q2-fungal-traits

bokulich-lab

q2-fungal-traits is a QIIME 2 plugin that annotates fungal taxonomic data with ecological traits and spore volumes derived from published fungal trait datasets. The plugin provides an annotate action that generates a metadata table containing fungal trait annotations and spore volume estimates based on the taxonomy of input sequences.

Installation instructions

For installation instructions head to the QIIME 2 Library.

How annotation works

The plugin links taxonomic assignments to known fungal trait datasets and produces a metadata table with:

  • ecological fungal lifestyle traits
  • estimated spore volumes

Trait and spore annotations are inferred from the taxonomy hierarchy, but the two reference datasets are matched differently.

Fungal trait matching

  • Fungal trait annotations are only attempted when both phylum and genus are present in the taxonomy input.
  • The FungalTraits dataset is matched on genus + phylum.
  • If either genus or phylum is missing, fungal trait annotation is skipped for that feature.

Spore volume matching

  • Spore volume annotations are only attempted for rows where the taxonomy contains kingdom and the kingdom is Fungi.
  • The spore dataset is then matched hierarchically using the available taxonomic ranks.

  1. Species level If a species match exists in the spore dataset, that value is used.

  2. Genus level fallback If no species-level match exists, the geometric mean of spore volumes within the genus is used.

  3. Family level fallback If no genus-level match exists, the geometric mean of spore volumes within the family is used.

  • The output records whether each spore value came from a species, genus, or family match.

Taxonomy requirements

  • Fungal trait annotation requires genus + phylum.
  • Spore volume annotation requires kingdom and at least one of species, genus, or family.
  • If only one of these two annotation paths can run, the plugin still returns the partial annotation.

Taxonomy string format and normalization

The input taxonomy is expected in standard QIIME 2 semicolon-separated format, for example:

k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Polyporales;f__Polyporaceae;g__Datroniella;s__Datroniella_minuta

The code extracts taxonomic ranks from the prefixed fields and normalizes matching keys so the input taxonomy can align with the reference datasets more reliably. The current normalization behavior includes:

  • surrounding whitespace around each rank is stripped
  • explicit empty ranks such as f__ are treated as missing values
  • square brackets [ and ] are removed
  • underscores _ and hyphens - are converted to spaces
  • repeated internal whitespace is collapsed
  • matching is case-insensitive via case folding
  • if a normalized species string does not already start with the normalized genus, the genus name is prepended before species-level matching so matching uses a consistent Genus species form

These normalized keys are used internally for matching only; the original taxonomy string is retained in the output metadata.

Data sources

The annotations rely on two curated fungal datasets.

Fungal trait dataset

Ecological trait data are derived from:

Põlme, S., Abarenkov, K., Henrik Nilsson, R. et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity 105, 1–16 (2020). https://doi.org/10.1007/s13225-020-00466-2

This dataset links ~10210 fungal genera to 17 ecological traits like lifestyle and fruit body type.

Spore volume dataset

Spore volume estimates are derived from:

Abrego, N., Furneaux, B., Hardwick, B. et al. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi. Nature 631, 835–842 (2024). https://doi.org/10.1038/s41586-024-07658-9

This dataset provides measured spore dimensions for ~30000 fungal species.

Usage

The plugin provides a single action: annotate.

This action takes taxonomic assignments as input and produces a metadata table with fungal trait annotations and spore volume estimates.

qiime fungal-traits annotate \
  --i-taxonomy taxonomy.qza \
  --o-metadata fungal_traits.qza

The metadata output can be examined in the browser:

qiime metadata tabulate \
  --m-input-file fungal_traits.qza \
  --o-visualization fungal_traits.qzv
qiime tools view fungal_traits.qzv

Output format

The annotate action produces a metadata table where each row corresponds to a feature (e.g., ASV or sequence) and columns contain taxonomic information, ecological trait annotations, and estimated spore volumes.

ColumnDescription
feature-idUnique identifier of the feature (e.g., ASV or sequence ID).
taxonTaxonomic assignment for the feature.
fungal_traits_genusGenus used for fungal trait matching.
primary_lifestylePrimary ecological lifestyle (e.g., saprotroph, pathogen, symbiont).
secondary_lifestyleSecondary lifestyle annotation if present.
comment_on_lifestyle_templateNotes or comments related to the lifestyle classification.
endophytic_interaction_capability_templateIndicates whether the genus has the capacity for endophytic interactions with plants.
plant_pathogenic_capacity_templateIndicates whether the genus includes plant pathogenic taxa.
decay_substrate_templateSubstrate type the fungus is associated with during decay (e.g., wood, litter).
decay_type_templateType of decay performed by the fungus (e.g., white rot, brown rot).
aquatic_habitat_templateIndicates whether taxa are associated with aquatic environments.
animal_biotrophic_capacity_templateIndicates whether taxa have biotrophic interactions with animals.
specific_hostsKnown host organisms associated with the fungus.
growth_form_templateMorphological growth form (e.g., filamentous mycelium, yeast-like).
fruitbody_type_templateType of fruiting body produced by the fungus.
hymenium_type_templateType of hymenium structure present in reproductive structures.
ectomycorrhiza_exploration_type_templateExploration type for ectomycorrhizal fungi.
ectomycorrhiza_lineage_templatePhylogenetic lineage associated with ectomycorrhizal fungi.
primary_photobiontPrimary photobiont partner in lichenized fungi.
secondary_photobiontSecondary photobiont partner if present.
mitospores_taxonTaxon used to match mitospore measurements.
mitospores_volumeEstimated volume of mitospores.
mitospores_matching_levelTaxonomic level used to determine mitospore volume (species, genus, or family).
meiospores_taxonTaxon used to match meiospore measurements.
meiospores_volumeEstimated volume of meiospores.
meiospores_matching_levelTaxonomic level used to determine meiospore volume (species, genus, or family).
multinucleate_sexual_spores_taxonTaxon used to match multinucleate sexual spore measurements.
multinucleate_sexual_spores_volumeEstimated volume of multinucleate sexual spores.
multinucleate_sexual_spores_matching_levelTaxonomic level used to determine multinucleate sexual spore volume (species, genus, or family).
multinucleate_asexual_spores_taxonTaxon used to match multinucleate asexual spore measurements.
multinucleate_asexual_spores_volumeEstimated volume of multinucleate asexual spores.
multinucleate_asexual_spores_matching_levelTaxonomic level used to determine multinucleate asexual spore volume (species, genus, or family).

Handling of duplicated entries in the fungal trait dataset

Three rows in the fungal traits dataset were exact duplicates and were removed.

Removed rows:

jrk02819 | Ascomycota | Dothideomycetes | Phaeotrichales | Phaeotrichaceae | Echinoascotheca | unspecified_saprotroph | filamentous_mycelium

jrk00124 | Ascomycota | Lecanoromycetes | Lecanorales | Lecanoraceae | Adelolecia | lichenized | non-aquatic | thallus_photosynthetic | apothecium_(hymenium_on_surface) | smooth | chlorococcoid

jrk10035 | Ascomycota | Sordariomycetes | Microascales | Ceratocystidaceae | Phialophoropsis | plant_pathogen | arthropod-associated | wood_pathogen | wood | blue-staining | non-aquatic | arthropod_ectosymbiont | Ambrosia_beetles_(Coleoptera:Curculionidae) | filamentous_mycelium | perithecium(hymenium_hidden,_narrow_opening) | closed

One genus entry was duplicated with differing completeness. The less complete row was removed.

Removed row:

jrk00561 | Ascomycota | Dothideomycetes | Dothideomycetes order incertae sedis | Paranectriellaceae | Paranectriella | | litter_saprotroph | | | no_endophytic_capacity | | leaf/fruit/seed | | non-aquatic | | | filamentous_mycelium

About

The q2-fungal-traits Python package was created from a template. To learn how to use QIIME 2, refer to the QIIME 2 User Documentation. To learn QIIME 2 plugin development, refer to Developing with QIIME 2.

q2-fungal-traits is a QIIME 2 plugin that annotates fungal taxonomic data with ecological traits and spore volumes derived from published fungal trait datasets. The plugin provides an annotate action that generates a metadata table containing fungal trait annotations and spore volume estimates based on the taxonomy of input sequences.

Installation instructions

For installation instructions head to the QIIME 2 Library.

How annotation works

The plugin links taxonomic assignments to known fungal trait datasets and produces a metadata table with:

  • ecological fungal lifestyle traits
  • estimated spore volumes

Trait and spore annotations are inferred from the taxonomy hierarchy, but the two reference datasets are matched differently.

Fungal trait matching

  • Fungal trait annotations are only attempted when both phylum and genus are present in the taxonomy input.
  • The FungalTraits dataset is matched on genus + phylum.
  • If either genus or phylum is missing, fungal trait annotation is skipped for that feature.

Spore volume matching

  • Spore volume annotations are only attempted for rows where the taxonomy contains kingdom and the kingdom is Fungi.
  • The spore dataset is then matched hierarchically using the available taxonomic ranks.

  1. Species level If a species match exists in the spore dataset, that value is used.

  2. Genus level fallback If no species-level match exists, the geometric mean of spore volumes within the genus is used.

  3. Family level fallback If no genus-level match exists, the geometric mean of spore volumes within the family is used.

  • The output records whether each spore value came from a species, genus, or family match.

Taxonomy requirements

  • Fungal trait annotation requires genus + phylum.
  • Spore volume annotation requires kingdom and at least one of species, genus, or family.
  • If only one of these two annotation paths can run, the plugin still returns the partial annotation.

Taxonomy string format and normalization

The input taxonomy is expected in standard QIIME 2 semicolon-separated format, for example:

k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Polyporales;f__Polyporaceae;g__Datroniella;s__Datroniella_minuta

The code extracts taxonomic ranks from the prefixed fields and normalizes matching keys so the input taxonomy can align with the reference datasets more reliably. The current normalization behavior includes:

  • surrounding whitespace around each rank is stripped
  • explicit empty ranks such as f__ are treated as missing values
  • square brackets [ and ] are removed
  • underscores _ and hyphens - are converted to spaces
  • repeated internal whitespace is collapsed
  • matching is case-insensitive via case folding
  • if a normalized species string does not already start with the normalized genus, the genus name is prepended before species-level matching so matching uses a consistent Genus species form

These normalized keys are used internally for matching only; the original taxonomy string is retained in the output metadata.

Data sources

The annotations rely on two curated fungal datasets.

Fungal trait dataset

Ecological trait data are derived from:

Põlme, S., Abarenkov, K., Henrik Nilsson, R. et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity 105, 1–16 (2020). https://doi.org/10.1007/s13225-020-00466-2

This dataset links ~10210 fungal genera to 17 ecological traits like lifestyle and fruit body type.

Spore volume dataset

Spore volume estimates are derived from:

Abrego, N., Furneaux, B., Hardwick, B. et al. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi. Nature 631, 835–842 (2024). https://doi.org/10.1038/s41586-024-07658-9

This dataset provides measured spore dimensions for ~30000 fungal species.

Usage

The plugin provides a single action: annotate.

This action takes taxonomic assignments as input and produces a metadata table with fungal trait annotations and spore volume estimates.

qiime fungal-traits annotate \
  --i-taxonomy taxonomy.qza \
  --o-metadata fungal_traits.qza

The metadata output can be examined in the browser:

qiime metadata tabulate \
  --m-input-file fungal_traits.qza \
  --o-visualization fungal_traits.qzv
qiime tools view fungal_traits.qzv

Output format

The annotate action produces a metadata table where each row corresponds to a feature (e.g., ASV or sequence) and columns contain taxonomic information, ecological trait annotations, and estimated spore volumes.

ColumnDescription
feature-idUnique identifier of the feature (e.g., ASV or sequence ID).
taxonTaxonomic assignment for the feature.
fungal_traits_genusGenus used for fungal trait matching.
primary_lifestylePrimary ecological lifestyle (e.g., saprotroph, pathogen, symbiont).
secondary_lifestyleSecondary lifestyle annotation if present.
comment_on_lifestyle_templateNotes or comments related to the lifestyle classification.
endophytic_interaction_capability_templateIndicates whether the genus has the capacity for endophytic interactions with plants.
plant_pathogenic_capacity_templateIndicates whether the genus includes plant pathogenic taxa.
decay_substrate_templateSubstrate type the fungus is associated with during decay (e.g., wood, litter).
decay_type_templateType of decay performed by the fungus (e.g., white rot, brown rot).
aquatic_habitat_templateIndicates whether taxa are associated with aquatic environments.
animal_biotrophic_capacity_templateIndicates whether taxa have biotrophic interactions with animals.
specific_hostsKnown host organisms associated with the fungus.
growth_form_templateMorphological growth form (e.g., filamentous mycelium, yeast-like).
fruitbody_type_templateType of fruiting body produced by the fungus.
hymenium_type_templateType of hymenium structure present in reproductive structures.
ectomycorrhiza_exploration_type_templateExploration type for ectomycorrhizal fungi.
ectomycorrhiza_lineage_templatePhylogenetic lineage associated with ectomycorrhizal fungi.
primary_photobiontPrimary photobiont partner in lichenized fungi.
secondary_photobiontSecondary photobiont partner if present.
mitospores_taxonTaxon used to match mitospore measurements.
mitospores_volumeEstimated volume of mitospores.
mitospores_matching_levelTaxonomic level used to determine mitospore volume (species, genus, or family).
meiospores_taxonTaxon used to match meiospore measurements.
meiospores_volumeEstimated volume of meiospores.
meiospores_matching_levelTaxonomic level used to determine meiospore volume (species, genus, or family).
multinucleate_sexual_spores_taxonTaxon used to match multinucleate sexual spore measurements.
multinucleate_sexual_spores_volumeEstimated volume of multinucleate sexual spores.
multinucleate_sexual_spores_matching_levelTaxonomic level used to determine multinucleate sexual spore volume (species, genus, or family).
multinucleate_asexual_spores_taxonTaxon used to match multinucleate asexual spore measurements.
multinucleate_asexual_spores_volumeEstimated volume of multinucleate asexual spores.
multinucleate_asexual_spores_matching_levelTaxonomic level used to determine multinucleate asexual spore volume (species, genus, or family).

Handling of duplicated entries in the fungal trait dataset

Three rows in the fungal traits dataset were exact duplicates and were removed.

Removed rows:

jrk02819 | Ascomycota | Dothideomycetes | Phaeotrichales | Phaeotrichaceae | Echinoascotheca | unspecified_saprotroph | filamentous_mycelium

jrk00124 | Ascomycota | Lecanoromycetes | Lecanorales | Lecanoraceae | Adelolecia | lichenized | non-aquatic | thallus_photosynthetic | apothecium_(hymenium_on_surface) | smooth | chlorococcoid

jrk10035 | Ascomycota | Sordariomycetes | Microascales | Ceratocystidaceae | Phialophoropsis | plant_pathogen | arthropod-associated | wood_pathogen | wood | blue-staining | non-aquatic | arthropod_ectosymbiont | Ambrosia_beetles_(Coleoptera:Curculionidae) | filamentous_mycelium | perithecium(hymenium_hidden,_narrow_opening) | closed

One genus entry was duplicated with differing completeness. The less complete row was removed.

Removed row:

jrk00561 | Ascomycota | Dothideomycetes | Dothideomycetes order incertae sedis | Paranectriellaceae | Paranectriella | | litter_saprotroph | | | no_endophytic_capacity | | leaf/fruit/seed | | non-aquatic | | | filamentous_mycelium

About

The q2-fungal-traits Python package was created from a template. To learn how to use QIIME 2, refer to the QIIME 2 User Documentation. To learn QIIME 2 plugin development, refer to Developing with QIIME 2.

q2-fungal-traits is a QIIME 2 plugin that annotates fungal taxonomic data with ecological traits and spore volumes derived from published fungal trait datasets. The plugin provides an annotate action that generates a metadata table containing fungal trait annotations and spore volume estimates based on the taxonomy of input sequences.

Installation instructions

For installation instructions head to the QIIME 2 Library.

How annotation works

The plugin links taxonomic assignments to known fungal trait datasets and produces a metadata table with:

  • ecological fungal lifestyle traits
  • estimated spore volumes

Trait and spore annotations are inferred from the taxonomy hierarchy, but the two reference datasets are matched differently.

Fungal trait matching

  • Fungal trait annotations are only attempted when both phylum and genus are present in the taxonomy input.
  • The FungalTraits dataset is matched on genus + phylum.
  • If either genus or phylum is missing, fungal trait annotation is skipped for that feature.

Spore volume matching

  • Spore volume annotations are only attempted for rows where the taxonomy contains kingdom and the kingdom is Fungi.
  • The spore dataset is then matched hierarchically using the available taxonomic ranks.

  1. Species level If a species match exists in the spore dataset, that value is used.

  2. Genus level fallback If no species-level match exists, the geometric mean of spore volumes within the genus is used.

  3. Family level fallback If no genus-level match exists, the geometric mean of spore volumes within the family is used.

  • The output records whether each spore value came from a species, genus, or family match.

Taxonomy requirements

  • Fungal trait annotation requires genus + phylum.
  • Spore volume annotation requires kingdom and at least one of species, genus, or family.
  • If only one of these two annotation paths can run, the plugin still returns the partial annotation.

Taxonomy string format and normalization

The input taxonomy is expected in standard QIIME 2 semicolon-separated format, for example:

k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Polyporales;f__Polyporaceae;g__Datroniella;s__Datroniella_minuta

The code extracts taxonomic ranks from the prefixed fields and normalizes matching keys so the input taxonomy can align with the reference datasets more reliably. The current normalization behavior includes:

  • surrounding whitespace around each rank is stripped
  • explicit empty ranks such as f__ are treated as missing values
  • square brackets [ and ] are removed
  • underscores _ and hyphens - are converted to spaces
  • repeated internal whitespace is collapsed
  • matching is case-insensitive via case folding
  • if a normalized species string does not already start with the normalized genus, the genus name is prepended before species-level matching so matching uses a consistent Genus species form

These normalized keys are used internally for matching only; the original taxonomy string is retained in the output metadata.

Data sources

The annotations rely on two curated fungal datasets.

Fungal trait dataset

Ecological trait data are derived from:

Põlme, S., Abarenkov, K., Henrik Nilsson, R. et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity 105, 1–16 (2020). https://doi.org/10.1007/s13225-020-00466-2

This dataset links ~10210 fungal genera to 17 ecological traits like lifestyle and fruit body type.

Spore volume dataset

Spore volume estimates are derived from:

Abrego, N., Furneaux, B., Hardwick, B. et al. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi. Nature 631, 835–842 (2024). https://doi.org/10.1038/s41586-024-07658-9

This dataset provides measured spore dimensions for ~30000 fungal species.

Usage

The plugin provides a single action: annotate.

This action takes taxonomic assignments as input and produces a metadata table with fungal trait annotations and spore volume estimates.

qiime fungal-traits annotate \
  --i-taxonomy taxonomy.qza \
  --o-metadata fungal_traits.qza

The metadata output can be examined in the browser:

qiime metadata tabulate \
  --m-input-file fungal_traits.qza \
  --o-visualization fungal_traits.qzv
qiime tools view fungal_traits.qzv

Output format

The annotate action produces a metadata table where each row corresponds to a feature (e.g., ASV or sequence) and columns contain taxonomic information, ecological trait annotations, and estimated spore volumes.

ColumnDescription
feature-idUnique identifier of the feature (e.g., ASV or sequence ID).
taxonTaxonomic assignment for the feature.
fungal_traits_genusGenus used for fungal trait matching.
primary_lifestylePrimary ecological lifestyle (e.g., saprotroph, pathogen, symbiont).
secondary_lifestyleSecondary lifestyle annotation if present.
comment_on_lifestyle_templateNotes or comments related to the lifestyle classification.
endophytic_interaction_capability_templateIndicates whether the genus has the capacity for endophytic interactions with plants.
plant_pathogenic_capacity_templateIndicates whether the genus includes plant pathogenic taxa.
decay_substrate_templateSubstrate type the fungus is associated with during decay (e.g., wood, litter).
decay_type_templateType of decay performed by the fungus (e.g., white rot, brown rot).
aquatic_habitat_templateIndicates whether taxa are associated with aquatic environments.
animal_biotrophic_capacity_templateIndicates whether taxa have biotrophic interactions with animals.
specific_hostsKnown host organisms associated with the fungus.
growth_form_templateMorphological growth form (e.g., filamentous mycelium, yeast-like).
fruitbody_type_templateType of fruiting body produced by the fungus.
hymenium_type_templateType of hymenium structure present in reproductive structures.
ectomycorrhiza_exploration_type_templateExploration type for ectomycorrhizal fungi.
ectomycorrhiza_lineage_templatePhylogenetic lineage associated with ectomycorrhizal fungi.
primary_photobiontPrimary photobiont partner in lichenized fungi.
secondary_photobiontSecondary photobiont partner if present.
mitospores_taxonTaxon used to match mitospore measurements.
mitospores_volumeEstimated volume of mitospores.
mitospores_matching_levelTaxonomic level used to determine mitospore volume (species, genus, or family).
meiospores_taxonTaxon used to match meiospore measurements.
meiospores_volumeEstimated volume of meiospores.
meiospores_matching_levelTaxonomic level used to determine meiospore volume (species, genus, or family).
multinucleate_sexual_spores_taxonTaxon used to match multinucleate sexual spore measurements.
multinucleate_sexual_spores_volumeEstimated volume of multinucleate sexual spores.
multinucleate_sexual_spores_matching_levelTaxonomic level used to determine multinucleate sexual spore volume (species, genus, or family).
multinucleate_asexual_spores_taxonTaxon used to match multinucleate asexual spore measurements.
multinucleate_asexual_spores_volumeEstimated volume of multinucleate asexual spores.
multinucleate_asexual_spores_matching_levelTaxonomic level used to determine multinucleate asexual spore volume (species, genus, or family).

Handling of duplicated entries in the fungal trait dataset

Three rows in the fungal traits dataset were exact duplicates and were removed.

Removed rows:

jrk02819 | Ascomycota | Dothideomycetes | Phaeotrichales | Phaeotrichaceae | Echinoascotheca | unspecified_saprotroph | filamentous_mycelium

jrk00124 | Ascomycota | Lecanoromycetes | Lecanorales | Lecanoraceae | Adelolecia | lichenized | non-aquatic | thallus_photosynthetic | apothecium_(hymenium_on_surface) | smooth | chlorococcoid

jrk10035 | Ascomycota | Sordariomycetes | Microascales | Ceratocystidaceae | Phialophoropsis | plant_pathogen | arthropod-associated | wood_pathogen | wood | blue-staining | non-aquatic | arthropod_ectosymbiont | Ambrosia_beetles_(Coleoptera:Curculionidae) | filamentous_mycelium | perithecium(hymenium_hidden,_narrow_opening) | closed

One genus entry was duplicated with differing completeness. The less complete row was removed.

Removed row:

jrk00561 | Ascomycota | Dothideomycetes | Dothideomycetes order incertae sedis | Paranectriellaceae | Paranectriella | | litter_saprotroph | | | no_endophytic_capacity | | leaf/fruit/seed | | non-aquatic | | | filamentous_mycelium

About

The q2-fungal-traits Python package was created from a template. To learn how to use QIIME 2, refer to the QIIME 2 User Documentation. To learn QIIME 2 plugin development, refer to Developing with QIIME 2.

q2-fungal-traits is a QIIME 2 plugin that annotates fungal taxonomic data with ecological traits and spore volumes derived from published fungal trait datasets. The plugin provides an annotate action that generates a metadata table containing fungal trait annotations and spore volume estimates based on the taxonomy of input sequences.

Installation instructions

For installation instructions head to the QIIME 2 Library.

How annotation works

The plugin links taxonomic assignments to known fungal trait datasets and produces a metadata table with:

  • ecological fungal lifestyle traits
  • estimated spore volumes

Trait and spore annotations are inferred from the taxonomy hierarchy, but the two reference datasets are matched differently.

Fungal trait matching

  • Fungal trait annotations are only attempted when both phylum and genus are present in the taxonomy input.
  • The FungalTraits dataset is matched on genus + phylum.
  • If either genus or phylum is missing, fungal trait annotation is skipped for that feature.

Spore volume matching

  • Spore volume annotations are only attempted for rows where the taxonomy contains kingdom and the kingdom is Fungi.
  • The spore dataset is then matched hierarchically using the available taxonomic ranks.

  1. Species level If a species match exists in the spore dataset, that value is used.

  2. Genus level fallback If no species-level match exists, the geometric mean of spore volumes within the genus is used.

  3. Family level fallback If no genus-level match exists, the geometric mean of spore volumes within the family is used.

  • The output records whether each spore value came from a species, genus, or family match.

Taxonomy requirements

  • Fungal trait annotation requires genus + phylum.
  • Spore volume annotation requires kingdom and at least one of species, genus, or family.
  • If only one of these two annotation paths can run, the plugin still returns the partial annotation.

Taxonomy string format and normalization

The input taxonomy is expected in standard QIIME 2 semicolon-separated format, for example:

k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Polyporales;f__Polyporaceae;g__Datroniella;s__Datroniella_minuta

The code extracts taxonomic ranks from the prefixed fields and normalizes matching keys so the input taxonomy can align with the reference datasets more reliably. The current normalization behavior includes:

  • surrounding whitespace around each rank is stripped
  • explicit empty ranks such as f__ are treated as missing values
  • square brackets [ and ] are removed
  • underscores _ and hyphens - are converted to spaces
  • repeated internal whitespace is collapsed
  • matching is case-insensitive via case folding
  • if a normalized species string does not already start with the normalized genus, the genus name is prepended before species-level matching so matching uses a consistent Genus species form

These normalized keys are used internally for matching only; the original taxonomy string is retained in the output metadata.

Data sources

The annotations rely on two curated fungal datasets.

Fungal trait dataset

Ecological trait data are derived from:

Põlme, S., Abarenkov, K., Henrik Nilsson, R. et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity 105, 1–16 (2020). https://doi.org/10.1007/s13225-020-00466-2

This dataset links ~10210 fungal genera to 17 ecological traits like lifestyle and fruit body type.

Spore volume dataset

Spore volume estimates are derived from:

Abrego, N., Furneaux, B., Hardwick, B. et al. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi. Nature 631, 835–842 (2024). https://doi.org/10.1038/s41586-024-07658-9

This dataset provides measured spore dimensions for ~30000 fungal species.

Usage

The plugin provides a single action: annotate.

This action takes taxonomic assignments as input and produces a metadata table with fungal trait annotations and spore volume estimates.

qiime fungal-traits annotate \
  --i-taxonomy taxonomy.qza \
  --o-metadata fungal_traits.qza

The metadata output can be examined in the browser:

qiime metadata tabulate \
  --m-input-file fungal_traits.qza \
  --o-visualization fungal_traits.qzv
qiime tools view fungal_traits.qzv

Output format

The annotate action produces a metadata table where each row corresponds to a feature (e.g., ASV or sequence) and columns contain taxonomic information, ecological trait annotations, and estimated spore volumes.

ColumnDescription
feature-idUnique identifier of the feature (e.g., ASV or sequence ID).
taxonTaxonomic assignment for the feature.
fungal_traits_genusGenus used for fungal trait matching.
primary_lifestylePrimary ecological lifestyle (e.g., saprotroph, pathogen, symbiont).
secondary_lifestyleSecondary lifestyle annotation if present.
comment_on_lifestyle_templateNotes or comments related to the lifestyle classification.
endophytic_interaction_capability_templateIndicates whether the genus has the capacity for endophytic interactions with plants.
plant_pathogenic_capacity_templateIndicates whether the genus includes plant pathogenic taxa.
decay_substrate_templateSubstrate type the fungus is associated with during decay (e.g., wood, litter).
decay_type_templateType of decay performed by the fungus (e.g., white rot, brown rot).
aquatic_habitat_templateIndicates whether taxa are associated with aquatic environments.
animal_biotrophic_capacity_templateIndicates whether taxa have biotrophic interactions with animals.
specific_hostsKnown host organisms associated with the fungus.
growth_form_templateMorphological growth form (e.g., filamentous mycelium, yeast-like).
fruitbody_type_templateType of fruiting body produced by the fungus.
hymenium_type_templateType of hymenium structure present in reproductive structures.
ectomycorrhiza_exploration_type_templateExploration type for ectomycorrhizal fungi.
ectomycorrhiza_lineage_templatePhylogenetic lineage associated with ectomycorrhizal fungi.
primary_photobiontPrimary photobiont partner in lichenized fungi.
secondary_photobiontSecondary photobiont partner if present.
mitospores_taxonTaxon used to match mitospore measurements.
mitospores_volumeEstimated volume of mitospores.
mitospores_matching_levelTaxonomic level used to determine mitospore volume (species, genus, or family).
meiospores_taxonTaxon used to match meiospore measurements.
meiospores_volumeEstimated volume of meiospores.
meiospores_matching_levelTaxonomic level used to determine meiospore volume (species, genus, or family).
multinucleate_sexual_spores_taxonTaxon used to match multinucleate sexual spore measurements.
multinucleate_sexual_spores_volumeEstimated volume of multinucleate sexual spores.
multinucleate_sexual_spores_matching_levelTaxonomic level used to determine multinucleate sexual spore volume (species, genus, or family).
multinucleate_asexual_spores_taxonTaxon used to match multinucleate asexual spore measurements.
multinucleate_asexual_spores_volumeEstimated volume of multinucleate asexual spores.
multinucleate_asexual_spores_matching_levelTaxonomic level used to determine multinucleate asexual spore volume (species, genus, or family).

Handling of duplicated entries in the fungal trait dataset

Three rows in the fungal traits dataset were exact duplicates and were removed.

Removed rows:

jrk02819 | Ascomycota | Dothideomycetes | Phaeotrichales | Phaeotrichaceae | Echinoascotheca | unspecified_saprotroph | filamentous_mycelium

jrk00124 | Ascomycota | Lecanoromycetes | Lecanorales | Lecanoraceae | Adelolecia | lichenized | non-aquatic | thallus_photosynthetic | apothecium_(hymenium_on_surface) | smooth | chlorococcoid

jrk10035 | Ascomycota | Sordariomycetes | Microascales | Ceratocystidaceae | Phialophoropsis | plant_pathogen | arthropod-associated | wood_pathogen | wood | blue-staining | non-aquatic | arthropod_ectosymbiont | Ambrosia_beetles_(Coleoptera:Curculionidae) | filamentous_mycelium | perithecium(hymenium_hidden,_narrow_opening) | closed

One genus entry was duplicated with differing completeness. The less complete row was removed.

Removed row:

jrk00561 | Ascomycota | Dothideomycetes | Dothideomycetes order incertae sedis | Paranectriellaceae | Paranectriella | | litter_saprotroph | | | no_endophytic_capacity | | leaf/fruit/seed | | non-aquatic | | | filamentous_mycelium

About

The q2-fungal-traits Python package was created from a template. To learn how to use QIIME 2, refer to the QIIME 2 User Documentation. To learn QIIME 2 plugin development, refer to Developing with QIIME 2.