soil metagenome Genome sequencing and assembly. soil metagenome

Research background and purpose BACKGROUND: Continuous cropping of Codonopsis codonopsis often leads to continuous cropping obstacles, resulting in a decrease in crop yield and quality. The problem is prominent in the intensive monoculture of high-value cash crops, which is a key problem facing global agriculture. Objective: To explore the structural and functional changes of rhizosphere microbial community under continuous cropping of Codonopsis codonopsis and Codonopsis rhubarb rotation by metagenomics, reveal the mechanism of continuous cropping obstacles, and provide scientific basis for alleviating obstacles and formulating prevention and control measures, so as to improve the yield and quality of Codonopsis codonopsis and promote the sustainable development of the industry. Experimental design and methods Design: The experiment was carried out in the vineyard of Gansu Agricultural University on April 15, 2022. Two groups were set up: continuous cropping (LS) and rotation cropping (DS, with rhubarb as the previous crop). Rhubarb reduces resource competition and maintains soil nutrient balance by virtue of its unique root characteristics. Its secretions can also inhibit harmful pathogenic bacteria. The row spacing of the experimental plot is 35 cm and the plant spacing is 9 cm. After uniformly applying basal fertilizer (urea and diammonium phosphate), the same fertilizer and water management is maintained throughout the process. Sampling: On September 20, 2022, Codonopsis pilosula plants were selected using the five - point sampling method. Rhizosphere soil was obtained by the shaking - root method, and then an appropriate amount of samples was collected by the quadrat method. Methods: Soil physicochemical properties were determined, such as pH measured by PB-10 pH meter (soil-water ratio 1:5), organic matter measured by potassium dichromate volumetric method, etc. Soil enzyme activities were determined with the help of Shanghai Tongwei Biochemical Kit. DNA-related experiments were carried out using the Illumina NovaSeq/Hiue HiSeq platform combined with the whole genome shotgun method, genes were predicted by MetaGeneMark, and the annotation function was compared with the protein database. Soil bacterial diversity index was calculated by QIIME, and the data were analyzed by R software. Research Results Soil physical and chemical properties: continuous cropping significantly reduced soil organic matter, available phosphorus, available potassium and nitrate nitrogen content, the decrease was 9.79%, 15.72%, 11.12%, 13.93%, respectively, ammonium nitrogen increased by about 2.65%, soil pH did not change significantly. Soil enzyme activity: Continuous cropping significantly reduced the activities of soil urease, sucrase, alkaline phosphatase and catalase in rhizosphere, with a decrease of 7.86%, 15.44%, 10.09% and 10.60% respectively. Microbial community: Continuous cropping reduced the diversity and richness of microbial community, and the Simpson and Shannon indices were lower in continuous cropping soils. At the phyla level, the relative abundance of actinomonas increased; at the genus level, the abundance of beneficial microorganisms such as Blastomonas, Pseudomonas, and Sphingomonas increased, and the abundance of Nitrospira, Nitrobacter, and Slow Rhizobium decreased. Microbial function: EggNOG analysis showed that functional clusters such as extracellular structure increased in continuous cropping soils, and functional clusters such as energy production increased in rotation soils. LEfSe analysis showed that the functional levels of KEGG pathways were significantly different between the two cropping modes.