Summary of Study ST002511
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001621. The data can be accessed directly via it's Project DOI: 10.21228/M85M6X This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST002511 |
| 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 |
| Olaf.Tyc@kgu.de | |
| Phone | +496963018046 |
| Submit Date | 2023-03-16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | GC-MS |
| Release Date | 2023-04-04 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001621 |
| Project DOI: | doi: 10.21228/M85M6X |
| 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 |
Subject:
| Subject ID: | SU002611 |
| Subject Type: | Bacteria |
| Subject Species: | Aspergillus niger;Bacillus subtilis |
| Taxonomy ID: | 5061;1423 |
Factors:
Subject type: Bacteria; Subject species: Aspergillus niger;Bacillus subtilis (Factor headings shown in green)
| mb_sample_id | local_sample_id | treatment | timepoint |
|---|---|---|---|
| SA252839 | A niger B subtilis interaction 3.2 | A. niger B. subtilis interaction | day 3 |
| SA252840 | A niger B subtilis interaction 3.1 | A. niger B. subtilis interaction | day 3 |
| SA252841 | A niger B subtilis interaction 5.1 | A. niger B. subtilis interaction | day 5 |
| SA252842 | A niger B subtilis interaction 5.2 | A. niger B. subtilis interaction | day 5 |
| SA252843 | A niger B subtilis interaction 5.3 | A. niger B. subtilis interaction | day 5 |
| SA252844 | A niger mono day 3.2 | A. niger mono | day 3 |
| SA252845 | A niger mono day 3.3 | A. niger mono | day 3 |
| SA252846 | A niger mono day 3.1 | A. niger mono | day 3 |
| SA252847 | A niger mono day 5.2 | A. niger mono | day 5 |
| SA252848 | A niger mono day 5.3 | A. niger mono | day 5 |
| SA252849 | A niger mono day 5.1 | A. niger mono | day 5 |
| SA252850 | B subtilis mono day 3.2 | B. subtilis mono | day 3 |
| SA252851 | B subtilis mono day 3.3 | B. subtilis mono | day 3 |
| SA252852 | B subtilis mono day 3.1 | B. subtilis mono | day 3 |
| SA252853 | B subtilis mono day 5.3 | B. subtilis mono | day 5 |
| SA252854 | B subtilis mono day 5.1 | B. subtilis mono | day 5 |
| SA252855 | B subtilis mono day 5.2 | B. subtilis mono | day 5 |
| SA252856 | Control day 3.1 | control | day 3 |
| SA252857 | Control day 3.3 | control | day 3 |
| SA252858 | Control day 3.2 | control | day 3 |
| SA252859 | Control day 5.3 | control | day 5 |
| SA252860 | Control day 5.2 | control | day 5 |
| SA252861 | Control day 5.1 | control | day 5 |
| Showing results 1 to 23 of 23 |
Collection:
| Collection ID: | CO002604 |
| 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 ID: | TR002623 |
| 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. |
Sample Preparation:
| Sampleprep ID: | SP002617 |
| 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. |
Combined analysis:
| Analysis ID | AN004135 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890B |
| Column | Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um) |
| MS Type | EI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 7200 QTOF |
| Ion Mode | POSITIVE |
| Units | m/z |
Chromatography:
| Chromatography ID: | CH003063 |
| 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). |
| Instrument Name: | Agilent 7890B |
| Column Name: | Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um) |
| Column Temperature: | 280°C |
| Flow Gradient: | - |
| Flow Rate: | 50 mL/min |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | GC |
MS:
| MS ID: | MS003882 |
| Analysis ID: | AN004135 |
| Instrument Name: | Agilent 7200 QTOF |
| Instrument Type: | QTOF |
| MS Type: | EI |
| 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. |
| Ion Mode: | POSITIVE |
