Combined pot experiments and subsequent DNA-SIP incubations reveal a core microbiota involved in modulating crop nitrogen uptake derived from soil

Abstract

Revealing the biological mechanisms of the amount of crop nitrogen (N) uptake derived from soil (NDS) is crucial for the prediction of eco-friendly and cost-effective N fertilizer management; however, there is a dearth of studies on this topic, especially on the comprehensive comparison under N-amended and non-amended conditions. Here, we conducted a pot experiment using soils with soil organic matter (SOM) gradients under 15N-labeled urea amended (+N) or non-amended (−N) to explore whether NDS was mediated by a group of core taxa or by individual keystone species. Our results showed that NDS increased with SOM, regardless of N input or not. In addition, NDS under −N conditions was 11.1 %–56.8 % higher than that under +N conditions. We revealed that in addition to SOM and nirS gene, a group of highly interactive core microbes connecting keystone species and some specific taxa made major contributions to NDS variations, though the composition of the core microbes under −N conditions differed from that under +N conditions. These interactive core microbes were considered as core microbiota, which was derived from one module of soil network and contained nirS-type denitrifier, further suggesting their important role in mediating the NDS. Combined with the results from stable isotope probing incubations, it was found that under −N conditions, NDS was negatively correlated with unclassified Rhodobacterales and RB41, both of which showed positive correlations with the unclassified Solibacterales, one of the keystone species identified by network analysis; under +N conditions, NDS was positively correlated with keystone species Skermanella identified by network analysis, and NDS and Skermanella were both positively correlated with Gaiellaceae, Bradyrhizobiaceae, and Solirubrobacter. Our results provide new insights into the factors driving NDS variations, and suggest that the core microbiota connecting keystone species and some specific taxa should be considered as a key factor in N fertilizer management strategies targeting the enhancement of N-use efficiency and agricultural sustainability.