Biology and Fertility of Soils

, Volume 48, Issue 5, pp 489–499 | Cite as

Manipulating the soil microbiome to increase soil health and plant fertility

  • Jacqueline M. Chaparro
  • Amy M. Sheflin
  • Daniel K. Manter
  • Jorge M. Vivanco


A variety of soil factors are known to increase nutrient availability and plant productivity. The most influential might be the organisms comprising the soil microbial community of the rhizosphere, which is the soil surrounding the roots of plants where complex interactions occur between the roots, soil, and microorganisms. Root exudates act as substrates and signaling molecules for microbes creating a complex and interwoven relationship between plants and the microbiome. While individual microorganisms such as endophytes, symbionts, pathogens, and plant growth promoting rhizobacteria are increasingly featured in the literature, the larger community of soil microorganisms, or soil microbiome, may have more far-reaching effects. Each microorganism functions in coordination with the overall soil microbiome to influence plant health and crop productivity. Increasing evidence indicates that plants can shape the soil microbiome through the secretion of root exudates. The molecular communication fluctuates according to the plant development stage, proximity to neighboring species, management techniques, and many other factors. This review seeks to summarize the current knowledge on this topic.


Microbiome Root exudates Plant growth promoting rhizobacteria (PGPRs) 



These studies were partially funded by NSF (MCB-0950857 to JMV). Funding for Jacqueline Chaparro was provided by the National Science Foundation for graduate students AGEP award #PO0000062901. We acknowledge the journal Biology and Fertility of Soils for inviting us to write this review article. Lastly, we apologize to those authors whose work could not be discussed because of the space limitations.


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Jacqueline M. Chaparro
    • 1
  • Amy M. Sheflin
    • 1
  • Daniel K. Manter
    • 2
  • Jorge M. Vivanco
    • 1
  1. 1.Center for Rhizosphere Biology and Department of Horticulture and Landscape ArchitectureColorado State UniversityFort CollinsUSA
  2. 2.Agricultural Research Service, Soil-Plant-Research UnitUnited States Department of AgricultureFort CollinsUSA

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