CO₂ fixation is the central mechanism of primary production in almost all ecosystems, and plays a major role in regulating the concentration of atmospheric CO₂. Carbon dioxide accounts for about 50% of the current global warming potential. Soil microorganisms that assimilate CO₂ are widely distributed, and have a great ability to adapt to environmental extremes, such as within volcanic sediments, lake wetlands and the submarine realm. Microbial CO₂ assimilation is of great significance to climate change mitigation and sustainable development for human beings.
It has now been well established that atmospheric concentration of CO₂ can be reduced significantly by adopting management practices to enhance CO₂ sequestration (storage) in cropland soils. Among the approaches for increasing CO₂ sequestration of croplands are soil fertilization management practices, such as returning crop residues to the soil, planting temporarily retired land with grass for stabilization, and integrating nutrient management strategies to diversified cropping systems. Paddy soils are distributed widely throughout the world, and generally are known for their production of greenhouse gasses (N₂O and CH₄). Numerous studies have used molecular techniques to investigate these microbial driving mechanisms. However, few studies have addressed the importance of microbial CO₂ fixation processes in paddy soils. Investigation of the impacts of long-term fertilization on the structure and abundance of CO₂ assimilating bacteria in paddy soils can provide a theoretical basis for the application of information on fertilization of paddy-rice fields. This type of research also may benefit the reduction of greenhouse gas emissions and increase carbon sequestration.
Although carbon fixating microorganisms exhibit a wide range of physiological and ecological traits, most photo- and chemoautotrophic bacteria use ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO), which catalyzes the first rate-limiting step in the Calvin cycle to incorporate atmospheric CO₂. The cbbL gene, which encodes the large subunit of the form I RubisCO is especially useful as a functional marker for significant phylogenetic analyses of CO₂ fixating microorganisms in different ecological systems.
In this study, soil samples were collected from a long-term fertilization experiment, which included a station that received no fertilization (CK), one treated with chemical fertilization (NPK), and one with NPK plus crop residue return (NPKS). The abundance, diversity, and composition of soil-CO₂ fixating bacteria were determined using Polymerase Chain Reaction (PCR), cloning and sequencing, and real-time quantitative PCR of the cbbL gene to explore the effects of long-term fertilization on the structure and abundance of the CO₂ fixation bacterial community. Based on sequence libraries of cbbL genes, our results clearly demonstrate that there was a significant response difference in community composition with respect to long-term fertilization regimes. A total of 165 cbbL genotypes from three different treatment soils were divided into 14 bacterial cbbL gene phylotypes, mainly including Bradyrhizobium, Ralstonia, and Thiobacillus. Facultative autotrophic bacteria, such as Bradyrhizobium and Ralstonia, dominated both in NPK and NPKS treatment soils, while growth of the obligate autotrophic bacteria, such as Thiobacillus and Nitrosospira, were suppressed. LUBSHUFF statistical analyses also demonstrated that cbbL gene libraries of CK, NPK and NPKS treatments were significantly different from one another. The Rarefaction curve indicated that fertilizer addition increases cbbL gene diversity. Thus, the NPK treatment had the highest curve. The abundance of the bacterial cbbL gene ranged from 3.35×10⁸-5.61×10⁸ copies g^-1 soil. Crop residue return NPKS had the highest abundance of bacterial cbbL gene, which was about one half the value of CK.Finally, application of chemicals and organic fertilizers in paddy ecosystems significantly influenced the CO₂ fixating bacterial community structure, and increased bacterial abundance and diversity. These results provide a strong basis for further investigation of fertilization on soil carbon sequestration potential and its related microbial mechanisms.