Soil represents the most substantial carbon store within terrestrial ecosystems, offering vital ecosystem services, including agricultural productivity, water purification, and climate modulation (Anikwe and Ife, 2023). Soil microorganisms are pivotal in upholding soil functionality, thereby sustaining ecosystem services and functional stability, encompassing primary production and nutrient turnover (Banerjee et al., 2018; Bu et al., 2023). Post-industrial human endeavors have precipitated widespread soil degradation, with the world’s agricultural soils forfeiting approximately 133bn tonnes of carbon, potentially impacting ecosystem productivity and atmospheric CO₂ levels (Sanderman et al., 2017). The principal contributors to soil carbon include plant detritus, root secretions, microbial biomass and necromass, alongside carbon fixation by autotrophic microbes (Mason et al., 2023). These autotrophs, as nature’s quintessential biosynthetic entities, are responsible for an estimated 0.6–4.9 Pg C yr⁻¹ of CO₂ fixation, equating to 25% of total anthropogenic CO₂ discharges (Bossio et al., 2020; Zheng Z. C. et al., 2022). Exhibiting remarkable adaptability across various ecosystems, they predominantly engage in the carbon cycle via the Calvin–Benson–Bassham (CBB) pathway, facilitated by the rate-limiting enzyme Rubisco (Li et al., 2020). The cbbL gene encodes Rubisco I’s large subunit, serving as a marker for carbon-fixing microbes and is extensively utilized to evaluate soil autotrophs’ CO₂ fixation capacity (Qin et al., 2021; Bu et al., 2023). However, extant research has chiefly concentrated on the influence of land stewardship and disparate soil regions on autotrophic microbial communities and their CO₂ fixation aptitude (Mukasa Mugerwa and McGee, 2017; Li et al., 2018; Zhou et al., 2019; Bu et al., 2023; Cheng et al., 2023), with a notable dearth of studies examining soil properties’ effects on autotrophic microorganisms and carbon dynamics.

Occupying 36% of China’s arable land, the red soil region is a critical contributor to the nation’s rice production, accounting for over 90% of the output (Huang and Zhao, 2014). Predominantly found in tropical and subtropical zones, these soils are subject to frequent alternations of high temperatures and rainfall, leading to severe erosion and leaching of alkali metal ions. Consequently, this results in elevated concentrations of iron and aluminum oxides, culminating in soil acidification (Xing et al., 2022). The dissolution of stable metal mineral-soil organic matter (SOM) complexes by acid rain further influence of SOM microbial mineralization (Moore et al., 2023). While prior research has concerned the interplay between autotrophic microorganisms, soil attributes, and various factors—including regional, soil type, and agricultural management influences—on these microorganisms’ carbon-fixation capabilities (Chu et al., 2016; Zhou et al., 2019; Wang et al., 2021), the feedback mechanisms and functional behaviors of autotrophic carbon-sequestering microbes in iron- and aluminum-rich acidic red soils remain largely uncharted.

Iron oxides can interact with soil organic carbon (SOC) in multiple ways: they may adsorb, complex with, and co-precipitate SOC, thereby enhancing its stabilization. Conversely, iron-reducing bacteria may facilitate dissimilatory Fe reduction, utilizing SOC and Fe as electron donors and acceptors, respectively, which can accelerate SOC decomposition (Moore et al., 2023; Yao Y. et al., 2023). Moreover, the diversity of vegetation types modulates soil physicochemical properties through processes such as litter decomposition and root exudation, subsequently affecting the composition and diversity of soil protozoa and microbial communities, as well as soil carbon-fixation rates (Bahadori et al., 2021; Bhattacharyya et al., 2022; Spohn et al., 2023; Yao Y. W. et al., 2023; Sun et al., 2024). For instance, Lynn et al. (2017) reported carbon-fixation rates of soil autotrophic microbes in wetland, grassland, and woodland soils to be 85.1, 21.9, and 32.9 mg C m⁻² d⁻¹, respectively. Similarly, Huang et al. (2022) observed notable disparities in carbon-fixation rates between forest and grassland soils in the Loess Plateau. These findings underscore the influence of vegetation types on soil carbon-fixation rates, which are pivotal for projecting the carbon-fixation potential of soil autotrophic microbes in the red soil region. Nonetheless, the underlying mechanisms of this influence remain to be elucidated.

This study seeks to explore the dynamic shifts in CO₂ fixation rates by autotrophic microorganisms within the red soil region and to furnish a theoretical framework for appraising the carbon-fixation potential of microbes across terrestrial ecosystems in the red soil regions of China. We examined the distribution patterns of soil carbon content and the CO₂ fixation. Employing bacterial 16S rRNA high-throughput sequencing, real-time fluorescent quantitative PCR, and stable isotope labeling techniques, we quantified the CO₂ fixation capacities of soil autotrophic microorganisms under different vegetation types. Additionally, we delineated the characteristics of soil autotrophic microbial communities, and identified the key biotic and abiotic determinants influencing carbon fixation.

The surface soil layer of PS and OS exhibited higher SOC, TP, and TN contents compared to other vegetation types, as indicated in Figure 1 and Supplementary Table S1. This disparity may be attributed to the application of inorganic or organic fertilizers, which are rich in nitrogen and phosphorus, on agricultural lands (Hao et al., 2019; Zheng F. J. et al., 2022). Conversely, SOC, DOC, MBC, and TN contents in BFS and CFS were superior to those in WS and OS, which can be ascribed to the enhanced absorption of soil nutrients during plant growth in the initial stages of vegetation restoration in WS (Zhu et al., 2023). As a result, WS exhibited a lower nutrient content relative to other vegetation cover types. The elevated SOC content in BFS and CFS suggests that the input of forest litter may compensate for the nutrient depletion following plant uptake (Pan et al., 2023). However, the humic acid produced by litter decomposition could further reduce soil pH (Rahim et al., 2024). Additionally, the organic acids secreted by coniferous forests, such as Cunninghamia lanceolat, to solubilize and assimilate phosphorus from soil minerals, also contribute to the reduction in soil pH (Pan et al., 2023). The highest SOC content recorded in CFS surface soil (18.11 g kg⁻¹) might be correlated with the shallow root depth of conifers and the retention of easily degradable rhizosphere sediments within the topsoil (Yan et al., 2018; Duan P. P. et al., 2023). In contrast, broadleaf trees, which possess a higher root biomass, allocate more carbon from decomposable roots to deeper soil strata (Panchal et al., 2022), potentially explaining the observed increase in MBC content in the deeper layer (0–50 cm) of BFS compared to CFS (Figure 1c).

Furthermore, iron plays a pivotal role in the fixation of soil organic carbon (Song et al., 2022). The forms of iron influence the accumulation and stability of soil carbon (Duan X. et al., 2023), where the interaction between iron minerals and organic matter may form an iron-soil organic carbon complex, potentially reducing the bioavailability of soil organic carbon to microorganisms (Herndon et al., 2017; Duan X. et al., 2023; Yang et al., 2023). This interaction may lead to enhanced carbon sequestration in deeper soils. Augmenting the sequestration of soil organic carbon not only ameliorates soil quality and fertility but also contributes to a primary strategy for mitigating global climate change (Nazir et al., 2024).

Environmental factors such as temperature, land use, nutrient content, and soil depth are significant determinants of CO₂ fixation by soil autotrophs (Bhattacharyya et al., 2022; Zhang et al., 2023). Liao et al. (2020) investigated the differences in soil carbon fixation rates between chemically and organically fertilized farmlands, attributing the diminished CO₂ fixation rate in chemically fertilized soils to decreased soil pH and increased nutrient concentrations. Additionally, Li et al. (2021) posited that alterations in the soil carbon-to-nitrogen (C/N) ratio significantly affect the rate of soil microbial carbon fixation, likely due to the ratio’s facilitation of microbial growth and metabolism, thus enhancing microbial carbon fixation processes. This study demonstrated that PS could sequester more CO₂, as shown in Supplementary Table S2, while farmland abandonment (wasteland) proved less conducive to soil carbon fixation. PS exhibited a higher rate of carbon fixation compared to other soil types, albeit lower than the CO₂ fixation rate of Tibetan Plateau soil (18–29 mg C kg⁻¹ soil d⁻¹) reported by Zhao et al. (2018). Prior research indicates that paddy field soil harbors a larger fraction of obligate autotrophic bacteria and exhibits greater ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCo) enzyme activity, with its CO₂ fixation rate being four times that of dryland and forest soils (Lynn et al., 2017; Liao et al., 2020). Numerous studies support the critical role of SOC in modulating carbon fixation rates (Bu et al., 2023), with variations in unstable soil organic matter altering the composition of the autotrophic bacterial community—specifically, the balance between obligate and facultative autotrophs—and thereby influencing microbial carbon fixation potential (Badger and Bek, 2008). Moreover, Fe_c and Fe_a are significantly correlated with the Rs and positively associated with SOC (Figure 6). Fe_c is likely to form complexes with simple SOC and organic acids via coordination bonds (Rezapour et al., 2015), while iron ions may act as electron acceptors for extrinsic iron reduction, affecting carbon fixation within autotrophic bacterial communities (Liu et al., 2019). The Spearman correlation heatmap (Figure 8) demonstrated that eight dominant bacterial species containing the cbbL gene were significantly correlated with pH value (p < 0.05), likely due to the sensitivity of soil microorganisms, particularly bacteria, to changes in soil pH (Fierer et al., 2007; Raniolo et al., 2023). Moreover, Fe, Fe_c and Fe_a showed significant correlations with dominant microbial genera (p < 0.05). Spearman correlation analysis also revealed significant correlations of TP with Mycolicibacterium, Sulfitobacter, Thiobacillus, and Thermomonospora. A global meta-analysis demonstrated that soil pH influences bacterial composition more strongly than spatial or climatic factors (biomes). Furthermore, an analysis of 942 soil bacterial genera found that only 0.8% were tolerant of low pH, whereas 21% were tolerant of high pH. Genera with an acidic pH optimum were more prevalent in humid climates (e.g., boreal forests, and tropical forests) (Zhou X. et al., 2024).

Soil microorganisms play a pivotal role in regulating the carbon budget balance at the soil-atmosphere interface through the assimilation of CO₂ and the mineralization and decomposition of soil organic matter (Tao et al., 2023; Ding et al., 2024; Wu et al., 2024; Yang et al., 2024). It is commonly posited by researchers that CO₂ fixation by soil autotrophic microorganisms predominantly occurs at the surface soil-atmosphere interface, leading to a frequent underestimation of the carbon fixation capacity of soil due to the overlooked contribution of deep soil microorganisms (Liao et al., 2023). An observed weak negative correlation between the abundance of the cbbL gene across various soil types and their CO₂ fixation capacity (Figure 4 and Supplementary Table S2) contrasts with findings by Li et al. (2021), who reported a positive correlation between the cbbL gene abundance and carbon fixation rates in the Tibetan Plateau and southern red soils. In contrast, Xiao et al. (2018) found no significant association between CO₂ fixation capabilities and cbbL gene abundance in erosive watershed and agricultural soils. This variance may be ascribed to the differing carbon assimilation potentials and metabolic strategies of autotrophs within the soil, as the abundance of autotrophic bacteria does not consistently correlate with CO₂ assimilation rates (Saini et al., 2011). Multiple linear regression analysis has identified SOC content and the Shannon index as the primary factors explaining variations in microbial carbon fixation rates (Supplementary Table S3). While previous research has indicated that alterations in tillage methods and vegetation succession can diminish microbial community diversity, the contrasting findings regarding community diversity in this study (Supplementary Table S4) may be attributed to the distinct influences exerted by different vegetation types on microbial populations (Zhao et al., 2019; Ramírez et al., 2020; Schmidt et al., 2021).

Obligate and facultative autotrophic bacteria are ubiquitous across all five vegetation types of soil. Certain microbial communities, including Proteobacteria, Actinobacteria, Armatimonadetes, and Planctomycetes, are recognized for their CO₂ fixation capabilities, as documented in previous studies (Vlaeminck et al., 2011; He et al., 2015; Bhattacharyya et al., 2022). The composition of carbon-fixing bacterial communities is known to vary across ecosystems; for instance, Rhodopseudomonas palustris, Bradyrhizobium, and Ralstonia eutropha are identified as predominant carbon fixation genera in wetlands (Lynn et al., 2017), while Sulfuritalea, Ferriphaselus, and Thiohalorhabdus dominate in karst region soils (Wang et al., 2021). The distinctive iron-rich and acidic conditions of the southern red soil region foster a unique carbon fixation bacterial community (Xing et al., 2022). Microbial co-occurrence network analysis has revealed the development and interactions within ecological niches, such as symbiosis, competition, and predation (Barberán et al., 2012; Hu et al., 2022), as depicted in Figure 5. PS microorganisms exhibit the most intricate co-occurrence network, suggesting that ecosystems with higher nutrient content possess enhanced stability and versatility (Wagg et al., 2019). Conversely, in barren ecosystems, oligotrophic species predominate with minimal predation competition, resulting in weaker interaction relationships. The co-occurrence network displays strong positive correlations and few negative correlations, indicating potential cooperation among microbes to adapt to similar niches (Liang et al., 2017). Facultative bacteria such as Bradyrhizobium and Mesorhizobium demonstrate versatile capabilities, thriving autotrophically via the Calvin cycle and utilizing energy from inorganic sources like nitrogen, sulfur compounds, and iron oxides (Selesi et al., 2005; Wang et al., 2021). Thiobacillus species, for example, are known to use organic substrates as electron donors and Fe as electron acceptors, facilitating dissimilatory Fe reduction, which enhances the microbial carbon utilization rate and strengthens the soil carbon reservoir by increasing the microbial carbon fraction content within the entombing effect (Liang et al., 2017; Yao Y. et al., 2023). Additionally, Odoricaulis and Methylibium participate in sulfur oxidation processes, while Bradyrhizobium forms symbiotic relationships with legumes, contributing to soil organic matter enhancement (Wang et al., 2021).

This study highlights the intricate interplay between soil carbon dynamics, microbial activity, and environmental factors in red soil ecosystems. The pronounced vertical variation in soil carbon content, which was more significant than horizontal distribution. The carbon fixation rate distribution revealed that PS exhibited nearly twice the fixation rate of WS, underscoring the important role of vegetation type in influencing carbon fixation. Both the Shannon index and SOC were key factors explaining the variability in soil carbon fixation rates across vegetation types. The results indicate that Fe and pH levels modulate carbon fixation by affecting SOC and the diversity of autotrophic bacterial communities. Although autotrophic carbon fixation contributed only 0.012 to 0.039% of total organic carbon within 40 days, its higher contribution in deeper soil layers emphasizes the importance of autotrophic carbon fixation in soils with low nutrient availability. Further research is needed to elucidate the mechanisms by which iron ions mediate microbial carbon fixation and facilitate the formation of stable carbon pools. These findings also have practical implications for sustainable agriculture and soil management. Targeted interventions, such as iron supplementation or pH regulation, could enhance microbial communities and improve carbon fixation. Additionally, this research supports the development of bio-based technologies, including microbial inoculants, to promote carbon storage and mitigate CO₂ emissions. A comprehensive understanding of microbial processes under different environmental conditions can inform the restoration of degraded red soils and guide climate mitigation strategies through improved soil carbon management. Advanced molecular tools—such as biomarker analysis, metagenomics combined with DNA-stable isotope probing, transcriptomics, and proteomics—will be crucial for identifying the specific microbial processes driving carbon fixation under both controlled and natural conditions. This research can provide a view for understanding the dynamic changes in microbial autotrophic CO₂ fixation rates in the red soil regions of China.