Sublethal effects of photoactive engineered nanomaterials on filamentous bacteriophage infection and E. coli gene expression in freshwater
Data files
Dec 22, 2025 version files 107.47 KB
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DLS_Mixture_size.xlsx
11.52 KB
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Gene_expression_data.xlsx
33.50 KB
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NMDS.R
9.96 KB
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Pearson_coefficient.R
906 B
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Phage_infection_data.xlsx
38.01 KB
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README.md
3.68 KB
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Zeta_potential_data.xlsx
9.90 KB
Abstract
Wide application and release of engineered nanomaterials (ENMs) into the environment require an understanding of their potential ecological impacts, particularly under real environmental conditions. Previously, we reported that low doses of photoactive ENMs exert significant sublethal stress on bacterial outer membranes under light in a freshwater medium, potentially increasing bacterial susceptibility to environmental stress and viral infection, and promoting microbial evolution and diversity. However, little is known about how ENMs may affect bacteriophage infection under environmental conditions. In this study, we investigated how two common photoactive ENMs, n-TiO2 and n-Ag, and their mixtures, on the infection of a filamentous coliphage, bacteriophage f1, at environmentally relevant concentrations under freshwater conditions, particularly by affecting cell surface structures (outer membrane and F-pili) and properties (zeta potential), and by altering the gene expression of the host bacteria. The phage infection was evaluated by plate counting using the double-layer agar method. Using RT-qPCR (reverse transcription quantitative polymerase chain reaction), we probed the mechanisms of how ENMs affect filamentous phage infection by measuring the gene expression of F-pili and membrane proteins (TolA and OmpF) on E. coli, relevant to the phage infection process, after being treated with the ENMs or their mixtures under light and dark conditions. We also investigated how ENMs and their mixtures affect the cell surface and the phage-host contact by visual observation from S/TEM micrographs and zeta potential measurements. Overall, our results provide mechanistic insight into the complex interactions among bacteria, bacteriophage, and ENMs under environmentally relevant conditions and further detail their potential ecological risks.
Dataset DOI: 10.5061/dryad.1zcrjdg3r
Description of the data and file structure
Files and variables
File: Pearson_coefficient.R
Description: This file includes coding using R to calculate Pearson's Correlation Coefficient between phage infection (raw data in "Phage_infection_data.xlsx") and outer membrane permeability (raw data will be provided upon requested as it was from a previous study cited in "Related works") with different ENMs treatment.
File: NMDS.R
Description: This file includes coding using R to generate NMDS (Non-metric Multidimensional Scaling) plots of all measurements in the study (phage infection, relative gene expression, and outer membrane permeability) generated by R. The raw data of phage infection can be found in "Phage_infection_data.xlsx", gene expression data can be found in "Phage_infection_data.xlsx", and outer membrane permeability data will be provided upon requested as it was from a previous study cited in "Related works".
File: Gene_expression_data.xlsx
Description: This file documents relative mRNA expression data calculated by "2^(-Delta Delta Ct)" method detailed in the file. The first sheet page lists relative mRNA expression data with individual ENM treatment. The second sheet page lists mRNA expression data with ENM mixtures relative to results with n-Ag exposure. The third sheet page lists mRNA expression data with ENM mixtures relative to results with no ENM exposure. Empty cells (filled with "null") in this file are left empty for formatting purposes and do not indicate missing data. Formatting in Excel files, including pages, merged cells, formulas, and text boxes, is essential for clear presentation and better organization of data.
File: Phage_infection_data.xlsx
Description: This file documents plate counts (sheet page 2-4) of phage infection using the Double-Layer-Agar method and processed phage infection data (sheet page 1). Empty cells (filled with "null") in this file are left empty for formatting purposes and do not indicate missing data. Some cells in the last two columns on sheet page 3 are left empty because they are either the control groups that do not require relative analysis or additional measurements that are already analyzed together with the other groups, and the results are shown in the corresponding groups. Formatting in Excel files, including pages, merged cells, formulas, and text boxes, is essential for clear presentation and better organization of data.
File: Zeta_potential_data.xlsx
Description: This file documents zeta potential measurements of ENMs in freshwater and the processed (average) data. Empty cells (filled with "null") in this file are left empty for formatting purposes and do not indicate missing data. Formatting in Excel files, including merged cells and formulas, is essential for clear presentation and better organization of data.
File: DLS_Mixture_size.xlsx
Description: This file documents aggregate size DLS measurements of ENMs in freshwater and the processed (average) data. Empty cells (filled with "null") in this file are left empty for formatting purposes and do not indicate missing data. Formatting in Excel files, including merged cells and formulas, is essential for clear presentation and better organization of data.
Code/software
Scripts of R ("ANOVA.R" and "NMDS.R") can be processed in R (https://www.r-project.org/).
