One of our current challenges is to quantify the mechanisms, capacity, and longevity of C stabilization in agricultural lands. The objectives of this study were to evaluate the long‐term (10 yr) role of C input in soil organic carbon (SOC) sequestration and to identify underlying mechanisms of C stabilization in soils. Carbon input and SOC sequestration, as governed by crop management strategies, were assessed across 10 Mediterranean cropping systems. Empirically derived relationships between yield and aboveground plus belowground crop biomass as well as estimates of C contributions from crop residues and manure amendments were used to quantify cumulative C inputs into each cropping system. Soil samples were separated into four aggregate size classes (>2000, 250–2000, 53–250, and <53 μm) and into three soil organic matter (SOM) fractions within the large (>2000 μm) and small (250–2000 μm) macroaggregates. Aggregate stability increased linearly with both C input (r2 = 0.75, p = 0.001) and SOC (r2 = 0.63, p = 0.006). Across the 10 cropping systems, annual soil C sequestration rates ranged from −0.35 to 0.56 Mg C ha−1 yr−1 We found a strong linear relationship (r2 = 0.70, p = 0.003) between SOC sequestration and cumulative C input, with a residue‐C conversion to SOC rate of 7.6%. This linear relationship suggests that these soils have not reached an upper limit of C sequestration (i.e., not C saturated). In addition, C shifted from the <53‐μm fraction in low C input systems to the large and small macroaggregates in high C input systems. A majority of the accumulation of SOC due to additional C inputs was preferentially sequestered in the microaggregates‐within‐small‐macroaggregates (mM). Hence, the mM fraction is an ideal indicator for C sequestration potential in sustainable agroecosystems.

We investigated the fate and rate of stabilization of root vs. residue C and the role of soil aggregates in root‐ vs. residue‐derived C accumulation within long‐term conventional (mineral fertilizer), low‐input (mineral fertilizer and cover crop), and organic (manure and cover crop) cropping systems. Both hairy vetch (Vicia dasycarpa Ten.) roots and residue were 13C labeled in situ and then traced into whole‐soil samples and three soil organic matter (SOM) fractions (coarse particulate organic matter [CPOM, >250 μm], microaggregates [53–250 μm], and silt and clay [<53 μm]). At the end of the maize (Zea mays L.) growing season, ∼52% of the root‐derived C was still present in the soil, while only ∼4% of residue‐derived C remained. These results suggest that root C contributes more to overall C stabilization than residue C, which supports a nascent body of research demonstrating greater retention of root‐derived than residue‐derived C in SOM. The ratio of root‐ to residue‐derived C (an indicator of relative root contribution) was higher in the microaggregates and silt‐and‐clay fractions than the CPOM of low‐input and conventional systems. In contrast, relative root contribution was greater in the whole soil of the organic (6.76) than the conventional (1.43) and low‐input cropping systems (3.24), and particularly greater in the CPOM of the organic system (7.53). This trend mirrored long‐term soil C stocks across the cropping systems, i.e., organic > low input = conventional, and suggests that the CPOM fraction is pivotal to short‐term accumulation of root‐derived C and, ultimately, to long‐term C sequestration under organic crop management.

This study coupled stable isotope probing with phospholipid fatty acid analysis (13C-PLFA) to describe the role of microbial community composition in the short-term processing (i.e., C incorporation into microbial biomass and/or deposition or respiration of C) of root- versus residue-C and, ultimately, in long-term C sequestration in conventional (annual synthetic fertilizer applications), low-input (synthetic fertilizer and cover crop applied in alternating years), and organic (annual composted manure and cover crop additions) maize-tomato (Zea mays – Lycopersicum esculentum) cropping systems. During the maize growing season, we traced 13C-labeled hairy vetch (Vicia dasycarpa) roots and residues into PLFAs extracted from soil microaggregates (53–250 μm) and silt-and-clay (<53 μm) particles. Total PLFA biomass was greatest in the organic (41.4 nmol g-1 soil) and similar between the conventional and low-input systems (31.0 and 30.1 nmol g-1 soil, respectively), with Gram-positive bacterial PLFA dominating the microbial communities in all systems. Although total PLFA-C derived from roots was over four times greater than from residues, relative distributions (mol%) of root- and residue-derived C into the microbial communities were not different among the three cropping systems. Additionally, neither the PLFA profiles nor the amount of root- and residue-C incorporation into the PLFAs of the microaggregates were consistently different when compared with the silt-and-clay particles. More fungal PLFA-C was measured, however, in microaggregates compared with silt-and-clay. The lack of differences between the mol% within the microbial communities of the cropping systems and between the PLFA-C in the microaggregates and the silt-and-clay may have been due to (i) insufficient differences in quality between roots and residues and/or (ii) the high N availability in these N-fertilized cropping systems that augmented the abilities of the microbial communities to process a wide range of substrate qualities. The main implications of this study are that (i) the greater short-term microbial processing of root- than residue-C can be a mechanistic explanation for the higher relative retention of root- over residue-C, but microbial community composition did not influence long-term C sequestration trends in the three cropping systems and (ii) in spite of the similarity between the microbial community profiles of the microaggregates and the silt-and-clay, more C was processed in the microaggregates by fungi, suggesting that the microaggregate is a relatively unique microenvironment for fungal activity.

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