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Cao Y, Li Z, Du P, Ji J, Sun W, Xu J, Liang B. Effects of different dwarfing interstocks on the rhizosphere, endophytic bacteria, and drought resistance of apple trees. Microbiol Res 2024; 283:127690. [PMID: 38461571 DOI: 10.1016/j.micres.2024.127690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/12/2024]
Abstract
Rootstock is commonly used to enhance plant resistance to drought stress. However, it is necessary to investigate the effects of different rootstock, interstock, and scion combinations on rhizosphere and root endophytic bacteria under drought stress. We conducted a pot experiment to investigate how interstock [SH40, Jizhen 1 (J1), and Jizhen 2 (J2)] affects the drought tolerance and nitrogen (N) uptake and utilization of apple trees under drought stress. The results showed that the total dry weight, total chlorophyll content, carotenoid content, photosynthesis rate, and N absorption and utilization efficiency of apple trees decreased significantly, whereas relative electrolyte leakage increased significantly under drought stress. Membership function analysis showed that the apple plants with the J1 interstock had the greatest drought resistance. In addition, drought treatment significantly affected the diversity and composition of rhizosphere and root endophytic communities in all three rootstock/interstock/scion combinations. Further analysis revealed that the relative abundance of the plant pathogen Ralstonia was significantly increased in J2 drought-treated roots, compared to the other groups, whereas those of some potentially beneficial bacteria (0134_terrestrial_group, Phenylobacterium, Ellin6067, Kribbella, Chloronema, and Streptomyces) increased significantly in the J1 drought-treated sample. Co-occurrence network analysis showed that some potentially beneficial bacteria (Ellin6067, S0134_terrestrial_group, Pedomicrobium, and Subgroup_10) were significantly positively correlated with N content. These modifications of the rhizosphere and endophytic bacterial communities may influence the drought resilience and N uptake efficiency of different combinations of interstocks and scions. This study is a much-needed step towards understanding the stress response mechanism of scion-rootstock combinations.
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Affiliation(s)
- Yang Cao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhongyong Li
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Peihua Du
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jiahao Ji
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Wei Sun
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jizhong Xu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Bowen Liang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071001, China.
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Castellano-Hinojosa A, Karlsen-Ayala E, Boyd NS, Strauss SL. Impact of repeated fumigant applications on soil properties, crop yield, and microbial communities in a plastic-mulched tomato production system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170659. [PMID: 38325480 DOI: 10.1016/j.scitotenv.2024.170659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
Pre-plant soil fumigation is widely applied to control nematodes, soil-borne fungal pathogens, and weeds in vegetable crops. However, most of the research evaluating the effect of fumigants on crop yield and soil microbial communities has been done on single compounds despite growers mainly applying fumigant combinations. We studied the effect of different fumigant combinations (chloropicrin, 1,3-dichloropropene, and metam potassium) on soil properties, crop yield, and the soil bacterial and fungal microbiome for two consecutive years in a plastic-mulched tomato production system in Florida (United States). While combinations of fumigants did not improve plant productivity more than the individual application of these products, application of fumigants with >60 % chloropicrin did significantly increase yield. Fumigant combinations had no significant effect on bacterial diversity, but fumigants with >35 % chloropicrin reduced soil fungal diversity and induced temporary changes in the soil bacterial and fungal community composition. These changes included short-term increases in the relative abundance of Firmicutes and Ascomycota, as well as decreases in other bacterial and fungal taxa. Repeated fumigation reduced network complexity and the relative abundance of several predicted bacterial functions and fungal guilds, particularly after fumigation and at end of harvest (3-months post fumigation). A structural equation model (SEM) showed fumigants not only directly impact crop yield, but they can also indirectly determine variations in plant productivity through effects on the soil microbiome. Overall, this study increases our understanding of the environmental and agricultural impacts of fumigants in a plastic-mulched tomato production system.
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Southwest Florida Research and Education Center, Department of Soil, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA
| | - Elena Karlsen-Ayala
- Southwest Florida Research and Education Center, Department of Soil, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA; Northern Research Station, United States Department of Agriculture, Forest Service, 51 Millpond Road, Hamden, CT 06517, USA
| | - Nathan S Boyd
- Gulf Coast Research and Education Center, Department of Horticulture, Institute of Food and Agricultural Sciences, University of Florida, 14625 C.R. 672, Wimauma, FL 33598, USA
| | - Sarah L Strauss
- Southwest Florida Research and Education Center, Department of Soil, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA.
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Andargie YE, Lee G, Jeong M, Tagele SB, Shin JH. Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere. FRONTIERS IN PLANT SCIENCE 2023; 14:1301698. [PMID: 38116158 PMCID: PMC10728675 DOI: 10.3389/fpls.2023.1301698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This is due to the involvement of various factors that determine microbiome assembly and result in an increased complexity of microbial networks. Thus, a comprehensive analysis of critical factors that influence microbiome assembly in the rhizosphere will enable scientists to design intervention techniques to reshape the rhizosphere microbiome structure and functions systematically. In this review, we give highlights on fundamental concepts in soil suppressiveness and concisely explore studies on how plants monitor microbiome assembly and homeostasis. We then emphasize key factors that govern pathogen-suppressive microbiome assembly. We discuss how pathogen infection enhances plant immunity by employing a cry-for-help strategy and examine how domestication wipes out defensive genes in plants experiencing domestication syndrome. Additionally, we provide insights into how nutrient availability and pH determine pathogen suppression in the rhizosphere. We finally highlight up-to-date endeavors in rhizosphere microbiome manipulation to gain valuable insights into potential strategies by which microbiome structure could be reshaped to promote pathogen-suppressive soil development.
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Affiliation(s)
- Yohannes Ebabuye Andargie
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Plant Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Setu Bazie Tagele
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
- Next Generation Sequencing (NGS) Core Facility, Kyungpook National University, Daegu, Republic of Korea
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Shi M, Qin T, Cheng Z, Zheng D, Pu Z, Yang Z, Lim KJ, Yang M, Wang Z. Exploring the Core Bacteria and Functional Traits in Pecan (Carya illinoinensis) Rhizosphere. Microbiol Spectr 2023; 11:e0011023. [PMID: 37310220 PMCID: PMC10433825 DOI: 10.1128/spectrum.00110-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/19/2023] [Indexed: 06/14/2023] Open
Abstract
Pecan (Carya illinoinensis) and Chinese hickory (Carya cathayensis) are important commercially cultivated nut trees. They are phylogenetically closely related plants; however, they exhibit significantly different phenotypes in response to abiotic stress and development. The rhizosphere selects core microorganisms from bulk soil, playing a pivotal role in the plant's resistance to abiotic stress and growth. In this study, we used metagenomic sequencing to compare the selection capabilities of seedling pecan and seedling hickory at taxonomic and functional levels in bulk soil and the rhizosphere. We observed that pecan has a stronger capacity to enrich rhizosphere plant-beneficial microbe bacteria (e.g., Rhizobium, Novosphingobium, Variovorax, Sphingobium, and Sphingomonas) and their associated functional traits than hickory. We also noted that the ABC transporters (e.g., monosaccharide transporter) and bacterial secretion systems (e.g., type IV secretion system) are the core functional traits of pecan rhizosphere bacteria. Rhizobium and Novosphingobium are the main contributors to the core functional traits. These results suggest that monosaccharides may help Rhizobium to efficiently enrich this niche. Novosphingobium may use a type IV secretion system to interact with other bacteria and thereby influence the assembly of pecan rhizosphere microbiomes. Our data provide valuable information to guide core microbial isolation and expand our knowledge of the assembly mechanisms of plant rhizosphere microbes. IMPORTANCE The rhizosphere microbiome has been identified as a fundamental factor in maintaining plant health, helping plants to fight the deleterious effects of diseases and abiotic stresses. However, to date, studies on the nut tree microbiome have been scarce. Here, we observed a significant "rhizosphere effect" on the seedling pecan. We furthermore demonstrated the core rhizosphere microbiome and function in the seedling pecan. Moreover, we deduced possible factors that help the core bacteria, such as Rhizobium, to efficiently enrich the pecan rhizosphere and the importance of the type IV system for the assembly of pecan rhizosphere bacterial communities. Our findings provide information for understanding the mechanism of the rhizosphere microbial community enrichment process.
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Affiliation(s)
- Mengting Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Tao Qin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zhitao Cheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Dingwei Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zhenyang Pu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zhengfu Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Kean-Jin Lim
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Menghua Yang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, Zhejiang, China
- Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, Hangzhou, Zhejiang, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
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