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The effect of microbial inoculant origin on the rhizosphere bacterial community composition and plant growth-promotion

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Abstract

Aims

Microbial inoculation has been proposed as a potential approach for rhizosphere engineering. However, it is still unclear to what extent successful plant growth-promoting effects are driven by the origin of the microbial inocula and which taxa are responsible for the plant-beneficial effects.

Methods

We conducted a microbial transplant experiment by using different microbial inocula (and nutrient controls) isolated from forest, soybean and tomato field soils and determined their effects on tomato plant biomass and nutrient assimilation in sterilized tomato soil. Rhizosphere bacterial communities were compared at the end of the experiment and correlative and machine learning analyses used to identify potential keystone taxa associated with the plant growth-promotion.

Results

Microbial inoculants had a clear positive effect on plant growth compared to control nutrient inoculants. Specifically, positive effects on the plant biomass were significantly associated with microbial inoculants from the forest and soybean field soils, while microbial inoculants from the forest and tomato field soils had clear positive effects on the plant nutrient assimilation. Soil nutrients alone had relatively minor effects on rhizosphere bacterial communities. However, the origin of microbial inoculants had clear effects on the structure of bacterial community structure with tomato and soybean inoculants having positive effects on the diversity and abundance of bacterial communities, respectively. Specifically, Streptomyces, Luteimonas and Enterobacter were identified as the potential keystone genera affecting plant growth.

Conclusions

The origin of soil microbiome inoculant can predictably influence plant growth and nutrient assimilation and that these effects are associated with certain key bacterial genera.

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Acknowledgements

This research was financially supported by the Natural Science Foundation of Jiangsu Province (BK20181068, BK20170467), the National Natural Science Foundation of China (31801952, 31470100), the Natural Science Research Program of Huai’an (HAB201829) and the Natural Science Research Project of Jiangsu Higher Education Institutions (18KJA180002). V-P.F. is supported by the Royal Society Research Grants (RSG\R1\180213 and CHL\R1\180031) at the University of York.

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Authors and Affiliations

  1. Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian, 223300, People’s Republic Of China

    Yian Gu, Ke Dong, Wei Yang, Yaner Yan, Naisen Liu, Nikolai Borisjuk & Yuming Luo

  2. Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700, AB, Wageningen, The Netherlands

    Stefan Geisen

  3. Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huaian Academy of Agricultural Sciences, Huai’an, 223300, People’s Republic Of China

    Dalu Gu

  4. Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK

    Ville-Petri Friman

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  1. Yian Gu
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  2. Ke Dong
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Fig. S1

Bacterial phyla of shared OTUs present in the tomato rhizosphere treated with different microbial inoculants. We detected 134 shared OTUs between three microbial inoculant treatments and most of these OTUs belonged to Proteobacteria, Actinobacteria, Bacteroidetes and Gemmatimonadetes (PDF 148 kb)

Fig. S2

Bacterial phyla significantly different between microbial and nutrient inoculants treatments. Corrected p-values were calculated using Student’s t test (p < 0.05). (PDF 161 kb)

Fig. S3

Associations between plant growth-promoting traits and bacterial community composition of tomato rhizosphere soils amended with nutrient and microbial inoculants. (a) Random forest model results showing the mean predictor importance (percentage of increase in mean square error (MSE)) of bacterial taxa in affecting plant growth. Different bar colors denote the direction of effects and asterisks above the bars indicate the significance levels (**, p < 0.01; *, p < 0.05). (b) Correlation between the bacterial community diversity (Shannon diversity) and mean plant growth-promotion (z-score) (PDF 171 kb)

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Gu, Y., Dong, K., Geisen, S. et al. The effect of microbial inoculant origin on the rhizosphere bacterial community composition and plant growth-promotion. Plant Soil 452, 105–117 (2020). https://doi.org/10.1007/s11104-020-04545-w

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