## 1 Introduction  
Karst ecosystem is an ecosystem restricted by geological background which accounts for one-third of the national land area in China [1]. In karst area (KA) with high temperature and humidity, the dissolution of carbonate brings a large amount of calcium ion ( Ca2+) and HCO3- into soil. HCO3- combines with H+ in the water to generate Carbon dioxide (CO2), which increases soil CO2 concentration [2]. The carbonate weathering consumes CO2 and represent large sinks for atmospheric CO2 that can influence global carbon balance [3, 4]. Thereby, carbon cycles during the weathering of carbonate rocks are very important [5], and biological activities catalyze and regulate this process of weathering, thus resulting in alkaline soils rich in calcium [6]. This process also alters soil microbial communities involved in carbon cycling within KA. CO2 is the most important greenhouse gases (GHG) [7] and the global CO2 imbalance is one of the most critical problems for the global carbon cycle [8]. Soil respiration was an important process of CO2 emission and initially used to describe soil metabolic processes [9], and soil aeration, temperature, moisture, and microbial communities influence respiration [10]. Microbial respiration accounts for more than 80% of all soil respiration [11],which indicated that microbes were the main contributor to soil CO\({}_{2}\) emissions [12]. In general, long-term inundation slows down the degradation process of soil organic matter in paddy field, which is conducive to the accumulation of soil organic carbon (SOC). The degradable organic carbon in paddy soil increase aboveground and underground biomass of rice [13], thus enhancing the outflow of root exudates and increasing the microbial biomass [14]. Both decreasing the ratio of carbon to nitrogen [15] and increasing the exogenous organic matter [16] retard soil respiration and increase SOC accumulation in paddy soils. The soil characterized by neutral alkalinity, the metal ions (including Ca\({}^{2+}\)) can not only combine with inorganic carbon [17; 18], but also with carboxyl group of soil organic matter, which changed the microbial community and its utilization of organic matter, thus affecting soil respiration [14; 19]. Consequently, soil respiration and its relation with microbe in rice fields of KA are critical for the accumulation and stability of SOC. Both bacteria and fungi are important microbial taxa that synergistically interact with soil respiration during rice cultivation [20; 21] and determine the carbon sequestration potential of paddy fields [22]. The inter-roots of rice colonization can rapidly limit oxygen and establish anaerobic zones that lead to some microbial populations performing the anaerobic respiration of nitrates and carbonates, thereby accelerating the release of photosynthetically fixed carbon through roots into the surrounding soils [23]. The input of carbon substrates drives the structural and functional changes in soil microbial communities, making the assimilated carbon of microorganisms more stable than aboveground and root-derived carbon [24]. SOC played an important pole in shaping the pattern of soil bacteria and fungi community structures [25], which indicated that increasing biomasses of root and litter stimulated microbial growth in KA [26]. In addition, bacterial and fungal populations are able to increase the stability of calcareous SOC [27] that might reduce the decomposition of soil organic matter. For example, _Flavobacterium_ and _Lysobacter_ dominated the karst area communities and exhibited relative abundances of 1.24-14.73%,which _Flavobacterium_ can decompose organic matter and _Lysobacter_ can synthesize organic matter using CO\({}_{2}\) as a carbon source [25]. Further, numerous bacterial and fungal taxa (such as _Bradyrhizobium_, _Herbspirillum_, _Cellulomonas_, _Blackococcus_, some endophytes and ectomycorrhiz) that are symbiotic with moss plants in KA are able to increase the peroxidase activity of mosses, thereby enhancing the photosynthetic efficiency of the plants [28].