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Xu X, Luo Q, Wei Q, Jiang S, Dong C, Faruque MO, Huang Z, Xu Z, Yin C, Zhu Z, Hu X. The Deterioration of Agronomical Traits of the Continuous Cropping of Stevia Is Associated With the Dynamics of Soil Bacterial Community. Front Microbiol 2022; 13:917000. [PMID: 35847059 PMCID: PMC9277660 DOI: 10.3389/fmicb.2022.917000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/12/2022] [Indexed: 11/25/2022] Open
Abstract
Stevia rebaudiana Bertoni is grown worldwide as an important, natural sweetener resource plant. The yield of steviol glycosides (SVglys) is greatly influenced by continuous cropping. In this study, we collected the roots, rhizosphere soils, and bulk soils from 2 years of continuous cropping (Y2) and 8 years of continuous cropping (Y8). A high-throughput sequencing technology based on Illumina Hiseq 2500 platform was used to study the structure and diversity of bacterial communities in the roots and soils of stevia with different years of continuous cropping. The results demonstrated that although the content of a group of SVglys was significantly increased in stevia of long-term continuous cropping, it inhibited the growth of plants and lowered the leaf dry weight; as a result, the total amount of SVglys was significantly decreased. Meanwhile, continuous cropping changed the physicochemical properties and the bacterial composition communities of soil. The different sampling sources of the root, rhizosphere soil, and bulk soil had no impact on the richness of bacterial communities, while it exhibited obvious effects on the diversity of bacterial communities. Continuous cropping had a stronger effect on the bacterial community composition in rhizosphere soil than in root and bulk soil. Based on linear discriminant analysis effect size (LEfSe), in the rhizosphere soil of Y8, the relative abundance of some beneficial bacterial genera of Sphingomonas, Devosia, Streptomyces, and Flavobacterium decreased significantly, while the relative abundance of Polycyclovorans, Haliangium, and Nitrospira greatly increased. Moreover, the soil pH and nutrient content, especially the soil organic matter, were correlated with the relative abundance of predominant bacteria at the genus level. This study provides a theoretical basis for uncovering the mechanism of obstacles in continuous stevia cropping and provides guidance for the sustainable development of stevia.
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Affiliation(s)
- Xinjuan Xu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan, China
| | - Qingyun Luo
- Department of Traditional Chinese Medicinal Materials, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Qingyun Luo
| | - Qichao Wei
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan, China
| | - Shangtao Jiang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization/Educational Ministry Engineering Center of Resource-Saving Fertilizers/Jiangsu Collaborative Innovation Center of Solid Organic Waste, Nanjing Agricultural University, Nanjing, China
| | - Caixia Dong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization/Educational Ministry Engineering Center of Resource-Saving Fertilizers/Jiangsu Collaborative Innovation Center of Solid Organic Waste, Nanjing Agricultural University, Nanjing, China
| | - Mohammad Omar Faruque
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chittagong, Bangladesh
| | - Zhongwen Huang
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan, China
| | - Zhenghua Xu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Changxi Yin
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zaibiao Zhu
- Department of Traditional Chinese Medicinal Materials, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xuebo Hu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Xuebo Hu
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Khan AL, Asaf S, M. Abed RM, Ning Chai Y, N. Al-Rawahi A, Mohanta TK, Al-Rawahi A, Schachtman DP, Al-Harrasi A. Rhizosphere Microbiome of Arid Land Medicinal Plants and Extra Cellular Enzymes Contribute to Their Abundance. Microorganisms 2020; 8:microorganisms8020213. [PMID: 32033333 PMCID: PMC7074696 DOI: 10.3390/microorganisms8020213] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 02/07/2023] Open
Abstract
Revealing the unexplored rhizosphere microbiome of plants in arid environments can help in understanding their interactions between microbial communities and plants during harsh growth conditions. Here, we report the first investigation of rhizospheric fungal and bacterial communities of Adenium obesum, Aloe dhufarensis and Cleome austroarabica using next-generation sequencing approaches. A. obesum and A. dhufarensis grows in dry tropical and C. austroarabica in arid conditions of Arabian Peninsula. The results indicated the presence of 121 fungal and 3662 bacterial operational taxonomic units (OTUs) whilst microbial diversity was significantly high in the rhizosphere of A. obesum and A. dhufarensis and low in C. austroarabica. Among fungal phyla, Ascomycota and Basidiomycota were abundantly associated within rhizospheres of all three plants. However, Mucoromycota was only present in the rhizospheres of A. obesum and A. dhufarensis, suggesting a variation in fungal niche on the basis of host and soil types. In case of bacterial communities, Actinobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia were predominant microbial phyla. These results demonstrated varying abundances of microbial structure across different hosts and locations in arid environments. Rhizosphere’s extracellular enzymes analysis revealed varying quantities, where, glucosidase, cellulase, esterase, and 1-aminocyclopropane-1-carboxylate deaminase were significantly higher in the rhizosphere of A. dhufarensis, while phosphatase and indole-acetic acid were highest in the rhizosphere of A. obesum. In conclusion, current findings usher for the first time the core microbial communities in the rhizospheric regions of three arid plants that vary greatly with location, host and soil conditions, and suggest the presence of extracellular enzymes could help in maintaining plant growth during the harsh environmental conditions.
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Affiliation(s)
- Abdul Latif Khan
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
- Correspondence: (A.L.K.); (A.A.-H.)
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Raeid M. M. Abed
- Sultan Qaboos University, College of Science, Biology Department, Muscat 123, Sultanate of Oman;
| | - Yen Ning Chai
- Department of Agronomy and Horticulture and Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (Y.N.C.); (D.P.S.)
| | - Ahmed N. Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
| | - Daniel P. Schachtman
- Department of Agronomy and Horticulture and Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (Y.N.C.); (D.P.S.)
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Sultanate of Oman; (S.A.); (A.N.A.-R.); (T.K.M.); (A.A.-R.)
- Correspondence: (A.L.K.); (A.A.-H.)
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Montanari-Coelho KK, Costa AT, Polonio JC, Azevedo JL, Marin SRR, Fuganti-Pagliarini R, Fujita Y, Yamaguchi-Shinozaki K, Nakashima K, Pamphile JA, Nepomuceno AL. Endophytic bacterial microbiome associated with leaves of genetically modified (AtAREB1) and conventional (BR 16) soybean plants. World J Microbiol Biotechnol 2018; 34:56. [PMID: 29594576 DOI: 10.1007/s11274-018-2439-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
Abstract
Plant leaves (phyllosphere) have a great potential for colonization and microbial growth, consisting of a dynamic environment in which several factors can interfere with the microbial population structure. The use of genetically modified (GM) plants has introduced several traits in agriculture, such as the improvement of plant drought tolerance, as observed in the AtAREB1 transcription factor overexpression in soybean (Glycine max L. Merrill). The present study aimed at investigating the taxonomic and functional profile of the leaf microbial community of bacteria found in GM (drought-tolerant event 1Ea2939) and conventional (BR 16) soybean plants. Bacterial DNA was extracted from leaf samples collected from each genotype and used for microbial diversity and richness analysis through the MiSeq Illumina platform. Functional prediction was performed using the PICRUSt tool and the STAMP v 2.1.3 software. The obtainment of the GM event 1Ea2939 showed minimum effects on the microbial community and in the potential for chemical-genetic communication, i.e. in the potential for symbiotic and/or mutualistic interaction between plants and their natural microbiota.
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Affiliation(s)
| | - Alessandra Tenório Costa
- Departamento de Biotecnologia, Genética e Biologia Celular (DBC), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Julio Cesar Polonio
- Departamento de Biotecnologia, Genética e Biologia Celular (DBC), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - João Lúcio Azevedo
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Renata Fuganti-Pagliarini
- Empresa Brasileira de Pesquisa Agropecuária, Centro Nacional de Pesquisa de Soja (EMBRAPA/Soja), Londrina, Brazil
| | - Yasunari Fujita
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | | | - Kazuo Nakashima
- Laboratory of Plant Molecular Physiology, Tokyo University, Tokyo, Japan
| | - João Alencar Pamphile
- Departamento de Biotecnologia, Genética e Biologia Celular (DBC), Universidade Estadual de Maringá, Maringá, Paraná, Brazil.
| | - Alexandre Lima Nepomuceno
- Empresa Brasileira de Pesquisa Agropecuária, Centro Nacional de Pesquisa de Soja (EMBRAPA/Soja), Londrina, Brazil
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Khan AL, Asaf S, Al-Rawahi A, Lee IJ, Al-Harrasi A. Rhizospheric microbial communities associated with wild and cultivated frankincense producing Boswellia sacra tree. PLoS One 2017; 12:e0186939. [PMID: 29053752 PMCID: PMC5650177 DOI: 10.1371/journal.pone.0186939] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Boswellia sacra, a frankincense producing endemic tree, has been well known for its cultural, religious and economic values. However, the tree has been least explored for the associated microsymbiota in the rhizosphere. The current study elucidates the fungal and bacterial communities of the rhizospheric regions of the wild and cultivated B. sacra tree populations through next generation sequencing. The sequence analysis showed the existence of 1006±8.9 and 60.6±3.1 operational taxonomic unit (OTUs) for bacterial and fungal communities respectively. In fungal communities, five major phyla were found with significantly higher abundance of Ascomycota (60.3%) in wild population and Basidiomycota (52%) in cultivated tree rhizospheres. Among bacterial communities, 31 major phyla were found, with significant distribution of Actinobacteria in wild tree rhizospheres, whereas Proteobacteria and Acidobacteria were highly abundant in cultivated trees. The diversity and abundance of microbiome varied significantly depending upon soil characteristics of the three different populations. In addition, significantly higher glucosidases, cellulases and indole-3-acetic acid were found in cultivated tree’s rhizospheres as compared to wild tree populations. for these plants to survive the harsh arid-land environmental conditions. The current study is a first comprehensive work and advances our knowledge about the core fungal and bacterial microbial microbiome associated with this economically important tree.
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Affiliation(s)
- Abdul Latif Khan
- UoN Chair of Oman’s Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa, Oman
| | - Sajjad Asaf
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ahmed Al-Rawahi
- UoN Chair of Oman’s Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa, Oman
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ahmed Al-Harrasi
- UoN Chair of Oman’s Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa, Oman
- * E-mail:
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