eDNA processes register the operations for managing data in the edna_utility and edna schemas. Environmental DNA (eDNA) metabarcoding is used in the AI4SH project to characterise soil biodiversity by sequencing DNA extracted directly from soil samples.

Process files

The eDNA process files are located at:

./setup/zzz/ai4sh/setup_processes/json_ai4sh/edna/

Process files in this directory register operations for:

  • Managing eDNA method reference catalogues (edna_utility tables)
  • Managing eDNA observations (edna tables)

eDNA utility catalogue processes

These processes manage the reference tables that describe the eDNA analytical pipeline. Each must be populated before eDNA observations that reference them can be entered.

Catalogue Description
Extraction method Protocol for extracting DNA from a soil sample (e.g. PowerSoil kit, CTAB method)
Amplification (PCR) PCR protocol including primers and cycling conditions
Purification Clean-up procedure for extracted or amplified DNA
Sequencing platform Sequencing technology (e.g. Illumina MiSeq, Oxford Nanopore)
Metabarcoding protocol Amplicon-based protocol for profiling community composition

All catalogue management processes for eDNA utility require a minimum user stratum of 4.

eDNA observation processes

eDNA observations use the same sample infrastructure as physicochemical observations. The soil sample is registered through the standard observation schema workflow (dataset → campaign → sampling log → sample), and the eDNA observation then references that sample along with the specific eDNA workflow records.

A complete eDNA observation registers:

  1. The source sample (linked to the standard observation schema)
  2. The extraction method applied to the sample
  3. The amplification protocol used
  4. The purification method
  5. The sequencing platform and run details
  6. The metabarcoding protocol and taxonomic assignment method
  7. The detected taxa with their abundances (linked to observation_utility.taxa)

eDNA observation management processes require a minimum user stratum of 3.

Integration with observation_utility.taxa

Detected taxa in eDNA results are stored using the Linnean classification hierarchy in observation_utility (order, family, genus, species, specimen). Before eDNA observations can be inserted, the relevant taxa must be registered via the observation utility manage_classification process. This links eDNA biodiversity results to the same taxonomic framework used for macrofauna and other biological observations, enabling cross-method biodiversity analyses from the same database.

Access level

  • eDNA utility catalogue management: minimum stratum 4
  • eDNA observation management: minimum stratum 3

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