Evaluating the lettuce metatranscriptome with MinION sequencing for future spaceflight food production applications

Abstract

Healthy plants are vital for successful, long-duration missions in space, as they provide the crew with life support, food production, and psychological benefits. The microorganisms that associate with plant tissues play a critical role in improving plant health and production. To that end, we developed a methodology to investigate the transcriptional activities of the microbiome of red romaine lettuce, a key salad crop that was grown under International Space Station (ISS)-like conditions. Microbial transcripts enriched from host–microbe total RNA were sequenced using the Oxford Nanopore MinION sequencing platform. Results show that this enrichment approach was highly reproducible and could be an effective approach for the on-site detection of microbial transcriptional activity. Our results demonstrate the feasibility of using metatranscriptomics of enriched microbial RNA as a potential method for on-site monitoring of the transcriptional activity of crop microbiomes, thereby helping to facilitate and maintain plant health for on-orbit space food production.

Cerium oxide nanomaterial regulates endophytic and rhizospheric bacteria of wheat to enhance resistance under simulated microgravity stress

“…Previous research has predominantly centered on assessing the effects of nanomaterials including CeO 2 NP under Earth-based conditions, yet our understanding of their potential bene ts under specialized environmental challenges, such as microgravity, remains limited. In the space ight environment, particularly under microgravity conditions, plants encounter signi cant adversities that frequently lead to impaired growth and increased vulnerability to diseases, largely owing to the disruption of plant-associated microbial ecosystems induced by the altered gravitational condition 11 . Root-associated microbial communities serve as key mediators for plant health and stress resistance, and their dynamic interactions can be ne-tuned by CeO 2 NP, offering new possibilities for space agriculture 38 .…”

“…Within the unique environments of space ight, plants confront an array of abiotic stressors, most notably microgravity. This shift in gravitational forces frequently leads to impaired growth and an enhanced vulnerability to diseases, primarily stemming from the disturbance of plant-associated microbial communities 11 . For example, soybean and wheat seedlings grown in space ight conditions are more susceptible to diseases, potentially caused by pathogenic invasion or dysbiosis 12,13 .…”

Unraveling plant–microbe interactions: can integrated omics approaches offer concrete answers?

“…In the past few years, a number of innovative methods have been developed to contribute to understanding plant–microbe interactions. For instance, Haveman et al (2021) utilized the MinION sequencing platform to perform a comparative analysis of lettuce microbiomes across temporal and spatial scales, to identify key drivers involved in plant growth and development. Such temporal and spatial scale comparisons will allow us to decipher how plant microbiomes change under environmental perturbations, and eventually contribute to improving plant health.…”

Tapping into Plant–Microbiome Interactions through the Lens of Multi-Omics Techniques

“…Metatranscriptome data analysis mainly involves quality control, transcriptome assembly, taxonomic profiling, functional annotation of transcript, pathway analysis, and differential gene expression analysis ( Figure 2 ). Shotgun data are used for metatranscriptome studies, but in recent times, long-read sequencers have been used for sequencing the metatranscriptomics samples [ 93 ].…”