Table 1: Summary of meta-data for each column in MycoDB including variable name, description, the type and range of data for each column, and the number of levels in each variable

From: MycoDB, a global database of plant response to mycorrhizal fungi

Table 1: Summary of meta-data for each column in MycoDB including variable name, description, the type and range of data for each column, and the number of levels in each variable
Variable Description Variable Type (range) Levels (#studies/level)
EXPERIMENTID A numerical identifier for unique experiments. Publications can contain multiple experiments, which can contain multiple studies. Multiple studies may have the same EXPERIMENTID value. Discrete
(5 to 1460)
917
CTLTRTSETID A numerical identifier for studies that use the same control mean value to calculate effect sizes. Multiple studies may have the same CTLTRTSETID value. Discrete
(78 to 15852)
2134
NONCTLTRTSETID A unique numerical identifier for individual studies, i.e., observations of plant response to mycorrhizal inoculation. Discrete
(75 to 15854)
4010
LASTNAME1 Last name of the first author of the paper. Categorical 334
LASTNAME2 Last name of the second author of the paper. Categorical 316
PAPERYEAR Year the paper was published. Discrete
(1976 to 2010)
34
JOURNALNAME Name of journal in which the article was published. Categorical 117
PAPERTITLE Title of the publication. Categorical 438
PAPERDATASOURCENAME The database construction Phase in which a paper was included in MycodB. Categorical 2004 Search (1698)
Sept 2010 Main Search (2312)
EFFECTSIZE1 Effect size of fungal inoculation on plant biomass calculated as a log response ratio:
ln(trt_massctrl_mass)
Negative values indicate a parasitic plant-fungal relationship; values close to 0 indicate a commensalistic plant-fungal relationship; positive values indicate a mutualistic plant-fungal relationship.
Continuous
(−4.68 to 7.38)
NA
ESTVAR1 Estimated within-study variance calculated as:
σ2=1ctrl_reps+1trt_reps
Continuous
(0.01 to 2.0)
NA
ESTVAR3 Estimated within-study variance calculated according to Equation 1 from Hedges et al. (1999):
σ2=trt_sd2trt_reps×trt_mass2+ctrl_sd2ctrl_reps×ctrl_mass2
Continuous
(0.000112 to 2.29)
NA
ctrl_mass Average mass of plants from the non-inoculated control. Value refers to whole plant biomass if given. If not, value is shoot biomass. Units are in grams. Continuous NA
ctrl_reps Number of replicates used for the non-inoculated control. This value was set as ‘1’ if the publication did not provide data on replication. Continuous NA
ctrl_sd Standard deviation (s.d.) for average mass of plants from the non-inoculated control. s.d. was calculated from SE and other measures of dispersion. If none was given, this value was set to NA Continuous NA
trt_mass Average mass of plants from the inoculated treatment. Value refers to whole plant biomass if given. If not, value is shoot biomass. Continuous NA
trt_reps Number of replicates used for the inoculated treatment. This value was coded as ‘1’ if the publication did not provide data on replication Continuous NA
trt_sd Standard deviation (s.d.) for average mass of plants from the inoculated treatment. s.d. was calculated from SE and other measures of dispersion. If none was given, this value was set to NA Continuous NA
PlantFamily Family name of host plant Categorical 72; see Supplementary File 1 for complete list
PlantSpecies Plant host genus and specific epithet combined into a single variable (e.g., zea_mays) Categorical 351; see Supplementary File 1 for complete list
FungalGenus Fungal genus name according to phylogenetic structure as of July 2013. Categorical 54; see Supplementary File 1 for complete list
PLANTLIFEHISTORY Life history strategy of the plant host. Categorical annual_biennial (1331)
perennial (2649)
unknown (30)
FUNGROUP Functional group category of host plant in study. Photosynthetic pathway, nitrogen fixing capabilities, and whether the plant is herbaceous (i.e., forb) or woody are summarized. Categorical C3 grass (297)
C4 grass (328)
Nfixforb (740)
Nfixwood (426)
nonNforb (853)
nonNwood (1366)
NONMYCOCONTROL Indicates whether additional measures were taken in a study to experimentally control for the effects of non-mycorrhizal soil microbes. Microbial wash indicates that either inoculum or experimental background soil was filtered in an attempt to remove mycorrhizal fungal propagules and then the filtrate was added to the non-inoculated control. Other indicates a different method was utilized to experimentally control for non-mycorrhizal microbes. Categorical microbial wash (756)
none (2871)
other (383)
NONMYCOCONTROL2 A consolidated version of NONMYCOCONTROL. Studies are coded as to whether non-mycorrhizal microbes were added or not. Categorical microbes_added (1139)
mics_not_added (2871)
FERTP Variable to indicate whether phosphorus fertilizer was added to both inoculated and control treatments. Categorical Pno (2151)
Pyes (1859)
FERTN Variable to indicate whether nitrogen fertilizer was added to both inoculated and control treatments. Categorical Nno (1699)
Nyes (2311)
INOC.COMPLEXITY Indicates whether multiple species or a single species of mycorrhizal fungi were added to inoculated treatments. For Whole, whole soil inoculum was added as inoculum, which likely contained multiple species of fungi, but it cannot be confirmed. Categorical Multi (369)
Single (3499)
Whole (142)
STERILIZED Indicates whether the background soil was sterilized or not. Categorical STERno (1041)
STERyes (2969)
MYCORRHIZAETYPE Study examined the addition of either arbuscular mycorrhizal (AM) fungi or ectomycorrhizal (EM) fungi. Categorical AM (2984)
EM (1026)
LOCATION Describes the experimental setting of each study. Lab indicates any controlled environmental setting such as greenhouse or growth chamber. Categorical field (291)
lab (3719)
DOMESTICATED Describes the degree of agricultural domestication of plant host. Domesticated indicates plants bred selectively as crops or for ornamental purposes, forage crops are planted in pastures and available in a seed mix, and wild indicates no artificial selective breeding. Studies on EM fungi are listed as NA as they were not coded for domestication. Categorical DOMESTICATED (1912)
FORAGECROP (321)
WILD (751)
NA (1026)
Rua2016 Indicates studies that were used in the Ruá et al. 2016 meta-analysis to explore local adaptation in AM fungi. Categorical NO (3683)
YES (327)
Loc_Ad_appropriate Indicates studies that have a known location of origin for at least two of the three experimental components (i.e., plants, fungi, soil) and could be assigned an LA_Code (see below). Categorical NO (2607)
YES (1403)
LA_Code Degree of sympatry or allopatry among plant host, fungal symbiont, and background soil for each study. NA indicates studies that were not coded for local adaptation and include all studies on EM fungi. Categorical See Table 2 for description of levels; NA (2609)
Plant_Lat Latitude in decimal degrees of the origin location of the plant host. Continuous (−35.3 to 69.0) NA
Plant_Long Longitude in decimal degrees of the origin location of the plant host. Continuous (−157.8 to 157.7) NA
Fung_Lat Latitude in decimal degrees of the origin location of the fungal symbiont. Continuous (−45.9 to 69.57) NA
Fung_Long Longitude in decimal degrees of the origin location of the fungal symbiont. Continuous (−123.3 to 174.5) NA
Soil_Lat Latitude in decimal degrees of the origin location of the background soil. Continuous (−40.6 to 63.4) NA
Soil_Long Longitude in decimal degrees of the origin location of the background soil. Continuous (−123.2 to 158.0) NA
AM_single_genus Denotes studies where plants were inoculated with AM fungi from a single known genus, and therefore can be used in phylogenetic analyses. Categorical YES (2398)
NO (1612)
EM_single_genus Denotes studies where plants were inoculated with EM fungi from a single known genus, and therefore can be used in phylogenetic analyses. Categorical YES (1003)
NO (3007)