Soils are a complex substrate with the highest biodiversity on Earth (Wagg et al., 2019), and forms the largest activated land carbon pool (Crowther et al., 2016; Zhou et al., 2020). It is well-known that land use changes drive global change and affect the carbon and nitrogen cycles at the ecosystem level (Li et al., 2016). The dynamics of soil carbon and nitrogen under changes in different soil types are important for illustrating carbon and nitrogen cycle mechanisms and have thus been a focus of research (Guo and Gifford, 2002). The massive addition of chemical fertilizers by the agriculture industry has posed substantial environmental risks, including by serious damage to soil chemical properties (Idkowiak, 2004), resulting in a significant increase in emissions of greenhouse gas emissions (Zhang et al., 2013), nutrient damage, and disturbances of the soil microbial communities (Postma-Blaauw et al., 2010; Qiu et al., 2016).

Soil microbes drive the soil to achieve functions that facilitate soil carbon and nitrogen nutrient cycling, organic matter decomposition, transformation, as well as help suppress soil-borne diseases (Philippot et al., 2013; Ling et al., 2014; Finzi et al., 2015; Pieterse et al., 2016). It is well known that soils in the tropics are one of the essential terrestrial carbon pools globally (Jobbágy and Jackson, 2000), in which soil microorganisms play a key role in adjusting net soil carbon storage by mineralization of plant residues and soil organic matter. Previous work has found that nitrogen fertilization can have direct or indirect impact on soil microorganisms by introducing nutrients and altering soil physicochemical properties (Geisseler and Scow, 2014; Aparna et al., 2016). Current research suggests high correlations between changes in soil microbial community, land utilization, or management way and microbial-induced eco-system functions (Colman and Schimel, 2013; Bonner et al., 2018). As is well known, soil bacterial communities are important in biogeochemical cycle (Jenkins et al., 2017), and because soil bacteria respond rapidly to changes under the soil condition, it is often served as early bio-indicators of altered soil quality (Chen et al., 2017). Knorr et al. (2005) propose that nitrogen addition may potentially either promote or impede litter decomposition, a phenomenon seemingly tied to the nitrogen content accessible to plants (Hobbie, 2015). Nitrogen addition significantly changed the relative abundance of bacteria and fungi. The impact on soil microorganisms was subject to numerous factors, including differences in nitrogen addition time, soil hydrothermal conditions, elevation gradients, and vegetation types, as observed in different studies (Xu et al., 2021). Therefore, we can utilize high-throughput sequencing technology, which provides rough information about the entire microbial biodiversity in the background of complex environments and different farming practices (Bowles et al., 2014; Fierer, 2017; Beaudry et al., 2021).

Microorganisms also serve as the major decomposers of plant material because of their specific capacity to produce a large number of enzymes that degrade simple molecules (e.g., cellulose) and more complex plant-derived compounds (e.g., lignin) (Romaní et al., 2006). Soil microbes transform and utilize a variety of soil carbon substrates, take up carbon into their biomass, stabilize carbon, and emit CO₂ in the soil (Bardgett et al., 2008; Wei et al., 2018). In agricultural production, straw addition is one of the main approaches for conventional exogenous carbon addition, and its decomposition and transformation involve a complex, long-term process of microbial community activity (Pausch and Kuzyakov, 2012). Crop straw, as a natural raw material, is rich in N, P, K and many other essential elements for plant growth. The addition of crop residues to the field is an important way to promote soil fertility and improve crop growth, which is important for the development of sustainable agriculture (Witt et al., 2000; Song et al., 2015). A large body of evidence shows that different characteristics ofcrop residues (straw) and environment factors can alter soil microbial communities’ diversity (Feng and Simpson, 2009; Merilä et al., 2010). Ma et al. found a significant positive effect of straw addition on soil microbial biomass, activity, and communities structure (Yu et al., 2016; Ma et al., 2019), resulting in an increase in soil grain structure and water-stabilized agglomerate content, which improves soil nutrients and water containment (Yin et al., 2015; Fierer, 2017). Other research found a significant increase in biomass of bacteria and actinomycete with short-term additions of crop straw to fields in Jiang Yan, China (Chen et al., 2017). The addition of carbon sources can indeed influence the physical and chemical properties as well as the microbial activity of farmland soil. It has been found that the incorporation of straw addition can improve soil structure, rendering it loser and more porous, while also increasing microbial and enzyme activities in the soil (Eagle et al., 2000; Sapkota, 2012). Biological nitrogen fixation stands as the second-largest contributor to soil nitrogen, trailing only behind mineral nitrogen, comprising approximately 16% of the global nitrogen input (Ollivier et al., 2011). The introduction of nitrogen, however, reduces the abundance and diversity of nitrogen-fixing microorganisms, with nitrate nitrogen emerging as one of the main influencing factors (Qin, 2021). The available nitrogen content in the soil showed a negative correlation with the community structure and abundance of nitrogen-fixing microorganisms. Furthermore, the addition of nitrogen fertilizer inhibited the growth of nitrogen-fixing microorganisms, resulting in a decrease in the diversity of nitrogen-fixing microorganisms in the soil (Hou et al., 2014). However, studies have shown that appropriate nitrogen fertilizer addition can increase the content of organic carbon in soil and increase the abundance of nitrogen-fixing bacteria, thereby promoting the nitrogen fixation capability of soil nitrogen-fixing microorganisms (Orr et al., 2012). Additional studies have also indicated that the abundance and community of nitrogen-fixing bacteria did not exhibit significant differences from the control group following nitrogen fertilization (Ogilvie et al., 2008; Berthrong et al., 2014). Therefore, exploring different types of soils assumes great significance in elucidating biological nitrogen fixation mechanisms. In conclusion, we propose several hypotheses, (1) Carbon and nitrogen supplementation alters the soil chemistry and bacterial composition of different utilization types; (2) Differences exist in the effects of different types of organic carbon (such as rice straw and roots) on soil properties and microorganisms, and the addition of organic carbon (straw) improves the nitrogen fixation capacity of organisms. Through this study, we aim to clarify the differences in bacterial responses to carbon and nitrogen within diverse land use types and to explore the potential of biological nitrogen fixation.

Land use practices determine plant community composition and soil management strategies, both of which affect soil physicochemical characteristics (Batlle-aguilar et al., 2011; Wolińska et al., 2017). Basic soil chemical properties were used as an indicator of nutrient content, and soil properties were obviously different across land utilization types. SOM plays a significant role in different ecosystem and soil fertility, determining the nutrient sequestration capacity of the soil (Dutta et al., 2003). Crop residues are well-known additives used to preserve and enhance soil fertility (Bhattacharyya et al., 2001) by sustaining or enhancing soil organic carbon (Li et al., 2018), which improves microbial activity and function, as well as plant biomass production and C sequestration (Jin et al., 2018). This study has showed that the addition of organic carbon (rice straw and root) along with inorganic nitrogen leads to an increase in the content of the soil insoluble organic C and SOC content. These findings generally consistent with the previous studies. A large body of results has found that below-ground C inputs (root biomass and root exudates) form stable carbon more efficiently than above-ground C inputs from litter (Cotrufo et al., 2015; Sokol et al., 2019; Sokol and Bradford, 2019; Witzgall et al., 2021). Moreover, our study found that the level of insoluble organic carbon in RR treatment was higher than that in the RS treatment. This suggests that belowground plant residues contributed a more significant contribution to SOC than aboveground biomass, a finding that is mostly consistent with previous studies.

The C metabolism characteristics of soil microbial communities can reveal the biological effectiveness and functional richness (Banning et al., 2012). Average CO₂ production rate is often used to infer soil microbial activity and reveals the ability of soil microbial communities to use particular C sources (Sinsabaugh et al., 2013). Previous work has demonstrated that larger residue C inputs may drive higher rates of C sequestration (Clapp et al., 2000). It is widely acknowledged that soil respiration can demonstrate biological activity and decomposition of organic residue (Santos et al., 2012; Ferreira et al., 2014). A high microbial respiration rate might indicate high microbial productivity in an ecosystem (Islam and Weil, 2000). Here, we showed that the addition of a combination of straw and inorganic nitrogen increased microbial respiration and improved nutrient conversion efficiency, consistent with previous studies, but the effect of adding rice straw was more obvious. Studies have presented a mixed picture regarding the impact of nitrogen-fixing microorganisms. On one hand, nitrogen addition has been shown to reduce both the abundance and diversity of nitrogen-fixing microorganisms. However, it’s worth nothing that certain studies have highlighted that judicious nitrogen fertilizer application can actually improve the organic carbon content in the soil and increase and abundance of nitrogen-fixing bacteria, thereby bolstering the nitrogen-fixing capability of soil microorganisms. In some instances, studies have even indicated that the abundance and community composition of nitrogen-fixing bacteria remained largely unchanged when compared to the control group following nitrogen fertilization (Ogilvie et al., 2008; Orr et al., 2012). In this study, the nitrogen fixation potential of different types of soil showed a significant decrease after the nitrogen addition. This reduction was primarily manifested in a significant decrease in the abundance of ¹⁵N and nifH genes, which further confirmed that the addition nitrogen reduces the biological nitrogen fixation capacity of soil microorganisms.

Microbial diversity is considered to be a crucial component in global C cycle. However, bacterial communities are often overlooked in stoichiometric nutrient cycling studies (McGuire and Treseder, 2010; Graham et al., 2014). Changes in bacterial community and diversity also alter soil fertility, pH and other environmental conditions (Samaddar et al., 2018; Li et al., 2019). Zhaoxiang et al. (2020) suggested that bacterial community structure is strongly influenced by soil organic matter content and TN. In this study, the CK and RR microbial communities in NS were mainly affected by ION, while other treatments were mainly affected by NH₄⁺, NO₃⁻, CO₂, and IOC. In addition to the CK treatment, other treatments’ effects on microbial community characteristics had a greater influence on other types of soil, indicating that soil physicochemical factors were an important factor regulating soil microbial community composition. The effect of these factors was different across soil types: IOC had an obvious influence on community composition under different treatments in HS, and NH₄⁺ was a dominant factor in DS. Previous studies demonstrate that as microbial community composition changes in response to land use change, microbial functional diversity decreases. Agricultural intensification has been shown to change community composition to change microbial functional diversity. The reduction of functional diversity has been identified as a widespread trend as land-use intensification increases, and this has been associated with specific environmental conditions and bacterial groups (Benslama et al., 2021). Additionally, member of the order Actinomycetales are major contributors to carbohydrate and amino acid metabolism in differ environments (Verastegui et al., 2014; Xia et al., 2015; De la Cruz-Barrón et al., 2016). We found that, with the higher the soil use intensity (HS, DS, and PS), the lower the bacterial richness and diversity, this shows that tillage mode is one of the important factors affecting soil microorganisms, especially bacterial communities. And the relative abundance of different bacterial phyla in NS was quite different from other types of soils. In NS, the relative abundance of Firmicutes under RSN treatment was significantly higher than in other treatments. In HS and DS, the relative abundance of Actinobacteria was the highest, and it was lower under RSN treatment than in CK. In PS, each treatment type significantly increased the relative abundance of Actinobacteria to a greater extent than in other soil types, Therefore, the influence of actinomycetes in different types of soil is the most obvious.

In different ecosystems, soil microbes play an essential role in organic matter decomposition and nutrient cycles, thereby enhancing nutrient availability for plants. At the same time, microbes act as a sensitive indicator that can be used to predict future soil biological conditions and can be used to inform agricultural practices (Hartmann et al., 2015). Recent work found that SOC content and soil ecological environment were significantly improved through the application of crop residue treatments (Tang et al., 2019), which enhanced the soil environment and C and nutrient availability to support soil microbial proliferation. Additionally, adding SOM at regular intervals may enhance the level of microbial activities; improve carbon and nitrogen cycle, and soil microbial diversity (Van Bruggen et al., 2006). We found that the addition of RS to NS and RR to DS led to a significant increase in microbial diversity. This indicates that the microbial communities in natural forest soil and banana garden soil are more sensitive to the response of exogenous organic carbon. Previous findings have shown that soil microbial community diversity was higher with crop residue treatments (Frasier et al., 2016). PCoA showed significant differences in bacterial communities, who documented changes in microbial community composition under straw application (Bei et al., 2018). A recent long-term experiment found no significant effect of maize straw application and fertilization on bacterial community structure at the phylum level (Xia et al., 2019). Here, our results revealed that in natural forest soil, the addition of rice straw and roots had a significant effect on bacterial communities, the RSN group was clearly separated from other treatments. In healthy banana soil and diseased banana soil, the degree of separation between each treatment decreased, but in paddy soil, the CK treatment is clearly separated from the other treatments, the results showed that the effects of organic carbon addition on different soil bacteria types were significantly different, with the addition of nitrogen increased the degree of impact.

We have demonstrated that exogenous carbon and nitrogen addition significantly affected soil physicochemical properties, bacterial communities and biological nitrogen fixation. Specifically, the addition of rice straw increased the absorption and utilization of nitrate nitrogen by microorganisms. On the other hand, the addition of rice roots (RR) did not increase the absorption capacity of microorganisms to absorb inorganic nitrogen but does increase the content of poorly soluble organic carbon. Furthermore, it is important to note that the addition of rice straw increased microbial respiration and the utilization efficiency of N₂ utilization. This showed that, across different soil utilization types, the addition of rice straw increases nitrogen fixation capacity by increasing the activity. Moreover, as soil types change, the number and variety of bacteria decrease progressively due to the addition of exogenous carbon (rice straw) and nitrogen, and microbial respiration intensity emerges as an important factor influencing the differences in the structure of bacterial communities. The addition of inorganic nitrogen further reduces bacterial diversity and richness, consequently reducing the ability of soil microorganisms to resist the environment challenges. In light of these findings, it is evident that the addition of rice straw and ammonium nitrate caused the accumulation of ammonium nitrogen in the soil environment, resulting in reduced bacterial diversity and richness. Therefore, we believe that for the implementation of soil nutrient retention strategies in agricultural practices while concurrently reducing the application of ammonium nitrogen. This approach is essential to maintain a healthy soil environment during agricultural production.

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found at: https://www.ncbi.nlm.nih.gov/, PRJNA906297.

CH: Writing – original draft. KL: Methodology, Writing – original draft. JL: Resources, Writing – original draft. PF: Resources, Writing – original draft. YR: Writing – review & editing. ZJ: Writing – review & editing.