Connecting the Lab and the Field: Genome Analysis of Phyllobacterium and Rhizobium Strains and Field Performance on Two Vegetable Crops

José David Flores-Félix,Raúl Rivas,Eustoquio Martínez-Molina,Fernando González-Andrés,Encarna Velázquez,Andrea Squartini

doi:10.3390/agronomy11061124

Abstract

The legume nodules are a rich source not only of rhizobia but also of endophytic bacteria exhibiting plant growth-promoting mechanisms with potential as plant biostimulants. In this work we analyzed the genomes of Phyllobacterium endophyticum PEPV15 and Rhizobium laguerreae PEPV16 strains, both isolated from Phaseolus vulgaris nodules. In silico analysis showed that the genomes of these two strains contain genes related to N-acyl-homoserine lactone (AHL) and cellulose biosynthesis, involved in quorum sensing and biofilm formation, which are essential for plant colonization. Several genes involved in plant growth promotion such as those related to phosphate solubilization, indole acetic acid production, siderophore biosynthesis and nitrogen fixation were also located in both genomes. When strains PEPV15 and PEPV16 were inoculated in lettuce and carrot in field assays, we found that both significantly increased the yield of lettuce shoots and carrot roots by more than 20% and 10%, respectively. The results of this work confirmed that the genome mining of genes involved in plant colonization and growth promotion is a good strategy for predicting the potential of bacterial strains as crops inoculants, opening new horizons for the selection of bacterial strains with which to design new, effective bacteria-based plant biostimulants.

Highlights

New perspectives in agriculture include the use of technologies able to reduce its impact on the environment through a maximization of the efficiency in the use of resources
The aims of this study were: (i) to perform a comparative in silico analysis of the whole genomes of two strains isolated from common bean nodules, Phyllobacterium endophyticum PEPV15 and Rhizobium laguerreae PEPV16 [30,31], which have similar in vitro plant growth patterns and are able to colonize lettuce and carrot roots and to promote the growth of the edible parts of these plants in pre-field studies carried out in microcosm conditions [32,33,34,35], and (ii) to carry out preliminary assays in commercial fields in order to evaluate the potential of these two strains as biostimulants of lettuce and carrot plants, two vegetables widely consumed worldwide in which the effects of the inoculation of rhizobia or legume nodule endophytic bacteria have not been studied to date
We detected the production of acyl-homoserine lactone (AHL) in both strains after dilutions 1:125 and 1:3126 for the strains PEPV15 and PEPV16, respectively. In agreement with these results, we found in the genome of the strain PEPV16 a gene encoding a N-acyl-L-homoserine lactone (AHL) synthase and in that of strain PEPV15 a gene encoding a GNAT family N-acetyltransferase involved in AHL biosynthesis [54]

Summary

Introduction

New perspectives in agriculture include the use of technologies able to reduce its impact on the environment through a maximization of the efficiency in the use of resources. Several studies on the diversity of PGPB [3] and their potential to colonize plant roots [4] and to exhibit in vitro plant growth promotion mechanisms have been published [5] These bacteria can inhabit the plant rhizosphere or the inner tissues of plants [6], plant endophytes being the most efficient inoculants [7]. For this reason, in the past year, several research studies have evaluated ways of increasing plant growth by using bacterial endophytes isolated from non-legume plants [8,9] and from legume nodules [10,11,12,13,14,15,16,17,18]. These nodules contain the rhizobia responsible for their formation and for symbiotic nitrogen fixation as well as other bacterial endophytes with different plant growth promotion mechanisms [19,20,21,22]

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