Metataxonomic insights into the effects of enhanced nitrogen addition on the bacterial communities in the tropical paddy soil of West Bengal, India

Abstract

In relation to global rice cultivation, nitrogen (N) is fundamental for paddy soil and crop productivity; however, the exploitation of synthetic N fertilisation in the global agri-food system has emerged as a major environmental concern. In this study, the effects of various synthetic N-compounds on paddy soil bacterial communities, including species abundance, diversity, and interactions, were investigated under four different N-amended [NO2-, NO3-, NH4+, and urea] conditions using a microcosm-based culturomics approach. The N-amendments altered soil properties, adversely impacting microbial abundance, diversity, and community composition. The 16S rRNA gene qPCR and amplicon sequencing indicated a negative effect of N on bacterial and archaeal abundance, species diversity, and richness. Our analyses revealed the predominance and cosmopolitan distribution of Proteobacteria, Bacilli, Anaerolineae, and Bacteroidota, their extensive adaptability and metabolic versatility under different N-amended conditions. Soil microbial community exhibited distinct responses to added N-substrates, with some bacterial taxa (Sphingomonadales) showing enhanced abundances while others were inhibited (Thermodesulfovibrionia and Clostridiales). The core-community across N-amended sets exhibited 68% taxonomic variation from its native counterpart, with two most abundant members of native soil, Nitrosomonadaceae and Beijerinckiaceae, diminishing, while Bacillaceae, Pseudomonadaceae, and Sphingomonadaceae became more prominent and resilient under N-amended conditions. The co-occurrence network highlighted that though total and core soil communities responded to N-amendments with an increased abundance of copiotroph bacteria, oligotrophs thrived under nutrient-limited conditions, serving as keystone taxa during prolonged fertilisation. These findings elucidate how synthetic N inputs restructure paddy soil microbiomes and alter their ecological functioning.