Journal: PLoS ONE

Article Title: Self-Organization, Layered Structure, and Aggregation Enhance Persistence of a Synthetic Biofilm Consortium

doi: 10.1371/journal.pone.0016791

Figure Lengend Snippet: ( A ) The synthetic symbiotic consortium. The blue population cannot synthesize diaminopimelate or lysine; when cultured without lysine or diaminopimelate, this population forms only a scant biofilm. The yellow population cannot form biofilms alone but is otherwise healthy. It synthesizes C4HSL, which diffuses freely and activates production of diaminopimelate in the blue population. Yellow cells become bound within the biofilm formed by the blue population and rescue growth. Together, the two populations form viable biofilms that persist. ( B ) The symbiotic consortium functions as designed. The blue population control forms a biofilm which eventually dies (blue bars), and the yellow population accumulates very little biomass (insignificant, not shown). When the yellow and blue populations are inoculated into a flow chamber in a 50/50 mixture, more biomass accumulates than in either control (solid yellow areas, total yellow biomass in the biofilm; solid blue areas, total blue biomass in the biofilm; the sum of blue and yellow areas is the overall total biomass in the biofilm at each time point; all errors are s.d.). All biofilm measurements were derived from images quantified with COMSTAT .

Article Snippet: All image-based measurements were calculated using the COMSTAT biofilm image processing package in Matlab .

Techniques: Cell Culture, Control, Derivative Assay

Journal: PLoS ONE

Article Title: Self-Organization, Layered Structure, and Aggregation Enhance Persistence of a Synthetic Biofilm Consortium

doi: 10.1371/journal.pone.0016791

Figure Lengend Snippet: ( A ) After 80 hours, the blue population remains primarily near the substrate while the yellow population forms clumps attached to the blue population, as shown in this cross-sectional projection taken at 1/3 the total height of the biofilm. ( B ) After 80 hours of growth, the yellow population begins to exhibit a consistently larger biomass median (yellow lines, throughout figure) than the blue population (blue lines, throughout figure), revealing that the yellow population grows further from the substrate while the blue population remains close to the substrate. (The biomass median indicates the average distance from the substrate at which cells of a given population are found.) Gray bars, plotted against the right-hand axis, indicate total biomass accumulation for the entire consortium at each time-point throughout the figure (errors throughout figure are s.d.). ( C ) Maximum total biomass accumulated by the downstream biofilm is double that in the initial biofilm (compare gray bars in [B] and [C]). Additionally, the downstream biofilm assumes the layered structure more quickly: the biomass medians reveal structure after 24 hours of growth. ( D ) When aggregates are disrupted prior to transfer, leaving all else constant, this treated effluent can form biofilms, but they never exhibit the layered structure or growth advantage. ( E ) The layered structure is recovered when the sorted blue-and-yellow aggregate fraction forms downstream biofilms. In fact, the consortium starts with this structure, exhibiting it by 24 hours after inoculation. Further, maximum total biomass accumulation is more than double the highest amount observed in the predecessor (illustrated in [D]), suggesting recovery of the growth advantage. ( F ) The single-cell fraction consists of more than 99% yellow cells, and thus neither the blue population nor the layered structure nor any growth advantage is evident in the downstream biofilm it forms. This biofilm accumulates less biomass than the biofilm formed by the aggregate fraction (compare to grey bars in [E]). ( G ) Here, effluent is taken from the treated biofilms, which are less productive and do not exhibit structure (illustrated in [D]). Although this effluent is left untreated, it forms initially dense, monomorphic, and primarily yellow downstream biofilms that do not exhibit layered structure. These biofilms consistently lose biomass.

Article Snippet: All image-based measurements were calculated using the COMSTAT biofilm image processing package in Matlab .

Techniques:

Journal: Scientific Reports

Article Title: ciaR impacts biofilm formation by regulating an arginine biosynthesis pathway in Streptococcus sanguinis SK36

doi: 10.1038/s41598-017-17383-1

Figure Lengend Snippet: The impact of ciaR mutation on biofilm formation. ( A ) The biofilms of WT, Δ ciaR and Δ ciaR / ciaR were cultured in a 96-well plate in BM media for 24 hours. Biomass was measured by crystal violet staining. ( B ) Biofilms of WT and Δ ciaR cultured in 4-well chambers after being washed with PBS buffer. ( C ) Biofilms grown in 4-well chambers were stained by SYTO9 and propidium iodide. Fluorescence (left) and differential interference microscopy images (middle) were obtained by confocal laser scanning microscopy. Fluorescence images were analyzed by COMSTAT script, and heat maps of biofilm thickness were generated, which showed the distribution of biomass in biofilms (right). ( D ) The fluorescence images were analyzed by COMSTAT. Biofilm biomass, average thickness, propidium iodide signal and roughness coefficient were quantified, respectively. All the data in Fig. 1D were compared with their WT control. *P ≤ 0.05, **P ≤ 0.01, Student’s t- test. Means and standard deviations from triplicate experiments are shown.

Article Snippet: These biofilms were subsequently observed by confocal laser scanning microscopy (CLSM) and quantified using a COMSTAT script in Matlab software .

Techniques: Mutagenesis, Cell Culture, Staining, Fluorescence, Microscopy, Confocal Laser Scanning Microscopy, Generated, Control

Journal: Scientific Reports

Article Title: ciaR impacts biofilm formation by regulating an arginine biosynthesis pathway in Streptococcus sanguinis SK36

doi: 10.1038/s41598-017-17383-1

Figure Lengend Snippet: Biofilm formation of WT and Δ ciaR under flow cell conditions. Strains were marked by different fluorescent reporters and then cultured in a flow cell system. Image in Fig. 5C was obtained by CLSM. Others were recorded by the fluorescence microscopy. Biofilm biomass was quantified by COMSTAT software. ( A ) The biofilms biomass of WT and Δ ciaR in the flow cell system at different time points. ( B ) WT and Δ ciaR were co-cultured in the flow cell channel and biofilm biomass was measured. ( C ) After being co-cultured for 4 days, the structure of biofilm formed by WT – Δ ciaR was examined by CLSM. For each sample in Fig. 5A and B, ten images from fluorescence microscopy were obtained to calculate the means and standard deviations. *P ≤ 0.05, **P ≤ 0.01, Student’s t- test.

Article Snippet: These biofilms were subsequently observed by confocal laser scanning microscopy (CLSM) and quantified using a COMSTAT script in Matlab software .

Techniques: Cell Culture, Fluorescence, Microscopy, Software