Data Package Metadata View Summary

Within-plant coexistence of viruses across nitrogen and phosphorus supply rates

General Information

Data Package:

Local Identifier:

edi.1602.1

Title:

Within-plant coexistence of viruses across nitrogen and phosphorus supply rates

Alternate Identifier:

DOI PLACE HOLDER

Abstract:

Most species can be coinfected by multiple pathogens that may interact through shared resources (i.e., resource competition) or the host immune system (i.e., apparent competition). Community theory developed for free-living organisms suggests that coinfecting pathogens can persist if they satisfy the mutual invasion criterion of coexistence, establishing infections in hosts that are already infected. Furthermore, the likelihood of coexistence may depend on host nutrition which can affect shared resources and host immunity. Here we apply the novel approach of combining a dynamical model and experimental mutual invasibility trials to explore the effects of host nutrient supply on the coexistence of two viral plant pathogens. We focus on among-pathogen interactions mediated by shared resources. First, we used a model to generate hypotheses about how nitrogen (N) and phosphorus (P) supply rates affect the ability of two plant viruses to invade established infections of the other virus. Then, we experimentally manipulated the N and P supplied to oats (Avena sativa) in a growth chamber experiment and tested mutual invasion of two RNA viral pathogens, BYDV-PAV and CYDV-RPV. Nutrient supplies ranged from rates that barely kept hosts alive up to high, but sub-toxic, rates. Model simulations suggested that the viruses were more likely to invade established infections either when they could replicate at lower N and P concentrations or when plant N and P concentrations increased due to a combination of nutrient supply rates and resident virus nutrient use. In the experiment, each virus successfully invaded hosts infected by the other and had consistent growth rates across N and P supply rates. Our results suggest that BYDV-PAV and CYDV-RPV can coexist across a wide range environmental nutrient supply, which is consistent with the high levels of co-occurrence of these two viruses in field populations.

Publication Date:

2024-03-17

For more information:
Visit:	DOI PLACE HOLDER

Time Period

Begin:

2015-08-29

End:

2015-12-21

People and Organizations
Contact:	Kendig, Amy E (Minnesota Department of Natural Resources) [ email ]
Creator:	Kendig, Amy E (Minnesota Department of Natural Resources)
Creator:	Seabloom, Eric W (University of Minnesota)
Creator:	Pell, Bruce (Lawrence Technological University)
Creator:	Yang, Kuang (Arizona State University)
Creator:	Borer, Elizabeth T (University of Minnesota)

Data Entities
Data Table Name:	Plant data
Description:	experiment information at the scale of a plant
Data Table Name:	qPCR data
Description:	raw qPCR sample data
Other Name:	Data processing
Description:	code to process qPCR data
Other Name:	Experiment data analysis
Description:	code to analyze qPCR data
Other Name:	Model parameters
Description:	code to estimate simulation model parameters
Other Name:	Model simulations
Description:	code to run model simulations
Other Name:	Model settings
Description:	code for figures and model settings, referenced by other scripts

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1602/1/675c148f244e7ea3f39db00eceb72fd8
Name:	Plant data
Description:	experiment information at the scale of a plant
Number of Records:	415
Number of Columns:	16

Table Structure

Object Name:

plant_data.csv

Size:

34312 bytes

Authentication:

dfa42e8f70e0beef2cd21e827de7d973 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

set

sample

nutrient

inoculation

time

invasion

replicate

expt_notes

no_analysis

freezer_bag_ID

extraction_date

tube_label

extraction_mass.mg

shoot_mass.g

extraction_notes

planned_qPCR_group

Definition:

Experimental block

unique sample ID

nutrient treatlment

primary virus inoculation

harvesting time interval (sequential)

indicator variable of whether inoculation treatment included invasion

replicate of nutrient-inoculation treatment

notes about experiment

indicator variable of whether sample should be omitted from analysis

ID for freezer storage

date of RNA extraction

unique sample ID for RNA sample tube

mass of plant tissue used for RNA extraction

mass of aboveground plant tissue

notes about RNA extraction

planned group for qPCR

Storage Type:

string

float

string

float

string

float

string

date

string

float

string

float

Measurement Type:

nominal

ratio

nominal

ratio

nominal

ratio

nominal

dateTime

nominal

ratio

nominal

ratio

Measurement Values Domain:

Definition

Experimental block

Definition

unique sample ID

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	L
Definition	grown with low treatment
Source

Code Definition

Code	N
Definition	grown with elevated N treatment
Source

Code Definition

Code	NP
Definition	grown with elevated N and P treatment
Source

Code Definition

Code	P
Definition	grown with elevated P treatment
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	PAV
Definition	primary inoculation with BYDV-PAV
Source

Code Definition

Code	RPV
Definition	primary inoculation with CYDV-RPV
Source

Unit	dimensionless
Type	natural
Min	1
Max	5

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	I
Definition	invasion inoculation (primary/resident and secondary/invader)
Source

Code Definition

Code	S
Definition	single virus inoculation
Source

Unit	dimensionless
Type	natural
Min	1
Max	3

Definition

notes about experiment

Unit	dimensionless
Type	natural
Min	1
Max	1

Definition

ID for freezer storage

Format	MM/DD/YY
Precision

Definition

unique sample ID for RNA sample tube

Unit	milligram
Type	real
Min	13.9
Max	55

Unit	gram
Type	real
Min	0.0387
Max	0.5822

Definition

notes about RNA extraction

Unit	dimensionless
Type	natural
Min	1
Max	20

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

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/1602/1/fd70c12b2064d7170859542ccff42168
Name:	qPCR data
Description:	raw qPCR sample data
Number of Records:	4221
Number of Columns:	23

Table Structure

Object Name:

qPCR_data_compiled.csv

Size:

550436 bytes

Authentication:

4bf5d3c6382ae203f1392d8d53ee2d51 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

well

sample

target

task

reporter

quencher

cycle

cycle_mean

cycle_sd

quantity

quantity_mean

quantity_sd

auto_threshold

threshold

auto_baseline

baseline_start

baseline_end

comments

high_sd

no_amp

outlier_rg

exp_fail

q_group

Definition:

position of sample in 96-well plate

ID assigned to sample

virus species being targeted for qPCR

purpose of the sample

fluorescent dye probe used to detect amplification

molecule attached to the 3' end of the probes to prevent the reporter from emitting signal while the probe is still intact

PCR cycle at which the fluorescence meets the threshold in the amplification plot (lower concentration samples take longer and have higher cycle numbers)

the mean of the cycles associated with a single sample-target combination

the standard deviation of the cycles associated with a single sample-target combination

the automatically estimated amount of target in the well, based on cycle and standard curve

the mean of the quantities associated with a single sample-target combination

the standard deviation of the quantities associated with a single sample-target combination

indicator variable for whether or not the threshold was set automatically

the level of fluorescence above the baseline and within the exponential amplification region

indicator variable for whether or not the baseline was set automatically

the lower end of the cycle range that defines background fluorescence

the upper end of the cycle range that defines background fluorescence

comments entered during qPCR analysis

indicator that the cycle_sd value is high relative to a predetermined threshold

indicator that the sample did not amplify (no fluorescence detected at or above the threshold)

indicator that the well cycle has a large deviation from other replicate wells in the same sample-target combination (outlier in replicate group)

indicator that the automatic algorithm failed for the well (exponential algorithm failed)

qPCR group in which the sample was analyzed (numbered in order of analysis)

Storage Type:

string

float

string

float

string

float

string

float

Measurement Type:

nominal

ratio

nominal

ratio

nominal

ratio

nominal

ratio

Measurement Values Domain:

Definition

position of sample in 96-well plate

Definition

ID assigned to sample

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	PAV
Definition	well is set up to detect and quantify BYDV-PAV (primers and probes)
Source

Code Definition

Code	RPV
Definition	well is set up to detect and quantify CYDV-RPV (primers and probes)
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	NTC
Definition	no template control
Source

Code Definition

Code	STANDARD
Definition	standard
Source

Code Definition

Code	TEST
Definition	standard test
Source

Code Definition

Code	UNKNOWN
Definition	no amplification control or sample
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	FAM
Definition	probe reporter for BYDV-PAV
Source

Code Definition

Code	VIC
Definition	probe reporter for CYDV-RPV
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	NFQ-MGB
Definition	used for all probes
Source

Definition

PCR cycle at which the fluorescence meets the threshold in the amplification plot (lower concentration samples take longer and have higher cycle numbers)

Unit	dimensionless
Type	real
Min	14.03070354
Max	44.98464966

Unit	dimensionless
Type	real
Min	0.009116388
Max	2.694843054

Unit	dimensionless
Type	real
Min	4.479950428
Max	5129248768

Unit	dimensionless
Type	real
Min	4.479950428
Max	5129248768

Unit	dimensionless
Type	real
Min	0.923508286
Max	104710624

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	TRUE
Definition	automatic threhold used
Source

Unit	dimensionless
Type	real
Min	0.013750629
Max	0.040314762

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	TRUE
Definition	automatic baseline used
Source

Unit	dimensionless
Type	natural
Min	3
Max	3

Unit	dimensionless
Type	natural
Min	4
Max	44

Definition

comments entered during qPCR analysis

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	N
Definition	no
Source

Code Definition

Code	Y
Definition	yes
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	N
Definition	no
Source

Code Definition

Code	Y
Definition	yes
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	N
Definition	no
Source

Code Definition

Code	Y
Definition	yes
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	N
Definition	no
Source

Code Definition

Code	Y
Definition	yes
Source

Unit	dimensionless
Type	natural
Min	1
Max	22

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

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

Code	NA
Expl	not applicable

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Non-Categorized Data Resource

Name:

Data processing

Entity Type:

unknown

Description:

code to process qPCR data

Physical Structure Description:

Object Name:

qPCR_data_processing.R

Size:

16499 bytes

Authentication:

1adf3c2530b74dde45cfec00b9120688 Calculated By MD5

Externally Defined Format:

Format Name:

text/plain

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/1602/1/08fa9c0a2e18301dd14e18c393fb4280

Non-Categorized Data Resource

Name:

Experiment data analysis

Entity Type:

unknown

Description:

code to analyze qPCR data

Physical Structure Description:

Object Name:

qPCR_analysis.R

Size:

26524 bytes

Authentication:

346b1a3a78e65f788cfcd2e48462618a Calculated By MD5

Externally Defined Format:

Format Name:

text/plain

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/1602/1/41835b4fd8594945307eb7d96c0c3806

Non-Categorized Data Resource

Name:

Model parameters

Entity Type:

unknown

Description:

code to estimate simulation model parameters

Physical Structure Description:

Object Name:

ode_fit_parameter_estimation.R

Size:

16617 bytes

Authentication:

09fd1729722ed33c4c3709a1d45ee25e Calculated By MD5

Externally Defined Format:

Format Name:

text/plain

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/1602/1/070606e19f541292152f93ab9569ba7f

Non-Categorized Data Resource

Name:

Model simulations

Entity Type:

unknown

Description:

code to run model simulations

Physical Structure Description:

Object Name:

ode_simulations.R

Size:

36467 bytes

Authentication:

eb4d0c98339e4c2a10c26b08b1f6a6ab Calculated By MD5

Externally Defined Format:

Format Name:

text/plain

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/1602/1/fae09ee7ee94d44af1c430a8735c8448

Non-Categorized Data Resource

Name:

Model settings

Entity Type:

unknown

Description:

code for figures and model settings, referenced by other scripts

Physical Structure Description:

Object Name:

model_settings.R

Size:

35795 bytes

Authentication:

ca70392d19e52b052c3c8c518c459c6c Calculated By MD5

Externally Defined Format:

Format Name:

text/plain

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/1602/1/d73b73c2be77892eaf79f6fd815755d4

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	viruses, grasses, nitrogen, phosphorus, disease, species interactions

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:

We performed in silico and in vivo mutual invasions tests with BYDV-PAV and CYDV-RPV across N and P supply rates. We first developed a model and then performed an experiment, both of which evaluated the outcomes of viral mutual invasion tests in the host Avena sativa L. cv. Coast Black Oat grown with one of four resource availability treatments (low N and P, elevated N, elevated P, or elevated N and P). The model combined within-host nutrient concentrations with viral dynamics to identify virus characteristics that could influence whether primary infections prevented or enabled secondary infections, depending on resource availability. Model results indicated that high nutrient requirements of the invading virus or high use of a limited nutrient by the resident virus could prevent mutual invasion. Our empirical results indicated, however, that mutual invasion was possible for either BYDV-PAV or CYDV-RPV regardless of resource availability. Please see paper (additional info) for more specific methods.

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:

Amy E Kendig

Organization:

Minnesota Department of Natural Resources

Email Address:

aekendig@gmail.com

Id:

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

Individual:

Eric W Seabloom

Organization:

University of Minnesota

Email Address:

seabloom@umn.edu

Id:

https://orcid.org/0000-0001-6780-9259

Individual:

Bruce Pell

Organization:

Lawrence Technological University

Email Address:

bpell@ltu.edu

Id:

https://orcid.org/0000-0003-1358-8061

Individual:

Kuang Yang

Organization:

Arizona State University

Email Address:

kuang@asu.edu

Id:

https://orcid.org/0000-0003-2774-4133

Individual:

Elizabeth T Borer

Organization:

University of Minnesota

Email Address:

borer@umn.edu

Id:

https://orcid.org/0000-0003-2259-5853

Contacts:

Individual:

Amy E Kendig

Organization:

Minnesota Department of Natural Resources

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:

2015-08-29

End:

2015-12-21

Sampling Site:

Description:

St. Paul, MN, USA

Site Coordinates:

Longitude (degree):

-93.18

Latitude (degree):

44.98

Project

Parent Project Information:

Title:

No project title to report

Personnel:

Individual:

Eric W Seabloom

Organization:

University of Minnesota

Email Address:

seabloom@umn.edu

Id:

https://orcid.org/0000-0001-6780-9259

Role:

Principal Investigator

Funding:

NSF DEB-1015805

Related Project:

Title:

No project title to report

Personnel:

Individual:

Elizabeth T Borer

Organization:

University of Minnesota

Email Address:

borer@umn.edu

Id:

https://orcid.org/0000-0003-2259-5853

Role:

Principal Investigator

Funding:

NSF DEB-1015805

Maintenance

Maintenance:

Description:	completed
Frequency:

Additional Info

Additional Information:

This dataset is associated with the paper "Within-plant coexistence of viruses across nitrogen and phosphorus supply rates" by Kendig et al (2024). Please reference this open-access paper for methods: [insert doi]

R script outputs can be found here: https://github.com/aekendig/virus-coexistence

Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'emlEditor'
        |     |     |___text '\n            '
        |     |     |___element 'app'
        |     |     |     |___text 'EMLassemblyline'
        |     |     |___text '\n            '
        |     |     |___element 'release'
        |     |     |     |___text '3.5.5'
        |     |     |___text '\n         '
        |     |___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

Within-plant coexistence of viruses across nitrogen and phosphorus supply rates

Data Entities

Data Table

Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

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

Additional Metadata

Recently Added

Recently Updated

Data Package Metadata View Summary

Within-plant coexistence of viruses across nitrogen and phosphorus supply rates

+/- Data Entities

Data Table

Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

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

+/- Additional Metadata

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance

Additional Info

Additional Metadata