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Table 1 Genomic features of the microorganisms used in the simplified soil microcosm

From: Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

Microbial straina Typeb Main biological characteristics of microbial species Genome version Reference and databasec Genome featuresd
Length Genes
Azorhizobium caulinodans ORS 571 B Gram-negative, nitrogen fixing bacterium both free-living in soil and in symbiotic interaction with plants GCA_000010525.1 [54, 86] 5.4 4781
Bacillus subtilis subsp. subtilis 168 B Gram-positive, common in soil and the rhizosphere GCA_000009045.1 [55, 87] 4.2 4371
Cupriavidus metallidurans CH34 B Gram-negative, also found in soil, adaptable to heavy metal stress GCA_000196015.1 [56, 88] 6.9 6829
Pseudomonas protegens Pf-5 B Gram-negative, common in soil, biocontrol agent GCA_000012265.1 [57, 89] 7.1 6212
Debaryomyces hansenii CBS 767 Y Salt-tolerant multilateral budding yeast of water and soil v1.0 [58, 90] 12.1 6272
Pichia stipitis CBS 6054 Y Budding yeast in soil and beetle gut v2.0 [60, 91] 15.4 5807
Saccharomyces cerevisiae S288c Y Ubiquitous budding yeast, also found in soil R64-1-1 [44, 45] 12.2 7126
Schizosaccharomyces pombe 972 h Y Fission yeast, isolated from soil ASM294v2 [61, 92] 12.6 7018
Aspergillus niger CBS 513.88 FF Ubiquitous in soil, saprophyte and pathogen of plants CADRE [62, 93] 33.9 14,445
Fusarium oxysporum f. sp. lycopersici 4287 FF Ubiquitous in soil, phytopathogen FO2 [64, 94] 60.0 18,066
Penicillium chrysogenum Wisconsin 54-1255 FF Ubiquitous, also found in soil, equipped with antifungal properties v1.0 [63, 95] 32.2 13,671
Trichoderma atroviride IMI 206040e BA Ubiquitous, also found in soil, biocontrol agent TRIAT v2.0 [65, 96] 36.1 11,863
Armillaria mellea DSM 3731f PP Soil inhabitant and polyphagous plant root pathogen v1.0 [66, 97] 84.2 14,473
Microcosm genomeg      322.2 120,934
  1. aThe simplified soil microcosm was obtained through inoculation of four bacteria (B), four yeasts (Y) and three filamentous fungi (FF) with sequenced genomes into a soil matrix. The plant pathogen (PP) and its biocontrol agent (BA) were also introduced
  2. bSoil microorganisms are classified as: bacterium (B), yeast (Y), filamentous fungus (FF), biocontrol agent (BA) and plant pathogen (P)
  3. cReferences and databases of the downloaded genome versions
  4. dGenome length (Mbp) and number of genes in the reference genome
  5. eThe reference genome of T. atroviride IMI 206040 was used to align read pairs deriving from T. atroviride SC1
  6. fThe reference genome of A. mellea DSM 3731 was used to align read pairs deriving from A. mellea M6132
  7. gThe microcosm genome was obtained by merging the data of 13 soil microorganisms and was used as a reference for RNA-Seq alignment