Endophytic Microbiota Comparison of Dendrobium huoshanense Root and Stem in Different Growth Years

Abstract

The endophytic microbiome in medicinal plants is rich and diverse, but few studies have followed the endophytic microbiome of medicinal plants in different tissues with their growth. In this study, we examined the endophytic bacterial and fungal community structures associated with both the stem and root compartments of Dendrobium huoshanense at different growth years via high-throughput sequencing of 16S rRNA genes and nrDNA fragments of internal transcribed spacer regions. Results indicated that more diverse prokaryotic and fungal operational taxonomic units were detected in roots than in stems, and the alpha diversity of endophytic prokaryotic significantly differed among the 1-, 2-, and 3-year-old roots. The dominant bacterial phyla Proteobacteria Firmicutes, Actinobacteria, Bacteroidetes, and Acidobacteria, and fungal phyla Ascomycota, Basidiomycota, and Ascomycota were detected in the stems and roots with 3 growth years. Moreover, linear discriminant effect size analysis revealed 138 differentially abundant taxonomic clades in the bacterial level, and 197 in the fungal level in six groups. Our results provide evidence for endophytic microbiota communities depending on the tissues and growth years of D. huoshanense. The results from this study should be useful to better understand medicinal plant-microbe interactions.

Key words

Dendrobium huoshanense - endophytic microbiota - overlap - growth years

• References

• 1 Givnish TJ, Spalink D, Ames M, Lyon SP, Hunter SJ, Zuluaga A, Iles WJ, Clements MA, Arroyo MT, Leebens-Mack J, Endara L, Kriebel R, Neubig KM, Whitten WM, Williams NH, Cameron KM. Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proc Biol Sci 2015; 282: 2108-2111
• 2 Teixeira da Silva JA, Jin X, Dobránszki J, Lu J, Wang H, Zotz G, Cardoso JC, Zeng S. Advances in Dendrobium molecular research: Applications in genetic variation, identification and breeding. Mol Phylogenet Evol 2016; 95: 196-216
• 3 Zha XQ, Deng YY, Li XL, Wang JF, Pan LH, Luo JP. The core structure of a Dendrobium huoshanense polysaccharide required for the inhibition of human lens epithelial cell apoptosis. Carbohydr Polym 2017; 155: 252-260
• 4 Fang Q, Wang JF, Zha XQ, Cui SH, Cao L, Luo JP. Immunomodulatory activity on macrophage of a purified polysaccharide extracted from Laminaria japonica . Carbohydr Polym 2015; 13: 66-73
• 5 Ng TB, Liu J, Wong JH, Ye X, Wing Sze SC, Tong Y, Zhang KY. Review of research on Dendrobium, a prized folk medicine. Appl Microbiol Biotechnol 2012; 93: 1795-1803
• 6 Zhao YJ, Han BX, Peng HS, Peng DY. [Research on evolution and transition of quality evaluation of Shihu]. Chin Tradit Herbal Drugs 2016; 41: 1348-1353
• 7 Berendsen RL, Pieterse CM, Bakker PA. The rhizosphere microbiome and plant health. Trends Plant Sci 2012; 17: 478-486
• 8 McCormick MK, Lee Taylor D, Juhaszova K, Burnett jr. RK, Whigham DF, OʼNeill JP. Limitations on orchid recruitment: not a simple picture. Mol Ecol 2012; 21: 1511-1523
• 9 Těšitelová T, Kotilínek M, Jersáková J, Joly FX, Košnar J, Tatarenko I, Selosse MA. Two widespread green Neottia species (Orchidaceae) show mycorrhizal preference for Sebacinales in various habitats and ontogenetic stages. Mol Ecol 2015; 24: 1122-1134
• 10 Hajong S, Kumaria S, Tandon P. Comparative study of key phosphorus and nitrogen metabolizing enzymes in mycorrhizal and non-mycorrhizal plants of Dendrobium chrysanthum Wall. ex Lindl. Acta Physiol Plant 2013; 35: 2311-2322
• 11 Zhang JY, Zhang N, Liu YX, Zhang X, Hu B, Qin Y, Xu H, Wang H, Guo X, Qian J, Wang W, Zhang P, Jin T, Chu C, Bai Y. Root microbiota shift in rice correlates with resident time in the field and developmental stage. Sci China Life Sci 2018; 61: 3-11
• 12 Chaparro JM, Badri DV, Vivanco JM. Rhizosphere microbiome assemblage is affected by plant development. ISME J 2014; 8: 790-803
• 13 Köberl M, Schmidt R, Ramadan EM, Bauer R, Berg G. The microbiome of medicinal plants: diversity and importance for plant growth, quality, and health. Front Microbiol 2013; 4: 400
• 14 Zhang YZ, Wang ET, Li M, Li QQ, Zhang YM, Zhao SJ, Jia XL, Zhang LH, Chen WF, Chen WX. Effects of rhizobial inoculation, cropping systems and growth stages on endophytic bacterial community of soybean roots. Plant Soil 2011; 347: 147-161
• 15 Shi S, Nuccio E, Herman DJ, Rijkers R, Estera K, Li J, da Rocha UN, He Z, Pett-Ridge J, Brodie EL, Zhou J, Firestone M. Successional trajectories of rhizosphere bacterial communities over consecutive seasons. MBio 2015; 6: e00746
• 16 Yuan Y, Yu M, Zhang B, Liu X, Zhang J. Comparative nutritional characteristics of the three major Chinese Dendrobium species with different growth years. PLoS One 2019; 14: e022266
• 17 Ryan RP, Germaine K, Franks A, Ryan DJ, Dowling DN. Bacterial endophytes: recent developments and applications. FEMS Microbiol Lett 2008; 278: 1-9
• 18 Jin H, Yang XY, Yan ZQ, Liu Q, Li XZ, Chen JX, Zhang DH, Zeng LM, Qin B. Characterization of rhizosphere and endophytic bacterial communities from leaves, stems and roots of medicinal Stellera chamaejasme L. Syst Appl Microbiol 2014; 37: 376-385
• 19 Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, Dombrowski N, Münch PC, Spaepen S, Remus-Emsermann M, Hüttel B, McHardy AC, Vorholt JA, Schulze-Lefert P. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 2015; 528: 364-369
• 20 Wang W, Zhai Y, Cao L, Tan H, Zhang R. Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.). Microbiol Res 2016; 188 – 189: 1-8
• 21 Compant S, Mitter B, Colli-Mull JG, Gangl H, Sessitsch A. Endophytes of grapevine flowers, berries, and seeds: identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization. Microb Ecol 2011; 62: 188-197
• 22 Yan Y, Zhang SC, Zhang JY, Ma PD, Duan JL, Liang ZS. Effect and mechanism of endophytic bacteria on growth and secondary metabolite synthesis in Salvia miltiorrhiza hairy roots. Acta Physiol Plant 2014; 36: 1095-1105
• 23 Xing X, Ma X, Men J, Chen Y, Guo S. Phylogenetic constrains on mycorrhizal specificity in eight Dendrobium (Orchidaceae) species. Sci China Life Sci 2017; 60: 536-544
• 24 Parthibhan S, Rao MV, Kumar TS. Culturable fungal endophytes in shoots of Dendrobium aqueum, Lindley – An imperiled orchid. Ecolog Genet Genomics 2017; 3 – 5: 18-24
• 25 Zhang PL, Wang GK, Liang YM, Ma ZH, Liu HT, Hang J, Wu J, Wang G. Distribution of endophytic fungi in Dendrobium huoshanense from different habitats by green shield sequencing. J Anhui Univ Chin Med 2018; 37: 77-82
• 26 Liu T, Greenslade A, Yang S. Levels of rhizome endophytic fungi fluctuate in Paris polyphylla var. yunnanensis as plants age. Plant Divers 2017; 31: 60-64
• 27 Asraful Islam SM, Math RK, Kim JM, Yun MG, Cho JJ, Kim EJ, Lee YH, Yun HD. Effect of plant age on endophytic bacterial diversity of balloon flower (Platycodon grandiflorum) root and their antimicrobial activities. Curr Microbiol 2010; 61: 346-356
• 28 Guo LD, Huang GR, Wang Y. Seasonal and tissue age influences on endophytic fungi of Pinus tabulaeformis (Pinaceae) in the Dongling Mountains, Beijing. J Integr Plant Biol 2008; 50: 997-1003
• 29 Chen NF, Dai J, Li YT, Dai YF, Han BX, Chen CW, Chen ND, Yao HJ, Zhang L, Li WQ, He XL, Gao JS, Li MH, Ye QM, Huang XW, Yao WX. Technical specification of seedlings breeding of Dendrobium huoshanense . China Patent LY/T2449-2015, 2015
• 30 Wang Y, Li HH, Tan GH, Li SN, Yan ML, Zhang WM. [Study on communities of endophytic fungi from Pogostemon cablin and their antimicrobial activities]. Chin J Chin Mater Med 2017; 42: 657-662
• 31 Fan L, Wang Z, Chen M, Qu Y, Li J, Zhou A, Xie S, Zeng F, Zou J. Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment. Sci Total Environ 2019; 657: 1194-1204