Data Package Metadata View Summary

Emerging fungal pathogen differentially affects three native plant species that compete with an invasive grass

General Information

Data Package:
Local Identifier:	edi.63.2
Title:	Emerging fungal pathogen differentially affects three native plant species that compete with an invasive grass
Alternate Identifier:	DOI PLACE HOLDER
Abstract:	This data package includes data and code from an experiment testing the effects of a leaf spot fungal infection and competition from the invasive (to the U.S.) grass Microstegium vimineum on the performance of three native grass species: Dichanthelium clandestinum, Elymus virginicus, and Eragrostis spectabilis. The experiment was performed between June and September of 2019 in a greenhouse on the University of Florida campus in Gainesville, FL, USA. The leaf spot infection is caused by the fungal pathogen Bipolaris gigantea, which has recently emerged on populations of M. vimineum in the U.S. We tested the hypothesis that infection of B. gigantea would both directly and indirectly affect the native grass species by measuring the change in biomass of each species with and without pathogen inoculation (direct effects) and by measuring the effect of pathogen inoculation on M. vimineum competition through changes in native grass biomass across a density gradient of M. vimneum (indirect effects). The code includes statistical analyses and figures. The code was run using R (version 4.0.1).
Publication Date:	2020-12-05

Time Period

Begin:

2019-06-26

End:

2019-09-12

People and Organizations
Contact:	Kendig, Amy E. (University of Florida) [ email ]
Creator:	Kendig, Amy E. (University of Florida)
Creator:	Svahnstrom, Vida J. (University of St. Andrews)
Creator:	Adhikari, Ashish (University of Florida)
Creator:	Harmon, Philip F. (University of Florida)
Creator:	Flory, S. Luke (University of Florida)

Data Entities
Data Table Name:	Biomass data
Description:	biomass data collected from Microstegium and native plants
Data Table Name:	Infection data
Description:	infection data collected from Microstegium and native plants
Other Name:	Biomass analysis
Description:	code to analyze biomass data
Other Name:	Infection analysis
Description:	code to analyze infection data

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/63/2/705814fd516e1ca5f804f1f6dca1bbc2
Name:	Biomass data
Description:	biomass data collected from Microstegium and native plants
Number of Records:	120
Number of Columns:	7

Table Structure

Object Name:

biomass_20190912.csv

Size:

3196 bytes

Authentication:

f7d5c06e92c8ab858937f327bd874b14 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

treatment

density

species

replicate

mv_biomass

nat_biomass

notes

Definition:

Pathogen inoculation treatment

Microstegium vimineum seeds planted per pot

Native species planted in the center of the pot

ID for pots within a density-pathogen inoculation-species treatment combination (1 to 4)

Oven-dried aboveground weight of all Microstegium vimineum

Oven-dried aboveground weight of the native plant

Notes recorded during experiment

Storage Type:

string

float

string

float

string

Measurement Type:

nominal

ratio

nominal

ratio

nominal

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	W
Definition	water with 0.1% Tween 20 was applied to plants (mock inoculation control)
Source

Code Definition

Code	F
Definition	fungal spore solution (Bipolaris gigantea) applied to plants (pathogen inoculation)
Source

Unit	dimensionless
Type	whole
Min	0
Max	100

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	V
Definition	the native species Elymys virginicus was in the pot
Source

Code Definition

Code	S
Definition	the native species Eragrostis spectabilis was in the pot
Source

Code Definition

Code	C
Definition	the native species Dichantheleum clandestinum was in the pot
Source

Unit	dimensionless
Type	natural
Min	1
Max	4

Unit	gram
Type	real
Min	0.08
Max	13.4

Unit	gram
Type	real
Min	0.0091
Max	4.1542

Definition

Notes recorded during experiment

Missing Value Code:

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/63/2/8931574e61ed5a1cb687081d798f1bbb
Name:	Infection data
Description:	infection data collected from Microstegium and native plants
Number of Records:	120
Number of Columns:	11

Table Structure

Object Name:

infection_20190809.csv

Size:

3494 bytes

Authentication:

4cca0e4555eae29262cb654de098627c Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

treatment

density

species

replicate

mv_leaves_infec

mv_leaves_stem_1

mv_leaves_stem_2

mv_leaves_stem_3

native_leaves_infec

native_leaves

notes

Definition:

Pathogen inoculation treatment

Microstegium vimineum seeds planted per pot

Native species planted in the center of the pot

ID for pots within a density-pathogen inoculation-species treatment combination (1 to 4)

Number of Microstegium vimineum leaves with brown lesions

Total number of leaves on a Microstegium vimineum seedling (replicate 1)

Total number of leaves on a Microstegium vimineum seedling (replicate 2)

Total number of leaves on a Microstegium vimineum seedling (replicate 3)

Number of native plant leaves with brown lesions

Total number of leaves on a seedling

Notes recorded during experiment

Storage Type:

string

float

string

float

string

Measurement Type:

nominal

ratio

nominal

ratio

nominal

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	W
Definition	water with 0.1% Tween 20 was applied to plants (mock inoculation control)
Source

Code Definition

Code	F
Definition	fungal spore solution (Bipolaris gigantea) applied to plants (pathogen inoculation)
Source

Unit	dimensionless
Type	whole
Min	0
Max	100

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	V
Definition	the native species Elymys virginicus was in the pot
Source

Code Definition

Code	S
Definition	the native species Eragrostis spectabilis was in the pot
Source

Code Definition

Code	C
Definition	the native species Dichantheleum clandestinum was in the pot
Source

Unit	dimensionless
Type	natural
Min	1
Max	4

Unit	dimensionless
Type	whole
Min	0
Max	59

Unit	dimensionless
Type	natural
Min	4
Max	52

Unit	dimensionless
Type	natural
Min	3
Max	50

Unit	dimensionless
Type	natural
Min	5
Max	25

Unit	dimensionless
Type	whole
Min	0
Max	2

Unit	dimensionless
Type	natural
Min	3
Max	10

Definition

Notes recorded during experiment

Missing Value Code:

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Code	NA
Expl	not applicable

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Non-Categorized Data Resource

Name:

Biomass analysis

Entity Type:

unknown

Description:

code to analyze biomass data

Physical Structure Description:

Object Name:

biomass_analysis.R

Size:

20592 bytes

Authentication:

f53626dba3bf4098c48afa6384b41b51 Calculated By MD5

Externally Defined Format:

Format Name:

text/plain

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/63/2/b5e0212ce3ac079c339d46a3e46ea633

Non-Categorized Data Resource

Name:

Infection analysis

Entity Type:

unknown

Description:

code to analyze infection data

Physical Structure Description:

Object Name:

infection_analysis.R

Size:

22416 bytes

Authentication:

27b0cec23d3954ff83590d207d276a97 Calculated By MD5

Externally Defined Format:

Format Name:

text/plain

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/63/2/fed7314c906ad2dc154adab94251f90c

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:
LTER	plants, species interactions, invasive species, disease, fungi

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:

Motivation: Plant communities can experience species invasions and infectious disease at the same time, but it is unclear what the consequences are, partly because most investigations feature only one native species. We examined the effects of disease and invasion on three native species. The invasive species is Microstegium vimineum, a forest understory grass, which hosts fungi in the genus Bipolaris that are spreading across the invaded range.

Design: In a greenhouse experiment, we manipulated, pathogen inoculation, native species identity, and M. vimineum density to measure the effects of disease, competition from an invasive plant, and both on the biomass production of the native species. We used two inoculation treatments (pathogen inoculation with a spore solution of Bipolaris gigantea and a mock inoculation control), three native species (Elymus virginicus, Eragrostis spectabilis, and Dichanthelium clandestinum), and five levels of M. vimineum density (0, 2, 10, 50, 100 seeds per pot). Crossing these three treatments in a full-factorial design led to 30 treatments with four replicate pots each.

Measurements: We quantified disease incidence by counting the number of M. vimineum leaves per pot with lesions and then counting the total number of leaves on three seedlings (or two when only two were available). For the native plants, we counted the number of leaves with lesions and the total number of leaves per plant when plants had lesions. At the end of the experiment, we harvested aboveground biomass, oven-dried it to a constant weight, and weighed it.

Analysis: We used the brms package to fit Bayesian models to each response variable. We fit a binomial linear regression to disease incidence data for M. vimineum with native species identity, M. vimineum density, and their interaction as the explanatory variables. We could not fit a model to the disease incidence data for the native species because there were too few data points. We fit a linear regression to M. vimineum biomass with pathogen inoculation treatment, native species identity, M. vimineum density (represented with a linear and quadratic term), and their interactions as the explanatory variables. We fit a Beverton-Holt function to native plant biomass across the range of M. vimineum density values with different parameters for each native species-pathogen inoculation treatment combination.

People and Organizations

Publishers:

Organization:

Environmental Data Initiative

Email Address:

info@environmentaldatainitiative.org

Web Address:

https://environmentaldatainitiative.org

Creators:

Individual:

Amy E. Kendig

Organization:

University of Florida

Email Address:

aekendig@gmail.com

Id:

https://orcid.org/0000-0002-2774-1795

Individual:

Vida J. Svahnstrom

Organization:

University of St. Andrews

Email Address:

vjs5@st-andrews.ac.uk

Individual:

Ashish Adhikari

Organization:

University of Florida

Email Address:

adhikariashish@ufl.edu

Individual:

Philip F. Harmon

Organization:

University of Florida

Email Address:

pfharmon@ufl.edu

Id:

https://orcid.org/0000-0003-2288-5148

Individual:

S. Luke Flory

Organization:

University of Florida

Email Address:

flory@ufl.edu

Id:

https://orcid.org/0000-0003-3336-8613

Contacts:

Individual:

Amy E. Kendig

Organization:

University of Florida

Email Address:

aekendig@gmail.com

Id:

https://orcid.org/0000-0002-2774-1795

Temporal, Geographic and Taxonomic Coverage

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

Time Period

Begin:

2019-06-26

End:

2019-09-12

Sampling Site:

Description:

Gainesville, FL, USA

Site Coordinates:

Longitude (degree):

-82.36

Latitude (degree):

29.64

Project

Parent Project Information:

Title:

No project title to report

Personnel:

Individual:

S. Luke Flory

Organization:

University of Florida

Email Address:

flory@ufl.edu

Id:

https://orcid.org/0000-0003-3336-8613

Role:

Principal Investigator

Funding:

USDA 2017-67013-26870

Maintenance

Maintenance:

Description:	completed
Frequency:

Additional Info

Additional Information:

This dataset is associated with the manuscript Emerging fungal pathogen on an invasive grass differentially affects native species by Kendig et al., submitted to PLOS ONE.

R script outputs can be found here: https://github.com/aekendig/native-plant-reu

Other Metadata

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

Emerging fungal pathogen differentially affects three native plant species that compete with an invasive grass

Data Entities

Data Table

Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

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 Info

Recently Added

Recently Updated

Data Package Metadata View Summary

Emerging fungal pathogen differentially affects three native plant species that compete with an invasive grass

+/- Data Entities

Data Table

Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

+/- 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 Info

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance

Additional Info