Summary of Study ST004211
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 PR002654. The data can be accessed directly via it's Project DOI: 10.21228/M8KV8T This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004211 |
| Study Title | Lost and Found: Rediscovering Microbiome-Associated Phenotypes that Reshape Agricultural Sustainability |
| Study Summary | Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification—key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and exudate metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. These findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture. These maize root exduate metabolomics data are a subset of this larger project and make up a phenotyping for candidate lines. |
| Institute | University of Arizona |
| Last Name | Favela |
| First Name | Alonso |
| Address | Forbes Building |
| alonsof@arizona.edu | |
| Phone | 14802552527 |
| Submit Date | 2025-07-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-10-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002654 |
| Project DOI: | doi: 10.21228/M8KV8T |
| Project Title: | Lost and Found: Rediscovering Microbiome-Associated Phenotypes that Reshape Agricultural Sustainability |
| Project Summary: | Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification—key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. Our findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture. ---- These maize root exduate metabolomics data are a subset of this larger project and make up a phenotyping for candidate lines. |
| Institute: | University of Arizona |
| Department: | School of Plant Sciences |
| Laboratory: | Favela Lab |
| Last Name: | Favela |
| First Name: | Alonso |
| Address: | Forbes Building |
| Email: | alonsof@arizona.edu |
| Phone: | 4802552527 |
Subject:
| Subject ID: | SU004363 |
| Subject Type: | Plant |
| Subject Species: | Zea mays |
| Taxonomy ID: | 4577 |
Factors:
Subject type: Plant; Subject species: Zea mays (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype |
|---|---|---|---|
| SA485458 | Blank MS2 | Blank | NA |
| SA485459 | Blank MS1 | Blank | NA |
| SA485460 | B73 2 | Maize Exudates | B73 |
| SA485461 | B73 1 | Maize Exudates | B73 |
| SA485462 | B73 6 | Maize Exudates | B73 |
| SA485463 | B73 5 | Maize Exudates | B73 |
| SA485464 | B73 3 | Maize Exudates | B73 |
| SA485465 | B73 4 | Maize Exudates | B73 |
| SA485466 | Z21 5 | Maize Exudates | NIL021 |
| SA485467 | Z21 4 | Maize Exudates | NIL021 |
| SA485468 | Z21 2 | Maize Exudates | NIL021 |
| SA485469 | Z21 3 | Maize Exudates | NIL021 |
| SA485470 | Z21 1 | Maize Exudates | NIL021 |
| SA485471 | Z47 6 | Maize Exudates | NIL047 |
| SA485472 | Z47 1 | Maize Exudates | NIL047 |
| SA485473 | Z47 5 | Maize Exudates | NIL047 |
| SA485474 | Z47 4 | Maize Exudates | NIL047 |
| SA485475 | Z47 3 | Maize Exudates | NIL047 |
| SA485476 | Z47 2 | Maize Exudates | NIL047 |
| SA485477 | Pooled MS2 | Pool | NA |
| SA485478 | Pooled QC1 | Pool | NA |
| SA485479 | Pooled QC2 | Pool | NA |
| SA485480 | Pooled QC3 | Pool | NA |
| Showing results 1 to 23 of 23 |
Collection:
| Collection ID: | CO004356 |
| Collection Summary: | Root exudates were collected from candidate BNI NILs to assess whether these lines exhibit distinct exudation profiles, in addition to previously observed differences in root tissue metabolomes. Seeds were sterilized prior to introduction to the hydroponic environment with a dilute bleach and ethanol solution, as in (2). To collect exudates, seedlings of B73, NIL021, and NIL047 were grown for four weeks in sterilized Hoagland’s nutrient solution with inert glass beads as a support matrix. Plants were maintained in a Hettich growth chamber under a 12 h light / 12 h dark photoperiod. At the time of sampling, plants were hydroponically extracted in a series of washes. First, the existing growth solution was drained and replaced with fresh deionized water (“trap solution”) to induce an osmotic shock response and stimulate exudation. Following a short incubation, the trap solution was removed and collected. A total of 40 mL of hydroponic exudate was recovered per plant. |
| Sample Type: | Maize root exudates |
Treatment:
| Treatment ID: | TR004372 |
| Treatment Summary: | No further treatment. This is a genotype study. |
Sample Preparation:
| Sampleprep ID: | SP004369 |
| Sampleprep Summary: | To capture the chemical diversity of root exudates, we conducted untargeted metabolomic profiling using both reverse phase liquid chromatography (RP-LC) and hydrophilic interaction liquid chromatography (HILIC) coupled to high-resolution mass spectrometry. RP-LC was used to analyze non-polar to moderately polar metabolites, while HILIC enabled the detection of highly polar and ionic compounds that are often poorly retained on reverse phase columns. This complementary approach allowed for broader metabolite coverage of root exudation chemistry. As with the root tissue analysis, metabolite identifications derived from these LC-MS datasets are considered putative due to limitations in compound libraries and structural resolution. |
Combined analysis:
| Analysis ID | AN007004 | AN007005 |
|---|---|---|
| Chromatography ID | CH005317 | CH005318 |
| MS ID | MS006701 | MS006702 |
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) | Waters ACQUITY Premier HSS T3 (150 x 2.1mm, 1.8um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Orbitrap Exploris 480 | Thermo Orbitrap Exploris 480 |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | Area | Area |
Chromatography:
| Chromatography ID: | CH005317 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 45 C |
| Flow Gradient: | 0–3 min held at 1% B; 3–19 min 1% B – 95% B; 19–20 min 95% B. |
| Flow Rate: | 300 μL/min |
| Solvent A: | 10% acetonitrile/90% water; 10 mM ammonium acetate; 0.1 % formic acid |
| Solvent B: | 50% acetonitrile/50% water; 10 mM ammonium acetate; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH005318 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY Premier HSS T3 (150 x 2.1mm, 1.8um) |
| Column Temperature: | 45 C |
| Flow Gradient: | 0–3 min held at 1% B; 3–19 min 1% B – 95% B; 19–20 min 95% B. |
| Flow Rate: | 300 μL/min |
| Solvent A: | 100% Water; 0.1% formic acid |
| Solvent B: | 100% Methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS006701 |
| Analysis ID: | AN007004 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Samples were analyzed in both positive and negative ionization modes using HCD (higher-energy collision dissociation). The HESI source parameters were set as follows: spray voltage 3.5 or 2.5 kV for positive and negative modes respectively; capillary temperature 350 °C; S lens RF level 50 arbitrary units, and aux gas heater temperature 350 °C. Full MS scan data were acquired at a resolving power of 120,000 FWHM at m/z 200 with the scanning range of m/z 65–975. The automatic gain control (AGC) target was set at 50%, with the maximum injection time of 100 ms. The data dependent acquisition (dd-MS2) parameters used to obtain product ion spectra were as follows: resolving power 30,000 FWHM at m/z 200, AGC target of 50% ions with maximum injection time is set to auto, isolation width 1.2 m/z, and HCD collision energies of: 20, 40, 80 %. For data generated, confident metabolite identifications were made using Thermo Compound Discoverer 3.3. For RP and HILIC positive and negative mode, spectra were aligned using an adaptive curve with a maximum of 0.5 min RT shift respectively and a 5-ppm mass tolerance. Peaks were selected based on a minimum intensity of 1 × 10⁶ and a chromatographic S/N of 3. Detected features were grouped based on a mass tolerance of 5 ppm and a RT tolerance of 0.5. Compounds were assigned based on Isotopic pattern, RT, MS1, and/or MS2. All identifications and integrated peaks were manually validated and exported for statistical analysis. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS006702 |
| Analysis ID: | AN007005 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Samples were analyzed in both positive and negative ionization modes using HCD (higher-energy collision dissociation). The HESI source parameters were set as follows: spray voltage 3.5 or 2.5 kV for positive and negative modes respectively; capillary temperature 350 °C; S lens RF level 50 arbitrary units, and aux gas heater temperature 350 °C. Full MS scan data were acquired at a resolving power of 120,000 FWHM at m/z 200 with the scanning range of m/z 65–975. The automatic gain control (AGC) target was set at 50%, with the maximum injection time of 100 ms. The data dependent acquisition (dd-MS2) parameters used to obtain product ion spectra were as follows: resolving power 30,000 FWHM at m/z 200, AGC target of 50% ions with maximum injection time is set to auto, isolation width 1.2 m/z, and HCD collision energies of: 20, 40, 80 %. For data generated, confident metabolite identifications were made using Thermo Compound Discoverer 3.3. For RP and HILIC positive and negative mode, spectra were aligned using an adaptive curve with a maximum of 0.5 min RT shift respectively and a 5-ppm mass tolerance. Peaks were selected based on a minimum intensity of 1 × 10⁶ and a chromatographic S/N of 3. Detected features were grouped based on a mass tolerance of 5 ppm and a RT tolerance of 0.5. Compounds were assigned based on Isotopic pattern, RT, MS1, and/or MS2. All identifications and integrated peaks were manually validated and exported for statistical analysis. |
| Ion Mode: | POSITIVE |
