Bioenergetic control of soil carbon dynamics across depth

Earth’s soils contain more carbon in soil organic matter (SOM) than vegetation and the atmosphere combined, but predicting how this reservoir responds to global change is uncertain. Although roughly half of global soil organic carbon (SOC) is stored below 30 cm, SOC turnover time increases from decades/centuries in topsoil to millennia in subsoil, and mechanisms for this depth-dependency remain debated. Proposed explanations include stabilization via mineral protection and physical separation limiting microbial access, and to a lesser extent suboptimal environmental conditions in well-aerated mineral soils. An alternative or complementary view posits strong energy limitation of deep-soil decomposers. Bioenergetic frameworks suggest SOC persists when the energy gained from catabolism is insufficient to offset the energetic costs (notably exoenzyme biosynthesis) required to access and depolymerize SOC. Deep SOC has been observed to have lower energy density and higher thermal stability, implying diminished energy quality with depth. Root-driven processes (rhizosphere priming) can accelerate deep SOC decomposition by providing fresh, energy-rich substrates and by increasing SOC accessibility (e.g., through organic ligands and physical perturbations). The authors hypothesize that slow deep SOC dynamics result from poor SOC energy quality coupled with low root energy supply due to sparse roots at depth. They test this by integrating radiocarbon and thermal analyses with long-term incubations in the presence/absence of continuously 13C/14C-labelled plants across three contrasting mineralogies (cambisol, vertisol, and andosol).

Prior work highlights multiple mechanisms for deep SOC persistence: (1) reduced accessibility to microbes and enzymes via mineral protection (associations with reactive minerals) and physical separation due to low SOC density and spatial heterogeneity; (2) suboptimal conditions (low temperature, anoxia) which are key in permafrost/peatlands but less supported in well-aerated mineral soils; and (3) energy limitation of microbial metabolism in deep environments. Theoretical models emphasize that exoenzyme production costs can limit decomposition unless energy returns exceed investments. A bioenergetic perspective evaluates SOC energy quality through energy density and activation energy, with prior observations of decreased energy density and increased thermal stability at depth indicating poorer energy quality. Rhizosphere priming literature shows roots can stimulate decomposition by supplying labile C and by disrupting organo-mineral associations via organic ligands or altering moisture regimes; however, how mineral reactivity modulates priming sensitivity at depth remained unclear. Meta-analyses also suggest soil type/mineralogy strongly influences deep SOC dynamics and persistence.

Study design: Three temperate, well-aerated mineral soil types in long-term grasslands in Auvergne, France were selected: eutric cambisol (granite parent material), chromic vertisol (basalt), and silandic andosol (trachyandesite). A factorial design crossed two depths (topsoil and subsoil) with three soil types (six treatments, four replicates each). Intact 20-cm soil cores were collected: topsoil from 5–25 cm (A horizon), subsoil from B horizon (cambisol 40–60 cm; vertisol 55–75 cm; andosol 35–55 cm). Field characterization: Cores were sieved (2 mm) and subsampled. SOC concentration, total N, and δ13C were measured by EA-IRMS. SOC fractions were isolated by particle-size fractionation after complete dispersion: <50 µm as mineral-associated organic matter (MAOM) and >50 µm as particulate organic matter (POM); C content determined by EA. Radiocarbon Δ14C of SOC was measured by AMS (ECHOMICADAS, LSCE). SOC turnover time (t) was estimated using a time-dependent, homogeneous one-pool model relating SOC Δ14C to atmospheric Δ14C and radioactive decay (λ=1.21×10−4 yr−1), run from 50 kyr BP to 2016 over t=1–30,000 yr to invert Δ14C to t. Thermal analyses and bioenergetic metrics: Rock-Eval 6 Turbo ramped pyrolysis-oxidation with evolved gas analysis quantified kinetics of SOC thermal decomposition; a regularized inverse method yielded the continuous activation energy distribution, from which mean (µE) and SD (σE) were calculated. Thermal stability indices included T90-HxCy-pyrolysis and T50-CO2 during pyrolysis and oxidation. Hydrogen and oxygen indices (HI, OI) served as proxies for H:C and O:C. Differential scanning calorimetry (TGA-DSC 3+) measured the net enthalpy of combustion (ΔE) over 185–600 °C; ΔE per SOC amount (kJ mol−1 SOM) was computed and used to derive the degree of reduction (YSOC=ΔE/Qo with Qo=109.04 kJ mol−1 per degree of reduction). Return-on-energy-investment (ROI) was defined as ΔE/µE. Microbial biomass C was determined by chloroform fumigation-extraction (0.5 M K2SO4; kEC=0.45). Root density (g dm−3) was measured from dried root mass per core volume. Mineralogical characterization included pHwater, clay content (pipette method), XRD for phyllosilicates, cation exchange capacity and exchangeable cations (cobalt hexamine), and selective dissolutions (citrate-dithionite, oxalate, pyrophosphate) for reactive Fe, Al, Si phases; organo-metal complexes were estimated as Ap−xSip. Plant isotopic labelling and incubations: Microcosms comprised stacked intact cores (three per column) from the same layer, placed in 60-cm PVC pots. Four planted and four unplanted microcosms per treatment (total 48). The C3 grass Dactylis glomerata was grown under greenhouse conditions for 279 days with continuous dual labelling using fossil-fuel CO2 (δ13C≈−35.23‰, Δ14C≈0‰) to deplete plant isotopic signatures; daytime labelled air maintained ~400 ppm CO2. Soil moisture was held at 85±5% WHC via drip irrigation; planted subsoil microcosms received mineral fertilization to match nutrient status with planted topsoil. Two incubation series were conducted at 21.5 °C: (1) Whole microcosm closed-chamber incubations at multiple times (days 76, 139, 174, 201, 242, 272; n=288). CO2 flux and δ13C were measured to partition respiration into native SOC (soil) vs plant-derived components via isotopic mixing equations. (2) At day 279, soil columns were separated into original cores (depth positions) and incubated in 3 L flasks for 24 h (n=144). CO2 was trapped in NaOH; concentrations measured by TOC analyzer, δ13C by EA-IRMS. For subsoil (selected treatments), Δ14C of respired CO2 was measured by AMS to estimate mean age of respired native SOC. Post-incubation, plant and soil materials were analyzed for C, N, δ13C; subsoil root Δ14C measured for selected cases. Rhizosphere priming effect (RPE) was quantified as percent change in native SOC decomposition rate (kSOC) in planted vs unplanted soils. Relationships of kSOC and RPE to plant activity metrics (respiration of plant/root-derived OC, living root density, net rhizodeposition) were analyzed across soil types and depths. Statistical analyses used linear models with soil type as a fixed effect; partial regression plots and effect sizes were reported; n sizes: 12 field cores for Table 1 metrics, 288 microcosm and 144 soil-core incubations for series 1 and 2 respectively.

• Depth gradients: SOC turnover time increased on average 6.9-fold with depth (from 1096±340 to 7566±2033 years), while Δ14C became more negative (−75.8% to −375.8%), [SOC] decreased by 59.4%, POM fraction decreased by 67.9%, and MAOM fraction increased by 6.1% (Table 1).
• Bioenergetic signature: Energy density (ΔE) declined by 27.6% with depth (175.1→126.7 kJ mol−1 SOM). Degree of reduction (YSOC) declined from 3.05 to 2.26, consistent with lower HI (−50%) and higher OI (+23%). Mean activation energy (µE) increased (+2.4 kJ mol−1 SOM) and σE increased (+0.70 kJ mol−1 SOM). Thermal stability indices (T90-HxCy-pyrolysis, T50-CO2-pyrolysis, T50-CO2-oxidation) were all higher in subsoil.
• Energy quality and persistence: ROI (ΔE/µE) declined from 1.10 to 0.78 with depth (−28.7%) and was strongly related to longer SOC turnover times (Fig. 2a). Root density declined by 95.6% (3.21→0.14 g dm−3) and was also tightly linked to longer SOC turnover (Fig. 2b).
• Baseline decomposition without roots: Native SOC decomposition rate (kSOC) in unplanted subsoil was ~3.0-fold smaller than in unplanted topsoil across soil types, mirroring radiocarbon-inferred slower dynamics.
• Rhizosphere priming: Roots markedly accelerated kSOC in both topsoil and subsoil, with proportionally much stronger effects in subsoil. At high plant activity (respiration of plant-derived OC ≈9.94 g C-CO2 m−2 d−1), RPE averaged +64% (topsoil) vs +411% (subsoil). At high root density (≈3.57 g dm−3), RPE averaged +138% (topsoil) vs +535% (subsoil). Subsoil and topsoil kSOC converged at high root activity/density (Figs. 3b, 4b).
• Age of respired C: In unplanted subsoil, respired CO2 Δ14C indicated decomposition of millennia-old SOC (mean ages ~1950–2900 years for cambisol and andosol). With high root densities, mean ages of respired native deep SOC reached ~9,000 years (cambisol) and ~17,000 years (andosol) (Fig. 5).
• Mineralogy effects: Across soil types (cambisol, vertisol, andosol), the depth-related decline in ROI and root density consistently explained slower SOC dynamics. However, sensitivity to priming varied: the andosol (rich in SRO minerals and organo-metal complexes) showed the strongest RPE at high plant activity/root density; vertisol showed intermediate responses; cambisol the weakest among the three. Vertisol SOC exhibited high thermal stability and low Δ14C and OI, suggesting substantial pyrogenic SOC and possibly minor fossil C inputs.

Findings support a bioenergetic control on the depth-dependency of SOC dynamics. Deep SOC exhibits poorer energy quality—lower energy density (lower YSOC, fewer C–H bonds, more oxidized C) and higher activation energy barriers—reducing the net return-on-energy-investment for decomposers and leading to slower turnover. This bioenergetic limitation is exacerbated by low root density in subsoil, limiting energy supply (rhizodeposition) needed to subsidize exoenzyme production and other metabolic costs. Experiments showed that when root activity/density is high, deep SOC decomposition accelerates and can mobilize millennia-old carbon, indicating that energy limitation can be alleviated by root-derived inputs. Mineral interactions contribute to the bioenergetic signature: broader activation energy distributions and increased thermal stability at depth reflect stronger bonding and mineral protection. Contrary to the expectation that strong mineral protection reduces priming, soils with higher mineral reactivity (e.g., andosols) showed greater priming sensitivity, likely because root exudate ligands disrupt organo-mineral associations, increasing accessibility when energy supply is sufficient. Abiotic constraints (temperature, moisture, oxygen) are unlikely to fully explain depth trends in these well-aerated soils, given lower kSOC in subsoils under standardized incubation conditions and the observed decrease in YSOC with depth. The study integrates accessibility and bioenergetic perspectives, proposing they are interdependent: mechanisms limiting accessibility often impose energetic costs, thereby driving persistence when energy supply is low; conversely, rhizosphere processes can overcome both accessibility and energetic constraints when plants invest sufficient energy.

The study demonstrates that the persistence of deep SOC in temperate, well-aerated mineral soils is governed by bioenergetic constraints—low energy density and high activation energy—combined with low root energy supply at depth. A simple ROI metric (ΔE/µE) and root density jointly predict the depth-dependency of SOC turnover across contrasting mineralogies. Root activity can strongly prime deep SOC decomposition, leading to respiration of millennia-old carbon, especially in mineralogically reactive soils where organo-mineral bonds can be disrupted by exudates. These insights caution that global-change-driven increases in rooting depth or management promoting deep-rooted species may destabilize persistent deep SOC and reduce long-term carbon storage. Future work should construct comprehensive SOC budgets balancing priming-induced losses versus potential formation, extend evaluations beyond well-aerated temperate soils, and integrate bioenergetics with accessibility in predictive models.

• Radiocarbon-based turnover estimates assume a homogeneous one-pool SOC model at steady state, an acknowledged simplification that may mask multi-pool dynamics.
• AMS measurements of Δ14C for respired CO2 were limited to selected treatments (cambisol and andosol subsoils) due to cost, reducing generality for the vertisol.
• Microcosm/soil-core approaches, despite efforts to preserve structure, may still introduce disturbance relative to in situ conditions; greenhouse conditions and fertilization of subsoil treatments may influence plant–soil interactions.
• Study systems were temperate, well-aerated mineral soils; findings may not generalize to permafrost, peatlands, or persistently waterlogged environments where abiotic constraints dominate.
• Potential contributions of pyrogenic or fossil carbon (particularly in the vertisol) complicate interpretation of turnover times and thermal signatures.