Abstract
Background and Aims
Rhizosphere microorganisms play an important role in promoting plant growth and maintaining soil health. Bacillus altitudinis LZP02 (LZP02) is an efficient plant growth-promoting rhizobacterium that interacts closely with rice radicals. However, the mechanisms mediating the rhizosphere interactions of beneficial strains of microorganisms in native soil are mostly unclear.
Methods
This study analysed the rhizosphere-enriched taxonomic and functional properties of the rhizosphere-associated microbiome and determined how they were affected by LZP02 using metagenome sequencing and ITS sequencing after the inoculation of LZP02 in soil. And microorganisms from the rice rhizosphere were identified and cultivated using high-throughput sequencing.
Results
LZP02 stimulated some beneficial bacteria, such as Novosphingobium, Acidovorax, Sphingomonas, and Devosia, to the rhizosphere. The enrichment of functional attributes, nitrogen metabolism and bacterial chemotaxis demonstrated an increase in active microbe-microbe interactions in the rhizosphere. This study showed that LZP02 stimulated plant growth in three ways: (1) by increasing the relative abundance of most rhizosphere-enriched genus; (2) by increasing the relative abundance of the functional attributes involved in microbe-microbe interactions; and (3) by enriching functional components that are essential for plant fitness, such as nitrogen fixation and bacterial chemotaxis in the rhizosphere microbiome. Finally, inoculation of enriched single strains or synthetic consortia isolated from the radical-associated microbiome using high-throughput cultivation could improve plant growth.
Conclusion
This study proposes a new mechanism by which LZP02 influences the nitrogen metabolism of rhizosphere microorganisms and bacterial chemotaxis for rice growth by reshaping the rhizosphere microbiome.
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Data availability
Raw data used in this study are available in the NCBI under the bioproject, accession no. PRJNA918597 and accession no. PRJNA919054. The raw data of high-throughput are available in the GSA: CRA007016.
Abbreviations
- PGPR:
-
Plant growth-promoting rhizobacteria
- BCAAs:
-
Branched chain amino acids
- LZP02:
-
Bacillus altitudinis LZP02
- LB:
-
Luria-Bertani broth
- CFU:
-
Colony forming unit
- PCR:
-
Polymerase chain reaction
- ASV:
-
Amplicon sequencing variant
- RDP:
-
Ribosomal database project
- ORFs:
-
Open reading frames
- KEGG:
-
Encyclopedia of genes and genomes
- TSB:
-
Trypticase soy broth
- OD:
-
Optical density
- PCoA:
-
Principal coordinate analysis
- LDA:
-
Linear discriminant analysis
- LEfSe:
-
Linear discriminate effect size
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Acknowledgements
The authors give thanks to Wang Zhigang and Chen Wenjing for their excellent technical assistance. Sequencing support was provided by Shanghai Majorbio Bio-pharm Technology Co., Ltd and Sangon Biotech (Shanghai) Co., Ltd.
Funding
This work was funded by the Outstanding Youth Fund project of Heilongjiang Province in China (JQ2023D001), the Key Research and Development Projects of Heilongjiang in China (GA21B007).
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W.N.C. wrote and edited the paper. W.N.C., W.J.C., and Z.G.W. conceived the overall study design. W.J.C. and Y.L.H. performed soil and radical sampling. W.N.C. conducted the experiments and prepared the figures and bioinformatics analysis. W.J.C. and Y.L.H. provided critical guidance in the analysis. Z.G.W. was involved in revising the manuscript and approving the final version.
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Chang, W., Chen, W., Hu, Y. et al. Bacillus altitudinis LZP02 improves rice growth by reshaping the rhizosphere microbiome. Plant Soil 498, 279–294 (2024). https://doi.org/10.1007/s11104-023-06435-3
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DOI: https://doi.org/10.1007/s11104-023-06435-3