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Characterization of a Plant Growth-Promoting Endohyphal Bacillus subtilis in Fusarium acuminatum from Spiranthes sinensis

LAN FANG

LAN FANG

College of Agriculture, Yangtze UniversityJingzhou, China
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FANG, LAN
, 
XIAO ZHENG

XIAO ZHENG

College of Agriculture, Yangtze UniversityJingzhou, China
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ZHENG, XIAO
, 
ZHENGXIANG SUN

ZHENGXIANG SUN

College of Agriculture, Yangtze UniversityJingzhou, China
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SUN, ZHENGXIANG
, 
YANYAN LI

YANYAN LI

Tobacco Research Institute of Hubei ProvinceWuhan, China
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LI, YANYAN
, 
JIANXIN DENG

JIANXIN DENG

College of Agriculture, Yangtze UniversityJingzhou, China
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DENG, JIANXIN
 and 
YI ZHOU

YI ZHOU

College of Agriculture, Yangtze UniversityJingzhou, China
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ZHOU, YI
  
Mar 24, 2023
Characterization of a Plant Growth-Promoting Endohyphal Bacillus subtilis in Fusarium acuminatum from Spiranthes sinensis's Cover Image
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Article Category: ORIGINAL PAPER
Published Online: Mar 24, 2023
Page range: 29 - 37
Received: Nov 10, 2022
Accepted: Feb 03, 2023
DOI: https://doi.org/10.33073/pjm-2023-007
Keywords
© 2023 LAN FANG et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
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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).
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.
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).
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.
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.

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–

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
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