Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.
Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.
Curr Biol. 2017 Jun 5;27(11):R541-R549. doi: 10.1016/j.cub.2017.03.075.
The study of marine microbial ecology has been completely transformed by molecular and genomic data: after centuries of relative neglect, genomics has revealed the surprising extent of microbial diversity and how microbial processes transform ocean and global ecosystems. But the revolution is not complete: major gaps in our understanding remain, and one obvious example is that microbial eukaryotes, or protists, are still largely neglected. Here we examine various ways in which protists might be better integrated into models of marine microbial ecology, what challenges this will present, and why understanding the limitations of our tools is a significant concern. In part this is a technical challenge - eukaryotic genomes are more difficult to characterize - but eukaryotic adaptations are also more dependent on morphology and behaviour than they are on the metabolic diversity that typifies bacteria, and these cannot be inferred from genomic data as readily as metabolism can be. We therefore cannot simply follow in the methodological footsteps of bacterial ecology and hope for similar success. Understanding microbial eukaryotes will require different approaches, including greater emphasis on taxonomically and trophically diverse model systems. Molecular sequencing will continue to play a role, and advances in environmental sequence tag studies and single-cell methods for genomic and transcriptomics offer particular promise.
经过几个世纪的相对忽视，基因组学揭示了微生物多样性的惊人程度，以及微生物过程如何改变海洋和全球生态系统。但革命尚未完成：我们的理解仍存在重大差距，一个明显的例子是，微生物真核生物，或原生生物，仍然在很大程度上被忽视。在这里，我们研究了将原生生物更好地纳入海洋微生物生态学模型的各种方法，这将带来哪些挑战，以及为什么理解我们工具的局限性是一个重要的关注点。在某种程度上，这是一个技术挑战——真核生物的基因组更难描述——但真核生物的适应性比细菌的代谢多样性更依赖于形态和行为，而不能像代谢那样容易从基因组数据中推断出来。因此，我们不能简单地追随细菌生态学的方法，期望取得类似的成功。要理解微生物真核生物，需要采用不同的方法，包括更加重视分类学和营养多样性的模式系统。分子测序将继续发挥作用，环境序列标签研究和单细胞基因组学和转录组学方法的进步尤其有希望。
