Nitrification is a critical link of the nitrogen biogeochemical cycle, and the nitrogen flux in the nitrification in terrestrial ecosystems is 330 Tg (Kuypers et al., 2018). It is a biological process that converts ammonia to nitrate through microorganism catalysis and plays a vital role in global ecosystems. Nitrification mainly consists of two processes, namely, nitrite oxidation and ammonia oxidation. Specifically, ammonia is first oxidized into nitrite by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) (Konneke et al., 2005), and then nitrite is oxidized into nitrate by nitrite-oxidizing bacteria (NOB) (Teske et al.,1994). Daims' group (2015) and Van Kessel' group (2015) respectively discovered a new microorganism for direct oxidization of ammonia to nitrate, which is called comammox (CMX) Nitrospira bacteria (NB). These bacteria are widely present in artificial engineering systems, including sewage treatment systems (Xia et al., 2018b) and nitrification reactors (Zhao et al., 2021), and they are also found in natural ecosystems such as salt marshes (Wang et al., 2021), agricultural soils (Wang et al., 2019), riparian soils (Wang et al., 2021), lake sediments (Shi Y et al., 2020), and forest soils (Li et al., 2020).
All known CMX NB belong to Nitrospira sublineage II, which can be further divided into clade A and B (Daims et al., 2015). In 2018, Xia and colleagues (2018a) first proposed to divide the clade A of CMX bacteria into clade A.1 and A.2. In 2021, clade A.2 was divided into clade A.2.1 and A.2.2 (Sun et al., 2021). A new clade A.3 was discovered in 2019 (Li et al., 2019). There are certain differences in the physiological properties of clade A and B (Hu and He 2017), and these differences result in spatial and temporal differentiation (Jiang et al., 2020; Wang et al., 2021) to adapt to different environmental conditions.
With the increase in depth, soil physicochemical properties will change. Various ammonia-oxidizing microorganisms have different adaptabilities to ammonia and oxygen, which contributes to bacterial differentiation with increasing soil depth, and this differentiation enables ammonia-oxidizing microorganisms to occupy a wider range of ecological niches. Previous reseach has demonstrated that the average abundance of all the AOA, AOB, and comammox are dramatically reduced with the increasing soil depth in forest, grassland, and farmlands (Hu et al., 2021). However, in the purple paddy soil in Chongqing, China, the abundance of AOA and AOB is dramatically reduced along the soil depth direction, and the abundance of CMX clade A is raised significantly with increasing soil profile depth, but clade B exhibits no similar pattern (Wan et al., 2019). The abundance of AOA gene has been shown to decrease with depth while that of AOB gene is decreased in semi-arid soils in southern Australia (Banning et al., 2015). In the sediments of a high-altitude freshwater wetland in Yunnan Province, China, AOA diversity is decreased with increasing sediment depth, whereas AOB diversity is not significantly correlated with sediment depth (Liu et al., 2014). The comammox diversity in bottom sediments (5–10 cm) was higher than that on the surface (0–1 cm) and in middle sediments (1–5 cm) from the tidal flats of the Yangtze Estuary in China (Jiang et al., 2019 ). These phenomena indicate that these ammonia-oxidizing microorganisms have the ability to vertically differentiate in different habitats to adapt to diverse natural environments.
The Three Gorges Dam is the largest water conservancy project with the largest comprehensive benefit in the world (He et al., 2011). After the completion of the Three Gorges Dam, the water level in the Reservoir area is 175 m in winter and 145 m in summer with a periodic flooding-exposure hydro-fluctuation (HF) area of 348 km2 on both sides of the Reservoir area. Numerous studies have shown that periodic flooding-exposure can change the material transformation process in the soil in the HF zone and increase the content of organic matter in the soil (Guo et al., 2016). Oxygen content in the soil, especially in the topsoil, changes dramatically during the flooding-exposure period, thus affecting the growth of CMX NB, making them more prone to vertical differentiation.
In this study, the natural and artificial HF zones of the Three Gorges Reservoir (TGR) area were chosen to assess the diversity of ammonia-oxidizing microorganisms and the abundance of AOA, AOB, and CMX NB in the soil. The aim of this research was to reveal the vertical differentiation of CMX NB with soil depth in the natural and artificial HF zones.