The rhizosphere and cropping system, but not arbuscular mycorrhizae, affect ammonia oxidizing archaea and bacteria abundances in two agricultural soils

Cassandra J. Wattenburger, Jessica Gutknecht, Quan Zhang, Thomas Brutnell, Kirsten Hofmockel, Larry Halverson

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


Arbuscular mycorrhizal fungi (AMF) form symbioses with roots that can enhance plant nutrition. While AMF have been shown to have a role in soil nitrogen (N) cycling, it is unclear whether AMF affect N cycling microbes such as ammonia-oxidizing bacteria (AOB) and archaea (AOA), which convert ammonium into nitrite in the first step of nitrification. In this study, we examined the effects of AMF on AOA and AOB abundances within the corn rhizosphere and bulk soil of conventional (corn-soybean rotation with inorganic fertilizer) and diversified (corn-soybean-oats/alfalfa-oats rotation with composted manure) systems. We hypothesized that AMF would decrease AOA and AOB abundances in a cropping-system dependent manner, possibly due to competition for ammonium. We grew corn deficient or proficient in AMF symbiosis in microcosms for 10 weeks. At the end of the experiment, both soils planted with the AMF-proficient corn genotype had higher ammonium and lower nitrate pool sizes compared to the same soils planted with the AMF-deficient corn genotype. Likewise, total plant N was higher in the AMF-proficient genotype compared to the AMF-deficient genotype. Despite changes in soil inorganic N pool sizes, AOA and AOB abundances were unaffected by plant AMF-proficiency. Instead, AOA abundance was greater in the rhizosphere than in the bulk soil regardless of cropping system, and AOB abundance was greater in the conventional than the diversified cropping system soil regardless of proximity to the root. These data indicate that 1) AMF did not affect AOA or AOB abundance in these N-rich soils but other factors such as root proximity and inorganic fertilization did and 2) AOA and AOB have differing ecological niches within rhizosphere and bulk soil that should be considered when managing for nitrogen losses.

Original languageEnglish (US)
Article number103540
JournalApplied Soil Ecology
StatePublished - Jul 2020

Bibliographical note

Funding Information:
Funding: This work was supported by the United States Department of Agriculture [grant number 2014-67019-21628 ] and University of Minnesota internal funding. This material is based upon work supported by Larry Halverson while serving at the U.S. NSF. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the U.S. NSF. We thank Guillaume Bay, Gregory Watson, and Alyssa Nease for their assistance in collecting and processing samples. Thank you to Nathan Johnson for creating the art for figure three.

Publisher Copyright:
© 2020


  • Agricultural management
  • Ammonia oxidizing archaea
  • Ammonia oxidizing bacteria
  • Arbuscular mycorrhizal fungi
  • Rhizosphere soil


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