Changes in the diversity of pecan (Carya illinoinensis) rhizosphere microbial community with different nitrogen fertilization, a case study in Oklahoma pecan orchard

Pecan (Carya illinoinensis) is primarily native to North America and is known as the leading nut produced in Oklahoma. Since the prices of fertilizers have increased and the activity of soil microbes may greatly affect fertilizer utilization, it is important to investigate the effect of fertilization on microbes. Samples were collected from pecan trees receiving full nitrogen (70 lbs/acre), half nitrogen (35 lbs/acre), and no nitrogen (0 lbs/acre) fertilization in an orchard. Microbes were characterized by using the next generation sequencing and annotated into functional groups (trophic mode and nitrogen related) by FUNGuild and FAPROTAX. Our results showed the core fungal genera in this orchard were Tuber and Hymenoscyphus, while the core bacterial families were Chitinophagaceae, Xanthobacteraceae, and Chthoniobacteraceae. Among them, the pecan truffle Tuber lyonii was the dominant fungus. In association with an increase of nitrogen fertilization, the Simpson Index (SI) of fungi in roots was decreased, and the presence of pathotroph (such as Monographella cucumerina and Lectera longa) was increased, implying that the risk of plant infection by pathogens was increased. The pecan with half rate of nitrogen fertilizer had the highest colonization of symbiotrophic fungi, the lowest presence of pathotrophic fungi, and the highest relative abundance of Tuber. The relative abundances of bacteria related to nitrate reduction, nitrogen respiration, and nitrate respiration were found to be the highest in pecan with half rate of nitrogen fertilizer, which might imply the highest efficiency of nitrogen fertilizer utilization in this treatment. It revealed that applying half the recommended nitrogen rate of fertilizer could improve beneficial microbe presence, perhaps increasing nitrogen uptake and decreasing nitrogen needed for optimum production.