Growth-promoting Effects of a Rhizosphere Growth-promoting Bacterium Leclercia adecarboxylata LN01 in Maize Plants and Its Whole-genome Analysis

doi:10.13560/j.cnki.biotech.bull.1985.2024-0487

Abstract

Abstract:

【Objective】Beneficial plant inter-root microorganisms can enhance soil-crop interactions and promote crop growth. The aim of this paper is to investigate the growth promotion mechanism of strain LN01, a maize PGPR (Plant growth-promoting rhizobacteria) strain, on maize plants.【Method】Firstly, 16S rRNA and whole genomics sequencing were used to clarify the taxonomic status of strain LN01. Secondly, a pot experiment was conducted to validate the growth-promoting effects of strain LN01 on maize. Whole-genome data mining was performed to identify genes related to plant growth promotion, and carbon-nitrogen analyzers, molybdenum-antimony colorimetric methods, flame photometers, Salkowski colorimetric methods, and Chrome Azurol Sulfonate（CAS）blue qualitative detection plates were used to study the nitrogen fixation, phosphate solubilization, potassium solubilization, indole-3-acetic acid（IAA）production, and siderophore capabilities of strain LN01.【Result】The strain LN01 promoted biomass accumulation in maize plants and effectively increased soil nutrient content. Strain LN01 was identified as Leclercia adecarboxylata. There were gene clusters in strain LN01's genome for these, including iron acquisition（fhuBCDEF, afuABC, efeOBU, and fepCDG）, phosphate solubilization（pstABCS, phoABER, phnACDEFGHIJKLP, and ugpABCE）, biological nitrogen fixation（nirBCD, nasA, glnA, gltBD, and nrtABC）, potassium solubilization（kdpABC, kefBCFG, trkAH, and kup）and IAA biosynthesis（trpABSCFRGD）. The biogenic gene synthesis clusters for four secondary metabolites that promoted plant growth, including non-ribosomal peptide synthases（NRPS）, terpenes, thiopeptides, and aryl polyenes, were identified throughout the genome by antiSMASH analysis. Strain LN01 had the capacity of nitrogen fixation, phosphate solubilizing activity, potassium solubilizing capacity, and IAA production by 15.14, 58.33, 15.6 and 42.2 mg/L, respectively, as well as iron-carrier production capacity.【Conclusion】Strain LN01 possesses genes related to nitrogen-fixing and phosphorus-solubilizing, potassium solubilization, iron carrier production and IAA secretion, which helps maize plants fix nutrients and promote maize plant development.

Key words: Leclercia adecarboxylata LN01, rhizosphere growth-promoting bacteria, whole-genome sequencing, growth-promoting effect

ZHANG Ting, WAN Yu-xin, XU Wei-hui, WANG Zhi-gang, CHEN Wen-jing, HU Yun-long. Growth-promoting Effects of a Rhizosphere Growth-promoting Bacterium Leclercia adecarboxylata LN01 in Maize Plants and Its Whole-genome Analysis[J]. Biotechnology Bulletin, 2025, 41(1): 263-275.

Figures/Tables 12

References 48

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培养基Medium	组分Composition/（g·L^-1）
NBRIP 培养基^[12] National Botanical Research Institute's phosphate medium	葡萄糖10.0，Ca₃ (PO₄)₂ 5.0，MgCl₂ ·6H₂O 0.2， (NH₄)₂SO₄ 0.1，琼脂20.0，液体培养基不加琼脂
亚历山大罗夫培养基^[13] Alexandrov medium	蔗糖5.0，Na₂HPO₄ 2.0，MgSO₄ 0.5，CaCO₃ 0.1，FeCl₃ 0.005，钾长石1.0，溴百里酚蓝（100 mg/L）20 mL，琼脂20.0，pH 7.0
解钾液体发酵培养基^[14] Potassium bacteria medium	蔗糖10.0，Na₂HPO₄ 1.0，MgSO₄ 1.0，CaCO₃ 0.1，FeCl₃ 0.005，钾长石10.0，(NH₄)₂SO₄ 0.5
阿须贝无氮培养基^[15] Ashby’S medium	KH₂PO₄0.2，MgSO₄0.2，NaCl 0.2，CaCO₃ 5.0，甘露醇10.0，CaSO₄ 0.1，琼脂20.0，pH 7.0，液体培养基不加琼脂
牛肉膏蛋白胨培养基^[16] Nutrient broth medium	蛋白胨10.0，NaCl 5.0，牛肉膏3.0，琼脂20.0，pH 7.0，液体培养基不加琼脂
CAS培养基Chrome azurol sulfonate medium	CAS培养基10.87，琼脂20.0，pH 7.0

培养基Medium	组分Composition/（g·L^-1）
NBRIP 培养基^[12] National Botanical Research Institute's phosphate medium	葡萄糖10.0，Ca₃ (PO₄)₂ 5.0，MgCl₂ ·6H₂O 0.2， (NH₄)₂SO₄ 0.1，琼脂20.0，液体培养基不加琼脂
亚历山大罗夫培养基^[13] Alexandrov medium	蔗糖5.0，Na₂HPO₄ 2.0，MgSO₄ 0.5，CaCO₃ 0.1，FeCl₃ 0.005，钾长石1.0，溴百里酚蓝（100 mg/L）20 mL，琼脂20.0，pH 7.0
解钾液体发酵培养基^[14] Potassium bacteria medium	蔗糖10.0，Na₂HPO₄ 1.0，MgSO₄ 1.0，CaCO₃ 0.1，FeCl₃ 0.005，钾长石10.0，(NH₄)₂SO₄ 0.5
阿须贝无氮培养基^[15] Ashby’S medium	KH₂PO₄0.2，MgSO₄0.2，NaCl 0.2，CaCO₃ 5.0，甘露醇10.0，CaSO₄ 0.1，琼脂20.0，pH 7.0，液体培养基不加琼脂
牛肉膏蛋白胨培养基^[16] Nutrient broth medium	蛋白胨10.0，NaCl 5.0，牛肉膏3.0，琼脂20.0，pH 7.0，液体培养基不加琼脂
CAS培养基Chrome azurol sulfonate medium	CAS培养基10.87，琼脂20.0，pH 7.0

菌株LN01特征 Characteristics of LN01	数值 Value
Genome size/bp	5 379 004
GC content/%	55.1
Chromosome	1
Plasmid	6
tRNA	87
rRNA（5S, 16S, 23S）	25
Protein-coding genes（CDS）	5 004
Genomic islands	14
Secondary metabolite gene clusters	4
Genes assigned to NR	4 873
Genes assigned to COGs	4 085
Genes assigned to GO	2 793
Genes assigned to KEGG	3 285
Genes assigned to Pfam	4 400
Genes assigned to Swiss-Prot	4 219

菌株LN01特征 Characteristics of LN01	数值 Value
Genome size/bp	5 379 004
GC content/%	55.1
Chromosome	1
Plasmid	6
tRNA	87
rRNA（5S, 16S, 23S）	25
Protein-coding genes（CDS）	5 004
Genomic islands	14
Secondary metabolite gene clusters	4
Genes assigned to NR	4 873
Genes assigned to COGs	4 085
Genes assigned to GO	2 793
Genes assigned to KEGG	3 285
Genes assigned to Pfam	4 400
Genes assigned to Swiss-Prot	4 219

促生特性 PGP traits	基因 Gene
IAA	trpA trpB trpS trpCF trpR trpGD ipdC amiE patB
Potassium solubilization and uptake	kdpA kdpB kdpC kefB kefC kefF kefG trkA trkH kup
Siderophore	tonB exbB fhuB fhuC fhuD fhuE fhuF efeO efeB efeU fepD fepG fepC ftsB afuB afuC afuA
Nitrogen generation	glnG nirB nirC nirD nasA nrtA nrtB nrtC nrtB nasA nirA glnA gltB gltD
Phosphate solubilization and uptake	pstS pstC pstA pstB phnA phnC phnD phnE phnF phnG phnH phnI phnJ phnK phnL phnN phnP phoA phoB phoE phoR ugpA ugpB ugpC ugpE