Characteristics of ammonia oxidation microbial abundance and community structure in paddy soils of rice–crayfish symbiosis farming system

Objectives To study the abundance and community structure of ammonia-oxidizing microbes in paddy soil under rice-crayfish farming system, for deeper understanding the changing trend of the microbial ecosystem under the system.

Methods The study was carried out at the Base of Agricultural College, Yangtze University in Jingzhou, Hubei Province. The comparison of conventional mid-season rice planting model (MR), and rice-crayfish symbiosis farming system (CR) was conducted using the technology of real-time fluorescence quantitative PCR and the platform of Illumina Miseq high-throughput sequencing to study the impact of rice-crayfish farming system on the abundance, diversity and community structure of ammonia oxidation microbes in different soils.

Results Rice-crayfish farming system significantly increased the content of soil nitrate, total carbon and total nitrogen. However, the effects on soil pH, alkali-hydrolyzable nitrogen, carbon and nitrogen ratio in soil were insignificant. The copy number of AOA amoA gene and AOB amoA gene was 3.13 × 10⁵ and 7.01 × 10⁵/g dry soil) respectively under CR system, while the copy number of AOA amoA gene and AOB amoA gene was 1.41 × 10⁵ and 3.87 × 10⁵ /g dry soil, respectively under MR system. The number of soil AOA and AOB was significantly higher in CR system, and the number of AOB was significantly higher than that of AOA in both CR and MR system. The α community diversity index indicated that CR system significantly decreased the community diversity of soil AOA but did not significantly affect the community diversity of soil AOB. Analysis of Venn results showed that CR system increased the number of species of AOA amoA gene and changed the species composition of AOB amoA gene, accompanied by the decrease in the number of species AOB amoA. At the generic level, norank_c_environmental_samples_p_Thaumarchaeota, unclassified_k_norank_d_Archaea, norank_c_environmental_samples_p_Crenarchaeota, norank_p_environmental_samples_k_norank were the predominant phyla of AOA, and their relative abundance accounted to 99.25%–99.46% of AOA total sequence of amoA gene. Moreover, CR significantly increased relative value of abundance of norank_c_environmental_samples_p_Crenarchaeota at the AOA genus level. unclassified_k_norank_d_Bacteria, norank_f_environmental_samples, norank_o_environmental_samples_c_Betaproteobacteria, unclassified_o_Nitrosomonadales were the main genus group of AOB, and their relative abundance was 97.78%–98.49%.The CR system significantly increased the relative abundance of norank_o_environmental_samples_c_Betaproteobacteria and unclassified_o_Nitrosomonadales at the AOB gene level. Redundancy analysis (RDA) showed that the community structure of soil AOA and AOB was similarly affected by the physical and chemical properties of soil. The most influential factor for community structure of soil AOA and AOB was nitrate nitrogen, followed by total carbon and ammonium nitrogen, alkali-hydrolyzable nitrogen, and pH. Based on the analysis of distance of RDA projecting, the effect of CR system on soil AOA community structure was greater than that of AOB, and MR was similar to CR in terms of the system to the community structure of soil AOB.

Conclusions Rice-crayfish symbiosis farming system has significantly decreased the diversity of AOA communities, but does not significantly affect AOB communities. Rice-crayfish symbiosis farming system also significantly increases the abundance of AOA and AOB and significantly affects the structure of the community. Soil nitrate nitrogen, total carbon, ammonium nitrogen, alkali-hydrolyzable nitrogen and pH affect soil microbial quantity and diversity, which are the main reasons for community structure changes.