Coesel Sacha N, van Creveld Shiri Graff, Dugenne Mathilde, Henderikx-Freitas Fernanda, White Angelicque E, Armbrust E Virginia
School of Oceanography, University of Washington, Seattle, WA 98195, United States.
Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI 96822, United States.
ISME J. 2025 Jan 2;19(1). doi: 10.1093/ismejo/wraf079.
Unicellular plankton form the foundation of the marine food web, driving carbon fixation and cycling essential biogeochemical elements in marine ecosystems. Carbon biomass, often measured as a bulk property, serves as a common "currency" for ecologists. The increasing availability of metatranscriptomic data presents an opportunity to add taxonomic and functional resolution to ecological models and yet, aligning transcript counts with carbon biomass estimates remains a challenge. Here, we combine 30 quantitative metatranscriptome samples with Imaging FlowCytobot-derived carbon biomass estimates and demonstrate a robust, proportional (log-log scale) relationship between transcript concentration and carbon biomass estimates across abundant protist taxa. Further, we show that dinoflagellates exhibit a transcript-to-biomass ratio ~ 6.4-fold higher than other protist groups, consistent with their known transcriptional divergence. These findings provide a means to address overrepresentation of dinoflagellate transcript levels in metatranscriptome data. Moreover, this study establishes an entrée for integrating metatranscriptomics into carbon biomass-based ecological models, enhancing the interpretability and applicability of transcriptomic data in ecosystem research and modeling.
单细胞浮游生物构成了海洋食物网的基础，推动着海洋生态系统中的碳固定和关键生物地球化学元素的循环。碳生物量通常作为一个整体属性来衡量，是生态学家常用的一种“货币”。宏转录组数据的可得性不断提高，为生态模型增添分类学和功能分辨率提供了契机，然而，将转录本计数与碳生物量估计值进行匹配仍然是一项挑战。在此，我们将30个定量宏转录组样本与成像流式细胞仪得出的碳生物量估计值相结合，证明了在丰富的原生生物类群中，转录本浓度与碳生物量估计值之间存在稳健的比例关系（对数-对数尺度）。此外，我们发现甲藻的转录本与生物量之比比其他原生生物类群高约6.4倍，这与其已知的转录差异一致。这些发现为解决宏转录组数据中甲藻转录水平过度代表的问题提供了一种方法。此外，本研究为将宏转录组学整合到基于碳生物量的生态模型中提供了一条途径，增强了转录组数据在生态系统研究和建模中的可解释性和适用性。
