Summary of Study ST004041

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 PR002533. The data can be accessed directly via it's Project DOI: 10.21228/M8784B 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 IDST004041
Study TitleSpatio-temporal phytoplankton dynamics of metabolite production depending on weather conditions
Study TypeEnvironmental metabolomics
Study SummaryIn this study, we investigate the temporal and spatial dynamics of phytoplankton community and the production of their primary and secondary untargeted metabolites in response to local meteorological events. Thus, we collected water samples in two points of the Aydat Lake (France): near the inflowing waters from Veyre River and at the middle of the lake during the 2021 summer. Untargeted intracellular metabolites were measured using ultra-high-performance liquid chromatography coupled with a high-resolution mass spectrometer, as well as phytoplankton biovolume and diversity and physicochemical lake’s parameters.
Institute
Muséum Nationale d'Histoire Naturelle
DepartmentAviv
LaboratoryUMR 7245 MCAM
Last NameMarie
First NameBenjamin
Address12 rue Buffon, Paris, Île-de-france, 75005, France
Emailbmarie@mnhn.fr
Phone01-40-79-32-12
Submit Date2025-07-08
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2025-08-05
Release Version1
Benjamin Marie Benjamin Marie
https://dx.doi.org/10.21228/M8784B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002533
Project DOI:doi: 10.21228/M8784B
Project Title:Spatio-temporal disparities in phytoplankton dynamics and metabolite production depending on environmental conditions
Project Type:Environmental metabolomics
Project Summary:Various studies suggest that global change is causing an increase in phytoplankton biomass, cyanobacteria prevalence and cyanotoxin production. Metabolomics approaches in natural system hold great promise in investigating the factors leading to variations in phytoplankton successions and subsequent cyanotoxin production. However, eco-metabolomics studies are still scarce in literature and suffer to adequately unravel the biologically relevant variables under environmental changes. In this study, we investigate the temporal and spatial dynamics of phytoplankton community and the production of their primary and secondary untargeted metabolites in response to seasonal variations. Thus, we collected water samples in two points of the Aydat Lake (France): near the inflowing waters from Veyre River and at the middle of the lake during the 2021 summer. Untargeted intracellular metabolites were measured using ultra-high-performance liquid chromatography coupled with a high-resolution mass spectrometer, as well as phytoplankton biovolume and diversity and physicochemical lake’s parameters. Our results highlight the existence of local metabolomic niches, as we report significant difference in the intra-cellular content in metabolites between the 2 sampling sites, separated by only 200m, while phytoplankton communities were similar.
Institute:Muséum Nationale d'Histoire Naturelle
Last Name:Marie
First Name:Benjamin
Address:12 rue Buffon, Paris, Île-de-france, 75005, France
Email:bmarie@mnhn.fr
Phone:01-40-79-32-12

Subject:

Subject ID:SU004187
Subject Type:Water sample

Factors:

Subject type: Water sample; Subject species: - (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Site (Z inflow L middle lake) profondeur (m) date
SA467056KL0_4_20_1_1610Filtered lake water L 0 13/9
SA467057KL0_2_18_1_1608Filtered lake water L 0 13/9
SA467058KL0_3_19_1_1609Filtered lake water L 0 13/9
SA467059KL0_1_17_1_1607Filtered lake water L 0 13/9
SA467060GL0_4_36_1_1510Filtered lake water L 0 16/8
SA467061GL0_3_35_1_1509Filtered lake water L 0 16/8
SA467062GL0_2_34_1_1508Filtered lake water L 0 16/8
SA467063GL0_1_33_1_1507Filtered lake water L 0 16/8
SA467064LL0_1_25_1_1617Filtered lake water L 0 17/9
SA467065LL0_2_26_1_1618Filtered lake water L 0 17/9
SA467066LL0_3_27_1_1619Filtered lake water L 0 17/9
SA467067LL0_4_28_1_1620Filtered lake water L 0 17/9
SA467072AL0_2_2_1_1410Filtered lake water L 0 23/7
SA467073AL0_1_1_1_1409Filtered lake water L 0 23/7
SA467074AL0_3_3_1_1411Filtered lake water L 0 23/7
SA467075AL0_4_4_1_1412Filtered lake water L 0 23/7
SA467076HL0_1_41_1_1517Filtered lake water L 0 23/8
SA467077HL0_4_44_1_1520Filtered lake water L 0 23/8
SA467078HL0_3_43_1_1519Filtered lake water L 0 23/8
SA467079HL0_2_42_1_1518Filtered lake water L 0 23/8
SA467080ML0_4_36_1_1630Filtered lake water L 0 23/9
SA467081ML0_3_35_1_1629Filtered lake water L 0 23/9
SA467082ML0_2_34_1_1628Filtered lake water L 0 23/9
SA467083ML0_1_33_1_1627Filtered lake water L 0 23/9
SA467084BL0_3_19_1_1435Filtered lake water L 0 26/7
SA467085BL0_1_17_1_1433Filtered lake water L 0 26/7
SA467086BL0_2_18_1_1434Filtered lake water L 0 26/7
SA467087BL0_4_20_1_1436Filtered lake water L 0 26/7
SA467088NL0_4_44_1_1640Filtered lake water L 0 27/9
SA467089NL0_3_43_1_1639Filtered lake water L 0 27/9
SA467090NL0_2_42_1_1638Filtered lake water L 0 27/9
SA467091NL0_1_41_1_1637Filtered lake water L 0 27/9
SA467068DL0_1_9_1_1477Filtered lake water L 0 2/8
SA467069DL0_4_12_1_1480Filtered lake water L 0 2/8
SA467070DL0_3_11_1_1479Filtered lake water L 0 2/8
SA467071DL0_2_10_1_1478Filtered lake water L 0 2/8
SA467092CL0_2_2_1_1468Filtered lake water L 0 28/7
SA467093CL0_1_1_1_1467Filtered lake water L 0 28/7
SA467094CL0_4_4_1_1470Filtered lake water L 0 28/7
SA467095CL0_3_3_1_1469Filtered lake water L 0 28/7
SA467096IL0_4_4_1_1590Filtered lake water L 0 30/8
SA467097IL0_3_3_1_1589Filtered lake water L 0 30/8
SA467098IL0_1_1_1_1587Filtered lake water L 0 30/8
SA467099IL0_2_2_1_1588Filtered lake water L 0 30/8
SA467100EL0_3_19_1_1489Filtered lake water L 0 5/8
SA467101EL0_4_20_1_1490Filtered lake water L 0 5/8
SA467102EL0_2_18_1_1488Filtered lake water L 0 5/8
SA467103EL0_1_17_1_1487Filtered lake water L 0 5/8
SA467104JL0_4_12_1_1600Filtered lake water L 0 6/9
SA467105JL0_1_9_1_1597Filtered lake water L 0 6/9
SA467106JL0_2_10_1_1598Filtered lake water L 0 6/9
SA467107JL0_3_11_1_1599Filtered lake water L 0 6/9
SA467108FL0_1_25_1_1497Filtered lake water L 0 9/8
SA467109FL0_3_27_1_1499Filtered lake water L 0 9/8
SA467110FL0_4_28_1_1500Filtered lake water L 0 9/8
SA467111FL0_2_26_1_1498Filtered lake water L 0 9/8
SA467112KL15_4_24_1_1615Filtered lake water L 1.5 13/9
SA467113KL15_1_21_1_1612Filtered lake water L 1.5 13/9
SA467114KL15_2_22_1_1613Filtered lake water L 1.5 13/9
SA467115KL15_3_23_1_1614Filtered lake water L 1.5 13/9
SA467116GL15_2_38_1_1513Filtered lake water L 1.5 16/8
SA467117GL15_3_39_1_1514Filtered lake water L 1.5 16/8
SA467118GL15_4_40_1_1515Filtered lake water L 1.5 16/8
SA467119GL15_1_37_1_1512Filtered lake water L 1.5 16/8
SA467120LL15_1_29_1_1622Filtered lake water L 1.5 17/9
SA467121LL15_3_31_1_1624Filtered lake water L 1.5 17/9
SA467122LL15_4_32_1_1625Filtered lake water L 1.5 17/9
SA467123LL15_2_30_1_1623Filtered lake water L 1.5 17/9
SA467128AL15_1_5_1_1415Filtered lake water L 1.5 23/7
SA467129AL15_2_6_1_1416Filtered lake water L 1.5 23/7
SA467130AL15_3_7_1_1417Filtered lake water L 1.5 23/7
SA467131AL15_4_8_1_1418Filtered lake water L 1.5 23/7
SA467132HL15_4_48_1_1525Filtered lake water L 1.5 23/8
SA467133HL15_2_46_1_1523Filtered lake water L 1.5 23/8
SA467134HL15_1_45_1_1522Filtered lake water L 1.5 23/8
SA467135HL15_3_47_1_1524Filtered lake water L 1.5 23/8
SA467136ML15_3_39_1_1634Filtered lake water L 1.5 23/9
SA467137ML15_1_37_1_1632Filtered lake water L 1.5 23/9
SA467138ML15_2_38_1_1633Filtered lake water L 1.5 23/9
SA467139ML15_4_40_1_1635Filtered lake water L 1.5 23/9
SA467140BL15_4_24_1_1442Filtered lake water L 1.5 26/7
SA467141BL15_2_22_1_1440Filtered lake water L 1.5 26/7
SA467142BL15_1_21_1_1439Filtered lake water L 1.5 26/7
SA467143BL15_3_23_1_1441Filtered lake water L 1.5 26/7
SA467144NL15_1_45_1_1642Filtered lake water L 1.5 27/9
SA467145NL15_4_48_1_1645Filtered lake water L 1.5 27/9
SA467146NL15_3_47_1_1644Filtered lake water L 1.5 27/9
SA467147NL15_2_46_1_1643Filtered lake water L 1.5 27/9
SA467124DL15_1_13_1_1482Filtered lake water L 1.5 2/8
SA467125DL15_2_14_1_1483Filtered lake water L 1.5 2/8
SA467126DL15_3_15_1_1484Filtered lake water L 1.5 2/8
SA467127DL15_4_16_1_1485Filtered lake water L 1.5 2/8
SA467148CL15_3_7_1_1474Filtered lake water L 1.5 28/7
SA467149CL15_1_5_1_1472Filtered lake water L 1.5 28/7
SA467150CL15_2_6_1_1473Filtered lake water L 1.5 28/7
SA467151CL15_4_8_1_1475Filtered lake water L 1.5 28/7
SA467152IL15_3_7_1_1594Filtered lake water L 1.5 30/8
SA467153IL15_4_8_1_1595Filtered lake water L 1.5 30/8
SA467154IL15_1_5_1_1592Filtered lake water L 1.5 30/8
SA467155IL15_2_6_1_1593Filtered lake water L 1.5 30/8
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 224

Collection:

Collection ID:CO004180
Collection Summary:Lake Aydat (45.6°N; 2.9°E) is in the French Massif Central, around 15 km southwest of Clermont Ferrand, at 837 m above sea level. The monitoring of Lake Aydat has been conducted from August 05th, 2021, to September 27th, 2021. Weekly and sporadic surface lake water samples are taken both prior to and following precipitation events. At each depth (0 or 1.5 m) and location (L=inflow; Z=center of the lake), approximately 10 liters of lake water collected with a Van Dorn bottle are then pre-filtered through a 250-micrometer Nylon filter to remove larger particles and kept phytoplankton, and then transferred into 15-liter containers. The lake water is immediately filtered in the laboratory using a 150-μm Nylon membrane to avoid the presence of zooplankton in the lake samples. For each depth and location, one liter of lake water is filtered on 10-μm nylon membranes using ultra-fast filtration and then are immediately transferred into 15 mL sterile falcon tubes and quickly flash-frozen in liquid nitrogen to preserve the samples for metabolomics analysis.
Sample Type:Algae
Collection Location:Aydat lake (France)
Collection Frequency:Weekly
Collection Duration:2 month
Volumeoramount Collected:10 L
Storage Conditions:-20℃

Treatment:

Treatment ID:TR004196
Treatment Summary:No treatment was applied to the water samples, that were collected accordingly. For each depth and location, one liter of lake water is filtered on 10-μm nylon membranes using ultra-fast filtration and then are immediately transferred into 15 mL sterile falcon tubes and quickly flash-frozen in liquid nitrogen to preserve the samples for metabolomics analysis. This process, known as quenching, is performed as quickly as possible to ensure a reliable method and minimize any disturbance to the endo-metabolism of cells. The filtration time for each sample is less than 30 seconds, and the Falcon tubes are kept at -20°C until the day of extraction. This procedure is applied four times to ensure four replicates of each sample per site and depth. Blanks are performed by filtering 1 liter of sterile ultra-pure water.
Treatment Protocol ID:Phytoplankton sampling was performed by filtering on 10-μm nylon membranes without any specific treament
Treatment Protocol Filename:No treatment
Treatment Protocol Comments:No treatment
Treatment:Phytoplankton sampling was performed by filtering on 10-μm nylon membranes without any specific treament
Treatment Compound:No treatment
Treatment Route:No treatment
Treatment Dose:No treatment
Treatment Dosevolume:No treatment
Treatment Doseduration:No treatment
Treatment Vehicle:No treatment

Sample Preparation:

Sampleprep ID:SP004193
Sampleprep Summary:On the day of extraction, we rinse the filter with 1 mL of sterile MQ water mixed with 0.1% NaCl and then vortex it. The filter is then centrifuged at 4°C (5,000 g, 5 min) with the Falcon tube cap attached, and we transfer the pellet to an Eppendorf tube. The Eppendorf tube is centrifuged at 4°C (15000 g, 10 min) and the supernatant is discarded, allowing us to weigh the pellet. We adjust the volume of an ice-cold solvent mixture, composed of methanol, acetonitrile, and water in a 2:2:1 ratio, according to the weighed biomass: 100 μL of the ice-cold solvent mixture corresponds to 1 mg of biomass. For the blank, we systematically add 200 μL of the mixture. Next, we subject the samples to mechanical disruption through three cycles of freezing and thawing using liquid nitrogen, alternating with three cycles of sonication. Each sonication cycle lasts 15 seconds and is performed at a power of 40% using a Fisherbrand™ Model 120 Sonic Dismembrator. Throughout this process, we keep the samples in ice. After extraction, the samples are centrifuged at 4°C (15000 g, 10 min) before being transferred into 40 μL vials (AR0-9973-13, Verex™ Vial Kit) and stored at -80°C until the detection of metabolites. In total, we extract 224 samples through four serial extractions, with a blank sample added systematically in each serial.
Processing Storage Conditions:-80℃
Extract Storage:On ice

Chromatography:

Chromatography ID:CH005076
Chromatography Summary:The extracts are further analyzed by injecting 2 μL of the solution onto a C18 column (Polar Advantage II 2.5 pore, Thermo) using an ultra-high-performance liquid chromatography (UHPLC) system (ELUTE, Bruker). The elution is done at a flow rate of 300 μL.min-1 with a linear gradient of acetonitrile in 0.1% formic acid (5 to 90%) over a period of 21 minutes. Next, we analyze the individual metabolite content using a high-resolution electrospray ionization hybrid quadrupole time-of-flight (ESI-Qq-TOF) mass spectrometer (Compact, Bruker) operating in positive auto MS/MS mode.
Instrument Name:ELUTE BRUKER
Column Name:Thermo Acclaim Polar Advantage II (150 x 3mm,3um)
Column Temperature:40
Flow Gradient:Linear gradient of 5-90% B over 21 min
Flow Rate:300 uL/min
Internal Standard:Sodium formate
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN006680
Laboratory Name:PtSMB
Analysis Type:MS
Operator Name:Benjamin MARIE
Chromatography ID:CH005076
Has Rt:1
Rt Units:Seconds
Results File:ST004041_AN006680_Results.txt
Units:Peak area (counts)
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