Microbial Ecology

, Volume 73, Issue 2, pp 417–434 | Cite as

Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure

  • Suzanne L. Ishaq
  • Stephen P. Johnson
  • Zach J. Miller
  • Erik A. Lehnhoff
  • Sarah Olivo
  • Carl J. YeomanEmail author
  • Fabian D. MenalledEmail author
Soil Microbiology


Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P < 0.001) and had more discriminant taxa delineating groups (linear discriminant analysis). Living inoculum soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P < 0.05), and more discriminant taxa than conventionally farmed inoculum-treated soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition.


16S rRNA Avena fatua Amaranthus retroflexus Conventional farming Illumina MiSeq Organic farming Soil microbial diversity 



The authors would like to thank Dr. Tiffanie Nelson, Montana State University, for her instruction in PRIMER and R. We also thank the farmers who allowed us to collect soil samples from their fields, Ali Thornton, Jesse Hunter, Madi Nixon, Ceci Welch, and Ethan Mayes who provided assistance with the greenhouse study. Further thanks to Subodh Adhikari, Sean McKenzie, and Wyatt Holmes for their help in gathering soil samples, and Dr. Cathy Zabinski for her insight on belowground ecology.

Compliance with Ethical Standards


This work was conducted with funding provided by the USDA-OREI (Grant MONB00365), USDA-ORG (2011-04960), and the Montana University System Research Initiative: 51040-MUSRI2015-02.

Supplementary material

248_2016_861_MOESM1_ESM.docx (20 kb)
Supplementary Table 1 (DOCX 19 kb)
248_2016_861_MOESM2_ESM.docx (38 kb)
Supplementary Table 2 (DOCX 38 kb)
248_2016_861_MOESM3_ESM.docx (23 kb)
Supplementary Table 3 (DOCX 23 kb)
248_2016_861_MOESM4_ESM.docx (528 kb)
Supplementary Fig. 1 (DOCX 527 kb)
248_2016_861_MOESM5_ESM.docx (280 kb)
Supplementary Fig. 2 (DOCX 279 kb)
248_2016_861_MOESM6_ESM.docx (320 kb)
Supplementary Fig. 3 (DOCX 320 kb)


  1. 1.
    Schnitzer SA, Klironomos JN, HilleRisLambers J et al (2011) Soil microbes drive the classic plant diversity–productivity pattern. Ecology 92:296–303. doi: 10.1890/10-0773.1 CrossRefPubMedGoogle Scholar
  2. 2.
    Zak DR, Homes WE, White DC et al (2003) Plant diversity, soil microbial communities, and ecosystem function: are there any links? Ecology 84:2042–2050CrossRefGoogle Scholar
  3. 3.
    Hartmann M, Frey B, Mayer J et al (2015) Distinct soil microbial diversity under long-term organic and conventional farming. ISME J 9:1177–1194. doi: 10.1038/ismej.2014.210 CrossRefPubMedGoogle Scholar
  4. 4.
    Grayston SJ, Wang SQ, Campbell CD, Edwards AC (1998) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30:369–378. doi: 10.1016/s0038-0717(97)00124-7 CrossRefGoogle Scholar
  5. 5.
    Brussaard L, de Ruiter PC, Brown GG (2007) Soil biodiversity for agricultural sustainability. Agric Ecosyst Environ 121:233–244. doi: 10.1016/j.agee.2006.12.013 CrossRefGoogle Scholar
  6. 6.
    Schmidt TM, Waldron C (2015) Microbial diversity in soils of agricultural landscapes and its relation to ecosystem function. In: Hamilton SK, Doll JE, Roberston GP (eds) The ecology of agricultural landscapes: long-term research on the path to sustainability. Oxford University Press, New York, pp 135–157Google Scholar
  7. 7.
    Griffiths BS, Ritz K, Bardgett RD et al (2000) Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship. Oikos 90:279–294. doi: 10.1034/j.1600-0706.2000.900208.x CrossRefGoogle Scholar
  8. 8.
    Atlas RM, Horowitz A, Krichevsky M, Bej AK (1991) Response of microbial populations to environmental disturbance. Microb Ecol 22:249–256. doi: 10.1007/BF02540227 CrossRefPubMedGoogle Scholar
  9. 9.
    van der Heijden MGA, Klironomos JN, Ursic M et al (1998) Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396:69–72. doi: 10.1038/23932 CrossRefGoogle Scholar
  10. 10.
    Hayat R, Ali S, Amara U et al (2010) Soil beneficial bacteria and their role in plant growth promotion: a review. Ann Microbiol 60:579–598CrossRefGoogle Scholar
  11. 11.
    Nannipieri P, Ascher J, Ceccherini MT et al (2003) Microbial diversity and soil functions. Eur J Soil Sci 54:655–670. doi: 10.1046/j.1351-0754.2003.0556.x CrossRefGoogle Scholar
  12. 12.
    Bardgett RD, van der Putten WH (2014) Belowground biodiversity and ecosystem functioning. Nature 515:505–511. doi: 10.1038/nature13855 CrossRefPubMedGoogle Scholar
  13. 13.
    Karlen DL, Wollenhaupt NC, Erbach DC et al (1994) Long-term tillage effects on soil quality. Soil Tillage Res 32:313–327CrossRefGoogle Scholar
  14. 14.
    Lupwayi NZ, Rice WA, Clayton GW (1998) Soil microbial diversity and community structure under wheat as influenced by tillage and crop rotation. Soil Biol Biochem 30:1733–1741. doi: 10.1016/S0038-0717(98)00025-X CrossRefGoogle Scholar
  15. 15.
    Menalled FD, Gross KL, Hammond M (2001) Weed aboveground and seedbank community responses to agricultural management systems. Ecol Appl 11:1586–1601CrossRefGoogle Scholar
  16. 16.
    Pollnac FW, Maxwell BD, Menalled FD (2009) Using species-area curves to examine weed communities in organic and conventional spring wheat systems. Weed Sci 57:241–247. doi: 10.1614/WS-08-159.1 CrossRefGoogle Scholar
  17. 17.
    Harbuck KSB, Menalled FD, Pollnac FW (2009) Impact of cropping systems on the weed seed banks in the northern Great Plains, USA. Weed Biol Manag 9:160–168. doi: 10.1111/j.1445-6664.2009.00334.x CrossRefGoogle Scholar
  18. 18.
    Thakur MP, Milcu A, Manning P et al (2015) Plant diversity drives soil microbial biomass carbon in grasslands irrespective of global environmental change factors. Glob Chang Biol 21:4076–4085. doi: 10.1111/gcb.13011 CrossRefPubMedGoogle Scholar
  19. 19.
    Postma-Blaauw MB, de Goede RGM, Bloem J et al (2010) Soil biota community structure and abundance under agricultural intensification and extensification. Ecology 91:460–473CrossRefPubMedGoogle Scholar
  20. 20.
    Flohre A, Rudnick M, Traser G et al (2011) Does soil biota benefit from organic farming in complex vs. simple landscapes? Agric Ecosyst Environ 141:210–214. doi: 10.1016/j.agee.2011.02.032 CrossRefGoogle Scholar
  21. 21.
    DeAngelis KM, Brodie EL, DeSantis TZ et al (2009) Selective progressive response of soil microbial community to wild oat roots. ISME J 3:168–178CrossRefPubMedGoogle Scholar
  22. 22.
    Wieland G, Neumann R, Backhaus H (2001) Variation of microbial communities in soil, rhizosphere, and rhizoplane in response to crop species, soil type, and crop development. Appl Environ Microbiol 67:5849–5854. doi: 10.1128/AEM.67.12.5849-5854.2001 CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Duineveld BM, Kowalchuk GA, Keijzer A et al (2001) Analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol 67:172–178. doi: 10.1128/AEM.67.1.172-178.2001 CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Germida JJ, Siciliano SD, Renato de Freitas J, Seib AM (1998) Diversity of root-associated bacteria associated with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum L.). FEMS Microbiol Ecol 26:43–50. doi: 10.1111/j.1574-6941.1998.tb01560.x CrossRefGoogle Scholar
  25. 25.
    Hao JJ, Davis RM (2009) Effect of soil inoculum density of Fusarium oxysporum f. sp. vasinfectum on disease development in cotton. Plant Dis 93:1324–1328CrossRefGoogle Scholar
  26. 26.
    Ballaminutt N, Matheus DR (2007) Characterization of fungal inoculum used in soil remediation. Braz J Microbiol 28:249–252Google Scholar
  27. 27.
    White D, Crosbie JD, Atkinson D, Killham K (1994) Effect of an introduced inoculum on soil microbial diversity. FEMS Microbiol Ecol 14:169–178CrossRefGoogle Scholar
  28. 28.
    Griffiths B, Ritz K, Wheatley R et al (2001) An examination of the biodiversity–ecosystem function relationship in arable soil microbial communities. Soil Biol Biochem 33:1713–1722. doi: 10.1016/S0038-0717(01)00094-3 CrossRefGoogle Scholar
  29. 29.
    Johnson SP, Miller ZJ, Lehnhoff EA, Miller PR, Menalled FD (2016) Cropping systems modify the impacts of biotic plant-soil feedbacks on wheat (Triticum aestivum L.) growth and competitive ability. Weed Res (in press)Google Scholar
  30. 30.
    Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700PubMedPubMedCentralGoogle Scholar
  31. 31.
    Caporaso JG, Lauber CL, Walters WA et al (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108(Suppl):4516–4522. doi: 10.1073/pnas.1000080107 CrossRefPubMedGoogle Scholar
  32. 32.
    Masella AP, Bartram AK, Truszkowski JM et al (2012) PANDAseq: paired-end assembler for illumina sequences. BMC Bioinforma 13:31. doi: 10.1186/1471-2105-13-31 CrossRefGoogle Scholar
  33. 33.
    Luo C, Tsementzi D, Kyrpides N et al (2012) Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 7:e30087. doi: 10.1371/journal.pone.0030087 CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Kozich JJ, Westcott SL, Baxter NT et al (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79:5112–5120. doi: 10.1128/AEM.01043-13 CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Edgar RC, Haas BJ, Clemente JC et al (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200. doi: 10.1093/bioinformatics/btr381 CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12:1889–98. doi: 10.1111/j.1462-2920.2010.02193.x CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Chao A, Shen T-J (2010) Program SPADE (Species Prediction And Diversity Estimation). Available at:
  40. 40.
    Burnham KP, Overton WS (1979) Robust estimation of population size when capture probabilities vary among animals. Ecology 60:927. doi: 10.2307/1936861 CrossRefGoogle Scholar
  41. 41.
    Jost L (2006) Entropy and diversity. Oikos 113:363CrossRefGoogle Scholar
  42. 42.
    Good IJ (1953) On population frequencies of species and the estimation of population parameters. Biometrika 40:237–264CrossRefGoogle Scholar
  43. 43.
    Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, UrbanaGoogle Scholar
  44. 44.
    Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. J Ecol 18:117–143. doi: 10.1111/j.1442-9993.1993.tb00438.x Google Scholar
  45. 45.
    Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Envir Microbiol 71:8228–8235. doi: 10.1128/AEM.71.12.8228-8235.2005 CrossRefGoogle Scholar
  46. 46.
    R Core Team (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
  47. 47.
    Beals EW (1984) Bray-Curtis ordination: an effective strategy for analysis of multivariate ecological data. Adv Ecol Res 14:1–55CrossRefGoogle Scholar
  48. 48.
    Langille MGI, Zaneveld J, Caporaso JG et al (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–821. doi: 10.1038/nbt.2676 CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Parks DH, Tyson GW, Hugenholtz P, Beiko RG (2014) STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30:3123–3124. doi: 10.1093/bioinformatics/btu494 CrossRefPubMedPubMedCentralGoogle Scholar
  50. 50.
    Tiemann LK, Grandy AS, Atkinson EE et al (2015) Crop rotational diversity enhances belowground communities and functions in an agroecosystem. Ecol Lett 18:761–771. doi: 10.1111/ele.12453 CrossRefPubMedGoogle Scholar
  51. 51.
    Wolfe BE, Klironomos JN (2005) Breaking new ground: soil communities and exotic plant invasion. Bioscience 55:477. doi: 10.1641/0006-3568(2005)055[0477:BNGSCA]2.0.CO;2 CrossRefGoogle Scholar
  52. 52.
    Bollen GJ (1969) The selective effect of heat treatment on the microflora of a greenhouse soil. Neth J Plant Pathol 75:157–163. doi: 10.1007/BF02137211 CrossRefGoogle Scholar
  53. 53.
    Margosch D, Ehrmann MA, Buckow R et al (2006) High-pressure-mediated survival of Clostridium botulinum and Bacillus amyloliquefaciens endospores at high temperature. Appl Environ Microbiol 72:3476–3481. doi: 10.1128/AEM.72.5.3476-3481.2006 CrossRefPubMedPubMedCentralGoogle Scholar
  54. 54.
    Yap JM, Goldsmith CE, Moore JE (2013) Integrity of bacterial genomic DNA after autoclaving: possible implications for horizontal gene transfer and clinical waste management. J Hosp Infect 83:247–249. doi: 10.1016/j.jhin.2012.11.016 CrossRefPubMedGoogle Scholar
  55. 55.
    Rocha EPC (2016) Using sex to cure the genome. PLoS Biol 14:e1002417. doi: 10.1371/journal.pbio.1002417 CrossRefPubMedPubMedCentralGoogle Scholar
  56. 56.
    Tillman D (1982) Resource competition and community structure. Princeton University Press, PrincetonGoogle Scholar
  57. 57.
    Smith JL, Paul EA (1990) The significance of soil microbial biomass estimations. In: Bollag J, Stotsky G (eds) Soil biochemistry. Marcel Dekker, New York, pp 357–396Google Scholar
  58. 58.
    Fierer N, Ladau J, Clemente JC et al (2013) Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342:621–624. doi: 10.1126/science.1243768 CrossRefPubMedGoogle Scholar
  59. 59.
    Bergmann GT, Bates ST, Eilers KG et al (2011) The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem 43:1450–1455. doi: 10.1016/j.soilbio.2011.03.012 CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Wu H, Fang Y, Yu J, Zhang Z (2014) The quest for a unified view of bacterial land colonization. ISME J 8:1358–69. doi: 10.1038/ismej.2013.247 CrossRefPubMedPubMedCentralGoogle Scholar
  61. 61.
    Burns JH, Anacker BL, Strauss SY, Burke DJ (2015) Soil microbial community variation correlates most strongly with plant species identity, followed by soil chemistry, spatial location and plant genus. AoB Plants 7:plv030. doi: 10.1093/aobpla/plv030 CrossRefPubMedPubMedCentralGoogle Scholar
  62. 62.
    Matson PA (1997) Agricultural intensification and ecosystem properties. Science 277:504–509. doi: 10.1126/science.277.5325.504 CrossRefPubMedGoogle Scholar
  63. 63.
    Bever JD, Platt TG, Morton ER (2012) Microbial population and community dynamics on plant roots and their feedbacks on plant communities. Annu Rev Microbiol 66:265–283. doi: 10.1146/annurev-micro-092611-150107 CrossRefPubMedPubMedCentralGoogle Scholar
  64. 64.
    Wagg C, Jansa J, Schmid B, van der Heijden MGA (2011) Belowground biodiversity effects of plant symbionts support aboveground productivity. Ecol Lett 14:1001–1009CrossRefPubMedGoogle Scholar
  65. 65.
    Mazzoleni S, Bonanomi G, Incerti G et al (2015) Inhibitory and toxic effects of extracellular self-DNA in litter: a mechanism for negative plant-soil feedbacks? New Phytol 205:1195–210. doi: 10.1111/nph.13121 CrossRefPubMedGoogle Scholar
  66. 66.
    Singh HP, Batish DR, Kohli RK (1999) Autotoxicity: concept, organisms, and ecological significance. CRC Crit Rev Plant Sci 18:757–772. doi: 10.1080/07352689991309478 CrossRefGoogle Scholar
  67. 67.
    Wood SA, Almaraz M, Bradford MA et al (2015) Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture. Front Microbiol 6:90. doi: 10.3389/fmicb.2015.00090 CrossRefPubMedPubMedCentralGoogle Scholar
  68. 68.
    Shi S, Nuccio E, Herman DJ et al (2015) Successional trajectories of rhizosphere bacterial communities over consecutive seasons. MBio 6:e00746. doi: 10.1128/mBio.00746-15 PubMedPubMedCentralGoogle Scholar
  69. 69.
    Frey-Klett P, Garbaye J, Tarkka M (2007) The mycorrhiza helper bacteria revisited. New Phytol 176:22–36. doi: 10.1111/j.1469-8137.2007.02191.x CrossRefPubMedGoogle Scholar
  70. 70.
    Qasem JR (1995) Allelopathic effects of Amaranthus retroflexus and Chenopodium murale on vegetable crops. Allelopath J 2:49–66Google Scholar
  71. 71.
    Eisenhut M, Ruth W, Haimovich M et al (2008) The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants. Proc Natl Acad Sci U S A 105:17199–17204CrossRefPubMedPubMedCentralGoogle Scholar
  72. 72.
    Yingping F, Lemeille S, Talla E et al (2014) Unravelling the cross-talk between iron starvation and oxidative stress responses highlights the key role of PerR (alr0957) in peroxide signalling in the cyanobacterium Nostoc PCC 7120. Environ Microbiol Rep 6:468–475. doi: 10.1111/1758-2229.12157 CrossRefPubMedGoogle Scholar
  73. 73.
    Schumacher WJ, Thill DC, Lee GA (1983) Allelopathic potential of wild oat (Avena fatua) on spring wheat (Triticum aestivum) growth. J Chem Ecol 9:1235–1245. doi: 10.1007/BF00982225 CrossRefPubMedGoogle Scholar
  74. 74.
    Iannucci A, Fragasso M, Platani C, Papa R (2013) Plant growth and phenolic compounds in the rhizosphere soil of wild oat (Avena fatua L.). Front Plant Sci 4:509. doi: 10.3389/fpls.2013.00509 CrossRefPubMedPubMedCentralGoogle Scholar
  75. 75.
    Mandal SM, Chakraborty D, Dey S (2010) Phenolic acids act as signaling molecules in plant-microbe symbioses. Plant Signal Behav 5:359–368CrossRefPubMedPubMedCentralGoogle Scholar
  76. 76.
    Barkovskii A, Bouillant ML, Monrozier LJ, Balandreau J (1995) Azospirillum strains use phenolic compounds as intermediates for electron transfer under oxygen-limiting conditions. Microb Ecol 29:99–114. doi: 10.1007/BF00217426 CrossRefPubMedGoogle Scholar
  77. 77.
    Westerberg K, Elväng AM, Stackebrandt E, Jansson JK (2000) Arthrobacter chlorophenolicus sp. nov., a new species capable of degrading high concentrations of 4-chlorophenol. Int J Syst Evol Microbiol 50 Pt 6:2083–92. doi: 10.1099/00207713-50-6-2083 CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Suzanne L. Ishaq
    • 1
    • 2
  • Stephen P. Johnson
    • 2
  • Zach J. Miller
    • 3
  • Erik A. Lehnhoff
    • 4
  • Sarah Olivo
    • 1
  • Carl J. Yeoman
    • 1
    Email author
  • Fabian D. Menalled
    • 2
    Email author
  1. 1.Department of Animal and Range SciencesMontana State UniversityBozemanUSA
  2. 2.Department of Land Resources and Environmental SciencesMontana State UniversityBozemanUSA
  3. 3.Western Agriculture Research CenterMontana State UniversityBozemanUSA
  4. 4.Department of Entomology, Plant Pathology and Weed ScienceNew Mexico State UniversityLas CrucesUSA

Personalised recommendations