Effects of Garlic Rotation and Organic Fertilizer Application on Bacterial Community Structure in Rhizosphere Soil of Continuous Cropping Tomato

Abstract

16S/18S/ITS's amplicon and metagenome sequencing had been used extensively to investigate the root mi- crobial community structure of crops and model plants. In this study, the rhizosphere soils of the continuous cropping (Control), garlic rotation and organic fertilizer application tomato plants were taken as the test samples, respectively, to measure the microbial community structure and soil enzyme activities. The results showed that both planting modes had significant effects on the microecology of continuous cropping tomato rhizosphere soil. After garlic rotation, the diversity (Shannon index and Simpson index) and relative abundance (Ace index and Chao1 index) of soil bacterial community decreased significantly in the early stage, but increased significantly in the later stage. These changes could be significantly alleviated by the application of organic fertilizer. During the whole growth period of tomato plants, the activities the six soil enzymes (sucrase, catalase, urease, protease, amylase and alkaline phosphatase) were all the highest in the organic fertilizer application plot, followed by the rotation plot and the continuous cropping plot. With the extension of planting time, the activities of soil protease, urease and alkaline phosphatase increased gradually, while that of sucrase decreased gradually. Catalase activity initially increased and then decreased, while amylase activity did not change significantly with time. After garlic rotation, mortality rate of tomato plants decreased significantly, and all growth indexes were significantly better than those of the control treatment. To sum up, garlic/tomato rotation can effectively improve the soil environment and alleviate the continuous cropping obstacle of tomatoes in greenhouse. Moreover, rotation combining with organic fertilizer application can acquire the most obvious mitigation effect.

Aggregate size matters: The impact of soil aggregation on microbial community assembly and suppression of tomato Ralstonia disease

“…With the long-term monoculture of tomatoes, these fields suffered seriously from tomato bacterial wilt caused by a soil-borne pathogen Ralstonia solanacearum (Liu et al, 2018;. In the 7th cropping cycle from which we collected the samples, the disease incidence of these field blocks ranged from approximately 21.4% to 68.8% (Zhao, 2020) based upon visible symptoms of tomato bacterial wilt (e.g., initial wilting of upper leaves followed by complete wilting of all leaves) (Vanitha et al, 2009).…”

“…PCR amplicons (Supplementary Information) total soil DNA were subjected to DNA sequencing using an Illumina Miseq PE250 platform (Illumina Inc., CA, US) at Personal Biotechnology Co., Ltd. (Shanghai, China) to determine the bacterial community compositions. The raw rhizosphere amplicon sequencing data was obtained from Zhao (Zhao, 2020), which was processed using the same protocol for DNA extraction and MiSeq sequencing, as described in the Supplementary Information.…”

“…We used rhizosphere amplicon sequencing data from Zhao (2020) to identify the ASV that corresponds to the pathogen of tomato Ralstonia disease and its potential inhibitors in the rhizosphere, which allowed us to investigate their distribution across soil aggregate size classes. The rhizosphere samples were the soils that remained on the tomato roots after being shaken, they were collected by root wash and centrifugation.…”

“…In addition to the newly generated data from the whole soil and soil aggregate samples, bioinformatics analysis also included rhizosphere sample data from Zhao (Zhao, 2020). Raw paired-end reads were processed using QIIME2-2021.8 (Bolyen et al, 2019) according to the standard pipeline.…”