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Application of N2-fixing Paenibacillus triticisoli BJ-18 changes the compositions and functions of the bacterial, diazotrophic, and fungal microbiomes in the rhizosphere and root/shoot endosphere of wheat under field conditions

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Abstract

From 2015 to 2018, we continuously applied the diazotroph Paenibacillus triticisoli BJ-18 as an inoculant to soil cropped winter wheat under field condition. Based on 16S rRNA, nifH, ITS, and shotgun metagenome sequencing, we investigated the influences of diazotroph on the composition and function of the bacterial, diazotrophic, and fungal communities in the rhizosphere and root/shoot endosphere of wheat in 2018. P. triticisoli BJ-18 significantly increased soil total N, available P, organic matter, nitrogenase activity, and wheat yield. The diversities of the rhizospheric bacterial community were higher in the inoculation treatment than the non-inoculation treatment, while the relative abundances of rhizospheric fungal, endospheric bacterial, and diazotrophic communities were lower in the inoculation treatment. Paenibacillus became dominant in the rhizosphere and root, and also the relative abundance of indigenous diazotrophs was increased by inoculation. The microbial inoculation also significantly increased the relative abundances of indigenous plant growth-promoting microbes (Bacillus, Klebsiella, and Podospora) but decreased the relative abundances of indigenous pathogenic fungi (Alternaria). Notably, some nitrogenase gene abundances were significantly enriched by inoculation. These results demonstrated that P. triticisoli BJ-18, acting as a keystone species, can change (optimize) the composition and function of plant microbiome to promote plant growth and productivity.

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Data availability

The DNA reads have been deposited at NCBI with SRA accession nos. SRP218978, SRP224781, SRP223722, and SRP223975.

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Funding

This work was supported by the National Key Research and Development Program of China (Grant No. 2017YFD0200800).

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  1. State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, 100094, People’s Republic of China

    Yongbin Li, Minyang Wang & Sanfeng Chen

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  1. Yongbin Li
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  2. Minyang Wang
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Contributions

SFC designed the study and edited and reviewed the manuscript. YBL performed all experiments and wrote the original manuscript. MYW assayed wheat biomass.

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Correspondence to Sanfeng Chen.

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Fig. S1

The rarefaction curves of rhizospheric bacteria (A), root endophytic bacteria (B), shoot endophytic bacteria (C), root endophytic diazotroph (D), shoot endophytic diazotroph (E) and rhizospheric fungi (F) based on OTUs level. (PDF 449 kb)

Table S1

Data statistics of shotgun metagenomic sequencing. (DOCX 15 kb)

Table S2

Microbial α-and β-diversity significances (P-values) between sample variables, and β-dissimilarities of intra- and inter-group comparisons. ANOSIM: analysis of similarities. (DOCX 17 kb)

Table S3

Good’s coverage of microbial communities in the wheat rhizosphere, roots and shoots. (DOCX 18 kb)

Table S4

Pearson’s correlation coefficient analysis between the abundances of nif genes and soil nitrogenase activity/total N content. (DOCX 15 kb)

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Li, Y., Wang, M. & Chen, S. Application of N2-fixing Paenibacillus triticisoli BJ-18 changes the compositions and functions of the bacterial, diazotrophic, and fungal microbiomes in the rhizosphere and root/shoot endosphere of wheat under field conditions. Biol Fertil Soils 57, 347–362 (2021). https://doi.org/10.1007/s00374-020-01528-y

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