Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions

Stien Beirinckx,Jeroen Raes,Caroline De Tender,Annelies Haegeman,Jane Debode,Tom Viaene,Dirk Inzé,Fien Amery,Raul Tito,Steven Vandenabeele,Hilde Nelissen,Sofie Goormachtig

doi:10.1186/s40168-020-00833-w

Abstract

BackgroundWhen maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. As some endophytes are beneficial for plants under stress conditions, we analyzed the impact of chilling temperatures on the root microbiome and examined whether microbiome-based analysis might help to identify bacterial strains that could promote growth under these temperatures.ResultsWe investigated how the maize root microbiome composition changed by means of 16S rRNA gene amplicon sequencing when maize was grown at chilling temperatures in comparison to ambient temperatures by repeatedly cultivating maize in field soil. We identified 12 abundant and enriched bacterial families that colonize maize roots, consisting of bacteria recruited from the soil, whereas seed-derived endophytes were lowly represented. Chilling temperatures modified the root microbiome composition only slightly, but significantly. An enrichment of several chilling-responsive families was detected, of which the Comamonadaceae and the Pseudomonadaceae were the most abundant in the root endosphere of maize grown under chilling conditions, whereas only three were strongly depleted, among which the Streptomycetaceae. Additionally, a collection of bacterial strains isolated from maize roots was established and a selection was screened for growth-promoting effects on juvenile maize grown under chilling temperatures. Two promising strains that promoted maize growth under chilling conditions were identified that belonged to the root endophytic bacterial families, from which the relative abundance remained unchanged by variations in the growth temperature.ConclusionsOur analyses indicate that chilling temperatures affect the bacterial community composition within the maize root endosphere. We further identified two bacterial strains that boost maize growth under chilling conditions. Their identity revealed that analyzing the chilling-responsive families did not help for their identification. As both strains belong to root endosphere enriched families, visualizing and comparing the bacterial diversity in these communities might still help to identify new PGPR strains. Additionally, a strain does not necessarely need to belong to a high abundant family in the root endosphere to provoke a growth-promoting effect in chilling conditions.DbrweUq9ovAceYzJQLfj4HVideo abstract.

Highlights

When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase
Identification of the main root microbiome families of maize grown in field soil To identify the main bacterial community of the maize root endosphere, grown in field soil, two experiments were carried out
I.e., bulk soil or root endosphere, was the major variance driver (87.15% and 86.25% for experiments I and II, respectively) for the differences in the bacterial community composition as found by the PERMANOVA analysis (P < 0.001) and illustrated in the Bray-Curtis dissimilarity-based principal coordinate analysis (PCoA) plot (Fig. 1a). In both maize grown in the field and in pots, five highly abundant phyla were significantly enriched (P < 0.001) in the root endosphere compared to the bulk soil: Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, and Actinobacteria (Additional file 1: Table S4)

Summary

Introduction

When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. Due to its subtropical origin, cultivation of maize in the Northern hemisphere is rather challenging because of chilling spring temperatures [1]. These chilling temperatures, on average 17 °C during the day and 12 °C during the night, retard plant development, eventually resulting in yield losses [2,3,4]. As well in the plant roots, i.e. the root endosphere, and as in the closely surrounding soil, the rhizosphere, microbial communities are established that can affect plant fitness [6]. The root endospherecolonizing microbes are expected to engage in robust interactions with the plant roots, but they could have been acquired by vertical transmission of seed microbes besides recruitment from the soil [14,15,16]

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Results

Discussion

Conclusion