Soil Carbon Sequestration: A Mechanistic Perspective on Limitations and Future Possibilities

Abstract

Climate change, driven by rising atmospheric concentrations of greenhouse gases (GHGs) such as CO₂, poses the most pressing environmental challenges today. Soil carbon (C) sequestration emerges as a crucial strategy to mitigate this issue by capturing atmospheric CO₂ and storing it in soil organic carbon (SOC), thereby reducing GHG levels and enhancing soil health. Although soil is the largest terrestrial C sink, capable of storing between 1500–2400 petagrams (Pg) of C, the practical potential for SOC sequestration through regenerative practices is still widely debated. This review examines the biotic, abiotic, structural, physical, and chemical limitations that constrain soil C sequestration, along with the human dimensions that influence these processes. It explores the role of plant physiology, root architecture, microbial interactions, and environmental factors in determining the efficacy of SOC sequestration. Furthermore, it discusses the potential innovative strategies, including photosynthetic modifications, root system engineering, microbial bioengineering, and the application of advanced materials such as C-capturing minerals, poly-carboxylic compounds, and nanomaterials, to enhance C capture and storage in soils. By providing a comprehensive understanding of these factors, this review aims to inform future research and policy development, offering pathways to optimize soil C sequestration as a viable tool for climate change mitigation.

1. Introduction

Climate change, driven by rising atmospheric concentrations of greenhouse gases (GHGs) such as carbon dioxide (CO₂), is one of the most pressing environmental challenges of our time. According to the Global Carbon Budget 2024, fossil fuel CO₂ emissions are projected to rise by 0.8% in 2024, reaching a record 37.4 Pg CO₂ yr⁻¹. Total CO₂ emissions, which include contributions from land-use changes, are expected to reach 41.6 Pg CO₂ yr⁻¹ in 2024, marking a 2.0% increase over the previous year [1].

Soil carbon (C) sequestration may offer a natural and effective approach in reducing atmospheric CO₂ levels, thereby contributing to climate change mitigation efforts [2]. This process involves capturing atmospheric CO₂ and storing it in the soil as organic C, effectively lowering atmospheric GHG levels and improving soil quality and fertility. Soil is the largest sink of terrestrial C, with an estimated 1500 to 2400 Pg of C, which is more than the amount in terrestrial vegetation (~500–600 Pg C) and the atmosphere (~860 Pg C) combined [1,3,4]. This significant capacity positions soil as a critical component in the global carbon cycle and a key focus for research aimed at mitigating climate change.

The global potential of soil organic C (SOC) sequestration through regenerative practices is estimated at 0.9 ± 0.3 Pg C yr ⁻¹, which may offset one-fourth of the annual increase in atmospheric CO₂ [5]. Small changes in soil C stocks can have large effects on the atmospheric concentration of CO₂. For instance, there are several studies indicating the potential of increasing SOC by 0.4% annually, a target proposed by the “4 per 1000” initiative, which could significantly offset anthropogenic CO₂ emissions [6,7]. However, many studies have also challenged and discussed the practical limitations of achieving such targets [8,9,10]. Conversely, poor soil management can release significant amounts of CO₂, with estimates suggesting cropland soils have lost approximately 50% of their original SOC content globally [3,11].

Although the potential of soil C sequestration is widely recognized, claims about its sequestration efficiency and subsequent environmental impact, especially considering agricultural systems, vary. Some estimates suggest that with appropriate practices, soil C sequestration could contribute to more than 10% of the global mitigation effort required by 2050 [12]. Others caution about the overestimation of the soil’s capacity due to limitations such as saturation effects and reversibility [10]. Investigating the limitations of soil C sequestration is critical for realistic appraisals of its role in climate change mitigation. These limitations encompass varying soil types, land-use practices, climate change impacts, management practices, and the capacity of the soil as a system.

Moreover, issues with the permanence of sequestered C, its measurement, and verification remain challenging [13,14]. Innovative approaches in land management, crop selection, and farming practices tailored to regional conditions are being researched for their potential to enhance C sequestration [15,16,17,18]. The most discussed pathways for soil C sequestration include practices such as the restoration of degraded lands, cover cropping, crop rotation, conservation tillage, organic farming, compost and manure application and biochar application [18,19,20]. These practices contribute to increased soil C levels through improvements in soil structure, increased biomass production, and enhanced microbial activity [17,18]. Yet, the pathway to maximizing soil C sequestration is riddled with complexities, with both well founded and speculative claims surrounding it. A holistic understanding is imperative, from varying soil types, moisture regimes, and microbial interactions, to the broader challenges of biophysiochemical and environmental limitations. These challenges underscore the need for an integrated approach that synergizes scientific research, technological innovation, and policy frameworks. This technical review investigates the mechanistic theories of soil C sequestration, its limitations, and its future possibilities. A comprehensive understanding of SOC sequestration will help us intervene in specific pathways to improve overall sequestration efficiency.

In recognizing the soil’s capacity to function as a C sink, this paper categorizes limitations of soil C sequestration into five main groups: (a) biotic, which includes plant physiology (photosynthesis) and architecture (root architecture), as well as plant–microbe interactions (root exudates, microbial interactions, and C use efficiency); (b) abiotic, which encompasses environmental factors such as temperature, moisture, nutrient availability, and CO₂ concentration; (c) structural and physical characteristics, covering soil characteristics such as texture and aggregate stability; (d) chemical interaction, discussing the kinetics of mineralization and different C pools; and (e) the human dimension, including management, policy, and sociology. This review primarily focuses on the biotic, abiotic, physical, and chemical limitations of soil C sequestration (Figure 1), weaving human management aspects into the discussion where necessary. By doing so, it provides an integrated understanding of the soil ecosystem characteristics that limit C storage capacity while acknowledging the role of the human dimension in optimizing the sequestration processes. Additionally, this study proposes several potential approaches for improving soil C sequestration, summarizing both emerging and conceptual ideas that could inform innovative strategies in this field (Figure 2). The findings of this study are crucial for measuring, monitoring, predicting, and intervening in existing soil C sequestration pathways and can serve as guide for future research and development, particularly in formulating innovative methods to enhance C sequestration.

2. Methodology

This review used a structured literature synthesis approach aimed at providing a mechanistic understanding of soil C sequestration, including its biotic, abiotic, chemical, and physical limitations, and evaluating emerging innovations that could enhance C storage in soil. The methodology comprised four sequential steps: (1) defining thematic categories and keywords, (2) conducting a systematic literature search, (3) applying inclusion and exclusion criteria, and (4) data extraction.

2.1. Search Strategy and Databases

A comprehensive search was conducted across multiple scientific databases, including Web of Science, Scopus, ScienceDirect, SpringerLink, and Google Scholar, covering the period from 1990 to 2025. Keywords were combined using Boolean operators and grouped by major themes such as the following:

• “Soil carbon sequestration” AND (“biotic limitation” OR “microbial necromass” OR “carbon use efficiency”)
• “Abiotic limitation” AND (“temperature sensitivity” OR “moisture variability”)
• “Mineral-associated organic matter” OR “MAOM formation”
• “Biochar” OR “nanomaterials” OR “MOF” AND “carbon storage”
• “Microbial gene editing” OR “synthetic microbiome” AND “soil C”
• “Root architecture” OR “rhizosphere exudation” AND “carbon stabilization”
• “Carbon sequestration” AND “economic feasibility” OR “scalability”
• “Carbon sequestration” AND “agronomic management”
• “Carbon sequestration” AND “biodiversity”

2.2. Inclusion and Exclusion Criteria

Studies were included if they met the following conditions:

○

Presented empirical or modeling-based evidence on soil C mechanisms (biological, chemical, or physical);

○

Addressed field, mesocosm, or laboratory scales with relevance to agricultural soils;

○

Discussed limitations, unresolved contradictions, or novel interventions related to C sequestration;

○

Were peer-reviewed articles, reviews, or meta-analyses published in English.

Studies were excluded if they

○

Lacked mechanistic details or were purely descriptive without quantitative data;

2.3. Data Extraction and Synthesis

Approximately 412 articles were initially retrieved. After screening titles, abstracts, and full texts, 245 publications were selected for final synthesis. These were categorized into five analytical domains:

• Photosynthetic and root-level constraints;
• Microbial contributions and limitations (necromass, respiration, viral shunt);
• Environmental/abiotic factors (temperature, moisture, pH);
• Soil structural and mineralogical influences (texture, aggregation, MAOM);
• Emerging interventions and scalability (engineered materials, microbial engineering).

Within each domain, findings were coded thematically, emphasizing contradictory results, quantitative benchmarks, and evidence gaps. A limitations–solutions matrix was constructed and used to derive research priorities based on mechanistic tractability and scalability potential.

3. Limitations

3.1. Biotic Limitations

The biotic domain comprises the source–sink continuum responsible for generating, translocating, and biologically transforming carbon entering the soil system. In mechanistic order it evaluates (i) the photosynthetic source strength that fixes atmospheric CO₂ and establishes the gross carbon budget; (ii) root architectural characteristics that control the depth-resolved allocation of assimilates; (iii) the chemodiversity of root tissues and exudates that mediates rhizosphere priming, aggregate formation, and precursor chemistry for mineral-associated organic carbon (MAOC); and (iv) microbial processing efficiencies—including cellular carbon-use efficiency, viral lysis, and predator–prey regulation—that ultimately partition incoming carbon between respiratory loss and the necromass pool. Together, these biotic controls define the upper theoretical limit (biological ceiling) of soil carbon sequestration against which subsequent abiotic and physicochemical constraints must be interpreted.

3.1.1. Photosynthetic Capacity and C Allocation

Photosynthesis sets the upper limit for soil C sequestration by controlling the principal C input into the soil [21]. The efficiency of C fixation varies by species and is influenced by CO₂ concentration, light intensity, temperature, water availability, and nutrient status. Rubisco, critical for CO₂ fixation, is highly sensitive to the CO₂/O₂ ratio [22]. Elevated atmospheric CO₂ has boosted net land C sinks from 1.2 ± 0.5 Pg C yr⁻¹ in the 1960s to 3.1 ± 0.6 Pg C yr⁻¹ in the 2010s [23]. However, enhanced biomass under high CO₂ can stimulate microbial priming, causing variable SOC responses [24]. A meta-analysis of 108 eCO₂ experiments found that the SOC stock decreased when plant biomass increased substantially, though grasslands showed an 8 ± 2% increase, and forests remained unchanged (0 ± 2%) [25]. The frequency of negative responses rises sharply on P-limited soils, questioning the universality of eCO₂ mitigation potential [26] and what multi-element threshold could flip eCO₂ from a sink to a source.

Different plant species modulate soil C storage through unique allocation patterns (roots vs. shoots) and tissue turnover. Woody biomass and deep root systems generally form more stable C pools [27]. Environmental stressors such as drought and nutrient scarcity reduce plant growth, thus lowering soil C inputs. Tools for estimating sequestration often focus on aboveground biomass and rarely capture belowground C contributions accurately, complicating species rankings with respect to soil C sequestration potential. Native plants with deeper roots generally yield higher long-term C storage [28]. Photosynthetic efficiency (<4.5% of solar energy for C3 plants and ~6% for C4 plants) is limited by incomplete light interception, photorespiration, and Rubisco’s oxygenation activity [29,30,31]. Plant autotrophic respiration releases approximately 50% of the CO₂ fixed by photosynthesis back to the atmosphere [32] (Figure 1). Nutrient constraints (especially nitrogen and phosphorus) further complicate biomass and root carbon allocation [33,34]. Improving our understanding of source–sink dynamics under changing CO₂ concentration, temperature, and precipitation is key to enhancing soil C sequestration.

3.1.2. Root Architecture

Root traits—branching intensity, depth, length density, diameter, and clustering—strongly influence soil aggregation and SOM stabilization [35]. Fine roots (<0.2 mm) promote 1000–2000 μm macroaggregates, while slightly thicker roots (0.2–1 mm) create larger macroaggregates (>2000 μm) [36]. Grasses with extensive fibrous roots excel at forming macroaggregates in topsoil, while variable root diameters can have mixed effects on microaggregate stabilization [35,37]. The effectiveness of root size classes also depends on soil type and existing SOC levels [38]. Deep-rooted species deposit root-derived C at greater depths, aiding stable organo–mineral associations on under-saturated mineral surfaces. Simulation studies show that certain maize root architectures can enhance drought tolerance, biomass accumulation, and deeper C deposition [39]. Roots contain ~45.6% carbon and contribute 30–40% of SOC, often with multi-millennial turnover in deep soil [24,40,41]. Adopting deep-rooted crops can add ~1 Pg C yr⁻¹ globally [42,43] and improve microbial stabilization—especially in N₂-fixing species that produce more amino acids, boosting microbial biomass and necromass formation [42]. Root-derived C inputs range from 0.1 to 2.8 t C ha⁻¹ yr⁻¹, with ectomycorrhizal associations generally storing ~70% more soil C than arbuscular mycorrhizal systems [43,44,45]. However, rhizosphere priming may destabilize SOC, with studies reporting a 380% increase to a 50% reduction in decomposition rates [24,46,47]. Approximately one-third of total SOC mineralization in temperate forests is root-driven [48].

3.1.3. Plant-Root Chemical Composition, Rhizodeposition, and Plant–Microbe Interactions

Root chemical composition—proportions of cellulose, hemicellulose, lignin, tannins, waxes, suberin, and cutin—governs decomposition rates and SOC stability [49,50,51]. Lignin resists degradation but is not universally inert; bacteria (Streptomyces, Rhodococcus, and Pseudomonas) and fungi can metabolize it [52]. Aliphatic compounds such as suberin and cutin, rich in long-chain fatty acids, often form more recalcitrant C pools [50,53]. This necessitates further evaluation of compound-specific decay rates and under simultaneous N:P enrichment and different climatic conditions.

Root tissues contribute up to 9% to mineral-associated organic carbon (MAOC) formation and 19% to particulate organic carbon (POC) [53]. Rhizodeposition—the release of organic/inorganic exudates—can account for 3–5% of plant fixed C and influences up to 46% of stable belowground C [53,54]. While rhizodeposits stimulate aggregation, microbial growth, and MAOC formation, they can also trigger SOC priming [55]. Allocation patterns vary by plant type (annual vs. perennial) and developmental stage [54,56], yet largely unexplored. Isotope-tracer incubations show certain root exudate chemistries stimulate priming that offsets up to >30% of the sequestered C [57]. This raises a challenge: can breeding deep-root ideotypes avoid co-selecting high-priming exudate profiles?

3.1.4. Microorganisms

Soil microorganisms play a dual function in the carbon cycle: they mineralize SOC to CO₂ and form a stable microbial necromass that can become physically or chemically protected in the mineral matrix [58]. Microbial necromass refers to the non-living structural remains of the cells—peptidoglycan, chitin, amino-sugars, and intracellular macromolecules—that persist after lysis. Necromass are quantified with biomarkers that are absent or rare in plant tissues, such as amino sugars muramic acid (bacterial) and glucosamine/galactosamine (fungal-derived); their concentration in acid-hydrolyzed soil extracts, multiplied by empirically derived C-conversion factors, yields an estimate of necromass-C [59]. Emerging methods, including compound specific ¹³C/¹⁵N isotopic analyses, amino acid profiling, and NanoSIMS imaging, also allow necromass assessment [60]. Using amino-sugar proxies, necromass is estimated to constitute 50–80% of total SOC, with a land-use gradient of ~51% in cropland, 47% in grassland, and 35% in forests within the upper 20 cm [61,62,63]. Fungal necromass is often more resistant to decay than bacterial necromass because of its melanin- and chitin-rich cell walls, which are more stable against microbial degradation [64].

Soil viruses can redirect carbon cycle via the viral shunt, i.e., viral lysate can simultaneously prime decomposition and add fresh necromass. Recent studies have shown that bacteriophage activity can enhance bacterial turnover, generating necromass but also potentially increasing CO₂ emission [65,66]. Protist and nematode grazing can further modulate the size and stoichiometry of the microbial community, influencing carbon use efficiency (CUE) and substrate production. Carbon use efficiency (CUE)—the fraction of substrate C retained in new microbial biomass—responds to substrate reduction state and nutrient stoichiometry. High-energy, N-rich inputs can raise potential CUE, but copiotrophic taxa frequently offset this advantage through higher respiratory costs [59,67,68]. In addition, biological soil crust (biocrusts)—complex communities of cyanobacteria, algae, lichens, mosses, and fungi—also play a vital role in SOC sequestration, especially in arid, semi-arid, and polar ecosystems [69]. Aerobic vs. anaerobic conditions also affect C turnover: in permanently waterlogged soils, mineralization is 60–95% slower due to limited oxidative enzyme activity [70]. However, quantitative understanding of microbial turnover, including virus-mediated C balances across depth and soil types, predator-driven shifts in CUE and necromass especially in deep soil, necromass persistence under shifting aerobic/anaerobic conditions, threshold moisture/redox conditions that flip necromass from stable to labile pools, remains a knowledge gap. (See

Table 1. Recent evidence on biotic limitations to soil organic carbon (SOC) sequestration and challenges.

Processes	Current Understanding	Contradictions	SOC Implications	Knowledge Gaps	References
Photosynthetic C supply	Net land sink driven mainly by rising CO2: 1.2 ± 0.2 Pg C yr−1 (1960–1969) → 3.5 ± 0.8 Pg C yr−1 (2011–2020).	Extreme heat/drought in 2023 drove the land sink near zero, indicating climatic overrides on CO2-fertilization.	Confirms that additional plant C input is available for sequestration but is increasingly counter balanced by warming feedback	Understanding partitioning of above- and belowground C allocation at global scale in changing plant productivity under elevated CO2. Lack of photo–respiration tradeoffs and nutrient feedback to MRV models and tools.	[71,72]
eCO2 effects on plant–soil allocation	Meta-analysis of 108 eCO2 experiments: SOC rose 8 ± 2% in grasslands, remained 0 ± 2% in forests; greatest plant biomass gains frequently reduced SOC via nutrient mining.	Five-year mountain beech–spruce FACE found no detectable SOC change despite eCO2.	Demonstrates allocation trade-off; nutrient constraints limit conversion of extra NPP to stable SOC	Evaluation of threshold points where nutrient addition flips the trade-off is necessary.	[25,73]
Root architecture (“Steep, Cheap & Deep” maize)	Roots contain ~45.6% carbon and contribute 30–40% of SOC, often with multi-millennial turnover in deep soil. Root-derived C inputs range from 0.1 to 2.8 t C ha−1 yr−1.	13CO2 tracing shows root activity after thaw increased SOC loss by 31% via priming of deep pools.	Deep inputs target sub-saturated mineral surfaces → higher MAOC potential	Mechanistic drivers of bimodal rooting (species traits vs. soil constraints) remain unresolved. Lack of in situ measurements of how deep-root inputs translate into MAOC vs. primed losses. Standardized protocols for sampling > 1 m depths are still scarce, impeding trait-based breeding and model calibration.	[74,75,76]
Belowground C allocation fraction	Belowground NPP 24.7 Pg C yr−1 = 46% of terrestrial C fixation.	Exudate additions raised mineralization and DOC, converting “resistant” SOC into CO2 (meta-analysis).	Large flux highlights leverage of root/rhizodeposition pathways	Chemical fate of this flux (POC vs. MAOC) remains poorly constrained.	[57,77]
Root chemistry and rhizodeposition	Rhizodeposits supply up to ~5% of GPP; contribute 10–40% of MAOC depending on soil mineralogy.	High-N litter trials increase mineralization of lignin, reducing its assumed recalcitrance.	Confirms chemical gateway to stable pools	Need compound-specific turnover rates under drought, high temperature, and high CO2.	[78,79]
Microbial biomass vs. necromass	Amino-sugar proxies show 50–80% of SOC is necromass; cropland 51%, grassland 47%, forest 35% (0–20 cm).	Isotopically labelled necromass became mineral-associated in 3 days, but 50% respired within 8 months under intensive management.	Validates necromass as dominant stable pool	Quantitative understanding of microbial turnover, including virus-mediated C balances across depth and soil types, predator-driven shifts in CUE and necromass, especially in deep soil and under shifting aerobic/anaerobic conditions.	[64,80]
Soil viral shunt	Viral addition raised cumulative respiration by 30% over 41 d within one soil and altered DOC/N coupling.	Mesocosms with elevated virus abundance reduced respiration by 3–6% via a kill-the-host strategy.	Viral-induced lysis can both liberate DOC (priming) and add necromass	Quantify net C balance across soil types, moisture regimes and agronomic managements.	[81,82]
Mycorrhizal type	Forest plots with high ectomycorrhizal (EcM) dominance stored significantly more soil C (model and inventory of >4000 plots).	Fertility-gradient study shows EcM fungi either accelerate or slow decomposition depending on N/P status.	Points to mycorrhizal trait filtering as a management lever	Determine absolute % increase and mechanisms (enzyme repression vs. litter quality) in non-boreal biomes.	[83,84]

).

3.2. Abiotic Limitations

Abiotic parameters impose the environmental boundary conditions that modulate every biotic pathway described in Section 3.1. Specifically, Section 3.2 quantifies how temperature, hydrological status, nutrient stoichiometry, and atmospheric CO₂ concentration regulate (i) enzyme kinetics of SOM decomposition, (ii) moisture-controlled oxygen diffusion and redox chemistry, (iii) elemental coupling that feeds back on microbial carbon-use efficiency, and (iv) the progressive saturation of reactive mineral surfaces. By constraining reaction rates, sorption equilibria, and microbial energetics, these factors determine the realized fraction of the biotic sequestration potential and govern the stability of stored carbon under future climate trajectories.

3.2.1. Temperature and Moisture

The temperature sensitivity of SOC decomposition varies with soil texture, mineralogy, and moisture (87–90%) [85,86,87]. Protected C (MAOC) is less temperature-sensitive, particularly in fine-textured soils. An increase of 10 °C can elevate the decomposition of unprotected C by 28% compared to protected C. This effect is amplified in cooler regions (<15 °C) [86]. Global warming has reduced particulate organic matter (POM) stocks by ~33% at soil depths of 20–90 cm [88]. Soil moisture accounts for ~90% of inter-annual variability in global land C uptake [89]. In humid regions, higher root abundance and greater interaction with minerals enhance MAOC formation; in arid areas, decomposition is often surface-limited [90]. Topography modulates moisture effects on SOC decomposition: shallow xeric soils (dry/low moisture content) show maximal temperature sensitivity at intermediate moisture, while deeper mesic soils (moderate to well-balanced moisture content) exhibit rising sensitivity with increasing moisture [91]. These complexities highlight the need to consider both temperature and moisture as one integrated unit in managing soil C stocks.

3.2.2. Nutrients

Essential nutrients (N, P, K, Mo) strongly affect soil C sequestration by regulating plant productivity and microbial processes. Nitrogen fertilization can elevate new C retention by ~30.3% and total C by ~6.1% [92], enhancing MAOC and POC formation through improved plant inputs and microbial CUE [93,94,95]. N enrichment can also stimulate hydrolytic enzymes and suppress oxidative enzymes, increasing recalcitrant C by ~22.7%. However, meeting large-scale sequestration goals with added N is unrealistic [96], and high N inputs may induce SOC priming and water-quality issues [97,98]. Phosphorus limits plant and microbial growth, particularly in highly weathered soils [99]. While P fertilization can boost biomass, overuse may alter soil pH, harm beneficial mycorrhizal fungi, and increase SOC mineralization [100,101]. Potassium indirectly supports C sequestration by maintaining plant health and photosynthetic capacity [102]. Molybdenum deficiencies reduce biological N fixation and microbial enzyme activities, limiting SOC storage [103,104,105]. Optimizing nutrient availability is therefore essential, but large-scale fertilization poses environmental and economic challenges.

3.3. Structural and Physical Soil Characteristics

Soil C sequestration is constrained by the finite capacity of mineral surfaces to stabilize organic matter [106]. Clay minerals and Fe/Al oxides form organo–mineral complexes that protect SOC from microbial decomposition [107]. However, these reactive surfaces can become saturated, diminishing the marginal gains of additional C inputs [108,109,110]. Some studies argue that mineral surfaces remain partly unoccupied, and thus there is potential for additional sequestration [111,112], but actual limits vary by mineralogy and management. Soil C saturation is determined by evaluating the relationship between MAOC, which constitutes the more stable fraction of SOC, and silt-plus-clay content as proxies for reactive mineral surfaces. Key influencing factors include soil texture, mineral composition, climate, land use, and management practices. Cropland soils often show a ~50% saturation deficit in fine fractions, suggesting unrealized C sequestration capacity under conventional practices [113,114]. Mineral-associated organic carbon is currently at 42% of its global saturation capacity in top soils and 21% in subsoils [115]. Shifting management may redefine this equilibrium [116]. Soil aggregates offer physical protection for SOC. Protective capacity is often organized with a soil aggregate hierarchy. Microaggregates (<250 μm) can trap SOC for decades to centuries, whereas macroaggregates (>250 μm) provide shorter-term protection [117,118,119]. However, microbial extracellular enzymes can still access aggregate-protected C [120]. Changes in land use or management, especially intensive tillage, may disrupt aggregates, releasing sequestered C. The aggregate system is dynamic, subject to constant turnover of formation and breakdown. The temporal lag between the initial carbon input and its final stabilization thus needs to be measured and verified, as short-term increases in SOC may reflect accumulation in the transient macroaggregate pool rather than true long-term sequestration.

3.4. Chemical Limitations

Physical protection within aggregates provides a crucial shield; however, most stable carbon storage in mineral soil is achieved through chemical stabilization. SOC comprises pools with differing turnover times: labile POC decomposes within months to years, while MAOC can persist for decades or centuries [121,122]. Although MAOC is considered as most stable C pools, emerging evidence suggests large MAOC pools remain susceptible to relatively rapid decomposition by microbial exogenous enzymes [122]. While microbial roles are well recognized in MAOC formation, the rates and efficiencies of microbial C conversion to MAOC across diverse soil types, climatic conditions, and management regimes are still a knowledge gap. Further, the vulnerability of existing MAOC stocks to destabilization under global warming, different moisture conditions, and land-use change needs more research. Organo–mineral associations via cationic bridging and chelation, especially with Fe/Al oxides, Ca, and Mg, is critical for longer-term SOC stabilization [123,124,125,126]. Calcium, in particular, is important for both alkaline and acidic soils [127]. In addition, stoichiometric controls on organic matter, especially the balance of carbon, nitrogen, and phosphorus (C: N:P), are key to SOC dynamics. While microbial biomass typically exhibits a relatively constrained C: N:P ratio (often around 60:7:1), soil organic matter with higher ratios—commonly when the C: N exceeds about 30:1 and the C:P surpasses roughly 200:1—tends to trigger nutrient mining of N and P by microbes, resulting in lower CUE and higher SOM mineralization, especially from older, stable pools [128]. Microbial dissimilatory iron reduction can mobilize dissolved organic carbon and Fe(II), linking iron redox cycling to SOC mineralization [129,130]. Soil pH and redox potential modulate OM solubility, nutrient availability, and decomposition rates [131,132]. SOC mineralization follows first-order kinetics, but as much as 90% of added OM may be rapidly mineralized to CO₂, limiting sequestration efficiency. Over time, soils can approach “sink saturation,” requiring impractically large organic inputs to further increase SOC stocks [133]. Consequently, while soil C sequestration remains a key climate mitigation pathway, its effectiveness is constrained by biological, physicochemical, and management factors that must be strategically addressed. (See

Table 2. Synthesis of abiotic (temperature, moisture, nutrient), structural, and chemical constraints on soil carbon (SOC) sequestration, including contradictory findings and knowledge gaps.

Processes	Current Understanding	Contradictory Findings	SOC Implication	Knowledge Gaps	References
Temperature and moisture	SOC responds negatively to increasing temperature, with a coefficient of 0.24. Earth system model analysis shows that frequent droughts can reduce the current land carbon sink by 2–3 Gt C per year. Unprotected POC is more sensitive than protected carbon; >28% higher loss with 10 °C increase in temperature.	Field warming in temperate forests often yields Q10 < 1.5 with no net SOC loss, likely due to substrate depletion.	Temperature sensitivity is ecosystem dependent, lab-predictions can overestimate field losses.	Precise moisture thresholds at which MAOC flips from sink to source and representation of VOC-C pathways released during drought–rewet pulses.	[134,135]
Nitrogen fertilization	Meta-analysis of long-term N fertilization found it increased SOC stocks by a mean of 4–7%.	Nitrogen addition can increase SOC loss, and there is no significant impact on SOC content.	Nutrient additions can redistribute carbon between soil pools (from POC to MAOC) rather than uniformly increasing the total SOC stock. The net outcome depends on the balance of production and decomposition.	Defining multi-element thresholds (N, P, and micronutrients) that maximize net SOC sequestration without causing nutrient saturation, priming of old carbon loss, or eutrophication.	[136,137]
Textural limitation (soil saturation)	Globally, subsoils (30–100 cm) in croplands are estimated to be, on average, at only 46% of their C saturation capacity, indicating a large potential sink.	In soils rich in reactive minerals such as Andisols, SOC can reach an apparent saturation point where additional carbon inputs do not lead to further SOC accrual, implying mineralogy-specific ceilings on storage.	The potential for SOC sequestration varies strongly with soil mineralogy. Universal “carbon deficit” models fail to capture these mineral-specific limitations, especially in volcanic and oxide-rich soils.	The specific chemical or physical mechanisms that drive the early onset of carbon saturation in soils rich in iron and aluminum oxides.	[138]
Chemical pools of carbon (MAOC)	Radiocarbon (14C) dating of bulk MAOC often reveals mean residence times of hundreds to thousands of years, suggesting long-term stability.	Despite its old average age, a significant fraction of MAOC can be rapidly mineralized. Studies using enzyme additions have shown that newer, more labile MAOC can be decomposed within years, especially under nutrient enrichment.	The persistence of MAOC is controlled more by its physical and chemical accessibility to microbes and enzymes rather than its intrinsic chemical structure or age. This stability can be modulated by nutrient status.	Partitioning the loss of MAOC into distinct pathways (enzyme-driven decomposition vs. physical desorption from minerals) under the combined pressures of global warming and fertilization.	[139]

POC—particulate organic carbon; MAOC—mineral-associated organic carbon.

).

4. Possibilities and Opportunities

4.1. Photosynthetic Modification

Enhancing CO₂ sequestration through photosynthetic modifications offers several promising strategies, including optimizing C fixation pathways, improving light utilization, modifying photoprotection mechanisms, delaying senescence, and refining canopy architecture [140,141]. One approach is to increase CO₂ availability in C3 and C4 plants by introducing CO₂ channels and bicarbonate transporters into their photosynthetic cells [142]. Another strategy involves reducing photorespiration by sequestering Rubisco in compartments with elevated CO₂ concentrations, a method that has shown promise in rice [143,144]. Maximizing photosynthesis also requires effectively utilizing high midday light intensities while protecting plants from photo-oxidation. Enhancing photoprotection mechanisms can strike a balance between preventing damage and maximizing light use, thereby increasing productivity [141,145]. Delaying senescence, through genetic modifications such as manipulating cytokinin synthesis or suppressing ethylene biosynthesis, can extend the photosynthetic period, as seen in tobacco and tomatoes [146,147]. Further improvements include accelerating light adaptation, for instance by speeding up the interconversion of violaxanthin and zeaxanthin in the xanthophyll cycle, and increasing photosystem II subunits, both of which enhance photosynthesis [30]. Expanding the range of wavelengths absorbed by chloroplast light-harvesting antennae, which currently absorb only 400–700 nm (less than 50% of solar energy), offers another opportunity for improvement [148]. Simulation models and an AI neural net framework can help explore and optimize these enhancements [30,149]. Dynamic systems models of canopy photosynthesis can optimize canopy architecture and physiology—such as leaf morphology, leaf angle, photosystem antenna size, and Rubisco kinetics—to maximize CO₂ uptake [150]. These models can also guide breeding programs by identifying optimal allele combinations to achieve maximum canopy photosynthetic rates [150]. The “smart canopy” concept enhances light harvesting and biomass production by designing canopies with more vertical upper leaves, high catalytic Rubisco in the upper canopy, and high specificity Rubisco in the lower canopy. The upper canopy should have fewer antenna pigments per photosystem, while the lower canopy should have larger antennae serving fewer reaction centers [141]. These diverse strategies, from genetic engineering to optimizing canopy architecture, present significant opportunities for enhancing CO₂ sequestration.

4.2. Modification of Root Systems and Rhizodeposition

Enhancing belowground C sequestration through root system modification and rhizodeposition presents a promising approach to increasing SOC storage. Recent advances in genome-driven breeding and marker-assisted selection have focused on increasing root biomass, optimizing root architecture, and prolonging root lifespan and C outputs. For example, expressing the Deeper Rooting 1 (DRO1) gene in rice has been shown to double the root depth and biomass [151,152], significantly contributing to C sequestration in deeper soil layers. In maize and wheat, enhancing the development of multiseriate cortical sclerenchyma increases root tensile strength, promoting deeper rooting and greater shoot biomass in compacted soils [153,154]. Modifications such as increasing root diameter and enhancing root hair development also play critical roles. Larger diameter roots (>5 mm) decompose 4.6 times slower than smaller roots, resulting in longer C storage in soils [155]. Additionally, roots with more extensive root hairs can enhance soil aggregate stability, which helps protect organic compounds from decomposition by reducing their accessibility to microbial activity in the rhizosphere [156]. Deep-rooted crops such as lucerne and Kernza have demonstrated that C inputs to deeper soil layers can result in greater C stabilization, particularly since rhizodeposition is most concentrated in the topsoil and diminishes with depth [157]. Elevated CO₂ levels have been shown to alter root morphology and enhance belowground carbon sequestration. Meta-analyses reveal increases in root length, diameter, total root mass (+28.8%), and fine root mass (+27.7%) under elevated CO₂ conditions, along with a reduction in the proportion of roots in the topsoil (−8.4%) [158]. These findings suggest that rising CO₂ levels may promote deeper root systems, potentially reducing the risk of C loss from topsoil disturbances, but it is a double edge sword, as increasing CO₂ can increase global warming. Rhizodeposition, the release of organic compounds from roots, plays a crucial role in SOC stabilization. Innovative strategies, including enhancing the secretion of organic acids such as succinic acid and amino acids such as aspartic acid, can significantly increase net MAOM carbon accumulation by reducing the priming effect [159]. Utilizing stable ¹³C tracer techniques to measure root exudate-derived SOC can offer insights into the pathways and quality of C accumulation in the rhizosphere [160]. Specific genomic editing and breeding approaches to release compounds such as suberin as root exudates can potentially improve the soil C sequestration [161]. These strategies underscore the importance of modifying root systems and rhizodeposition processes to enhance SOC sequestration, contributing to climate change mitigation and soil health improvement [162]. By targeting breeding and management practices that optimize root traits and root retention in soil, the potential for C sequestration in agricultural systems can be significantly enhanced.

4.3. C-Capturing Minerals

The development and application of C-capturing minerals offers a cutting-edge approach to enhancing soil C sequestration, especially where geological sequestration is not viable. These minerals are designed or modified to react with atmospheric CO₂, converting it into stable mineral forms that can be permanently stored in the soil. This process, known as mineral carbonation, provides a promising strategy for sequestering C in a form that is resistant to decomposition and re-release into the atmosphere [163,164]. Mineral carbonation involves the reaction of CO₂ with naturally occurring or engineered minerals, such as silicates and oxides, to form stable carbonate compounds. While this process occurs naturally through the weathering of silicate rocks, it can be significantly accelerated through engineered interventions. For example, silicate minerals such as olivine ((Mg,Fe)₂SiO₄) can capture and convert CO₂ into stable carbonates such as magnesium carbonate, which can remain in the soil for millennia. Forsterite, a magnesium-rich form of olivine, is particularly effective, with C sequestration efficiencies reaching up to 1.25 g CO₂ g⁻¹ of forsterite as the upper theoretical limit [165,166]. Recent research has focused on developing engineered silicate minerals optimized for faster and more efficient CO₂ capture. These tailored minerals maximize surface area and reactivity, enhancing their interaction with CO₂ and accelerating the formation of stable carbonates [167]. Studies have demonstrated that certain engineered minerals can increase the rate of CO₂ capture by up to 30 times compared to natural processes, making them highly effective for large-scale C sequestration efforts [168]. Integrating C-capturing minerals into soil management practices holds significant potential for enhancing soil carbon storage. For instance, applying finely ground silicate minerals to agricultural soils can facilitate the capture of atmospheric CO₂ directly in the field, while simultaneously improving soil fertility by releasing essential nutrients such as magnesium (Mg) and calcium (Ca) as the minerals weather [169]. However, Mn plays a complex role in soil carbon dynamics. It can enhance the recovery of litter C in MAOM, contributing to C stabilization in soil [170], whereas other studies suggest that it may also accelerate the decomposition of SOM, leading to increased CO₂ emissions. This dual role underscores the need for a deeper understanding of the underlying mechanisms for their impact on soil carbon processes.

Advancements in AI technologies have further improved the design and optimization of new minerals for CO₂ sequestration. AI algorithms can model interactions between engineered minerals and CO₂, leading to the creation of materials that are more efficient and cost-effective in capturing and storing carbon [171,172]. Researchers at the U.S. Department of Energy’s Argonne National Laboratory have utilized generative AI models to develop metal–organic frameworks (MOFs) with CO₂ sequestration capacities exceeding 2 mmol g⁻¹, surpassing 96.9% of structures in the hypothetical MOF dataset [173]. However, while the potential of C-capturing minerals is considerable, their large-scale application requires careful consideration of environmental impacts and cost-effectiveness. Sustainable sourcing and processing of these minerals are crucial to avoiding negative environmental consequences, and the economic feasibility of deploying these technologies on a broad scale remains a key factor in their widespread adoption.

4.4. Synthetic Poly-Carboxylic Compounds

The development of poly-carboxylic compounds to mimic or enhance the functions of naturally occurring organic acids, such as citric and tartaric acid, which have a strong affinity for binding with SOM, can significantly improve soil C sequestration. Poly-carboxylic acids, which contain multiple carboxyl groups (-COOH), interact strongly with soil minerals, particularly iron and aluminum oxides [174]. These interactions promote the formation of stable complexes between the poly-carboxylic acids and OM, effectively trapping C and making it less vulnerable to microbial degradation [175,176]. Recent research has focused on synthesizing biodegradable poly-carboxylic compounds tailored to specific soil types and environmental conditions to maximize their effectiveness in C sequestration [177]. These compounds can be integrated into soil management practices, particularly in systems with low OM content or degraded soils, where C retention is a priority. Additionally, they can be combined with other soil treatments, such as biochar or mineral additives, to further enhance the stability of SOC [178]. However, their environmental impacts and economic feasibility must be carefully evaluated to ensure sustainable and cost-effective large-scale applications, which will be critical to their adoption in soil management practices.

4.5. Phytolith Formation

Phytoliths are microscopic, amorphous silica deposits formed within plant tissues by the uptake and polymerization of soluble silicic acid from soil, often referred to as “plant stones” due to their durability and persistence, long after plant decay, thereby playing a critical role in long-term C sequestration. During their formation, a fraction of organic C—typically between 0.2% and 5.8%—becomes occluded within the silica matrix to form phytolith-occluded carbon (PhytOC), which is highly resistant to microbial decomposition, with turnover times estimated to range from 433 to 1018 years [179]. In tropical and subtropical regions, PhytOC accumulation rates have been reported at 7.2–8.8 kg ha⁻¹ yr⁻¹, contributing up to 37% of the global mean long-term soil organic carbon accumulation rate [180]. However, the magnitude of sequestration varies among species and is influenced by factors such as soil pH, moisture, and other environmental conditions. Agronomic practices, including silicon fertilizer amendments and the incorporation of silicon-rich rice husk biochar, have been shown to increase phytolith formation in crops such as rice and oats by three- to fivefold [181,182,183] and contribute to the terrestrial carbon pool [184]. Additionally, the selection and cultivation of high-phytolith species such as bamboo and sugarcane, together with breeding high-biomass cultivars with enhanced silicon uptake—through the identification and manipulation of key genes, such as Lsi1 and Lsi2, involved in silicon transport and the phytolith formation pathway can further improve SOC stocks. It is important, however, to balance these approaches because excessive phytolith production may reduce overall biomass and nutrient uptake, and long-term silicon fertilization can alter soil pH and microbial communities.

4.6. Responsive Hydrogels

Responsive hydrogels, particularly superabsorbent polymers (SAPs), are designed to absorb large amounts of water and nutrients and release them gradually in response to specific stimuli such as moisture, pH, or CO₂ levels [185]. For instance, CO₂—responsive hydrogels can increase their hydrophilicity under acidic conditions, promoting greater C sequestration in soils with fluctuating pH levels [186]. Research by Shaikh et al. (2020) demonstrated that integrating hydrogels into soil management practices in semi-arid regions significantly increased water retention and reduced nitrogen losses, suggesting potential for enhanced C sequestration [187]. Additionally, in soilless farming, or film farming, hydrogel technology can reduce water consumption by up to 90% while boosting crop productivity. A field study in Dubai reported that this approach increased crop yield and biomass quality by 30–50%, saved water resources by 1.3–2 times, and protected the topsoil from pathogens and salinization, thereby extending the service life of soil conditioners by 2–4 times [188]. Similar results have been observed in Saudi Arabia [189]. However, traditional hydrogels have drawbacks such as slow degradation and low energy efficiency, which can raise environmental concerns. To address these issues, optimizing the physical and chemical interactions between hydrogels and soil particles can create a more stable environment for carbon storage. The development and use of biodegradable hydrogels ensure they break down over time without leaving harmful residues in the soil [190]. Additionally, solid sorbent-based carbon capture systems, such as sustainable carbon-capture hydrogels (SCCH), which have demonstrated excellent CO₂ uptake of 3.6 mmol g⁻¹ (400 ppm) at room temperature [191], are essential for maintaining soil health and preventing long-term environmental impacts.

4.7. Nanomaterials

Nanomaterials, including nanoporous materials, nano-hollow structures, nanocomposites, and nanocrystalline particles, represent a promising frontier in enhancing soil C sequestration. By interacting with SOM at the molecular level, these materials can significantly improve the stability and retention of C in soils [192]. Their high surface area, reactive sorption capacity, fast reaction rates, thermal stability, durability, and strong adsorption capabilities enable them to bind organic C compounds more effectively than traditional materials such as activated carbon, zeolites, and mesoporous silica [193]. Although there are mixed responses regarding the impact of nanomaterials on soil microbial populations and activity, optimizing their dosage could make them a powerful tool for capturing and storing CO₂. The use of nanomaterials in soil can lead to the formation of stable C-mineral complexes, macro-aggregates, and micro-aggregates that are resistant to microbial degradation. For instance, graphene-based materials can improve the soil aggregation [194] and the stability of SOM by creating physical barriers that protect organic C from microbial attack, while C nanotubes, as nano-membrane materials, have been found to boost the adsorption capacity of CO₂ [193]. Nano-sized CaCO₃-derived CaO is a promising material for CO₂ absorption. Similarly, nano-magnesium oxide has shown potential to enhance soil structure by increasing total porosity, reducing soil density, and improving the mean weight diameter (MWD) of soil aggregates [195]. Nano-silica has also shown potential to stabilize soil aggregates [196] and increase the coefficient of permeability and the compression index. Despite their potential, several environmental and practical considerations must be addressed. The long-term impacts of nanomaterials on soil ecosystems require careful study to avoid negative effects on soil health and microbial communities [193]. Indeed, nanomaterials can affect soil microorganisms through (i) direct toxicity, (ii) changes in toxin or nutrient bioavailability, (iii) interactions with natural organic compounds, and (iv) interactions with toxic compounds that may alter their toxicity [193]. Additionally, the cost and scalability of nanomaterial production and application are critical factors in determining their feasibility for widespread use in soil management practices. Integrating nanomaterials into soil management strategies could revolutionize C sequestration efforts, particularly in agricultural settings where maintaining soil health is crucial [197]. Future research should focus on optimizing the design and application of these materials to maximize their C sequestration potential while ensuring they are safe and sustainable for long-term use.

4.8. Microbial Modification

Soil microbes—bacteria, archaea, fungi, and viruses—play a central role in the decomposition and transformation of OM, directly influencing the stabilization and retention of SOC [198]. Microbial biomass, particularly dead microbial cells or necromass, can become a significant C sink, contributing to the formation of stable OM [59]. Certain microbial groups, such as Arbuscular Mycorrhizal Fungi (AMF), facilitate the transfer of C from labile to recalcitrant pools and their aggregation to soil particles by producing the glycoprotein glomalin-related soil protein (GRSP) [199]. Many studies have established that it is possible to improve the CUE and sequestration in soils by selecting, promoting, and introducing beneficial microbial species and consortia to support SOM elemental coupling, as well as microorganism-derived enzymes responsible for the transformation of organic compounds [67]. At the same time, the adaptability and competitive nature of introduced microbes in comparison to native microbes, as long as their long-term effectiveness, also remain debatable. Advances in gene editing technologies, such as CRISPR-Cas9, can help in engineering microbes to enhance their C sequestration and subsequent C stabilization efficiency, especially by engineering subunits of rubisco rbcS (ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit) [200,201], which help convert atmospheric CO₂ into organic C through the Calvin cycle. Engineering microbes to express extracellular polymeric substance (EPS) biosynthesis genes can enhance soil particle aggregation and stabilize carbon within the soil matrix [202], while modifications related to the reductive tricarboxylic acid (TCA) cycle can further improve C fixation and sequestration [203,204].

The success of microbial applications and subsequent C sequestration strategies will depend on various environmental factors, including soil type, pH, moisture, temperature, and agronomic practices. Tailoring microbial interventions to specific soil and crop conditions is crucial for maximizing their effectiveness. Environmental changes, such as elevated CO₂ concentrations, could alter plant rhizodeposition patterns, affecting microbial selectivity. Identifying plant-derived metabolites that promote the selection of specific microbial groups will be essential for the success of these strategies.

However, the long-term stability of engineered microbial communities in natural environments must be carefully evaluated to ensure sustained benefits. While laboratory studies have shown promising results, applying these microbial modifications in the field will require further extensive research. Long-term field trials are necessary to assess the durability and scalability of these microbial interventions across different agricultural and natural ecosystems.

4.9. Deliberate Phage Infection

Bacteriophages, or phages, have the unique ability to regulate bacterial populations through lytic pathways, enabling the deliberate reshaping of microbial communities and contributing to the formation of necromass. By selectively targeting and lysing specific bacterial groups, phages release organic matter and influence key nutrient cycling processes [205]. For example, phages can effectively control populations of Acidobacteria, Verrucomicrobia, and Deltaproteobacteria—bacteria that are crucial in organic matter degradation [206]. By reducing the abundance of bacteria that are highly active in carbon mineralization, phage interventions can slow the breakdown of organic matter, thereby enhancing SOC retention. This strategy is particularly beneficial in soils where certain bacterial taxa dominate carbon cycling, as phage interventions can redirect microbial activity towards pathways that conserve carbon. Additionally, during the lytic cycle, phages contribute to carbon cycling by releasing bacterial necromass. This process, known as the “viral shunt,” refers to the diversion of organic carbon from microbial biomass into dissolved organic matter through viral lysis, leading to the turnover of approximately 20% of oceanic microbial biomass daily and the release of around 3 gigatons of carbon annually [207,208]. In drought-stressed environments, phages can also control pathogenic microbes, thereby enhancing plant growth and resilience. Improved plant growth under stress conditions can indirectly contribute to SOC retention by increasing root biomass and rhizodeposition. Furthermore, studies suggest that phages can be selected and applied in drought conditions to establish mutualistic relationships with plants, aiding their survival under abiotic stress and promoting greater carbon input into the soil through enhanced plant growth and root development. Future research should focus on understanding the long-term impacts of phage applications on microbial community stability and soil health, as well as on developing targeted phage treatments that can be integrated into broader soil management strategies [205] (See

Table 3. Soil carbon sequestration limitations and corresponding solutions.

Limitation	Solution	Applicability and Target Systems	Scalability and Economic Feasibility	Current Status	Select References
Photosynthetic Capacity	Photosynthetic Modification	Primarily targets major C3 crops (wheat, rice, soybeans) that have lower photosynthetic efficiency than C4 crops. Most effective in high-input agricultural systems where light and nutrients are not limiting factors.	Low–medium. High R&D costs. Regulatory hurdles for genetically modified organisms (GMOs) are significant. Once developed, scaling through seed distribution is feasible, but requires widespread farmer adoption and adapted agronomic practices.	Laboratory/Early Field Trials. Researchers have successfully engineered modifications in model plants (tobacco) and some crops, demonstrating yield increases. Not yet commercially available.	[31,209,210]
Root Architecture and C Allocation	Modification of Root Systems and Genetic Engineering	Broadly applicable to all annual and perennial cropping systems, especially in regions with deep soils or those prone to drought. Essential for moving carbon into more stable, deeper soil layers.	Medium. Breeding is a proven, scalable pathway. Genetic engineering faces similar regulatory and public acceptance hurdles as photosynthetic modification. The perennial grain Kernza® is an early commercial example.	Research for early commercialization. Specific genes (e.g., DRO1) identified and tested. Perennial grain varieties such as Kernza® are available on a limited commercial scale. Widespread availability of deep-rooting staple crops is still years away.	[42,151]
Priming Effect and Root Chemistry	Modification of Rhizodeposition and Root Chemistry	Applicable to agricultural systems where maximizing the efficiency of carbon inputs is critical, particularly in soils with low carbon saturation potential or where organic amendments are used.	Low. Requires advanced genetic selection and engineering, making R&D costs high. The link between specific exudates and long-term carbon stabilization needs more field validation before commercial breeding efforts can be scaled.	Conceptual/Laboratory Research. Specific compounds have been identified that reduce priming in lab settings. Breeding programs are beginning to consider root chemistry as a selection trait, but it is not yet a primary focus.	[211]
Microbial CUE and Necromass Formation	Microbial Modification and Management (Bio-fertilizers)	Best suited for degraded soils or intensive agricultural systems where native microbial communities may be suboptimal. Efficacy is highly dependent on soil type, climate, and management practices.	High. Production of microbial inoculants is well established and relatively low cost. The main challenge is ensuring product stability (shelf life) and consistent performance across diverse field conditions.	Commercially available. Bio-fertilizers and microbial soil amendments are widely available, but their specific formulation for carbon sequestration is an emerging market. Product consistency and efficacy remain variable.	[212]
Viral and Predator–Prey Dynamics	Deliberate Phage Infection	Highly targeted approach, potentially useful for controlling specific microbial groups known to accelerate carbon loss in certain high-value agricultural systems (e.g., horticulture) or in bioremediation contexts.	Very low. Phage therapy for soil applications is highly complex. Identifying, isolating, and deploying effective phages at a field scale is a massive logistical and ecological challenge. Cost-prohibitive for broadacre agriculture currently.	Conceptual/Early Laboratory Research. Phage biology is well understood, but its application for manipulating broad soil ecosystem functions such as carbon cycling is in its infancy. No field-scale applications for this purpose exist.	[213,214]
Temperature and Moisture Stress	Responsive Hydrogels	Most applicable to arid and semi-arid regions, sandy soil with low water-holding capacity, and high-value horticulture to mitigate drought stress and improve water use efficiency.	Medium–low. The cost of hydrogels can be prohibitive for large acres of row crops. Concerns about the long-term fate and potential microplastic pollution from non-biodegradable polymers limit scalability. Biodegradable options are emerging but are more expensive.	Commercially Available/Niche Application. Used in horticulture, landscaping, and forestry. Research into biodegradable hydrogels and their large-scale agricultural use is ongoing.	[187,188]
Nutrient Limitation	Precision Nutrient Management and Bio-fertilizers	Universally applicable to all managed agricultural systems. Essential for optimizing plant growth and carbon inputs while minimizing environmental impacts such as nitrous oxide emissions and nutrient runoff.	High. Technology for precision application (e.g., variable rate technology) is commercially available and becoming more affordable. Bio-fertilizers are scalable. The main barrier is upfront investment and farmer training.	Commercially available and increasingly adopted. Widely adopted in developed agricultural economies. Continued innovation focuses on integrating more data layers (soil sensors, satellite imagery) for higher precision.	[215,216]
Carbon Saturation	C-Capturing Minerals (Enhanced Weathering)	Best suited for acidic agricultural soils where crushed silicate rocks (such as basalt) can provide a liming co-benefit. Requires accessible sources of suitable rock and infrastructure for grinding and transport.	Medium. Scalability is limited by the proximity of farms to rock quarries, transportation costs, and the energy required for grinding. Supply chains need to be developed. Potentially very large scale if logistical and economic hurdles are overcome.	Field Trials and early commercial projects. Several startups and research projects are conducting large-scale field trials. Carbon credits from enhanced weathering are being sold on the voluntary market, but the science of measurement, reporting, and verification (MRV) is still developing.	[217]
Chemical Instability of SOC	Synthetic Poly-carboxylic Compounds	Potential application in degraded soils or as an additive to other organic amendments (e.g., compost) to increase the formation of stable organo–mineral complexes.	Low. Currently, these are specialty chemicals, not produced at a scale or cost suitable for agriculture. The environmental impact and long-term stability of synthetic polymers in soil require extensive study.	Conceptual/Laboratory Research. The principles of organo–mineral stabilization are well known. Some commercial products use carboxylic acids as fertilizer additives, but their design for long-term carbon sequestration is not established.	[218]
Limited Formation of Stable C Pools	Phytolith Formation Enhancement	Applicable to crops that are high in silica accumulators, such as rice, sugarcane, wheat, and bamboo. Most effective in soils with available silicon or where silicon-based fertilizers are applied.	Medium. Application of silicate amendments (e.g., slag, diatomaceous earth, rice husk biochar) is logistically feasible. Breeding for higher silica uptake is a viable long-term strategy.	Research/Field Trials. The role of PhytOC in carbon sequestration is well documented. Field trials applying silicon sources have shown increased phytolith production. It is not yet a mainstream, managed sequestration practice.	[219,220]
Physical Protection and Aggregation	Nanomaterials and Biochar	Biochar: widely applicable across most soil types and systems. Nanomaterials: highly experimental, targeted for specific soil conditioning challenges such as improving aggregation or water retention.	Biochar: High. Scalable, with production systems ranging from small on-farm units to large industrial plants. Cost and quality control are key variables. Nanomaterials: very low. Production costs are extremely high, and major concerns about ecotoxicity and environmental fate prevent any consideration for large-scale agricultural use at present.	Biochar: commercially Available and increasingly adopted. A well-established soil amendment with a growing market. Nanomaterials: laboratory research. Exclusively in the research phase for soil applications; no commercial use in agriculture for sequestration.	[221,222,223]

).

5. Management and Human Dimension

While mechanistic feedback and inherent limitations constrain soil C sequestration efficiency, agronomic managements and human interventions play a crucial role in the stabilization and release of soil C. Regenerative soil health management strategies—including conservation tillage, cover cropping, residue management, crop–livestock integration, and the application of soil amendments such as coal char, biochar, and manure—have shown positive impact in boosting soil C levels.

Conservation tillage, along with residue retentions, enhances soil aggregation, promotes biological activity, and increases C sequestration. Cover crops also significantly contribute to the improvement of potentially mineralizable carbon (PMC), permanganate-oxidizable C (POX-C), organic C content, microbial activity, and soil aggregate stability [224]. Studies by Blanco Canqui (2022) showed that cover crops could sequester between 0.2 and 0.92 Mg C ha⁻¹ yr⁻¹, with an average of 0.41 Mg C ha⁻¹ yr⁻¹, as observed across 77 comparative studies [17]. The greatest increases in SOC were mostly observed in soils with low C content (<1% C) and after five years of cover cropping, particularly when biomass production exceeded 2.0 Mg ha⁻¹. The amount of C stored was closely correlated with the biomass produced by cover crops and the duration of cover cropping. Integrating livestock into cropping systems can further enhance soil C levels by increasing net primary productivity (NPP), promoting belowground biomass allocation, improving nutrient cycling, and stimulating soil biological activity [225].

Soil amendments such as biochar also contribute to C storage, either directly, by adding C to the soil, or indirectly, through negative priming effects [226]. A global meta-analysis by Gross et al. (2021) found that biochar application in field studies resulted in an absolute increase of 13.0 Mg ha⁻¹ in SOC, representing a 29% relative increase [227]. Vegetation restoration of degraded and eroded ecosystems can significantly increase SOC stock, as reported up to 14–38.8% compared to baseline [228,229,230]. Diverse plant communities contribute to a variable carbon-to-nitrogen (C: N) ratio by providing litter with heterogeneous biochemical compositions—particularly in structural compounds such as lignin and cellulose—and by offering a range of carbon inputs stemming from species-specific growth patterns. These variations can, under conducive conditions, enhance SOC accumulation [231,232].

The effectiveness of C sequestration is strongly influenced by various regional environmental and soil and site-specific factors, including climate, soil type, soil physicochemical characteristics, crop types, system disturbances, and human activities. In arid and semi-arid regions, challenges such as low precipitation, high temperatures, and rapid organic matter decomposition necessitate water-efficient strategies. Conservation tillage can increase SOC by 9% over a decade in sandy soils, while reforestation with native species enhances SOC by 20% in degraded thorn woodlands [233]. In temperate regions, where historical SOC depletion and intensive agriculture pose challenges, rotational grazing, cover cropping, no-tillage, agroforestry, and biochar have proven particularly effective in enhancing soil C stocks [234,235,236]. Tropical and humid regions face high decomposition rates, soil acidity, and nutrient leaching, requiring SOC-preserving techniques. Cover cropping can be a strategic practice to improve SOC in such cases [237]. Mediterranean climates, characterized by seasonal drought, erosion, and low biomass production, benefit from organic amendments and soil conservation techniques. Olive mill waste compost can increases SOC in mediterranean climatic zone [238]. Manure and compost applications have been widely effective in all environments, supporting SOC accumulation across diverse conditions.

Government policies related to climate and agriculture, including incentives and regulatory measures, are also critical in either advancing or impeding C storage efforts. For example, the 4 per 1000 Initiative aims to increase SOC stocks by 0.4% annually, offsetting global GHG emissions through improved agricultural land and soil management practices [7]. Policies and market support that promote sustainable agricultural practices provide subsidies for cover crops, support climate-smart technologies, and encourage the use of organic amendments can significantly enhance soil C sequestration and agricultural productivity. In the United States, voluntary conservation programs such as the Environmental Quality Incentives Program (EQIP) and the Conservation Stewardship Program (CSP) offer financial assistance to farmers for adopting conservation practices on their farms. In Michigan, for instance, from 2008 to 2019, approximately 13% of EQIP payments, totaling around USD 21.7 million, were allocated for cover crops. Each dollar spent on EQIP cover crop payments led to an increase of 0.01 hectares in the area [239]. Crucially, effective policy implementation requires robust systems for measuring, monitoring, reporting, and verifying C sequestration. Farm profitability and sustainability are key drivers influencing decisions on crop selection, management practices, and participation in beneficial policies and incentive programs [187]. To effectively enhance soil C sequestration, it is crucial to promote regenerative agricultural practices supported by policies that value ecosystem services. This approach should calculate the return on investment (ROI) in agriculture not solely based on yield, but through a comprehensive assessment that includes environmental benefits and improvements to human health. Such a holistic strategy can significantly contribute to both direct and indirect C sequestration in soils.

6. Future Research Directions

Despite the growing implementation of regenerative agriculture and other practice-based strategies to enhance soil organic carbon (SOC), these approaches often lack predictability and scalability across diverse agroecosystems. The temporal dynamics of SOC accrual under different agronomic management remain uncertain and are modulated by climate variability, edaphic properties, and legacy land use. Consequently, while these practices are integral to sustainable agriculture, there is a pressing need for a complementary research agenda that directly targets the mechanistic underpinnings of SOC stabilization. The following sections outline five research priorities aimed at unraveling and engineering the biological, chemical, and physical interactions that govern carbon persistence in soils.

i.

Engineering the Plant-Microbe-Mineral Interface for Carbon Persistence

Soil carbon stabilization is mediated by complex interactions among root exudates, microbial communities, and mineral surfaces. However, current research examines these components in isolation. Future studies should focus on integrating plant breeding with microbiome engineering to construct synergistic plant–microbe systems that enhance carbon stabilization. Research should investigate the co-selection of crop root traits and specific microbial consortia to optimize the conversion of rhizodeposits into mineral-associated organic matter (MAOM) and elucidate the signaling compounds and metabolic exchanges that facilitate this process.

ii.

Quantifying the Net Carbon Balance of the Soil Viral Shunt and Microbial Predation

Viral lysis and microbial predation significantly influence necromass formation and labile carbon flux, yet their net impact on SOC dynamics remains unresolved. A key research priority should be to quantify the balance between microbial necromass generation and respiratory carbon loss induced by bacteriophages and protists, focusing on variability across soil types, hydrological regimes, and management practices.

iii.

Developing Multi-Functional “Smart” Soil Amendments

Traditional soil amendments such as biochar or lime offer limited, singular functionalities. Future soil conditioners must simultaneously address multiple constraints to SOC persistence. Research should prioritize the design of composite materials—such as polymer–clay–nutrient hydrogels or mineral-infused biochars—that concurrently improve water retention, sorption capacity, and soil aggregation.

iv.

Elucidating Mechanisms of Deep Soil Carbon Persistence

Most SOC research focuses on surface soils (0–30 cm), overlooking the substantial sequestration potential of subsoils. Understanding deep carbon dynamics is essential for modeling long-term SOC storage. Future research should involve globally coordinated deep soil surveys (>1 m) across pedoclimatic gradients, characterizing root inputs, microbial community structure, and mineral associations in subsoils.

v.

Assessing Ecological and Economic Feasibility of Advanced Interventions

Innovations developed in laboratory settings must be evaluated for their long-term ecological integrity, economic viability, and social acceptability to enable widespread adoption. Research should include comprehensive life cycle assessments (LCAs) and techno-economic analyses (TEAs) of interventions such as nanomaterials, synthetic microbiomes, or functionalized amendments. This will aid in assessing trade-offs in terms of carbon footprint, ecotoxicity potential, and economic returns.

7. Summary

This review comprehensively explores the complex mechanisms and limitations of soil carbon (C) sequestration, highlighting the integral role of biotic, abiotic, structural, and chemical factors. Soil C sequestration remains a key strategy in climate change mitigation due to the vast C storage potential of soils, exceeding that of the atmosphere and terrestrial biomass combined. However, the efficacy of this strategy is constrained by multifaceted interactions across biological processes, soil mineral properties, and environmental conditions. Biotic factors, including plant productivity, root system traits, and microbial community dynamics, regulate both C inputs and stabilization processes. Root exudation, rhizodeposition, and necromass formation are central to SOC persistence but vary with species traits, nutrient availability, and environmental stressors. Abiotic constraints such as temperature and moisture regimes influence microbial activity and SOC decomposition, often interacting with soil texture and mineralogy to modulate protection mechanisms. Physical stabilization via aggregates and mineral associations plays a central role, yet the protective capacity of soil is finite and varies with depth, mineral type, and disturbance history. Chemical processes, including cation bridging, chelation, and redox cycling, further influence SOM stabilization by governing molecular interactions with reactive surfaces. While mineral-associated organic carbon (MAOC) is widely considered stable, recent findings suggest its accessibility may be modulated by enzymatic activity, nutrient stoichiometry, and environmental perturbations. Although regenerative agricultural practices have demonstrated potential for enhancing SOC, their success is variable and often context-dependent. There are challenges in achieving long-term stabilization, especially under scenarios of climate variability and shifting land use. Future success in enhancing SOC stocks will hinge not only on improving practice-based approaches but also on addressing critical knowledge gaps through targeted research. Mechanistic advances in areas such as the plant–microbe–mineral interface, the role of microbial predation and viral lysis, and deep soil dynamics will be pivotal. The development of multi-functional amendments and rigorous ecological-economic evaluation further emphasize the need for precision interventions. Advancing SOC sequestration requires a transdisciplinary research framework that integrates ecological theory, soil systems biology, material science, and policy design.