Long-Term Organic Nutrient Management Fosters the Eubacterial Community Diversity in the Indian Semi-arid Alfisol as Revealed by Length Heterogeneity–PCR

Abstract

Agricultural practices influence the community structure and functional diversity of soil microorganisms. In the present study, the impact of nutrient-management systems on the changes in the biological properties of Indian semi-arid Alfisol was assessed. The long-term organically managed (OGF) and inorganically fertilized (IGF) soils from century-old experimental plots were compared for eubacterial diversity using amplicon length heterogeneity PCR (LH-PCR) targeting three hypervariable domains (V1, V1_V2, and V3) of 16S rRNA gene. Of these domains, V1_V2 could discriminate the bacterial communities between the soil types. The relative ratios of amplicons differed between OGF and ICF soils, and eubacterial diversity was decreased substantially because of the inorganic chemical fertilizers, as compared to organic amendments. The Bray–Curtis similarity index and diversity indices of amplicons were greater in OGF soil than in ICF soil. This polyphasic approach revealed that the diversity and functionality of the soil eubacterial community were encouraged by long-term organic manures more than inorganic chemical fertilizers.

Keywords:

• 16S rRNA gene
• amplicon length heterogeneity
• eubacterial diversity
• organic manures
• QPCR

Acknowledgment

We thank S. Chellamuthu, Professor of Soil Science, Tamil Nadu Agricultural University, Coimbatore, India, for his guidance and valuable suggestions for soil sampling from the long-term experimental plots.