Miliute I., Buzaite O., Baniulis D., Stanys V. Bacterial endophytes in agricultural crops and their role in stress tolerance: A review. Differentiation and Variability in the Rhizosphere and Endosphere Biotransformation of ginsenoside Rb1 to ginsenoside Rg3 by endophytic bacterium, Yan H., Jin H., Fu Y., Yin Z., Yin C. Production of rare ginsenosides Rg3 and Rh2 by endophytic bacteria from, Luo S.L., Dang L.Z., Li J.F., Zou C., Zhang K.Q., Li G.H. In addition, the chloroplast structure of the spots was complete. Wang Y, Wang H, Cheng H, Chang F, Wan Y, She X. PeerJ. In this study, we asked three main questions: (1) Are leaf spots related to colonization by microorganisms? First Report of Anthracnose of Tricyrtis macropoda Caused by Colletotrichum gloeosporioides in Korea. Mitochondrial, chloroplast, plant, and protoplast entries were deleted, and the unclassified contaminant sequences were filtered out. This research received no external funding. Photosynthetica 41, 8389. Ethyl acetate extracts from 21 isolates of endophytic fungi from roots, leaves, stems, and seeds of P. notoginseng showed activity against one or more of five fungal root rot pathogens of ginseng with extracts from five endophytes having activity against all pathogens tested [44]. Polar Biol. Figure 3. Bookshelf A comprehensive study of the microbiomics and metabonomics of the spots and green parts of leaves was performed. Tricyrtis macropoda was collected from the northern slope of the Qinling Mountains in China at 1072940E, 340138N and an altitude of 1,644 at 10 m interval. Sun X., Guo L.D. How plants recruit their microbiome? Analyzing metagenomic data from bacterial endophytes of P. ginseng also showed the presence of ACC deaminase genes [19]. Guilds of mycorrhizal fungi and their relation to trees ericads orchids and liverworts in a neotropical mountain rain forest. Compared with the inoculation with the wild strains E5 and S1, the inoculation with engineered strains E5P and S1P significantly increased wilt resistance and promoted plant growth, respectively. Endophytic fungi harbored in, Tan Y., Cui Y., Li H., Kuang A., Li X., Wei Y., Ji X. Rhizospheric soil and root endogenous fungal diversity and composition in response to continuous, Xing X., Guo S., Fu J. Biodiversity and distribution of endophytic fungi associated with, Park Y.H., Kim Y.C., Park S.U., Lim H.S., Kim J.B., Cho B.K., Bae H. Age-dependent distribution of fungal endophytes in, Fu Y., Yin Z.H., Wu L.P., Yin C.R. Lignin engineering in field-grown poplar trees affects the endosphere While some endophytes were specific to a plant age, other endophytes, such as B. amyloliquefaciens and B. aryabhattai, were found in plants of all ages. Endophytic bacterial communities in ginseng and their antifungal activity against pathogens. Plant. (2011). This research showed the relationship between endophytic microorganisms and metabolites, and the findings advance our understanding of endophyte-plant interactions and provide a new direction for investigating the relationship between endophytes and phenotypes. The leaves of Tricyrtis macropoda have an unusual spotted pattern. J. Plant Dis. (F) Venn diagram of fungi. results from a variety of mechanisms, such as epidermal cells, intercellular space, mesophyll cells, chloroplast variation and crystal interaction, which strengthen the white spots in the seedlings (Wang Z. X. et al., 2016; Chen et al., 2017). Chlorophyll in leaves is an important photosynthetic pigment (Pilar et al., 2016). Endosphere microbiome comparison between symptomatic and - PLOS However, there is also considerable variation between different plants and different fungal endophytes. Among those isolates, other mechanisms for improved nutrition were the ability to solubilize phosphate, which was found in half of the isolates with Lysinibacillus fusiformis, B. cereus and B. megaterium having the highest phosphate solubilization activities, but only seven isolates produced siderophores for possible iron scavenging. Two Enterobacter endophytes from P. ginseng seeds had the ability to produce IAA [39]. For example, an Arthrinium sp. (B) Microscopic image of a cross-section of the green part of the blade, with a magnification of 16 10. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". 46, 12141221. Isolates with these activities were mostly from roots and were Bacillus species, which are well-known antibiotic producers, with B. amyloliquefaciens subsp. doi: 10.1093/acprof:oso/9780199661596.001.0001, Gu, Z. Y., Zhu, J., Hao, Q., Yuan, Y. W., Duan, Y. W., Men, S. Q., et al. Light response and chlorophyll fluorescence parameters in dicranopteris dichotoma with light intensity and nitrogen treatments. Funct. The word microbiota (microbiome) has been used to describe this ecological community of tree-associated pathogenic, mutualistic, and commensal microorganisms. For P. notoginseng, Zheng et al. FC: the data curation. FOIA For P. quinquefolius, direct 16S rDNA sequencing showed that leaves, stems and roots also had Proteobacteria, Actinobacteria, Bacteroidetes, Plantomycetes and Acidobacteria as the most abundant phyla, with Proteobacteria being the most abundant in all tissues, ranging from 41 to 73% [23]. In this study, we apply an advanced network mapping theory for mapping the genetic architecture of microbial interaction networks in the leaf microbiome of Arabidopsis ( Brachi et al., 2022 ). 142, 211227. Thus, there is a close relationship between plant metabolites and endophytes, which may be caused by the production of metabolites by the endophytes, an influence on host secondary metabolite production, or more complex hostmicroorganism interactions. Using this setup, we performed a cross-sectional characterization of plant transcriptomes in the presence or absence of a complex microbial community. Physiol. J Ginseng Res. [43] used culturing to find that roots had both the highest abundance and diversity, with isolates in nine genera, seeds had the second highest abundance but third highest diversity, stems had the third highest abundance but second highest diversity, and leaves had both the lowest abundance and diversity, with isolates in only four genera. In addition, patterns can be formed on the leaves of many angiosperms, such as stripes, spots, or complex designs [e.g., Orchidaceae (Goodyera schlechtendaliana Rchb. This study examines how inoculation with live soil influences the assembly of the endosphere microbiome of leaves and roots of chrysanthemum. Bacterial endophytes can increase plant growth by affecting hormones in Panax species, such as indoleacetic acid (IAA) production that stimulates plant cell elongation. Microbiome complexity and the rules of microbiotic community assemblage are not yet fully understood. 52, 19211926. Similarly, 97% and 3% of 89 fungal endophyte isolates obtained from P. notoginseng belonged to the Ascomycota and Zygomycota, respectively, and among the 23 genera, the most common were Alternaria and Penicillium, both belonging to the Ascomycota [43]. A study on the functional characteristics of the endophytic community of rice roots showed that plant endophytes may participate in the metabolic processes of rice (Vain et al., 2014). doi: 10.1093/aob/mcs025, Shirke, P. A., and Pathre, U. V. (2003). We selected metabolites satisfying the following criteria as potential markers: (1) high confidence [| P(corr)| > 0.6] in discrimination between the spots and green parts of leaves, (2) mean intensities in leaf spots that were significantly different from those in the green parts of leaves (P < 0.05), and (3) a minimum two-fold change in level between leaves and green spots. Bacterial and fungal diversity in the shoot tips and roots increased with the development of the banana plantlets. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. [19], Dong et al. U.S.A. 112, 911920. eCollection 2020. Authors Yan Wang 1 , Huyin Cheng 2 , Fan Chang 1 , Le Zhao 3 , Bin Wang 4 , Yi Wan 1 , Ming Yue 5 Affiliations Oikos. The UNITE database for molecular identification of fungi recent updates and future perspectives. (A) PCoA of the bacterial community at the OTU level based on the binary Jaccard algorithm. Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including bacteria, fungi and archaea.The microbial communities inside the root and in the rhizosphere are distinct from . The bacterial groups belonging to the Enterobacteriaceae family with different relative abundances were detected in all the samples. However, no further description was given. Xiong et al. Abarenkov K., Nilsson R. H., Larsson K. H., Alexander I. J., Eberhardt U., Erland S., et al. Microbiome 5, 25. This result is different from previous studies. *Correspondence: Ming Yue, yueming@nwu.edu.cn, Beneficial Microbiota Interacting with the Plant Immune System, View all Root-associated (rhizosphere and endosphere) microbiomes of the Grand Naine and the affinity of endophytes to the host. Zheng Y.K., Miao C.P., Chen H.H., Huang F.F., Xia Y.M., Chen Y.W., Zhao L.W. In contrast, ITS2 rRNA sequencing of P. notoginseng tissues showed that leaves had the highest diversity of fungi compared to roots and stems [26]. doi: 10.1016/j.tplants.2012.04.001, Berg, G., Grube, M., Schloter, M., and Smalla, K. (2014). To better show the distribution of microbial differences in plant leaves, we calculated the proportion of OTUs in specific areas of plant leaves and the OTUs shared by different areas (Figures 5E,F). The plant microbiome is a key determinant of health and productivity. The rhizosphere microbiome and plant health. Similarly, alpha diversity parameters (ACE, Chao1, Shannon, and Simpson indices) of the microbiome of the green leaf parts and spots were not significantly different. Before As regards the diversity of endophytic microorganisms in leaves, there was no significant difference in the diversity of endophytic bacteria, but in our study, Proteobacteria were significantly enriched in the leaf. Pigments and active ingredients in leaves of seven Eucommia ulmoides variation types. In general, all tissues of the plant host have microbial communities: at the soil root interface (rhizosphere), inside the plant tissue (root, stem, leaf endosphere), and at the air-plant interface (phyllosphere environment), and rhizocompartments includes nodule endophytes, root endophytes, rhizosphere, and root zone [ 11 ]. Forest Microbiology | ScienceDirect Proc. doi: 10.1126/science.1195568. Microbiol. 1-Aminociclopropane-1-carboxylate (ACC)-degrading bacteria having been widely studied for their use in alleviating abiotic stresses in plants. Acta Bot. Archaeal endophytes are much less studied but have been found by DNA-based detection, such as 16S rRNA sequencing, and mostly belong to the Cenarchaea and Euryarchaea [11]. Selected species with an abundance greater than 0.5% are displayed in the figure and combined other species into Others; Unassigned represents the species without taxonomic annotation. The endophyte had endo-1,4--D-glucanase, exo-1,4--D-glucanase, -1,3-glucanase and -glucosidase activities that were induced when fungal cell walls were included as a substrate. (2016). (1980). Biochem. Fragaria chiloensis cryptic virus: A new strawberry virus found in. While not tested on a ginseng disease, the extract reduced infection of Arabidopsis leaves by B. cinerea. Structural variability and niche differentiation in the rhizosphere and I thank Saeideh Jafarpour for assistance in helping format this publication. The endosphere of ginseng contains a variety of fungal, bacterial, archaeal and viral endophytes. Two tightly linked genes coding for NADdependent malic enzyme and dynaminrelated protein are associated with resistance to Cercospora leaf spot disease in cowpea (Vigna unguiculata (L.) Walp.). Plant growth-promoting activities for bacterial and fungal endophytes isolated from medicinal plant of. Hara, N. (1957). Cercospora in Guatemala. However, the mechanisms of leaf spot formation in T. macropoda are currently unclear. At the genus level, Cercospora, Colletotrichum, and Aspergillus in Ascomycota accounted for 40.88% of the endophytic fungi in this study (Figure 5D) and differed significantly in abundance between the two leaf parts (P < 0.05). (E) Venn diagram of bacteria. The editor and reviewer's affiliations are the latest provided on their Loop research profiles and may not reflect their situation at the time of review. LC-MS/MS analyses were performed using a UHPLC system (1,290, Agilent Technologies) with a UPLC HSS T3 column (2.1 mm 100 mm, 1.8 m) coupled to a Q Exactive instrument (Orbitrap MS, Thermo). Proc Natl Acad Sci USA. Their abundance and diversity are generally affected by environmental and plant developmental factors similar to that of bacterial endophytes. Compared to bacterial endophytes, there have been fewer studies of fungal endophyte abundance and diversity in ginseng. Analysis of endophytic microbial community diversity in leaves. Plants | Free Full-Text | Changes in Microbial Community Structure in Root microbiome assembly is a multistep process shaped by both soil type and host differences ( 6, 10 ). Virus infection improves drought tolerance. In this study, we analyzed the division of fungi and bacteria at different levels. Then, Usearch (version 11)1 was used for follow-up analysis of biological information. The endophytic Enterobacteriaceae strains Enterobacter sp. Plant Microbiome: Composition and Functions in Plant - SpringerLink Ginseng (Panax) is a genus of herbaceous perennial plants in the Araliaceae that are both harvested from the wild and cultivated commercially and are used as a medicinal herb primarily due to secondary metabolites in the roots, particularly a variety of ginsenosides (teriterpenoid saponins) [16]. The rhizoplane microbiome of diseased samples presented a more intense microbial network than that of healthy samples, but the endosphere microbiome showed exactly the opposite variation. Kloepper J.W., Ryu C.M. Panax species contain a wide range of endophytes, similar to other plants. It also showed the ability to solubilize phosphate and produce siderophores. Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field grown poplar trees. Endosphere Microbiome and Metabolic Differences Between the Spots and Green Parts of Tricyrtis macropoda Leaves Front Microbiol. It appears that many bacterial endophytes have the potential to promote ginseng growth through manipulation of plant hormones. Unable to load your collection due to an error, Unable to load your delegates due to an error. The endosphere microbiome The plant microbiome consists of diverse microbial communities on the outside surface and in internal tissues of the host plant. Insects can also act as endophyte vectors when feeding on sap and pollinating [4]. (PDF) FOREST MICROBIOLOGY (VOLUME 1): TREE MICROBIOME - ResearchGate (2007). One hundred and eighty of the 578 isolates . Ginsenosides can also be altered within ginseng tissues by bacterial endophyte inoculation. The widespread occurrence of endosphere microbes with the ability to metabolize ginsenosides or produce ginsenosides in culture indicates that although the endophyte species found in ginseng are not unique, their genomes may differ from isolates of the same species in other environments, having altered or unique genes to help them grow in the specialized conditions of the ginseng apoplast. The effects of water stress on PhotosystemII in wheat. Using direct ITS2 sequencing, Wei et al. Methods: Although archaea and viruses have been detected in symptomless ginseng plants, little is known about them. Among 53 fungal endophytes from roots and seeds of P. notoginseng, two were found to produce saponins in potato dextrose broth with an Aspergillus isolate synthesizing Re Rd, and 20(S)-Rg3 and a Fusarium isolate synthesizing Rb1, Rd and 20(S)-Rg3 [49]. Dang H, Zhang T, Wang Z, Li G, Zhao W, Lv X, Zhuang L. BMC Plant Biol. However, treatments for gummosis have not been systemically established and studies of the microbiome closely related to this plant disease are lacking. An additional analysis of rhizosphere and endosphere bacterial microbiome at the phylum level in moso bamboo indicated that the main dominant bacteria of rhizosphere are Proteobacteria . The Venn diagram shows the numbers of OTUs in two leaf parts, with the number shown in the overlapping part of the diagrams indicating the total number of OTUs shared between the two leaf parts and the numbers shown in the non-overlapping parts indicating the numbers of unique OTUs in each part. doi: 10.1093/jxb/erv456, Shasmita, D. M., Pradipta, K., Mohapatra, S. K., Naik, A., and Mukherjee, K. (2019). 2017 Feb 23;5(1):25. doi: 10.1186/s40168-017-0241-2. Asian and American ginsengA Review. Hence, the leaf color pattern may help T. macropoda to be well adapted to strong-light environments in the seedling stage, which is likely the result of long-term coevolution between plants and microorganisms. The abscissa represents the different experimental groups,, Alpha diversity of the microbiome communities in different parts. Bacterial Endophytes and Their Effects on Plants and Uses in Agriculture. (C) Microscopic image of a cross-section of a spot on the blade, with a magnification of 16 10. A notable change was higher abundance of the pathogen, Cylindrocarpon, in 3- versus 1- and 2-year-old roots. Difference of microbiome variability between rhizosphere and endospheric in Ricinus communis L As a highly active transition zone between plants and soil, the rhizosphere provides an ideal environment for the growth, development, and reproduction of microbial communities (Vandenkoornhuyse et al., 2015). The endosphere of ginseng contains a variety of fungal, bacterial, archaeal and viral endophytes. Plant sex affects plant-microbiome assemblies of dioecious Venn Diagram: a package for the generation of highlycustomizable Venn and Euler diagrams in R. BMC Bioinformatics 12:35. doi: 10.1186/1471-2105-12-35. Keywords: The Endosphere Microbiome of Ginseng - PMC [20] and up to 10,351 operational taxonomic units (OTUs) by Hong et al. 2022 Oct 13;13:1009395. doi: 10.3389/fpls.2022.1009395. The horizontal and vertical coordinates are the two characteristic values that explain most of the variation between samples, and the amount of variation explained is expressed as a percentage. A clear example of a bacterial root endophyte inducing ISR in ginseng is a soil drench with the bacterial endophyte, B. amyloliquefaciens, from P. ginseng roots that induced resistance against Phytophthora cactorum and upregulated the P. ginseng ISR defense-related markers genes, PgPR5 (thaumatin-like), PgPR10 (ribonuclease) and PgCAT (ROS scavenging), in leaves following P. cactorum inoculation [35]. [51] found the antifungal compound, falcarinol, from the endophytic fungus, a Paecilomyces sp., isolated from P. ginseng, and the fungus inhibited the fungal plant pathogen, Pyricularia oryzae, and four human pathogenic fungi. (2020). The value of F0 is closely related to the light-catching antenna system, the state of PSII reaction centers (Sun et al., 2015), and the concentration of chlorophyll (Shasmita et al., 2019; Zhang, 2019). National Pharmacopoeia Commission (2015). Wilson D. Endophyte: The evolution of a term, and clarification of its use and definition. Resistance associated metabolite profiling of Aspergillus leaf spot in cotton through nontargeted metabolomics. Genet. Biotechnol. 2015 ). The values of Fv/Fm and Fv/Fo vary very little under non-stress conditions (Shirke and Pathre, 2003; Kumud et al., 2011), and the Fv/Fm or Fv/F0 values between spots and non-spots areas were not significantly different (Table 1), which also indicated that uneven colonization of leaves by fungi did not cause stress effects on the plants. Leaf spot of Polygonatum odoratum caused by Colletotrichum spaethianum. Thus far, there is limited information about them, and it is not known if they are affected by factors such as plant development and stress. However, nutrient. Kb were isolated on Enterobacteriaceae selective medium and further engineered by expressing 1-aminocyclopropane-1-carboxylate (ACC) deaminase on the bacterial cell walls (designated as E5P, S1P, and KbP, respectively). Disclaimer, National Library of Medicine Notably, the relative abundance of root endosphere Otu956 (genus Streptomyces) was strongly linked to the carotene hydroxylase 2 gene, encoding a key enzyme in the transformation of carotenoids. Microb Cell Fact. The .gov means its official. Cercospora can cause necrotic damage to the leaves, thus leading to suborbicular, oil-stained brown spots on the leaf surface (Chupp, 1954; Xie et al., 2017), and Cercospora can cause frog eye spots in cigar tobacco in Hainan (Zhao et al., 2020). The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Environ. (2018). 51, 19471954. Plant Prot. 8600 Rockville Pike 39, 619638. doi: 10.1007/s00300-013-1410-9, Chen, H. M., Chen, H. M., Wu, H. X., Yan, B., Zhao, H. G., Liu, F. H., et al. The relative abundance of Fusarium associated with the wilt disease did not increase during the wilting process. Cercospora in Guatemala. Plant microbiome highlights the importance of endosphere microbiome for growth and health of the host plant. [46] isolated 81 fungal endophytes and showed that the fewest species among nine fungal endophytes isolates was in 1-year-old roots while the most was in 3-year-old roots. Unplanted soil pots were used as a control to differentiate plant effects from general edaphic factors. (2011). doi: 10.1016/j.tplants.2018.05.003, Ingrid, K., Ingeborg, H., Sabrina, S., Juan, P. S., Michael, W., Markus, P., et al. 19, 672687. (A) Electrospray ionization positive mode. First report of Cercospora nicotianae causing frog eye spot in Cigar Tobacco in Hainan, China. They are high-interest targets for sustainable food production and the protection of agri-food systems from biotic stress and adverse environmental conditions. Changes in the diversity of the endophytic microbial community and metabolites were studied, and the effect of T. macropoda leaf spots on photosynthesis was examined by chlorophyll fluorescence. Physiol. The samples were vortexed for 30 s, homogenized at 40 Hz for 4 min, and sonicated for 5 min in an ice-water bath. In addition, we analyzed the differences in microorganisms at different levels. Taxon discrimination of the root endosphere was also very clear at the order, genus, and species levels. Multidisciplinary Digital Publishing Institute (MDPI). Plant microbiome structure and functions are shaped by several factors, including host genotype and developmental stage, the presence or absence of diseases, and environmental conditions. Microbiome 5, 2542. Field application of T. citrinoviride also showed decreased levels of foliar infection by A. panax associated with induced expression of several ginsenoside biosynthesis and defense genes. Averaged over the years, fungal endophyte diversity and abundance were highest over the years in roots, followed by leaves and lowest in stems. At this point, the study of archaeal endophytes has been primarily limited to detection in plants. 27, 3037. For fungi, a total of 7.33% of the OTUs were unique to the spots and 10.78% were unique to the green parts. doi: 10.1023/a:1025864513663, Shu, J., Yu, Z. H., Sun, W. X., Zhao, J., Li, Q. L., Tang, L. H., et al. Wilson D. Ecology of Woody Plant Endophytes. The UNITE database for molecular identification of fungi recent updates and future perspectives. Age-dependent Distribution of Fungal Endophytes in Panax ginseng Roots Cultivated in Korea. Banana endosphere microbiome structure varied during plant growth and wilting processes. PCA scores of different parts of the leaves. 9, 1323. Alkaloid and ketone metabolites were decreased in the green parts compared with the spots, and amino acids, organic acids, lipids, and other compounds were increased in the green parts compared with the spots. The cellulase KORRIGAN is part of the cellulose synthase complex. An endophytic isolate of T. gamsii from P. notoginseng roots coiled around the hyphae of four plant pathogenic fungi in culture, typical for mycoparasitism by Trichoderma [50].
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