Data Package Metadata View Summary

Effects of freshwater salinization on a salt-naïve planktonic eukaryote community

General Information

Data Package:
Local Identifier:	edi.516.2
Title:	Effects of freshwater salinization on a salt-naïve planktonic eukaryote community
Alternate Identifier:	DOI PLACE HOLDER
Abstract:	Salinization of freshwater ecosystems is a widespread issue, but evidence of ecological effects on aquatic eukaryote communities remains scarce. We experimentally exposed naive planktonic communities of a north-temperate, freshwater lake to a gradient of chloride (Cl-) concentration (0.27-1400 mg Cl-.L-1) with in-situ mesocosms. Following six weeks of exposure, we measured changes in the diversity, composition, and abundance of eukaryotic 18S rRNA gene. Total phytoplankton biomass remained unchanged, but we observed a shift in dominant phytoplankton groups with elevated salt concentration, from Cryptophyta and Chlorophyta that dominated in lower chloride concentrations (<185 mg Cl-.L-1) to Ochrophyta that dominated at higher conductivity (>185 mg Cl-.L-1). Most zooplankton and rotifer taxa were sensitive to the salinity and disappeared at low chloride concentrations (<40 mg Cl-.L-1). While ciliates thrived at low chloride concentrations (<185 mg Cl-.L-1), fungal groups dominated at intermediate chloride concentrations (185 mg Cl-.L-1 to 640 mg Cl-.L-1), and only phytoplankton remained at the highest chloride concentrations (> 640 mg Cl-.L-1).
Publication Date:	2021-10-27

Time Period

Begin:

2018-07-23

End:

2018-08-03

People and Organizations
Contact:	Derry, Alison (UQAM, PI) [ email ]
Creator:	Astorg, Louis (UQAM, PhD student)
Creator:	Gagnon, Jean-Christophe (UQAM, MSc student)
Creator:	Lazar, Cassandre (UQAM, PI)
Creator:	Derry, Alison (UQAM, PI)
Associate:	Lazar, Cassandre (UQAM, PI, DNA extraction and sequencing)

Data Entities
Data Table Name:	Environmental variable
Description:	Set of environmental variables measured in mesocosms
Data Table Name:	Chlorophyll a
Description:	Measures of chlorophyll a in the mesocosms
Data Table Name:	ASV table
Description:	ASV sequence count table
Data Table Name:	ASVs taxonomy
Description:	Taxonomy of the different ASV sequences
Data Table Name:	Conductivity_chloride_relationship
Description:	Provide conductivity chloride concentration realtionship from 21 mesocosms at the start of the experiement

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/516/2/1b8dc89c064f7099a9493a77b76dd4ac
Name:	Environmental variable
Description:	Set of environmental variables measured in mesocosms
Number of Records:	19
Number of Columns:	10

Table Structure

Object Name:

env.csv

Size:

1082 byte

Authentication:

417417fd9b84f0a9305ed8919ef5da31 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

mesocosm

Temp (C)

Cond (SPC)

Sal (ppt)

DO (%)

treatment

time

date

Column Name:

mesocosm

Temp (C)

Conductivity

Sal (ppt)

DO (%)

treatment

time

date

Definition:

mesocosm name

Water tmperature in celsius

Water conductivity microS.cm-2

Water salinity

Water pH

Water dissolved oxygene

Salt (NaCl) treatment level

Sampling time t0 = start, t1=week 3, t2=week6

Sampling dates

Water Total Phosphorus

Storage Type:

string

float

string

dateTime

float

Measurement Type:

nominal

ratio

nominal

dateTime

ratio

Measurement Values Domain:

Definition

mesocosm name

Unit	celsius
Type	real

Unit	microS.cm-2
Type	real

Unit	part per trillion
Type	real

Unit	no unit
Type	real

Unit	percent
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No NaCl added
Source

Code Definition

Code	3
Definition	Level of NaCl number 3
Source

Code Definition

Code	5
Definition	Level of NaCl number 5
Source

Code Definition

Code	8
Definition	Level of NaCl number 8
Source

Code Definition

Code	11
Definition	Level of NaCl number 11
Source

Code Definition

Code	13
Definition	Level of NaCl number 13
Source

Code Definition

Code	15
Definition	Level of NaCl number 15
Source

Code Definition

Code	18
Definition	Level of NaCl number 18
Source

Code Definition

Code	20
Definition	Level of NaCl number 20
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	t0
Definition	Start of the experiment
Source

Code Definition

Code	t1
Definition	Sampling three weeks after the start of the experiment
Source

Code Definition

Code	t2
Definition	Sampling six weeks after the start of the experiment
Source

Format	DD-MM-YYYY
Precision

Unit	microgramPerLiter
Type	real

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/516/2/c304212ddea8800e84aa7c496f73920b
Name:	Chlorophyll a
Description:	Measures of chlorophyll a in the mesocosms
Number of Records:	19
Number of Columns:	5

Table Structure

Object Name:

Chla_18S.csv

Size:

446 byte

Authentication:

59a99863ae6284d4e2ac25de3c226a12 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

nom

Chla

WEEK

CONC

conductivity

Column Name:

nom

Chla

WEEK

CONC

conductivity

Definition:

Mesocosm name

Water chlorophyll a concentration

Sampling week, Lac = lac reference

Salt (NaCl) treatment level

Water conductivity

Storage Type:

string

float

string

float

Measurement Type:

nominal

ratio

nominal

ratio

Measurement Values Domain:

Definition

Mesocosm name

Unit	microgramPerLiter
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	3
Definition	Sampling three weeks after the start of the experiment
Source

Code Definition

Code	6
Definition	Sampling six weeks after the start of the experiment
Source

Code Definition

Code	Lac
Definition	Start of the experiment
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No NaCl added
Source

Code Definition

Code	3
Definition	Level of NaCl number 3
Source

Code Definition

Code	5
Definition	Level of NaCl number 5
Source

Code Definition

Code	8
Definition	Level of NaCl number 8
Source

Code Definition

Code	11
Definition	Level of NaCl number 11
Source

Code Definition

Code	13
Definition	Level of NaCl number 13
Source

Code Definition

Code	15
Definition	Level of NaCl number 15
Source

Code Definition

Code	18
Definition	Level of NaCl number 18
Source

Code Definition

Code	20
Definition	Level of NaCl number 20
Source

Unit	microS.cm-2
Type	real

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/516/2/a7107503dd56e0cc2fed45833a051c8b
Name:	ASV table
Description:	ASV sequence count table
Number of Records:	920
Number of Columns:	20

Table Structure

Object Name:

ASV_counts.csv

Size:

44698 byte

Authentication:

80fdaed45dfbc57528b8017d0b93c850 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

ASV

T0Meseuc

T3S0

T3S11

T3S13

T3S15

T3S18

T3S20

T3S3

T3S5

T3S8

T6S0euc

T6S11

T6S13

T6S15

T6S18

T6S20

T6S3

T6S5

T6S8

Column Name:

ASV

T0Meseuc

T3S0

T3S11

T3S13

T3S15

T3S18

T3S20

T3S3

T3S5

T3S8

T6S0euc

T6S11

T6S13

T6S15

T6S18

T6S20

T6S3

T6S5

T6S8

Definition:

ASV number

ASV sequence number in mesocosm of salt treatment 0 at the start of the experiement

ASV sequence number in mesocosm T3S0

ASV sequence number in mesocosm T3S11

ASV sequence number in mesocosm T3S13

ASV sequence number in mesocosm T3S15

ASV sequence number in mesocosm T3S18

ASV sequence number in mesocosm T3S20

ASV sequence number in mesocosm T3S3

ASV sequence number in mesocosm T3S5

ASV sequence number in mesocosm T3S8

ASV sequence number in mesocosm T6S0

ASV sequence number in mesocosm T6S11

ASV sequence number in mesocosm T6S13

ASV sequence number in mesocosm T6S15

ASV sequence number in mesocosm T6S18

ASV sequence number in mesocosm T6S20

ASV sequence number in mesocosm T6S3

ASV sequence number in mesocosm T6S5

ASV sequence number in mesocosm T6S8

Storage Type:

string

float

Measurement Type:

nominal

ratio

Measurement Values Domain:

Definition

ASV number

Unit	number
Type	real

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Unit	number
Type	integer

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/516/2/f53f0eda82ad8f5f4f451303a86f3967
Name:	ASVs taxonomy
Description:	Taxonomy of the different ASV sequences
Number of Records:	920
Number of Columns:	8

Table Structure

Object Name:

ASVs_taxonomy.csv

Size:

45301 byte

Authentication:

5dde3fb45162d1b04652cfea31e2df3b Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

ASV

domain

phylum

class

order

family

genus

species

Column Name:

ASV

domain

phylum

class

order

family

genus

species

Definition:

ASV number

Taxonomic domain of ASV

Taxonomic phylum of ASV

Taxonomic class of ASV

Taxonomic order of ASV

Taxonomic family of ASV

Taxonomic genus of ASV

Taxonomic species of ASV

Storage Type:

string

Measurement Type:

nominal

Measurement Values Domain:

Definition

ASV number

Definition

Taxonomic domain of ASV

Definition

Taxonomic phylum of ASV

Definition

Taxonomic class of ASV

Definition

Taxonomic order of ASV

Definition

Taxonomic family of ASV

Definition

Taxonomic genus of ASV

Definition

Taxonomic species of ASV

Missing Value Code:

Code	NA
Expl	Not known

Code	NA
Expl	Not known

Code	NA
Expl	Not known

Code	NA
Expl	Not known

Code	NA
Expl	Not known

Code	NA
Expl	Not known

Code	NA
Expl	Not known

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/516/2/24958aa7d587e9915d6907e2c119dd6a
Name:	Conductivity_chloride_relationship
Description:	Provide conductivity chloride concentration realtionship from 21 mesocosms at the start of the experiement
Number of Records:	21
Number of Columns:	4

Table Structure

Object Name:

Conductivity_chloride_relationship.csv

Size:

575 byte

Authentication:

26658f3e0b4412f19b438480d0ce6979 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Bag

Cond (SPC)

date

Cl (mg/L)

Column Name:

Bag

Cond (SPC)

date

Cl (mg/L)

Definition:

Bag salt level treatment

Specific water conductivity

Sampling date

Chloride concentration

Storage Type:

float

dateTime

float

Measurement Type:

ratio

dateTime

ratio

Measurement Values Domain:

Unit	number
Type	integer

Unit	microS.cm-2
Type	real

Format	DD-MM-YYYY
Precision

Unit	milligramPerLiter
Type	real

Missing Value Code:

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:
(No thesaurus)	Salinization, 18S rRNA metabarcoding, Freshwater, Eukaryote community, Chloride, Plankton

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:

The mesocosm experiment was implemented with water and biological communities from Lake Croche (45°59'17.34" N / 74° 0'20.75" O) (Fig. 1), which is located at the Station de biologie des Laurentides de l’Université de Montréal (Québec, Canada). Lake Croche is a salt-naïve oligo-mesotrophic lake situated in the Laurentian region of Québec, which lies within the Canadian Shield, and has a low ambient chloride concentration of 0.27 mg Cl-.L-1. The experimental design involved 21 mesocosms, from which we focused DNA sampling on 9 mesocosms (Fig. 1). The experiment was conducted for 6 weeks (June 23 to August 3, 2018). Lake water used to fill the mesocosms was sampled and analyzed at the beginning of the experiment (hereafter referred as ‘start’), and each mesocosm was sampled after 3 weeks and after 6 weeks from the start of the experiment. Initial chloride concentrations were measured along with conductivity from water samples collected from the mesocosms following the NaCl addition. Conductivity was subsequently utilized as a proxy of chloride concentration because of a strong relationship between chloride and conductivity in this experiment (R2 = 0.986, p = <2e-16), and further analysis were performed using calculated chloride concentration from conductivity measures.

To detect changes in the diversity, relative abundance, and community composition of planktonic eukaryotes, we analyzed eukaryotic 18S rRNA gene diversity from water samples collected from the mesocosms at the start of the experiment, and at each of weeks 3 and 6 of the experiment in 9 different mesocosms. DNA field sampling methods and laboratory methods for filtration, DNA extraction, PCR amplification and sequencing are provided in Appendix. For bioinformatics of 18S metabarcoding, the DADA2 (Callahan et al. 2016) workflow was used. Pseudo-pooling was used to infer Amplicon Sequence Variants (ASVs). ASVs refer to single DNA sequences recovered from a high-throughput marker gene analysis and are used to classify groups of species based on DNA sequences. We applied a variance stabilizing transformation method to normalize sampling depth in the different samples (McMurdie and Holmes 2014). We investigated the potential positive relationship between sampling depth and ASV diversity in the different samples which was actually found to be negative. Furthermore, we used R 4.0.3 (R Core Team 2020) phyloseq package (McMurdie and Holmes 2013) rarefaction function to analyze rarefied data. We therefore chose to report non-rarefied data in the main sections of the manuscript. Sequences are available at http://www.ncbi.nlm.nih.gov/bioproject/733220.

People and Organizations

Publishers:

Organization:

Environmental Data Initiative

Email Address:

info@environmentaldatainitiative.org

Web Address:

https://environmentaldatainitiative.org

Id:

https://ror.org/0330j0z60

Creators:

Individual:

Louis Astorg

Organization:

UQAM

Position:

PhD student

Email Address:

louisastorg@msn.com

Individual:	Jean-Christophe Gagnon
Organization:	UQAM
Position:	MSc student

Individual:	Cassandre Lazar
Organization:	UQAM
Position:	PI

Individual:	Alison Derry
Organization:	UQAM
Position:	PI

Contacts:

Individual:

Alison Derry

Organization:

UQAM

Position:

Email Address:

derry.alison@uqam.ca

Associated Parties:

Individual:

Cassandre Lazar

Organization:

UQAM

Position:

Email Address:

lazar.cassandre@uqam.ca

Role:

DNA extraction and sequencing

Metadata Providers:

Individual:

Louis Astorg

Organization:

UQAM

Position:

PhD student

Email Address:

louisastorg@msn.com

Temporal, Geographic and Taxonomic Coverage

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

Time Period

Begin:

2018-07-23

End:

2018-08-03

Sampling Site:

Description:

Site Coordinates:

Longitude (degree):

-74.017093

Latitude (degree):

45.976633

Project

Parent Project Information:

Title:

Effects of freshwater salinization on a salt-naïve planktonic eukaryote community

Personnel:

Individual:

Louis Astorg

Organization:

UQAM

Position:

PhD student

Email Address:

louisastorg@msn.com

Role:

First author

Individual:

Alison Derry

Organization:

UQAM

Position:

Email Address:

derry.alison@uqam.ca

Role:

designed the study, conducted field work

Maintenance

Maintenance:

Description:	No maintenance
Frequency:

Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n        '
        |___element 'metadata'
        |     |___text '\n            '
        |     |___element 'unitList'
        |     |     |___text '\n                '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = ' microS.cm-2'
        |     |     |     |  \___attribute 'name' = ' microS.cm-2'
        |     |     |     |___text '\n                    '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n                '
        |     |     |___text '\n                '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'part per trillion'
        |     |     |     |  \___attribute 'name' = 'part per trillion'
        |     |     |     |___text '\n                    '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n                '
        |     |     |___text '\n                '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'no unit'
        |     |     |     |  \___attribute 'name' = 'no unit'
        |     |     |     |___text '\n                    '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n                '
        |     |     |___text '\n                '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'microS.cm-2'
        |     |     |     |  \___attribute 'name' = 'microS.cm-2'
        |     |     |     |___text '\n                    '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n                '
        |     |     |___text '\n            '
        |     |___text '\n        '
        |___text '\n    '

Additional Metadata

additionalMetadata
        |___text '\n        '
        |___element 'metadata'
        |     |___text '\n            '
        |     |___element 'emlEditor'
        |     |        \___attribute 'app' = 'ezEML'
        |     |        \___attribute 'release' = '2021.10.22'
        |     |___text '\n        '
        |___text '\n    '

Copyright 2024 Environmental Data Initiative. This material is based upon work supported by the National Science Foundation under grants #2223103 and #2223104. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Please contact us with questions, comments, or for technical assistance regarding this web site or the Environmental Data Initiative. Please read our privacy policy to know what information we collect about you and to understand your privacy rights.

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

Data Package Metadata View Summary

Effects of freshwater salinization on a salt-naïve planktonic eukaryote community

Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Data Package Usage Rights

Keywords

Methods and Protocols

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

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Parent Project Information:

Maintenance

Additional Metadata

Additional Metadata

Recently Added

Recently Updated

Data Package Metadata View Summary

Effects of freshwater salinization on a salt-naïve planktonic eukaryote community

+/- Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

+/- Data Package Usage Rights

+/- Keywords

+/- Methods and Protocols

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

+/- People and Organizations

+/- Temporal, Geographic and Taxonomic Coverage

+/- Project

Parent Project Information:

+/- Maintenance

+/- Additional Metadata

+/- Additional Metadata

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance

Additional Metadata

Additional Metadata