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. 2022 May 14;25(6):104406. doi: 10.1016/j.isci.2022.104406
REAGENT or RESOURCE SOURCE IDENTIFIER
Chemicals, peptides, and recombinant proteins
Lysogeny Broth (LB) Carl Roth GmbH Catalog # X964.2
Tryptic Soy Broth (TSB) Sigma-Aldrich Catalog # 22098-500G-F
Agar Carl Roth GmbH Catalog # 5210.2
Potassium Hydrogen Phosphate Carl Roth GmbH Catalog # P749.2
Potassium Dihydrogen Phosphate Carl Roth GmbH Catalog # 3904.1
MOPS Carl Roth GmbH Catalog # 6979.3
Magnesium chloride hexahydrate Carl Roth GmbH Catalog # 2189.1
Manganese(II) chloride Carl Roth GmbH Catalog # T881.3
Zinc chloride Carl Roth GmbH Catalog # T887.1
Thiamine Carl Roth GmbH Catalog # T911.1
Calcium chloride Carl Roth GmbH Catalog # 5239.1
Ammonium chloride Carl Roth GmbH Catalog # K298.2
Glycerol Carl Roth GmbH Catalog # 7533.1
Cellobiose Carl Roth GmbH Catalog # 5840.3
Xylan from beechwood Carl Roth GmbH Catalog # 4414.3
Starch from potatoes Carl Roth GmbH Catalog # 9441.1
Potassium hydroxide Carl Roth GmbH Catalog # 6751.1
Sodium hypochlorite VWR Catalog # 27900.296
Murashige and Skoog basal salts mixture Sigma-Aldrich Catalog # M5519
Spectinomycin dihydrochloride VWR J61820.14
Experimental models: Organisms/strains
DK1042: B. subtilis NCIB 3610 comlQ12I (Konkol et al., 2013) Strain DK1042
TB500.1: DK1042 amyE::Phyperspank-gfp SpecR (Mhatre et al., 2017) N/A
TB501.1: DK1042 amyE::Phyperspank-mKATE2 SpecR (Dragoš et al., 2018a) N/A
TB530.1: DK1042 amyE::Phyperspank-gfp SpecRhag::KmR N/A
TB531.1: DK1042 amyE::Phyperspank-mKATE2 SpecRhag::KmR N/A
DTUB310: DK1042 Ev6.1 amyE::Phyperspank-gfp SpecR This study N/A
DTUB311: DK1042 Ev6.1 amyE::Phyperspank-mKATE2 SpecR
DTUB312: DK1042 Ev7.3 amyE::Phyperspank-gfp SpecR
DTUB313: DK1042 Ev7.3 amyE::Phyperspank-mKATE2 SpecR
D749: Pedobacter sp (Lozano-Andrade et al., 2021) N/A
D757: Rhodococcus globerulus N/A
D763: Stenotrophomas indicatrix N/A
D764: Chryseobacterium sp N/A
MC1061: Escherichia coli K-12 F¯ λ¯ Δ(ara-leu)7697 [araD139]B/r Δ(codB-lacI)3 galK16 galE15 e14¯ mcrA0 relA1 rpsL150(StrR) spoT1 mcrB1 hsdR2(r¯ m+) (Casadaban et al., 1980) N/A
Arabidopsis thaliana Col-0 NASC N/A
Recombinant DNA
pTB497.1 (van Gestel et al., 2014) N/A
pTB498.1 (Dragoš et al., 2018b) N/A
Software and algorithms
Zen 3.1 Software Carl Zeiss, Oberkochen, Germany https://www.zeiss.com/corporate/int/home.html
ImageJ (Schindelin et al., 2012) https://imagej.nih.gov/ij/
OriginPro 2020 OriginLab, Northampton, MA, USA https://www.originlab.com/
R Studio RStudio, Boston, MA, USA https://www.rstudio.com/
bcl2fastq (v2.17.1.14) Illumina, San Diego, CA, USA https://www.illumina.com/
CLC Genomics Workbench Qiagen, Hilden, Germany https://digitalinsights.qiagen.com
SOAPnuke (v1.5.6) (Chen et al., 2018) https://github.com/BGI-flexlab/SOAPnuke
breseq (v0.35.7) (Deatherage and Barrick, 2014) https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing
Others
Glass beads Ø0.25-0.5 mm, Carl Roth GmbH Catalog # A553.1