Elsevier

Applied Soil Ecology

Volume 158, February 2021, 103784
Applied Soil Ecology

Inoculation with plant growth-promoting bacteria alters the rhizosphere functioning of tomato plants

https://doi.org/10.1016/j.apsoil.2020.103784Get rights and content

Highlights

  • Tomato rhizosphere metabolome was investigated upon PGPB inoculation.

  • Accumulation of rhizosphere compounds was dependent of the inoculated bacterium.

  • Inoculation with PGPB influenced the metabolism of the rhizosphere microbiome.

  • Key metabolites in plant-bacteria interactions were detected.

Abstract

Inoculation with plant growth-promoting bacteria (PGPB) represents an efficient method in sustainable agriculture to improve nutrients availability and crop production in diverse environmental conditions. In the present work, untargeted metabolomics and community-level physiological profiles (CLPP) approaches were employed to investigate the shaping of tomato rhizosphere functioning and potential metabolic activity imposed by rhizosphere-associated microbiome, following inoculation with two different PGPB (Enterobacter sp. 15S and Pseudomonas sp. 16S). Significant increases in root and shoot dry biomass were observed in both inoculated treatments, when compared to uninoculated plants (p < 0.05). The untargeted metabolomics allowed discriminating the metabolic profiles of tomato rhizosphere, with distinct modulations imposed by either Enterobacter 15S or Pseudomonas 16S. Flavonoids and other phenolics were among the most frequently identified differential metabolites in the rhizosphere from both Enterobacter 15S and Pseudomonas 16S inoculated plants. Nevertheless, other metabolites like phytohormones and amino acids were also decisive to this specific modulation. The metabolic activity profile rhizosphere-associated microbiome of tomato plants unveiled by the CLPP analysis was congruent with the metabolomic data and reinforced the influence exerted by the bacterial inoculation on modulating the rhizosphere microbiome functioning. In particular, the microbiome associated with control and 16S-treated plants showed a higher functional diversity than those treated with Enterobacter 15S. Carbohydrates, carboxylic acids, amino acids, and polymers were the main classes of substrates which contributed to such differences.

Introduction

The rhizosphere is defined as the soil volume that is greatly influenced by root activity, thus showing distinct physical, chemical and biological characteristics from bulk soil (Hinsinger et al., 2005). Important processes related to growth, nutrition and health of plants, as well those related to the biogeochemical cycles take place in the rhizosphere, in part due to the higher density and metabolic activity of its microbiome compared to the bulk soil microbiome (Mendes et al., 2013). Inoculation with beneficial bacteria, also known as plant growth-promoting bacteria (PGPB), constitutes a powerful tool towards sustainable agriculture due to their positive influence on plant development through multiples mechanisms: they may provide nutrients, alleviate biotic and abiotic stresses and secrete phytohormones and phytochelators (Bulgarelli et al., 2013; Gouda et al., 2018; Pii et al., 2015a). The most common bacteria which have been used in inoculation studies mainly include different genera of diazotrophic bacteria, like Rhizobium, Bradyrhizobium and Azospirillum, or P-solubilizing bacteria, like Pseudomonas and Bacillus (Bashan et al., 2014). However, in the last years, the possibility of using of other genera with the potential of improving the plant growth, such as Burkholderia, Herbaspirillum, Enterobacter, Streptomyces, Erwinia, Rhodococcus, Azotobacter, Gluconacetobacter, Klebsiella and Pantoea among others, has been also explored (Santos et al., 2017; Souza et al., 2015).

Through roots, plants actively release a large variety of organic and inorganic compounds called rhizodeposits or root exudates (Uren, 2007), many of which have biological activity on other organisms. Root exudates mainly consist of low molecular weight organic compounds such as amino acids, organic acids, sugars, phenolic compounds and high molecular weight compounds such as polysaccharides and proteins (Badri and Vivanco, 2009; Zhalnina et al., 2018). The complexity of the root exudates is related to its functional multiplicity, albeit its composition depends on genetics, developmental and environmental influences; on the other hand, the active modulation of qualitative and quantitative root exudation profiles by the plant can modify the rhizosphere and soil properties to ensure a better adaptation to the environmental conditions (Vives-Peris et al., 2020). Furthermore, root exudates represent an important nutrient source for rhizosphere microorganisms; therefore, any variation in their concentration and composition can playing an active role in shaping the rhizosphere microbiome, by exerting either positive, negative or neutral effects on microbial growth (Canarini et al., 2019).

Insights of the reciprocal metabolic and signaling feedbacks established between plants and microorganisms in the rhizosphere can be investigated by the application of complementary high-throughput approaches, such as untargeted metabolomics and the community-level physiological profiling (CLPP) (Lladó and Baldrian, 2017; Mhlongo et al., 2018). In this context, the exploration of the biotic processes occurring in the rhizosphere, especially the relationships between the plants and their associated microbiota, could provide new management approaches for agriculture, by favoring the establishment of beneficial interactions aiming at improving both the plant nutrition and the protection against environmental stresses (Gupta et al., 2015; Zhalnina et al., 2018). Hence, since studies comparing the response to PGPB inoculation on the variability in root exudation of dicots and the modulation of the metabolic activity of rhizosphere microbial communities are scarcely described, the aim of this work was to investigate the effect of the inoculation with different species of beneficial bacteria (Enterobacter sp. 15S and Pseudomonas sp. 16S) on the functioning and metabolic versatility of tomato rhizosphere using two integrative approaches: i) untargeted metabolomics by UHPLC-ESI/QTOF-MS and (ii) CLPP using Biolog EcoPlates.

Section snippets

Bacterial strains

Enterobacter sp. 15S and Pseudomonas sp. 16S (both strains within the class Gammaproteobacteria) were originally isolated from horticultural soils under conventional and organic management, respectively. These bacteria were selected from the results of a previous screening (Zuluaga et al., 2020) based on their diverse plant growth promotion traits (i.e., IAA production, phosphate solubilization and siderophores production) and their ability to enhance tomato growth. The strains are deposited in

Plant-growth response to inoculation

The effects of bacterial inoculation on plant biomass responses after 40 days of growth in rhizoboxes system are shown in Fig. 1. Root and shoot biomass of tomato plants inoculated with Enterobacter 15S were significantly increased by more than 40% as compared to control plants; similarly, the inoculation with Pseudomonas 16S caused a significantly higher accumulation of both root and shoot biomass (over 50%) with respect to control plants. No significant differences in plant biomass

Discussion

With the increased need of developing sustainable agriculture practices to feed the growing world population, agricultural bioinputs such as PGPB inoculants have emerged as important tools to reduce the use of agrochemicals. Nonetheless, an integrative understanding of the functional dynamics and crosstalks developed in soil-plant-microorganism interrelationships is needed for a better exploitation of PGPB potentials in extensive crop systems (Wezel et al., 2014). Here, we studied the changes

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

This work was supported by the Instituto Nacional de Ciência e Tecnologia de Microrganismos Promotores do Crescimento de Plantas Visando a Sustentabilidade Agrícola e Responsabilidade Ambiental (INCT-MPCPAgro), CNPq, Fundação Araucária and Londrina State University. The authors thank the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for granting scholarships to Mónica Y. A. Zuluaga (PDSE 88881.189485/2018-01).

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