Soil microorganisms, as an active participant of soil ecosystem, are the drivers for transformation and cycling of nutrient elements, such as carbon, nitrogen, phosphorus, sulfur, and so on. They are also involved in metabolism processes, directly affecting the earth's biochemical cycle (Gao et al., 2020). Microbial-biogeography studies have focused greatly on community structure, and on how their diversity and composition respond to local abiotic and biotic factors of soil (Fierer, 2017; Gao et al., 2020). It is reported that the soil microbial community structure and diversity are impacted by environmental changes or human disturbance, such as soil ages (Shanmugam & Kingery, 2018), environmental stress (Sinha et al., 2009; Jiang et al., 2020; Zhang et al., 2020), natural succession process (Zhang et al., 2016), allelopathic plant effect (Hortal et al., 2015; Kong et al., 2008), continuous cropping (Ying et al., 2012), long-term crop rotation (D'Acunto et al., 2018), and fertilization (Zhang et al., 2019). For a long time, impacts from planting types have been considered as one of the most important factors that change the diversity of soil microbial communities (Deng et al., 2019; Guo et al., 2020).
In addition to environmental factors, interspecies interactions also have a strong impact on microbial communities. Microorganisms, such as bacteria and fungi, always coexist and interact with each other in various habitats and positively or negatively interact with each other (D'Acunto et al., 2018), contributing significantly to biodiversity and biomass, and affecting essential soil processes and function (Bahram et al., 2018). For example, bacteria act as plant rhizobacteria which are beneficial to their hosts with nutrients, and fungi known as plant symbionts are helpful for plant health (Fisher et al., 2012). Additionally, molecular communications between bacterial and fungal communities are highly relevant for sustainable soil management (Lemanceau et al., 2016). For example, fungi usually play a key role in the decomposition of complex organic compounds, producing small molecules, which are then further decomposed by bacteria in the same habitat. Moreover, many fungal groups can secrete large amounts of antibacterial compounds, causing bacterial antibiotic resistance (Bahram et al., 2018). Bacteria may contribute to nutrient provision for plants, e.g., performing important steps of the nitrogen cycle, including nitrogen fixation, nitrification, and denitrification (Nelson & Sadowsky, 2015; Meng et al., 2017). The interactions between bacteria and fungi, such as the binding of soil bacterial and fungal spores, the injection of molecules into fungal spores by bacteria, the production of volatiles by bacteria, and the degradation of fungal cell walls, have been summarized by a previous study (Miransari, 2011). Therefore, it is important to investigate both bacteria and fungi at the same biotopes.
Co-occurrence network analysis provides new insight into the interaction of microbial taxa in the complex community by employing a more standard suite of analytical approaches. In general, the inter association between taxa may help to reveal the niche shared by community members (such as bacteria, archaea and fungi), or may help to reveal the more direct symbiotic relationship between community members (Barberati et al., 2012). But reliable network analysis is based on deep exploring patterns in large and complex datasets, which are more difficult to detect using the standard alpha/beta diversity metrics widely used in microbial ecology (Proulx et al., 2005). Fortunately, due to the advances in barcoded pyrosequencing technique (Feng et al., 2014; de Vries et al., 2018; Wang et al., 2020), it is now possible to generate microbial datasets using network analysis approaches in highly diverse communities, like those found in soils, to explore co-occurrence patterns. Exploring co-occurrence patterns between soil microorganisms can help to decipher inter- or intra-phyla interactions related to biotic factors, habitat affinities or shared common physiology to guide more focused research.
The Taige Canal is located in the economically developed and densely populated Taihu Basin. The Taihu Basin has sufficient water, light and heat resources, which greatly support the development of agriculture. The major planting methods operated by farmers in this area are rice-wheat rotation (Zhou et al., 2012). It is a typical region of the Yangtze River Delta, which is the most developed region in Chinese agriculture ecosystem. With the adjustment of the industrial structure and the renewal of farmers' ideas, some wheat fields have been replaced with orchards. The area of farmland has decreased, and the planting area of various orchards has increased year by year in the Yangtze River Delta (Ji et al., 2008; Min et al., 2020). Due to changes in planting methods, the amount of fertilization, plant density, and the content of elements such as N and P in the soil, the structure and diversity of microbial communities have changed. The co-occurrence networks help to determine associations between microbial groups. However, few studies focus on the co-occurrence network of microbial communities in response to changes in planting patterns. Therefore, we addressed the following questions: 1) Do soil microorganisms tend to co-occurrence networks of microbe-microbe intra-reaction patterns in soils? 2) Which taxa are generalists and how these ecological categories (niche differentiation) shape network structure?