Soil nutrient cycling and microbiome responses to Bt rice cultivation

The composition and function of rhizosphere microbiomes depend on interactions between plant roots and soil nutrient conditions. However, the influence of genetic variation of plant species on root-associated microorganisms and their nutrient cycling activities remains poorly understood.

Here, cultivation of Bt rice cultivar T1C-1, its parental cultivar Minghui 63, and the conventional cultivar Zhonghua11 was conducted in a randomized block design with nine replicate plots. The microorganisms, enzymes, and metabolites that were differentially abundant in soils from the 3 cultivars were evaluated with metagenomic and metabolomic analyses. The study aimed to elucidate the effects of Bt rice cultivation on soil microbial community characteristics.

Cultivation of the Bt rice variety T1C-1 led to higher soil total nitrogen (TN), ammonium-N (NH₄⁺-N), nitrate-N (NO₃⁻-N), and nitrite-N (NO₂⁻-N) concentrations compared to soils of the parental cultivar Minghui 63. Metagenomic analyses revealed that rhizosphere bacterial community compositions significantly differed among cultivars, but this was not observed for fungal and nematode communities. The bacterial community Shannon diversity index was positively associated with soil nutrient multifunctionality (SNM) that was evaluated as the ability to perform multiple nutrient cycling processes. These results highlight the importance of biodiversity as a major driver of root microhabitat ecosystem functioning.

Metagenomic and metabolomic analyses suggested that Bt rice cultivation alters soil C and N cycling, possibly by influencing the functioning of soil microbiomes. Our results provide insight into ecological effects of the cultivation of Bt crops on soil community as well as key knowledge for their overall risk assessment.