The soil carbon cycle determined by GeoChip 5.0 in sugarcane and soybean intercropping systems with reduced nitrogen input in South China

Agricultural soil is the most important carbon (C) pool on the Earth's surface and is also a source or sink of greenhouse gases. The C cycle is one of the important biogeochemical processes in the agroecosystem and requires microorganisms to participate in many of the important C cycling pathways, such as C fixation, C degradation, and methane metabolism. Insight into the functions of microbial communities in the C cycle can provide a better understanding of the response and feedback of soil microbes with respect to global climate change. The microarray GeoChip 5.0 was used in this study to detect the specific genes linking C cycling and soil microbial-mediated processes and to evaluate the abundance, diversity and similarity of the detected genes responding to different nitrogen (N) application levels under intercropping treatment. Our results indicated that compositional changes in soil microbial communities elicited by N input have functional implications for C cycling and storage in agroecosystems. We further identified a sugarcane (Saccharum officinarum) field as a C sink in this intercropping system, in which sugarcane/soybean (Glycine max) (1:2) strip intercropping (SB2) at the N1 application rate (SB2-N1) had the largest C sequestration potential and net C balance among all the treatments. Most of the functional genes involved in C cycling with regards to fixation and degradation were separately identified after 4 years of N fertilization and intercropping treatments, and environmental factors were central in shaping the functional gene structure related to the C cycles. Overall, our results suggested that reduced N application combined with intercropping treatment mediates ecosystem functions and may have profound feedback effects on global climate change.