Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation

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60 Scopus citations


Incorporation of organic material into soils is an important element of organic farming practices that can affect the composition of the soil bacterial communities that carry out nutrient cycling and other functions crucial to crop health and growth. We conducted a field experiment to determine the effects of cover crops and fertilizers on bacterial community structure in agricultural soils under long-term organic management. Illumina sequencing of 16S rDNA revealed diverse communities comprising 45 bacterial phyla in corn rhizosphere and bulk field soil. Community structure was most affected by location and by the rhizosphere effect, followed by sampling time and amendment treatment. These effects were associated with soil physicochemical properties, including pH, moisture, organic matter, and nutrient levels. Treatment differences were apparent in bulk and rhizosphere soils at the time of peak corn growth in the season following cover crop and fertilizer application. Cover crop and fertilizer treatments tended to lower alpha diversity in early season samples. However, winter rye, oilseed radish, and buckwheat cover crop treatments increased alpha diversity in some later season samples compared to a no-amendment control. Fertilizer treatments and some cover crops decreased relative abundance of members of the ammonia-oxidizing family Nitrosomonadaceae. Pelleted poultry manure and Sustane® (a commercial fertilizer) decreased the relative abundance of Rhizobiales. Our data point to a need for future research exploring how (1) cover crops influence bacterial community structure and functions, (2) these effects differ with biomass composition and quantity, and (3) existing soil conditions and microbial community composition influence how soil microbial populations respond to agricultural management practices.

Original languageEnglish (US)
Pages (from-to)9331-9341
Number of pages11
JournalApplied Microbiology and Biotechnology
Issue number21
StatePublished - Nov 1 2016

Bibliographical note

Funding Information:
This project was funded by the CERES Trust and supported by fellowships from the USDA National Needs Program and the MnDRIVE Initiative.

Publisher Copyright:
© 2016, Springer-Verlag Berlin Heidelberg.


  • 16S rRNA
  • Community structure
  • Cover crops
  • Manure
  • Organic agriculture
  • Sequence analysis
  • Soil


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