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Using Illumina-Based Sequence Analysis to Guide Probiotic Candidate Selection and Isolation

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Abstract

Selection for probiotic candidates by in vivo experimental trials is time and labor consuming; more informed strategy is needed to select successful probiotic candidates. The aim of the study was to elucidate the microbial taxa transmitted from maize seeds to seedlings during the germination process of maize and their probiotic effects. The bacterial and fungal taxa in kernel germs and sprouts were analyzed by Illumina-based sequencing. The sprouts contained more diverse fungi than those in germs. The bacterial species (OTUs) declined with the germination from germs to the sprouts. However, the endophytic fungal diversity increased during the germination process. Seed-borne dominant bacterial genera Bacillus, Halomonas, and Shewanella and dominant fungal genera Aspergillus were also detected in sprouts. The spore-forming bacteria BS3 isolated directly from sprouts could promote growth of maize seedling and resistance to F. verticillioides under F. verticillioides-infested soils. The results suggested that maize contained core bacterial and fungal taxa during the development from seeds to sprouts, and the core endophytes showed more intimate correlation with host plants than did other microbial taxa. Illumina-based sequence analysis is feasible to guide probiotic candidate selection and isolation.

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References

  1. Peiffer JA, Ley RE (2013) Exploring the maize rhizosphere microbiome in the field: a glimpse into a highly complex system. Commun Integr Biol 6:e25117. doi:10.4161/cib.25117

    Article  Google Scholar 

  2. Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, Buckler ES, Ley RE (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci U S A 110:6548–6553

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. 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 

  4. Silva DAF, Cotta SR, Vollú RE, Jurelevicius DA, Marques JM, Marriel IE, Seldin L (2014) Endophytic microbial community in two transgenic maize genotypes and in their near-isogenic non-transgenic maize genotype. BMC Microbiol 14:332. doi:10.1186//s12866-014-0332-1

    Article  PubMed  PubMed Central  Google Scholar 

  5. Berlec A (2012) Novel techniques and findings in the study of plant microbiota: search for plant probiotics. Plant Sci 193-194:96–102

    Article  CAS  PubMed  Google Scholar 

  6. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Turner TR, James EK, Poole PS (2013) The plant microbiome. Genome Biol 14:209 http://genomebiology.com/2013/14/6/209

    Article  PubMed  PubMed Central  Google Scholar 

  8. 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 

  9. Rebollar EA, Antwis RE, Becker MH, Belden LK, Bletz MC, Brucker RM, Harrison XA, Hughey MC, Kueneman JG, Loudon AH, Mckenzie V, Medina D, Minbiole KPC, Rollins-Smith LA, Walke JB, Weiss S, Woodhams DC, Harris RN (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 

  10. Shi Y, Yang H, Zhang T, Sun J, Lou K (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. Podolich O, Ardanov P, Zaets I, Pirttilä AM, Kozyrovska N (2015) Reviving of the endophytic bacterial community as a putative mechanism of plant resistance. Plant Soil 388:367–377

    Article  CAS  Google Scholar 

  12. Liu Y, Zuo S, Zou Y, Wang J, Song W (2013) Investigation on diversity and population succession dynamics of endophytic bacteria from seeds of maize (Zea mays L., Nongda 108) at different growth stages. Ann Microbiol 63:71–79

    Article  Google Scholar 

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

    Article  PubMed  Google Scholar 

  14. 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:e30438. doi:10.1371/journal.pone.0030438

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

  16. Johnston-Monje D, Mousa WK, Lazarovits G, Raizada MN (2014) Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize. BMC Plant Biol 14:233. doi:10.1186/s12870-014-0233-3

    Article  PubMed  PubMed Central  Google Scholar 

  17. Rijavec T, Lapanje A, Dermastia M, Rupnik M (2007) Isolation of bacterial endophytes from germinated maize kernels. Can J Microbiol 53:802–808

    Article  CAS  PubMed  Google Scholar 

  18. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Degnan PH, Ochman H (2012) Illumina-based analysis of microbial community diversity. ISME J 6:183–194

    Article  CAS  PubMed  Google Scholar 

  20. Wang W, Zhai Y, Cao L, Tan H, Zhang R (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 

  21. Hernández-Rodríguez A, Heydrich-Pérez M, Acebo-Guerrero Y, Valle MGV, Hernández-Lauzardo AN (2008) Antagonistic activity of Cuban native rhizobacteria against Fusarium verticillioides (Sacc.) Nirenb. in maize (Zea mays L.) Appl Soil Ecol 39:180–186

    Article  Google Scholar 

  22. Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22:5271–5277

    Article  PubMed  Google Scholar 

  23. Ondov BD, Bergman NH, Phillippy AM (2011) Interactive metagenomic visualization in a web browser. BMC Bioinf 12:385

    Article  Google Scholar 

  24. 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 

  25. Flores-Felix JD, Silva LR, Rivera LP, Marcos-Garcia M, Garcia-Fraile P, Martinez-Molina E, Mateos PF, Velazquez E, Andrade P, Rivas R (2015) 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  PubMed  PubMed Central  Google Scholar 

  26. Ferreira A, Quecine MC, Lacava PT, Oda S, Azevedo JL, Araújo WL (2008) Diversity of endophytic bacteria from Eucalyptus species seeds and colonization of seedlings by Pantoea agglomerans. FEMS Microbiol Lett 287:8–14

    Article  CAS  PubMed  Google Scholar 

  27. Barret M, Briand M, Bonneau S, Préveaux A, Valière S, Bouchez O, Hunault G, Simoneau P, Jacques M-A (2015) Emergence shapes the structure of the seed microbiota. Appl Environ Microbiol 81:1257–1266

    Article  PubMed  PubMed Central  Google Scholar 

  28. Cavaglieri L, Orlando J, Rodríguez MI, Chulze S, Etcheverry M (2005) Biocontrol of Bacillus subtilis against Fusarium verticillioides in vitro and at the maize root level. Res Microbiol 156:748–754

    Article  CAS  PubMed  Google Scholar 

  29. Pérez-García A, Romero D, de Vicente A (2011) Plant protection and growth stimulation by microorganisms: biotechnological application of bacilli in agriculture. Curr Opin Biotechnol 22:187–193

    Article  PubMed  Google Scholar 

  30. Gond SK, Bergen MS, Torres MS, White JF Jr (2015a) Endophytic Bacillus spp. produce antifungal lipopeptides and induce host defence gene expression in maize. Microbiol Res 172:79–87

    Article  CAS  PubMed  Google Scholar 

  31. Gond SK, Bergen MS, Torres MS, White JF Jr, Kharwar RN (2015b) Effect of bacterial endophyte on expression of defense genes in Indian popcorn against Fusarium moniliforme. Symbiosis 66:133–140

    Article  CAS  Google Scholar 

  32. Johnston-Monje D, Lundberg DS, Lazarovits G, Reis VM, Raizada MN (2016) Bacterial populations in juvenile maize rhizospheres originate from both seed and soil. Plant Soil. doi:10.1007/s11104-016-2826-0

  33. Cavaglieri LR, Passone A, Etcheverry MG (2004) Correlation between screening procedures to select root endophytes for biological control of Fusarium verticillioides in Zea mays L. Biol Control 31:259–267

    Article  Google Scholar 

  34. Amin N (2013) Diversity of endophytic fungi from root of maize var. Pulut (waxy corn local variety of South Sulawesi, Indonesia). Int J Curr Microbiol App Sci 2:148–154

    Google Scholar 

  35. Niaz I, Dawar S (2009) Detection of seed mycoflora in maize (Zea mays L.). Pak J Bot 443–451

  36. Brown RL, Cotty PJ, Cleveland TE (1991) Reduction in aflatoxin content of maize by atoxigenic strains of Aspergillus flavus. J Food Prot 54:623–626

    Article  CAS  PubMed  Google Scholar 

  37. Brown RL, Cleveland TE, Payne GA, Woloshuk CP, Campbell KW, White DG (1995) Determination of resistance to aflatoxin production in maize kernals and detection of fungal colonization using an Aspergillus flavus transformant expressing Escherichia coli β-glucuronidase. Phytopathology 85:983–989

    Article  CAS  Google Scholar 

  38. Desjardins AE, Plattner RD, Nelsen TC, Leslie JF (1995) Genetic analysis of fumonisin production and virulence of Gibberella fujikuroi mating population A (Fusarium moniliforme) on maize (Zea mays) seedlings. Appl Environ Microbiol 61:79–86

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Marín S, Sanchis V, Ramos AJ, Vinas I, Magan N (1998a) Environmental factors, in vitro interactions, and niche overlap between Fusarium moniliforme, F. proliferatum, and F. graminearum, Aspergillus and Pencillium species from maize grain. Mycol Res 102:931–837

    Google Scholar 

  40. Marín S, Sanchis V, Sáenz R, Ramos AJ, Vinas I, Magan N (1998b) Ecological determinants for germination and growth of some Aspergillus and Penicillium spp. from maize grain. J Appl Microbiol 84:25–36

    Article  PubMed  Google Scholar 

  41. Marín S, Sanchis V, Arnau F, Ramos AJ, Magan N (1998c) Colonisation and competitiveness of Aspergillus and Penicillium species on maize grain in the presence of Fusarium moniliforme and Fusarium proliferatum. Int J Food Microbiol 45:107–117

    Article  PubMed  Google Scholar 

  42. Orsi RB, Corrêa B, Possi CR, Schammass EA, Nogueira JR, Dias SMC, Malozzi MAB (2000) Mycoflora and occurrence of fumonisins in freshly harvested and stored hybrid maize. J Stored Prod Res 36:75–87

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Laboratory, Henan Provincial People’s Hospital, Zhengzhou, 450003, China

    Wenfeng Wang, Yi Li, Wangsen Qin & Changyi Sun

  2. School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China

    Hongming Tan & Lixiang Cao

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  1. Wenfeng Wang
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  2. Yi Li
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Correspondence to Lixiang Cao.

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Wang, W., Li, Y., Qin, W. et al. Using Illumina-Based Sequence Analysis to Guide Probiotic Candidate Selection and Isolation. Probiotics & Antimicro. Prot. 10, 478–484 (2018). https://doi.org/10.1007/s12602-017-9298-2

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