Department of Biology, Dalhousie University, Halifax, NS, Canada.
Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada.
ISME J. 2022 Feb;16(2):569-579. doi: 10.1038/s41396-021-01084-9. Epub 2021 Sep 4.
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.
蛋白质的产生和利用在微生物中受到强烈选择，但尚不清楚蛋白质组水平的特征与生态策略有何关系。我们通过原位宏蛋白质组学方法鉴定和量化了南极浮游植物繁殖过程中的真核微生物和细菌的蛋白质组特征。不同的分类群，而不是不同的环境条件，根据核糖体和光合蛋白质组的比例形成了不同的聚类，我们提出这些特征与生态差异有关。我们定义并使用了一种蛋白质组代理来表示调控成本，结果表明，SAR11 的调控成本是我们在南大洋夏季研究地点观察到的所有分类群中最低的。甲藻的调控成本低于硅藻，这可能是罗斯海甲藻向硅藻繁殖的基础。我们通过评估宏蛋白质组学中的各种偏倚来源来进行这些蛋白质组特征推断，为该领域的研究人员提供了实用的建议。我们已经量化了真核生物和细菌分类群中的几种蛋白质组特征（核糖体和光合蛋白质组比例、调控成本），然后可以将其纳入反映资源分配策略的微生物群落基于特征的模型中。
