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

Abstract

Background: When 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. Results: We 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. Conclusions: Our 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.

Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units

“…To confirm the results of the soil dataset and to evaluate the differences in metabarcoding methods on samples with reduced diversity, we examined the bacterial communities of a root-related dataset, referred to below as the plant dataset. This dataset contained bacterial sequences of two plant-related compartments, the rhizosphere, i.e., the soil closely surrounding the root, and the endosphere, i.e., the inside of the plant root of field soilgrown maize (Zea mays L.) [24]. Fig.…”

“…To create the culture-based mock bacterial community with 254 bacterial isolates (Table S6 A), maize roots were sterilized and crushed [24]. Diluted suspensions were plated and incubated.…”

Microbial Diversity of Upland Rice Roots and Their Influence on Rice Growth and Drought Tolerance

“…Microbial-based plant biotechnology has been proven to be more effective than plant breeding and genetic improvement methods [ 13 ]. A recent study has shown that endophytes improve plant tolerance against abiotic stresses such as salinity, drought and cold [ 6 , 14 , 15 , 16 , 17 , 18 , 19 ]. PGPB and fungi can alleviate abiotic stresses of their host plants via a variety of mechanisms [ 20 , 21 , 22 ].…”

Long-Term Bacterial Fertilizer Application Improves Eucalyptus Growth and Yields through Altering Soil Quality

“…In our study site, we carried out a plantation of bare root eucalyptus seedlings (3600 eucalyptus ha -1 ). We selected eucalyptus as the focal crops for our research because eucalyptus is the most prominent pulp and wood material in Guangxi [4]. Bare-root eucalyptus (DH32-29, a clone of Eucalyptus urophylla x E. grandis) seedlings were supplied by Dongmen tree farm, Guangxi, China (seedling quality examination certi cate number 2011-029) and planted using three-dimensional holes (20 cm * 20 cm * 20 cm) for each individual.…”

“…The utility of bacterial fertilizers has been studied in crops such as maize (Beirinckx et al 2020 (Santos et al 2018). However, to our knowledge, few studies have focused on the effects of sludge and PGPR on forest plantations, as well as on understanding the underlying mechanisms via soil quality alteration.…”