Fig 1.
Metagenome sequence reads (in RPM) of T6SS core genes from 3.0 and 0.2 μm water size fractions by sample date.
Samples span seasons and broad ranges of environmental conditions such as high and low chlorophyll level, toxic phytoplankton bloom, and nutrient levels. Twenty-one bacterial genera from several classes known to harbor five core T6SS genes were confirmed and are present at varying rpm across samples.
Fig 2.
Heatmap profile showing the abundance of various T6SS-bearing bacterial genera from 2014–2015 samples.
(A) Particle-attached (3.0 μm) filter size fraction. (B) Free-living (0.2 μm) filter size fraction. OTU abundance relative to per-sample geometric mean is based on clr transformed values of sequence reads belonging to each bacterial genus across duplicate or triplicate samples.
Table 1.
Differential abundance of T6SS-bearing bacteria between filter sizes.
Fig 3.
Heatmap of the global distribution of T6SS hcp and vgrg gene sequences.
Reads per million (rpm) mapped reads taken from TARA Oceans metagenome dataset. Hotspots of T6SS abundance appear in the South Atlantic and Indian Ocean gyres, known areas with extremely low biomass and low nutrient concentration. Reads matching known hcp and vgrg gene sequences were acquired using BLAST+ 2.9.0. Map was built using data from R Natural Earth. Code is available at https://github.com/M-Kempnich/Presence-and-abundance-of-T6SS.
Fig 4.
Redundancy analysis (RDA) demonstrating the association between abundance of T6SS-bearing bacteria and environmental characteristics from SC Wharf time series data.
(A) Relationships of particle- attached (3.0 μm water fraction) community and (B) free-living (0.22 μm water fraction) community with physico-chemical-biological parameters. Considered environmental factors were toxic Pseudo-nitzschia (Toxic Pn, cells/mL, nitrate (NO3, μM), ammonia (NH3, μM), phosphate (PO4, μM), silicate (Si, μM) concentrations, chlorophyll concentration (chl, mg/m3), and water temperature (Temp, ˚C)). Arrow length represents strength of the relationship of each environmental parameter to the composition of T6SS-bearing bacteria. Colored circles represent bacterial genera with T6SS.
Fig 5.
RDA analysis showing the association of T6SS reads (in rpm) and environmental variables from the TARA Oceans metagenome samples.
Colored circles represent T6SS vgrG and hcp gene reads from eight bacterial genera. Six environmental variables that contributed to the variation of the global T6SS reads were plotted and these include number of autotroph cells (cells/ml), nitrite-nitrate (NO2+NO3, μM), oxygen concentration (O2, μmol/kg), bacterial functional richness (Tax. Rich.) and water sample depth (Depth, meters). Arrow length represents strength of the relationship of each environmental parameter to the composition of T6SS-bearing bacteria. * indicates significant environmental variable (p < 0.005).