; Gels; Lubricants
PubMed: 37806847
DOI: 10.1016/j.clae.2023.102064