Journal of Plant Growth Regulation

, Volume 38, Issue 1, pp 93–102 | Cite as

Insights into Endophytic Bacterial Community Structures of Seeds Among Various Oryza sativa L. Rice Genotypes

  • Jun Zhang
  • Caiwen Zhang
  • Jing Yang
  • Ruijie Zhang
  • Jusheng Gao
  • Xia Zhao
  • Juanjuan Zhao
  • Dongfang Zhao
  • Xiaoxia ZhangEmail author


This study aimed to investigate the endophytic bacterial communities among various rice seed genotypes, to define the core microbiome and to further explore the relationship between rice genotypes and their endophytic bacterial flora. Simple sequence repeats molecular marker technology was used to investigate the genetic polymorphism in five different genotypes of rice. Endophytic bacterial communities in rice seeds were investigated using the Illumina-based 16S rRNA gene. The results showed that rice genotype had little impact on the diversity and richness of endophytic bacteria in seeds. The various rice genotypes do not have significantly different communities of endophytic bacterial in seeds, but the endophyte abundance distributions are obviously different, especially the dominant endophytic genera. Some phyla, such as Acidobacteria, Fusobacteria, Chlamydiae and Gemmatimonadetes, were first detected in rice seeds using high-throughput sequencing technique. As expected, five different rice genotypes were found to have a shared microbiome. At the genus level, Pantoea (28.33–72.77%), Acinetobacter (0.16–34.23%) and Xanthomonas (3.20–13.51%), which are probably the core microflora in indica rice seeds, served as the dominant genera that coexisted in all rice seeds tested. However, the current studies cannot confirm the correlation of rice phylogeny and seed bacterial microbiome clearly, but provide some clues of technical possibility and valuable experiences for the future study.


Rice phylogeny Seed endophytic bacteria Correlation High-throughput sequencing Core microbiome 



We thank Prof. Yang-Sheng Li of Wuhan University for offering rice seeds. We thank Dr. Yan-Zhong Luo of Biotechnology Research Institute, Chinese Academy of Agricultural Sciences for excellent technical assistance.


This work was supported by the National Natural Science Foundation of China (Grant No. 31670005).

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

344_2018_9812_MOESM1_ESM.doc (308 kb)
Online Resource (DOC 307 KB)


  1. Adams PD, Kloepper JW (2002) Effect of host genotype on indigenous bacterial endophytes of cotton (Gossypium hirsutum L.). Plant Soil 240:181–189CrossRefGoogle Scholar
  2. Chang P, Gerhardt KE, Huang XD, Yu XM, Glick BR, Gerwing PD, Greenberg BM (2014) Plant growth-promoting bacteria facilitate the growth of barley and oats in salt-impacted soil: implications for phytoremediation of saline soils. Int J Phytoremediat 16:1133–1147CrossRefGoogle Scholar
  3. Compant S, Mitter B, Coli-Mull JG, Gangl H, Sessitsch A (2011) Endophytes of grapevine flowers, berries, and seeds, identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization. Microbial Ecol 62:188–197CrossRefGoogle Scholar
  4. Doty SL, Oakley B, Xin G, Kang JW, Singleton G, Khan Z, Vajzovic A, Staley JT (2009) Diazotrophic endophytes of native black cottonwood and willow. Symbiosis 47:23–33CrossRefGoogle Scholar
  5. Ebeltagy A, Nishioka K, Suzuki H, Sato T, Sato Y, Morisaki H, Mitsui H, Minamisawa K (2000) Isolation and characterization of endophytic bacteria from wild and traditionally cultivated rice varieties. Soil Sci Plant Nutr 46:617–629CrossRefGoogle Scholar
  6. Edgar RC (2013) UPARSE, highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998CrossRefGoogle Scholar
  7. Edwards J, Johnson C, Santosmedellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci 112:911–920CrossRefGoogle Scholar
  8. Gandhi A, Muralidharan G (2016) Assessment of zinc solubilizing potentiality of Acinetobacter sp. isolated from rice rhizosphere. Eur J Soil Biol 76:1–8CrossRefGoogle Scholar
  9. Gitaitis R, Walcott R (2007) The epidemiology and management of seedborne bacterial diseases. Annu Rev Phytopathol 45:371–397CrossRefGoogle Scholar
  10. Granér G, Persson P, Meijer J, Alström S (2003) A study on microbial diversity in different cultivars of Brassica napus in relation to its wilt pathogen, Verticillium longisporum. FEMS Microbiol Lett 224:269–276CrossRefGoogle Scholar
  11. Grum M, Camloh M, Rudolph K, Ravnikar M (1998) Elimination of bean seed-borne bacteria by thermotherapy and meristem culture. Plant Cell Tissue Organ Cult 52:79–82CrossRefGoogle Scholar
  12. Hardoim PR, Andreote FD, Reinhold-Hurek B, Sessitsch A, Overbeek LSV, Elsas JDV (2011) Rice root-associated bacteria, insights into community structures across 10 cultivars. FEMS Microbiol Ecol 77:154–164CrossRefGoogle Scholar
  13. Hardoim PR, Hardoim CCP, van Overbeek LS, van Elsas JD (2012) Dynamics of seed-borne rice endophytes on early plant growth stages. PLoS ONE 7:e30438CrossRefGoogle Scholar
  14. Huang Y, Kuang Z, Wang W, Cao L (2016) Exploring potential bacterial and fungal biocontrol agents transmitted from seeds to sprouts of wheat. Biol Control 98:27–33CrossRefGoogle Scholar
  15. Jiang XY, Gao JS, Xu FH, Cao YH, Tang X, Zhang XX (2013) Diversity of endophytic bacteria in rice seeds and their secretion of indole acetic acid. Acta Microbiologica Sinica 53:269–275 (in Chinese)Google Scholar
  16. Johnston-monje D, Raizada MN (2011) Conservation and diversity of seed associated endophytes in zea across boundaries of evolution, ethnography and ecology. PLoS ONE 6:e20396CrossRefGoogle Scholar
  17. Kong Y (2011) Btrim, a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics 98:152–153CrossRefGoogle Scholar
  18. Kruasuwan W, Thamchaipenet (2016) A diversity of culturable plant growth-promoting bacterial endophytes associated with sugarcane roots and their effect of growth by co-inoculation of diazotrophs and actinomycetes. J Plant Growth Regul 35:1–14CrossRefGoogle Scholar
  19. Lamit LJ, Lau MK, Sthultz CM, Wooley SC, Whitham TG, Gehring CA (2014) Tree genotype and genetically based growth traits structure twig endophyte communities. Am J Bot 101:467–478CrossRefGoogle Scholar
  20. Liu L, Liu Y, Song W (2009) Indigenous bacterial community diversity in hybrid rice (Oryza sativa L.) seed. Biotechnol Bull 1:95–111 (in Chinese)Google Scholar
  21. Liu Y, Zuo S, Xu L, Zou Y, Song W (2012) Study on diversity of endophytic bacterial communities in seeds of hybrid maize and their parental lines. Arch Microbiol 194:1001–1012CrossRefGoogle Scholar
  22. Liu Y, Li H, Li J, Cao Y, Yao S, Bai F, Tan W, Cheng C (2013) Investigation on diversity of endophytic bacterial community in Xisha wild Noni (Morinda citrifolia L.) seed. Biotechnol Bull 65:142–147 (in Chinese)Google Scholar
  23. López-López A, Rogel MA, Ormeño-Orillo E, Martínez-Romero J, Martínez-Romero E (2010) Phaseolus vulgaris seed-borne endophytic community with novel bacterial species such as Rhizobium endophyticum sp. nov. Syst Appl Microbiol 33:322–327CrossRefGoogle Scholar
  24. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Ri TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90CrossRefGoogle Scholar
  25. Magoč T, Salzberg SL (2011) FLASH, fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963CrossRefGoogle Scholar
  26. Mano H, Tanaka F, Watanabe A, Kaga H, Okunishi S, Morisaki H (2006) Culturable surface and endophytic bacterial flora of the maturing seeds of rice plants (Oryza sativa) cultivated in a paddy field. Microbes Environ 21:86–100CrossRefGoogle Scholar
  27. Marques JM, Silva TFD, Vollú RE, Blank AF, Smalla K, Seldin L (2015) Bacterial endophytes of sweet potato tuberous roots affected by the plant genotype and growth stage. Appl Soil Ecol 96:273–281CrossRefGoogle Scholar
  28. Mastretta C, Taghavi S, van der Lelie D, Mengoni A, Galardi F, Gonnelli C, Braca T, Boulet J, Weyens N, Vangronsveld J (2009) Endophytic bacteria from seeds of Nicotiana tabacum can reduce cadmium phytotoxicity. Int J Phytoremediat 11:251–267CrossRefGoogle Scholar
  29. Nair DN, Padmavathy S (2014) Impact of endophytic microorganisms on plants, environment and humans. Sci World J 2014:250693CrossRefGoogle Scholar
  30. Nelson EB (2004) Microbial dynamics and interactions in the spermosphere. Ann Rev Phytopathol 42:271–309CrossRefGoogle Scholar
  31. Okunishi S, Sako K, Mano H, Imamura A, Morisaki H (2005) Bacterial flora of endophytes in the maturing seed of cultivated rice (Oryza sativa). Microbes Environ 20:168–177CrossRefGoogle Scholar
  32. Qin Y, Pan X, Yuan Z (2016) Seed endophytic microbiota in a coastal plant and phytobeneficial properties of the fungus Cladosporium cladosporioides. Fungal Ecol 24:53–60CrossRefGoogle Scholar
  33. Rastogi G, Tech JJ, Coaker GL, Leveau JH (2010) A PCR-based toolbox for the culture-independent quantification of total bacterial abundances in plant environments. J Microbiol Methods 83:127–132CrossRefGoogle Scholar
  34. Rosenblueth M, López-López A, Martínez J, Rogel MA, Toledo I, Martínez-Romero E (2010) Seed bacterial endophytes: common genera, seed-to-seed variability and their possible role in plants. Acta Hortic 938:39–48Google Scholar
  35. Sachdev D, Nema P, Dhakephalkar P, Zinjarde S, Chopade B (2010) Assessment of 16S rRNA gene-based phylogenetic diversity and promising plant growth-promoting traits of Acinetobacter community from the rhizosphere of wheat. Microbiol Res 165:627–638CrossRefGoogle Scholar
  36. Sasaki K, Ikeda S, Ohkubo T, Kisara C, Sato T, Minamisawa K (2013) Effects of plant genotype and nitrogen level on bacterial communities in rice shoots and roots. Microbes Environ 28:391–395CrossRefGoogle Scholar
  37. Shade A, Handelsman J (2012) Beyond the Venn diagram, the hunt for a core microbiome. Environ Microbiol 14:4–12CrossRefGoogle Scholar
  38. Sobolev VS, Orner VA, Arias RS (2013) Distribution of bacterial endophytes in peanut seeds obtained from axenic and control plant material under field conditions. Plant Soil 371:367–376CrossRefGoogle Scholar
  39. Suzuki W, Sugawara M, Miwa K, Morikawa M (2014) Plant growth-promoting bacterium Acinetobacter calcoaceticus P23 increases the chlorophyll content of the monocot Lemna minor (duckweed) and the dicot Lactuca sativa (lettuce). J Biosci Bioeng 118:41–44CrossRefGoogle Scholar
  40. Trotel-aziz P, Couderchet M, Biagianti S, Aziz A (2008) Characterization of new bacterial biocontrol agents Acinetobacter, Bacillus, Pantoea and Pseudomonas spp. mediating grapevine resistance against Botrytis cinerea. Environ Exp Bot 64:21–32CrossRefGoogle Scholar
  41. Truyens S, Weyens N, Cuypers A, Vangronsveld J (2015) Bacterial seed endophytes: genera, vertical transmission and interaction with plants. Environ Microbiol Rep 7:40–50CrossRefGoogle Scholar
  42. Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A (2015) The importance of the microbiome of the plant holobiont. New Phytol 206:1196–1206CrossRefGoogle Scholar
  43. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267CrossRefGoogle Scholar
  44. Wang W, Zhai Y, Cao L, Tan H, Zhang R (2016a) Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.). Microbiol Res 188–189:1–8CrossRefGoogle Scholar
  45. Wang W, Zhai Y, Cao L, Tan H, Zhang R (2016b) Illumina-based analysis of core actinobacteriome in roots, stems, and grains of rice. Microbiol Res 190:12–18CrossRefGoogle Scholar
  46. Xie GL, Soad A, Swings J, Mew TW (2003) Diversity of Gram negative bacteria antagonistic against major pathogens of rice from rice seed in the tropic environment. J Zhejiang Univ Sci A 4:463–468CrossRefGoogle Scholar
  47. Yan J, Shu CH, Tian C, Wang YS, Xiao QM, Chen W, Chao J (2014) Isolation and identification of endophytic bacteria in seeds of tobacco variety K326. Hunan Agric Sci 18:21–27 (in Chinese)Google Scholar
  48. Zhang XX, Zhang RJ, Gao JS, Wang XC, Fan FL, Ma XT, Yin HQ, Zhang CW, Feng K, Deng Y (2017) Thirty-one years of rice-rice-green manure rotations shape the rhizosphere microbial community and enrich beneficial bacteria. Soil Biol Biochem 104:208–217CrossRefGoogle Scholar
  49. Zou YY, Liu L, Liu Y, Zhao L, Deng QY, Wu J, Zhuang W, Song W (2012) Diversity of indigenous bacterial communities in Oryza sativa seeds of different varieties. Chin J Plant Ecol 36:880–890 (in Chinese)CrossRefGoogle Scholar

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Authors and Affiliations

  1. 1.Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
  2. 2.State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
  3. 3.Qiyang Agro-ecosystem of National Field Experimental Station, Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesQiyangChina
  4. 4.China Center of Industrial Culture Collection (CICC)China National Research Institute of Food and Fermentation IndustriesBeijingChina
  5. 5.State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC)Guangdong Institute of MicrobiologyGuangzhouChina

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