Drawing of Suillus ectomycorrhizha, spores; soil nematode, fungus, bacteria, protists; plant grass rhizosphere network

DNA databases

UNITE database for fungal ITS
Greengenes database for bacteria & archaea 16S
SILVA database for 16S/18S
Arbuscular Mycorrhizal Fungi (MaarjAM) database

Naive Bayes classifiers for working through QIIME
The good folks at QIIME keeps updated 16S/18S files of these databases:
SILVA 132 99% OTUs full-length sequences
SILVA 132 99% OTUs from 515F/806R region of sequences
Greengenes 13_8 99% OTUs full-length sequences
Greengenes 13_8 99% OTUs from 515F/806R region of sequences

We keep the UNITE classifier updated
UNITE v7.2 (01.12.2017) trained on QIIME2 2018.11

Organismal life history (guild) databases

FUNGuild database for fungal trophic functional traits
NEMAGuild database for nematode trophic functional traits
Hawai`i Plant Host & Pathogen database
Australian Quarantined plant pests & Diseases (Q-Bank)

Trait databases

DEEMY database for mycorrhizal fungal traits
fungaltraits (funfun) database for fungal traits
TRY for plant traits
NodDB database for plants with root‐symbiotic nitrogen fixation
Global Biotraits database for lots of organisms

Systematics Databases

Index Fungorum
Plant of the World
Index to Organism names (ION)
GenBank Taxonomy

Abiotic & Environmental Databases

Global Climate Data (Worldclim)
World Soil Information (ISRIC)
FAO Soils Portal
Vector and raster map data