The Influence of Soil Fertilization on the Distribution and Diversity of Phosphorus Cycling Genes and Microbes Community of Maize Rhizosphere Using Shotgun Metagenomics.

Matthew Enebe,Olubukola Babalola

doi:10.3390/genes12071022

Abstract

Biogeochemical cycling of phosphorus in the agro-ecosystem is mediated by soil microbes. These microbes regulate the availability of phosphorus in the soil. Little is known about the response of functional traits of phosphorus cycling microbes in soil fertilized with compost manure (derived from domestic waste and plant materials) or inorganic nitrogen fertilizers at high and low doses. We used a metagenomics investigation study to understand the changes in the abundance and distribution of microbial phosphorus cycling genes in agricultural farmlands receiving inorganic fertilizers (120 kg N/ha, 60 kg N/ha) or compost manure (8 tons/ha, 4 tons/ha), and in comparison with the control. Soil fertilization with high level of compost (Cp8) or low level of inorganic nitrogen (N1) fertilizer have nearly similar effects on the rhizosphere of maize plants in promoting the abundance of genes involved in phosphorus cycle. Genes such as ppk involved in polyphosphate formation and pstSABC (for phosphate transportation) are highly enriched in these treatments. These genes facilitate phosphorus immobilization. At a high dose of inorganic fertilizer application or low compost manure treatment, the phosphorus cycling genes were repressed and the abundance decreased. The bacterial families Bacillaceae and Carnobacteriaceae were very abundant in the high inorganic fertilizer (N2) treated soil, while Pseudonocardiaceae, Clostridiaceae, Cytophagaceae, Micromonosporaceae, Thermomonosporaceae, Nocardiopsaceae, Sphaerobacteraceae, Thermoactinomycetaceae, Planococcaceae, Intrasporangiaceae, Opitutaceae, Acidimicrobiaceae, Frankiaceae were most abundant in Cp8. Pyrenophora, Talaromyces, and Trichophyton fungi were observed to be dominant in Cp8 and Methanosarcina, Methanobrevibacter, Methanoculleus, and Methanosphaera archaea have the highest percentage occurrence in Cp8. Moreover, N2 treatment, Cenarchaeum, Candidatus Nitrososphaera, and Nitrosopumilus were most abundant among fertilized soils. Our findings have brought to light the basis for the manipulation of rhizosphere microbial communities and their genes to improve availability of phosphorus as well as phosphorus cycle regulation in agro-ecosystems.

Highlights

Driven by the need to increase crop yield, farmers worldwide have resorted to employing either organic or inorganic fertilizers to boost soil fertility
There was a significant difference in the relative abundance of these bacterial families (p < 0.001) within the fertilized and unfertilized maize rhizosphere soil samples
The principal component analysis and principal coordinate analysis of the fungal genus are contained in Figures S1 and S2 and are described in the discussion section

Summary

Introduction

Driven by the need to increase crop yield, farmers worldwide have resorted to employing either organic or inorganic fertilizers to boost soil fertility. Microbes capable of producing organic acid through carbon metabolism as well as the synthesis of hydrolytic enzyme such as phosphatase are capable of phosphorus mineralization and solubilization [7,8]. Abiotic factors like drying and rewetting of soil, temperature, pH, and soil depth [13,14] determine the extent of phosphorus availability in the soil and its reactivity. Microbes secreting organic acids (e.g., pyruvic acid, gluconic acid) that facilitate the solubilization of phosphate minerals are called phosphate solubilizing bacteria As these acids are derived from organic carbon compounds via the tricarboxylic acid cycle, there is a close relation between carbon utilization by bacteria and phosphorus availability. In the soluble inorganic forms, phosphorus exists in soil as phosphodiesters, phosphomonoesters or phytates (in the organic forms) and as metallophosphates [23]

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