Table S4 from Diatoms dominate the eukaryotic metatranscriptome during spring in coastal ‘dead zone’ sediments.

An important characteristic of marine sediments is the oxygen concentration that affects many central metabolic processes. There has been a widespread increase in hypoxia in coastal systems (referred to as ‘dead zones’) mainly caused by eutrophication. Hence, it is central to understand the metabolism and ecology of eukaryotic life in sediments during changing oxygen conditions. Therefore, we sampled coastal ‘dead zone’ Baltic Sea sediment during autumn and spring, and analysed the eukaryotic metatranscriptome from field samples and after incubation in the dark under oxic or anoxic conditions. Bacillariophyta (diatoms) dominated the eukaryotic metatranscriptome in spring and were also abundant during autumn. A large fraction of the diatom RNA reads was associated with the photosystems suggesting a constitutive expression in darkness. Microscope observation showed intact diatom cells and these would, if hatched, represent a significant part of the pelagic phytoplankton biomass. Oxygenation did not significantly change the relative proportion of diatoms nor resulted in any major shifts in metabolic ‘signatures’. By contrast, diatoms rapidly responded when exposed to light suggesting that light is limiting diatom development in hypoxic sediments. Hence, it is suggested that diatoms in hypoxic sediments are on ‘standby’ to exploit the environment if they reach suitable habitats.

海洋沉积物的一项核心特征为其氧浓度，该参数可调控诸多关键代谢过程。当前沿海生态系统中低氧区（又称‘死亡区’）的规模呈广泛扩张趋势，其主要诱因是水体富营养化。因此，解析氧浓度波动条件下沉积物内真核生物的代谢与生态特征，已成为相关研究的核心议题。

为此，本研究于秋季与春季采集波罗的海沿海‘死亡区’的沉积物样本，并针对野外原位样本，以及经黑暗、有氧或厌氧条件培养后的样本，开展了真核生物宏转录组（eukaryotic metatranscriptome）分析。

春季样本的真核生物宏转录组以硅藻门（Bacillariophyta，diatoms）占绝对主导，秋季样本中硅藻的丰度亦处于较高水平。硅藻的RNA测序读段中有较大比例与光系统相关，这提示硅藻在黑暗环境中仍存在组成型基因表达。

显微镜观测结果显示，沉积物中存在完整的硅藻细胞；若此类细胞得以复苏，将构成远洋浮游植物生物量的重要组成部分。氧浓度变化并未显著改变硅藻的相对占比，也未引发代谢特征的显著偏移。与之形成鲜明对比的是，硅藻在暴露于光照后会快速产生响应，这表明光照是限制低氧沉积物中硅藻生长发育的关键限制因子。

综上，本研究提出推测：低氧沉积物中的硅藻处于‘待命’状态，一旦抵达适宜生境，便可快速利用环境资源实现种群扩张。