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.

健康的植物对于成功的长期太空任务至关重要，因为它们为机组人员提供生命支持、食物生产和心理益处。与植物组织相关的微生物在改善植物健康和生产方面发挥着关键作用。为此，我们开发了一种方法来研究红色生菜微生物组的转录活动，这是一种在类似国际空间站 (ISS) 的条件下种植的重要沙拉作物。使用 Oxford Nanopore MinION 测序平台对从宿主-微生物总 RNA 中富集的微生物转录本进行测序。结果表明，这种富集方法具有高度可重复性，可以成为现场检测微生物转录活性的有效方法。