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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
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BMC Genomics

ISSN: 1471-2164

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