Data Package Metadata   View Summary

Freshwater mussel metabolomics of Yahara Lakes, Madison, WI USA

General Information
Data Package:
Local Identifier:knb-lter-ntl.424.1
Title:Freshwater mussel metabolomics of Yahara Lakes, Madison, WI USA
Alternate Identifier:DOI PLACE HOLDER
Abstract:

Metabolomic profiles of unionids (Lampsilis siliquoidea) under varying loads of zebra mussels (Dreissena polymorpha) in a eutrophic lake chain in Wisconsin, USA. Metabolites were sourced from hemolymph.

Publication Date:2023-01-11
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
2017-06-01
End:
2017-09-15

People and Organizations
Contact:Butitta(Center for Limnology) [  email ]
Creator:Butitta, Vince L (Center for Limnology)

Data Entities
Data Table Name:
metab_mergedscaled_forEDI
Description:
Data table for metabolites collected from unionid (Lampsilis siliquoidea) hemolymph as well as zebra mussel loads on unionids
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-ntl/424/1/7cca7b94e301b8c3fe854c9e8ca007e1
Name:metab_mergedscaled_forEDI
Description:Data table for metabolites collected from unionid (Lampsilis siliquoidea) hemolymph as well as zebra mussel loads on unionids
Number of Records:32
Number of Columns:112

Table Structure
Object Name:metab_mergedscaled_forEDI.csv
Size:43460 byte
Authentication:1f0e55742a11da9113207b6037bbce31 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 IDlabelspeciesorganLakezebra_countzebra_mass_gzebra_drymass_glength_mmunionid_drymass_gsexglycogen_est_mg.gzebra_mussel_loadzymosterolxylosevalineureauraciltyrosinetryptophantrehalosethymidinethreoninethreonic_acidthreitoltagatosesucrosesuccinic_acidshikimic_acidserinesalicylic_acidriboseribonic_acidraffinosequinic_acidpyrogallolputrescinepseudo_uridineprolinepipecolinic_acidphenylalanineoxoprolineornithineoctanolnicotinic_acidN_acetylmannosaminemyo_inositolmethylhexosemethionine_sulfoxidemethioninemelezitosemannitolmaltotriosemaltosemalic_acidlyxitollysineleucinelactuloseisothreonic_acidisopentadecanoic_acidisoleucineinosinehydroquinoneguanosineglycineglycerol_alpha_phosphateglycerol_3_galactosideglycerolglyceric_acidglutaric_acidglutamineglutamic_acidglucose_6_phosphateglucose_1_phosphateglucosegluconic_acidgalactosegalactonic_acidgalactinolfumaric_acidfructoseepsilon_caprolactamdeoxypentitolcystinecitrullinecitric_acidcholesterolcellobiosecatecholcapric_acidbeta_alanineaspartic_acidasparaginearabitolalanineadenosineadenineX.6_deoxyglucoseX.5_methoxytryptamineX.5_hydroxynorvaline_NISTX.3_aminoisobutyric_acidX.3_4_dihydroxycinnamic_acidX.2_methylglyceric_acidX.2_ketoadipic_acidX.2_hydroxyvaleric_acidX.2_deoxytetronic_acidX.2_aminobutyric_acidX.1_monostearinX.1_monopalmitinX.1_5_anhydroglucitolX.1_2_4_benzenetriol
Column Name:ID  
label  
species  
organ  
Lake  
zebra_count  
zebra_mass_g  
zebra_drymass_g  
length_mm  
unionid_drymass_g  
sex  
glycogen_est_mg.g  
zebra_mussel_load  
zymosterol  
xylose  
valine  
urea  
uracil  
tyrosine  
tryptophan  
trehalose  
thymidine  
threonine  
threonic_acid  
threitol  
tagatose  
sucrose  
succinic_acid  
shikimic_acid  
serine  
salicylic_acid  
ribose  
ribonic_acid  
raffinose  
quinic_acid  
pyrogallol  
putrescine  
pseudo_uridine  
proline  
pipecolinic_acid  
phenylalanine  
oxoproline  
ornithine  
octanol  
nicotinic_acid  
N_acetylmannosamine  
myo_inositol  
methylhexose  
methionine_sulfoxide  
methionine  
melezitose  
mannitol  
maltotriose  
maltose  
malic_acid  
lyxitol  
lysine  
leucine  
lactulose  
isothreonic_acid  
isopentadecanoic_acid  
isoleucine  
inosine  
hydroquinone  
guanosine  
glycine  
glycerol_alpha_phosphate  
glycerol_3_galactoside  
glycerol  
glyceric_acid  
glutaric_acid  
glutamine  
glutamic_acid  
glucose_6_phosphate  
glucose_1_phosphate  
glucose  
gluconic_acid  
galactose  
galactonic_acid  
galactinol  
fumaric_acid  
fructose  
epsilon_caprolactam  
deoxypentitol  
cystine  
citrulline  
citric_acid  
cholesterol  
cellobiose  
catechol  
capric_acid  
beta_alanine  
aspartic_acid  
asparagine  
arabitol  
alanine  
adenosine  
adenine  
X.6_deoxyglucose  
X.5_methoxytryptamine  
X.5_hydroxynorvaline_NIST  
X.3_aminoisobutyric_acid  
X.3_4_dihydroxycinnamic_acid  
X.2_methylglyceric_acid  
X.2_ketoadipic_acid  
X.2_hydroxyvaleric_acid  
X.2_deoxytetronic_acid  
X.2_aminobutyric_acid  
X.1_monostearin  
X.1_monopalmitin  
X.1_5_anhydroglucitol  
X.1_2_4_benzenetriol  
Definition:individual mussel identificationunique ID code SpeciesSource tissue for metabolomic analysisLake IDcount of zebra musselsmass of zebra mussels in gramstotal dry mass of zebra mussels unionid length along major axisdry mass of unionid (soft tissue only)assesed via external shell morphologyglycogen estimate in mg per g foot tissuezebra mussel loadzymosterol relative concentrationxylose relative concentrationvaline relative concentrationurea relative concentrationuracil relative concentrationtyrosine relative concentrationtryptophan relative concentrationtrehalose relative concentrationthymidine relative concentrationthreonine relative concentrationthreonic acid relative concentrationthreitol relative concentrationtagatose relative concentrationsucrose relative concentrationsuccinic acid relative concentrationshikimic acid relative concentrationserine relative concentrationsalicylic acid relative concentrationribose relative concentrationribonic acid relative concentrationraffinose relative concentrationquinic acid relative concentrationpyrogallol relative concentrationputrescine relative concentrationpseudo uridine relative concentrationproline relative concentrationpipecolinic acid relative concentrationphenylalanineoxoproline relative concentrationornithine relative concentrationoctanol relative concentrationnicotinic acid relative concentrationn-acetylmannisamine relative concentrationmyo-inositol relative concentrationmethylhexose relative concentrationmethionine sulfoxide relative concentrationmethionine relative concentrationmelezitose relative concentrationmannitol relative concentrationmaltotriose relative concentrationmaltose relative concentrationmalic acid relative concentrationlyxitol relative concentrationlysine relative concentrationleucine relative concentrationlactulose relative concentrationisothreonic acidisopentadecnoic acid relative concentrationisoleucine relative concentrationinosine relative concentrationhydroquinine relative concentrationguanosine relative concentrationglycine relative concentrationglycerol a-phosphate relative concentrationglycerol 3-galatoside relative concentrationglycerol relative concentrationglyceric acid relative concentrationglutaric acid relative concentrationglutamine relative concentrationglutamic acid relative concentrationglucose 6-phosphate relative concentrationglucose 1-phosphate relative concentrationglucose relative concentrationgluconic acid relative concentrationgalactose relative concentrationgalactonic acid relative concentrationgalactinol relative concentrationfumarate relative concentrationfructose relative concentrationepsilon caprolactum relative concentrationdeoxypentitol relative concentrationcystine relative concentrationcitrulline relative concentrationcintric acid relative concentrationcholesterol relative concentrationcellobiose relative concentrationcatechol relative concentrationcapric acid relative concentrationbeta alanine relative concentrationaspartic acid relative concentrationasparagine relative concentrationarabitol relative concentrationalanine relative concentrationadenosine relative concentrationadenine relative concentration6-deoxyglucose relative concentration5-methoxytryptamine relative concentration5-hydroxynorvaline relative concentration3-aminoisobutyric acid 3-4-dihydroxycinnamic acid2-methylglyceric acid relative concentration2-ketoadipic acid relative concentrationhydroxyvaleric acid relative concentration2-deoxytetronic acid relative concentration2-aminobutyric acid 1-monostearin relative concentration1-monopalmitin relative concentration1-5-anhydroglucitol relative concentration1-2-4-benzenetriol relative concentration
Storage Type:string  
string  
string  
string  
string  
float  
float  
float  
float  
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string  
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Measurement Type:nominalnominalnominalnominalnominalratioratioratioratiorationominalratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratio
Measurement Values Domain:
Definitionindividual mussel identification
Definitionunique ID code
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeLampsilis silquoidea
Definitionspecies ID
Source
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codehemolymph
Definitionsource for metabolite sample
Source
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeKG
DefinitionLake Kegonsa
Source
Code Definition
CodeME
DefinitionLake Mendota
Source
Code Definition
CodeMO
DefinitionLake Monona
Source
Unitcount
Typeinteger
Unitgram
Typereal
Unitgram
Typereal
Unitmillimeter
Typereal
Unitgram
Typereal
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeF
Definitionfemale
Source
Code Definition
CodeM
Definitionmale
Source
Code Definition
Codenan
Definitionunindentified
Source
Unitmg/g
Typereal
Unitdimensionless
Typereal
Unitdimensionless
Typereal
Unitdimensionless
Typereal
Unitdimensionless
Typereal
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Missing Value Code:                    
Codenan
Explunable to identify sex with high confidence
CodeNA
ExplNot all unionids were able to be assessed for glycogen levels
                                                                                                                                                                                                       
Accuracy Report:                                                                                                                                                                                                                                
Accuracy Assessment:                                                                                                                                                                                                                                
Coverage:                                                                                                                                                                                                                                
Methods:                                                                                                                                                                                                                                

Data Package Usage Rights

This data package is released to the "public domain" under Creative Commons CC0 1.0 "No Rights Reserved" (see: https://creativecommons.org/publicdomain/zero/1.0/). It is considered professional etiquette to provide attribution of the original work if this data package is shared in whole or by individual components. A generic citation is provided for this data package on the website https://portal.edirepository.org (herein "website") in the summary metadata page. Communication (and collaboration) with the creators of this data package is recommended to prevent duplicate research or publication. This data package (and its components) is made available "as is" and with no warranty of accuracy or fitness for use. The creators of this data package and the website shall not be liable for any damages resulting from misinterpretation or misuse of the data package or its components. Periodic updates of this data package may be available from the website. Thank you.

Keywords

By Thesaurus:
freshwater musselunionid
physiologymetabolomics
(No thesaurus)freshwater mussels, stress
dreissenazebra mussel

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

Mussels that were collected for glycogen analysis were immediately placed on ice to preserve the tissue for later analysis (following Dunn and Ellis, 2005). In the lab, individuals were sexed via external shell morphology, dried in a drying oven to a constant mass, weighed, then approximately 10mg of foot tissue was collected and run for glycogen analysis (following Naimo et al. 1998). For mussels that were sampled for metabolomics analysis, in the field, immediately after collection, approximately 200uL of hemolymph was drawn from the anterior adductor muscle using a 27–29-gauge syringe, stored in a 2mL cryotube, and flash frozen in liquid nitrogen. Unionids were then scraped of all zebra mussels if present and returned to the benthos. All zebra mussels greater than length 5mm were counted and measured along the major axis of the shell. Cumulative dry weight of all zebra mussels was estimated using a standard conversion of length to dry weight for zebra mussels (Coughlan et al. 2021). Zebra mussel loads were calculated as total estimated zebra mussel dry mass divided by the total dry mass of the unionid soft tissue. Hemolymph samples were stored at -80˚C until they were shipped on dry ice to West Coast Metabolomics Center at UC-Davis for non-targeted analysis of primary metabolites. Metabolites were identified using gas chromatography time-of-flight mass spectroscopy (GC-TOF MS and their peak heights were normalized to the sum peak height of annotated compounds (mTIC-normalization) by the West Coast Metabolomics Center. Each metabolite was independently normalized to zero and standardized to one standard deviation.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@edirepository.org
Web Address:
https://edirepository.org
Id:https://ror.org/0330j0z60
Creators:
Individual: Vince L Butitta
Organization:Center for Limnology
Address:
Madison, WI 53706
Email Address:
vincent.butitta@gmail.com
Id:https://orcid.org/0000-0001-7569-4770
Contacts:
Individual: Butitta
Organization:Center for Limnology
Address:
Madison, WI 53706
Email Address:
vincent.butitta@gmail.com
Id:https://orcid.org/0000-0001-7569-4770

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2017-06-01
End:
2017-09-15
Geographic Region:
Description:Madison, Wisconsin, USA. Lakes in Yahara lake chain (Mendota, Monona, Kegonsa)
Bounding Coordinates:
Northern:  43.162564Southern:  42.945311
Western:  -89.508547Eastern:  -89.209169
Taxonomic Range:
General Coverage:All mussels were identified to species
Classification:
Rank Name:Kingdom
Rank Value:Animalia
Common Name:animals
Identifer:https://www.itis.gov
ID: 202423
Classification:
Rank Name:Subkingdom
Rank Value:Bilateria
Identifer:https://www.itis.gov
ID: 914154
Classification:
Rank Name:Infrakingdom
Rank Value:Protostomia
Identifer:https://www.itis.gov
ID: 914155
Classification:
Rank Name:Superphylum
Rank Value:Lophozoa
Identifer:https://www.itis.gov
ID: 914159
Classification:
Rank Name:Phylum
Rank Value:Mollusca
Common Name:molluscs
Identifer:https://www.itis.gov
ID: 69458
Classification:
Rank Name:Class
Rank Value:Bivalvia
Common Name:bivalves
Identifer:https://www.itis.gov
ID: 79118
Classification:
Rank Name:Subclass
Rank Value:Palaeoheterodonta
Identifer:https://www.itis.gov
ID: 79911
Classification:
Rank Name:Order
Rank Value:Unionoida
Identifer:https://www.itis.gov
ID: 79912
Classification:
Rank Name:Superfamily
Rank Value:Unionoidea
Identifer:https://www.itis.gov
ID: 982987
Classification:
Rank Name:Family
Rank Value:Unionidae
Identifer:https://www.itis.gov
ID: 79913
Classification:
Rank Name:Subfamily
Rank Value:Ambleminae
Identifer:https://www.itis.gov
ID: 983004
Classification:
Rank Name:Genus
Rank Value:Lampsilis
Identifer:https://www.itis.gov
ID: 79986
Classification:
Rank Name:Species
Rank Value:Lampsilis siliquoidea
Common Name:fatmucket
Identifer:https://www.itis.gov
ID: 80028

Project

Parent Project Information:

Title:Metabolomics of unionids (Lampsilis siliquoidea) experiencing stress from zebra mussel (Dreissena polymorpha) invasion
Personnel:
Individual: Vince L Butitta
Email Address:
vincent.butitta@gmail.com
Id:https://orcid.org/0000-0001-7569-4770
Role:graduate student researcher
Individual: Emily H Stanley
Organization:Center for Limnology
Email Address:
ehstanley@wisc.edu
Id:https://orcid.org/0000-0003-4922-8121
Role:Faculty adviosr
Additional Award Information:
Funder:National Science Foundation
Number:1440297
Title:LTER: Comparative Study of a Suite of Lakes in Wisconsin

Maintenance

Maintenance:
Description:

Dataset is complete and will not be updated

Frequency:notPlanned
Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'unitList'
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'mg/g'
        |     |     |     |  \___attribute 'name' = 'mg/g'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'estimate of glycogen in milligrams per gram dry foot tissue'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'count'
        |     |     |     |  \___attribute 'name' = 'count'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'count all and only zebra mussels greater than 5mm encrusted on unionids were enumerated'
        |     |     |     |___text '\n        '
        |     |     |___text '\n      '
        |     |___text '\n    '
        |___text '\n  '

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'emlEditor'
        |     |        \___attribute 'app' = 'ezEML'
        |     |        \___attribute 'release' = '2023.01.04'
        |     |___text '\n    '
        |___text '\n  '

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

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