The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts

Abstract

Microbial communities are highly responsive to environmental cues, and both their structure and activity can be altered in response to changing conditions. We hypothesized that host-associated microbial communities, particularly those colonizing host surfaces, can serve as in situ sensors to reveal environmental conditions experienced by both microorganisms and the host. For a proof-of-concept, we studied a model plant-soil system and employed a non-deterministic gene-centric approach. A holistic analysis was performed using plants of two species and irrigation with water of low quality to induce host stress. Our analyses examined the genetic potential (DNA) and gene expression patterns (RNA) of plant-associated microbial communities, as well as transcriptional profiling of host plants. Transcriptional analysis of plants irrigated with treated wastewater revealed significant enrichment of general stress-associated root transcripts relative to plants irrigated with fresh water. Metagenomic analysis of root-associated microbial communities in treated wastewater-irrigated plants, however, revealed enrichment of more specific stress-associated genes relating to high levels of salt, high pH and lower levels of oxygen. Meta-analysis of these differentially abundant genes obtained from other metagenome studies provided evidence of the link between environmental factors such as pH and oxygen and these genes. Analysis of microbial transcriptional response demonstrated that enriched gene content was actively expressed, which implies contemporary response to elevated levels of pH and salt. We demonstrate here that microbial profiling can elucidate stress signals that cannot be observed even through interrogation of host transcriptome, leading to an alternate mechanism for evaluating in situ conditions experienced by host organisms.Significance StatementThis study examines the potential for microbial communities to provide insight into stresses experienced by their eukaryotic host organisms, through profiling of metagenomes and metatranscriptomes. Our study uses plant host-associated microorganisms as an in vivo and in situ microsensor to identify environmental stresses experienced by the microbial community and by the plant. Transcriptionally active host-associated microbial communities are responsive in a highly specific manner to environmental conditions. Conversely, host transcriptome sequencing provides only a very general stress response. This study is a proof-of-concept for the use of microbial communities as microsensors, with a great potential for interrogation of a wide range of host systems.

Elucidating the Diversity and Potential Function of Nonribosomal Peptide and Polyketide Biosynthetic Gene Clusters in the Root Microbiome

“…Due to the potential biases associated with the above-described PCR-based approach, we analyzed previously reported ( 32 ) shotgun metagenomes of the same tomato and lettuce root samples ( n = 3 each). Assembled open reading frame (ORF) sequences from the metagenomes identified using Prodigal were aligned against the MIBiG database, generating a list of the 50 most abundant NRPSs and PKSs in each of the root data sets (representing the normalized abundance within samples by plotting the coefficient of variance [CV] for each gene) ( Fig.…”

“…In addition, as gene clusters are often silent or expressed under very specific conditions, we evaluated gene expression in parallel to gene occurrence to uncover active BGCs with ecological importance in the highly dynamic root ecosystem. Thus, in parallel to the shotgun metagenome analysis described above, we applied a similar analytical approach using the previously collected shotgun metatranscriptomes ( 32 ) to identify NRPSs and PKSs with enhanced expression in lettuce and/or tomato root microbiomes. Interestingly, 60% (30/50) and 46% (23/50) of the AD and KS domains that were highly abundant in the tomato and lettuce root samples, respectively, were highly expressed as well ( Fig.…”

“…Raw amplicon sequences are available via the MG-RAST data repository under accession number mgm4862150.3 . In addition, shotgun metagenome and metatranscriptome data sets of lettuce and tomato roots ( n = 3 for each data set type [hence, 6 for tomato and 6 for lettuce]) previously generated and analyzed from the same samples were also used for NRPS and PKS identification as described below ( 32 ). Shotgun sequence data are available via the NCBI Sequence Read Archive (SRA) data repository under project accession number PRJNA602301 .…”

“…Raw AD and KS amplicons from the tomato root, lettuce root, and tomato bulk soil microbial communities sequenced in this study are available via the MG-RAST data repository under accession number mgm4862150.3 . Previously sequenced shotgun metagenome and metatranscriptome data sets ( 32 ) are available via the NCBI SRA data repository under project accession number PRJNA602301 .…”

Elucidating the diversity and potential function of nonribosomal peptide and polyketide biosynthetic gene clusters in the root microbiome

“…Due to the potential biases associated with the above PCR-based approach, we analyzed previously published (32) shotgun metagenomes of the same tomato and lettuce root samples (n=3 each). Assembled open reading frame (ORF) sequences from the metagenomes identified using Prodigal were aligned against the MIBiG database, generating a list of the fifty most abundant NRPSs and PKSs in each of the root datasets (representing the normalized abundance within-samples by plotting the coefficient of variance (CV) for each gene, Fig.…”