diff --git a/.gitattributes b/.gitattributes index 7cc7aff8c361697485349db9c0baf488d86cd39f..23b3b4ce418bd15fb5c389f48c5bd3e7a9c5956f 100644 --- a/.gitattributes +++ b/.gitattributes @@ -2,3 +2,5 @@ /_publication/Getzke[[:space:]]et[[:space:]]al.[[:space:]]-[[:space:]]2023[[:space:]]-[[:space:]]Cofunctioning[[:space:]]of[[:space:]]bacterial[[:space:]]exometabolites[[:space:]]drives[[:space:]]r.pdf filter=lfs diff=lfs merge=lfs -text _publication/pnas.2221508120.sapp.pdf filter=lfs diff=lfs merge=lfs -text _publication/dataverse_files/Table[[:space:]]S2.xlsx filter=lfs diff=lfs merge=lfs -text +assays/Screen[[:space:]]for[[:space:]]antagonistic[[:space:]]interbacterial[[:space:]]interactions/dataset/Table[[:space:]]S2.xlsx filter=lfs diff=lfs merge=lfs -text +assays/Screen[[:space:]]for[[:space:]]antagonistic[[:space:]]interbacterial[[:space:]]interactions/dataset/pnas.2221508120fig01.jpg filter=lfs diff=lfs merge=lfs -text diff --git a/assays/Screen for antagonistic interbacterial interactions/README.md b/assays/Screen for antagonistic interbacterial interactions/README.md new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/Screen for antagonistic interbacterial interactions/dataset/.gitkeep b/assays/Screen for antagonistic interbacterial interactions/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/Screen for antagonistic interbacterial interactions/dataset/Table S2.xlsx b/assays/Screen for antagonistic interbacterial interactions/dataset/Table S2.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..3efd1aa456ec24ff7e3c79fff6e7982cb2cc3f89 --- /dev/null +++ b/assays/Screen for antagonistic interbacterial interactions/dataset/Table S2.xlsx @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c069c9709aa2030dcebe88d4341730a998802c92b0d05874b6c0c8729fb9d3c0 +size 4062801 diff --git a/assays/Screen for antagonistic interbacterial interactions/dataset/pnas.2221508120fig01.jpg b/assays/Screen for antagonistic interbacterial interactions/dataset/pnas.2221508120fig01.jpg new file mode 100644 index 0000000000000000000000000000000000000000..492e876470ff2a2269bbcd09cecfbbeb5ac0adbd --- /dev/null +++ b/assays/Screen for antagonistic interbacterial interactions/dataset/pnas.2221508120fig01.jpg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:dc6ad441e957998c488c858cc7b695edad1da236e9ab0b6b5bca382ed20fb5f5 +size 2822141 diff --git a/assays/Screen for antagonistic interbacterial interactions/isa.assay.xlsx b/assays/Screen for antagonistic interbacterial interactions/isa.assay.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..d640390bbbb0cae512737de896b0324818c265e0 Binary files /dev/null and b/assays/Screen for antagonistic interbacterial interactions/isa.assay.xlsx differ diff --git a/assays/Screen for antagonistic interbacterial interactions/protocols/.gitkeep b/assays/Screen for antagonistic interbacterial interactions/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/Screen for antagonistic interbacterial interactions/protocols/AntagonisticInterbacterialInteractions.md b/assays/Screen for antagonistic interbacterial interactions/protocols/AntagonisticInterbacterialInteractions.md new file mode 100644 index 0000000000000000000000000000000000000000..22b90fdf1c48c45bfaa252f724eb97438db9a6bb --- /dev/null +++ b/assays/Screen for antagonistic interbacterial interactions/protocols/AntagonisticInterbacterialInteractions.md @@ -0,0 +1,3 @@ +## Screen for antagonistic interbacterial interactions + +For the initial mBA experiment (**Fig. 1**), bacterial strains were cultured for seven days in 25% TSB (7.5 g/l Tryptic Soy Broth, Sigma-Aldrich). Briefly, 100 μl of a bacterial solution were resuspended in 50 ml cooled (~38 oC), but still molten, 25% TSA (15 g/l Bacto-Agar, Duchefa Biochemie) and poured into a square petri dish (120x120 mm). After medium solidification, 24 bacterial isolates were spotted on top of the medium using a multi-stamp replicator. The replicator was sterilized by dipping in 70% EtOH (v/v) followed by flaming and cooling. The screen comprising 39,204 binary interactions was conducted once and validated by randomly re-screening 7,470 interaction pairs as described above. All bacterial strains that showed antagonistic activity were rescreened two more times. For the *Ralstonia* inhibition screen, *R. solanacearum* GMI1000 was pre-cultured for two days in CPG medium (1% peptone, 0.5% glucose and 0.1% casamino acids; pH7.0). Before spotting the bacterial cultures, each CPG agar plate (1% Peptone, 0.5% D-glucose, 0.1% casamino acids and 1.5% agar; pH 7.0) was overlaid with 5 ml of *R. solanacearum* suspension (50 μl of pre-cultured *R. solanacearum* in pure sterile water). Excess *R. solanacearum* suspension was removed and the plates were briefly dried, then 5 μl of the bacterial culture were spotted onto the *R. solanacearum*-overlaid plates. All isolates were tested three times. For all subsequent halo assays, strains were cultivated in 50% TSB until turbidity, stored at 4 °C and diluted 1:10 in 50% TSB one day before the experiment. Bacterial cultures were pelleted at 4,000 rpm for 15 min. The resulting bacterial pellets were subsequently washed 3 times and resuspended in 1 ml 10 mM MgCl2. OD600 were measured and set depending on the strain. One hundred microliters bacterial culture were inoculated per 50 ml 25% TSA. After drying, up to nine different 3-μl droplets of bacterial suspensions with 0.4 OD600 were applied with equal distances. For all experiments, plates were incubated at 25 °C for up to 96 hours and photographs were taken thereafter for quantitative image analysis. The size of the halo of inhibition was measured using ImageJ with up to five separate measurements, which were subsequently averaged to reduce variation. Raw data of Fig. 1 are indicated in **Table 2**. diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index 157fd1f0fdd5f106896e00e56d4f8e70a4120e6d..9e238189d6ffe34f7a4e803f25e76361c4ee9372 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ diff --git a/studies/Bacterial culture conditions/isa.study.xlsx b/studies/Bacterial culture conditions/isa.study.xlsx index 1b5495d777214661aafbddba288560d3f5e7cf65..2b4080113d0be2185182ebe7282b28133a8e2664 100644 Binary files a/studies/Bacterial culture conditions/isa.study.xlsx and b/studies/Bacterial culture conditions/isa.study.xlsx differ diff --git a/studies/Plant Growth Conditions/isa.study.xlsx b/studies/Plant Growth Conditions/isa.study.xlsx index 8097240ae3a7d16bddc619b12feffa897c910052..49fcf1250fda1ce318ddcbd806d4a6e6f4e4c7a5 100644 Binary files a/studies/Plant Growth Conditions/isa.study.xlsx and b/studies/Plant Growth Conditions/isa.study.xlsx differ