The aeroponic rhizosphere microbiome: community dynamics in early succession suggest strong selectional forces

  • Jennifer W. Edmonds
  • Joshua D. Sackett
  • Hunter Lomprey
  • Heather L. Hudson
  • Duane P. MoserEmail author
Original Paper


In the last decade there has been increased interest in the manipulation of rhizosphere microbial communities in soilless systems (hydroponics) through the addition of plant growth promoting microbes (PGPMs) to increase plant nutrition, lower plant stress response, and control pathogens. This method of crop management requires documenting patterns in communities living in plant roots throughout the growing season to inform decisions on timing of application and composition of the supplemental PGPM consortium. As a contribution to this effort, we measured changes in the bacterial community through early succession (first 26 days) in plant root biofilms growing in an indoor commercial aeroponic system where roots were sprayed with a mist of nutrient-amended water. By 12 days following seed germination, a root-associated community had established that was distinct from the source communities found circulating in the system. Successional patterns in the community over the following 2 weeks (12–26 days) included changes in abundance of bacterial groups that have been documented in published literature as able to utilize plant root exudates, release plant hormones, or augment nutrient availability. Six bacterial families/genera (Hydrogenophilaceae, Rhizobium, Legionellaceae, Methylophilus, Massilia, or Herbaspirillum) were the most abundant in each root sample, comprising 8–37% of the microbiome. Given the absence of soil-associated microbial communities in hydroponic systems, they provide an ideal design for isolating plant–microbial interactions and identifying key components possibly contributing to plant health.


Community structure Illumina sequencing Hydroponics Proteobacteria 



Special thanks to Brittany Kruger for guidance and help with field sampling, and to Kristie Menjivar, Sara Munson, Daniel Walsh, and Heather Williams for laboratory assistance with DNA extractions. We particularly thank the owners of Indoor Farms of America, Ron Evans and David Martin, for allowing us to sample their aeroponic demonstration facility and for information regarding system engineering that guided our sampling protocol. Thanks also to Markus Berli and Kent Hoekman of CTREC for technical assistance over the life of this project contributing to the original project concept, and to Daniel Gerrity for use of laboratory instrumentation at UNLV.

Author’s contribution

JE (co-first author) aided with sampling, generated water chemistry data, analyzed portions of sequence data, and wrote and edited the original draft. JS (co-first author) designed study, lead sampling effort, coordinated lab analyses, analyzed sequence data, wrote portions of the original draft and edited the original draft. HL contributed to laboratory sample processing and to writing portions of the original draft. HH contributed to writing portions of the original draft. DM conceived and designed the study, aided with sampling, and edited the original draft.


This work was supported by a SEED Grant from Nevada’s National Aeronautics and Space Administration (NASA), Established Program to Stimulate Competitive Research, (EPSCoR) to Nevada State College, cooperative agreement number NNX13AB18A. Additional funding was provided by the Nevada State College provost office, the Desert Research Institute’s Clean Technologies and Renewable Energy Center (CTREC), and a Grant from the USDA (AWD-05-00000017) in collaboration with the University of Nevada Las Vegas.

Compliance with ethical standards

Conflict of interest

Authors JWE, JDS, HL, HLH, DPM declare they have no conflict of interest.

Supplementary material

10482_2019_1319_MOESM1_ESM.xlsx (496 kb)
Appendix S1. Sheet 1:Unrarefied OTU table including OTU numbers, OTU sequences, taxonomy, and OTU counts. Sheet 2:OTU table, rarefied to a depth of 10,000 sequences per sample, including OTU numbers, OTU sequences, taxonomy, and OTU counts. Uclust-assigned taxonomy was derived from the SILVA_128 curated reference database at 97% sequence identity (k = kingdom, p = phylum, c = class, o = order, f = family, g = genus, s = species). Sheet 3:Abundances of prokaryotic phyla detected in each sample. The Proteobacteria have been subdivided into classes. (XLSX 496 kb)


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Physical and Life SciencesNevada State CollegeHendersonUSA
  2. 2.Division of Earth and Ecosystems SciencesDesert Research InstituteLas VegasUSA
  3. 3.Division of Hydrologic SciencesDesert Research InstituteLas VegasUSA
  4. 4.School of Life SciencesUniversity of NevadaLas VegasUSA

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