Diversity and Metagenomic Profiling of Indigenous Bacterial Communities in Flooded Rice Paddy Soil using Next-Generation Sequencing (NGS)

Abstract

The objective of this research was to explore the composition and diversity patterns of microbial communities inhabiting flooded rice field soils in Yosowilangun District, Lumajang, as an environment characterized by harsh and challenging conditions. Through a metagenomic approach utilizing next-generation sequencing (NGS), a comprehensive analysis was performed on soil samples collected from submerged paddy ecosystems. The results revealed a significantly high level of microbial biodiversity, highlighting the complexity of the soil microbiome under anaerobic and acidic conditions. Taxonomic classification indicated the presence of 47 phyla, 113 classes, 257 orders, 574 families, 1.813 genera, and 4.199 distinct species. Overall, a total of 101.427 microbial species were recorded, and the diversity assessment using the Shannon-Wiener index yielded a value of 6.2267, suggesting a well-balanced and rich microbial ecosystem. Among the taxa detected, Sporacetigenium mesophilum emerged as the most prevalent species, followed by Anatilimnocola aggregata and Methylothermalis aethiopiae. The dominance of these particular microbes demonstrates a strong ecological adaptation to the low-oxygen and low-pH environment typical of inundated rice field soils. These findings underscore the ecological importance of flooded agricultural landscapes as reservoirs of microbial diversity, which may play vital roles in maintaining soil health and agricultural sustainability.