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Liu Z, Zhang C, Ma J, Peng Q, Du X, Sun S, Cheng J, Peng W, Chen L, Gu Z, Zhang W, Su P, Zhang D. Extraction Methods Determine the Quality of Soil Microbiota Acquisition. Microorganisms 2024; 12:403. [PMID: 38399807 PMCID: PMC10891820 DOI: 10.3390/microorganisms12020403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The soil microbiome plays a key role in plant health. Native soil microbiome inoculation, metagenomic profiling, and high-throughput cultivation require efficient microbe extraction. Sonication and oscillation are the most common methods used to extract soil microbiomes. However, the extraction efficiency of these methods has not been investigated in full. In this study, we compared the culturable microbe numbers, community structures, and alpha diversities among the different methods, including sonication, oscillation, and centrifugation, and their processing times. The study results showed that sonication significantly increases the culturable colony number compared with oscillation and centrifugation. Furthermore, the sonication strategy was found to be the main factor influencing extraction efficiency, but increased sonication time can aid in recovery from this impact. Finally, the extraction processing times were found to have a significant negative relationship with α-diversity among the extracted microbiota. In conclusion, sonication is the main factor for enriching in situ microbiota, and increased extraction time significantly decreases the α-diversity of the extracted microbiota. The results of this study provide insights into the isolation and utilization of different microorganism sources.
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Affiliation(s)
- Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Chi Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Qianze Peng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
| | - Xiaohua Du
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Shu'e Sun
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ju'e Cheng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Weiye Peng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lijie Chen
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Zepei Gu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Weixing Zhang
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Pin Su
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
| | - Deyong Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
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Cao Y, Lu N, Yang D, Mo M, Zhang KQ, Li C, Shang S. Root-knot nematode infections and soil characteristics significantly affected microbial community composition and assembly of tobacco soil microbiota: a large-scale comparison in tobacco-growing areas. Front Microbiol 2023; 14:1282609. [PMID: 38107871 PMCID: PMC10722292 DOI: 10.3389/fmicb.2023.1282609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/23/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction Tobacco root-knot nematode (RKN) is a highly destructive soil-borne disease worldwide. However, there is a lack of research on the relationship between RKN and tobacco root microbial community composition under large-scale geographical conditions in China. Methods In this study, we collected 65 samples from 28 main tobacco-growing areas across 10 provinces in China and conducted 16S rDNA sequencing to investigate the dynamic microbial changes in tobacco soil infected by RKN compared to healthy tobacco soil. Based on the analysis of rhizosphere soil bacterial communities, changes after RKN infection, and soil environmental factors. Results We found the 28 tobacco-growing areas could be divided into two distinct groups with different microbial compositions and varying responses to RKN infection. In group1 of the provinces of Anhui, Henan, Shanxi, and Heilongjiang, Vicinamibacteria dominated the bacterial community, while Acidobacteriae was present in low abundance. In contrast, group2 of the other six provinces (Yunnan, Guizhou, Chongqing, Guangxi, Hubei, and Shandong) exhibited an opposite pattern. After infected by RKN, the genera Chitinophaga increased significant in group 1, while the genera Rhodococcus in group 2 exhibited a substantial increase. Alpha-diversity analysis revealed that RKN-infected tobacco exhibited a richer and more diverse rhizosphere soil bacterial community compared to healthy tobacco in most growing areas. A total of 12 kinds of soil environmental factors were measured in healthy and RKN-infected tobacco soil, and based on the co-occurrence and correlation analysis between environmental factors and microbial species, the pH level, calcium (Ca), magnesium (Mg), phosphorus (P), iron (Fe), and sodium (Na) were identified as key environmental factors influencing the population composition of rhizosphere microorganisms during RKN infection. We observed that RKN infection further increased the pH in weakly alkaline group 1 soil, while weakly acidic group 2 soil experienced a further decrease in pH. Furthermore, we identified three genera as potential biocontrol or plant growth-promoting bacteria for tobacco. Discussion These findings provide valuable reference data for managing RKN disease in different tobacco-growing areas and contribute to the exploration of new and effective biological control methods.
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Affiliation(s)
- Yi Cao
- Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
| | - Ning Lu
- Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
| | - Dongmei Yang
- Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
| | - Minghe Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, China
| | - Caibin Li
- Bijie Tobacco Company of Guizhou Province, Bijie, Guizhou, China
| | - Shenghua Shang
- Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
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Zhang J, Fang H, Zhao Y, Zheng Y, Jiang J, Gu X. Responses of soil nutrients and rhizosphere microbial communities of a medicinal plant Pinelliaternata to vermicompost. 3 Biotech 2023; 13:353. [PMID: 37810193 PMCID: PMC10555985 DOI: 10.1007/s13205-023-03780-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
Vermicomposting is an important strategy for restoring soil function and fertility. However, information on the effects of vermicompost application in intensive Pinellia ternata planting systems has rarely been reported. Here, we focus on the effects of different vermicompost levels and chemical fertilizer (CF) strategies on soil chemical properties, soil enzymes, and soil rhizosphere microbial communities (bacteria and fungi) in a field experiment. Compared to no added fertilizers (CK), vermicompost was more effective than the CF treatment in increasing P. ternata yield. We found that the 5 t ha-1 vermicompost treatment (VC2) significantly increased the tuber yield by 44.43% and 6.55% compared to the CK and CF treatment, respectively, and water-soluble exudates by 6.56% and 9.63% (P < 0.05). The vermicompost and CF treatments significantly increased the total phosphorus (TP), urease (Ure), and soil catalase (Cat) contents (P < 0.05). Compared to the vermicompost and CK treatments, the CF treatment significantly decreased soil organic carbon (SOC), C/N ratio, and soil acid phosphatase (Pac) (P < 0.05). Redundancy analysis (RDA) showed that Ure and total potassium (TK) were the major drivers in the bacterial community, whereas TP, total nitrogen (TN), Pac, and TK were the major drivers in the fungal community. We also found a positive correlation between soil enzyme activities, including between Ure and bacterial genera (Clostridium, Pseudoclavibacter, Stella, Hyphomicrobium, Mesorhizobium, and Adlercreutzia). In summary, vermicompost application promotes P. ternata soil microecosystems and improves soil fertility, soil enzyme activities, and rhizosphere microbial structure and function. Vermicomposting is a novel and promising approach to sustainable ecological cultivation of Chinese herbs via the promotion of soil properties and beneficial organisms.
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Affiliation(s)
- Jianyun Zhang
- College of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
- Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
- International Joint Research Center on Resource Utilization and Quality Evaluation of Traditional Chinese Medicine of Hebei Province, Shijiazhuang, 050200 China
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137 China
| | - Huiyong Fang
- College of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
- Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
- International Joint Research Center on Resource Utilization and Quality Evaluation of Traditional Chinese Medicine of Hebei Province, Shijiazhuang, 050200 China
| | - Yunsheng Zhao
- College of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
- Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
- International Joint Research Center on Resource Utilization and Quality Evaluation of Traditional Chinese Medicine of Hebei Province, Shijiazhuang, 050200 China
| | - Yuguang Zheng
- Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
- International Joint Research Center on Resource Utilization and Quality Evaluation of Traditional Chinese Medicine of Hebei Province, Shijiazhuang, 050200 China
- Department of Pharmaceutical Engineering, Hebei Chemical and Pharmaceutical College, Shijiazhuang, 050026 China
| | - Jianming Jiang
- College of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
| | - Xian Gu
- College of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
- Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
- International Joint Research Center on Resource Utilization and Quality Evaluation of Traditional Chinese Medicine of Hebei Province, Shijiazhuang, 050200 China
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Wang H, Wu C, Zhang H, Xiao M, Ge T, Zhou Z, Liu Y, Peng S, Peng P, Chen J. Characterization of the belowground microbial community and co-occurrence networks of tobacco plants infected with bacterial wilt disease. World J Microbiol Biotechnol 2022; 38:155. [PMID: 35796795 DOI: 10.1007/s11274-022-03347-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/23/2022] [Indexed: 11/25/2022]
Abstract
Characterizing the microbial communities associated with soil-borne disease incidence is a key approach in understanding the potential role of microbes in protecting crops from pathogens. In this study, we compared the soil properties and microbial composition of the rhizosphere soil and roots of healthy and bacterial wilt-infected tobacco plants to assess their potential influence on plant health. Our results revealed that the relative abundance of pathogens was higher in diseased plants than in healthy plants. Moreover, compared with healthy plants, there was a significantly higher microbial alpha diversity in the roots and rhizosphere soil of diseased plants. In addition, we detected a lower abundance of certain plant microbiota, including species in the genera Penicillium, Trichoderma, and Burkholderia in the rhizosphere of diseased plants, which were found to be significantly negatively associated with the relative abundance of Ralstonia. Indeed, compared with healthy plants, the co-occurrence networks of diseased plants included a larger number of associations linked to plant health. Furthermore, structural equation modeling revealed that these specific microbes were correlated with disease suppression, thereby implying that they may play important roles in maintaining plant health. In conclusion, our findings provide important insights into the relationships between soil-borne disease incidence and changes in the belowground microbial community. These findings will serve as a basis for further research investigating the use of specific plant-associated genera to inhibit soil-borne diseases.
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Affiliation(s)
- Haiting Wang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha, 410004, Hunan, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Chuanfa Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Haoqing Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Mouliang Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Tida Ge
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha, 410004, Hunan, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Zhicheng Zhou
- Tobacco Research Institute of Hunan Province, Changsha, 410004, China
| | - Yongjun Liu
- Tobacco Research Institute of Hunan Province, Changsha, 410004, China
| | - Shuguang Peng
- Tobacco Research Institute of Hunan Province, Changsha, 410004, China
| | - Peiqin Peng
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha, 410004, Hunan, China.
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China.
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