Effects of Long-Term Application of Organic Fertilizer on Rare and Abundant Bacterial Sub-Communities in Greenhouse Tomato Soil

The objective of the present study was to distinguish the rare and abundant bacteria from the whole community and to explore their responses to long-term application of organic fertilizer respectively, so as to provide new insights into the relationships between soil biodiversity and ecosystem functioning under major agricultural activities.

Based on the long-term fertilization experiment of greenhouse tomato, soils were collected under four different treatments, including no fertilizer (M0), low organic fertilizer 5.68 t·hm^-2 (M1), medium organic fertilizer 8.52 t·hm^-2 (M2), and high organic fertilizer 11.36 t·hm^-2 (M3). Illumina MiSeq platform was used to analyze the diversity, community composition, co-occurrence network and potential functions differences of the rare and abundant bacterial sub-communities, and their various responses to long-term fertilization, to illustrate the key factors driving the distinct distribution patterns and responses for rare and abundant bacteria.

Compared with the abundant bacterial sub-community, the rare bacterial sub-community showed higher α- and β-diversity and distinct community composition, as well as potential functions. A functional prediction detected that abundant bacteria contributed primary functions in the greenhouse ecosystem, such as nutrient and energy metabolism, meanwhile rare bacteria contribute a substantial fraction of auxiliary functions (e.g., metabolism of cofactors), which indicated they played important roles in the functional redundancy of microbial communities. Contrasting responses of rare and abundant bacterial sub-communities to long-term fertilization were revealed in this study, in which the rare bacteria was more sensitive. Compared with no fertilizer, the long-term application of organic and chemical fertilizer significantly increased the OTU richness, Shannon diversity, and total relative abundance by 19.8%-53.8%, 5.8%-8.0%, and 1.1-1.2 times, respectively, and changed the community composition and structure of rare bacterial sub-communities. In addition, with the increased application rates of organic fertilizer, the OTU richness of rare bacteria also increased significantly, accompanied by obvious changing in community composition and structure. However, the abundant bacteria exhibited less sensitivity to long-term fertilization, with only the community composition altered. Besides, the co-occurrence network complexity increased with organic fertilizer rates, especially in rare sub-communities. Both the results of the NMDS and mantel test revealed that the controlling factors affecting rare and abundant bacterial sub-communities were different. A variety of soil factors associated with deterministic processes, i.e., SOC, soil nutrients of total N and P, Olsen-P and available K, and pH, as well as macro- and medium-aggregate, significantly influenced abundant bacteria. Structural equation model (SEM) further showed that soil organic matter and total phosphorus directly drove abundant bacterial diversity. On the other hand, less effects of environmental filtering and more scattered distribution patterns were found in rare bacteria, indicating different assemblies of rare and abundant sub-communities.

Compared with the abundant bacteria and the whole community, the rare bacteria sub-community showed higher diversity and unique community composition, which improved the functional redundancy of the microbial community. Long-term fertilization altered the whole bacterial community mainly by affecting rare bacteria (i.e., increasing diversity, changing community composition, increasing co-occurrence network complexity) rather than the abundant bacteria. The controlling factors that mediated the assembly of the rare and abundant bacterial sub-communities were also different.