Summary of Study ST004301

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 PR002717. The data can be accessed directly via it's Project DOI: 10.21228/M8FV8K 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.

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Study IDST004301
Study TitleMetabolomic profiling of three native North American ash trees (Fraxinus spp.) and their relationship to the Emerald ash borer (Agrilus planipennis) infestation
Study TypeResearch
Study SummaryThis study aimed to profile microbial communities associated with ash phloem and Emerald Ash Borer (EAB; Agrilus planipennis) larval guts and their relationship to ash phloem metabolites in three native susceptible North American ash species: Fraxinus pennsylvanica (green ash), F. nigra (black ash) and F. americana (white ash) using metabarcoding and widely targeted metabolomics to establish the first global metabolomic profile of phloem in these ash species. We examined interspecies differences in microbiota and metabolite profiles and interactions of ash phloem microbiota and metabolites in relation to EAB infestation. Samples of uninfested phloem, with no visible EAB infestation, but located adjacent to an EAB gallery (PhloemA – Pa) and infested phloem from an EAB gallery (infested phloem)(Gallery – G), each represented by two pooled phloem punch samples per tree, were collected from four trees of each ash species showing high EAB infestation signs to track the ‘within-tree’ metabolite variation in response to EAB infestation. We found that microbiota and metabolites in green ash showed a distinct response to EAB infestation compared to the other ash species. We also identified specific metabolites interacting with microbial communities in ash phloem and/or the EAB larval gut. Green ash also displayed a distinct global metabolite profile from the other two species and had the highest number of differentially regulated metabolites. However, green and white ash shared a strong upregulation of terpenoid compounds, several of which were among compounds significantly associated with microbial communities in green ash phloem or the EAB larval gut.
Institute
Cornell University
DepartmentCollege of Agricultural and Life Sciences
LaboratoryBushley Lab
Last NameBushley
First NameKathryn
Address538 Tower Road, Ithaca, NY, 14853
Emailkeb45@cornell.edu
Phone(607) 255-1276
Submit Date2025-10-10
Num Groups6
Total Subjects48
Study CommentsPairwise comparisons (PhloemA versus Gallery) in each tree species
PublicationsEnvironmental Microbiome in review
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-10-24
Release Version1
Kathryn Bushley Kathryn Bushley
https://dx.doi.org/10.21228/M8FV8K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002717
Project DOI:doi: 10.21228/M8FV8K
Project Title:Interactions between phloem microbiota and metabolomes in three North American ash species (Fraxinus spp.) susceptible to Emerald Ash Borer (Agrilus planipennis)
Project Type:Widely Targeted Metabolomics for Plants
Project Summary:This study aimed to profile microbial communities associated with ash phloem and Emerald Ash Borer (EAB; Agrilus planipennis) larval guts and their relationship to ash phloem metabolites in three native susceptible North American ash species: Fraxinus pennsylvanica (green ash), F. nigra (black ash) and F. americana (white ash) using metabarcoding and widely targeted metabolomics to establish the first global metabolomic profile of phloem in these ash species. We examined interspecies differences in microbiota and metabolite profiles and interactions of ash phloem microbiota and metabolites in relation to EAB infestation. Samples of uninfested phloem, with no visible EAB infestation, but located adjacent to an EAB gallery (PhloemA – Pa) and infested phloem from an EAB gallery (Gallery – G), each represented by two pooled phloem punch samples per tree, were collected from four trees of each ash species showing high EAB infestation signs to track the ‘within-tree’ metabolite variation in response to EAB infestation. We found that microbiota and metabolites in green ash showed a distinct response to EAB infestation compared to the other ash species. We also identified specific metabolites interacting with microbial communities in ash phloem and/or the EAB larval gut. Green ash also displayed a distinct global metabolite profile from the other two species and had the highest number of differentially regulated metabolites. However, green and white ash shared a strong upregulation of terpenoid compounds, several of which were among compounds significantly associated with microbial communities in green ash phloem or the EAB larval gut.
Institute:Cornell University
Department:College of Agricultural and Life Sciences
Laboratory:Bushley Lab
Last Name:Bushley
First Name:Kathryn
Address:538 Tower Road, Ithaca, NY, 14853
Email:keb45@cornell.edu
Phone:(607) 255-1276
Funding Source:NSF
Publications:Environmental Microbiome (in review)
Contributors:Judith Mogouong, Claire Yager, Kathryn Bushley

Subject:

Subject ID:SU004459
Subject Type:Plant
Subject Species:Fraxinus pennsylvanica, Fraxinus nigra, Fraxinus americana
Taxonomy ID:56036, 56031, 38872

Factors:

Subject type: Plant; Subject species: Fraxinus pennsylvanica, Fraxinus nigra, Fraxinus americana (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Species Type
SA505334F22TR040G1BPlant Black Gallery
SA505335F22TR053G1BPlant Black Gallery
SA505336F22TR041G1BPlant Black Gallery
SA505337F22TR044G1BPlant Black Gallery
SA505338F22TR053P1BPlant Black Phloem
SA505339F22TR041P1BPlant Black Phloem
SA505340F22TR040P1BPlant Black Phloem
SA505341F22TR044P1BPlant Black Phloem
SA505342F22ST122G1RPlant Green Gallery
SA505343F22ST120G1RPlant Green Gallery
SA505344F22ST1UG1RPlant Green Gallery
SA505345F22ST121G1RPlant Green Gallery
SA505346F22ST1UP1RPlant Green Phloem
SA505347F22ST120P1RPlant Green Phloem
SA505348F22ST122P1RPlant Green Phloem
SA505349F22ST121P1RPlant Green Phloem
SA505350F22TR130G1WPlant White Gallery
SA505351F22TR178G1WPlant White Gallery
SA505352F22TR180G1WPlant White Gallery
SA505353F22TR181G1WPlant White Gallery
SA505354F22TR130P1WPlant White Phloem
SA505355F22TR178P1WPlant White Phloem
SA505356F22TR180P1WPlant White Phloem
SA505357F22TR181P1WPlant White Phloem
Showing results 1 to 24 of 24

Collection:

Collection ID:CO004452
Collection Summary:Trees from three native North American ash species, including F. pennsylvanica (green), F. nigra (black), and F. americana (white) were sampled from natural forests in state or city parks near Ithaca, NY, U.S.A. F. pennsylvanica trees from Renwick woods natural area in Stewart Park, City of Ithaca (latitude 42.46037898, longitude -76.50254798, approx. elevation: 122 meters), F. nigra from Robert H. Treman State Park (latitude 42.39894499, longitude, -76.59105099, approx. elevation: 299 meters), and F. americana trees from Robert H. Treman State park (latitude 42.40109797, longitude -76.58934301, approx. elevation 316 meters). The uninfested phloem with no visible infestation, but located adjacent to a gallery (PhloemA – Pa), infested phloem from a gallery (Gallery – G) sample (region of phloem infested with emerald ash borer) types, each represented by two pooled punch samples, were collected from trees showing high infestation signs to track the ‘within-tree’ metabolite variation in response to EAB infestation and stored at -80ºC prior to metabolite extraction.
Sample Type:Plant
Collection Location:City of Ithaca, New-York, USA
Storage Conditions:-80℃

Treatment:

Treatment ID:TR004468
Treatment Summary:No treatment. This was an observation environmental study.

Sample Preparation:

Sampleprep ID:SP004465
Sampleprep Summary:Immediately after being removed from the -80ºC freezer, the samples were chilled in liquid nitrogen and lyophilized for approximately 72 h using a freeze-dry system (Labconco, Kansas City, MO, USA). The bark was gently removed, and each sample was wrapped in aluminum foil, labelled, placed in a plastic bag with desiccant, and shipped to MetWare Biotechnology Inc., MA, USA for metabolomics analysis. Samples were ground using a ball mill (30 Hz, 1.5 min) (MM 400, Retsh). For extraction, 50 mg of the ground tissue was mixed with 1.2 mL of -20ºC pre-cooled 70% methanol with internal standards. The mixture was then vortexed (30 sec every 30 min for a total of six times, centrifuged (12,000 rpm, 3 min, 4ºC), and the supernatant collected and filtered through a 0.22µm membrane filter. Extractions were run alongside internal standards on an ultra-performance liquid chromatography and tandem mass spectrometry (UPLC-MS/MS) system (Applied Biosystems Qtrap 6500, https://sciex.com/ accessed 03 April 2025). The UPLC-MS/MS was performed as described in Koski, et al. 16. The area of each chromatographic peak represents the relative abundance of the corresponding compound, and the mass spectrum peak of each metabolite in different samples was corrected based on retention time and peak distribution information to ensure the accuracy of qualitative and quantitative analysis.

Chromatography:

Chromatography ID:CH005442
Chromatography Summary:The data acquisition instruments consisted of Ultra Performance Liquid Chromatography (UPLC) (Ex-ionLC™ AD, https://sciex.com/) and tandem mass spectrometry (MS/MS) (Applied Biosystems QTRAP.
Instrument Name:ExionLC AD
Column Name:Agilent ZORBAX RRHD SB-C18 (100 x 2.1mm,1.8um)
Column Temperature:40
Flow Gradient:Elution gradient: 0.00 min, the proportion of B phase was 5%, within 9.00 min, the proportion of B phase increased linearly to 95%, and remained at 95% for 1 min, 10.00-11.10 min, the proportion of B phase decreased to 5%, and balanced at 5% upto 14 min;
Flow Rate:0.35 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN007163
Analysis Type:MS
Analysis Protocol File:eab-metabolomics-short-report_v2.pdf
Chromatography ID:CH005442
Num Factors:6
Num Metabolites:917
Units:relative abundance
  
Analysis ID:AN007164
Analysis Type:MS
Analysis Protocol File:eab-metabolomics-short-report_v2.pdf
Chromatography ID:CH005442
Num Factors:6
Num Metabolites:1005
Units:relative abundance
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