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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. Yeoman
  • Fabian D. Menalled
Soil Microbiology

Abstract

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.

Keywords

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

Notes

Acknowledgments

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

Funding

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

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Supplementary Table 1 (DOCX 19 kb)
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Supplementary Table 2 (DOCX 38 kb)
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Supplementary Table 3 (DOCX 23 kb)
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Supplementary Fig. 1 (DOCX 527 kb)
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Supplementary Fig. 2 (DOCX 279 kb)
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Supplementary Fig. 3 (DOCX 320 kb)

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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
  • Fabian D. Menalled
    • 2
  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

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