Hechler Robert M, Yates Matthew C, Chain Frédéric J J, Cristescu Melania E
Department of Biology, McGill University, Montréal, Québec, Canada.
Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada.
Mol Ecol. 2025 Jul;34(13):e17152. doi: 10.1111/mec.17152. Epub 2023 Oct 4.
To safeguard biodiversity in a changing climate, taxonomic information about species turnover and insights into the health of organisms are required. Environmental DNA approaches are increasingly used for species identification, but cannot provide functional insights. Transcriptomic methods reveal the physiological states of macroorganisms, but are currently species-specific and require tissue sampling or animal sacrifice, making community-wide assessments challenging. Here, we test whether broad functional information (expression level of the transcribed genes) can be harnessed from environmental RNA (eRNA), which includes extra-organismal RNA from macroorganisms along with whole microorganisms. We exposed Daphnia pulex as well as phytoplankton prey and microorganism colonizers to control (20°C) and heat stress (28°C) conditions for 7 days. We sequenced eRNA from tank water (after complete removal of Daphnia) as well as RNA from Daphnia tissue, enabling comparisons of extra-organismal and organismal RNA-based gene expression profiles. Both RNA types detected similar heat stress responses of Daphnia. Using eRNA, we identified 32 Daphnia genes to be differentially expressed following heat stress. Of these, 17 were also differentially expressed and exhibited similar levels of relative expression in organismal RNA. In addition to the extra-organismal Daphnia response, eRNA detected community-wide heat stress responses consisting of distinct functional profiles and 121 differentially expressed genes across eight taxa. Our study demonstrates that environmental transcriptomics based on extra-organismal eRNA can noninvasively reveal gene expression responses of macroorganisms following environmental changes, with broad potential implications for the biomonitoring of health across the trophic chain.
为了在气候变化的情况下保护生物多样性，需要有关物种更替的分类学信息以及对生物体健康状况的深入了解。环境DNA方法越来越多地用于物种鉴定，但无法提供功能方面的见解。转录组学方法可以揭示大型生物的生理状态，但目前具有物种特异性，并且需要组织采样或牺牲动物，这使得进行全群落评估具有挑战性。在这里，我们测试是否可以从环境RNA（eRNA）中获取广泛的功能信息（转录基因的表达水平），环境RNA包括大型生物的细胞外RNA以及整个微生物。我们将水蚤、浮游植物猎物和微生物定殖者暴露于对照（20°C）和热应激（28°C）条件下7天。我们对水箱水（完全去除水蚤后）中的eRNA以及水蚤组织中的RNA进行了测序，从而能够比较基于细胞外和细胞内RNA的基因表达谱。两种RNA类型都检测到了水蚤类似的热应激反应。利用eRNA，我们鉴定出32个水蚤基因在热应激后差异表达。其中，17个基因在细胞内RNA中也差异表达，并且表现出相似的相对表达水平。除了水蚤的细胞外反应外，eRNA还检测到了全群落的热应激反应，包括不同的功能谱以及八个分类群中的121个差异表达基因。我们的研究表明，基于细胞外eRNA的环境转录组学可以非侵入性地揭示大型生物在环境变化后的基因表达反应，这对整个营养链的健康生物监测具有广泛的潜在意义。
