DOI: 10.5061/dryad.1zcrjdg3r
title: Sublethal effects of photoactive engineered nanomaterials on filamentous bacteriophage infection and <em>E. coli</em> gene expression in freshwater

description: 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.
description: # **Sublethal effects of photoactive engineered nanomaterials on
 filamentous bacteriophage infection and** ***E. coli*** **gene expression
 in freshwater** Dataset DOI:
 [10.5061/dryad.1zcrjdg3r](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/](https://www.r-project.org/)).