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Li J, Hou L, Zhang G, Cheng L, Liu Y. Comparative Analysis of Rhizosphere and Endosphere Fungal Communities in Healthy and Diseased Faba Bean Plants. J Fungi (Basel) 2024; 10:84. [PMID: 38276030 PMCID: PMC10817651 DOI: 10.3390/jof10010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
This study used the ITS approach based on Illumina MiSeq sequencing to assess the endosphere and rhizosphere fungal communities in healthy and diseased faba bean plants. The findings indicate that the most predominant phyla in all samples were Ascomycota (49.89-99.56%) and Basidiomycota (0.33-25.78%). In healthy endosphere samples, Glomeromycota (0.08-1.17%) was the only predominant phylum. In diseased endosphere samples, Olpidiomycota (0.04-1.75%) was the only predominant phylum. At the genus level, Penicillium (0.47-35.21%) was more abundant in rhizosphere soil, while Paraphoma (3.48-91.16%) was predominant in the endosphere roots of faba bean plants. Significant differences were observed in the alpha diversity of rhizosphere samples from different germplasm resources (p < 0.05). The fungal community structures were clearly distinguished between rhizosphere and endosphere samples and between healthy and diseased endosphere samples (p < 0.05). Saccharomyces was significantly enriched in diseased endosphere samples, whereas Apiotrichum was enriched in healthy endosphere samples. Vishniacozyma and Phialophora were enriched in diseased rhizosphere samples, while Pseudogymnoascus was enriched in healthy rhizosphere samples. Diseased samples displayed more strongly correlated genera than healthy samples. Saprotrophs accounted for a larger proportion of the fungal microbes in rhizosphere soil than in endosphere roots. This study provides a better understanding of the composition and diversity of fungal communities in the rhizosphere and endosphere of faba bean plants as well as a theoretical guidance for future research on the prevention or control of faba bean root rot disease.
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Affiliation(s)
- Juan Li
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Lu Hou
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Gui Zhang
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Liang Cheng
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yujiao Liu
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
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Liu Y, Lu W, Li Y, Zhai B, Zhang B, Qin H, Xu P, Yang Y, Fan S, Wang Y, Li C, Zhao J, Ai J. Diversity of Endophytes of Actinidia arguta in Different Seasons. Life (Basel) 2024; 14:149. [PMID: 38276278 PMCID: PMC10819999 DOI: 10.3390/life14010149] [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: 12/12/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
The seasonal changes in environmental conditions can alter the growth states of host plants, thereby affecting the living environment of endophytes and forming different endophytic communities. This study employs Illumina MiSeq next-generation sequencing to analyze the 16SrRNA and ITS rDNA of endophytes in 24 samples of Actinidia arguta stem tissues across different seasons. The results revealed a high richness and diversity of endophytes in Actinidia arguta, with significant seasonal variations in microbial community richness. This study identified 897 genera across 36 phyla for bacteria and 251 genera across 8 phyla for fungi. Notably, 69 bacterial genera and 19 fungal genera significantly contributed to the differences in community structure across seasons. A distinctive feature of coexistence in the endophytic community, both specific and conservative across different seasons, was observed. The bacterial community in winter demonstrated significantly higher richness and diversity compared to the other seasons. Environmental factors likely influence the optimal timing for endophyte colonization. Solar radiation, temperature, precipitation, and relative humidity significantly impact the diversity of endophytic bacteria and fungi. In addition, seasonal variations show significant differences in the nutritional modes of fungal endophytes and the degradation, ligninolysis, and ureolysis functions of bacterial endophytes. This study elucidates the potential role of endophytes in assisting Actinidia arguta in adapting to seasonal changes and provides a theoretical basis for further exploration of functional microbial strains.
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Affiliation(s)
- Yingxue Liu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Wenpeng Lu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Yang Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (Y.L.); (B.Z.); (J.Z.)
| | - Boyu Zhai
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (Y.L.); (B.Z.); (J.Z.)
| | - Baoxiang Zhang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Hongyan Qin
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Peilei Xu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Yiming Yang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Shutian Fan
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Yue Wang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Changyu Li
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (Y.L.); (W.L.); (B.Z.); (H.Q.); (P.X.); (Y.Y.); (S.F.); (Y.W.); (C.L.)
| | - Jianjun Zhao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (Y.L.); (B.Z.); (J.Z.)
| | - Jun Ai
- College of Horticulture, Jilin Agricultural University, Changchun 130112, China
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Huang H, Huang H, Xia Z, Yang Y, Jiang X, Huang C, Yang Y, Wang D, Chen Z. Sequencing, Functional Annotation, and Interaction Prediction of mRNAs and Candidate Long Noncoding RNAs Originating from Tea Leaves During Infection by the Fungal Pathogen Causing Tea Leaf Spot, Didymella bellidis. PLANT DISEASE 2023; 107:2830-2834. [PMID: 37707825 DOI: 10.1094/pdis-05-22-1240-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Tea leaf spot caused by Didymella bellidis can seriously reduce the productivity and quality of tea (Camellia sinensis var. sinensis) leaves in Guizhou Province, southwest China. Analysis of the relationship between messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) of tea could provide insights into the plant-pathogen interaction. In this study, high-throughput sequencing of mRNAs and lncRNAs from tea leaves during infection by D. bellidis was conducted using the Illumina Novaseq 6000 platform. Infection by D. bellidis hyphae resulted in up- or downregulation of 553 and 191 of the differentially expressed mRNAs (DEmRNAs), respectively. As the S gene number (total number of genes with significantly differential expression annotated in the specified Gene Ontology [GO] database), three were enriched with respect to the defense response to the fungus at the biological process level. Expression of the DEmRNAs peroxidase 21 (TEA000222.1) and mcht-2 (TEA013240.1) originating from tea leaves were upregulated during challenge by D. bellidis hyphae, whereas expression of the LRR receptor-like serine/threonine-protein kinase ERECTA (TEA016781.1) gene was downregulated. The infection of D. bellidis hyphae resulted in up- or downregulation of 227 and 958 of the differentially expressed lncRNAs (DElncRNAs). The DEmRNAs associated with uncharacterized LOC101499401 (TEA015626.1), uncharacterized protein (TEA014125.1), structural maintenance of chromosomes protein 1 (TEA001660.1), and uncharacterized protein (TEA017727.1) occurred as a result of cis regulation by DElncRNAs MSTRG.20036, MSTRG.3843, MSTRG.26132, and MSTRG.56701, respectively. The expression profiling and lncRNA/mRNA association prediction in the tea leaves infected by D. bellidis will provide a valuable resource for further research into disease resistance.
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Affiliation(s)
- Honglin Huang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Hongke Huang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
- College of Tea Science, Guizhou University, Guiyang, Guizhou 550025, China
| | - Zhongqiu Xia
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
- College of Tea Science, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yuqin Yang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
- College of Tea Science, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xinyue Jiang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Chen Huang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yuanyou Yang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Delu Wang
- College of Forestry, Guizhou University, Guiyang, Guizhou 550025, China
| | - Zhuo Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
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Liu J, Abdelfattah A, Wasserman B, Wisniewski M, Droby S, Fazio G, Mazzola M, Wu X. Contrasting effects of genotype and root size on the fungal and bacterial communities associated with apple rootstocks. HORTICULTURE RESEARCH 2022; 9:6511261. [PMID: 35043188 PMCID: PMC8769040 DOI: 10.1093/hr/uhab013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 05/04/2023]
Abstract
The endophytic microbiome of plants is believed to have a significant impact on its physiology and disease resistance, however, the role of host genotype in determining the composition of the endophytic microbiome of apple root systems remains an open question that has important implications for defining breeding objectives. In the current study, the bacterial and fungal microbiota associated with four different apple rootstocks planted in April, 2018 in the same soil environment and harvested in May, 2019 were evaluated to determine the role of genotype on the composition of both the bacterial and fungal communities. Results demonstrated a clear impact of genotype and root size on microbial composition and diversity. The fungal community was more affected by plant genotype whereas the bacterial community was shaped by root size. Fungal and bacterial abundance was equal between different-sized roots however, significantly higher microbial counts were detected in rhizosphere samples compared to root endosphere samples. This study provides information that can be used to develop a comprehensive and readily applicable understanding of the impact of genotype and environmental factors on the establishment of plant microbiome, as well as its potential function and impact on host physiology.
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Affiliation(s)
- Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, 317 Honghe Road, Yongchuan District, Chongqing 402160, China
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
| | - Birgit Wasserman
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 220 Ag Quad Ln, Blacksburg, VA 24061, USA
- Corresponding authors: E-mails: ;
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Center, PO Box 15159 Rishon LeZion 7505101, Israel
| | - Gennaro Fazio
- United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Plant Genetic Resources Unit, 21 Crabapple Drive, Geneva, NY 14456, USA
| | - Mark Mazzola
- USDA-ARS, Tree Fruit Research Laboratory,
1104 North Western Ave., Wenatchee, WA 98801, USA
| | - Xuehong Wu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, 2 Youanmingyuan West Road, Haidan District, Beijing 100193, China
- Corresponding authors: E-mails: ;
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Dai Y, Wang Z, Leng J, Sui Y, Jiang M, Wisniewski M, Liu J, Wang Q. Eco-friendly management of postharvest fungal decays in kiwifruit. Crit Rev Food Sci Nutr 2021; 62:8307-8318. [PMID: 33998844 DOI: 10.1080/10408398.2021.1926908] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Kiwifruit is purchased by consumers worldwide and is increasing in demand. Unfortunately, kiwifruit is susceptible to postharvest decay caused by a variety of fungal pathogens, including Botrytis cinerea, Penicillium expansum, Alternaria alternata, Botryosphaeria dothidea, and Diaporthe spp. Among these pathogens, B. cinerea is the most prevalent and devastating. Infections by these fungal pathogens result in a deterioration in fruit quality and a reduction in marketable yield. Eco-friendly methods to control kiwifruit postharvest decay have been explored as alternatives to the use of synthetic fungicides. In this review, we provide an overview and discuss the virulence and pathogenesis of fungi that are causal agents of kiwifruit decay, especially B. cinerea, including recent molecular and genomic studies. Advances in pre- and postharvest measures for postharvest decay management, including biological control, physical applications, the use of natural compounds and plant hormones, and the use of combined methods, are also reviewed. Eco-friendly control measures are a critical component of an integrated management approach for sustainable production of kiwifruit. The need for further research on the use of microbial consortia for the management of postharvest diseases of kiwifruit is also discussed.
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Affiliation(s)
- Yuan Dai
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Zhenshuo Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jinsong Leng
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Yuan Sui
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Mingguo Jiang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Qi Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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