A saline soil is generally defined as one in which the electrical conductivity of the saturation extract in the root zone exceeds 4 dS m⁻¹ (approximately 40 mM NaCl) at 25°C and has an exchangeable sodium of 15% (Shrivastava and Kumar, 2015). Soil salinization is one of the most damaging environmental abiotic stresses, resulting in a substantial decrease in crop yield and quality, due to the accumulation of water-soluble salts in the surface soil layer that exceed normal values and have unfavorable physicochemical properties (Bai et al., 2023). Soil salinization is a global problem, affecting about 23% of the world’s arable land (Tang et al., 2023). In addition, salinized areas are growing at a rate of 10% per year due to low precipitation, large surface evaporation, weathering of native rocks, irrigation with saline water, and poor cultural practices. It is expected that more than 50% of arable land will be salinized by 2050 (Jamil and Ashraf, 2011). The salinization of arable land is also a common environmental disaster in coastal areas of China (Cui et al., 2021). Soil salinization in coastal areas is the result of multiple factors, including the transport of rivers, the toppling of seawater, the ocean currents, tides, and waves (Yang et al., 2021). A large acreage of quality land is coming under salinity every year. This poses serious limitations to crop productivity and limits sustainable land use. Any attempt to reduce the effects of salinity in plant systems may improve crop growth at high salinity. The amelioration of coastal saline soils is essential to sustainable agriculture in coastal zones. This could be an option to fill the gap in crop demand (Gupta et al., 2023).

Soil salinity is a prominent abiotic stressor that significantly impedes crop growth, with its impact intensifying over time (Chaves et al., 2009). Soil salinization imposes substantial limitations on achieving the full yield potential of crop cultivars. The escalating levels of soil salinization pose a grave threat to the overall crop production system, resulting in a sharp decline in both the quality and quantity of agricultural produce. The expansion of saline soil is expedited by intensive agricultural practices. Furthermore, salinity stress in plants adversely affects nutrient uptake, osmotic balance, membrane integrity, and overall growth, thereby disrupting the dynamics of the entire crop (Zhang et al., 2022). It also causes generation of excessive reactive oxygen species, which besides acting as signaling molecule, it can harm plant function and reduce productivity at higher concentrations (Czarnocka and Karpinski, 2018). A large acreage of quality land is coming under salinity every year. This poses serious limitations to crop productivity and limits sustainable land use.

Plant rhizosphere microhabitat is the most active microhabitat in soil, and it is also the main area for plants to obtain nutrients. In this microdomain, plant-microbial-soil-environment interactions jointly maintain the balance of the rhizosphere microecosystem and affect crop production. Plant-associated microbes play an important role in host nutrient utilization, stress tolerance, plant health, and adaptation (Yang et al., 2022; Pang et al., 2023). Soil microorganisms are not only the drivers of soil organic matter turnover and nutrient cycling, but also an important part of soil organic matter. Therefore, any effect of salt accumulation on microorganisms will affect the turnover process of soil organic matter (Setia et al., 2012). On the one hand, microorganisms reduce soil organic matter content through mineralization; on the other hand, microbial dead bodies in the turnover process of microorganisms account for 10–80% of soil organic matter content (Liang et al., 2019; Wang et al., 2021). Therefore, soil microorganisms act as “carbon pumps” in the turnover process of soil organic matter. It has been reported that microorganisms have a close relationship with plants in nutrient cycling and mitigating biotic and abiotic stresses (Meena et al., 2017). Microorganisms have the ability to maintain plant growth under salt-stress conditions, such as improving nutrient uptake, osmotic balance, ion balance, membrane stability, and overall growth (Sahu et al., 2021). Microorganisms that can mitigate the deleterious effects of soil salinization on plant growth and productivity are being exploited for sustainable agriculture, exploring that rhizosphere microorganisms can ameliorate the adverse effects of salt stress on different physiological parameters (Gupta et al., 2023).

In the agriculture sector, cotton is an important cash crop, which has strong adaptability to saline-alkali soil and is a pioneer crop for saline-alkali soil improvement (Guo et al., 2015). Given the increasing detrimental impacts of saline-alkali soil, it is important to characterize the different microbial systems of major crops such as cotton, so that the base of effective climate-adaptive cropping strategies can be expanded to prepare Chinese agriculture for the future. Therefore, it is necessary to evaluate the potential of cotton rhizosphere microorganisms in alleviating salt stress and excavate beneficial rhizosphere microorganisms.

Soil salinity is a widespread global issue that impacts approximately 20% of irrigated land (Shrivastava and Kumar, 2015). It poses a significant challenge to agriculture as it leads to a substantial reduction in crop yields. The presence of excessive salts in the soil interferes with plant growth and development, affecting nutrient uptake, water absorption, and overall plant health. This reduction in crop productivity has detrimental effects on food security and agricultural sustainability. Addressing soil salinity is crucial for maintaining and increasing crop yields to meet the growing demand for food worldwide. In this study, the impact of soil salinization on cotton growth, yield, soil properties, and microbial community structures was examined. The results showed that increasing soil salinity had detrimental effects, reducing soil stability, nutrient availability, and altering the composition of microbial communities. The study also found that cotton yield decreased with higher levels of soil salinization. Additionally, the diversity and structure of microbial communities in cotton rhizosphere soil were affected by soil salinization, with a decline in beneficial microbial groups. These findings provide valuable insights into the mechanisms through which saline-alkali soil affects soil microorganisms in cotton rhizosphere soil and offer guidance for improving saline-alkali soil using beneficial microorganisms.

Soil aggregates are the “cells” of soil and an important habitat for microorganisms. They are composed of soil particles (sand, silt, and clay) cemented with organic or inorganic substances (Six et al., 2000). The higher the proportion of large aggregates, the higher the aggregate stability. Soil aggregate stability affects microbial community structure, regulates oxygen divergence, and regulates water and nutrient transport, which in turn affect the formation and decomposition of soil organic matter (Six et al., 2004). The total amount of soil aggregate decreased with increasing soil salinization at the seedling, flowering and boll and flocculation stages, indicating that soil stability decreased with increasing salinity (Table 1). The contents of soil organic carbon, organic matter, AHN, AP, and AK are considered to be one of the important factors affecting soil bacterial community structure. These factors can affect soil physical and chemical properties and nutritional status, and then affect the survival and activities of soil microorganisms (Zhao et al., 2014). The contents of AHN, AP and AK in the rhizosphere soil of heavily saline-alkali soil were significantly lower than those of slight saline-alkali soil during the three investigated cotton growth periods (Table 2). Soil salinization is a common abiotic stress that reduces the water-extraction capacity of roots and disrupts plant metabolism, in turn affecting crop growth and yield in agroecosystems on a global scale (Yang et al., 2021). In this study, we evaluated the effects of different levels of saline-alkali soil on cotton yield and found that cotton yield indicators decreased with the increase of soil salinization (Table 3). These results indicate that salinization alters the physical and chemical properties of soil in coastal areas, resulting in decreased soil stability and nutrient availability. In addition, different soil physical and chemical environments may lead to different degrees of promoting, inhibiting, or reversing effects of cotton roots on the same bacterial community. These changes had a significant impact on cotton yield, resulting in decreased productivity.

Alpha diversity is used to measure the richness and diversity of a single soil sample. Chao1 measures the number of species (Eren et al., 2012). Shannon and Simpson indices are used to measure species diversity, which are affected by species richness and Community evenness in the sample community. Under the same species richness, the greater the evenness of each species in the community, the greater the diversity of the community was considered. Higher Shannon index values and higher Simpson index values indicate higher species diversity of the samples (Washington, 1984). The Chao1 index of each component showed that species richness in the heavy saline-alkali soil tended to be lower than that in the light saline-alkali soil. Shannon and Simpson indices showed that species diversity in the heavy saline-alkali soil tended to be lower than that in the light saline-alkali soil (Figure 1). The results of beta diversity analysis showed that there were significant differences in bacterial communities of soil with different degrees of salinization. The SS, FS, and GS of the soil samples from the slight saline-alkali soil were closer. SM, FM, and GM of the moderate saline-alkali soil samples were close to each other. The FH and GH of the heavy saline alkali soil samples were far from the other samples, and the samples between the two types of soil were separated from each other (Figure 2).

Microbial diversity and community structure play crucial roles in soil health. A diverse and balanced microbial community is indicative of a healthy soil ecosystem. Various types of microbes, including bacteria, fungi, protozoa, and viruses, contribute to important soil processes such as nutrient cycling, organic matter decomposition, and disease suppression (Howard and Hanna, 2015; Pereg and Mcmillan, 2015). Plants exert selective pressure on the structural and functional diversity of microbial populations through the root exudation, and in relation to soil properties, plant species, growth stage, and many other stress factors (Gomes et al., 2001). Plants provide abundant ecological niches for various microorganisms, including bacteria, fungi, protozoa, nematodes, and viruses, facilitating the formation of complex symbiotic relationships. These microorganisms interact with plants in the natural environment, participating in plant growth and development, influencing plant functional traits, maintaining species diversity, and promoting community structure stability, thereby establishing a plant–soil feedback effect (Agler et al., 2016). Plant root exudates serve as the basis for such plant–soil feedback, shaping specific microbial communities to meet host growth requirements. Microbial communities and plants, in turn, uphold the stability of structure and function in ecosystems by eliciting symbiotic or immune defense mechanisms (Hacquard et al., 2017). Salinity changes soil bacterial diversity and community structure. The effects of various factors, such as soil structure, texture, pH, water content, salinity, mineral content and organic content, on soil microbial communities have been widely confirmed (Berg and Smalla, 2009; Hill et al., 2019). Proteobacteria, Bacteroidetes, and Actinobacteria were the main bacterial communities in the southeastern coastal saline-alkali land (Li et al., 2018). Proteobacteria, one of the largest phyla of soil bacteria, play important roles in biogeochemical cycles, including carbon, nitrogen, sulfur, and iron cycles, and they are well known for their versatility and ability to perform multiple metabolic processes (Spain et al., 2009). Actinomycetes are widely distributed in soils and play a crucial role in nutrient cycling and defense mechanisms (Stach and Bull, 2005; Jose and Jha, 2017; Bull and Goodfellow, 2019). They have the ability to survive as endophytes within plant tissues, contributing to nutrient assimilation and promoting plant growth (Vurukonda et al., 2018). Additionally, Actinomycetes are known to drive nutrient cycling even in harsh environmental conditions (Bull et al., 1998). The Acidobacteriota phylum is highly versatile in adapting to various physiological and ecological conditions. It possesses the capacity to degrade complex carbon-containing compounds. Stressors affecting Acidobacteriota may influence the cycling processes of plant-derived organic matter (Singh et al., 2007; Kalam et al., 2020). Gemmatimonadota is able to adapt to alkaline and high salinity soils (Malard et al., 2019; Guan et al., 2021), and their abundance is influenced by organic nutrient concentrations in the soil and plays a crucial role in soil ecosystems (Deng et al., 2019; Liu et al., 2021). In this study, Proteobacteria, Actinobacteria, Gemmatimonadota, Bacteroidota, Actinobacteriota, and Chloroflexi were the dominating bacterial phyla in in the cotton rhizosphere soil of saline-alkali soil (Figure 3). Among them, Proteobacteria accounted for the highest proportion, which was consistent with the results of previous studies (Tian and Gao, 2014; Qiao et al., 2017). There were differences in rhizosphere bacterial community structure among different developmental stages and soil conditions (Figure 3; Supplementary Table S2). We found that the relative abundance of Proteobacteria in the heavily saline-alkali soil was higher than that in the moderately and slight saline-alkali soil at the seedling and boll opening stages of cotton. The relative abundance of Bacteroidota increased with increasing soil salinity during these three growth periods. This may be due to cotton increasing the relative abundance of Proteobacteria and Bacteroidetes by secreting root exudates to promote nutrient cycling in rhizosphere soil, which helps cotton adapt to the harsh environment of saline-alkali soil at different growth stages. The relative abundance of Actinomycetes in cotton rhizosphere soil in heavy saline-alkali soil was lower than that in moderate and slight saline-alkali soil, which might be due to the failure of Actinomycetes to adapt to high saline-alkali soil environment. Different growth stages can also affect the structure of bacterial communities in the rhizosphere. For example, the relative abundance of Proteobacteria in rhizosphere soil at the boll opening stage was higher than that at the seedling and blooming stages in the moderate and heavy saline-alkali soil. In the heavy saline-alkali soil, the relative abundance of Actinobacteriota at the seedling stage was higher than that at the boll opening and flowering stages. These results suggest that the relative abundance of microorganisms in the cotton rhizosphere is affected by the degree of soil salinity and the different growth stages.

LEfSe analysis was used to search for robust differential species, namely biomarkers, between soil samples from different saline-alkali sites (Figure 5). This study revealed that o_Chitinophagales, o_Rhizobiales, o_Burkholderiales, o_Vicinamibacterales, o_Gemmatimonadales, o_Rokubacteriales and f_Nitrosomonadacea were biomarkers of lightly saline-alkali soil. f_Hymenobacteraceae, o_Thermoanaerobaculales, o_Longimicrobiales and g_Sphingomonas were biomarkers of moderate saline-alkali soil. o_Cytophagales, o_Polyangiales, o_Sphingomonadales, f_Comamonadaceae, f_Oxalobacteracea, o_Xanthomonadales, o_Actinomarinales, s_Gemmatimonadacea, o_Tistrellales, o_SBR1031, o_Gemmatimonadota, o_Kiloniellales, o_Rhodobacterales, o_Pseudomonadales, o_Gammaproteobacteri were biomarkers of heavily saline-alkali soil. This suggests that these taxa may be important species for maintaining soil health in saline-alkali soils.

Microorganisms (including viruses, bacteria, archaea and protists) do not exist in isolation but form complex ecological interaction webs. Interactions within these ecological webs can have a positive impact (that is, a win), a negative impact (that is, a loss) or no impact on the species involved (Lidicker, 1979). Network analysis has been widely applied to explore the complex inter relationships and co-occurrence patterns of soil microbial communities (He et al., 2017; Sen and Fengzhi, 2018). Previous studies have shown that environmental changes can affect the complexity of soil microbial co-occurrence networks (Banerjee et al., 2019). In this study, we examined the effects of salinization on the co-occurrence network of bacterial communities in cotton rhizosphere soil (Figure 6). The results showed that soil salinization reduced the total nodes, average path length, graph diameter, betweenness centralization of the network. The results demonstrate that soil salinization significantly affects the diversity and structure of bacterial communities in cotton rhizosphere soil. As the degree of soil salinization increases, the relative abundance of certain beneficial bacterial groups in cotton rhizosphere soil decreases.

In this study, we combined soil nutrient analysis to compare and explain the bacterial community structure and functions in different saline-alkali soils and at different stages of cotton growth. This research provides a theoretical foundation for understanding how soil microorganisms maintain nutrient balance and drive ecosystem nutrient cycling. The findings deepen our understanding of the impact of saline-alkali soil on bacterial communities in cotton rhizosphere, and offer valuable insights for utilizing beneficial microorganisms to improve saline-alkali soil.

The original contributions presented in the study are included in the article/Supplementary material, further inquiries can be directed to the corresponding author.

GF: Conceptualization, Data curation, Investigation, Writing – original draft, Writing – review & editing. YWu: Data curation, Visualization, Formal Analysis, Writing – original draft, Writing – review & editing. CY: Visualization, Validation, Writing – original draft, Writing – review & editing. QZ: Methodology, Writing – review & editing. SW: Data curation, Project administration, Writing – original draft. MD: Investigation, Writing – review & editing. YWa: Data curation, Writing – review & editing. HQ: Investigation, Writing – original draft, Writing – review & editing. LG: Data curation, Investigation, Visualization, Writing – original draft, Writing – review & editing.