“I’ve Got the Magic in Me”: The Microbiome of Conventional vs Organic Production Systems

  • Andrea Sanchez-Barrios
  • Mohammad Radhi Sahib
  • Seth DeBoltEmail author


The term microbiome refers to the existence of multiple microbial genomes present in an environment in an association with a host. With the development of more precise sequencing approaches, identification of genus and families that were uncultivable microbes has been made possible. The current chapter explores the importance of understanding microbial communities and their association with agricultural production systems with particular attention to endophytic microorganisms. Agri-management practices and their relationship to the selection of microbial variation of taxa by plants and soil have been discussed in detail. The article also discusses how farming practices such as cover cropping and mulching mediate microbial community dynamics. Future perspectives on advancing sustainability by microbiome optimization are discussed.


Soil Microbiome Plant growth Expansion Endophyte Organic 



Work was supported by the National Science Foundation under Cooperative Agreement No. 1355438 and IOS-1256029. US Department of Agriculture Hatch funding and Altria Graduate Research Fellowship to ASB also supported this work.


  1. Adesemoye AO, Torbert HA, Kloepper JW (2009) Plant growth-promoting rhizobacteria allow reduced application rates of chemical fertilizers. Microb Ecol 58(4):921–929CrossRefPubMedGoogle Scholar
  2. Altmore C, Norvell WA, Bjorkman T, Harman GE (1999) Solubilization of phosphates and micronutrients by the plant growth promoting and biocontrol fungus Trichoderma harzianum Rifai. Appl Environ Microbiol 65:2926–2933Google Scholar
  3. Bacon CW, White JF (2016) Functions, mechanisms and regulation of endophytic and epiphytic microbial communities of plants. Symbiosis 68(1):87–98CrossRefGoogle Scholar
  4. Barrow JR, Lucero ME, Reyes-Vera I, Havstad KM (2008) Do symbiotic microbes have a role in plant evolution, performance and response to stress? Commun Integr Biol 1:69–73CrossRefPubMedPubMedCentralGoogle Scholar
  5. Biedrzycki ML, Jilany TA, Dudley SA, Bais HP (2010) Root exudates mediate kin recognition in plants. Commun Integr Biol 3:28–35CrossRefPubMedPubMedCentralGoogle Scholar
  6. Birtel J, Walser J-C, Pichon S, Bürgmann H, Matthews B (2015) Estimating bacterial diversity for ecological studies: methods, metrics, and assumptions. PLoS One 10(4):e0125356. doi: 10.1371/journal.pone.0125356 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Brabham C, Debolt S (2013) Chemical genetics to probe the cell wall. Front Plant Biotechnol 3:309Google Scholar
  8. Bulgarelli D, Rott M, Schlaeppi K, Ver Loren, van Themaat E et al (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91–95CrossRefPubMedGoogle Scholar
  9. Carbonetto B, Rascovan N, Álvarez R, Mentaberry A, Vázquez MP (2014) Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas. PLoS One 9:1–11CrossRefGoogle Scholar
  10. Deaker R, Roughley RJ, Kennedy IR (2004) Legume seed inoculation technology – a review. Soil Biol Biochem 36(8):1275–1288CrossRefGoogle Scholar
  11. Ding T, Melcher U (2016) Influences of plant species, season and location on leaf endophytic bacterial communities of non-cultivated plants. PLoS One 11(3):e0150895. doi: 10.1371/journal.pone.0150895 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Downie JA, Walker SA (1999) Plant responses to nodulation factors. Curr Opin Plant Biol 2:483–489CrossRefPubMedGoogle Scholar
  13. Feng Y, Motta AC, Reeves DW, Burmester CH, Van Santen E, Osborne JA (2003) Soil microbial communities under conventional till and no-till continuous cotton systems. Soil Biol Biochem 35:1693–1703CrossRefGoogle Scholar
  14. Foley JA, DeFries R, Asner GP, Barford C, Bonan G, Carpenter SR et al (2005) Global consequences of land use. Science 309:570–574CrossRefPubMedGoogle Scholar
  15. Gale WJ, Cambardella CA, Bailey TB (2000) Surface residue and root-derived carbon in stable and unstable aggregates. Soil Sci Soc Am J 64:196–201CrossRefGoogle Scholar
  16. Gopal M, Gupta A (2016) Microbiome selection could spur next-generation plant breeding strategies. Front Microbiol 7:1971–1977CrossRefPubMedPubMedCentralGoogle Scholar
  17. Hall TJ, Davis WEE (1990) Survival of Bacillus subtilis in silver sugar maple seedlings over a two-year period. Plant Dis 74:608–609CrossRefGoogle Scholar
  18. Hansen ML, Kregelund L, Nybroe O, Sorensen J (1997) Early colonization of barley roots by Pseudomonas fluorescens studied by immunofluorescence technique and confocal laser scanning microscopy. FEMS Microbiol Ecol 23:353e360CrossRefGoogle Scholar
  19. Hartmann M, Widmer F (2006) Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices. Appl Environ Microbiol 72:7804–7812CrossRefPubMedPubMedCentralGoogle Scholar
  20. Hartmann M, Frey B, Mayer J, Mader P, Widmer F (2015) Distinct soil microbial diversity under long-term organic and conventional farming. ISME J 9:1177–1194CrossRefPubMedGoogle Scholar
  21. Iniguez LA, Dong Y, Carter HD, Ahmer BMM, Stone JM, Triplett E (2005) Regulation of enteric endophytic bacterial colonization by plant defenses. Mol Plant-Microbe Interact 18:169–178CrossRefPubMedGoogle Scholar
  22. Kennedy A, Smith K (1995) Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 170:75–86CrossRefGoogle Scholar
  23. Kumar AS, Bais HP (2012) Wired to the roots: impact of root beneficial microbe interactions on the above ground plant physiology and protection. Plant Sign Behav 72:694–706Google Scholar
  24. Kumar A, Maurya BR, Raghuwanshi R (2014) Isolation and characterization of PGPR and their effect on growth, yield and nutrient content in wheat (Triticum aestivum L.) Biocatal Agric Biotechnol 3:121–128Google Scholar
  25. Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, Malfatti S, Glavina del Rio T, Jones CD, Tringe SG, Dangl JL (2015) Plant microbiome. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349:860–864CrossRefPubMedGoogle Scholar
  26. Li B, Lia Y-Y, Wua H-M, Zhanga F-F, Lia C-J, Lia X-X, Lambersb H, Long L (2016) Root exudates drive interspecific facilitation by enhancing nodulation and N2 fixation. PNAS 113:236496–236501Google Scholar
  27. Lundberg D et al (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90CrossRefPubMedPubMedCentralGoogle Scholar
  28. Lundberg DS, Yourstone S, Mieczkowski P, Jones CD, Dangl DL (2013) Practical innovations for high-throughput amplicon sequencing. Nat Methods 10:999–1002CrossRefPubMedGoogle Scholar
  29. Manzoni S, Jackson RB, Trofymow JA, Porporato A (2008) The global stoichiometry of litter nitrogen mineralization. Science 321:684–686CrossRefPubMedGoogle Scholar
  30. Parnell JJ, Berka R, Young HA, Sturino JM, Kang Y, Barnhart DM, DiLeo MV (2016) From the lab to the farm: an industrial perspective of plant beneficial microorganisms. Frontiers Plant Sci 7:1110. doi: 10.3389/fpls.2016.01110 CrossRefGoogle Scholar
  31. Paul EA (2007) Soil microbiology, ecology, and biochemistry in perspective. Soil microbiology, ecology and biochemistry, 3rd edn. Academic, San Diego, pp 3–24CrossRefGoogle Scholar
  32. Plett JM, Martin F (2011) Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes. Trends Genet 27:14–22CrossRefPubMedGoogle Scholar
  33. Rosenblueth M, Martinez-Romero E (2006) Bacterial endophytes and their interactions with hosts. Mol Plant-Microbe Interact 19:827–837CrossRefPubMedGoogle Scholar
  34. Schardl CL, Leuchtmann A, Spiering MJ (2004) Symbioses of grasses with seed borne fungal endophytes. Annu Rev Plant Biol 55:315–340CrossRefPubMedGoogle Scholar
  35. Schlaeppi K, Bulgarelli D (2015) The plant microbiome at work. Mol Plant-Microbe Interact 28:212–217CrossRefPubMedGoogle Scholar
  36. Seipke RF, Kaltenpoth M, Hutchings MI (2012) Streptomyces as symbionts: an emerging and widespread theme? FEMS Microbiol Rev 36:862–876CrossRefPubMedGoogle Scholar
  37. Singh BK, Bardgett RD, Smith P, Reay DS (2010) Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat Rev Micro 8:779–790CrossRefGoogle Scholar
  38. Soltani AA, Khavazi K, Asadi-Rahmani H, Omidvari M, Abaszadeh DP, Mirhoseyni H (2010) Plant growth promoting characteristics in some Flavobacterium spp. isolated from soils of Iran. J Agr Sci 4:106–115Google Scholar
  39. Stagnari F, Perpetuini G, Tofalo R, Campanelli G, Leteo F, Della Vella U, Schirone M, Suzzi G, Pisante M (2014) Long-term impact of farm management and crops on soil microorganisms assessed by combined DGGE and PLFA analyses. Front Microbiol 5:644CrossRefPubMedPubMedCentralGoogle Scholar
  40. Tokala R, Strap JL, Jung CM, Crawford DL, Salove MH, Deobald LA, Bailey FJ, Morra MJ (2002) Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC108 and the pea plant (Pisum sativum). Appl Environ Microbiol 68:2161–2171CrossRefPubMedPubMedCentralGoogle Scholar
  41. Tsurumaru H et al (2015) Metagenomic analysis of the bacterial community associated with the taproot of sugar beet. Microbes Environ 30:63–69CrossRefPubMedPubMedCentralGoogle Scholar
  42. Wagner MR, Lundberg DS, del Rio T, Tringe SG, Dangl JF, Mitchell-Olds T (2016) Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Comm 7:12151CrossRefGoogle Scholar
  43. Wang W, Wang H, Feng Y, Wang L, Xiao X, Xi Y, Luo X, Sun R, Ye X, Huang Y, Zhang Z, Cui Z (2016) Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River. Scientific Reports 6: Article number 35046Google Scholar
  44. Wilkinson V, Lucas RL (1969) Effects of herbicides on the growth of soil fungi. New Phytol 68:709–719CrossRefGoogle Scholar
  45. Xia Y, Greissworth E, Mucci C, Williams MA, DeBolt S (2013) Characterization of culturable bacterial endophytes of switchgrass (Panicum virgatum L.) and their capacity to influence plant growth. GCB Bioenergy 5:674–682CrossRefGoogle Scholar
  46. Xia Y, Petti C, Williams MA, DeBolt S (2014) Experimental approaches to study plant cell walls during plant-microbe interactions. Front Plant Sci 5:540CrossRefPubMedPubMedCentralGoogle Scholar
  47. Xia Y, Debolt S, Dreyer D, Scott D, Williams M (2015) Characterization of culturable bacterial endophytes and their capacity to promote plant growth from plants grown using organic or conventional practices. Front Plant Sci 6. doi: 10.3389/fpls.2015.00490

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Andrea Sanchez-Barrios
    • 1
  • Mohammad Radhi Sahib
    • 1
    • 2
  • Seth DeBolt
    • 1
    Email author
  1. 1.Department of HorticultureUniversity of KentuckyLexingtonUSA
  2. 2.Al Qasim Green UniversityBabylonIraq

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