{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002511","ANALYSIS_ID":"AN004135","VERSION":"1","CREATED_ON":"March 21, 2023, 8:29 am"},

"PROJECT":{"PROJECT_TITLE":"Enhanced niche colonization and competition during bacterial adaptation to a fungus","PROJECT_TYPE":"Fungal / bacterial interaction","PROJECT_SUMMARY":"Bacterial-fungal interactions (BFIs) influence microbial community performance of most ecosystems and elicit specific microbial behaviors, including the stimulation of specialized metabolite production. Using a simple BFI system encompassing the Gram-positive bacterium Bacillus subtilis and the black mold fungus Aspergillus niger, we established a co-culture experimental evolution method to investigate bacterial adaptation to the presence of a fungus. In the evolving populations, B. subtilis was rapidly selected for enhanced production of the lipopeptide surfactin and accelerated surface spreading that led to an inhibition of fungal expansion and environment acidification. These phenotypes were explained by specific mutations in the DegS-DegU two-component system. In the presence of surfactin, the fungal hyphae exhibited bulged cells with delocalized secretory vesicles and RlmA-dependent cell wall stress induction. Increased surfactin production generally enhances the competitive success of the bacterium against various Aspergillus species that likely explains the primary adaption path in the presence of A. niger.","INSTITUTE":"Netherlands Institute of Ecology","DEPARTMENT":"Microbial Ecology","LABORATORY":"GCMS Lab","LAST_NAME":"Tyc","FIRST_NAME":"Olaf","ADDRESS":"Theodor-Stern-Kai 7, Building 11, 60590 Frankfurt Germany","EMAIL":"Olaf.Tyc@kgu.de","PHONE":"016094726403"},

"STUDY":{"STUDY_TITLE":"Enhanced niche colonization and competition during bacterial adaptation to a fungus","STUDY_TYPE":"Fungal / bacterial interaction","STUDY_SUMMARY":"Enhanced niche 1 colonization and competition during bacterial adaptation to a fungus","INSTITUTE":"Netherlands Institute of Ecology","DEPARTMENT":"Microbial Ecology","LAST_NAME":"Tyc","FIRST_NAME":"Olaf","ADDRESS":"Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands","EMAIL":"Olaf.Tyc@kgu.de","PHONE":"+496963018046"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Aspergillus niger/Bacillus subtilis","TAXONOMY_ID":"5061/1423"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"A niger mono day 3.1",
"Factors":{"treatment":"A. niger mono","timepoint":"day 3"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0103 A niger mono 268208.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A niger mono day 3.2",
"Factors":{"treatment":"A. niger mono","timepoint":"day 3"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0105 A niger mono 268210.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A niger mono day 3.3",
"Factors":{"treatment":"A. niger mono","timepoint":"day 3"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0107 A niger mono 268213.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"B subtilis mono day 3.1",
"Factors":{"treatment":"B. subtilis mono","timepoint":"day 3"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0109 B sp  3610 anc mono 268233.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"B subtilis mono day 3.2",
"Factors":{"treatment":"B. subtilis mono","timepoint":"day 3"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0111 B sp  3610 anc mono 268237.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"B subtilis mono day 3.3",
"Factors":{"treatment":"B. subtilis mono","timepoint":"day 3"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0113 B sp  3610 anc mono 288253.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A niger B subtilis interaction 3.1",
"Factors":{"treatment":"A. niger B. subtilis interaction","timepoint":"day 3"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0115 A niger  B sp 3610 anc int 288255.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A niger B subtilis interaction 3.2",
"Factors":{"treatment":"A. niger B. subtilis interaction","timepoint":"day 3"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0119 A niger  B sp 3610 anc int 288258.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Control day 3.1",
"Factors":{"treatment":"control","timepoint":"day 3"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0121 TSB media control 288266.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Control day 3.2",
"Factors":{"treatment":"control","timepoint":"day 3"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0123 TSB media control 288269.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Control day 3.3",
"Factors":{"treatment":"control","timepoint":"day 3"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0125 TSB media control 288279.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A niger mono day 5.1",
"Factors":{"treatment":"A. niger mono","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0127 A niger mono 263895.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A niger mono day 5.2",
"Factors":{"treatment":"A. niger mono","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0129 A niger mono 268204.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A niger mono day 5.3",
"Factors":{"treatment":"A. niger mono","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0131 A niger mono 268209.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"B subtilis mono day 5.1",
"Factors":{"treatment":"B. subtilis mono","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0133 B sp  3610 anc mono 268221.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"B subtilis mono day 5.2",
"Factors":{"treatment":"B. subtilis mono","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0135 B sp  3610 anc mono 268223.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"B subtilis mono day 5.3",
"Factors":{"treatment":"B. subtilis mono","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0137 B sp  3610 anc mono 268234.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A niger B subtilis interaction 5.1",
"Factors":{"treatment":"A. niger B. subtilis interaction","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0139 A niger  B sp 3610 anc int 268236.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A niger B subtilis interaction 5.2",
"Factors":{"treatment":"A. niger B. subtilis interaction","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0141 A niger  B sp 3610 anc int 287345.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A niger B subtilis interaction 5.3",
"Factors":{"treatment":"A. niger B. subtilis interaction","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0143 A niger  B sp 3610 anc int 288245.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Control day 5.1",
"Factors":{"treatment":"control","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0145 TSB media control 288282.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Control day 5.2",
"Factors":{"treatment":"control","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0147 TSB media control 288288.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Control day 5.3",
"Factors":{"treatment":"control","timepoint":"day 5"},
"Additional sample data":{"RAW_FILE_NAME":"qtof-2017-0149 TSB media control 288289.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"For analysis and trapping of volatile organic compounds two-compartment glass Petri-dishes (Garbeva et al., 2014) containing 1% LB-A (Carl-Roth LB- Agar) were applied. The fungus Aspergillus niger was inoculated 24 hours before addition of the bacterial strain on the left side of the two compartment glass petri-dish and incubated overnight at 28 °C. The bacterial strain Bacillus subtilis 3610 was incubated overnight at 28 °C in LB- liquid medium (Carl-Roth LB- Medium). After overnight _incubation a volume of 2 µl of the grown Bacillus subtilis 3610 culture was spotted on the opposite side of the Aspergillus niger culture. The glass Petri-dishes were kept open for 25 min. for drying of the droplets. After the drying process plates were closed by a lid with an outlet connected to a steel trap containing 150 mg Tenax TA and 150 mg Carbopack B (Markes International Ltd) and incubated at 28 °C. The Tenax steel traps were collected after three and five days of incubation and stored at 4 °C until GC-Q-TOF analysis. As controls, glass Petri-dishes containing LB agar media without inoculated bacteria or fungi were used.","SAMPLE_TYPE":"Fungal/bacterial volatiles","COLLECTION_METHOD":"Tenax Trap","COLLECTION_LOCATION":"Wageningen, The Netherlands","COLLECTION_FREQUENCY":"3 days and 5 days","COLLECTION_DURATION":"5 min.","STORAGE_CONDITIONS":"4℃","COLLECTION_VIALS":"Tenax","STORAGE_VIALS":"Metal tubes"},

"TREATMENT":{"TREATMENT_SUMMARY":"The fungus Aspergillus niger was inoculated 24 hours before addition of the bacterial strain on the left side of the two compartment glass petri-dish and incubated overnight at 28 °C. The bacterial strain Bacillus subtilis 3610 was incubated overnight at 28 °C in LB- liquid medium (Carl-Roth LB- Medium). After overnight _incubation a volume of 2 µl of the grown Bacillus subtilis 3610 culture was spotted on the opposite side of the Aspergillus niger culture."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"The collected volatiles were desorbed from the traps using a desorption unit (Unity TD-100, Markes International Ltd., Llantrisant, UK) at 210 °C for 12 min (He flow 50 mL/min) and trapped on a cold trap at -10 °C. The volatiles were introduced into the GC-Q-TOF (model Agilent 7890B GC and the Agilent 7200A QTOF, Santa Clara, USA) by heating the cold trap for 12 min to 250 °C."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The volatiles were desorbed from the traps using an desorption unit (Unity TD-100, Markes International Ltd., Llantrisant, UK) at 210 °C for 12 min (He flow 50 mL/min) and trapped on a cold trap at -10 °C. The volatiles were introduced into the GC-Q-TOF (model Agilent 7890B GC and the Agilent 7200A QTOF, Santa Clara, USA) by heating the cold trap for 12 min to 250 °C. The used split ratio was 1:10 and the used column was a 30 × 0.25 mm ID RXI-5MS, film thickness 0.25 µm (Restek 13424-6850, Bellefonte, PA, USA). Temperature program was as follows: 39 °C for 2 min, from 39 °C to 95 °C at 3.5 °C/min, then to 165 °C at 4 °C/min, to 280 °C at 15 °C/min and finally to 320 °C at 30 °C/min, hold 7 min. The volatile organic compounds were ionized in EI mode at eV and mass spectra were acquired in full-scan-mode (30–400 U @ 5 scans/s). Mass-spectra were extracted with MassHunter Qualitative Analysis Software V B.06.00 Build 6.0.633.0 (Agilent Technologies, Santa Clara, USA).","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 7890B","COLUMN_NAME":"Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um)","SOLVENT_A":"-","SOLVENT_B":"-","FLOW_GRADIENT":"-","FLOW_RATE":"50 mL/min","COLUMN_TEMPERATURE":"280°C"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Netherlands Insitute of Ecology, NIOO-KNAW, Wageningen","OPERATOR_NAME":"Hans Zweers"},

"MS":{"INSTRUMENT_NAME":"Agilent 7200 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"The volatile organic compounds were ionized in EI mode at eV and mass spectra were acquired in full-scan-mode (30–400 U @ 5 scans/s). Mass-spectra were extracted with MassHunter Qualitative Analysis Software V B.06.00 Build 6.0.633.0 (Agilent Technologies, Santa Clara, USA). The obtained mass spectra were transformed to netCDF files and imported into MZmine V2.20 (Copyright © 2005-2012) MZmine Development Team) (Pluskal et al., 2010). Compounds were identified via their mass spectra using deconvolution function and local-minimum search algorithm in combination with two mass-spectral-libraries: NIST 2014 V2.20 (National Institute of Standards and Technology, USA http://www.nist.gov) and Wiley 7th edition spectral libraries and by their linear retention indexes (LRI). The LRI values were calculated by using AMDIS 2.72 (National Institute of Standards and Technology, USA). After deconvolution and mass identification peak lists containing the mass features of each treatment were exported as csv file format for further analysis.","MS_RESULTS_FILE":"ST002511_AN004135_Results.txt UNITS:m/z Has m/z:Yes Has RT:Yes RT units:Minutes"}

}