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      Comparison of Microbial Community of Rhizosphere and Endosphere in Kiwifruit

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          Abstract

          Understanding the microbial community and function are crucial knowledge for crop management. In this study, bacterial and fungal community structures both rhizosphere and endosphere in kiwifruit were analyzed to gain our knowledge in kiwifruit microbiome. Microbial community in rhizosphere was less variation than endosphere community. Functional prediction results demonstrated that abundance of saprotrophic fungi was similar in both rhizosphere and endosphere, but potential pathogenic fungi was more abundance in endosphere than in rhizosphere. This finding suggested that maintain healthy soil is the first priority to protect the host plant against biotic stresses.

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          Fungal endophytes: diversity and functional roles.

          R. Rodriguez, J F White, A. Arnold … (2009)
          All plants in natural ecosystems appear to be symbiotic with fungal endophytes. This highly diverse group of fungi can have profound impacts on plant communities through increasing fitness by conferring abiotic and biotic stress tolerance, increasing biomass and decreasing water consumption, or decreasing fitness by altering resource allocation. Despite more than 100 yr of research resulting in thousands of journal articles, the ecological significance of these fungi remains poorly characterized. Historically, two endophytic groups (clavicipitaceous (C) and nonclavicipitaceous (NC)) have been discriminated based on phylogeny and life history traits. Here, we show that NC-endophytes represent three distinct functional groups based on host colonization and transmission, in planta biodiversity and fitness benefits conferred to hosts. Using this framework, we contrast the life histories, interactions with hosts and potential roles in plant ecophysiology of C- and NC-endophytes, and highlight several key questions for future work in endophyte biology.
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            Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species

            Devin Coleman-Derr, Damaris Desgarennes, Citlali Fonseca-García … (2015)
            Summary Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semiarid and arid regions of Central and North America and are emerging as biofuel feedstocks. We examined prokaryotic and fungal communities in the rhizosphere, phyllosphere, leaf and root endosphere, as well as proximal and distal soil samples from cultivated and native agaves, through Illumina amplicon sequencing. Phylogenetic profiling revealed that the composition of prokaryotic communities was primarily determined by the plant compartment, whereas the composition of fungal communities was mainly influenced by the biogeography of the host species. Cultivated A. tequilana exhibited lower levels of prokaryotic diversity compared with native agaves, although no differences in microbial diversity were found in the endosphere. Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave–microbe interactions.
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              The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome

              M. A. Cregger, A. M. Veach, Z K Yang … (2018)
              Background Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in the plant niche-level microbiome, from rhizosphere soils to plant canopies, is imperative to gain a better understanding of how both the structural and functional processes of microbiomes impact the health of the overall plant holobiome. Using Populus trees as a model ecosystem, we characterized the archaeal/bacterial and fungal microbiome across 30 different tissue-level niches within replicated Populus deltoides and hybrid Populus trichocarpa × deltoides individuals using 16S and ITS2 rRNA gene analyses. Results Our analyses indicate that archaeal/bacterial and fungal microbiomes varied primarily across broader plant habitat classes (leaves, stems, roots, soils) regardless of plant genotype, except for fungal communities within leaf niches, which were greatly impacted by the host genotype. Differences between tree genotypes are evident in the elevated presence of two potential fungal pathogens, Marssonina brunnea and Septoria sp., on hybrid P. trichocarpa × deltoides trees which may in turn be contributing to divergence in overall microbiome composition. Archaeal/bacterial diversity increased from leaves, to stem, to root, and to soil habitats, whereas fungal diversity was the greatest in stems and soils. Conclusions This study provides a holistic understanding of microbiome structure within a bioenergy relevant plant host, one of the most complete niche-level analyses of any plant. As such, it constitutes a detailed atlas or map for further hypothesis testing on the significance of individual microbial taxa within specific niches and habitats of Populus and a baseline for comparisons to other plant species. Electronic supplementary material The online version of this article (10.1186/s40168-018-0413-8) contains supplementary material, which is available to authorized users.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Plant Pathol J
                Journal ID (iso-abbrev): Plant Pathol. J
                Title: The Plant Pathology Journal
                Publisher: Korean Society of Plant Pathology
                ISSN (Print): 1598-2254
                ISSN (Electronic): 2093-9280
                Publication date (Print): December 2019
                Publication date (Electronic): 12 December 2019
                Volume: 35
                Issue: 6
                Pages: 705-711
                Affiliations
                [1 ]Department of Plant Medicine and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
                [2 ]Division of Applied Life Science and Research Institute of Life Science, Gyeongsang National University, Jinju 58282, Korea
                [3 ]Department of Applied Biology, Chonnam National University, Gwangju 61185, Korea
                Author notes
                [* ]Corresponding author: Phone) +82-55-772-1922, FAX) +82-55-772-1929, E-mail) kwak@ 123456gnu.ac.kr
                [†]

                These authors contributed equally to this work.

                [¶]

                Current address: Research Institute of BIO Technology, CJ, Suwon 16495, Korea

                Handling Editor : Seo, Young-Su

                Author information
                https://orcid.org/0000-0003-2139-1808
                Article
                Publisher ID: ppj-35-705
                DOI: 10.5423/PPJ.NT.08.2019.0216
                PMC ID: 6901249
                SO-VID: 2413158f-d444-4445-aecf-85c198860bb8
                Copyright © © The Korean Society of Plant Pathology
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 06 August 2019
                Date revision received : 06 September 2019
                Date accepted : 08 September 2019
                Categories
                Subject: Note

                Keywords: endosphere,kiwifruit,microbial community,rhizosphere
                Data availability:
                Keywords: endosphere, kiwifruit, microbial community, rhizosphere

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