Fig. 1.
The endohyphal bacteria in Fusarium acuminatum YZU 172038.
(A, B) Fluorescent SYTO-9 nucleic acid stained hyphae under fluorescent microscopy (FN – fungal nucleus, BD – bacterial DNA), scale bars = 5 μm;
(C, D) bacteria (green signals pointed by white arrows) in hypha detected by the FISH method, scale bars = 5 μm; (E) PCR amplification of the 16S RNA gene (M – 2000 bp maker, 1 – YZU 172038); (F) colony morphology of EHB YZASR384 on LA medium;
(G) scanning electron microscopy of EHB YZASR384; (H) PCR amplification of endoglucanase gene (1 – EHB YZSR384, 2 – YZU 172038).
Fig. 2.
Phylogenetic tree of endohyphal strain YZSR384 using the neighbor-joining method based on the 16S rRNA gene sequences.
Bootstrap values (%) presented at the branches were calculated from 1,000 replications.
Fig. 3.
Plant growth promoting (PGP) assays for rice seeds using the culture broth of endophytic Fusarium acuminatum YZU 172038 (A, B) and its EHB Bacillus subtilis YZSR384 (C, D). The controls were PDB broth (A, B) and demineralized LB liquid (C, D).
Fig. 4.
Detection of the IAA production in EHB YZSR384 culture broth.
(A) Salkowski test of the negative control (left) and the EHB YZSR384 broth (right).
(B) The IAA concentration in different incubation times.
Table I
Genome properties of EHB Bacillus subtilis YZSR384.
| Feature | Bacillus subtilis YZSR384 |
|---|---|
| Genome size (bp) | 4,215,636 |
| GC content (%) | 43.51 |
| Total number of genes | 4444 |
| Number of CDSs | 4216 |
| tRNA genes | 87 |
| rRNA genes | 30 |
| tmRNA genes | 1 |
| Genomic islands | 4 |
| Genes allocated to Uniprot | 4,157 |
| Genes allocated to Refseq | 4,180 |
| Genes allocated to KEGG | 2,330 |
| Genes allocated to Pfam | 3,761 |
| Genes allocated to GO | 3,359 |
| Genes allocated to COG | 2,816 |
Table II
Genes associated with plant growth-promoting (PGP) traits for EHB Bacillus subtilis YZSR384.
| PGP activity | Gene | Function | Chromosome location |
|---|---|---|---|
| IAA production | trpS | Tryptophanyl-tRNA synthetase | 1218699–1217707 – |
| trpA | Tryptophan synthase subunit alpha | 2371911–2371108 – | |
| trpB | Tryptophan synthase subunit beta | 2373106–2371904 – | |
| trpF | Phosphoribosylanthranilate isomerase | 2373734–2373087 – | |
| trpC | Indole-3-glycerol phosphate synthase | 2374491–2373739 – | |
| trpD | Anthranilate phosphoribosyltransferase | 2375500–2374484 – | |
| trpE | Anthranilate synthase | 2377019–2375472 – | |
| Phosphate solubilization | phoD | Alkaline phosphatase | 283609–285360 + |
| phoB | Alkaline phosphatase | 621083–619695 – | |
| phoA | Alkaline phosphatase | 1018051–1016675 – | |
| phoH | Phosphate starvation-inducible protein | 2615049–2614090 – | |
| PhoP | Alkaline phosphatase synthesis transcriptional regulatory protein | 2978117–2977395 – | |
| phoR | Two-component sensor histidine kinase | 3236753–3238354 + | |
| pstB | Phosphate ABC transporter ATP-binding protein | 2577585–2576803 – 2578405–2577596 – | |
| pstA | Phosphate ABC transporter permease | 2579310–2578426 – | |
| pstC | Phosphate ABC transporter permease | 2580239–2579310 – | |
| pstS | Phosphate ABC transporter substrate-binding protein | 2581210–2580308 – | |
| Siderophore production | entB | Isochorismatase | 552212–552754 + 3288208–3287270 – |
| entC | Isochorismate synthase | 3153313–3151898 – 3153500–3153375 – 3291891–3291106 – | |
| entE | 2,3-dihydroxybenzoate-AMP ligase | 3289855–3288236 – | |
| entA | 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase | 3291080–3289884 – |