Production and use of proteins is under strong selection in microbes, but it is unclear how proteome-level traits relate to ecological strategies. We identified and quantified proteomic traits of eukaryotic microbes and bacteria through an Antarctic phytoplankton bloom using in situ metaproteomics. Different taxa, rather than different environmental conditions, formed distinct clusters based on their ribosomal and photosynthetic proteomic proportions, and we propose that these characteristics relate to ecological differences. We defined and used a proteomic proxy for regulatory cost, which showed that SAR11 had the lowest regulatory cost of any taxa we observed at our summertime Southern Ocean study site. Haptophytes had lower regulatory cost than diatoms, which may underpin haptophyte-to-diatom bloom progression in the Ross Sea. We were able to make these proteomic trait inferences by assessing various sources of bias in metaproteomics, providing practical recommendations for researchers in the field. We have quantified several proteomic traits (ribosomal and photosynthetic proteomic proportions, regulatory cost) in eukaryotic and bacterial taxa, which can then be incorporated into trait-based models of microbial communities that reflect resource allocation strategies.

蛋白质的生产和使用在微生物中受到强烈的选择，但尚不清楚蛋白质组水平的性状如何与生态策略相关。我们通过使用原位元蛋白质组学的南极浮游植物大量繁殖来鉴定和量化真核微生物和细菌的蛋白质组学特征。不同的分类群，而不是不同的环境条件，根据它们的核糖体和光合蛋白质组比例形成了不同的簇，我们认为这些特征与生态差异有关。我们定义并使用了监管成本的蛋白质组学代理，这表明 SAR11 的监管成本是我们在夏季南大洋研究地点观察到的任何分类群中最低的。与硅藻相比，触体植物的监管成本更低，这可能支持罗斯海中触体到硅藻的开花进程。我们能够通过评估元蛋白质组学中的各种偏差来源来推断这些蛋白质组学特征，为该领域的研究人员提供实用的建议。我们已经量化了真核生物和细菌类群中的几种蛋白质组学特征（核糖体和光合蛋白质组学比例、监管成本），然后可以将其纳入反映资源分配策略的基于特征的微生物群落模型中。