Climate, Soil, and Microbes: Interactions Shaping Organic Matter Decomposition in Croplands

Abstract

Soil organic matter (SOM) decomposition is a critical biogeochemical process that regulates the carbon cycle, nutrient availability, and agricultural sustainability of cropland systems. Recent progress in multi-omics and microbial network analyses has provided us with a better understanding of the decomposition process at different spatial and temporal scales. Climate factors, such as temperature and seasonal variations in moisture, play a critical role in microbial activity and enzyme kinetics, and their impacts are mediated by soil physical and chemical properties. Soil mineralogy, texture, and structure create different soil microenvironments, affecting the connectivity of microbial habitats, substrate availability, and protective mechanisms of organic matter. Moreover, different microbial groups (bacteria, fungi, and archaea) contribute differently to the decomposition of plant residues and SOM. Recent findings suggest the paramount importance of living microbial communities as well as necromass in forming soil organic carbon pools. Microbial functional traits such as carbon use efficiency, dormancy, and stress tolerance are essential drivers of decomposition in the soil. Furthermore, the role of microbial necromass, alongside live microbial communities, in the formation and stabilization of persistent SOM fractions is increasingly recognized. Based on this microbial perspective, feedback between local microbial processes and landscape-scale carbon dynamics illustrates the cross-scale interactions that drive agricultural productivity and regulate soil climate. Understanding these dynamics also highlights the potential for incorporating microbial functioning into sustainable agricultural management, which offers promising avenues for increasing carbon sequestration without jeopardizing soil nutrient cycling. This review explores current developments in intricate relationships between climate, soil characteristics, and microbial communities determining SOM decomposition, serving as a promising resource in organic fertilization and regenerative agriculture. Specifically, we examine how nutrient availability, pH, and oxygen levels critically influence these microbial contributions to SOM stability and turnover.

1. Introduction

Soil organic matter (SOM) decomposition in agricultural landscapes is a fundamental biogeochemical process governing terrestrial carbon cycling, nutrient availability, and ecosystem functioning. SOM is mainly produced by incomplete decomposition and transformation of crop residues by microbes [1]. Croplands, which occupy approximately 12% of the Earth’s ice-free land surface, serve as a dynamic interface where plant-derived organic materials undergo continuous transformation through complex interactions between climatic drivers, soil properties, and microbial communities [2].

The structural and chemical compositions of crop residues vary significantly, greatly affecting their decomposition rates and stabilization potential [3]. For instance, if recalcitrants such as lignin, tannins, and phenols are high in crop residues, they hinder residue decomposition [4]. Likewise, aboveground crop residues, including plant stems and leaves, demonstrate better organic matter (OM) quality than belowground residues, such as roots [5]. Similarly, substrate availability and quality directly influence soil microbial turnover [6]. Therefore, if substrate availability is interrupted, microbes may undergo dormancy or their biomass reduces following cell death, and a decrease in microbial biomass leads to the accumulation of microbial necromass, which is considered an important source of stable SOM. Because microbial necromasses are heterogeneous in nature, they are used as labile substrates by living microorganisms [7].

New paradigm changes have highlighted the importance of microbial necromass as a central driver of stable SOC pools and have shifted the focus away from traditional views of decomposition as a loss process [8,9]. This recognition has significant implications for understanding how agricultural practices affect long-term soil carbon pools and fertility. Additionally, modeling techniques and frameworks at the “meso-scale” to “micro-scale” have been developed that provide a more mechanistic characterization of decomposition (not just simple temperature and moisture functions), such as trait-based decomposition models that mechanistically represent microbial community dynamics.

This review integrates the current knowledge of climate–soil–microbe interactions in croplands and explores how they determine the cycling of organic matter at multiple scales, ranging from molecular to landscape. In general, the organic matter decomposition process varies across a hierarchy of scales. For instance, different chemical bonds are broken down by microbial enzymes at the molecular scale [10,11]. Conversely, at the microaggregate scale, organic matter is typically present in the bound form in soil aggregates, which physically protect its decomposition by enzymatic activity [12,13]. At the field scale, differences exist in soil texture, topology, and farming practices (like tillage and fertilization), resulting in variations in decomposition rates [11,14]. Finally, at the landscape scale, regional climate patterns, vegetation types, and land use are key determinants of large-scale carbon cycling dynamics [15,16]. The article also assesses the impact of climate variability on microbial decomposition processes, explores the impact of soil environmental factors as context-dependent modifiers, and evaluates how microbial functional ecology mediates decomposition outcomes. The critical feedback between decomposition processes and broader agroecosystem functioning, current modeling capabilities, and priority areas for future research is also highlighted.

2. Organic Matter and the Soil Microbial Engine

2.1. Composition and Fate of SOM in Croplands

The chemical composition of crop residues is a primary driver of decomposition. The initial chemical composition of different crops varies significantly in carbon, nitrogen, carbon–nitrogen (C–N) ratio, and major organic fractions, including the soluble fraction, hemicellulose, cellulose, and lignin. These variations, especially in the C–N ratio and lignin content, affect the rate and nature of microbial decomposition and the eventual SOM formation. For instance, a lower C–N ratio indicates a more easily decomposable material, whereas a higher lignin content implies higher recalcitrance [17].

The SOM in croplands consists of diverse carbon pools with varying degrees of stability and turnover rates [18,19]. Particulate organic matter represents a more labile fraction, primarily derived from plant residues, and is easily accessible for microbial decomposition [20,21]. Conversely, mineral-associated organic matter forms through organo–mineral interactions and represents the most persistent soil carbon pool [19,22]. Carbon transformation and stabilization within these fractions are strongly influenced by climate, soil texture, and microbial traits [23,24,25]. For example, higher temperature and optimum moisture content trigger particulate organic carbon (POC) degradation by stimulating microbial activity and enzyme kinetics, thereby reducing turnover times [23,25,26]. However, simultaneously, these climatic conditions can indirectly promote the formation of mineral-associated organic carbon (MAOC) by stimulating the degradation of complex organic matter into simpler, microbial-derived molecules, which can easily adsorb on mineral surfaces [23,27,28]. Additionally, fine-textured soils (such as, clays) provide greater surface area and pore spaces for organo–mineral associations and physical protection; hence, promoting MAOC formation and stability compared to sandy soils [29,30,31]. This is further mediated by microbial traits; certain microbial communities (for example, K-strategists) are more efficient in producing necromass and metabolic byproducts that preferentially form MAOC, even under nutrient limitation or during drying–rewetting cycles that induce cell lysis and subsequent adsorption [32,33,34,35]. Therefore, the interaction between climate-mediated microbial activity, soil mineralogy, and microbial functional diversity is the key determinant controlling carbon allocation between labile POC and stable MAOC pools [24,27,31]. Recent studies have demonstrated that cropland soils typically contain lower SOM concentrations than natural ecosystems owing to frequent disturbances and reduced carbon inputs [36,37].

The fate of SOM in agricultural systems is largely determined by the balance between organic matter inputs from crop residues, root exudates, and external amendments and outputs through microbial decomposition and soil respiration [38,39]. Crop residues contribute to varying amounts of carbon with different chemical compositions, affecting the decomposition rates and stabilization potential [40]. The conversion of forest or grassland to cropland typically results in substantial SOC loss, often exceeding 50% of the original stock within decades of cultivation [36]. However, improved management practices can partially restore these losses by enhancing carbon inputs and reducing decomposition rates [38].

2.2. Key Microbial Groups and Their Decomposition Roles

Soil microbial communities in croplands are dominated by bacteria and fungi, which exhibit distinct functional roles in organic matter decomposition [41,42]. Bacterial communities, particularly Proteobacteria and Bacteroidetes, are typically enriched in agricultural soils and respond rapidly to changes in substrate availability and environmental conditions [41,43]. These copiotrophic organisms excel at decomposing readily available organic compounds and are particularly abundant in the rhizosphere, where root exudates provide labile carbon sources [40,42]. Fungal communities, dominated by ascomycetes and basidiomycetes, play crucial roles in decomposing more recalcitrant plant materials through their extensive hyphal networks and specialized enzyme systems [41,44].

Different extracellular enzymes released by these microbial groups can degrade organic compounds into their bioavailable forms. For instance, β-1,4-glucosidase (BG) and cellobiohydrolase (CBH) are essential for decomposing cellulose [45], whereas polyphenol oxidase and peroxidase are involved in decomposing lignin [46]. Other enzymes, such as β-1,4-N-acetylglucosaminidase (NAG), leucine aminopeptidase (LAP), and alkaline phosphatase (AP), can assist in nutrient mineralization [47]. The comparative activities of BG:AP, BG:NAG, and NAG:AP have been proposed as indicators of nutrient acquisition strategies (carbon versus phosphorus, carbon versus nitrogen, and nitrogen versus phosphorus) [10,48]. Table 1 lists the major groups microorganisms responsible for decomposition of organic matter in croplands, emphasizing their distinct ecological strategies and management responses [49,50].

Besides enzyme profiles, microbial functional traits are also largely responsible for decomposition [51]. For instance, strategies of microbial dormancy and resistance are primarily important; many soil microbes may become dormant (spore formation or reduced metabolic activity) under unfavorable conditions (such as drought and nutrient starvation), allowing them to survive and rapidly reactivate when conditions become favorable [52]. This accelerated resuscitation leads to episodic release of carbon and nutrients [53]. Additionally, microbial growth strategies (mostly identified as r- and K-strategists) influence their resource management and participation in the decomposition process [54]. For example, r-strategists (such as, many Proteobacteria and Bacteroidetes) are often copiotroph, with high growth rates and encoded enzymes for degradation of labile carbon, resulting in a dominance under high substrate availability, but with a relatively smaller contribution to stable SOM [55]. In contrast, K-strategists (such as, many fungi and Acidobacteria) are oligotrophs, with lower growth rates, increased CUE activity, and stronger allocation to decomposing recalcitrant compounds (for example, ligninolytic enzymes). They also contribute to the stable microbial necromass and long-term carbon sequestration, particularly in nutrient-poor or stable environments [56,57]. Understanding these characteristics provides a mechanistic link between microbial functional ecology (from their enzyme repertoires, survival and growth strategies) and decomposition outcomes across diverse soil conditions [56].

Table 1. Key microbial groups involved in decomposition processes, their ecological strategies, and responses to climate and soil type and agricultural management practices.

Microbial Group	Primary Function	Habitat Preference	Response to Management	Influence of Climate and Soil Type	References
Proteobacteria	Rapid decomposition of labile organic compounds	Rhizosphere, nutrient-rich environments	Increases with fertilization and organic inputs	Favored by warmer temperatures and higher moisture in fertile, loamy soils.	[58,59,60,61]
Bacteroidetes	Decomposition of readily available substrates	Agricultural soils, organic-rich zones	Enhanced by agricultural practices	Prevalent in moist, neutral pH soils; sensitive to drought stress.	[62,63,64,65]
Ascomycetes	Decomposition of recalcitrant plant materials	Diverse soil environments	Sensitive to soil disturbance	Exhibit broad environmental tolerance; active across diverse soil types and moisture regimes, including dry conditions.	[66,67]
Basidiomycetes	Decomposition of complex organic compounds	Forest soils, organic matter-rich zones	Decreases with intensive cultivation	Prefer cooler, stable environments and higher moisture; dominant in forest soils with abundant lignin.	[68,69,70,71]
Actinobacteria	Decomposition of complex organic matter	Diverse soil conditions	Variable response to management	Resilient to desiccation and high pH; prominent in arid and alkaline soils.	[72,73,74]
Acidobacteria	Slow decomposition of stable organic compounds	Nutrient-poor, stable environments	Stable under low-input systems	Dominant in acidic, oligotrophic soils and stable, undisturbed environments; sensitive to rapid environmental shifts.	[60,75,76,77]

Table 1. Key microbial groups involved in decomposition processes, their ecological strategies, and responses to climate and soil type and agricultural management practices.

Microbial Group	Primary Function	Habitat Preference	Response to Management	Influence of Climate and Soil Type	References
Proteobacteria	Rapid decomposition of labile organic compounds	Rhizosphere, nutrient-rich environments	Increases with fertilization and organic inputs	Favored by warmer temperatures and higher moisture in fertile, loamy soils.	[58,59,60,61]
Bacteroidetes	Decomposition of readily available substrates	Agricultural soils, organic-rich zones	Enhanced by agricultural practices	Prevalent in moist, neutral pH soils; sensitive to drought stress.	[62,63,64,65]
Ascomycetes	Decomposition of recalcitrant plant materials	Diverse soil environments	Sensitive to soil disturbance	Exhibit broad environmental tolerance; active across diverse soil types and moisture regimes, including dry conditions.	[66,67]
Basidiomycetes	Decomposition of complex organic compounds	Forest soils, organic matter-rich zones	Decreases with intensive cultivation	Prefer cooler, stable environments and higher moisture; dominant in forest soils with abundant lignin.	[68,69,70,71]
Actinobacteria	Decomposition of complex organic matter	Diverse soil conditions	Variable response to management	Resilient to desiccation and high pH; prominent in arid and alkaline soils.	[72,73,74]
Acidobacteria	Slow decomposition of stable organic compounds	Nutrient-poor, stable environments	Stable under low-input systems	Dominant in acidic, oligotrophic soils and stable, undisturbed environments; sensitive to rapid environmental shifts.	[60,75,76,77]

Microbial community structure and diversity are important indicators of soil health [78]. Organic matter decomposition is a highly specialized process that depends on various microbial guilds, implying that management practices that influence microbial diversity, such as monoculture versus diverse crop rotations or the application of particular chemical fertilizers, will directly influence the decomposition rate and efficiency. For instance, the prevalence and activity of ligninolytic fungi are essential for the breakdown of recalcitrant molecules, with a significant impact on the rate of stable SOM formation [79]. The relative abundance and activity of bacterial and fungal communities significantly impact decomposition patterns and soil carbon cycling [43,80]. Therefore, planned rotation of crops increases microbial diversity and network complexity, which subsequently improves nutrient cycling and ecosystem functioning [40].

2.3. Microbial Necromass and Its Contribution to Stable SOM

Microbial necromass—the dead cells and cell-wall fragments of soil microbes—provides a critical link between fresh crop inputs and long-lived soil organic matter [32]. As microbes grow on crop residues, carbon is assimilated into biomass and ultimately released as necromass when cells die (via turnover, predation, or stress) [9,34]. This microbial residue carbon (bacterial and fungal necromass) is now recognized as a major SOM component [9,81]. Amino-sugar biomarker studies show necromass often makes up on around 30–60% of total SOC across ecosystems (higher in grasslands and croplands than in forests) [82,83]. For instance, cropland soils typically derive about half of their organic carbon from microbial necromass [84,85], reflecting the fact that large portions of crop-residue carbon are first cycled through the soil microbial communities [34].

Unlike fresh plant litter, microbial necromass is enriched in N-bearing compounds (amino sugars, proteins, lipids) and has strong affinity for mineral surfaces [86,87]. After cell death, these necromass molecules bind tightly to clay and silt particles or become physically trapped within soil microaggregates [88,89]. Through such organo–mineral associations and aggregate entombment, microbial necromass is effectively stabilized, forming MAOM that resists rapid decomposition [86,90]. This “microbial carbon pump” (MCP) pathway—where microbes transform plant carbon into cell biomass that is later preserved as necromass in protected soil pools—has been highlighted as a fundamental mechanism of soil carbon sequestration [32,34].

Field and modeling studies confirm the quantitative importance of necromass in croplands [85,91]. For instance, global surveys report that soil microbial necromass contributes roughly 50–51% of SOC in cultivated soils [82,84]. By comparison, contributions are ~33% in forests and ~60% in some grasslands [92]. Importantly, management practices strongly influence these fractions [93]. Long-term intensive tillage or monocropping tends to deplete microbial biomass and reduce necromass accumulation, whereas practices that support microbial activity (organic amendments, reduced disturbance, crop rotations) tend to boost necromass-derived carbon [85,94]. A recent meta-analysis found that “climate-smart” cropping systems (conservation tillage, nutrient management, organic inputs) increased soil microbial necromass by ~18% relative to conventional systems [93]. Thus, practices that enhance microbial growth and turnover (for example, adding compost or cover crops, improving soil fertility, minimizing soil disturbance) generally raise the share of SOC coming from stable microbial residues [95].

In summary, necromass provides a mechanistic bridge between crop residue inputs and stable soil carbon pools [32,96]. Crop residues supply the substrate, microbes convert a portion of that carbon into cell biomass, and after microbial death, the remnants are rapidly protected by mineral and aggregate processes [86]. This microbial pathway often sequesters carbon more effectively than direct plant-residue humification [96,97]. A future understanding of residue decomposition must therefore account not only for plant litter chemistry, but also for microbial growth, turnover, and necromass stabilization [9,81]. By integrating necromass dynamics with aggregate and mineral protection, it is possible to obtain a coherent framework linking substrate inputs to the long-term formation of stable SOM in croplands [88,98].

3. Climate Influences Decomposition Dynamics

3.1. Temperature Sensitivity of Microbial Processes and Enzyme Kinetics

Temperature significantly controls microbial decomposition processes by impacting enzyme kinetics and microbial metabolism [99,100]. The temperature sensitivity of SOM decomposition, commonly expressed as Q10 values, varies significantly among different SOM fractions and microbial processes, with particulate organic matter typically exhibiting higher temperature sensitivity than mineral-associated organic matter due to differences in substrate accessibility and protection mechanisms [20]. To clarify these complex interactions, Figure 1a,b illustrate generalized enzyme Q10 ranges and microbial CUE responses across varying temperature and moisture gradients. Enzyme Q10 typically peaks within an optimal temperature range, while microbial CUE can show more complex responses, potentially increasing or decreasing with warming depending on factors like substrate availability and microbial community shifts [101].

Temperature sensitivity patterns reveal intricate relationships between intracellular and extracellular processes that differ depending on the temperature range examined [101]. For instance, between 5 and 15 °C, both intra- and extracellular metabolic processes show similar temperature sensitivities. However, as temperature increases (15–37 °C), intracellular metabolic processes demonstrate higher temperature sensitivity. Conversely, at higher temperatures (26–37 °C), extracellular enzyme activity becomes more temperature sensitive, indicating that depolymerization of complex carbon compounds becomes increasingly sensitive to temperature changes [101]. Additionally, different enzymes exhibit varying Q10 values (1.78 to 3.28) [102], which reveal their unique catalytic efficiencies and thermal stabilities. For instance, cellulose-degrading enzymes (cellobiohydrolase) show higher temperature sensitivity, while protein-degrading enzymes (leucine aminopeptidase) demonstrate lower Q10 values but are highly sensitive to drought [103]. These enzyme-specific responses are crucial for predicting climate change impacts on decomposition processes, as the relative importance of different enzymatic pathways may shift under warming scenarios [104].

Beyond enzymatic processes, temperature and seasonal variations in moisture content directly impact overall microbial activity and enzyme kinetics through enzyme conformation, substrate diffusion, and microbial physiological state [105,106]. Microorganisms and their cellular metabolites are extremely sensitive to these environmental conditions [107,108]. Enzymes require specific temperature and moisture conditions for optimal three-dimensional structure and catalytic function, and any deviations can lead to enzyme denaturation or reduced activity [109,110]. For instance, drying–rewetting cycles alter substrate accessibility and enzyme-substrate diffusion rates, and microbial activity by causing osmotic stress, microbial dormancy, or reactivation [110,111]. During dry periods, low substrate diffusion along with desiccation stress limits the microbial activity and enzyme production, whereas rewetting exerts a “Birch effect” and results in reactivation of dormant microbes and the release of enzymes from lysed cells, hence, rapidly increasing microbial metabolic activity and SOM decomposition [103,112,113]. This dynamic interplay of temperature and moisture dictates the availability of water, microbial community structure, and the expression of enzymes, which are essential for both microbial metabolism and the movement of substrates to enzymes, thereby directly affecting decomposition rates [114].

Changes in soil temperature specifically influence microbial community composition by affecting metabolic processes, aeration, nutrient availability, microstructure connectivity, and microbial motility. These conditions exhibit different effects on bacteria and fungi, possibly because of their distinct composition and biology [115]. Moreover, microbial respiration increases under high thermal conditions (until certain limits), which affects both the quality and quantity of the organic matter [116,117]. Therefore, elevated temperatures within a suitable range positively affect soil nitrate content, likely due to fast decomposition of plant litter and organic matter, resulting in the accumulation of mineral nitrogen and the release of carbon dioxide [118]. Such temperature regimes are also dominated by fast-growing bacteria (such as Proteobacteria) that can decompose organic matter. Contrarily, fungi (such as saprotrophic fungi) tend to dominate low-temperature environments because of their capacity to decompose complex organic compounds, for instance, lignin [107].

Enzyme catalytic efficiency serves as the key determinant of temperature sensitivity [99,119] in soil carbon cycling, with important implications for predicting climate change impacts on decomposition processes [120]. This sensitivity is further regulated by nutrient availability, such as nitrogen and phosphorus fertilization, highlighting complex interactions within soil ecosystems [121]. Microbial carbon use efficiency (CUE) also demonstrates complex temperature dependencies that influence soil carbon cycling [122,123]. Warming can either increase or decrease CUE, depending on substrate quality, nutrient availability, and microbial community composition [123]. Recent studies have indicated that CUE is at least four times more important than other factors in determining global soil organic carbon storage [122]. The effects of temperature on decomposition are further modulated by soil moisture, nutrient availability, and substrate quality [99,100]. Long-term warming experiments have revealed that temperature sensitivity may decline over time owing to substrate depletion and microbial acclimation [100].

3.2. Moisture Effects on Soil Aeration, Redox, and Microbial Activity

Moisture conditions in the soil have a considerable influence on organic matter decomposition. Many biochemical reactions occurring in the soil are strongly affected by soil moisture conditions. They even affect organic matter content, mobility, gaseous exchange, microbial growth, activity, and community composition, and ultimately, decomposition of organic matter [124]. Moisture regulates decomposition by influencing oxygen availability, substrate diffusion, and microbial habitat connectivity [125]. Optimal moisture conditions for decomposition typically occur at intermediate levels that balance adequate substrate mobility with sufficient aeration for aerobic processes [126]. Soils that are rich in moisture, well-ventilated, and have neutral pH are believed to be ideal for organic matter decomposition [127,128]. Moreover, SOM turnover is regulated by precipitation, which is strongly associated with soil moisture [129]. Changes in precipitation trends also cause changes in soil moisture, thereby affecting substrate availability and organic matter decomposition [130].

Excessive moisture can create anaerobic conditions that shift microbial metabolism toward fermentation and methanogenesis, reduce decomposition rates, and alter carbon cycling pathways [100], leading to increased emission of methane in waterlogged croplands and a slower, less efficient breakdown of complex carbon compounds [131,132]. Regarding oxygen availability, aerobic microorganisms can effectively decompose organic matter, whereas mutualistic consortia are involved in anaerobic decomposition because single bacteria cannot perform complete decomposition. Similarly, the rate of aerobic decomposition is five to ten times higher than anaerobic decomposition [133]. Hence, oxygen availability serves as a critical regulator of decomposition pathways, with aerobic processes generally proceeding more rapidly than anaerobic processes [134]. Similarly, an oxygen-limited environment encourages the growth and activity of methanogenic archaea and facultative anaerobes compared with aerobic conditions, favoring the growth of Actinobacteria and fungi [133]. A recent study has demonstrated that oxygen availability regulates the quality of soil-dissolved organic matter by mediating microbial metabolism and iron oxidation, with implications for carbon cycling in agricultural systems [121]. In contrast, drought stress can limit microbial activity by reducing substrate diffusion and increasing osmotic stress [100,135], often resulting in microbial dormancy, reduced biomass, and the accumulation of less labile organic matter due to suppressed enzymatic activity [136,137]. Soil texture and structure significantly mediate the effects of moisture on decomposition by controlling pore size distribution and water retention characteristics [125,138]. Fine-textured soils with high clay content tend to retain more moisture and provide better protection for organic matter through physical occlusion in micropores [138].

Aggregation promotes decomposition through improved microbial habitat and substrate accessibility while simultaneously protecting organic matter within aggregate cores [139,140]. Rabbi et al. [125] found that microbial decomposition of organic matter and wetting–drying cycles promote aggregation, highlighting the complex feedback between moisture fluctuations, microbial activity, and soil structure development [25,140]. Although all types of microorganisms (actinomycetes, bacteria, and fungi) are involved in aerobic and anaerobic degradation, fungi are more active in decomposing highly recalcitrant constituents owing to their ability to produce diverse extracellular enzymes [141]. These dynamics have important implications for understanding the decomposition responses to changing precipitation patterns under future changing scenarios [140,142].

The relationship between moisture, oxygen, and decomposition creates complex threshold behaviors in many soils, with slight changes in water content potentially triggering substantial shifts in decomposition rates and pathways when critical thresholds are crossed [143]. Moisture fluctuations, particularly wetting–drying cycles, can significantly influence decomposition through physical disruption of aggregates, osmotic stress on microbial communities, and substrate redistribution [139]. These dynamic processes often result in decomposition patterns that cannot be predicted from average moisture conditions alone, highlighting the importance of considering temporal variability in moisture regimes when assessing decomposition dynamics [140].

3.3. Climate Variability, Land Use Change, and Long-Term Shifts in OM Decomposition

Climate variability and extreme weather events have increasingly influenced SOM dynamics in agricultural systems [100]. Changes in precipitation patterns affect soil carbon decomposition through altered moisture regimes and increased frequency of drought–flood cycles [135]. Land use conversion from natural ecosystems to croplands represents one of the most significant drivers of soil carbon loss, with effects persisting for decades after initial conversion [36,144].

Sanderman et al. [145] developed a global soil organic carbon loss map induced by past land use changes, specifically transformation from natural to cultivated ecosystems, and estimated the SOC loss in the top two m of soil. Their analysis indicated loss of carbon over time, an extensive and pronounced influence of anthropogenic activities on terrestrial carbon pools, and the long-term persistence of these effects. The “soil carbon debt” associated with historical land use change highlights the need for widespread sustainable land management. This stresses that agricultural systems have been and remain a major source of CO₂ to the atmosphere, and the future development of such systems must focus on carbon sequestration to reverse this trend.

Land use change affects different soil environmental factors, biological interactions, and nutrient conditions, thereby shaping microbial communities [146]. For instance, changes from woodland to farmland or pasture decrease microbial abundance and diversity, possibly due to nutrient cycling performed by soil microbes [147]. Microorganisms largely facilitate changes in soil ecosystems, including degraded land. The biomass carbon, enzyme activity, and basal respiration of microbes are essential for determining their adaptation and response to degraded land [148,149]. Land use changes in croplands negatively impact all these indicators due to retarded microbial activity [150]. Similarly, a decrease in plant growth promoting rhizobacteria and unbalanced carbon and nitrogen cycling were observed in severely degraded subalpine meadows [151].

The magnitude of these effects varies with climate, soil type, and management intensity [19,37]. Long-term impacts of climate change on decomposition exhibit complex temporal dynamics with lag effects that may extend for several years. A four-year lag in soil organic carbon responses to elevated temperatures has been observed, highlighting the importance of considering temporal scales in climate impact assessments. Extreme precipitation events can trigger substantial nutrient leaching and alter the soil carbon cycling trajectories [100]. The interaction between climate change and land management creates nonlinear responses that challenge predictive modeling efforts [135,152]. A previous study found that elevated temperatures and abnormal precipitation significantly impact soil carbon and nitrogen dynamics, with important implications for agricultural sustainability under changing climatic conditions [25].

Climate–soil–management interactions create complex patterns of carbon sequestration potential across agricultural landscapes [153]. Emerging research has emphasized the importance of considering local soil conditions, climate projections, and management options when developing strategies to enhance soil carbon storage in croplands [120,154].

4. Soil Properties as Contextual Modifiers

4.1. Soil Aggregation, Texture, and Porosity: Regulators of Microbial Habitat and OM Protection

Soil aggregation provides fundamental control for organic matter protection and microbial habitat organization [155]. Macroaggregates (>250 μm) serve as dynamic structures that facilitate rapid carbon cycling, while microaggregates (<250 μm) provide long-term protection for organic matter through physical occlusion [125]. The microbial processing of organic matter drives aggregate formation and stability through the production of binding agents and extracellular polymeric substances [125]. The spatial distribution of bacteria between macro- and microaggregates creates distinct microenvironments with varying oxygen concentrations, nutrient availability, and microbial interactions [155]. The relationship between aggregation and organic matter protection is context-dependent and varies with the soil type, management history, and environmental conditions [125]. The mechanism by which soil mineralogy affects SOM protection and microbial habitat is depicted in Figure 2.

Soil texture exerts a fundamental control on organic matter decomposition through its influence on pore size distribution and microbial accessibility. Clay-rich soils typically exhibit slower decomposition rates because of enhanced organo–mineral interactions and reduced pore connectivity. Fine-textured soils, which are rich in clay particles, serve as microhabitats for the growth of slow decomposers, such as Actinobacteria and mycorrhizal fungi, whereas sandy soils have larger poor sizes that allow for better aeration and water retention, thus favoring the growth of copiotrophs, such as Proteobacteria [156]. Soil texture is the second most important indicator after pH for determining the soil microbial community.

Table 2. Influence of soil texture on microbial community and organic matter stabilization.

Soil Texture	Microbial Community Dominance	Impact on Organic Matter Decomposition	References
Clay-rich soils (fine-textured)	Actinobacteria, Mycorrhizal fungi	Slower decomposition due to microbial protection by clay particles	[134]
Sandy soils (coarse-textured)	Copiotrophs (for example, Proteobacteria)	Faster decomposition due to increased aeration and lower stabilization	[158]
Silt-loam soils	Balanced bacterial and fungal diversity	Moderate decomposition rate with good organic matter retention	[159]
High-clay aggregated soils	Fungal-dominated communities	Enhanced carbon stabilization through macroaggregate formation	[160]

presents the impact of soil texture on microbial community and organic matter stabilization. It has greater impact on alpha diversity of fungi than that of bacteria, as fungal species richness is favored in coarse-textured soils. Conversely, clay and silt soils facilitate the growth of filamentous bacteria and some fungi. Similarly, finer-textured soils have higher inherent potential for organic carbon degradation [157].

The relationship between texture and decomposition is mediated by the pore neck size, which determines whether microorganisms can access soil microsites [138]. Porosity influences decomposition by affecting water movement, gas diffusion, and microbial colonization patterns [125]. The total porosity and pore size distribution also determine substrate accessibility and microbial habitat connectivity. Sandy soils with larger pore sizes typically exhibit higher decomposition rates owing to improved aeration and reduced physical protection [138]. The interaction between texture and moisture creates complex feedback effects on decomposition, with clayey soils showing greater sensitivity to moisture variations [126].

4.2. Soil pH

Soil pH is one of the most important determinants of microbial community composition, enzyme activity, and organic matter stabilization [41,161]. Rhizosphere processes often reduce soil pH, particularly in neutral to alkaline soils, creating favorable conditions for particular microbial groups [42]. pH influences microbial community composition, diversity, biomass, and enzymatic activity but also the microbial turnover of organic matter and microbial-mediated mineralization of carbon and nitrogen [162]. The microbial decomposition of organic matter is also affected by soil pH. Near-neutral pH (approximately 7) is generally considered ideal for soil microbial enzymatic activity and organic matter decomposition, as it optimizes enzyme conformation and enhances the bioavailability of key nutrients directly required for microbial metabolic and enzymatic processes [10,163]. Conversely, extreme pH conditions can denature important intra- and extra-cellular enzymes, and select for specialized, often less diverse and less efficient, microbial guilds adapted to stress [164].

The acidic pH inhibits the growth of microorganisms, thereby negatively affecting the decomposition of organic matter. For instance, acidic conditions usually promote the growth of fungal communities over bacterial populations, thereby influencing decomposition pathways [165,166]. Moreover, toxic metals such as aluminum are abundant in acidic soils. These metals inhibit microbial enzymatic activity and form a strong bond with organic matter, thereby reducing its decomposition. Finally, alkaline pH also affects microbial activity [167], often suppressing key enzyme activities vital for decomposition and favoring distinct, alkali-tolerant bacterial groups such as Actinobacteria [168,169].

4.3. Nutrient Stoichiometry and Microbial CUE

Nutrient availability, particularly nitrogen and phosphorus, fundamentally alters decomposition dynamics by affecting microbial growth and enzyme production [21,119]. In particular, soil nitrogen and phosphorus affect the primary productivity and community composition of organic matter decomposers [170]. Studies have suggested that high nitrogen and phosphorus levels stimulate microbial decomposition of holocellulose and soluble compounds, which are preferentially lost during the early stages of decomposition [171]. However, during the secondary stages (when lignin dominates the substrate), nitrogen addition reduces the decomposition rate due to lignin binding with complex organic compounds, changes in the fungal community (that are lignocellulolytic), promotion of bacterial growth (which prefers carbohydrates and aromatic compounds) [172], and reduction in the production of lignolytic enzymes through gene regulation [173]. Similarly, nutrient-rich soils are dominated by copiotrophs (Actinobacteria and Proteobacteria), whereas nutrient-poor soils encourage the growth of oligotrophic bacteria (such as Firmicutes) and fungi that feed on recalcitrant organic matter [174,175]. This nutrient-driven microbial adaptation, including shifts in resource allocation, directly impacts microbial CUE and thus the rate and extent of SOM stabilization [175,176]. Under nutrient-limited conditions (for example, high C–N or C–P), microbes allocate more energy to produce nutrient-acquiring enzymes, causing excess carbon to be respired and reducing CUE; conversely, abundant nutrients (low C–N/P) tend to increase CUE [177,178].

Besides nitrogen and phosphorus, the carbon-to-nitrogen (C–N) ratio is also an important indicator of organic matter decomposition. Organic matter with a low C–N ratio contains more nitrogen that is readily available for microbes, leading to faster decomposition. Conversely, under a high C–N ratio, less nitrogen is readily available to microbes. Therefore, the decomposition process is slow, leading to nitrogen immobilization [179]. At the microbial level, changes in C–N ratios affect the expression of enzymes and nutrient-acquisition strategies of bacteria. For instance, a high C–N ratio (>25:1) indicates a nitrogen limitation to microbes, resulting in an upregulation of enzymes to acquire nitrogen (for example, N-acetylglucosaminidase and leucine aminopeptidase) and a downregulation of carbon-acquiring enzymes [180]. In contrast, low C–N ratios (<20:1) favor nitrogen mineralization because of an excessive release of nitrogen from microbial biomass [181]. However, thresholds are very important: a C–N ratio of about 20–25:1 is considered a critical threshold where neither strong net immobilization nor mineralization occurs, and microbial demand balances with the substrate supply. Nutrient ratios well above this threshold enhance nitrogen immobilization (thereby slowing carbon decomposition), while low ratios promote carbon decomposition and nitrogen release [182]. Microbial biomass C–N is typically low (averaging around 7:1) [183], so substrates with much higher C–N force microbes to immobilize N for their own stoichiometric needs, slowing decomposition [184].

5. Cross-Scale Interactions and Emergent Feedback

5.1. Feedback Between Microbial Activity and Soil Microenvironment

Microbial activity creates dynamic feedback that modifies soil microenvironmental conditions and subsequently influences decomposition processes [152]. Microbial respiration alters local pH and redox conditions, affecting nutrient availability and mineral–organic matter interactions [161]. Extracellular enzyme production by soil microorganisms modifies substrate accessibility and chemical composition of SOM pools [185]. These enzyme-catalyzed reactions may enhance or retard subsequent decomposition depending on the nature of the products formed and their reactivity [99].

The production of microbial necromass is a major feedback mechanism for the long-term storage of soil carbon [81]. Microbial–mineral interactions work as feedback processes [25]. Microbial activity can modify the surface properties of minerals by producing organic acids and siderophores, affecting their ability to stabilize organic matter [134]. Mineral surfaces, on the other hand, affect microbial community composition by changing substrate availability, water films, and predation protection [153]. The chemical composition of necromass is different from that of living biomass and is characterized by modified C–N ratios as well as increased resistance to decomposition. Mechanisms of microbial death influence necromass composition and their ultimate fate in soil [22]. In particular, the stabilization of microbial necromass is controlled by the adsorption of recalcitrant components, like chitin and peptidoglycans, on mineral surfaces, which generate stable organo–mineral complexes [32,186]. This phenomenon is especially promoted by iron and aluminum oxides, which strongly adsorb microbial residues [187,188]. Microorganisms also produce extracellular polymeric substances (EPSs), which adhere to minerals and provide physical protection to organic matter within biofilms [189]. Through variations in moisture and temperature, climate directly impacts microbial turnover and CUE; for instance, drying–rewetting cycles induce microbial mortality and necromass pulses [190], whereas optimal conditions increase CUE, thus channeling more carbon into biomass and potentially stable necromass [85,122].

The new paradigm of the “soil–microbe complex” underscores the mutualistic and intimate relationship between soil environment and microbial communities [153,154]. This perspective acknowledges that microorganisms are both responsive and can actively alter their habitat, which can generate feedback that influences decomposition dynamics over various timescales [120]. The MCP is an important component of this complex. It facilitates the sequestration of SOC by converting labile carbon into the more recalcitrant forms, such as microbial necromass and metabolic byproducts [191]. Metabolic byproducts are ultimately stabilized by adsorption of carbon to mineral surfaces or its physical protection into soil aggregates [192]. The MCP’s efficiency is largely dependent on the availability of nutrients and climate-induced changes in microbial community composition, which enhance microbial growth and necromass production and preferentially promote characteristics that enhance stable carbon allocation [34,193]. This process depicts the role of microbes in controlling the fate of carbon in the soil and, ultimately, the global carbon cycle [194].

5.2. Landscape-Level Implications of Local Decomposition Processes

Local decomposition processes collectively influence carbon cycling at the landscape scale via spatial heterogeneity and connectivity effects [152,195]. Soil formation processes and weathering patterns result in spatial variations in decomposition rates across landscapes [142,152]. Topographic gradients influence moisture distribution, temperature regimes, and erosion-deposition patterns that affect organic matter dynamics [153]. The interaction between local soil properties and regional climate creates complex spatial mosaics of decomposition [154,195].

Landscape-scale soil carbon storage depends on the spatial distribution of different soil types and their decomposition characteristics [120]. Wetland and lowland positions typically store more soil organic carbon than upland areas because of reduced decomposition rates under anaerobic conditions [195]. Agricultural land use patterns at the landscape scale influence regional carbon balances through edge effects and spatial connectivity [44]. Understanding these cross-scale interactions is essential for scaling local measurements to regional and global carbon cycle assessments [139].

The spatial configuration of agricultural landscapes creates important constraints on decomposition processes through effects on the microclimate, water movement, and organism dispersal [134,142]. Landscape features such as hedgerows, riparian buffers, and field margins can significantly influence decomposition patterns by altering temperature, moisture, and litter input quality. These edge effects create transition zones with distinct decomposition characteristics that differ from those of adjacent fields or natural areas [153]. The impact of various temporal and spatial scales on SOM decomposition in cropland systems is summarized in

Table 3. Impact of temporal and spatial scales on SOM decomposition in cropland systems.

Scale	Time Frame/Spatial Resolution	Key Processes	Dominant Drivers	Microbial–Mineral Interactions	References
Micro-scale	Seconds to days/µm–mm	Enzyme production, microbial respiration, and necromass formation	Temperature, pH, substrate quality	Enzyme-substrate binding, organo–mineral associations	[22,99]
Meso-scale	Weeks to seasons/cm–m	Root exudation, aggregate formation, CUE dynamics	Moisture cycles, root turnover	Rhizosphere activity, necromass input	[108,125]
Field-scale	Annual/plot–field (~10–1000 m2)	Litter decomposition, SOM pool turnover	Crop management, tillage, fertilization	Microbial diversity shifts, aggregate dynamics	[40,140]
Landscape-scale	Multi-year to decades/km2	Land use transitions, erosion, SOC sequestration	Climate variability, land cover change	Lateral carbon fluxes, ecosystem connectivity	[135,145]
Regional/Global	Decades to centuries/>103 km2	Carbon modeling, global sequestration trends	Climate change, policy, socioeconomic factors	Macroecological trends, soil carbon debt	[36,122]

. In particular, mesoscale consequences of decomposition at the landscape level arise from integrated molecular-level interactions. For example, the temperature dependance of any specific enzyme-substrate reaction at the molecular scale [196] is scaled up across millions of microbial cells through a soil pore network (micro-scale) to control the local respiration rates. Such localized biochemical processes, which are often spatially heterogeneous because of soil texture, moisture, and nutrient hot-spots across a field, then translate to field-scale differentiated carbon fluxes [197]. At the broader landscape scale, the integrated outcome of these field-scale differences, as modulated by factors such as regional climatic gradients, land use type (for example, forest patches versus cropland), and hydrologic connectivity, gives rise to the regional net ecosystem carbon balance [101,198]. Regional carbon dynamics can be assessed and predicted using spatial modeling frameworks and geospatial tools, such as Geographic Information Systems (GISs) and remote sensing data, which integrate diverse environmental datasets to map and monitor carbon fluxes and stocks across complex landscapes [199]. For instance, satellite-derived vegetation indices (e.g., NDVI) can be integrated with climate models and soil maps within GIS platforms to simulate regional decomposition rates and predict long-term soil organic carbon (SOC) sequestration [200]. This allows researchers to assess the landscape-scale impact of land use changes, such as reforestation or agricultural management practices, on carbon balances and to identify hotspots of carbon loss or gain [201]. Accordingly, the sub-micron scale chemical interactions between soil minerals and individual organic compounds dictate the mass balance of the whole SOC pool in a watershed [202].

6. Decomposition, Carbon Sequestration, and Cropland Sustainability

6.1. Balancing Decomposition and Carbon Stabilization

Regenerative agricultural systems must balance the beneficial aspects of organic matter decomposition for nutrient cycling with the need for long-term carbon sequestration [39]. Decomposition provides essential nutrients for crop growth but simultaneously releases CO₂ into the atmosphere [38]. The challenge lies in optimizing management practices to maintain adequate nutrient mineralization while maximizing carbon stabilization in persistent soil pools [21]. Recent research has demonstrated that targeting mineral-associated organic matter formation can enhance carbon sequestration without compromising nutrient availability [19].

Thresholds of soil organic carbon are important drivers of effective management interventions. For instance, soils with low carbon concentrations show a different response to nitrogen fertilization compared to soils rich in carbon, which might have implications for carbon sequestration strategies. Partitioning between particulate and mineral-associated organic matter pools may differ depending on the initial amount of soil organic carbon and management history [20,21]. Knowledge of these threshold effects is important for target-specific implementation of carbon sequestration strategies in different agricultural systems [140]. Recent studies also indicate that short-term warming promotes carbon stabilization in mineral-associated fractions in abandoned croplands, implying a strong interaction between climate change and carbon stabilization [25,140]. Microbial CUE is critical in connecting the formation of POC/MAOC to the carbon sequestration strategies [122,203]. For instance, higher CUE indicates that more carbon is assimilated into microbial biomass and then stable necromass, directly enhancing MAOC formation rather than CO₂ efflux [122]. Soil physical properties, such as texture (for example, clay content) and aggregate stability, strongly affect the dynamics of POC and MAOC by controlling physical protection and establishing a microenvironment for microbial activity [204,205]. Fine-textured soils are rich in reactive mineral surfaces that favor the formation of MAOC by stronger organo-mineral associations [204,206]. Under different climate regimes, the balance shifts; in warm and wet conditions, rapid POC decomposition is often linked to increased MAOC formation through microbial turnover and concomitant necromass production [207]. In contrast, severe drought can decrease these processes by inhibiting microbial activity and the disruption of physical protection [207,208]. Therefore, effective SOC sequestration strategies must incorporate land management practices that increase microbial CUE and effects on soil aggregation and consider site-specific climatic conditions to ensure maximum transformation of labile POC to stable MAOC [205,208].

The concept of carbon saturation has been established to interpret the diminishing potential of soil carbon sequestration in agricultural systems [142]. This perspective acknowledges that soil has a limited capacity to stabilize organic matter, with potential consequences for the long-term efficacy of carbon sequestration strategies [134]. Management practices that affect unsaturated carbon pools are more likely to enhance soil carbon storage than those that target saturated fractions [153]. Practices that enhance microbial CUE and promote the stabilization of microbial products may be adopted as ecological strategies to synchronize improvements in nutrient cycling and carbon sequestration [120].

6.2. Role of Microbial Communities in SOC Formation and Loss

Microbial communities contribute to both the loss of soil carbon by decomposition and its formation via necromass production and SOM stabilization [32,209]. This trade-off is modulated by the microbial CUE, community structure, and environmental conditions [210]. The ultimate fate of soil organic carbon is affected by microbial properties such as enzyme production profiles and stress tolerance [211]. Recent research has highlighted that microbial functional diversity is more important than taxonomic diversity in predicting soil carbon outcomes [212]. Unlike taxonomic richness, functional diversity reflects differences in microbial strategies for carbon acquisition, transformation, and stabilization [213,214,215]. Communities with diverse functional traits—such as complementary enzyme systems and metabolic pathways—are better equipped to process a broader range of substrates and direct more carbon into necromass and stable SOM components [9,12,81,216].

Farming methods that promote beneficial microbial communities can simultaneously improve soil carbon sequestration and crop productivity. Cover crops and diverse rotations increase the diversity of microorganisms and the quality of carbon input. Low tillage practices help preserve soil structure and habitat for microbes and promote increased carbon retention [217,218,219]. The combinatorial effect of these practices leads to synergistic changes exceeding the sum of individual management impacts [220,221]. Lu et al. [140] described that catalytic efficiency of soil enzymes can predict temperature sensitivity of soil carbon cycling, underscoring the role of microbially mediated processes in carbon kinetics.

The emerging concept of the MCP emphasizes the central role of microorganisms in transforming plant inputs into stable SOM [25]. This perspective highlights the importance of considering not only the quantity of carbon inputs but also their processing efficiency within the soil microbial community [134,142]. Management practices that enhance microbial CUE while promoting the formation of stable microbial products offer promising pathways for simultaneously improving nutrient cycling and carbon sequestration in cropland systems [153].

Mechanistically, beyond necromass formation, MCP’s efficiency in enhancing SOC sequestration also depends on several other microbial processes, including direct synthesis of recalcitrant microbial metabolites and EPS that act as glues for soil aggregate formation, physically protecting organic matter from decomposition [222]. Additionally, microbial resource acquisition strategies modulate the MCP. For instance, competitive interactions among microbial groups can drive a higher proportion of assimilated carbon toward stable biomass and byproducts rather than respiration [223]. Specific microbial taxa, particularly those with slower growth rates (K-strategists) and high investment in complex biopolymer synthesis, are disproportionately important in forming stable carbon forms via the MCP [224]. Furthermore, the enzymatic breakdown of complex plant litter into simpler compounds by microbes often results in the formation of novel, chemically altered organic molecules that are more prone to adsorption onto mineral surfaces or occlusion within aggregates, representing another facet of the MCP [192]. This highlights a broader feedback loop where microbial activity not only processes carbon inputs but actively transforms them into persistent forms, driven by both intrinsic microbial traits and extrinsic environmental conditions. The interplay between climate (shifts in temperature and moisture regimes) and soil properties (mineral composition and aggregate stability) directly dictates the optimal conditions for these MCP-related mechanisms, influencing microbial community composition toward taxa and metabolic pathways that favor stable SOC formation [122]. The role of different microbial taxa in decomposition processes under different environments is illustrated in Figure 3.

6.3. Effects of Agricultural Practices on Decomposition Dynamics

Different agricultural management practices exert varying influences on decomposition processes and soil carbon cycling. These practices collectively influence microbial traits such as CUE and enzyme activities, which critically determine the fate of SOM [225,226]. Regenerative practices, including cover cropping, reduced tillage, diverse rotations, and agroforestry, generally enhance SOC accumulation [38,227]. Carbon sequestration rates for woody perennial and arable land uses indicate the contribution of different regenerative practices to achieving sequestration in arable cropland systems. Studies indicate that agroforestry and double cover crops have the higher mean sequestration rates, while other practices have a lesser but positive effect on below-ground carbon sequestration [228,229]. These diverse practices increase microbial diversity, CUE, and enzyme activities, thereby promoting greater SOM stabilization [230]. No-till systems combined with cover crops maximize the potential for SOM accumulation [231]. Crop rotation and diversity enhance microbial community complexity and functional redundancy, leading to more stable decomposition [227].

Tillage practices also significantly influence decomposition through their effects on soil structure, aggregate stability, and microbial habitat. Conventional tillage disrupts stable mineral-associated organic matter, resulting in a net loss of SOM [232]. High-intensity tillage and disturbance reduce microbial biomass and efficiency, undermining CUE and SOM protection [233]. Conversely, reduced or no-till systems help maintain soil aggregates and microbial habitats, often leading to higher microbial CUE and enhanced SOC retention [234]. Although the ratio of Gram-positive to Gram-negative bacteria increases with increasing land degradation, the ratio of bacteria to fungi decreases. Generally, fresh organic inputs are preferred by Gram-negative bacteria, whereas Gram-positive bacteria favor recalcitrant or low-quality organic matter for decomposition [235]. These results indicate changes in the quality of SOM and a decrease in microbial ecosystem stability, which may be attributed to the high carbon content that transits microbial communities from commensals to oligotrophic groups and an increase in the soil pH of degraded lands, generating physiological pressure on soil microbes and affecting their competition and reproduction. Conversely, fungi are less sensitive to soil pH than bacteria and are generally more resistant to intense land degradation [236].

Conventional agricultural practices can also lead to environmental disturbances such as water and soil pollution and reduced soil health [237]. These practices often involve intensive use of synthetic fertilizers, pesticides, and other chemical inputs. Excessive use of these chemicals can suppress microbial CUE and enzyme activities, undermining SOM formation and soil health [238]. If applied in excessive concentrations, chemical fertilizers and pesticides can result in the loss of organic matter, a reduction in cellulose-decomposing bacteria, and an increase in soil salinity, thereby affecting the soil structure, nutrients, and microbial diversity and abundance. Hence, conventional farming significantly decreases soil earthworm community, food webs, and microbial diversity [170,239,240]. Soil has the specific ability to filter, adsorb, and precipitate substances. Therefore, soil exposure to biologically active chemicals, such as heavy metals, pesticides, polychlorinated biphenyls and furans, polycyclic carbohydrates, petroleum products, and dioxins, significantly influences soil quality, microbial biocenosis, and ultimately human health [241]. Soil fungi and bacteria play essential roles in pollutant migration, morphological transformation, and decomposition [241,242]. Gram-positive bacteria prefer utilizing complex pollutants more than Gram-negative bacteria [243]. Although soil microbes can actively degrade pollutants, these pollutants may significantly affect microbial ecological succession and kill various microbes, resulting in the loss of resistance in the soil ecosystem.

Persistent organic pollutants further illustrate these impacts. For example, dichlorodiphenyltrichloroethane affects soil respiration and reduces microbial growth and activity. Specifically, it decreases the bacterial and actinomycete counts and inhibits the growth of Trichoderma viride, Botryotrichum species, Alternaria humicola, Sepedonium species, Helmintosporium sativum, Botrytis, Rhizoctonia solani, Mucor species, Azotobacter, and nodulation. Similarly, other pollutants, including aldrin and polychlorinated biphenyls, negatively affect soil fertility, inhibit the growth of nematodes and the nitrifying bacterium Nitrobacter agilis, and decrease the nitrite-oxidizing bacterial count [244,245]. Furthermore, heavy metals may accumulate in high concentrations in the soil. They are persistent and cannot be degraded through metabolic processes, negatively affecting microbial diversity, activity, and biomass [246]. Overall, chemical pollutants tend to lower microbial enzyme activities and CUE, weakening decomposition and SOM protection [247].

Site-specific and precision management strategies (for example, variable-rate fertilizer applications and targeted cover crop use) further influence soil microbial processes. By tailoring interventions to local soil and climate conditions, these approaches can maximize microbial efficiency and carbon retention [248]. The timing and intensity of management interventions create promising effects that persist over multiple growing seasons [40]. Recent research has highlighted the potential of precision management approaches for optimizing decomposition processes based on site-specific soil and climate conditions [153]. These approaches recognize that optimal management strategies vary considerably across different landscape positions and soil types, necessitating spatially explicit recommendations [120]. The development of decision support tools that integrate decomposition science with precision agriculture technologies offers promising opportunities for optimizing both agricultural productivity and environmental outcomes [121].

7. Future Research Directions

Although there has been considerable progress, some key knowledge gaps are still present in the SOM decomposition in croplands. First, there is a lack of comprehensive understanding of the contributions of soil fauna (arthropods, nematodes, and earthworms) to OM decomposition; especially their trophic relationships with microbial communities and impact on microbial CUE and enzyme expression. Therefore, fauna-mediated turnover should be incorporated into trait-based decomposition frameworks in future studies. Second, the soil–microbiome–plant interaction is not only complex but poorly characterized at field scales. Trait-based experimental designs in relation to root exudation, microbial growth kinetics, and necromass formation are required among diverse crop species to determine crop-specific SOM stabilization. Third, the climate change impact on soil microbiomes under different moisture/warming is required to be extensively investigated in the climatic zones. Long-term field trials are essential to predict how precipitation changes, temperature extremes, and drought interact to influence microbial traits (dormancy, enzyme allocation, and necromass production) and thereby MAOM formation. Fourth, there is a pressing need for the standardization of microbial trait measurements such as CUE, growth efficiency, and enzyme stoichiometry across agricultural systems. This allows for cross-study comparisons and model calibration, especially for trait-explicit biogeochemical models, such as MIMICS and CORPSE. Fifth, combining the multi-omics data (metagenomics, transcriptomics, and metabolomics) with the soil physico-chemical models is a major frontier. This is important in the context of quantifying microbial contributions to SOM persistence and predicting community shifts; for example, relationships between the abundance of ligninolytic enzyme genes and soil aggregation models to infer the decomposition of recalcitrant carbon. Sixth, it is necessary to scale up the laboratory results to more realistic field and landscape conditions. Although much of our current understanding originates from these lab microcosms, decomposition performed under natural conditions is spatially heterogeneous. Furthermore, connecting field mesocosms with remote sensing and geospatial modeling (soil moisture sensors, thermal infrared imaging, and NDVI) may efficiently scale microbial-driven decomposition. Lastly, inter-disciplinary efforts need to focus on applicable technologies. With the integration of sensor networks, in situ probes, and HTS of DNA/RNA sequencing, in situ monitoring of soil respiration and redox dynamics can be developed to follow a microbial response. It appears that AI/ML, using multi-site, multi-omics data, can generate adaptive predictive decomposition models for a specific soil–climate–crop combination that would allow for greater accuracy in these predictions.

8. Conclusions

This review emphasizes the critical importance of climate–soil–microbe interactions on SOM decomposition, which is influential in sustaining crop land, carbon sequestration, and nutrient availability. The advancement of multi-omics technologies and microbial network approaches has provided unprecedented understanding of these dynamics at different spatial and temporal scales, highlighting the crucial roles of climate and soil in shaping such dynamics. Microbes are the central players in decomposition, with different groups like bacteria that act on labile carbon, and the fungi that release specialized enzymes to break down recalcitrant materials play distinct complementary roles. Importantly, microbial functional traits, including CUE, dormancy, and growth strategy, are key to decomposition responses and to the fate of carbon in the soil. The formation of microbial necromass, dead microbial cells stabilized by mineral association, is a major component of stable SOM and contributes as a key mechanism in long-term carbon sequestration through the MCP. An enhanced knowledge of these microbial processes directly supports climate-smart agriculture. This suggests that harnessing microbial functioning in sustainable management would provide opportunities for improving carbon sequestration and nutrient cycling. Regenerative farming systems, including cover crops, reduced tillage, agroforestry, and diverse rotations are effective strategies to increase soil microbial diversity, CUE, and enzyme activities, which can favor greater SOM stabilization and agriculture productivity. This highlights the importance of regionally specific recommendations that consider soil, climate, and economic status for the successful and widespread adoption of sustainable organic carbon management. This paper therefore links theoretical developments with their application. In principle, it integrates a mechanistic, multi-scale approach to SOM dynamics, moving beyond simplistic conceptualizations by emphasizing the MCP and the importance of microbial functional diversity. Operationally, it leads to decision-support strategies for developing climate-resilient agricultural systems. By highlighting microbial functions and responses to management, this work guides farmers and policy makers toward successful regenerative strategies that improve both soil health and global food security.