Wheat Rhizosphere Metagenome Reveals Newfound Potential Soil Zn-Mobilizing Bacteria Contributing to Cultivars’ Variation in Grain Zn Concentration

Abstract

An effective solution to global human zinc (Zn) deficiency is Zn biofortification of staple food crops, which has been hindered by the low available Zn in calcareous soils worldwide. Many culturable soil microbes have been reported to increase Zn availability in the laboratory, while the status of these microbes in fields and whether there are unculturable Zn-mobilizing microbes remain unexplored. Here, we use the culture-independent metagenomic sequencing to investigate the rhizosphere microbiome of three high-Zn (HZn) and three low-Zn (LZn) wheat cultivars in a field experiment with calcareous soils. The average grain Zn concentration of HZn was higher than the Zn biofortification target 40 mg kg–1, while that of LZn was lower than 40 mg kg–1. Metagenomic sequencing and analysis showed large microbiome difference between wheat rhizosphere and bulk soil but small difference between HZn and LZn. Most of the rhizosphere-enriched microbes in HZn and LZn were in common, including many of the previously reported soil Zn-mobilizing microbes. Notably, 30 of the 32 rhizosphere-enriched species exhibiting different abundances between HZn and LZn possess the functional genes involved in soil Zn mobilization, especially the synthesis and exudation of organic acids and siderophores. Most of the abundant potential Zn-mobilizing species were positively correlated with grain Zn concentration and formed a module with strong interspecies relations in the co-occurrence network of abundant rhizosphere-enriched microbes. The potential Zn-mobilizing species, especially Massilia and Pseudomonas, may contribute to the cultivars’ variation in grain Zn concentration, and they deserve further investigation in future studies on Zn biofortification.

Cross Talk Between Zinc-Solubilizing Bacteria and Plants: A Short Tale of Bacterial-Assisted Zinc Biofortification

“…PR3) with 75% RDF (recommended dose of fertilizers) showed an improved level of Zn uptake (323.8 g/h) in wheat (191). Recently, the metagenomics-based study revealed the existence of potential Zn-mobilizing species, particularly Massilia and Pseudomonas sp., that could form a functional community in increasing Zn concentration in grains of wheat varieties (192). More recent studies that decipher the microbial-assisted improvement in the plant yield and Zn content of crop plants are listed in Table 2.…”

“…Molecular approaches of culture-independent methods for determining the functional gene or microbial diversity in soil have been developed considerably in the recent past. Metagenomics also offers new perspectives to identify the existence and abundance of certain microorganisms or functional genes specific for soil Zn mobilization or increasing root Zn uptake, mainly the synthesis of OAs and siderophores (192).…”

Seed endophytic bacterial profiling from wheat varieties of contrasting heat sensitivity

“…When comparing the presence of Zn-mobilizing species such as Adhaeribacter , Janthinobacterium , Massilia , and Pseudomonas in rhizospheric and bulk soil of wheat, it was observed that the relative abundance was higher in the rhizosphere that could articulate the local community structure to improve the plant growth by mobilizing nutrients ( Wang et al., 2021 ). Acinetobacter was highly prominent, while Pantoea , Pseudomonas , and Paracoccus were also detected from the endosperm of T. aestivum cv.…”

Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production

“…The authors of these studies advise reducing the spreading of ARG from amendment onto the lettuce leaf surface as this may influence human health negatively. Many other scientific questions can be tackled using metagenomics, such as Zn availability in grains for biofortification ( Wang et al, 2021 ), or the detection of foodborne pathogens in production chains ( Yang et al, 2016 ).…”