Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations

TL;DR

This study investigates the root microbiome of squash plants in arid and humid environments, demonstrating that microbiome diversity and functional genes associated with drought tolerance can be transplanted and analyzed in controlled settings.

Contribution

It provides evidence that in situ microbiome diversity and functional traits related to drought adaptation can be transferred and studied ex-situ in greenhouse conditions.

Findings

Distinct microbiomes in arid and humid soils identified

Arid microbiomes contain unique bacterial genera and genes for drought tolerance

Microbiome transplantation maintains diversity and functional traits in controlled environments

Abstract

Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N=48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The Beta-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. With shotgun metagenomic sequencing of rhizospheres (N=6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.