Cold Acclimation in Brachypodium Is Accompanied by Changes in Above-Ground Bacterial and Fungal Communities

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.

Differential Impacts of Road De-icers on Freshwater Bacterial Communities

“…It can be challenging to recover taxonomic information for bacteria in a background of algal DNA since chloroplast sequences share homology with bacterial 16S rRNA gene sequences. Previously in analogous situations, we used peptide nucleic acid plastid clamps with other bacterial 16S rRNA primers in amplicon protocols, but 99% of the sequences still returned plastid DNA [51,52]. The procedure used here resulted in only 0.03% of the ASVs corresponding to chloroplast sequences and demonstrated that the judicious selection of V3-V4 16S rRNA gene primers [33], in conjunction with the deployment of algal blockers, was successful.…”

Apple Root Microbiome as Indicator of Plant Adaptation to Apple Replant Diseased Soils

“…Plants are sessile organisms and are constantly exposed to environmental stresses. However, they can mitigate the effect of these stresses by deploying environmental microbiomes for their protection [ 35 ]. Host plants continuously shape root-associated microbial communities according to changes in biotic and abiotic factors [ 3 , 36 , 37 , 38 ].…”

Brachypodium Antifreeze Protein Gene Products Inhibit Ice Recrystallisation, Attenuate Ice Nucleation, and Reduce Immune Response

“…The requirement for at least partial immune suppression is likely temporary. Once freezing takes place, the absence of free water may make pathogens less threatening and certainly, by the end of the CA period, the above-ground microbial community in Brachypodium changes so that whereas P. syringae accounted for 8% of the taxa prior to transfer to 4 °C, 6 days later, this taxon had disappeared [ 45 ].…”