Abstract
Shifts in microbiota undoubtedly support host plants faced with abiotic stress, including low temperatures. Cold-resistant perennials prepare for freeze stress during a period of cold acclimation that can be mimicked by transfer from growing conditions to a reduced photoperiod and a temperature of 4 °C for 2–6 days. After cold acclimation, the model cereal, Brachypodium distachyon, was characterized using metagenomics supplemented with amplicon sequencing (16S ribosomal RNA gene fragments and an internal transcribed spacer region). The bacterial and fungal rhizosphere remained largely unchanged from that of non-acclimated plants. However, leaf samples representing bacterial and fungal communities of the endo- and phyllospheres significantly changed. For example, a plant-beneficial bacterium, Streptomyces sp. M2, increased more than 200-fold in relative abundance in cold-acclimated leaves, and this increase correlated with a striking decrease in the abundance of Pseudomonas syringae (from 8% to zero). This change is of consequence to the host, since P. syringae is a ubiquitous ice-nucleating phytopathogen responsible for devastating frost events in crops. We posit that a responsive above-ground bacterial and fungal community interacts with Brachypodium’s low temperature and anti-pathogen signalling networks to help ensure survival in subsequent freeze events, underscoring the importance of inter-kingdom partnerships in the response to cold stress.
Highlights
Following QIIME2 processing, it was determined through diversity analysis and Principal coordinate analysis (PCoA) using Bray–Curtis dissimilarities that the microbial compositions associated with the kits were significantly different than the Brachypodium leaf (p < 0.001 16S, p < 0.05 ITS, pairwise PERMANOVA) and rhizosphere microbiomes (p < 0.001 16S, p < 0.05 ITS, pairwise PERMANOVA) (Figure S5)
In the CA rhizosphere, the genera identified by shotgun metagenomic and 16S rRNA amplicon sequences, as well as shotgun metagenomics and ITS amplicon sequencing, were well correlated (R2 = 0.93 and R2 = 0.88, respectively) (Figure S6)
Both the changes in microbial community profiles following CA and the functional role of these plant beneficials suggest that commercial growers could see some benefit from the inoculation of mixed community strains, including Streptomyces sp
Summary
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Plants are at the mercy of an array of abiotic stresses, and, as winter approaches in mid- to high-latitudes and altitudes, one such stress is low temperature. Plants employ various strategies that allow them to recognise and cope with the cold [1]. Perennials undergo a period of cold acclimation, which in a few days of low temperature exposure allows them to physiologically prepare for freezing conditions
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