Skip to main content
SpringerLink
Log in

Evaluation of Probiotic Diversity from Soybean (Glycine max) Seeds and Sprouts Using Illumina-Based Sequencing Method

  • Published:
Probiotics and Antimicrobial Proteins Aims and scope Submit manuscript

Abstract

There is increasing interest in the use of plant probiotics as environmental-friendly and healthy biofertilizers. The study aimed at selecting for novel probiotic candidates of soybean (Glycine max). The bacteriome and mycobiome of soybean sprouts and seeds were analyzed by Illumina-based sequencing. Seeds contained more diverse bacteria than those in sprouts. The seeds contained similar fungal diversity with sprouts. Total 15 bacterial OTUs and 4 fungal OTUs were detected in seeds and sprouts simultaneously, suggesting that the sprouts contained bacterial and fungal taxa transmitted from seeds. The Halothiobacillus was the most dominant bacterial genus observed and coexisted in seeds and sprouts. The OTUs belonged to Ascomycota were the most dominant fungal taxa observed in seeds and sprouts. Halothiobacillus was firstly identified as endophytic probiotics of soybean. The results suggested that sprouts might contain diverse plant probiotics of mature plants and Illumina-based sequencing can be used to screen for probiotic candidates.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Flores-Felix JD, Marcos-Garcia M, Silva LR et al (2015) Rhizobium as plants probiotic for strawberry production under microcosm conditions. Symbiosis 67:25–32

    Article  CAS  Google Scholar 

  2. Flores-Felix JD, Silva LR, Rivera LP et al (2015a) Plants probiotics as a tool to produce highly functional fruits: the case of Phyllobacterium and vitamin C in strawberries. PLoS One 10(4):e0122281

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Nicolaisen M, Justesen AF, Knorr K et al (2014) Fungal communities in wheat grain show significant co-existence patterns among species. Fungal Ecol 11:145–153

    Article  Google Scholar 

  4. Links MG, Demeke T, Gräfenhan T et al (2014) Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds. New Phytol 202:542–553

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Ofek M, Hadar Y, Minz D (2011) Colonization of cucumber seeds by bacteria during germination. Environ Microbiol 13:2794–2807

    Article  PubMed  Google Scholar 

  6. Fett WF, Cooke PH (2005) A survey of native microbial aggregates on alfalfa, clover and mung bean sprout cotyledons for thickness as determined by confocal scanning laser microscopy. Food Microbiol 22(2–3):253–259

    Article  Google Scholar 

  7. Weiss A, Hertel C, Grothe S et al (2007) Characterization of the cultivable microbiota of sprouts and their potential for application as protective cultures. Syst Appl Microbiol 30:483–493

    Article  CAS  PubMed  Google Scholar 

  8. Ding H, Fu TJ, Smith MA (2013) Microbial contamination in sprouts: how effective is seed disinfection treatment? J Food Sci 78:R495–R501

    Article  CAS  PubMed  Google Scholar 

  9. Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663

    Article  CAS  PubMed  Google Scholar 

  10. Shi Y, Yang H, Zhang T et al (2014) Illumina-based analysis of endophytic bacterial diversity and space-time dynamics in sugar beet on the north slope of Tianshan mountain. Appl Microbiol Biotechnol 98:6375–6385

    Article  CAS  PubMed  Google Scholar 

  11. Wang W, Zhai Y, Cao L et al (2016) Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.) Microbiol Res 188-189:1–8

    Article  PubMed  Google Scholar 

  12. Kõljalg U, Nilsson RH, Abarenkov K et al (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22:5271–5277

    Article  CAS  PubMed  Google Scholar 

  13. Kemp PF, Aller JY (2004) Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol Ecol 47:161–177

    Article  CAS  PubMed  Google Scholar 

  14. Huang Y, Kuang Z, Deng Z, Zhang R, Cao L (2017) Endophytic bacterial and fungal communities transmitted from cotyledons and germs in peanut (Arachis hypogaea L.) sprouts. Environ Sci Pollut Res. doi:10.1007/s11356-017-9254-4

  15. Rebollar EA, Antwis RE, Becker MH et al (2016) Using “omics” and integrated multi-omics approaches to guide probiotic selection to mitigate chytridiomycosis and other emerging infectious disease. Front Microbiol 7:68

    Article  PubMed  PubMed Central  Google Scholar 

  16. Hung PQ, Kumar SM, Govindsamy V et al (2007) Isolation and characterization of endophytic bacteria from wild and cultivated soybean varieties. Biol Fertil Soils 44:155–162

    Article  Google Scholar 

  17. Li JH, Wang ET, Chen WF et al (2008) Genetic diversity and potential for promotion of plant growth detected in nodule endophytic bacteria of soybean grown in Heilongjiang province of China. Soil Biol Biochem 40:238–246

    Article  CAS  Google Scholar 

  18. Bethlenfalvay GJ, Brown MS, Ames RN et al (1988) Effects of drought on host and endophyte development in mycorrhizal soybeans in relation to water use and phosphate uptake. Physiol Plant 72:565–571

    Article  CAS  Google Scholar 

  19. Kuklinsky-Sobral J, Araujo WL, Mendes R et al (2004) Isolation and characterization of soybean-associated bacteria and their potential for plant growth promotion. Environ Microbiol 6:1244–1251

    Article  CAS  PubMed  Google Scholar 

  20. Kuklinsky-Sobral J, Araujo WL, Mendes R et al (2005) Isolation and characterization of endophytic bacteria from soybean (Glycine max) grown in soil treated with glyphosate herbicide. Plant Soil 273:91–99

    Article  CAS  Google Scholar 

  21. Chi F, Shen SH, Cheng HP et al (2005) Ascending migration of endophytic rhizobia, from roots to leaves, inside rice plants and assessment of benefits to rice growth physiology. Appl Environ Microbiol 71:7271–7278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Chee PP, Fober KA, Slightom JL (1989) Transformation of soybean (Glycine max) by infecting germinating seeds with Agrobacterium tumefaciens. Plant Physiol 91:1212–1218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Cakmakci R, Donmez F, Aydin A et al (2006) Growth promotion of plant growth-promoting rhizobacteria under greenhouse and two different field soil conditions. Soil Biol Biochem 38:1482–1487

    Article  CAS  Google Scholar 

  24. 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:e20396. doi:10.1371/journal.pone.0020396

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Truyens S, Weyens N, Cuypers A et al (2014) Bacterial seed endophytes: genera, vertical transmission and interaction with plants. Environ Microbiol Rep. doi:10.1111/1758-2229.12181

  26. Anandham R, Janahiraman V, Gandhi PI et al (2014) Early plant growth promotion of maize by various sulfur oxidizing bacteria that uses different thiosulfate oxidation pathway. Afr J Microbiol Res 48:439–447

    Google Scholar 

  27. Anandham R, Sridar R, Nalayini P et al (2007) Potential for plant growth promotion in groundnut (Arachis hypogaea L.) cv. ALR-2 by co-inoculation of sulfur-oxidizing bacteria and Rhizobium. Microbiol Res 162:139–153

    Article  CAS  PubMed  Google Scholar 

  28. Krepski ST, Hanson TE, Chan CS (2012) Isolation and characterization of a novel biomineral stalk-forming iron-oxidizing bacterium from a circumneutral groundwater seep. Environ Microbiol 14:1671–1680

    Article  CAS  PubMed  Google Scholar 

  29. Hemming BC (1986) Microbial-iron interactions in the plant rhizosphere: an overview. J Plant Nutr 9:505–521

    Article  CAS  Google Scholar 

  30. Radhakrishnan R, Khan AL, Kang SM et al (2015) A comparative study of phosphate solubilization and the host plant growth promotion ability of Fusarium verticillioidesRK01 and Humicolasp. KNU01 under salt stress. Ann Microbiol 65:585–593

    Article  CAS  Google Scholar 

  31. Sibounnavong P, Keoudone C, Soytong K et al (2010) A new mycofungicide from Emericella nidulans against tomato wilt caused by Fusarium oxysporum f. sp. lycopersici in vivo. J Agric Technol 6:19–30

    Google Scholar 

  32. Abadias M, Usall J, Anguera M et al (2008) Microbiological quality of fresh, minimally-processed fruit and vegetables, and sprouts from retail establishments. Int J Food Microbiol 123:121–129

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This study was supported by the Natural Science Foundation of Guangdong Province (Grant No. 2015A030313355), the Youth Elite Project of Guangzhou University of Chinese Medicine (Grant No. QNYC20170103), the Guangdong Provincial Administration of Traditional Chinese Medicine (Grant No. 20152114), and the Chinese National Natural Science Foundation (Grant No. 31400111).

Author information

Author notes

  1. Yali Huang and Miaomiao Zhang contributed equally to this work.

Authors and Affiliations

  1. College of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China

    Yali Huang & Miaomiao Zhang

  2. School of Basic Courses, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China

    Zujun Deng

  3. School of Life Sciences, Sun Yat-sen University, Guangzhou, China

    Lixiang Cao

Authors
  1. Yali Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Miaomiao Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zujun Deng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lixiang Cao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Yali Huang or Lixiang Cao.

Ethics declarations

Conflict of Interest

The authors declare that they have no conflict of interest.

Funding

This study was funded by the Natural Science Foundation of Guangdong Province (Grant No. 2015A030313355), the Youth Elite Project of Guangzhou University of Chinese Medicine (Grant No. QNYC20170103), and the Chinese National Natural Science Foundation (Grant No. 31400111) and the Guangdong Provincial Administration of Traditional Chinese Medicine (Grant No. 20152114).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Huang, Y., Zhang, M., Deng, Z. et al. Evaluation of Probiotic Diversity from Soybean (Glycine max) Seeds and Sprouts Using Illumina-Based Sequencing Method. Probiotics & Antimicro. Prot. 10, 293–298 (2018). https://doi.org/10.1007/s12602-017-9305-7

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12602-017-9305-7

Keywords

Search

Navigation