Tillage systems can changes in soil organic carbon dynamics and soil microbial biomass by changing aggregate formation and C distribution within the aggregate. However, the effects of tillage method or straw return on soil organic C (SOC) have showed inconsistent results in different soil/climate/ cropping systems. Soil TOC and labile organic C fractions contents were significantly affected by straw returns, and were higher under straw return treatments than non-straw return at three depths. The soil organic carbon (SOC) stock in bulk soil was 40.2-51.1% higher in the 0.00-0.05 m layer and 11.3-17.0% lower in the 0.05-0.20 m layer in NT system no-tillage without straw (NT-S) and with straw (NT+S), compared to the MP system moldboard plow without straw (MP-S) and with straw (MP+S), respectively. Residue incorporation caused a significant increment of 15.65% in total water stable aggregates in surface soil (0– 15 cm) and 7.53% in sub-surface soil (15–30 cm). In surface soil, the maximum (19.2%) and minimum (8.9%) proportion of total aggregated carbon was retained with >2 mm and 0.1–0.05 mm size fractions, respectively. At 0–7 cm depth, soil MBC was significantly higher under plowing tillage than rotary tillage, but EOC was just opposite. Rotary tillage had significantly higher soil TOC than plowing tillage at 7–14 cm depth. However, at 14– 21 cm depth, TOC, DOC and MBC were significantly higher under plowing tillage than rotary tillage except for EOC. A considerable proportion of the total SOC was found to be captured by the macro-aggregates (>2–0.25 mm) under both surface (67.1%) and sub-surface layers (66.7%) leaving rest amount in micro-aggregates and ‘silt + clay’ sized particles. Application of inorganic fertilizer could sustain soil organic carbon (SOC) concentrations, whereas long-term application of manure alone or combined with NPK (M and NPK + M) significantly increased SOC contents compared with the unfertilized control. Manure application significantly increased the proportion of large macro-aggregates (> 2000 µm) compared with the control, while leading to a corresponding decline in the percentage of micro-aggregates (53–250 µm). Carbon storage in the intra-aggregate particulate organic matter within micro-aggregates was enhanced from 9.8% of the total SOC stock in the control to 19.7% and 18.6% in the M and NPK + M treatments, respectively. The shift in SOC stocks towards micro-aggregates is beneficial for long-term soil C sequestration. Moreover, the differences in the micro-aggregate protected C accounted, on average, for 39.8% of the differences in total SOC stocks between the control and the manure-applied treatments. Thus, we suggest that the micro-aggregate protected C is promising for assessing the impact of conventional and conservation agriculture on SOC storage in the vertisol. Soil disturbance by tillage leads to destruction of the protective soil aggregate. This in turn exposes the labile C occluded in these aggregates to microbial breakdown. The present study found that SOC change was significantly influenced by the crop residue retention rate and the edaphic variable of initial SOC content.

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