The variability of bacterial communities in both the endosphere and ectosphere of different niches in Chinese chives (Allium tuberosum)


Autoři: Yuxin Wang aff001;  Chaonan Wang aff001;  Yizhu Gu aff001;  Pingzhi Wang aff001;  Weitang Song aff001;  Jinhai Ma aff002;  Xiaofei Yang aff002
Působiště autorů: College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China aff001;  Henan Jiuxing Institute of Biotechnology, Pingdingshan, Henan, China aff002
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: 10.1371/journal.pone.0227671

Souhrn

Deciphering the various types of interactions between plants and their microbiomes is a hot topic for research in ecology as well as in plant sciences and agronomy. To analyse and compare the differences in microbial communities in different compartments of Chinese chives, high-throughput sequencing technology was employed to amplify and sequence the V5-V6 region of the 16S rDNA of microorganisms in the leaves, phylloplanes, stems, roots and rhizospheres of Chinese chives. The sequences were clustered by operational taxonomic units (OTUs), and the community composition of bacteria between the endosphere (inner tissues) and ectosphere (outer surfaces) of Chinese chives was analysed based on the OTU. Overall, the results indicated that the endophytic bacteria in Chinese chives mainly include Proteobacteria, Actinobacteria, and Actinomycetes. Alpha diversity index analysis and OTU number analysis showed that the bacterial diversity and richness of the underground plant compartments were higher than those of the above-ground parts. PCoA based on the OTU level showed that the vertical stratification structure of plants and compartments had significant effects on the bacterial community structure. The richness of endophytic bacteria also varied greatly among the different varieties of Chinese chive. A considerable number of endophytic bacteria form symbiotic and mutually beneficial relationships with host plants, which play an important role in regulating host growth, metabolism and stress resistance. Further investigations are needed to uncover the evolution of interactions between plants and endophytes.

Klíčová slova:

Bacteria – Biomarkers – Community structure – Leaves – Plants – Rhizosphere – Sequence databases – Species diversity


Zdroje

1. Lopez-Velasco G, Carder P A, Welbaum G E, Ponder M A. Diversity of the spinach (Spinacia oleracea) spermosphere and phyllosphere bacterial communities. Fems Microbiology Letters. 2013; 346(2): 146–154. doi: 10.1111/1574-6968.12216 23859062

2. Kaihui L, Xiaowei D, Hong-Fei W, Xiaomei Z, Wael NH, Mohammed AM et al. Eukaryotic microbial communities in hypersaline soils and sediments from the alkaline hypersaline Huama Lake as revealed by 454 pyrosequencing. Antonie van Leeuwenhoek. 2014;105(5): 871–80. doi: 10.1007/s10482-014-0141-4 24563154

3. Qin S, Xing K, Jiang J, Xu L, Li W. Biodiversity, bioactive natural products and biotechnological potential of plant-associated endophytic actinobacteria. Appl Microbiol Biotechnol. 2011; 89(3): 457–473. doi: 10.1007/s00253-010-2923-6 20941490

4. Hongwei L, Lilia CC, Mark C, Eugenie S, Paul GD, Corné MJP, et al. Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria. Front Microbiol. 2017; 8: 2552. https://doi.org/10.3389/fmicb.2017.02552 29312235

5. Philippe V, Achim Q, Marie D, Amandine LV, Alexis D. The importance of the microbiome of the plant holobiont. New Phytologist. 2015; 206(4): 1196–206. doi: 10.1111/nph.13312 25655016

6. Shakya M, Gottel N, Castro H, Yang ZK, Gunter L, Labbé J, et al. A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees. PloS one. 2013; 8(10): e76382. doi: 10.1371/journal.pone.0076382 24146861

7. Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P. Structure and Functions of the Bacterial Microbiota of Plants. In: Merchant SS, editor Annual Review of Plant Biology. Annu Rev Plant Biol. 2013; 64: 807–38. doi: 10.1146/annurev-arplant-050312-120106 23373698

8. Van Elsas JD, Chiurazzi M, Mallon CA, Elhottova D, Kristufek V, Salles JF. Microbial diversity determines the invasion of soil by a bacterial pathogen. Proceedings of the National Academy of Sciences of the United States of America. 2012; 109(4) 1159–64. doi: 10.1073/pnas.1109326109 22232669

9. Wu X, Monchy S, Taghavi S, Zhu W, Ramos J, van der Lelie D. Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida. Fems Microbiol Rev. 2011; 35(2): 299–323. doi: 10.1111/j.1574-6976.2010.00249.x 20796030

10. Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A. The importance of the microbiome of the plant holobiont. New Phytol. 2015; 206(4SI):1196–206.

11. Pierre G. What makes a specialized endophyte special? Molecular Ecology. 2018; 27(15): 3037–39. doi: 10.1111/mec.14775 30133874

12. Yao L, Hu Z, Wang L, Zhou J, Li W. Research development of the relationship between plant endophyte and host. Ecology and Environmental Sciences. 2010; 19(7): 1750–54. chinese

13. Tang XL, Olatunji OJ, Zhou Y, Hou XL. 2017. Allium tuberosum: antidiabetic and hepatoprotective activities. Food Res Int. 2017; 102:681–9. doi: 10.1016/j.foodres.2017.08.034 29196001

14. Riley D, Barber SA. Bicarbonate accumulation and pH changes at the soybean root-soil interface. Soil Sci Soc Am Proc. 1969; 33: 905–8.

15. Xiangwei G, Chunjuan L, Jing L, Yan L, Qinghua Y, Weili Z, Pu Y, et al. Responses of rhizosphere soil properties, enzyme activities and microbial diversity to intercropping patterns on the Loess Plateau of China. Soil & Tillage Research, 2019; 195, 104355. https://doi.org/10.1016/j.still.2019.104355

16. Wiebke S, Grafe TU, Ivonne M, Ingolf SD, Alexander K. Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies. Microb Ecol. 2016; 71(4):938–53. doi: 10.1007/s00248-015-0723-3 26790863

17. Bram B, Michiel ODB, Sofie T, Sascha T, Nele W, Wout B, Jaco V. Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies. Front Microbiol. 2016; 7: 650. doi: 10.3389/fmicb.2016.00650 27242686

18. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–20. doi: 10.1093/bioinformatics/btu170 24695404

19. Magoc T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011; 27(21): 2957–63. doi: 10.1093/bioinformatics/btr507 21903629

20. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011; 27(16): 2194–200. doi: 10.1093/bioinformatics/btr381 21700674

21. Yile A, Hongqi L, Liping Z, Sikandar A, Zhongguo Y. The linear random forest algorithm and its advantages in machine learning assisted logging regression modeling. J Petrol Sci Eng. 2019; 174: 776–89.

22. Mohammad ET, Saeb K, Mary L, Jesus S, Adrian UNC. Diversity of endophytes across the soil-plant continuum for Atriplex spp. in arid environments. Journal of Arid Land. 2016; 8(2): 241–53.

23. Davide B, Matthias R, Klaus S, Emiel VLVT, Nahal A, Federica A, et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature. 2012; 488: 91–5. doi: 10.1038/nature11336 22859207

24. Derek SL, Sarah LL, Sur HP, Scott Y, Jase G, Stephanie M, et al. Defining the core Arabidopsis thaliana root microbiome. Nature. 2012; 488(7409): 86–90. doi: 10.1038/nature11237 22859206

25. Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proceedings of the National Academy of Sciences. 2015; 112(8): E911–20.

26. Stéphane H, Ruben G, Antonio G, Stijn S, Gail A, Sarah L, et al. Microbiota and host nutrition across plant and animal kingdoms. Cell Host Microbe. 2015; 17(5): 603–16. doi: 10.1016/j.chom.2015.04.009 25974302

27. Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM. The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol. 2006; 57: 233–266. doi: 10.1146/annurev.arplant.57.032905.105159 16669762

28. Walker TS, Bais HP, Grotewold E, Vivanco JM. Update on root exudation and rhizosphere biology: root exudation and rhizosphere biology. Plant Physiol. 2003; 132: 44–51.

29. Beckers B, Op De Beeck M, Weyens N, Boerjan W, Vangronsveld J. Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. Microbiome. 2017; 5: 25. https://doi.org/10.1186/s40168-017-0241-2. 28231859

30. Maida I, Chiellini C, Mengoni A, Bosi E, Firenzuoli F, Fondi M, et al. Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plantEchinacea purpurea. Environ Microbiol. 2016; 18(8): 2357–65. doi: 10.1111/1462-2920.12911 26013664

31. Suárez-Moreno ZR, Vinchira-Villarraga DM, Vergara-Morales DI, Castellanos L, Ramos FA, Guarnaccia C, et al. Plant-Growth Promotion and Biocontrol Properties of Three Streptomyces Isolates to Control Bacterial Rice Pathogens. Front Microbiol. 2019; 10: 290. doi: 10.3389/fmicb.2019.00290 30858835

32. Sy A, Timmers ACJ, Knief C, Vorholt JA. Methylotrophic metabolism is advantageous for Methylobacterium extorquens during colonization of Medicago truncatula under competitive conditions. Appl Environ Microbiol. 2005;71: 7245–52. doi: 10.1128/AEM.71.11.7245-7252.2005 16269765

33. Galbally IE, Kirstine W. The production of methanol by flowering plants and the global cycle of methanol. J Atmos Chem. 2002; 43: 195–229.

34. Dong M, Yang Z, Cheng G, Peng L, Xu Q, Xu J. Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum. Front Microbiol. 2018; 9: 267. doi: 10.3389/fmicb.2018.00267 29515548

35. Schlatter D, Kinkel L, Thomashow L, Weller D, Paulitz T. Disease suppressive soils: new insights from the soil microbiome. Phytopathology. 2017;107: 1284–97. doi: 10.1094/PHYTO-03-17-0111-RVW 28650266


Článek vyšel v časopise

PLOS One


2020 Číslo 1