Blaskowski Stephen, Roald Marie, Berube Paul M, Braakman Rogier, Armbrust E Virginia
Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
School of Oceanography, University of Washington, Seattle, WA, USA.
Sci Adv. 2025 Apr 4;11(14):eadr4310. doi: 10.1126/sciadv.adr4310.
Microbes respond to changes in their environment by adapting their physiology through coordinated adjustments to the expression levels of functionally related genes. To detect these shifts in situ, we developed a sparse tensor decomposition method that derives gene co-expression patterns from inherently complex whole community RNA sequencing data. Application of the method to metatranscriptomes of the abundant marine cyanobacteria and identified responses to scarcity of two essential nutrients, nitrogen and iron, including increased transporter expression, restructured photosynthesis and carbon metabolism, and mitigation of oxidative stress. Further, expression profiles of the identified gene clusters suggest that both cyanobacteria populations experience simultaneous nitrogen and iron stresses in a transition zone between North Pacific oceanic gyres. The results demonstrate the power of our approach to infer organism responses to environmental pressures, hypothesize functions of uncharacterized genes, and extrapolate ramifications for biogeochemical cycles in a changing ecosystem.
微生物通过对功能相关基因的表达水平进行协调调整来适应其生理状态，从而对环境变化做出反应。为了原位检测这些变化，我们开发了一种稀疏张量分解方法，该方法从本质上复杂的整个群落RNA测序数据中推导基因共表达模式。将该方法应用于丰富的海洋蓝细菌的元转录组，确定了对两种必需营养素（氮和铁）稀缺的反应，包括转运蛋白表达增加、光合作用和碳代谢重组以及氧化应激的缓解。此外，所鉴定基因簇的表达谱表明，这两种蓝细菌种群在北太平洋环流之间的过渡区同时经历氮和铁胁迫。结果证明了我们的方法在推断生物体对环境压力的反应、推测未表征基因的功能以及推断变化的生态系统中生物地球化学循环的影响方面的强大作用。
