Notes

Fig S3A,B and D are images.

Setup packages and plotting for the notebook:

# Check packages
source("../../../tools/package_setup.R")

# Load packages
library(tidyverse)
library(cowplot)
library(kableExtra)
library(broom)
library(modelr)

# Code display options
knitr::opts_chunk$set(tidy.opts=list(width.cutoff=60),tidy=FALSE, echo = TRUE, message=FALSE, warning=FALSE, fig.align="center", fig.retina = 2)

# Load plotting tools
source("../../../tools/plotting_tools.R")


#Modify the plot theme
theme_set(theme_notebook())

Fig. S3C - DNase colony TOTO-1 measurement

Let’s read in the data and make the plot:

pRdata <- read_csv('../../../../data/Spectroscopy/TOTO_DAPI_extracts.csv') %>% rename(TOTO=`1uM_TOTO_avg_(535nm)`,DAPI=`1uM_DAPI_avg_(445nm)`) %>%  
  gather(key='dye',value='fluor',TOTO, DAPI) %>% 
  separate(X1,sep=' ',c('added','Treatment','Replicate')) %>% 
  mutate(id=paste(added,Treatment,dye,sep = " ")) %>% 
  group_by(id) %>% 
  mutate(mean = ifelse(Replicate=='1',mean(fluor),NA))

# Plot layout
toto_plot <- ggplot(pRdata %>% filter(dye=='TOTO') %>% filter(id!="with ctDNA TOTO"),aes(x=id,y=fluor))+
  geom_col(aes(y=mean), fill = "light gray") +
  geom_jitter(height=0,width=0.1,shape =21, size = 1)

# Plot styling 
toto_plot_styled <- toto_plot +
  labs(x = NULL, y = 'TOTO-1 Fluorescence (A.U.)') + 
  scale_x_discrete(breaks = c('no ctDNA TOTO','no DNase TOTO','with DNase TOTO'), 
                   labels=c("-","+ buffer", "+ buffer\n+ DNase"))
    
toto_plot_styled

Fig. S3E - Colony biofilm eDNA quantification

Let’s read in the raw well data and the metadata:

df_biofilms <- read_csv("../../../../data/Spectroscopy/2019_11_22_std_wt_dphz_postCTdna.csv") %>%  gather(key = "well", value = "FluorInt", -wavelength)

df_meta <- read_csv("../../../../data/Spectroscopy/2019_11_22_well_metadata.csv")

df_toto <- left_join(df_biofilms, df_meta, by = c('well')) %>% filter(wavelength == 535)

df_toto %>% kable() %>% kable_styling(bootstrap_options = 'condensed') %>%
    scroll_box(width = "100%", height = "400px")

wavelength	well	FluorInt	strain	toto_added	ctDNA_added	well_std_conc	bio_rep	tech_rep
535	A1	37448	std	TRUE	TRUE	50.0000000	1	1
535	A2	36204	std	TRUE	TRUE	25.0000000	1	1
535	A3	35944	std	TRUE	TRUE	12.5000000	1	1
535	A4	32623	std	TRUE	TRUE	6.2500000	1	1
535	A5	23778	std	TRUE	TRUE	3.1250000	1	1
535	A6	15091	std	TRUE	TRUE	1.5625000	1	1
535	A7	9899	std	TRUE	TRUE	0.7812500	1	1
535	A8	7085	std	TRUE	TRUE	0.3906250	1	1
535	A9	6164	std	TRUE	TRUE	0.1953125	1	1
535	A10	3926	std	TRUE	TRUE	0.0976562	1	1
535	A11	4527	std	TRUE	TRUE	0.0488281	1	1
535	A12	3075	std	TRUE	TRUE	0.0244141	1	1
535	B1	12139	WT	TRUE	TRUE	NA	1	1
535	B2	13446	WT	TRUE	TRUE	NA	2	1
535	B3	11074	WT	TRUE	TRUE	NA	3	1
535	B4	11370	WT	TRUE	TRUE	NA	4	1
535	B5	12068	WT	TRUE	TRUE	NA	5	1
535	B6	11855	WT	TRUE	TRUE	NA	6	1
535	B7	10123	WT	TRUE	FALSE	NA	1	2
535	B8	11827	WT	TRUE	FALSE	NA	2	2
535	B9	9761	WT	TRUE	FALSE	NA	3	2
535	B10	10182	WT	TRUE	FALSE	NA	4	2
535	B11	9634	WT	TRUE	FALSE	NA	5	2
535	B12	11566	WT	TRUE	FALSE	NA	6	2
535	C1	10915	WT	TRUE	FALSE	NA	1	3
535	C2	10894	WT	TRUE	FALSE	NA	2	3
535	C3	9651	WT	TRUE	FALSE	NA	3	3
535	C4	10147	WT	TRUE	FALSE	NA	4	3
535	C5	11910	WT	TRUE	FALSE	NA	5	3
535	C6	12036	WT	TRUE	FALSE	NA	6	3
535	C7	130	WT	FALSE	FALSE	NA	1	4
535	C8	190	WT	FALSE	FALSE	NA	2	4
535	C9	119	WT	FALSE	FALSE	NA	3	4
535	C10	124	WT	FALSE	FALSE	NA	4	4
535	C11	144	WT	FALSE	FALSE	NA	5	4
535	C12	138	WT	FALSE	FALSE	NA	6	4
535	E1	23490	dPHZ	TRUE	TRUE	NA	1	1
535	E2	22622	dPHZ	TRUE	TRUE	NA	2	1
535	E3	24901	dPHZ	TRUE	TRUE	NA	3	1
535	E4	14964	dPHZ	TRUE	TRUE	NA	4	1
535	E5	19109	dPHZ	TRUE	TRUE	NA	5	1
535	E6	14650	dPHZ	TRUE	TRUE	NA	6	1
535	F1	22498	dPHZ	TRUE	FALSE	NA	1	2
535	F2	13008	dPHZ	TRUE	FALSE	NA	2	2
535	F3	15141	dPHZ	TRUE	FALSE	NA	3	2
535	F4	18463	dPHZ	TRUE	FALSE	NA	4	2
535	F5	14572	dPHZ	TRUE	FALSE	NA	5	2
535	F6	17939	dPHZ	TRUE	FALSE	NA	6	2
535	G1	25159	dPHZ	TRUE	FALSE	NA	1	3
535	G2	12442	dPHZ	TRUE	FALSE	NA	2	3
535	G3	14663	dPHZ	TRUE	FALSE	NA	3	3
535	G4	15324	dPHZ	TRUE	FALSE	NA	4	3
535	G5	13968	dPHZ	TRUE	FALSE	NA	5	3
535	G6	16661	dPHZ	TRUE	FALSE	NA	6	3
535	H1	235	dPHZ	FALSE	FALSE	NA	1	4
535	H2	164	dPHZ	FALSE	FALSE	NA	2	4
535	H3	500	dPHZ	FALSE	FALSE	NA	3	4
535	H4	191	dPHZ	FALSE	FALSE	NA	4	4
535	H5	208	dPHZ	FALSE	FALSE	NA	5	4
535	H6	221	dPHZ	FALSE	FALSE	NA	6	4

Now let’s make the plot:

bg_means <- df_toto %>% filter(strain != 'std' & tech_rep == 4) %>% group_by(strain) %>% summarise(mean = mean(FluorInt))

plot_eDNA <- ggplot(df_toto %>% filter(strain != 'std') %>% mutate(facet_labels = ifelse(strain =='dPHZ', paste0('\u0394','phz'), strain)), 
       aes(x = factor(tech_rep), y = FluorInt)) + 
  geom_line(data = . %>% filter(tech_rep<4), aes(group = bio_rep), color = 'light gray')+
  geom_hline(data = bg_means, aes(yintercept = mean), linetype = 2, color = 'light gray') +
  geom_point(data = . %>% filter(tech_rep<4), aes(fill = factor(ctDNA_added)), shape = 21) + 
  geom_jitter(data = . %>% filter(tech_rep==4), aes(x = 2), width = 1, shape = 21, color = 'light gray')+
  facet_wrap(~facet_labels, scales = 'free') + ylim(0, 30000) + guides(fill = F)

# Plot styling

plot_eDNA_styled <- plot_eDNA + 
  labs(x = 'Technical replicates', y = 'TOTO-1 Fluorescence (A.U.)')

plot_eDNA_styled

Create Figure

theme_set(theme_figure())

fig_s3 <- plot_grid( toto_plot_styled,plot_eDNA_styled, align = 'hv', axis = 'tblr', ncol = 2, rel_widths = c(1,2), scale = 0.95, labels = c('C','E'), label_size = 12)

fig_s3

save_plot("../../../../figures/supplement/phz2019_Fig_S3.pdf", fig_s3, base_width = 7, base_height = 2)

sessionInfo()

## R version 3.5.3 (2019-03-11)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS  10.15.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] lubridate_1.7.4   hms_0.5.3         modelr_0.1.5     
##  [4] broom_0.5.2       kableExtra_1.1.0  cowplot_0.9.4    
##  [7] viridis_0.5.1     viridisLite_0.3.0 knitr_1.23       
## [10] forcats_0.4.0     stringr_1.4.0     dplyr_0.8.3      
## [13] purrr_0.3.3       readr_1.3.1       tidyr_1.0.0      
## [16] tibble_2.1.3      ggplot2_3.3.0     tidyverse_1.3.0  
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_0.2.5 xfun_0.7         haven_2.2.0      lattice_0.20-38 
##  [5] colorspace_1.4-1 vctrs_0.3.1      generics_0.0.2   htmltools_0.4.0 
##  [9] yaml_2.2.0       rlang_0.4.6      pillar_1.4.2     glue_1.3.1      
## [13] withr_2.1.2      DBI_1.0.0        dbplyr_1.4.2     readxl_1.3.1    
## [17] lifecycle_0.1.0  munsell_0.5.0    gtable_0.3.0     cellranger_1.1.0
## [21] rvest_0.3.5      evaluate_0.14    labeling_0.3     highr_0.8       
## [25] Rcpp_1.0.2       scales_1.0.0     backports_1.1.4  webshot_0.5.1   
## [29] jsonlite_1.6     fs_1.3.1         gridExtra_2.3    digest_0.6.21   
## [33] stringi_1.4.3    grid_3.5.3       cli_1.1.0        tools_3.5.3     
## [37] magrittr_1.5     crayon_1.3.4     pkgconfig_2.0.3  ellipsis_0.3.0  
## [41] xml2_1.2.2       reprex_0.3.0     assertthat_0.2.1 rmarkdown_1.13  
## [45] httr_1.4.1       rstudioapi_0.10  R6_2.4.0         nlme_3.1-137    
## [49] compiler_3.5.3

Figure S3

Extracellular DNA promotes efficient extracellular electron transfer by pyocyanin in Pseudomonas aeruginosa biofilms.

Scott H. Saunders, Edmund C.M. Tse, Matthew D. Yates, Fernanda Jiménez Otero, Scott A. Trammell, Eric D.A. Stemp, Jacqueline K. Barton, Leonard M. Tender and Dianne K. Newman

Notes

Fig. S3C - DNase colony TOTO-1 measurement

Fig. S3E - Colony biofilm eDNA quantification

Create Figure