Processes that lead to soil organic carbon (SOC) protection depend on both soil porosity and structure organization, as well as chemical and biological properties. In particular, the soil micro-nano porosity (<30 μm) regulates microorganism accessibility to the soil pore system and offers surfaces for organic carbon adsorption and intercalation into soil minerals. The aim of this work was to investigate how pore size distribution can selectively protect specific carbon pools in different aggregate size fractions, by considering the effects of long-term application of farmyard manure (FYM) and mineral (Min) fertilization. Macroaggregates (250–2000 μm), microaggregates (53–250 μm), and silt–clay (<53 μm) fractions of three different soils (clayey, peaty, and sandy) were separated by wet sieving technique and then subjected to chemical and physical analysis. Sample porosity and pore size distribution were analyzed using mercury intrusion porosimetry (MIP), while SOC chemical structure was characterized by means of nuclear magnetic resonance (13C cross-polarization–magic angle spinning nuclear magnetic resonance (CP MAS 13C NMR)) and diffuse reflectance infrared Fourier transform (DRIFT) spectroscopies. Results showed that FYM increased organic (OC) and humic carbon (HC) content compared to the Min fertilization and unfertilized soils. However, it caused a gradual decrease in O,N-alkyl C, and alkyl C of humic C from macroaggregate to silt–clay fractions, suggesting an advanced state of humic component degradation as revealed by CP MAS 13C NMR, DRIFT analyses. MIP analysis showed a clear increase of micropores (5–30 μm) and cryptopores (0.0035–0.1 μm) from macroaggregate to silt–clay fractions, while minor differences were observed among the treatments. The application of principal component analysis to mineral soil fractions identified the formation of three main clusters, where (i) macroaggregates of clayey soil were mainly associated to cryptopores and OC and (ii) microaggregates and silt–clay fraction were mainly isolated by carbonyl C, ultramicropores, and total porosity. The third cluster was associated with medium and fine sand of the sand soil fraction as coupled with O,N-alkyl C, anomeric C, mesopores, and HC/OC ratio. Overall, this study indicates that pore size distribution may be a valuable indicator of soil capacity to sequester carbon, due to its direct influence on SOC linkages with soil aggregates and the positive effects against SOC decomposition phenomena. In this context, micropore- to nanopore-dominated structures (e.g., clayey soil) were able to protect OC compounds by interacting with mineral surfaces and intercalation with phyllosilicates, while meso/macropore-dominated structures (i.e., sandy soil) exhibited their low ability to protect the organic components.
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