Can microbiome functional profile elucidate hidden stress in its host?

A wealth of evidence has been amassed that links environmental cues to changes in microbial community structure and function. We hypothesized that host-associated microbial communities can serve as in situ sensors to reveal environmental conditions experienced by both microorganisms and the host. Plant response to prolonged unidentified environmental stress caused by irrigation with water of lower quality, was studied. A holistic view of plant root soil continuum was applied, focusing on plant host, associated root microbiome and the surrounding soil.
Amplicon sequencing of 16S ribosomal RNA (rRNA) gene revealed that the root microbiome composition was affected similarly by the plant type and irrigation water quality.
Further, we examined the transcriptional profiling of host plants, as well as genetic potential (metagenome) and gene expression patterns (metatranscriptome) of the associated microbial communities.
Due to the general nature of host response, it was not efficiently indicative for the type of stress it was exposed to. In contrast, metagenomic analysis of the root-associated microbial communities irrigated with treated wastewater, revealed enrichment of specific stress-associated genes relating to high levels of salt, high pH and lower levels of oxygen. Metatranscriptome profile demonstrated contemporary response to elevated levels of pH and salt. Meta-analysis of these differentially abundant genes obtained from several available metagenome studies, provided evidence that links pH and oxygen to the observed enriched genes.
The current study provides a proof-of-concept for the use of microbial communities as microsensors, with great potential for examination of a wide range of host systems.