Abstract
The effects of fertilizer regime on bulk soil microbial communities have been well studied, but this is not the case for the rhizosphere microbiome. The aim of this work was to assess the impact of fertilization regime on wheat rhizosphere microbiome assembly and 16S rRNA gene-predicted functions with soil from the long term Broadbalk experiment at Rothamsted Research. Soil from four N fertilization regimes (organic N, zero N, medium inorganic N and high inorganic N) was sown with seeds of Triticum aestivum cv. Cadenza. 16S rRNA gene amplicon sequencing was performed with the Illumina platform on bulk soil and rhizosphere samples of 4-week-old and flowering plants (10 weeks). Phylogenetic and 16S rRNA gene-predicted functional analyses were performed. Fertilization regime affected the structure and composition of wheat rhizosphere bacterial communities. Acidobacteria and Planctomycetes were significantly depleted in treatments receiving inorganic N, whereas the addition of high levels of inorganic N enriched members of the phylum Bacteroidetes, especially after 10 weeks. Bacterial richness and diversity decreased with inorganic nitrogen inputs and was highest after organic treatment (FYM). In general, high levels of inorganic nitrogen fertilizers negatively affect bacterial richness and diversity, leading to a less stable bacterial community structure over time, whereas, more stable bacterial communities are provided by organic amendments. 16S rRNA gene-predicted functional structure was more affected by growth stage than by fertilizer treatment, although, some functions related to energy metabolism and metabolism of terpenoids and polyketides were enriched in samples not receiving any inorganic N, whereas inorganic N addition enriched predicted functions related to metabolism of other amino acids and carbohydrates. Understanding the impact of different fertilizers on the structure and dynamics of the rhizosphere microbiome is an important step toward developing strategies for production of crops in a sustainable way.
Highlights
MATERIALS AND METHODSThe development and application of synthetic fertilizers fueled the green revolution and massively expanded our ability to produce food (Stevenson et al, 2013)
Mantel test indicated that relative abundance of Operational taxonomic units (OTUs) assigned to bacterial communities correlated with soil parameters such as pH, %N, %C, %Inorganic carbon (IC) and C:N ratio (R = 0.6328, p = 0.0001) (Table 2)
The phylum Bacteroidetes was negatively correlated with high %IC and C:N, Cyanobacteria was negatively correlated with high %N and %C, whereas Gemmatimonadetes was negatively correlated with high C:N
Summary
MATERIALS AND METHODSThe development and application of synthetic fertilizers fueled the green revolution and massively expanded our ability to produce food (Stevenson et al, 2013). It is well known that soil microbial communities influence plant growth, health and resource use efficiency, especially the subset that are recruited by plants to form the root microbiome (Berendsen et al, 2012; Mendes et al, 2013). Understanding and optimizing microbial communities for enhanced crop growth is a considerable challenge, but one that we can begin to tackle due to advances in next-generation sequencing technologies (Mendes et al, 2013). An understanding of the effect of agricultural practices such as fertilization regime on the presence or absence of pathogens and beneficial microbes is essential to ascertain if microbiome manipulation can be optimized to contribute to sustainable intensification of agriculture (Bakker et al, 2012; Hartmann et al, 2015; Quiza et al, 2015)
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