Environmental, molecular, and life history data associated with ecological and evolutionary nematode responses to soil phosphorus availability, McMurdo Dry Valleys, Antarctica

Summary

Abstract: 

Elemental stoichiometry is a useful theoretical framework for understanding the sources and controls on nutrient availability that can structure the composition, diversity, and life history of biotic communities. One such relationship, as postulated by the growth rate hypothesis (GRH), is that organismal development rate is positively linked to cellular phosphorus (P). To test the GRH as part of the McMurdo Dry Valleys Long Term Ecological Research (LTER) program, we examined the effects of phosphorus (P) availability both in situ and in vitro, on the evolution of growth and development of free-living soil nematodes (primarily Plectus murrayi) that occur in the McMurdo Dry Valleys of Antarctica. During the 2008-2009 austral summer, we collected soils from two glacial till sequences, the Ross Sea till and Taylor II till, occurring in the Lake Fryxell and Lake Bonney basins, respectively, of Taylor Valley. Through a variety of subsequent analyses, we generated the environmental, molecular, and life history trait data contained herein. In addition, this package contains body size and biomass data for nematodes isolated from soil samples collected during the 1999-2000 and 2004-2005 austral summers.

Date Range: 

December 4, 1999 to June 30, 2016
Data Citation
Xue, X., Adhikari, B.N., Ball, B.A., Barrett, J.E., Miao, J., Perkes, A., Martin, M., Simmons, B.L., Wall, D.H., Adams, B.J. 2021. Environmental, molecular, and life history data associated with ecological and evolutionary nematode responses to soil phosphorus availability, McMurdo Dry Valleys, Antarctica. Environmental Data Initiative. DOI: 10.6073/pasta/4478f48a6ff6cfc0b221cfa14a6a0dfa. Dataset accessed 18 May 2022.
Dataset(s)

Description: 

Nematode biomass data

Variables (click to expand): 

DATASET_CODE
  • Label: Dataset code
  • Definition: Internal dataset code.
  • Type: Nominal
  • Missing values: None specified
YEAR
  • Label: Year
  • Definition: Year of sample collection.
  • Type: Date/time
  • Date format: YYYY
  • Missing values: None specified
BASIN
  • Label: Lake basin
  • Definition: Lake basin of sample collection site (i.e., Fryxell or Bonney).
  • Type: Nominal
  • Missing values: None specified
LOCATION
  • Label: Sample location
  • Definition: Location of sample collection (i.e., F6 or SSLB = South Side Lake Bonney). Samples were collected from control plots located in the BEE experiment.
  • Type: Nominal
  • Missing values: None specified
TREATMENT
  • Label: Treatment
  • Definition: Experimental treatment. In this case, samples were collected from c=control plots located in the BEE experiment.
  • Type: Nominal
  • Missing values: None specified
REPLICATE
  • Label: Replicate
  • Definition: Sample replicate number.
  • Type: Nominal
  • Missing values: None specified
SEX
  • Label: Sex
  • Definition: Gender of nematode (i.e., m=male, f=female).
  • Type: Nominal
  • Missing values: None specified
LENGTH_UM
  • Label: Length
  • Definition: Length of nematode.
  • Type: Physical quantity
  • Unit: micrometer
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
WIDTH_UM
  • Label: Width
  • Definition: Width of nematode.
  • Type: Physical quantity
  • Unit: micrometer
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
BIOMASS_UM
  • Label: Biomass
  • Definition: Biomass of nematode.
  • Type: Physical quantity
  • Unit: microgram
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
BIOMASS_CORR_UM
  • Label: Corrected biomass
  • Definition: Corrected nematode biomass (refer to methods for specifics).
  • Type: Physical quantity
  • Unit: microgram
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified

Description: 

Manifest table for genomic data archived in NCBI

Variables (click to expand): 

DATASET_CODE
  • Label: Dataset code
  • Definition: Internal dataset code.
  • Type: Nominal
  • Missing values: None specified
BIOPROJECT_ACCN
  • Label: BioProject Accession Number
  • Definition: NCBI BioProject accession number.
  • Type: Nominal
  • Missing values: None specified
SRA_EXPT_ACCN
  • Label: SRA Experiment Accession Number
  • Definition: NCBI Sequence Read Archive (SRA) accession number associated with the experiment.
  • Type: Nominal
  • Missing values: None specified
SRA_RUN_ACCN
  • Label: SRA Run Accession Number
  • Definition: NCBI Sequence Read Archive (SRA) accession number associated with the sequencing run.
  • Type: Nominal
  • Missing values: None specified
EXPT_NAME
  • Label: Experiment name
  • Definition: Name of the experiment in the NCBI data portal.
  • Type: Nominal
  • Missing values: None specified
SAMPLE_NAME
  • Label: Sample name
  • Definition: Name of the sample in the NCBI data portal.
  • Type: Nominal
  • Missing values: None specified
SPECIES
  • Label: Species
  • Definition: Abbreviated code for the species name of the associated organism. Matches nematode species name codes used elsewhere in this data package. C_elegans = Caenorhabditis elegans. P_murrayi = Plectus murrayi.
  • Type: Nominal
  • Missing values: None specified
P_MEDIA
  • Label: Phosphorus media
  • Definition: Phosphorus media type (i.e., rich or poor) that associated nematode populations were reared on. Matches codes used elsewhere in this data package.
  • Type: Nominal
  • Missing values: None specified
LIBRARY_NAME
  • Label: Library name
  • Definition: Name of the sequencing library in the NCBI data portal.
  • Type: Nominal
  • Missing values: None specified
LIBRARY_STRATEGY
  • Label: Library strategy
  • Definition: Library strategy employed, where RNA-Seq = random sequencing of whole transcriptome.
  • Type: Nominal
  • Missing values: None specified
LIBRARY_SOURCE
  • Label: Library source
  • Definition: Library source, where TRANSCRIPTOMIC = Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries).
  • Type: Nominal
  • Missing values: None specified
LIBRARY_LAYOUT
  • Label: Library layout
  • Definition: Library layout, where the options are single or paired-end.
  • Type: Nominal
  • Missing values: None specified
SEQUENCING_PLATFORM
  • Label: Sequencing platform
  • Definition: Sequencing platform used.
  • Type: Nominal
  • Missing values: None specified
SEQUENCING_INSTRUMENT
  • Label: Sequencing instrument
  • Definition: Model of sequencing instrument used.
  • Type: Nominal
  • Missing values: None specified
SEQUENCING_DESIGN
  • Label: Sequencing design
  • Definition: Description of the sequencing design.
  • Type: Nominal
  • Missing values: None specified
FILE_TYPE
  • Label: File type
  • Definition: File type
  • Type: Nominal
  • Missing values: None specified

Description: 

Nematode life history traits

Variables (click to expand): 

DATASET_CODE
  • Label: Dataset code
  • Definition: Internal dataset code.
  • Type: Nominal
  • Missing values: None specified
SPECIES
  • Label: Species
  • Definition: Abbreviated code for the species name of the associated organism. Matches nematode species name codes used elsewhere in this data package. C_elegans = Caenorhabditis elegans. P_murrayi = Plectus murrayi.
  • Type: Nominal
  • Missing values: None specified
P_MEDIA
  • Label: Phosphorus media
  • Definition: Phosphorus media type (i.e., rich or poor) that associated nematode populations were reared on. Matches codes used elsewhere in this data package.
  • Type: Nominal
  • Missing values: None specified
REPLICATE
  • Label: Replicate
  • Definition: Sample replicate number.
  • Type: Nominal
  • Missing values: None specified
TOTAL_EGG_COUNT
  • Label: Total egg count
  • Definition: Total number of eggs laid.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
HATCH_RATE
  • Label: Hatch rate
  • Definition: Egg hatch rate.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
EGG_LENGTH_MM
  • Label:
  • Definition: Egg length.
  • Type: Physical quantity
  • Unit: millimeter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
EGG_VOLUME_MM3
  • Label:
  • Definition: Egg volume.
  • Type: Physical quantity
  • Unit: cubicMillimeter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
DAYS_TO_EMERGE
  • Label: Emerge days
  • Definition: Number of days to emergence (hatching). The number of days since the egg is laid until it is hatched.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
DAYS_TO_ADULT
  • Label: Pre-adult days
  • Definition: Number of days from hatching (emergence day) until adult stage.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
DAYS_TO_PREGNANCY
  • Label: Adult days
  • Definition: Number of days from adult day (DAYS_TO_ADULT) to pregnancy.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
PREGNANCY_DAY
  • Label: Pregnant day
  • Definition: Day when eggs were first observed.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
EGGLAY_DAY
  • Label: Lay egg day
  • Definition: Day of start of laying eggs.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
DEATH_DAY
  • Label: Dead day
  • Definition: The day of nematode death.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
ADULT_LENGTH_MM
  • Label:
  • Definition: Adult length.
  • Type: Physical quantity
  • Unit: millimeter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
ADULT_VOLUME_MM3
  • Label:
  • Definition: Adult volume.
  • Type: Physical quantity
  • Unit: cubicMillimeter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified

Description: 

Environmental (soil) and nematode somatic phosphorus

Variables (click to expand): 

DATASET_CODE
  • Label: Dataset code
  • Definition: Internal dataset code.
  • Type: Nominal
  • Missing values: None specified
SAMPLE_TYPE
  • Label: Sample type
  • Definition: Code for sample type, i.e., sample blank or bulk soils.
  • Type: Nominal
  • Missing values: None specified
BASIN
  • Label: Lake basin
  • Definition: Lake basin of sample collection site (i.e., Fryxell or Bonney).
  • Type: Nominal
  • Missing values: None specified
LOCATION
  • Label: Sample location
  • Definition: Location of sample collection (i.e., F6 or SSLB = South Side Lake Bonney). Samples were collected from control plots located in the BEE experiment.
  • Type: Nominal
  • Missing values: None specified
REPLICATE
  • Label: Replicate
  • Definition: Sample replicate number.
  • Type: Nominal
  • Missing values: None specified
PO4_DILUTED_EXT_MGL
  • Label: PO4 in diluted extracts
  • Definition: PO4 content in extracted samples that were diluted.
  • Type: Physical quantity
  • Unit: milligramsPerLiter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
EXT_DILUTION_FACTOR
  • Label:
  • Definition: Extract dilution factor
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
PO4_UNDILUTED_EXT_MGL
  • Label: PO4 in undiluted extracts
  • Definition: PO4 content in extracted samples that were undiluted.
  • Type: Physical quantity
  • Unit: milligramsPerLiter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
EXT_VOLUME_L
  • Label: Extract volume
  • Definition: Volume of extract.
  • Type: Physical quantity
  • Unit: liter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
PO4_ENTIRE_EXT_MGL
  • Label: PO4 in entire extract
  • Definition: PO4 content in entire sample extracts.
  • Type: Physical quantity
  • Unit: milligramsPerLiter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
PO4_ENTIRE_EXT_CORR_MGL
  • Label: Corrected PO4 in entire extract
  • Definition: Corrected PO4 content in entire sample extracts (-blank). Refer to methods for specifics.
  • Type: Physical quantity
  • Unit: milligramsPerLiter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
SOIL_EXT_G
  • Label: Soil extract weight
  • Definition: Weight of soil extract.
  • Type: Physical quantity
  • Unit: grams
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
SOIL_MOISTURE_PCT
  • Label: Soil moisture
  • Definition: Soil moisture percentage.
  • Type: Physical quantity
  • Unit: percent
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
SOIL_DRYWT_G
  • Label: Soil dry weight
  • Definition: Weight of dry soil.
  • Type: Physical quantity
  • Unit: grams
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
PO4_SOIL_R1_MGG
  • Label: Soil phosphorus
  • Definition: Phosphorus content of soil replicate 1.
  • Type: Physical quantity
  • Unit: milligramsPerLiter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
PO4_SOIL_R2_MGG
  • Label: Soil phosphorus
  • Definition: Phosphorus content of soil replicate 2.
  • Type: Physical quantity
  • Unit: milligramsPerLiter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
PO4_SOIL_R3_MGG
  • Label: Soil phosphorus
  • Definition: Phosphorus content of soil replicate 3.
  • Type: Physical quantity
  • Unit: milligramsPerLiter
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified

Description: 

qPCR of 18S rRNA expression from field-collected samples

Variables (click to expand): 

DATASET_CODE
  • Label: Dataset code
  • Definition: Internal dataset code.
  • Type: Nominal
  • Missing values: None specified
BASIN
  • Label: Lake basin
  • Definition: Lake basin of sample collection site (i.e., Fryxell or Bonney).
  • Type: Nominal
  • Missing values: None specified
LOCATION
  • Label: Sample location
  • Definition: Location of sample collection (i.e., F6 or SSLB = South Side Lake Bonney). Samples were collected from control plots located in the BEE experiment.
  • Type: Nominal
  • Missing values: None specified
SPECIES
  • Label: Species
  • Definition: Abbreviated code for the species name of the associated organism. Matches nematode species name codes used elsewhere in this data package. C_elegans = Caenorhabditis elegans. P_murrayi = Plectus murrayi.
  • Type: Nominal
  • Missing values: None specified
FOLD_CHANGE
  • Label:
  • Definition: Expression fold change.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
SE
  • Label:
  • Definition: Standard error
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified

Description: 

qPCR of 18S rRNA and Beta actin expression from laboratory-reared animals

Variables (click to expand): 

DATASET_CODE
  • Label: Dataset code
  • Definition: Internal dataset code.
  • Type: Nominal
  • Missing values: None specified
PCR_POSITION
  • Label:
  • Definition: Cell number on the PCR machine.
  • Type: Nominal
  • Missing values: None specified
SPECIES
  • Label: Species
  • Definition: Abbreviated code for the species name of the associated organism. Matches nematode species name codes used elsewhere in this data package. C_elegans = Caenorhabditis elegans. P_murrayi = Plectus murrayi.
  • Type: Nominal
  • Missing values: None specified
P_MEDIA
  • Label: Phosphorus media
  • Definition: Phosphorus media type (i.e., rich or poor) that associated nematode populations were reared on. Matches codes used elsewhere in this data package.
  • Type: Nominal
  • Missing values: None specified
REPLICATE
  • Label: Replicate
  • Definition: Sample replicate number.
  • Type: Nominal
  • Missing values: None specified
SYBR_CT
  • Label: CtSYBR
  • Definition: Ct value for each cell. CtSYBR = threshold cycle.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified
SYBR_TARGET
  • Label: TargetSYBR
  • Definition: Targeted gene name. TargetSYBR = targeted gene name; 18s = small ribosomal subunit RNA; Bactin = beta-actin.
  • Type: Nominal
  • Missing values: None specified

Description: 

Fecundity of C. elegans and P. murrayi in P-poor and P-rich media

Variables (click to expand): 

DATASET_CODE
  • Label: Dataset code
  • Definition: Internal dataset code.
  • Type: Nominal
  • Missing values: None specified
SPECIES
  • Label: Species
  • Definition: Abbreviated code for the species name of the associated organism. Matches nematode species name codes used elsewhere in this data package. C_elegans = Caenorhabditis elegans. P_murrayi = Plectus murrayi.
  • Type: Nominal
  • Missing values: None specified
P_MEDIA
  • Label: Phosphorus media
  • Definition: Phosphorus media type (i.e., rich or poor) that associated nematode populations were reared on. Matches codes used elsewhere in this data package.
  • Type: Nominal
  • Missing values: None specified
REPLICATE
  • Label: Replicate
  • Definition: Sample replicate number.
  • Type: Nominal
  • Missing values: None specified
DAY
  • Label: Day
  • Definition: Observation day (1-20).
  • Type: Nominal
  • Missing values: None specified
EGG_COUNT
  • Label: Egg count
  • Definition: Number of eggs laid on the day of observation.
  • Type: Physical quantity
  • Unit: dimensionless
  • Maximum: Not specified
  • Minimum: Not specified
  • Precision: Not specified
  • Missing values: None specified

Short name: 

SOILS_GRH

Dataset ID: 

266