Metagenomic analysis of agricultural soils under organic and inorganic fertilization
Abstract
Soil fertilization is an age-old agricultural practice aimed at increasing soil nutrition and soil health. Recently, agriculturists have come to the realization that inorganic fertilizer application over time could result in no corresponding increase in crop yield. Organic manure has been shown to be beneficial to soil health and in promotion of soil ecosystems’ biodiversity. A healthy soil is one in which the microbes present are viable and performing their activities in nutrient cycling and sustaining plant health. However, increased fertilization of agricultural soils has resulted in a series of environmental degradation effects. This necessitates the adoption of a suitable strategy for increasing soil fertility without distorting the stability of the soil micro and macro ecosystems. In this study, we employed shotgun metagenomics sequencing to understand the effects of fertilization with organic and inorganic fertilizers at different concentrations on the soil microbiome structure, diversity and function at the maize rhizosphere. The soil samples were sourced from maize plants rhizosphere treated with compost manure at a concentration of 8 tons and 4 tons per hectare as well as from the ones treated with 120 kg and 60 kg per hectare inorganic fertilizers (NPK – 20:7:3) and control. The pH of the soil was 4.97, thus slightly acidic. Other physicochemical properties of the soil were determined. The effects of these fertilizers were investigated on carbon, nitrogen, and phosphorus cycling genes. It was equally evaluated for the genes involved in bacterial chemotaxis and disease suppression in the soil. The different fertilizer doses and types have effects on the microbial communities and their basic functions in the soil. Proteobacteria and Bacteroidetes were distributed in all the treated samples, with Proteobacteria and Actinobacteria being very abundant in high dose of compost manure (Cp8), low inorganic fertilizer (N1) and the control (Cn0) treatments. Firmicutes were most abundant in high inorganic fertilizer (N2) treated soils and low compost manure (Cp4) treatments. Besides, the results showed that fungi were selected and enriched by high and low compost manure, while archaea were mostly supported by high dose of inorganic fertilizer and high compost manure treatments. Functional genes involved in carbon, nitrogen and phosphorus cycling were highly enhanced in the maize rhizosphere under high compost, lower inorganic fertilizer and
the control. Disease suppressive genes such as genes for antibiotics, antifungal, nematicides and siderophores production were abundant in the maize rhizosphere. Bacterial chemotaxis were observed to be high in these treatments. On the other hand, low compost manure and high inorganic fertilizers tended to suppress these microbial beneficial functions. This implies that there is higher chance of disease development and poor crop yield in a soil treated with these nutrients at the specified concentrations. They do not promote biodiversity due to inorganic fertilizers’ associated soil acidification and salinization and low compost manure induced nutrients starvation to soil microbes and hence their observed negative effects. Therefore, to achieve a sustainable agriculture in maintaining biodiversity within the soil ecosystem and increasing crop yield under a semi-arid condition, higher doses of compost manure and lower inorganic fertilizer should be the desired fertilization choice. Maize plants could be harnessed through intercropping practice to enable other plants to benefit from their enrichment of soil microbial community structure and functions through rhizosphere effects.