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Article

Revolutionizing Salinized Farmland: How Salt-Controlled Irrigation Transforms Microbial Diversity and Soil Organic Matter in a Salt-Alkali Soil

by
Xu Yang
1,
Ruihong Yu
1,2,3,*,
Guanglei Yu
1,
Yansong Bai
1,
Muhan Li
1,
Zeyuan Liu
1,
Shen Qu
1,
Ping Miao
4,
Hongli Ma
4,
Tao Zhang
5 and
Yonglin Jia
6
1
Inner Mongolia Key Laboratory of River and Lake Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
2
Key Laboratory of Mongolian Plateau Ecology and Resource Utilization, Ministry of Education, Hohhot 010021, China
3
Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot 010018, China
4
River and Lake Protection Center, Ordos Water Conservancy Bureau, Ordos 017000, China
5
Hohhot Hydrology and Water Resources Branch Center, Hohhot 010021, China
6
The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
*
Author to whom correspondence should be addressed.
Agronomy 2025, 15(4), 956; https://doi.org/10.3390/agronomy15040956
Submission received: 18 March 2025 / Revised: 7 April 2025 / Accepted: 10 April 2025 / Published: 14 April 2025
(This article belongs to the Section Agricultural Biosystem and Biological Engineering)
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Versions Notes

Abstract

:
China is one of the countries most seriously affected by soil salinization, while the impact of salt-controlled irrigation on the relationship between soil dissolved organic matter (DOM) and microbial in farmland affected by salinization remains largely unexplored. We conducted a comprehensive survey of soil DOM and a microbial survey of Ordos’s salinized farmland in China before and after salt-controlled irrigation. Our findings reveal a reduction of 18.4 mg/L in surface soil (0–10 cm) DOC following irrigation, whereas the subsurface soil (20–40 cm) DOC increased by 20.7 mg/L. Moreover, irrigation led to an increase in the aromaticity and humification of the soil, with the salt content of the subsurface soil rising from 2.7 to 3.7 mg/g. Additionally, the total dissolved solids (TDS) in the drained water were 2463 mg/L higher than in the irrigation water (1416.3 mg/L). This suggests that the DOM and salts from the surface soil either leached into deeper layers or were lost via runoff. Furthermore, SEM analysis and a Mantel test revealed that microbial composition significantly influenced soil DOM contents, especially increased levels of Marmoricola and MND1, which are associated with decomposing organic matter and may contribute to the leaching of soil DOM in deep layers following irrigation.

1. Introduction

Approximately 10% of the cultivated land in nearly 100 countries worldwide are affected by salinization [1]. With the intensification of climate warming, the global salinized land area is growing at an annual scale of 1.0~1.5 ha [2]. China is one of the countries most seriously affected by soil salinization, with a total saline-alkali land area of 99.13 million ha [3]. Accordingly, the measures to control saline-alkali land are also important measures for food production security in the coming years.
In recent years, strategies for the recovery of salinized land have been studied and developed [4]. Such strategies mainly involve the cultivation of salt-tolerant crops [5], water-saving irrigation [6], back-filling of guest soil [7], modifying agent application [8], and water conservation measures [9]. Particularly, water-saving irrigation is widely used in arid and semi-arid regions, including controlled irrigation, drip irrigation, and rain-gathering irrigation [10]. It can modify the physical state, microbial activity, and crop growth of soil, resulting in reduced soil salinization risk and water consumption [5]. Although salt-leaching irrigation is known to mitigate salt buildup by flushing excess salts below the root zone [11,12,13,14], this practice can inadvertently increase the soil’s water content, salinity, pH, and nutrient levels [15,16]. Liu et al. [11] demonstrated that irrigation, particularly when combined with precipitation and a balanced use of brackish and freshwater, enhances salt leaching in the North China Plain, with irrigated croplands achieving greater salt reduction (61%) compared to unirrigated grasslands (42%). Zhao et al. [12] revealed that large-scale drip irrigation in Kalamiji Oasis lowered groundwater levels (0.5 m yr−1) and increased soil salinity in shelterbelts compared to farmlands. These contrasting findings underscore the necessity for further investigation into how salt-controlled irrigation affects soil characteristics.
As the largest organic matter reservoir in terrestrial ecosystems [17,18], soil microorganisms are integral to the formation of soil organic matter through the decomposition and transformation of plant inputs [19,20], especially dissolved organic matter (DOM), which is vital for regulating key biogeochemical processes such as nutrient cycling and organic material storage. The dynamics of soil DOM turnover [21], influenced by environmental factors and input material, are critical in determining soil fertility, productivity, and ecosystem development [1]. Recent studies have demonstrated that salt-controlled irrigation in saline soils increased the diversity of soil microorganisms and the relative abundance of dominant phyla [5]. Notably, a reciprocal relationship exists between soil microorganisms and DOM: while microorganisms break down carbon compounds, they also contribute to the preservation of carbon molecules through various metabolic processes [22,23,24]. Nonetheless, the potential consequences of microbial community shifts induced by salt-pressure irrigation on the content and composition of soil DOM remain largely unexplored. This leads us to question whether forms of irrigation aimed at reducing salinity may alter soil DOM composition while affecting the soil’s microbial community structure, ultimately affecting the soil’s properties? This is of great significance for the rational application of salt-controlled irrigation and for ensuring the fertility of salinized soil.
Hence, the objective of this research is to investigate the impact of salt-controlled irrigation on the relationship between soil DOM and microbial populations in farmland affected by salinization. We hypothesized that soil DOM would be influenced by microbial communities both before and after irrigation. To test this hypothesis, we examined the changes in DOM and microbial communities across four soil types: crop soil (S), crop + straw soil (S-S), crop + mulch soil (S-M), and crop + mulch + straw soil (S-SM). The analysis of soil DOM components was performed using 3D fluorescence spectroscopy, while microbial community diversity and abundance were assessed using 16S rRNA sequencing. By applying multivariate statistical analysis, we aimed to clarify the composition and distribution of soil microorganisms and soil DOM both before and after irrigation, with the ultimate goal of exploring their interactions.

2. Materials and Methods

2.1. Study Area and Sample Collection

The irrigation region is located on the southern side of the Yellow River. A combined length of 412 km covers the primary irrigation system along the course of the Yellow River, mainly including Changhaibai, Muye, Balahai, Jianshe, and Dugui irrigation area (109°10′–106°80′, 39°0′–40°42′, Figure 1); the total irrigated area reaches 27,940 ha. The diversion of Yellow River water for agricultural irrigation has significantly boosted crop yields in this region.
Salt-controlled irrigation, an agricultural technique designed to ameliorate saline-alkali soils, facilitates the downward migration of accumulated salts below the crop root zone through increased irrigation volume. The fundamental principle involves utilizing water infiltration to mobilize soluble salts, thereby reducing rhizosphere salinity and ensuring optimal crop growth. However, excessive irrigation may compromise soil structure, induce nutrient leaching, and potentially trigger secondary salinization. To assess the impact of salt-controlled irrigation on soil surface and subsurface organic matter characteristics, we conducted sampling before and after a large centralized saline-controlled irrigation; the samples were collected in September 25 (prior to intensive irrigation implementation) and November 25 (following irrigation cessation) in 2023. A total of sixty-eight samples were gathered from various locations within the irrigation region situated on the southern side of the Yellow River, encompassing surface soil (0–10 cm), subsurface soil (30–40 cm), irrigation canal surface water, and Yellow river water (Figure 1). A sampling depth of 40 cm was selected to encompass the primary root zone of crops and capture the dominant salt redistribution zone during leaching irrigation. At each soil sample site (Table S1), three composite samples were obtained by collecting individual samples at different points along a diagonal line spanning an area of 10 × 10 m and subsequently mixing them in situ. Hence, a total of forty soil composite samples were gathered from both the surface and subsurface layers of the irrigated agricultural land, both prior to and subsequent to irrigation. Soil samples were carefully enclosed in aluminum foil pouches for preservation, following which, they were placed inside a freezer set at 4 °C for subsequent analysis. To obtain surface water samples (Table S2), stainless steel buckets underwent preliminary cleaning with Milli-Q water. These buckets were then utilized to collect 2 L of surface water (0–10 cm) from the central region of the irrigation canal and stored within a cooling box maintained at 4 °C until further processing [25].

2.2. Soil Physical and Chemical Properties and Microbial Analysis

Soil and water physicochemical properties and soil microbial analysis methods are listed in Support Information Texts S3 and S4.

2.3. Statistical Analysis

The Mantel test was utilized to examine the correlation between the distance matrix of environmental variables and both the microbial community matrix and DOM composition matrix (based on Bray−Curtis distance). Redundancy analysis (RDA) was employed to depict the relationship between microbial communities and environmental factors. Structural equation modeling (SEM) was constructed using Smartpls 3.0 software to assess the direct and indirect impacts of soil DOC contents, soil properties (pH, TN, TC, salt, sobs, ace, and chao), as well as soil DOM characteristics (CDOM, SUVA254, SR, E2/E3, FI, BIX, HIX, and fluorescent component).
The application of SEM proves to be highly advantageous when examining intricate associations among predictors frequently observed in environmental ecosystems, as it facilitates the division of causal impacts among numerous variables and the distinction between direct and indirect effects of model predictors [26]. The objective of utilizing SEM in this study was to analyze the soil attributes (including microbial composition) and characteristics of soil DOM in relation to soil DOC levels before and after irrigation. Prior to model calculation, we established a pre-existing model based on our current understanding of how environmental variables influence soil DOC levels (Figure S1).

3. Results

3.1. Changes in Soil Organic Matter Before and After Irrigation

The soil TC contents was influenced by the type of soil covering material. As shown in Figure 2, before salt-controlled irrigation, the control soil exhibited the lowest TC content (13.3 mg/g), followed by S-S soil (13.7 mg/g), S-SM soil (14.0 mg/g), with S-M soil showing the highest TC content with 15.8 mg/g. Salt-controlled irrigation significantly increased soil TC content, with surface soil TC increasing from 15.7 to 17.1 mg/g and subsurface soil TC increasing from 11.9 to 13.3 mg/g. Notably, both before and after salt-controlled irrigation, surface soil had higher TC contents (0.6–12.0 mg/kg, p < 0.05) compared to subsurface soil.
Salt-controlled irrigation significantly increased the TOC contents of the S-S soil, S-M soil and S-SM soil by 0.26–1.5 mg/g. This observation suggests that irrigation promotes the release of organic carbon in soil straw and mulch film. S-M soil also has the highest TOC concentration than another soil. However, the difference between the surface and subsurface soil TOC is not significant in each soil. In particular, salt-controlled irrigation decreased the surface soil DOC by 18.4 mg/L, but increased the subsurface soil DOC by 20.7 mg/L. The S-S has the highest DOC than other soil.
Salt-controlled irrigation obviously increased soil CDOM, with the most pronounced enhancement observed in the S-SM, where CDOM levels rose from 0.14 (before irrigation) to 2.38 (after irrigation). The UV-Vis absorbance optical indices of soils are presented in Table S3. Before irrigation, the highest SUVA254 value was observed in the S-S soil sample (0.128), whereas after-irrigation, this value shifted to the S-SM soil sample (0.181). These findings indicate that the SUVA254 values of both surface and subsurface soils were higher before irrigation compared to after irrigation. Before irrigation, values of E2/E3 and SR were lower in surface soil than subsurface soil, which might indicate the relatively larger percentage of high molecular weight in surface soil, while after irrigation, the relative molecular weight of surface and subsurface soil did not change significantly. In particular, S-SM exhibited the highest relative molecular weight of DOM.
Fluorescence indicators were employed to identify the associations between changes in DOM, FI, and BIX values, which are linked to the proportion of organic matter derived from microorganisms and its level of humification, while HIX value was correlated with microbial material. The salinity control irrigation led to an increase in soil aromaticity and humification levels. As present in Table S4, irrigation intensifies the soil humification, which is consistent with the optical indices of UV–Vis absorbance in soils, the mean FI increased from 2.04 before irrigation to 3.38 after irrigation, whereas BIX also increased slightly by 0.11 after irrigation. Especially after irrigation, the humification degree of the subsurface soil was more obvious than that of the surface soil (p < 0.05), while the microbial material (represented by HIX value) was more abundant than that in the top soil. However, the humification degree of soil with different characteristics did not show obvious regular changes before and after irrigation.
Using EEM-PARAFAC analysis (refer to Figure S2), four distinct DOM components in soil were identified before and after salt-controlled irrigation. Although the relative proportions of these components remained largely consistent after irrigation, their fluorescence intensities differed significantly between surface and subsurface soils. As shown in Figure 3, the fluorescence intensity of protein-like (tryptophan-like) components (C1) in surface soil was 4.7–7.1 times higher than subsurface soil, and microbial humic-like fluorophores (C3) in surface soil was 3.5 times higher than in subsurface soil, while the terrestrial humic-like fluorophores (C2, C4) in surface soil was 0.32–0.75 times lower than in subsurface soil.

3.2. The Soil and Surface Water Quality Before and After Irrigation

There was no significant change in soil pH before and after salt-controlled irrigation (Table S5). However, the salt content of subsurface soil increased from 2.7 to 3.7 mg/g across four soil types following irrigation, representing a 1.0 mg/g elevation compared to surface soil levels.
Surface water quality before and after irrigation was analyzed (Tables S6–S11). The pH of surface water is 9.1 before irrigation and increases to 9.6 after irrigation; there was no significant difference in pH between irrigation water and drained water. The contents of DO were relatively uniform with values from 7.6 to 15.4 mg/L before and after irrigation. However, irrigation significantly increased the content of TDS in drained water, which was 2463 mg/L higher than that of irrigation water (1416.3 mg/L); the salt also increased by 1.4 g/L.
In both sampling periods, Na+ was the dominant cation in the groundwater, followed by Mg+, Ca2+, and K+. Before irrigation, Cl− was the most dominant major anion in the groundwater, followed by SO42−, HCO3−, CO32−, and F−. While after irrigation, SO42− become the most dominant major anion, followed by Cl−, HCO3−, CO32−, and F−. Before irrigation, surface water chl-a decreased significantly from 17.989 to 3.592 μg/L after irrigation; the chl-a of drainage water was significantly higher than irrigation water (p < 0.05), while after irrigation, the chl-a content in irrigation water and drainage water tended to be consistent. Before irrigation, the TN and NO3−-N contents of irrigation water were significantly higher than those of drained water (p < 0.05), while after irrigation, the TN content of drained water was 5.463 mg/L higher than that of irrigation water and the NH4+-N content was 0.152 mg/L higher than that of irrigation water.

3.3. The Microbial Composition of Soil Before and After Irrigation

The α-diversity index, calculated from 16S rRNA sequencing data, revealed significant variations in bacterial community diversity across soil layers. Before irrigation, the richness and diversity of bacteria in the surface soil consistently exceeded that of subsurface soil (Table S12). However, irrigation had a significant impact on enhancing the richness and diversity of bacteria in the subsurface soil (Student’s test, p < 0.05), indicating that the salt-controlled irrigation may affect the microbial composition of the underlying soil, which was the same result with the soil BIX values. There was no significant difference in microbial diversity among four soil properties, and, therefore, in the subsequent microbial analysis, we do not discuss the differences between different soil properties separately.
The composition of soil microbial community is presented in Figure 4a; at the phylum level, Actinobacteriota (24.1% ± 8.42), Proteobacteria (19.6% ± 5.72), Chloroflxi (15.0% ± 6.15), and Acidobacteriota (11.0% ± 7.5) were the most abundant phyla before and after irrigation in the soil. At the genus level, we analyzed soil samples from both surface and subsurface layers collected before and after irrigation. The focus initially was to determine any significant differences between groups based on dominant genera (refer to Figure S3). The findings indicate that among the 15 most abundant species, there was a significant difference (p < 0.05) observed in 9 species, 5 species have the highly significance difference (p < 0.01), and 1 species p < 0.005. Furthermore, after irrigation, the 15 dominant genus in subsurface soil were significant difference between the subsurface soil before irrigation, and the abundance of 12 dominant species was higher after irrigation than before irrigation (Figure 4b). Moreover, the changes in subsurface soil community composition at genus level were most obvious after irrigation (p < 0.05) (Figure 4c).
The Mantel test was used to evaluate the influence of external environmental factors (such as soil physicochemical characteristics and DOM composition) on the microbial community before and after irrigation (Figure 5a). Of all the parameters investigated, those significantly associated with the composition of DOM were found to be directly linked to microbial factors. Moreover, the parameters linked to microorganisms exhibited strong correlations with DOM, suggesting that microorganisms played a crucial role in shaping the molecular structure of DOM.
The salt, soil DOC content, and DOM fluorescence proxies (FI and BIX) before and after irrigation showed strong associations with the microbial community composition of the soil (p < 0.05). Compared to the surface soil, the subsurface soil microbial community composition had a stronger relationship with the soil environmental factors, especially the soil DOM peculiarity. At the same time, irrigation enhanced the correlation between soil environmental factors and the composition of microbial communities. To assess the alignment between soil DOM characteristics and microbial community composition following irrigation, a Procrustes analysis was conducted (Figure S4). This further supported that the alterations in soil DOM and soil microorganisms exhibited a strong correlation subsequent to after irrigation (M2 = 0.032, p < 0.05). These results further reveal that there is a strong correlation between the composition of bacterial and DOM characteristic in soil cores and soil physicochemical indexes. The strong correlation observed between DOM characteristics (such as DOC contents and BIX) and microbial parameters (including Shannon and Chao indices) further emphasizes the interdependence of these variables.
RDA was employed to provide additional insights into the impact of environmental factors on microbial variability (Figure 5c). For redundancy analysis, only those factors exhibiting a variance inflation factor (VIF) value < 10 among the significantly correlated parameters were considered. The results show that the environmental factors closely related to microbial community changed before and after irrigation. More specifically, before irrigation, BIX, DOC, pH, and salinity were identified as the primary contributors to the variance, whereas after irrigation, the key factors shifted to pH, TOC, and CDOM. The analysis results are slightly different from those of the Mantel test, potentially attributable to the combined analysis of surface and subsurface soil samples.
To characterize soil metabolic potential, a comprehensive analysis using FAPROTAX identified 3886 operational taxonomic units (OTUs) that were classified into 50 distinct functional groups (Figure S5). The function of surface and subsurface soil before and after irrigation was analyzed, respectively. As shown in Figure S5, irrigation had significant effects on microbial functions of surface soil and subsurface soil. The functions of methanotrophy, anoxygenic photoautotrophy, ligninolysis, and anoxygenic photoautotrophy oxidation in surface soil increased after irrigation, while the functions of aerobic ammonia oxidation decreased. In subsurface soil after irrigation, the functions of chlorate reducers and dark thiosulfate oxidation decreased, but the functions of thiosulfate respiration and chloroplasts increased.

3.4. Key Factors Affecting Soil Dissolved Organic Matter Before and After Irrigation

DOC content was used as an index representing soil organic matter, and the effects of microbial composition and organic matter composition on DOC before and after salt-controlled irrigation were analyzed by SEM. As shown in Figure 6, microbial diversity indices were the main primary drivers of soil DOC content, the sobs and ace indices had direct effects on the soil DOC, and the chao index had indirect affected the soil DOC before and after salt-controlled irrigation. Especially, the negative correlation between chao index and soil DOC contents became more significant after irrigation, and the sobs and ace index always elicited a dominant promoting effect on soil DOC contents. The UV index and fluorescence index, which represent the properties of organic matter, have significant changes on the SEM results of soil DOC concentration before and after irrigation (Figure 6b,d). Soil DOC content was positively influenced by SR, HIX, and microbial humic-like fluorophores C3 before irrigation, while BIX exhibited a significant negative impact on soil DOC content. While after irrigation, E2/E3, FI, CDOM, and HIX both elicit a dominant promoting effect on soil DOC content, the terrestrial humic-like fluorophores C2 and microbial humic-like fluorophores C3 has a significant negative correlation with soil DOC content.

4. Discussion

4.1. Effects of Salt-Controlled Irrigation on Soil and Water Quality

Salt-controlled irrigation is distinct from traditional methods due to its multiple benefits. In autumn, it replenishes soil moisture before winter, enhances soil health by stimulating microbial activity and nutrient cycling, and improves soil structure and organic matter. This practice lowers soil salinity, flushes accumulated salts from the root zone, and creates a more favorable growing environment, ultimately boosting crop growth and sustainability. However, it is essential to monitor changes in the physicochemical properties of surface water and soil in irrigated areas. The present study identifies significant salt changes in soil and surface water after irrigation. Irrigation exhibited the salt content of the subsurface soil, while the TDS in drained water already exceeded that of irrigation water after irrigation. This phenomenon indicates that salt-controlled irrigation has an obvious scouring effect on soil salt. Following irrigation, surface soil salt either penetrates into the deep soil layer or is carried away through runoff. A similar result was reported by Tong [3] after a flood irrigation of saline-alkali soil. In addition, after irrigation, the TN content of drained water was 5.463 mg/L higher than that of irrigation water, and the NH4+-N content was 0.152 mg/L higher than that of irrigation water. This is attributed to irrigation reducing the cohesion of the soil colloid, which changes the granule structure, making the granules split into small single-grain unstructured soil, caused the loss of soil nutrients [25]. While soil pH did not change during the study, a similar result was reported by Rusan [27] and Marzieh Farhadkhani [28] after the long-term irrigation of farmland. The alteration in granule structure resulted in the fragmentation of granules into individual grains, leading to a decline in soil nutrient content. Although there were no significant variations observed in soil pH throughout the investigation, analogous findings were documented by Rusan and Marzieh Farhadkhani following prolonged irrigation practices on agricultural land.
Overall, our study reveals significantly elevated concentrations of pollutants in drainage water following irrigation, including TDS, TN, and NH4+-N. These findings indicate that current irrigation practices may lead to soil nutrient leaching and secondary salinization risks. Salt accumulation in subsurface soil layers could potentially reduce crop productivity, while nutrient-enriched drainage water may trigger algal blooms in receiving water bodies, posing threats to aquatic ecosystems.

4.2. Factors Affecting Microbial and DOM Compositions in Salt Farmland

The microbial community is crucial for preserving the ecological function of farmlands. Alterations in soil microbial characteristics serve as reliable indicators of soil quality [29], given their higher dynamism and sensitivity compared to physical or chemical soil properties [23]. Previous research has shown that the long-term irrigation, ambient temperature and humidity, ultraviolet radiation levels, soil moisture and pH levels, interactions with native soil microorganisms, and the irrigation methods employed, as well as the specific plant species grown, can all influence the abundance and activity of microorganisms in soil [23,24]. In our presence study, the richness and diversity of bacteria in the surface soil was always higher than that in the subsurface soil before irrigation (Table S12). However, irrigation significantly enhanced the richness and diversity of bacteria in subsurface soil, with 12 dominant species showing increased abundance post-irrigation (Figure 4b). Overall, environmental variables were found to shape microbial community structure differentially between surface and subsurface soils (Figure 5). The Mantel analysis showed that soil salinity affects the composition of subsurface microbial community. These findings are consistent with the results presented by Guo et al. regarding the abundance and diversity of denitrifying communities, along with their potential denitrification activity in soils exposed to wastewater irrigation, which can be significantly influenced by the soil’s physicochemical properties as well as the pollutants present [30]. Moreover, UV radiation from natural sunlight may play a crucial role in deactivating microorganisms within arid and semi-arid regions. Additionally, it is widely recognized that water acidity levels [29], redox conditions determined by pH levels, and solar radiation exposure greatly impact the availability of light energy in microbial habitats; hence, these factors hold significant influence over microbial community assembly [31,32,33].
Soil organic carbon is crucial for enhancing nutrient availability, water retention, and overall soil health, which are essential for the growth and productivity of crops and other plants. Our results demonstrate that salt-controlled irrigation significantly increased TC content in both surface (from 15.7 to 17.1 mg/g) and subsurface soils (from 11.9 to 13.3 mg/g) (Figure 2). We suspect that this is mainly due to the carbon inputs from irrigation water, which enhances organic carbon accumulation in agricultural soils, consequently raising TOC levels [23]. In addition to the quantity of SOM, alterations in its composition resulting from the utilization of reclaimed wastewater for irrigation are observed in the irrigated soils [34]. In particular, irrigation decreased the surface soil DOC, while increasing the subsurface soil significantly; the S-S soil has the highest DOC than other soil (Figure 2). The primary reasons are as follows: (1) The movement of soil DOC from the surface to the subsurface induced by irrigation. (2) Post-irrigation shifts in surface and subsurface soil microbial community composition led to differential soil carbon decomposition rates. Recent research indicates that the decomposition of soil organic matter in different soil layers is primarily influenced by factors such as its accessibility, concentration, bioavailability [35], and biodergradability [22] rather than being predominantly affected by any inherent recalcitrance of DOM molecules [20]. Furthermore, the microbial processing of organic molecules [36] is closely linked to alterations in DOM within the environment. The degradation efficiency of DOM is significantly influenced by its molecular characteristics [37]. Therefore, the microbial population adjusts to and breaks down essential DOM elements based on their specific molecular characteristics at distinct depths [20]. This microbial decomposition results in alterations in the composition of DOM as soil depth varies [22].

4.3. Mechanism of Microbial Control on DOM Characteristics with Salt-Controlled Irrigation

As the primary component of soil organic matter that is highly mobile and readily accessible to organisms, the heterogeneity of DOM is closely associated with microbial processes [38]. Microbes play a crucial role in the generation, utilization, and alteration of DOM, particularly in agricultural soil subjected to intricate human activities, especially in farmland soil with complex human disturbance. Greater microbial diversity supports more diverse metabolic pathways, driving continuous DOM recycling, transformation, and molecular reorganization. This ultimately impacts the molecular weight, chemical composition, oxidation state, and accessibility of DOM [20,39]. In addition, the microbial community structure and activity can be influenced by the functional complexity of DOM components [40]. For example, the presence of protein components in DOM promotes the abundance of copiotrophic bacteria like Proteobacteria and Acidobacteria [41], while elevated levels of organic acids suppress soil microbial activity [42].
In this study, the Mantel test was used to evaluate the effects of external environmental factors on the microbial community before and after irrigation (Figure 5a). The parameters significantly related to DOM composition were the microorganisms index. Procrustes analysis (Figure S4) further demonstrated that the changes in soil DOM and soil microorganisms were closely linked after irrigation. SEM analysis (Figure 6) also showed that the microbial diversity index was the main factor driving soil DOC contents. Overall, microorganisms were found to be the main factor causing changes in soil carbon; this may have finally resulted in soil humification and leaching DOC. Microbial activity enhanced the chemical variety of soil DOM, while diverse DOM served as a source of energy for microbial growth. These intricate interconnections established a complex network between microorganisms and DOM. Additionally, the accumulation of organic carbon in soil relied on the carbon input from aboveground vegetation, with microorganisms also contributing by utilizing easily degradable compounds to form stable organic matter, thus leading to the formation of a persistent soil carbon reservoir [43].
Future research should focus on several key areas: Firstly, analyzing the variations in microbial responses under different saline-alkaline soil types and irrigation conditions to develop more targeted soil improvement strategies. Secondly, examining the long-term effects of salt-controlled irrigation on soil functionality, including carbon cycling and nutrient dynamics, to optimize irrigation management, enhance soil health, and provide a scientific basis for the sustainable use of saline-alkaline lands.

5. Conclusions

Our study investigates the relationship between dissolved organic matter (DOM) and microbial diversity in salinized farmland soils under salt-controlled irrigation. We conducted comprehensive DOM and microbial analyses of salinized farmland soils in Ordos, China, both before and after irrigation. The results demonstrate that irrigation decreased the surface soil while increased the subsurface soil DOC. At the same time, the irrigation increased the degree of aromaticity and humification of the soil. SEM and Mantel tests revealed that microbial community composition was the primary factor controlling soil DOM content. In particular, increased levels of Marmoricola and MND1, which are associated with decomposing organic matter, may lead to leaching of soil carbon after irrigation. The metabolic activities of microorganisms led to an enhancement in the variety and amount of organic matter in soil, while the diverse organic matter served as a source of energy for microbial growth. These intricate connections formed a complex network between microorganisms and organic matter.
The Southern bank of the Yellow River implements a large-scale salt-flushing irrigation in autumn each year to control soil salinity and enhance soil fertility. Research has shown that autumn salt-flushing irrigation does reduce the salt content in the surface soil, but it also decreases the content of soluble organic carbon in the surface soil. Additionally, the nitrogen and phosphorus content flowing from farmland into drainage channels significantly increases, posing a pollution risk to drainage water sources. Therefore, it is recommended that strict control over salt concentration and irrigation volume be exercised during salt-flushing irrigation to avoid excessive use leading to soil salinization and water pollution issues. It is also advised to enhance soil improvement and management to mitigate potential risks. Furthermore, with the global salinized land area gradually increasing, our research of great significance for understanding the relationship between organic carbon and microbial communities in salinized soil with salt-controlled irrigation, which played an important role in the development of soil organic matter as well as the formation of stable soil carbon pool in salinized farmland. Future studies should be encouraged to expand the research depth to reveal the effects of soil DOM changes induced by microbial action on crop growth after irrigation.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agronomy15040956/s1, Figure S1. A priori model according of the impact of environmental variables on soil DOC contents. Figure S2. PARAFAC model output showing the four different fluorescent components (Comp 1: protein-like (tryptophan-like) components, Comp 2: terrestrial humic-like fluorophores, Comp 3: microbial humic-like fluorophores, Comp 4: terrestrial humic-like fluorophores). Figure S3. The differences dominant genera of soil samples between before and after irrigation. Figure S4. Procrustes analysis of microbial community composition and soil DOM characteristic after irrigation. Figure S5. FAPROTAX analysis of soil before and after irrigation. Table S1. Locations of soil sampling sites. Table S2. Locations of groundwater sampling sites. Table S3. Summary of soil sample ultraviolet fluorescence index. Table S4. Summary of soil three-dimensional fluorescence index. Table S5. Summary of soil properties. Table S6. Physical index of surface water sample before irrigation. Table S7. Ion index of groundwater sample before irrigation. Table S8. Chemical index of groundwater sample before irrigation. Table S9. Physical index of groundwater sample after irrigation. Table S10. Ion index of groundwater sample before irrigation. Table S11. Chemical index of groundwater sample after irrigation. Table S12. Soil α diversity index. Text S1. Calculation methods of Ultraviolet spectrophotometer index. Text S2. Calculation methods of 3D Fluorescence. Text S3. Soil microbial analysis. Text S4. Soil microbial analysis. References [44,45,46,47,48,49,50,51,52,53] are cited in supplementary file.

Author Contributions

Conceptualization, X.Y.; methodology, G.Y. and Y.B.; software, M.L.; validation, Z.L., S.Q. and P.M.; formal analysis, H.M.; investigation, T.Z.; resources, Y.J.; data curation, R.Y.; writing—original draft preparation, X.Y.; writing—review and editing, R.Y.; visualization, X.Y.; supervision, X.Y.; project administration, R.Y.; funding acquisition, R.Y. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the Ordos Science and Technology Major Project (Grant No. ZD20232303), National Natural Science Foundation of China (Grant No. 52279067), and Project of Key Laboratory of River and Lake in Inner Mongolia Autonomous Region (Grant No. 2022QZBZ0003).

Data Availability Statement

Data are unavailable due to privacy or ethical restrictions.

Acknowledgments

The authors are grateful to the colleagues for their help in the field and the reviewers for their valuable comments.

Conflicts of Interest

The authors declare no conflicts of interest.

References

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Agronomy 15 00956 g001
Figure 1. Sampling sites for surface water and soil within a representative irrigation region situated alongside the southern side of the Yellow River.
Figure 1. Sampling sites for surface water and soil within a representative irrigation region situated alongside the southern side of the Yellow River.
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Figure 2. TC (mg/g) (a), TOC (mg/g) (b), DOC (mg/L) (c) in soil before and after irrigation. Black bars indicate surface soil (0–10 cm), and red bars indicate subsurface soil (30–40 cm). Data are presented as mean ± SD (n = 3).
Figure 2. TC (mg/g) (a), TOC (mg/g) (b), DOC (mg/L) (c) in soil before and after irrigation. Black bars indicate surface soil (0–10 cm), and red bars indicate subsurface soil (30–40 cm). Data are presented as mean ± SD (n = 3).
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Figure 3. Before and after irrigation, the soil exhibited varying proportions of four fluorescent constituents (from Comp1 to Comp4).
Figure 3. Before and after irrigation, the soil exhibited varying proportions of four fluorescent constituents (from Comp1 to Comp4).
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Figure 4. Comparison of taxonomic differences in soil samples at the phylum level. (a) Relative abundance (%) of microbial community composition in surface and subsurface soils before and after irrigation; significant differences are marked with asterisks. (b) Top 15 dominant genera with significant differences between surface and subsurface soils after irrigation (ANOVA, p < 0.05). (c) Boxplot of soil microbial gene abundance (reads per million) before and after irrigation.
Figure 4. Comparison of taxonomic differences in soil samples at the phylum level. (a) Relative abundance (%) of microbial community composition in surface and subsurface soils before and after irrigation; significant differences are marked with asterisks. (b) Top 15 dominant genera with significant differences between surface and subsurface soils after irrigation (ANOVA, p < 0.05). (c) Boxplot of soil microbial gene abundance (reads per million) before and after irrigation.
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Figure 5. Relationships between microbial communities, dissolved organic matter (DOM), and environmental parameters. (a) Mantel test analysis of microbial–DOM–parameter correlations. Edge width indicates Mantel’s r value (strength of correlation), and color denotes statistical significance. Pairwise Pearson’s correlation coefficients between parameters are shown in the heatmap (color gradient). (b,c) RDA of soil microbial composition (gene level) before (b) and after (c) irrigation. Arrows represent environmental variables, and their length/direction indicate influence strength. Explained variance (%) of each RDA axis is given in parentheses.
Figure 5. Relationships between microbial communities, dissolved organic matter (DOM), and environmental parameters. (a) Mantel test analysis of microbial–DOM–parameter correlations. Edge width indicates Mantel’s r value (strength of correlation), and color denotes statistical significance. Pairwise Pearson’s correlation coefficients between parameters are shown in the heatmap (color gradient). (b,c) RDA of soil microbial composition (gene level) before (b) and after (c) irrigation. Arrows represent environmental variables, and their length/direction indicate influence strength. Explained variance (%) of each RDA axis is given in parentheses.
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Figure 6. SEM analyzing direct and indirect effects of environmental factors on soil DOC content before (a,b) and after (c,d) irrigation. Negative and positive effects are indicated by red and blue lines, respectively, while those not directly related to soil DOC contents are represented by grey dotted lines.
Figure 6. SEM analyzing direct and indirect effects of environmental factors on soil DOC content before (a,b) and after (c,d) irrigation. Negative and positive effects are indicated by red and blue lines, respectively, while those not directly related to soil DOC contents are represented by grey dotted lines.
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MDPI and ACS Style

Yang, X.; Yu, R.; Yu, G.; Bai, Y.; Li, M.; Liu, Z.; Qu, S.; Miao, P.; Ma, H.; Zhang, T.; et al. Revolutionizing Salinized Farmland: How Salt-Controlled Irrigation Transforms Microbial Diversity and Soil Organic Matter in a Salt-Alkali Soil. Agronomy 2025, 15, 956. https://doi.org/10.3390/agronomy15040956

AMA Style

Yang X, Yu R, Yu G, Bai Y, Li M, Liu Z, Qu S, Miao P, Ma H, Zhang T, et al. Revolutionizing Salinized Farmland: How Salt-Controlled Irrigation Transforms Microbial Diversity and Soil Organic Matter in a Salt-Alkali Soil. Agronomy. 2025; 15(4):956. https://doi.org/10.3390/agronomy15040956

Chicago/Turabian Style

Yang, Xu, Ruihong Yu, Guanglei Yu, Yansong Bai, Muhan Li, Zeyuan Liu, Shen Qu, Ping Miao, Hongli Ma, Tao Zhang, and et al. 2025. "Revolutionizing Salinized Farmland: How Salt-Controlled Irrigation Transforms Microbial Diversity and Soil Organic Matter in a Salt-Alkali Soil" Agronomy 15, no. 4: 956. https://doi.org/10.3390/agronomy15040956

APA Style

Yang, X., Yu, R., Yu, G., Bai, Y., Li, M., Liu, Z., Qu, S., Miao, P., Ma, H., Zhang, T., & Jia, Y. (2025). Revolutionizing Salinized Farmland: How Salt-Controlled Irrigation Transforms Microbial Diversity and Soil Organic Matter in a Salt-Alkali Soil. Agronomy, 15(4), 956. https://doi.org/10.3390/agronomy15040956

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