A microbiome engineering framework to evaluate rhizobial symbionts of legumes

Kenjiro W Quides,Hagop S Atamian

doi:10.1007/s11104-021-04892-2

Abstract

BackgroundFor well over a century, rhizobia have been recognized as effective biofertilizer options for legume crops. This has led to the widespread use of rhizobial inoculants in agricultural systems, but a recurring issue has emerged: applied rhizobia struggle to provide growth benefits to legume crops. This has largely been attributed to the presence of soil rhizobia and has been termed the ‘rhizobial competition problem.’ScopeMicrobiome engineering has emerged as a methodology to circumvent the rhizobial competition problem by creating legume microbiomes that do not require exogenous rhizobia. However, we highlight an alternative implementation of microbiome engineering that focuses on untangling the complexities of the symbiosis that contribute to the rhizobial competition problem. We outline three approaches that use different starting inocula to test hypotheses to overcome the rhizobial competition problem.ConclusionsThe approaches we suggest are targeted at various stages of the legume-rhizobium symbiosis and will help us uncover underlying molecular mechanisms that contribute to the rhizobial competition problem. We conclude with an integrative perspective of these different approaches and suggest a path forward for future research on legumes and their complex microbiome.

Highlights

There has been an attempt to inoculate rhizobia into the soil of legume crops to reduce or replace the use of expensive and polluting nitrogen fertilizer (Ferguson et al 2010; Tilman et al 2002)
Rhizobia are commercially available as elite inoculants that are selected for application to agricultural fields based on their capacity to improve legume growth and yield through nitrogen fixation (USDA 2015)
The problem is strong competition with the existing soil rhizobia community, native or naturalized, that limits survivorship in the soil and access to host tissue. This phenomenon, whereby elite inoculants struggle to provide benefit in agricultural fields that is comparable to the benefit observed under controlled settings, has been termed the ‘rhizobial competition problem’ (RCP; Triplett and Sadowsky 1992)

Summary

Conclusions

The approaches we suggest are targeted at various stages of the legume-rhizobium symbiosis and will help us uncover underlying molecular mechanisms that contribute to the rhizobial competition problem. We conclude with an integrative perspective of these different approaches and suggest a path forward for future research on legumes and their complex microbiome.

Introduction

Concluding thoughts and future directions