Genome-wide transcriptome profiling provides insights into the responses of maize (Zea mays L.) to diazotrophic bacteria



We applied for the first time a high-throughput transcriptome approach to elucidate biochemical and physiological mechanisms controlling early events in the interaction between maize seedlings and different beneficial diazotrophic bacteria.


mRNA transcriptomes from maize (Zea mays L.) seedlings were characterized seven days after inoculation with Azospirillum brasilense sp245 and Herbaspirillum seropedicae HRC54. The expression profiles of selected genes were validated by quantitative reverse transcription–polymerase chain reaction analysis.


Transcriptome profiling revealed a total of 764 and 3595 differentially expressed genes (DEGs) in maize when exclusively associated with A. brasilense and H. seropedicae, respectively, whereas 455 DEGs were shared by both treatments. Our results support the modulation of the host nitrogen metabolism and phytohormone responses by both diazotrophic bacteria as well as distinct activation of host immune responses.


Diazotrophic bacteria modulate maize metabolism, with some common responses to both beneficial bacteria, while others are specific to each bacterial species. This study provides a valuable contribution on how these beneficial bacteria might amend host metabolism to improve growth and fitness.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6



abscisic acid


auxin response factor




bri1-ems-suppressor 1


coiled-coil receptor, nucleotide-binding sites, and leucine-rich repeated domains


counts per million


damage-associated molecular patterns


days after inoculation


differentially expressed genes




gene ontology


gibberellic acids


basic helix-loop-helix


homeobox domain


indole acetic acid


membrane-based interactome network database


multidimensional scaling


nitrate reductase


nitrite reductase


nitrogen use efficiency


pattern recognition receptors


pattern trigger immunity


quantitative reverse transcription–polymerase chain reaction


receptor-like cytoplasmic kinases


cysteine receptor-like kinase


receptor-like kinase


recognition peronospora parasítica




salicylic acid


toll and interleukin receptor, nucleotide-binding sites, and leucine-rich repeated domains


transcription factors


  1. Amaral FP, Bueno JCF, Hermes VS, Arisi ACM (2014) Gene expression analysis of maize seedlings (DKB240 variety) inoculated with plant growth promoting bacterium Herbaspirillum seropedicae. Symbiosis 62:41–50

    CAS  Google Scholar 

  2. Ashfield T, Ong LE, Nobuta K, Schneider CM, Innes RW (2004) Convergent evolution of disease resistance gene specificity in two flowering plant families. Plant Cell 16:309–318

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Baldani JI, Baldani VL (2005) History on the biological nitrogen fixation research in graminaceous plants: special emphasis on the Brazilian experience. An Acad Bras Ciênc 77:549–579

    CAS  PubMed  Google Scholar 

  4. Baldani J, Caruso L, Baldani VL et al (1997) Recent advances in BNF with non-legume plants. Soil Biol Biochem 29:911–922

    CAS  Google Scholar 

  5. Bartel B, Fink GR (1995) ILR1, an amidohydrolase that releases active indole-3-acetic acid from conjugates. Science 268:1745–1748

    CAS  PubMed  Google Scholar 

  6. Bashan Y, Holguin G, De-Bashan LE (2004) Azospirillum-plant relationships: physiological, molecular, agricultural, and environmental advances (1997-2003). Can J Microbiol 50:521–577

    CAS  PubMed  Google Scholar 

  7. Bastián F, Cohen A, Piccoli P, Luna V, Bottini* R, Baraldi R, Bottini R (1998) Production of indole-3-acetic acid and gibberellins A1 and A3 by Acetobacter diazotrophicus and Herbaspirillum seropedicae in chemically-defined culture media. Plant Growth Regul 24:7–11

    Google Scholar 

  8. Benschop JJ, Mohammed S, O’Flaherty M et al (2007) Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis. Mol Cell Proteomics 6:1198–1214

    CAS  PubMed  Google Scholar 

  9. Bhattacharjee RB, Singh A, Mukhopadhyay SN (2008) Use of nitrogen-fixing bacteria as biofertiliser for non-legumes: prospects and challenges. Appl Microbiol Biotechnol 80:199–209

    CAS  PubMed  Google Scholar 

  10. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. Botta AL, Santacecilia A, Ercole C, Cacchio P, del Gallo M (2013) In vitro and in vivo inoculation of four endophytic bacteria on Lycopersicon esculentum. New Biotechnol 30:666–674

    CAS  Google Scholar 

  12. Brandt R, Cabedo M, Xie Y, Wenkel S (2014) Homeodomain leucine-zipper proteins and their role in synchronizing growth and development with the environment. J Integr Plant Biol 56:518–526

    CAS  PubMed  Google Scholar 

  13. Brusamarello-Santos LCC, Pacheco F, Aljanabi SMM, Monteiro RA, Cruz LM, Baura VA, Pedrosa FO, Souza EM, Wassem R (2012) Differential gene expression of rice roots inoculated with the diazotroph Herbaspirillum seropedicae. Plant Soil 356:113–125

    CAS  Google Scholar 

  14. Brusamarello-Santos LC, Gilard F, Brulé L et al (2017) Metabolic profiling of two maize (Zea mays L.) inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense. PloS one 12:e0174576.

  15. Canellas LP, Olivares FL, Okorokova-Façanha AL, Façanha AR (2002) Humic acids isolated from earthworm compost enhance root elongation, lateral root emergence, and plasma membrane H+-ATPase activity in maize roots. Plant Physiol 130:1951–1957

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Canellas LP, Balmori DM, Médici LO, Aguiar NO, Campostrini E, Rosa RCC, Façanha AR, Olivares FL (2013) A combination of humic substances and Herbaspirillum seropedicae inoculation enhances the growth of maize (Zea mays L.). Plant Soil 366:119–132

    CAS  Google Scholar 

  17. Carvalho TLG, Ballesteros HGF, Thiebaut F, Ferreira PCG, Hemerly AS (2016) Nice to meet you: genetic, epigenetic and metabolic controls of plant perception of beneficial associative and endophytic diazotrophic bacteria in non-leguminous plants. Plant Mol Biol 90:561–574

    CAS  PubMed  Google Scholar 

  18. Castillo P, Molina R, Andrade A, Vigliocco A, Alemano S, Cassán FD (2015) Phytohormones and other plant growth regulators produced by pgpr: the genus Azospirillum. In: Cassán F, Okon Y, Creus C (eds) Handbook for Azospirillum. Springer, Cham, pp 115–138

    Google Scholar 

  19. Cavalcante JJV, Vargas C, Nogueira EM et al (2007) Members of the ethylene signalling pathway are regulated in sugarcane during the association with nitrogen-fixing endophytic bacteria. J Exp Bot 58:673–686

    CAS  PubMed  Google Scholar 

  20. Creus CM, Graziano M, Casanovas EM, Pereyra MA, Simontacchi M, Puntarulo S, Barassi CA, Lamattina L (2005) Nitric oxide is involved in the Azospirillum brasilense-induced lateral root formation in tomato. Planta 221:297–303

    CAS  PubMed  Google Scholar 

  21. Cui MH, Yoo KS, Hyoung S, Nguyen HTK, Kim YY, Kim HJ, Ok SH, Yoo SD, Shin JS (2013) An Arabidopsis R2R3–MYB transcription factor, AtMYB20, negatively regulates type 2C serine/threonine protein phosphatases to enhance salt tolerance. FEBS Lett 587:1773–1778

    CAS  PubMed  Google Scholar 

  22. da Fonseca Breda FA, da Silva TFR, dos Santos SG et al (2018) Modulation of nitrogen metabolism of maize plants inoculated with Azospirillum brasilense and Herbaspirillum seropedicae. Arch Microbiol 201:547–558

    PubMed  Google Scholar 

  23. Da K, Nowak J, Flinn B (2012) Potato cytosine methylation and gene expression changes induced by a beneficial bacterial endophyte, Burkholderia phytofirmans strain PsJN. Plant Physiol Biochem 50:24–34

    CAS  PubMed  Google Scholar 

  24. Dangl JL, Jones JD (2001) Plant pathogens and integrated defence responses to infection. Nature 411:826–833

    CAS  PubMed  Google Scholar 

  25. Davies PJ (2005) Plant hormones: biosynthesis, signal transduction, action. Springer Netherlands

  26. Díaz-Zorita M, Canigia MVF, Bravo OÁ et al (2015) Field evaluation of extensive crops inoculated with Azospirillum sp. In: Cassán F, Okon Y, Creus C (eds) Handbook for Azospirillum. Springer, Cham, pp 435–445

    Google Scholar 

  27. Divi UK, Krishna P (2009) Brassinosteroid: a biotechnological target for enhancing crop yield and stress tolerance. New Biotechnol 26:131–136

    CAS  Google Scholar 

  28. Dobbelaere S, Croonenborghs A, Thys A, Vande Broek A, Vanderleyden J (1999) Phytostimulatory effect of Azospirillum brasilense wild type and mutant strains altered in IAA production on wheat. Plant Soil 212:153–162

    Google Scholar 

  29. Doerks T, Copley R, Bork P (2001) DDT–a novel domain in different transcription and chromosome remodeling factors. Trends Biochem Sci 26:145–146

    CAS  PubMed  Google Scholar 

  30. Du L, Ali GS, Simons KA et al (2009) Ca2+/calmodulin regulates salicylic-acid-mediated plant immunity. Nature 457:1154–1158

    CAS  PubMed  Google Scholar 

  31. Du Z, Zhou X, Ling Y et al (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:W64–W70.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. Dubois M, van den Broeck L, Inzé D (2018) The pivotal role of ethylene in plant growth. Trends Plant Sci 23:311–323

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Eisen JA, Sweder KS, Hanawalt PC (1995) Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res 23:2715–2723

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186.

    CAS  Article  PubMed  Google Scholar 

  35. Gourion B, Berrabah F, Ratet P, Stacey G (2015) Rhizobium–legume symbioses: the crucial role of plant immunity. Trends Plant Sci 20:186–194

    CAS  PubMed  Google Scholar 

  36. Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM (2007) Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol 8:R7.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  37. Halbach T, Scheer N, Werr W (2000) Transcriptional activation by the PHD finger is inhibited through an adjacent leucine zipper that binds 14-3-3 proteins. Nucleic Acids Res 28:3542–3550

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79:293–320

    PubMed  PubMed Central  Google Scholar 

  39. He J-X, Gendron JM, Sun Y, Gampala SS, Gendron N, Sun CQ, Wang ZY (2005) BZR1 is a transcriptional repressor with dual roles in brassinosteroid homeostasis and growth responses. Science 307:1634–1638

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Hoagland DR, Arnon DI (1950) The water-culture method for growing plants without soil. Calif Agr Exp St a Cir 347:1–32

    Google Scholar 

  41. Hu H-C, Wang Y-Y, Tsay Y-F (2009) AtCIPK8, a CBL-interacting protein kinase, regulates the low-affinity phase of the primary nitrate response. Plant J 57:264–278

    CAS  PubMed  Google Scholar 

  42. Hungria M, Campo RJ, Souza EM, Pedrosa FO (2010) Inoculation with selected strains of Azospirillum brasilense and A. lipoferum improves yields of maize and wheat in Brazil. Plant Soil 331:413–425

    CAS  Google Scholar 

  43. Jakoby M, Weisshaar B, Dröge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci 7:106–111

    CAS  PubMed  Google Scholar 

  44. James EK, Gyaneshwar P, Mathan N, Barraquio WL, Reddy PM, Iannetta PPM, Olivares FL, Ladha JK (2002) Infection and colonization of rice seedlings by the plant growth-promoting bacterium Herbaspirillum seropedicae Z67. Mol Plant-Microbe Interact 15:894–906

    CAS  PubMed  Google Scholar 

  45. Janzen RA, Rood SB, Dormaar JF, McGill WB (1992) Azospirillum brasilense produces gibberellin in pure culture on chemically-defined medium and in co-culture on straw. Soil Biol Biochem 24:1061–1064

    CAS  Google Scholar 

  46. Jiang Z, Liu X, Peng Z et al (2010) AHD2. 0: an update version of Arabidopsis hormone database for plant systematic studies. Nucleic Acids Res 39:D1123–D1129

    PubMed  PubMed Central  Google Scholar 

  47. Jin J, Tian F, Yang D-C et al (2017) PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res 45:D1040–D1045

    CAS  PubMed  Google Scholar 

  48. Jones JD, Dangl JL (2006) The plant immune system. Nature 444:323–329

    CAS  PubMed  Google Scholar 

  49. Jones AM, Xuan Y, Xu M, Wang RS, Ho CH, Lalonde S, You CH, Sardi MI, Parsa SA, Smith-Valle E, Su T, Frazer KA, Pilot G, Pratelli R, Grossmann G, Acharya BR, Hu HC, Engineer C, Villiers F, Ju C, Takeda K, Su Z, Dong Q, Assmann SM, Chen J, Kwak JM, Schroeder JI, Albert R, Rhee SY, Frommer WB (2014) Border control—a membrane-linked interactome of Arabidopsis. Science 344:711–716

    CAS  PubMed  Google Scholar 

  50. Kapulnik Y, Okon Y, Henis Y (1985) Changes in root morphology of wheat caused by Azospirillum inoculation. Can J Microbiol 31:881–887

    Google Scholar 

  51. Kechid M, Desbrosses G, Rokhsi W, Varoquaux F, Djekoun A, Touraine B (2013) The NRT2.5 and NRT2.6 genes are involved in growth promotion of Arabidopsis by the plant growth-promoting rhizobacterium (PGPR) strain Phyllobacterium brassicacearum STM196. New Phytol 198:514–524

    CAS  PubMed  Google Scholar 

  52. Kiełbowicz-Matuk A (2012) Involvement of plant C2H2-type zinc finger transcription factors in stress responses. Plant Sci 185:78–85

    PubMed  Google Scholar 

  53. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  54. Le MH, Cao Y, Zhang X-C, Stacey G (2014) LIK1, a CERK1-interacting kinase, regulates plant immune responses in Arabidopsis. PLoS One 9:e102245.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  55. Lefebvre B, Timmers T, Mbengue M, Moreau S, Herve C, Toth K, Bittencourt-Silvestre J, Klaus D, Deslandes L, Godiard L, Murray JD, Udvardi MK, Raffaele S, Mongrand S, Cullimore J, Gamas P, Niebel A, Ott T (2010) A remorin protein interacts with symbiotic receptors and regulates bacterial infection. Proc Natl Acad Sci 107:2343–2348

    CAS  PubMed  Google Scholar 

  56. Lezhneva L, Kiba T, Feria-Bourrellier A-B, Lafouge F, Boutet-Mercey S, Zoufan P, Sakakibara H, Daniel-Vedele F, Krapp A (2014) The Arabidopsis nitrate transporter NRT 2.5 plays a role in nitrate acquisition and remobilization in nitrogen-starved plants. Plant J 80:230–241

    CAS  PubMed  Google Scholar 

  57. Lin W, Okon Y, Hardy RW (1983) Enhanced mineral uptake by Zea mays and Sorghum bicolor roots inoculated with Azospirillum brasilense. Appl Environ Microbiol 45:1775–1779

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Lin F, Jiang L, Liu Y, Lv Y, Dai H, Zhao H (2014) Genome-wide identification of housekeeping genes in maize. Plant Mol Biol 86:543–554.

    CAS  Article  PubMed  Google Scholar 

  59. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408

    CAS  Google Scholar 

  60. Lopez-Gomez M, Sandal N, Stougaard J, Boller T (2012) Interplay of flg22-induced defence responses and nodulation in Lotus japonicus. J Exp Bot 63:393–401

    CAS  PubMed  Google Scholar 

  61. Lozano-Durán R, Macho AP, Boutrot F, Segonzac C, Somssich IE, Zipfel C (2013) The transcriptional regulator BZR1 mediates trade-off between plant innate immunity and growth. Elife 2:e00983.

    Article  PubMed  PubMed Central  Google Scholar 

  62. Luna E, Pastor V, Robert J, Flors V, Mauch-Mani B, Ton J (2011) Callose deposition: a multifaceted plant defense response. Mol Plant-Microbe Interact 24:183–193

    CAS  PubMed  Google Scholar 

  63. Luo J, Zhou J, Li H, Shi W, Polle A, Lu M, Sun X, Luo ZB (2015) Global poplar root and leaf transcriptomes reveal links between growth and stress responses under nitrogen starvation and excess. Tree Physiol 35:1283–1302

    CAS  PubMed  Google Scholar 

  64. Macho AP, Zipfel C (2014) Plant PRRs and the activation of innate immune signaling. Mol Cell 54:263–272

    CAS  PubMed  Google Scholar 

  65. McCarthy DJ, Chen Y, Smyth GK (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res 40:4288–4297

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Meyer J, Berger DK, Christensen SA, Murray SL (2017) RNA-Seq analysis of resistant and susceptible sub-tropical maize lines reveals a role for kauralexins in resistance to grey leaf spot disease, caused by Cercospora zeina. BMC Plant Biol 17:197.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  67. Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW (2003) Genome-wide analysis of NBS-LRR–encoding genes in Arabidopsis. Plant Cell 15:809–834

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Müller B (2016) Characterization of UmamiTs in Arabidopsis: amino acid transporters involved in amino acid cycling, phloem unloading and the supply of symplasmically isolated sink tissues

  69. Nakano T, Suzuki K, Fujimura T, Shinshi H (2006) Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol 140:411–432

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Okushima Y, Fukaki H, Onoda M, Theologis A, Tasaka M (2007) ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis. Plant Cell 19:118–130

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Oliveira A, Urquiaga S, Döbereiner J, Baldani JI (2002) The effect of inoculating endophytic N2-fixing bacteria on micropropagated sugarcane plants. Plant Soil 242:205–215

    CAS  Google Scholar 

  72. Oliveira IJ, Fontes JRA, Pereira BFF, Muniz AW (2018) Inoculation with Azospirillum brasiliense increases maize yield. Chem Biol Technol Agric 5:6.

    CAS  Article  Google Scholar 

  73. Pedrosa FO, Monteiro RA, Wassem R, Cruz LM, Ayub RA, Colauto NB, Fernandez MA, Fungaro MHP, Grisard EC, Hungria M, Madeira HMF, Nodari RO, Osaku CA, Petzl-Erler ML, Terenzi H, Vieira LGE, Steffens MBR, Weiss VA, Pereira LFP, Almeida MIM, Alves LR, Marin A, Araujo LM, Balsanelli E, Baura VA, Chubatsu LS, Faoro H, Favetti A, Friedermann G, Glienke C, Karp S, Kava-Cordeiro V, Raittz RT, Ramos HJO, Ribeiro EMSF, Rigo LU, Rocha SN, Schwab S, Silva AG, Souza EM, Tadra-Sfeir MZ, Torres RA, Dabul ANG, Soares MAM, Gasques LS, Gimenes CCT, Valle JS, Ciferri RR, Correa LC, Murace NK, Pamphile JA, Patussi EV, Prioli AJ, Prioli SMA, Rocha CLMSC, Arantes OMN, Furlaneto MC, Godoy LP, Oliveira CEC, Satori D, Vilas-Boas LA, Watanabe MAE, Dambros BP, Guerra MP, Mathioni SM, Santos KL, Steindel M, Vernal J, Barcellos FG, Campo RJ, Chueire LMO, Nicolás MF, Pereira-Ferrari L, da Conceição Silva JL, Gioppo NMR, Margarido VP, Menck-Soares MA, Pinto FGS, Simão RCG, Takahashi EK, Yates MG, Souza EM (2011) Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PLoS Genet 7:e1002064.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  74. Pérez-Rodríguez P, Riano-Pachon DM, Corrêa LGG et al (2009) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res 38:D822–D827.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  75. Peterson KM, Shyu C, Burr CA, Horst RJ, Kanaoka MM, Omae M, Sato Y, Torii KU (2013) Arabidopsis homeodomain-leucine zipper IV proteins promote stomatal development and ectopically induce stomata beyond the epidermis. Development. 140:1924–1935.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  76. Pii Y, Mimmo T, Tomasi N, Terzano R, Cesco S, Crecchio C (2015) Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A review. Biol Fertil Soils 51:403–415

    CAS  Google Scholar 

  77. Pontier D, Picart C, Roudier F, Garcia D, Lahmy S, Azevedo J, Alart E, Laudié M, Karlowski WM, Cooke R, Colot V, Voinnet O, Lagrange T (2012) NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis. Mol Cell 48:121–132

    CAS  PubMed  Google Scholar 

  78. Presti L, Lanver D, Schweizer G et al (2015) Fungal effectors and plant susceptibility. Annu Rev Plant Biol 66:513–545

    PubMed  Google Scholar 

  79. Ramirez-Prado JS, Abulfaraj AA, Rayapuram N, Benhamed M, Hirt H (2018) Plant immunity: from signaling to epigenetic control of defense. Trends Plant Sci 23:833–844

    CAS  PubMed  Google Scholar 

  80. Rietz S, Dermendjiev G, Oppermann E, Tafesse FG, Effendi Y, Holk A, Parker JE, Teige M, Scherer GFE (2010) Roles of Arabidopsis patatin-related phospholipases a in root development are related to auxin responses and phosphate deficiency. Mol Plant 3:524–538

    CAS  PubMed  Google Scholar 

  81. Ristova D, Carré C, Pervent M et al (2016) Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root. Sci Signal 9:rs13–rs13

    PubMed  Google Scholar 

  82. Rivera D, Revale S, Molina R et al (2014) Complete genome sequence of the model rhizosphere strain Azospirillum brasilense Az39, successfully applied in agriculture. Genome Announc 2:e00683–14–e00683–14.

    Article  PubMed  PubMed Central  Google Scholar 

  83. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140.

    CAS  Article  PubMed  Google Scholar 

  84. Rodrigues CM, de Souza AA, Takita MA, Kishi LT, Machado MA (2013) RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes as a defense response. BMC Genomics 14:676.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  85. Rushton PJ, Somssich IE, Ringler P, Shen QJ (2010) WRKY transcription factors. Trends Plant Sci 15:247–258

    CAS  PubMed  Google Scholar 

  86. Santner A, Estelle M (2009) Recent advances and emerging trends in plant hormone signalling. Nature 459:1071–1078

    CAS  PubMed  Google Scholar 

  87. Sasse J, Martinoia E, Northern T (2018) Feed your friends: do plant exudates shape the root microbiome? Trends Plant Sci 23:25–41

    CAS  PubMed  Google Scholar 

  88. Sharma SB, Sayyed RZ, Trivedi MH, Gobi TA (2013) Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. SpringerPlus 2:587.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  89. Stracke R, Werber M, Weisshaar B (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol 4:447–456

    CAS  PubMed  Google Scholar 

  90. Supek F, Bošnjak M, Škunca N, Šmuc T (2011) REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One 6:e21800.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  91. Tatis PAD, Corzo MH, Cabezas JCO et al (2018) The overexpression of RXam1, a cassava gene coding for an RLK, confers disease resistance to Xanthomonas axonopodis pv. manihotis. Planta 247:1031–1042

    Google Scholar 

  92. Thiebaut F, Rojas CA, Grativol C, Motta M, Vieira T, Regulski M, Martienssen RA, Farinelli L, Hemerly AS, Ferreira PCG (2014) Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize. BMC Genomics 15:766.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  93. Tortora ML, Díaz-Ricci JC, Pedraza RO (2012) Protection of strawberry plants (Fragaria ananassa Duch.) against anthracnose disease induced by Azospirillum brasilense. Plant Soil 356:279–290

    CAS  Google Scholar 

  94. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks. Nat Protoc 7:562–578

    CAS  PubMed  PubMed Central  Google Scholar 

  95. Underwood W (2012) The plant cell wall: a dynamic barrier against pathogen invasion. Front Plant Sci 3:85.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  96. Vargas L, de Carvalho TLG, Ferreira PCG, Baldani VLD, Baldani JI, Hemerly AS (2012) Early responses of rice (Oryza sativa L.) seedlings to inoculation with beneficial diazotrophic bacteria are dependent on plant and bacterial genotypes. Plant Soil 356:127–137

    CAS  Google Scholar 

  97. Vibhuti M, Kumar A, Sheoran N, Nadakkakath AV, Eapen SJ (2017) Molecular basis of endophytic Bacillus megaterium induced growth promotion in Arabidopsis thaliana: revelation by microarray-based gene expression analysis. J Plant Growth Regul 36:118–130

    CAS  Google Scholar 

  98. Wang F, Kong W, Wong G, Fu L, Peng R, Li Z, Yao Q (2016) AtMYB12 regulates flavonoids accumulation and abiotic stress tolerance in transgenic Arabidopsis thaliana. Mol Gen Genomics 291:1545–1559

    CAS  Google Scholar 

  99. Wisniewski-Dyé F, Lozano L, Acosta-Cruz E, Borland S, Drogue B, Prigent-Combaret C, Rouy Z, Barbe V, Herrera AM, González V, Mavingui P (2012) Genome sequence of Azospirillum brasilense CBG497 and comparative analyses of Azospirillum core and accessory genomes provide insight into niche adaptation. Genes 3:576–602

    PubMed  PubMed Central  Google Scholar 

  100. Yamaguchi K, Yamada K, Kawasaki T (2013) Receptor-like cytoplasmic kinases are pivotal components in pattern recognition receptor-mediated signaling in plant immunity. Plant Signal Behav 8:e25662.

    CAS  Article  PubMed Central  Google Scholar 

  101. Yang H, Bogner M, Stierhof Y-D, Ludewig U (2010) H+-independent glutamine transport in plant root tips. PLoS One 5:e8917.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  102. Yang K, Qi L, Zhang Z (2014) Isolation and characterization of a novel wall-associated kinase gene TaWAK5 in wheat (Triticum aestivum). Crop J 2:255–266

    Google Scholar 

  103. Zamioudis C, Pieterse CMJ (2012) Modulation of host immunity by beneficial microbes. Mol Plant-Microbe Interact 25:139–150

    CAS  PubMed  Google Scholar 

Download references


The research was supported by Instituto Nacional de Ciência de Tecnologia (INCT) in Biological Nitrogen Fixation, Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Newton Fund grant (BB/N013476/1). PRH and HGFB were supported by CNPq posdoctoral and PhD fellowships, respectively. TLGC and CAR were supported by FAPERJ posdoctoral fellowships. ASH and PCGF receive support from a CNPq research grant.

Author information



Corresponding author

Correspondence to Adriana S. Hemerly.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Responsible Editor: Anton Hartmann.

Electronic supplementary material


(XLSX 12.1 kb)


(DOCX 126 kb)


(XLSX 1271 kb)


(XLSX 136 kb)


(XLSX 68 kb)


(XLSX 56 kb)


(XLSX 89 kb)


(XLSX 69 kb)

Fig. S1

Non-metric multidimensional scaling (MDS) ordination on RNA-seq library transcript abundance profiling of maize samples inoculated with Azospirillum brasilense (azos_in), Herbaspirillum seropedicae (herb_in) and mock-inoculated (uninoculated). (PDF 39 kb)

Fig. S2

Functional multidimesional scatterplots of GO enriched terms for biological process (a and b) and molecular function (c and d). Functional enriched GO terms identified in maize DEGs repressed (a and c) and induced (b after inoculation with Herbaspirillum seropedicae were independently analyzed with AgriGO and summarized using REVIGO semantic similarity-based scatterplots. For each category, enriched GO terms are plotted after the redundancy removal of semantic similarities. Semantically similar GO terms remain close together in the plot. Bubble color indicates adjusted p value for the false discovery rates, whereas large bubble size indicates more frequency count of the GO term in the underlying GO database. (PDF 603 kb)

Fig. S3

Mapman visualization of maize differentially expressed genes (DEGs) involved in biotic stress response when inoculated by both diazotrophic bacteria Azospirillum brasilense and Herbaspirillum seropedicae (a) or solely inoculated with A. brasilense (b) and H. seropedicae (c). Inoculated plants were compared to mock-inoculated plants and each block represents rescaled log2 ratios (red, induced; blue, repressed) of a specific DEG. (PDF 373 kb)

Fig. S4

Schematic representation of maize differentially expressed genes (DEGs) involved in auxin and brassinosteroids (BRs) metabolism when induced (red colors) or repressed (blue colors) after inoculation with Herbaspirillum seropedicae (square) or common to Azospirillum brasilense and H. seropedicae (circle) datasets. The genes arf1 and arf7 encode auxin response factor enzymes, while gene br6ox1 encodes a protein involved in the biosynthesis of BRs and the bzr1 gene is a positive regulator of the BR signaling pathway. (PDF 60 kb)

Fig. S5

Heatmap of transcription factor (TF) families from maize differentially expressed genes (DEGs) inoculated with diazotrophic bacteria Herbaspirillum seropedicae (Herb) and Azospirillum brasilense (Azos). Values are shown as log2 fold change related to mock-inoculated plants when induced (A) and repressed (B) by both diazotrophic bacteria, as well as induced (C) and repressed (D) in plants solely inoculated with H. seropedicae. The transcriptional regulatory families of AP2-EREBP, ethylene responsive factor; BES1, Brassinosteroids-related transcription factor; bHLH, basic Helix-Loop-Helix; C2C2, CONSTANS LIKE genes; MYB, Myb DNA-binding domain; ARF, Auxin Response Factor; HB, Homeobox KNOX1 KNOX2 domains; SBP, Squamosa promoter Binding Proteins domain; trihelix, helix-loop-helix-loop-helix; AUX_IAA, AUX_IAA domain; bZIP, basic region/leucine zipper motif; C2H2, zinc-finger domain; CCAAT, CBFB_NFYA CBFD_NFYB_HMF CCAAT-Dr1 NF-YB NF-YC domains; GNAT, Gcn5-related N-acetyltransferases; WRKY, WRKY domain; C3H, zf-CCCH domain; CAMTA, calmodulin binding transcription activators; orphans; PHD, plant homeodomain; SET, SET domain; SNF2, SNF2_N domain are shown. (PDF 115 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Hardoim, P.R., de Carvalho, T.L.G., Ballesteros, H.G.F. et al. Genome-wide transcriptome profiling provides insights into the responses of maize (Zea mays L.) to diazotrophic bacteria. Plant Soil 451, 121–143 (2020).

Download citation


  • Plant-microbe interactions
  • RNA-seq
  • Phytohormones
  • Nitrogen metabolism
  • Cell wall membrane receptors
  • Cytoplasmic receptors