Data Package Metadata View Summary

Leaf litter, soil, and periphyton gene expression along freshwater to marine gradients in Everglades National Park (FCE LTER), Florida, USA, January 2021 and April 2021

General Information

Data Package:

Local Identifier:

knb-lter-fce.1270.1

Title:

Leaf litter, soil, and periphyton gene expression along freshwater to marine gradients in Everglades National Park (FCE LTER), Florida, USA, January 2021 and April 2021

Alternate Identifier:

DOI PLACE HOLDER

Abstract:

We collected leaf litter, periphyton, and soil along freshwater to marine gradients at SRS-2, SRS-4, SRS-6, TS/PH-2, TS/Ph-3, TS/Ph-7a, and TS/Ph-10. Samples were collected in January and April of 2021 to understand how microbial communities respond to and influence the breakdown of organic matter along freshwater to marine transects. Data collection for this project is complete.

We selected n = 12 genes/gene families encoding for focal enzymes to investigate which are important to the breakdown of organic matter: Dioxygenases (associated with aerobic respiration), Sulfatases (associated with the release of sulfates from complex molecules), sulfite reductases (associated with sulfite reduction), methyl coenzyme M reductase and formylmethanofuran (associated with methanogenesis), nitrite reductases (associated with nitrite reduction), cellobiosidase, glucosidase, and xylosidase (associated with cellulose breakdown), phenol oxidase (associated with lignin breakdown), acid phosphatase (associated with phosphate acquisition in acidic environments), and alkaline phosphatase (associated with phosphate acquisition in basic environments). For each gene/family of interest, we searched all annotated transcripts for all entries corresponding to that gene/family and combined all values for a total expression.

We selected n = 6 monophyletic microbial functional groups, representing sulfate reducers, sulfate oxidizers, methane oxidizers, methanogens, nitrite oxidizers, and ammonia oxidizers associated with sulfate and methane cycling. We filtered all annotated transcripts for all species with the following in the name: in the name: ‘desulfo’ for sulfate reducers, ‘sulfito’ for sulfite oxidizers, ‘methylo’ for methyl/methane oxidizers, ‘methano’ for methanogens, ‘nitro’ for nitrite oxidizers, and ‘nitroso’ for aerobic ammonia oxidizers.

Publication Date:

2024-07-24

For more information:
Visit:	DOI PLACE HOLDER

Time Period

Begin:

2021

End:

2021

People and Organizations
Contact:	Information Manager (Florida Coastal Everglades LTER) [ email ]
Contact:	Anderson, Kenneth (Kent State University, Post-doctoral Scholar) [ email ]
Creator:	Anderson, Kenneth J (Kent State University, Post-doctoral Scholar)
Creator:	Kominoski, John S (Florida International University, Associate Professor)
Creator:	Choi, Chang Jae (University of Florida, Post-doctoral Scholar)
Creator:	Stingl, Ulrich (University of Florida, Assistant Professor)

Data Entities
Data Table Name:	FCE1270_FocalGenedata
Description:	Transcriptomic gene expression from deployed litter samples, soil samples, and periphyton samples.

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/knb-lter-fce/1270/1/1cc3807f30fe631a87fecf117bb49b44
Name:	FCE1270_FocalGenedata
Description:	Transcriptomic gene expression from deployed litter samples, soil samples, and periphyton samples.
Number of Records:	66
Number of Columns:	18

Table Structure

Object Name:

FCE1270_FocalGenedata.csv

Size:

11548 byte

Authentication:

37cfcb91a5c13d5aba8bd336b0f381d9 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

SITENAME

Species

Month

Type

Dioxygenases

Sulfatases

Sulfite Reductases

Formylmethanofuran

Nitrite reductases

Cellobiosidase

Glucosidase

Xylosidase

Phenol Oxidase

Alkaline phosphatase

Acid Phosphatase

k.dd

Salinity

Column Name:

SITENAME

Species

Month

Type

Dioxygenases

Sulfatases

Sulfite_Reductases

Formylmethanofuran

Nitrite_reductases

Cellobiosidase

Glucosidase

Xylosidase

Phenol_Oxidase

Alkaline_phosphatase

Acid_Phosphatase

k.dd

Salinity

Definition:

Name of LTER site

Species of Vegetation microbes were isolated from

Month during which samples were collected

This column groups by whether samples are from deployed leaf litter packs, periphyton, or soil.

Summed total relative expression of genes associated with dioxygenases

Summed total relative expression of genes associated with sulfatases

Summed total relative expression of genes associated with sulfite reductases

Summed total relative expression of genes associated with formylmethanofuran

Summed total relative expression of genes associated with nitrite reductases

Summed total relative expression of genes associated with cellobiosidases

Summed total relative expression of genes associated with glucosidases

Summed total relative expression of genes associated with xylosidases

Summed total relative expression of genes associated with phenol oxidases

Summed total relative expression of genes associated with alkaline phosphatases

Summed total relative expression of genes associated with acid phosphatases

leaf litter breakdown rate per degree day

water salinity

Total phosphorus in the water column

Storage Type:

string

float

Measurement Type:

nominal

ratio

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	SRS2
Definition	Site SRS-2
Source

Code Definition

Code	SRS4
Definition	Site SRS-4
Source

Code Definition

Code	SRS6
Definition	Site SRS-6
Source

Code Definition

Code	TS/Ph10
Definition	Site TS/Ph-10
Source

Code Definition

Code	TS/Ph2
Definition	Site TS/Ph-2
Source

Code Definition

Code	TS/Ph3
Definition	Site TS/Ph-3
Source

Code Definition

Code	TS/Ph7a
Definition	Site TS/Ph-7a
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Eleocharis
Definition	Eleocharis cellulosa
Source

Code Definition

Code	Mangrove
Definition	Rhizophora mangle
Source

Code Definition

Code	Periphyton
Definition	Mixed periphyton was collected for these samples.
Source

Code Definition

Code	Sawgrass
Definition	Cladium jamaicense
Source

Code Definition

Code	Soil
Definition	Soil from the top 10cm of the soil was collected for these samples
Source

Code Definition

Code	Thalassia
Definition	Thalassia testudinum
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1
Definition	January
Source

Code Definition

Code	4
Definition	April
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Litter
Definition	Samples from deployed leaf litter packs
Source

Code Definition

Code	Peri
Definition	Samples where periphyton was collected if present.
Source

Code Definition

Code	Soil
Definition	Samples where soil was collected from the top 10cm of the soil surface
Source

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	k.dd
Type	real

Unit	PSU
Precision	0.1
Type	real

Unit	micromolePerLiter
Precision	0.01
Type	real

Missing Value Code:

Code	NA
Expl	Soil and periphyton samples have no breakdown rate as they were environmental samples and not deployed leaf litter.

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
FCE Keyword List	FCE LTER, LTER, Florida Coastal Everglades LTER
LTER Controlled Vocabulary	microbes, decomposition, litter decomposition
LTER Core Research Areas	disturbance

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:

For each site and litter pair we collected a subset of 2-3 g wet mass of litter, a grab sample of soil, and a grab sample of periphyton for each site. All subsamples were preserved at -20°C until extraction, which took place up to a year after initial collection. Samples were sent to Novogene (Novogene Co. Ltd., Beijing, China) for the total RNA extraction followed by metatranscriptome sequencing. Briefly, the total RNA was extracted using TRIzol reagent (Rio et al. 2010) and the quality and quantity of the RNA were assessed using the Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and Nanodrop ND-1000 (ThermoScientific, Waltham, MA, USA), respectively. After the total RNA samples passed the quality check, cDNA libraries were prepared from total RNA using poly(A) enrichment of the mRNA to remove rRNA resulting in the construction of 250-300 bp insert cDNA libraries and sequenced by paired-end (PE) sequencing (PE 2 × 150 bp) using an Illumina NovaSeq 6000 platform (NovaSeq Reagent Kits, Illumina, Inc., San Diego, CA, USA).

Raw reads were processed using the Simple Annotation of Metatranscriptomes by Sequence Analysis 2.0 (SAMSA2) pipeline (Westreich et al. 2018) with slight modification. Briefly, low quality bases were trimmed using Trimmomatic v0.39 (Bolger et al. 2014) and overlapping paired-end reads were merged into single sequences using PEAR v0.9.11 (Zhang et al. 2014). Ribosomal RNA reads were removed with SortMeRNA v2.1 (Kopylova et al. 2012) and the cleaned transcripts were annotated by DIAMOND v0.9.36 (Buchfink et al. 2021) against the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (O'leary et al. 2016) for taxonomic and functional characterization. The resulting annotation files were aggregated and merged with custom Python and R scripts included in the SAMSA2 pipeline (Westreich et al. 2018).

We selected n = 12 genes/gene families encoding for focal enzymes to investigate which are important to the breakdown of organic matter: Dioxygenases (associated with aerobic respiration), Sulfatases (associated with the release of sulfates from complex molecules), sulfite reductases (associated with sulfite reduction), methyl coenzyme M reductase and formylmethanofuran (associated with methanogenesis), nitrite reductases (associated with nitrite reduction), cellobiosidase, glucosidase, and xylosidase (associated with cellulose breakdown), phenol oxidase (associated with lignin breakdown), acid phosphatase (associated with phosphate acquisition in acidic environments), and alkaline phosphatase (associated with phosphate acquisition in basic environments; Table 1). For each gene/family of interest, we searched all annotated transcripts for all entries corresponding to that gene/family and combined all values for a total expression.

References:

Bolger, A. M., M. Lohse, and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.

Buchfink, B., K. Reuter, and H.-G. Drost. 2021. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nature Methods 18: 366-368.

Kopylova, E., L. Noé, and H. Touzet. 2012. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28: 3211-3217.

O'leary, N. A. and others 2016. Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation. Nucleic Acids Research 44: D733-D745.

Rio, D. C., M. Ares, G. J. Hannon, and T. W. Nilsen. 2010. Purification of RNA using TRIzol (TRI reagent). Cold Spring Harbor Protocols 2010: pdb. prot5439.

Westreich, S. T., M. L. Treiber, D. A. Mills, I. Korf, and D. G. Lemay. 2018. SAMSA2: A standalone metatranscriptome analysis pipeline. BMC bioinformatics 19: 1-11.

Zhang, J., K. Kobert, T. Flouri, and A. Stamatakis. 2014. PEAR: A fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30: 614-620.

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:

Kenneth J Anderson

Organization:

Kent State University

Position:

Post-doctoral Scholar

Email Address:

kanderson624@gmail.com

Id:

https://orcid.org/0000-0002-1202-1453

Individual:

John S Kominoski

Organization:

Florida International University

Position:

Associate Professor

Email Address:

jkominos@fiu.edu

Id:

https://orcid.org/0000-0002-0978-3326

Individual:

Chang Jae Choi

Organization:

University of Florida

Position:

Post-doctoral Scholar

Email Address:

changjae.choi@ufl.edu

Id:

https://orcid.org/0000-0002-0831-7470

Individual:

Ulrich Stingl

Organization:

University of Florida

Position:

Assistant Professor

Email Address:

ustingl@ufl.edu

Id:

https://orcid.org/0000-0002-0684-2597

Contacts:

Organization:

Florida Coastal Everglades LTER

Position:

Information Manager

Address:

Florida International University,

11200 SW 8th Street, OE 148,

Miami, FL 33199 USA

Email Address:

fcelter@fiu.edu

Web Address:

https://fcelter.fiu.edu

Individual:

Kenneth Anderson

Organization:

Kent State University

Position:

Post-doctoral Scholar

Email Address:

kanderson624@gmail.com

Id:

https://orcid.org/0000-0002-1202-1453

Metadata Providers:

Organization:

Florida Coastal Everglades LTER

Address:

Florida International University,

11200 SW 8th Street, OE 148,

Miami, FL 33199 USA

Phone:

305-348-6054 (voice)

Email Address:

fcelter@fiu.edu

Web Address:

https://fcelter.fiu.edu

Id:

https://ror.org/03davk141

Temporal, Geographic and Taxonomic Coverage

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

Time Period

Begin:

2021

End:

2021

Sampling Site:

Description:

SRS2

Site Coordinates:

Longitude (degree):

-80.78520692

Latitude (degree):

25.54972811

Sampling Site:

Description:

SRS4

Site Coordinates:

Longitude (degree):

-80.96431016

Latitude (degree):

25.40976421

Sampling Site:

Description:

SRS6

Site Coordinates:

Longitude (degree):

-81.07794623

Latitude (degree):

25.36462994

Sampling Site:

Description:

TS/Ph2

Site Coordinates:

Longitude (degree):

-80.60690341

Latitude (degree):

25.40357188

Sampling Site:

Description:

TS/Ph3

Site Coordinates:

Longitude (degree):

-80.66271768

Latitude (degree):

25.25240534

Sampling Site:

Description:

TS/Ph7a

Site Coordinates:

Longitude (degree):

-80.63910514

Latitude (degree):

25.19080491

Sampling Site:

Description:

TS/Ph10

Site Coordinates:

Longitude (degree):

-80.68097374

Latitude (degree):

25.02476744

Taxonomic Range:

Classification:

Rank Name:

Kingdom

Rank Value:

Plantae

Common Name:

plants

Identifer:

https://www.itis.gov
ID: 202422

Classification:

Rank Name:

Subkingdom

Rank Value:

Viridiplantae

Common Name:

green plants

Identifer:

https://www.itis.gov
ID: 954898

Classification:

Rank Name:

Infrakingdom

Rank Value:

Streptophyta

Common Name:

land plants

Identifer:

https://www.itis.gov
ID: 846494

Classification:

Rank Name:

Division

Rank Value:

Tracheophyta

Common Name:

vascular plants

Identifer:

https://www.itis.gov
ID: 846496

Classification:

Rank Name:

Subdivision

Rank Value:

Spermatophytina

Common Name:

spermatophytes

Identifer:

https://www.itis.gov
ID: 846504

Classification:

Rank Name:

Class

Rank Value:

Magnoliopsida

Identifer:

https://www.itis.gov
ID: 18063

Classification:

Rank Name:

Superorder

Rank Value:

Rosanae

Identifer:

https://www.itis.gov
ID: 846548

Classification:

Rank Name:

Order

Rank Value:

Malpighiales

Identifer:

https://www.itis.gov
ID: 822428

Classification:

Rank Name:

Family

Rank Value:

Rhizophoraceae

Common Name:

mangroves

Identifer:

https://www.itis.gov
ID: 27789

Classification:

Rank Name:

Genus

Rank Value:

Rhizophora

Common Name:

mangrove

Identifer:

https://www.itis.gov
ID: 27790

Classification:

Rank Name:	Species
Rank Value:	Rhizophora mangle
Common Name:	American mangrove
Identifer:	https://www.itis.gov ID: 27791

Taxonomic Range:

Classification:

Rank Name:

Kingdom

Rank Value:

Plantae

Common Name:

plants

Identifer:

https://www.itis.gov
ID: 202422

Classification:

Rank Name:

Subkingdom

Rank Value:

Viridiplantae

Common Name:

green plants

Identifer:

https://www.itis.gov
ID: 954898

Classification:

Rank Name:

Infrakingdom

Rank Value:

Streptophyta

Common Name:

land plants

Identifer:

https://www.itis.gov
ID: 846494

Classification:

Rank Name:

Division

Rank Value:

Tracheophyta

Common Name:

vascular plants

Identifer:

https://www.itis.gov
ID: 846496

Classification:

Rank Name:

Subdivision

Rank Value:

Spermatophytina

Common Name:

spermatophytes

Identifer:

https://www.itis.gov
ID: 846504

Classification:

Rank Name:

Class

Rank Value:

Magnoliopsida

Identifer:

https://www.itis.gov
ID: 18063

Classification:

Rank Name:

Superorder

Rank Value:

Lilianae

Common Name:

monocots

Identifer:

https://www.itis.gov
ID: 846542

Classification:

Rank Name:

Order

Rank Value:

Poales

Identifer:

https://www.itis.gov
ID: 846620

Classification:

Rank Name:

Family

Rank Value:

Cyperaceae

Common Name:

sedges

Identifer:

https://www.itis.gov
ID: 39357

Classification:

Rank Name:

Genus

Rank Value:

Cladium

Common Name:

sawgrass

Identifer:

https://www.itis.gov
ID: 39877

Classification:

Rank Name:	Species
Rank Value:	Cladium jamaicense
Common Name:	Jamaica swamp sawgrass
Identifer:	https://www.itis.gov ID: 39878

Taxonomic Range:

Classification:

Rank Name:

Kingdom

Rank Value:

Viridiplantae

Common Name:

green plants

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 33090 (Viridiplantae)

Classification:

Rank Name:

Phylum

Rank Value:

Streptophyta

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 35493 (Streptophyta)

Classification:

Rank Name:

Subphylum

Rank Value:

Streptophytina

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 131221 (Streptophytina)

Classification:

Rank Name:

Class

Rank Value:

Magnoliopsida

Common Name:

flowering plants

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 3398 (Magnoliopsida)

Classification:

Rank Name:

Order

Rank Value:

Alismatales

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 16360 (Alismatales)

Classification:

Rank Name:

Family

Rank Value:

Hydrocharitaceae

Common Name:

tape-grass family

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 26319 (Hydrocharitaceae)

Classification:

Rank Name:

Genus

Rank Value:

Thalassia

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 55495 (Thalassia)

Classification:

Rank Name:	Species
Rank Value:	Thalassia testudinum
Identifer:	National Center for Biotechnology Information - Taxonomy (NCBI) Info for ID: 55497 (Thalassia testudinum)

Taxonomic Range:

Classification:

Rank Name:

Kingdom

Rank Value:

Viridiplantae

Common Name:

green plants

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 33090 (Viridiplantae)

Classification:

Rank Name:

Phylum

Rank Value:

Streptophyta

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 35493 (Streptophyta)

Classification:

Rank Name:

Subphylum

Rank Value:

Streptophytina

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 131221 (Streptophytina)

Classification:

Rank Name:

Class

Rank Value:

Magnoliopsida

Common Name:

flowering plants

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 3398 (Magnoliopsida)

Classification:

Rank Name:

Subclass

Rank Value:

Petrosaviidae

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 1437197 (Petrosaviidae)

Classification:

Rank Name:

Order

Rank Value:

Poales

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 38820 (Poales)

Classification:

Rank Name:

Family

Rank Value:

Cyperaceae

Common Name:

sedge family

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 4609 (Cyperaceae)

Classification:

Rank Name:

Subfamily

Rank Value:

Cyperoideae

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 986140 (Cyperoideae)

Classification:

Rank Name:

Genus

Rank Value:

Eleocharis

Common Name:

spikerushes

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 46324 (Eleocharis)

Classification:

Rank Name:	Species
Rank Value:	Eleocharis cellulosa
Identifer:	National Center for Biotechnology Information - Taxonomy (NCBI) Info for ID: 110283 (Eleocharis cellulosa)

Project

Parent Project Information:

Title:

LTER: Coastal Oligotrophic Ecosystem Research

Personnel:

Individual:

John Kominoski

Address:

Florida International University,

11200 S.W. 8th Street,

Miami, FL 33199 US

Email Address:

jkominos@fiu.edu

Id:

https://orcid.org/0000-0002-0978-3326

Role:

Lead Principal Investigator

Individual:	James Fourqurean
Id:	https://orcid.org/0000-0002-0811-8500
Role:	Co-Principal Investigator

Individual:	Evelyn Gaiser
Id:	https://orcid.org/0000-0003-2065-4821
Role:	Co-Principal Investigator

Individual:	Jennifer Rehage
Id:	https://orcid.org/0000-0003-0009-6906
Role:	Co-Principal Investigator

Individual:	Kevin Grove
Id:	https://orcid.org/0000-0001-9114-5050
Role:	Co-Principal Investigator

Abstract:

Coastal ecosystems like the Florida Everglades provide many benefits and services to society including protection from storms, habitat and food for important fisheries, support of tourism and local economies, filtration of fresh water, and burial and storage of carbon that offsets greenhouse gas emissions. The Florida Coastal Everglades Long Term Ecological Research (FCE LTER) program addresses how and why coastal ecosystems and their services are changing. Like many coastal ecosystems, the Florida Everglades has been threatened by diversion of fresh water to support urban and agricultural expansion. At the same time, sea-level rise has caused saltwater intrusion of coastal ecosystems which stresses freshwater species, causes elevation loss, and contaminates municipal water resources. However, restoration of seasonal pulses of fresh water may counteract these threats. Researchers in the FCE LTER are continuing long-term studies and experiments to understand how changes in freshwater supply, sea-level rise, and disturbances like tropical storms interact to influence ecosystems and their services. The science team is guided by a diversity and inclusion plan to attract diverse scientists at all career stages. The team includes resource managers – who use discoveries and knowledge from the FCE LTER to guide effective freshwater restoration – and an active community of academic and agency scientists, teachers and other educators, graduate, undergraduate, and high school students. The project has a robust education and outreach program that engages the research team with the general public to advance science discoveries and protection of coastal ecosystems.

Additional Award Information:

Funder:

National Science Foundation

Funder ID:

https://ror.org/021nxhr62

Number:

2025954

Title:

LTER: Coastal Oligotrophic Ecosystem Research

URL:

https://www.nsf.gov/awardsearch/showAward?AWD_ID=2025954&HistoricalAwards=false

Related Project:

Title:

FCE LTER IV: Drivers of Abrupt Change in the Florida Coastal Everglades

Personnel:

Individual:	Evelyn Gaiser
Id:	https://orcid.org/0000-0003-2065-4821
Role:	Lead Principal Investigator

Abstract:

Coastal ecosystems like the Florida Everglades provide many benefits to society. They protect coastlines from storms and store carbon. They provide habitat and food for important fisheries. They also support tourism and local economies, and store freshwater for millions of people. The Florida Coastal Everglades Long Term Ecological Research (FCE LTER) program addresses how and why coastal ecosystems are changing in response to sea level rise and the actions of people. Like many coastal ecosystems, the Florida Everglades are threatened by the diversion of freshwater to support urban and agricultural expansion. At the same time, sea level rise has caused coastal ecosystems to become saltier, threatening the freshwater supply, stressing freshwater plants, and causing the soils to collapse. When the soils beneath coastal wetlands disappear, seawater invades even more quickly. Researchers in the FCE LTER are continuing long-term studies and experiments to understand how these changes influence ecosystem functions and services. They are also developing tools for resource managers to create an effective freshwater restoration program. The science team includes an active community of graduate students. As a group, they reach the public through education and outreach activities, and regularly advise policy-makers on resource management decisions. The FCE LTER research program addresses how changing fresh and marine supplies of water influence coastal ecosystem dynamics through: (i) continued long-term assessment of changes in biogeochemistry, primary production, organic matter, and trophic dynamics in ecosystems along freshwater-to-marine gradients, (ii) maintenance of existing in situ and ex situ long-term experiments, (iii) use of high-resolution remote sensing, coupled with models to forecast landscape-scale changes, (iv) addition of synoptic satellite sites to capture discrete spatio-temporal responses to episodic disturbance, and (v) initiation of new experimental manipulations to determine drivers and mechanisms of resilience to saltwater intrusion. Data syntheses integrate month-to-annual and inter-annual data into models of water, nutrients, carbon, and species dynamics throughout the Everglades landscape to compare how ecosystems with different productivities and carbon stores respond (maintain, increase, or decline) to short- (pulses) and long-term changes (presses) in hydrologic connectivity. Understanding and predicting the drivers of abrupt changes in ecosystems is a key challenge in ecosystem ecology.

Additional Award Information:

Funder:

National Science Foundation

Funder ID:

https://ror.org/021nxhr62

Number:

1832229

Title:

LTER: Drivers of Abrupt Change in the Florida Coastal Everglades

URL:

https://www.nsf.gov/awardsearch/showAward?AWD_ID=1832229&HistoricalAwards=false

Maintenance

Maintenance:

Description:	knb-lter-fce.1270.1: Initial publication of dataset. Data collection is complete.
Frequency:

Other Metadata

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        |     |     |     |___text '\n               '
        |     |     |     |___element 'permit'
        |     |     |     |     |___text 'EVER-2019-SCI-0055'
        |     |     |     |___text '\n            '
        |     |     |___text '\n         '
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        |___element 'metadata'
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        |     |___element 'fetchedFromEDI'
        |     |        \___attribute 'dateFetched' = '2022-12-06'
        |     |        \___attribute 'packageID' = 'FCE Template'
        |     |___text '\n      '
        |___text '\n   '

Additional Metadata

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        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'importedFromXML'
        |     |        \___attribute 'dateImported' = '2022-12-06'
        |     |        \___attribute 'filename' = 'FCE Template.xml'
        |     |        \___attribute 'taxonomicCoverageExempt' = 'True'
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Additional Metadata

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        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'k.dd'
        |     |     |     |  \___attribute 'name' = 'k.dd'
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        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |     |___text 'We calculated the breakdown rate (k) for each sample as: k = ln(AFDMt/AFDM0) / days incubated. We calculated degree-days as: degree-days = summed daily mean water temperature °C / number of days deployed. We then scaled breakdown rate (k) by temperature as: k / degree-day.'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'PSU'
        |     |     |     |  \___attribute 'name' = 'PSU'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |     |___text 'Practical Salinity Units'
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        |     |        \___attribute 'release' = '2024.07.17'
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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

Leaf litter, soil, and periphyton gene expression along freshwater to marine gradients in Everglades National Park (FCE LTER), Florida, USA, January 2021 and April 2021

Data Entities

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

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Recently Added

Recently Updated

Data Package Metadata View Summary

Leaf litter, soil, and periphyton gene expression along freshwater to marine gradients in Everglades National Park (FCE LTER), Florida, USA, January 2021 and April 2021

+/- Data Entities

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

+/- Additional Metadata

+/- 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

Additional Metadata

Additional Metadata

Additional Metadata