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      Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding

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          Abstract

          Background

          Rice, which serves as a staple food for more than half of the world’s population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined.

          Results

          In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together.

          Conclusions

          This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12864-021-07587-1.

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          Most cited references52

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          The importance of the microbiome of the plant holobiont.

          Plants can no longer be considered as standalone entities and a more holistic perception is needed. Indeed, plants harbor a wide diversity of microorganisms both inside and outside their tissues, in the endosphere and ectosphere, respectively. These microorganisms, which mostly belong to Bacteria and Fungi, are involved in major functions such as plant nutrition and plant resistance to biotic and abiotic stresses. Hence, the microbiota impact plant growth and survival, two key components of fitness. Plant fitness is therefore a consequence of the plant per se and its microbiota, which collectively form a holobiont. Complementary to the reductionist perception of evolutionary pressures acting on plant or symbiotic compartments, the plant holobiont concept requires a novel perception of evolution. The interlinkages between the plant holobiont components are explored here in the light of current ecological and evolutionary theories. Microbiome complexity and the rules of microbiotic community assemblage are not yet fully understood. It is suggested that the plant can modulate its microbiota to dynamically adjust to its environment. To better understand the level of plant dependence on the microbiotic components, the core microbiota need to be determined at different hierarchical scales of ecology while pan-microbiome analyses would improve characterization of the functions displayed. © 2015 The Authors New Phytologist © 2015 New Phytologist Trust.
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            Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

            Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.
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              Bacterial seed endophytes: genera, vertical transmission and interaction with plants

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                Author and article information

                Contributors
                tranplamson@duytan.edu.vn , son.tran@ttu.edu
                tiancj@iga.ac.cn
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                17 April 2021
                17 April 2021
                2021
                : 22
                : 278
                Affiliations
                [1 ]GRID grid.9227.e, ISNI 0000000119573309, Northeast Institute of Geography and Agroecology, , Chinese Academy of Sciences, ; Changchun, 130102 Jilin China
                [2 ]GRID grid.410726.6, ISNI 0000 0004 1797 8419, University of Chinese Academy of Sciences, ; Beijing, 100049 China
                [3 ]GRID grid.464380.d, ISNI 0000 0000 9885 0994, Rice Research Institute, , Jiangxi Academy of Agricultural Sciences, ; Nanchang, 330200 China
                [4 ]GRID grid.444918.4, ISNI 0000 0004 1794 7022, Institute of Research and Development, , Duy Tan University, ; Da Nang, 550000 Vietnam
                [5 ]GRID grid.264784.b, ISNI 0000 0001 2186 7496, Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, , Texas Tech University, ; Lubbock, TX 79409 USA
                [6 ]GRID grid.464353.3, ISNI 0000 0000 9888 756X, Key Laboratory of Straw Biology and Utilization of the Ministry of Education, , Jilin Agricultural University, ; Changchun, 130118 Jilin Province China
                Author information
                http://orcid.org/0000-0003-1792-6005
                Article
                7587
                10.1186/s12864-021-07587-1
                8052703
                33865333
                be04b35b-3a74-4dec-a536-e21806452464
                © The Author(s) 2021

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 26 May 2020
                : 7 April 2021
                Funding
                Funded by: Special Foundation for Basic Research Program in Wild China of CAS
                Award ID: XDA23070501
                Award Recipient :
                Funded by: National Natural Science Foundation of China
                Award ID: 41920104008, 42007043, 41571255, 41701332
                Award Recipient :
                Funded by: Special Foundation for State Major Basic Research Program of China
                Award ID: 2016YFC0501202
                Award Recipient :
                Funded by: Key Laboratory Foundation of Mollisols Agroecology
                Award ID: 2020ZKHT-02
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2021

                Genetics
                cultivated rice,microbiota,endophytic,wild rice
                Genetics
                cultivated rice, microbiota, endophytic, wild rice

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