The shifts of maize soil microbial community and networks are related to soil properties under different organic fertilizers

Abstract

In recent years, organic fertilizer (OF) instead of chemical fertilizer is an effective way to improve the utilization efficiency of crop resources and the quality of agricultural products. However, knowledge of the effects of OF on soil microorganisms is still limited. The microbial communities in two soils of Yinchuan (P) and Guyuan (T) city were studied by high-throughput sequencing, and the correlation between their community structure and soil properties was analyzed. The 16S rRNA and ITS genes were targeted in DNA extracted from maize rhizosphere soils subjected to four OF level (0 (P1/T1), 4500 (P2/T2), 9000 (P3/T3), 13500 (P4/T4) kg/ha OF applied. Compared to the control treatment, OF treatments significantly changed soil chemical properties and microbial diversity. Additionally, OF treatments also shift composition of microbial community structure and the effects on Yinchuan (P-region) were larger than Guyuan (T-region). What's more, OF treatments also significantly affected the community composition of bacteria and fungi in the two regions, among which there were significant differences in the relative abundance of three phyla, four genera of bacteria, and eight phyla and nine genera of fungi among all OF treatments. Microbial network analysis showed that the high-OF treatments (P3 and P4) reduced the number of links in the microbial network at the genus level for the 16S rRNA gene, while increased that in T-region. Redundancy analysis (RDA) revealed that organic matter (OM) and available phosphorus (AP) were the main factors driving the bacterial and fungal community structure. In conclusion, this study demonstrated that OF treatments significantly affected soil C and P as well as the bacterial and fungal community compositions in wheat rhizosphere soils, which might affect soil biogeochemical cycles.

Introduction

Soil providing food, feed, fiber and medicine, is essential for human well-being (Raaijmakers and Mazzola, 2016). In recent years, the intensive application of chemical fertilizers in agricultural production lead to substantial environmental risks, including serious damage to soil physicochemical properties (Idkowiak, 2004), increase of greenhouse gas emissions (Zhang et al., 2013), loss of nutrients (Miao et al., 2011), and interference of soil microbial community (Postma-Blaauw et al., 2010; Qiu et al., 2016). Soil degradation caused by these factors reduces soil fertility, and further affects the production and nutritional quality of cash crops to some extent, thus threatening global food security. Therefore, in order to solve the series of problems, it is necessary to implement alternative management to replace mineral fertilizer (Ren et al., 2019). However, proper organic substitution not only can sustain the crop yield, but also can mitigate the impacts by the overuse of synthetic N fertilizer, such as waterbody eutrophication, greenhouse gas emissions, and biodiversity losses.

Organic fertilizer (OF) is made from some agricultural and animal husbandry wastes after fermentation and decomposition, of which the addition has a beneficial effect on soil quality because it improves soil porosity and increases the content of organic carbon (SOC), additionally, it also contains all the essential nutrients released slowly (Assis et al., 2020; Ji et al., 2020). It is found that appling OF can improve soil physicochemical properties, and enhance enzyme activity and beneficial microorganisms, so as to improve crop productivity (Wu et al., 2020).

Soil microorganisms, important component of ecosystem, are the drivers of soil functional processes, such as nutrient cycling, C sequestration, and N fixation (Finzi et al., 2015; Ling et al., 2014a; Philippot et al., 2013). Soil microorganisms are also considered to be responsible for the necessary biological processes for maintaining healthy soil and inhibiting plant diseases (Ling et al., 2014b), including driving nutrient cycling and organic matter transformation, improving plant productivity and helping to control soil borne diseases (Pieterse et al., 2016). More interestingly, soil microorganisms are vulnerable to positive or negative effects of soil management or disturbance, leading to changes in their classification and function (Cordovez et al., 2019). However, OF is an effective way to regulate soil microbial diversity and community structure (Tao et al., 2015). Sun et al. (2015) found that long-term application of OF can effectively promote the increase of soil microbial diversity. Luo et al. (2016) also found that OF increased the number of soil bacteria and fungi, but inhibited the growth of actinomycetes. In addition, application of OF can provide important nutrients for root microorganisms, regulate soil physicochemical properties, and create favorable conditions for microorganisms, meanwhile inhibit the growth of plant pathogens (Shen et al., 2014; Wen et al., 2015). With the upgradation of molecular biotechnology, the studies on the effects of OF on soil microorganisms have been becoming more and more popular. Ling et al. (2014b) analyzed the effect of continuous application of OF on soil bacterial diversity of watermelon continuous cropping by PCR-DGGE technology and adjusted the soil microbial community to an appropriate level, so as to maintain the health of plants. In soil microbiome, it has been shown that the application of OF may stimulate specific microbial communities (such as Pseudomonas, Streptomyces, Flavobacterium, etc.) related to inhibition of plant disease (Cha et al., 2016; Kwak et al., 2018). After the application of OF with biocontrol effect, a large number of functional bacteria propagate, and some beneficial microorganisms, such as actinomycetes, produce antibiotics (Zhao et al., 2016), which inhibit the reproduction of other harmful microorganisms, enhance the disease resistance ability of crops and guarantee the growth and development of crops (Yilmaz and Sönmez, 2017; Zhang et al., 2016). Numerous studies have showed fertilization directly or indirectly affects the soil microorganisms via the input of nutrients and altering the soil properties (Aparna et al., 2016; Chen et al., 2021a; Geisseler and Scow, 2014). Wu et al. (2021) found that dissolved organic carbon content was the main factor affecting microbial community composition. A study suggested that there were significant association of total nitrogen (TN), total phosphorus (TP) and available potassium (AK) with alternation of the bacterial community in cinnamon soil (Liu et al., 2021). Ji et al. (2020) also revealed that soil pH, soil organic C (SOC), microbial biomass C (MBC), and available potassium (AK) were the key characteristics that were significantly correlated with the variation of soil fungal community in a tea plantation with long-term fertilization. Therefore, identifying the key physicochemical parameters driving soil microbial community structure and understanding how the rhizosphere microbial community develops are the potential mechanisms for regulating soil microbial health and sustainable agriculture involving crop yield (Qiao et al., 2019; Sun et al., 2015).

Although there have been many studies on the effect of OF on soil microorganisms, but mainly for pathogenic bacteria, the impact on the overall microorganisms is still unknown. Therefore, we investigate the effects of OF on soil chemical properties, microbial diversity and community structure of maize, and analyzed the main factors driving the functional changes of soil microbial community, which can provide a certain theoretical and data basis for the rational utilization of OF and the study of microecology.