Metagenomic deciphering of microbial community structure, diversity and functionality of the soil-and-oil palm seedling system associated with fertilizer application

In well-run Malaysian oil palm plantations, fertilizer management is the highest field cost factor and is often associated with environmental concerns. While inorganic fertilizer effects on crop microbes like maize, wheat, and soybean are extensively studied, oil palm seedling microbial communities and responses, including root changes, microbial shifts, and nutrient uptake, remain insufficiently understood. This prompted the study to investigate microbial community composition, diversity, and functional attributes of the soil-and-oil palm seedling system (bulk soil, rhizosphere, rhizoplane, endosphere) subjected to NPK fertilization using an amplicon sequencing approach and bioinformatic analyses. The fertilizer application substantially (p < 0.05) increased soil physicochemical properties including base saturation, total phosphorus, exchangeable magnesium, and potassium. The inorganic fertilizer also increased significantly (p < 0.05) the foliar carbon and potassium content as well as the seedling’s dry weight. The taxonomic composition of microorganisms revealed Proteobacteria (44.91%), Ascomycota (37.42%), Cyanobacteria (22.85%), and Glomeromycota (12.56%) predominantly distributed across all samples. Alpha diversity demonstrated that the fertilizer application significantly reduced the bacteria across the soil-and-oil palm seedling system yet increased the fungal richness and diversity in bulk soil and rhizoplane. Moreover, the Principal Coordinate Analysis (PCoA) indicated the fertilizer application influenced the microbial communities mainly in the rhizosphere compared to other niches. However, the unfertilized soil enriched a higher number of discriminatory taxa compared to the fertilized based on linear discriminant analysis effect size (LEfSe) analysis. Apart from the enrichment of fungal pathogenicity due to the fertilizer application, the LEfSe also revealed that the treatment enriched functions related to nutrient cycling and plant growth promotions in the microbial communities. Several phyla members belonging to Proteobacteria, Actinobacteria, Acidobacteria, Ascomycota, and Basidiomycota were recognized as the network keystones as revealed by the co-occurrence network analysis. Based on canonical correspondence analysis, several environmental factors including pH, foliar total carbon and phosphorus, soil total phosphorus, and plant biomass were identified as the significant (p < 0.05) key drivers in determining the composition of the microbial communities. These findings provided insights into the microbial composition and potential functions in unfertilized and fertilized soil. The research reveals that the NPK application improves soil properties and seedling growth. To avoid over-fertilization and environmental harm, careful dosage and timing are crucial. While NPK use shifts microbial diversity towards fungi, a balanced community can be maintained by adding organic fertilizers or compost that support bacterial populations and nutrient supply. The study also emphasizes nutrient cycling and growth promotion through LEfSe analysis, suggesting benefits from specific microbial inoculants. Environmental factors like pH, nutrients, and plant biomass guide fertilizer strategies for optimal nutrient uptake and microbial relationships. For long-term sustainability, an integrated approach using inorganic and organic fertilizers is recommended for enhanced soil health and microbial diversity. This research underscores lasting benefits for soil and ecosystem resilience, beyond short-term gains.

Text 122810.pdf Download (1MB) Official URL or Download Paper: http://ethesis.upm.edu.my/id/eprint/18673

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