Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus Frankia.

Louis S. Tisa,Michael Goodfellow,Imen Nouioui,Lorena Carro,Maher Gtari,Faten Ghodhbane-Gtari,Jean Franco Castro,Vartul Sangal,Carlos Cortés-albayay,Hans-Peter Klenk

doi:10.3389/fmicb.2019.01457

Abstract

This study was designed to determine the plant growth promoting (PGP) potential of members of the genus Frankia. To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the Frankia genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (trpD), anthranilate synthases, and aminases (trpA and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (nif operon except for atypical Frankia) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in Frankia cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of Frankia casuarinae, F. inefficax, F. irregularis, and F. saprophytica. In short, these in silico genome analyses provide an insight into the PGP abilities of Frankia strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in Frankia strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that Frankia may have novel molecular mechanisms for cytokinin biosynthesis.

Highlights

Actinobacteria classified in the genus Frankia (Brunchorst, 1886) are well known for their ability to induce nitrogen-fixing nodules in over 200 species of dicotyledonous plants representing eight angiosperm families (Normand et al, 2014)
The prospect of selecting Frankia strains for targeted growth promotion of actinorhizal plants in marginal soils was bedeviled by the difficulty of growing these slow-growing bacteria and by the poor state of their systematics
The distribution of plant growth promoting (PGP) genes in the genomes was determined using the SEED server (Overbeek et al, 2014) with a focus on genes encoding for nitrogen fixation, phosphate solubilization, plant hormones, siderophores, lytic enzymes, and those modulating the effect of environmental stress

Summary

Introduction

Actinobacteria classified in the genus Frankia (Brunchorst, 1886) are well known for their ability to induce nitrogen-fixing nodules in over 200 species of dicotyledonous (actinorhizal) plants representing eight angiosperm families (Normand et al, 2014). The distribution of PGP genes within the genomes of representative Frankia strains was undertaken with particular reference to those associated with the synthesis of plant hormones, siderophores, and the regulation of phosphate metabolism.

Results

Conclusion