Using free-living protozoan biodiversity to resolve deep eukaryote evolution

真核生物是具有复杂细胞的生命形式。最常见的真核生物是动物、真菌和陆生植物。然而，这些只代表了真核生物“王国”的一小部分-有几十种藻类、寄生虫和自由生活的原生动物，它们是地球生物多样性的不同组成部分。事实上，自由生活的原生动物代表了今天存活的真核生物群体的大多数多样性，并且具有最古老的根源：它们产生了所有其他真核生物。它们也是生态系统中极其重要的组成部分，是其他微生物的主要捕食者。尽管如此，我们对自由生活的原生动物的了解远远少于其他真核生物。 拟议的研究计划包括3个项目，解决有关自由生活的原生动物的生物多样性和进化的基本问题：项目1：我们将使用细胞培养以及从无法培养的细胞中获得大量遗传数据的方法来分离可能代表“新王国”的原生动物。然后，我们将从大型遗传信息数据库中推断出进化树，将这些新群体置于生命进化树上。项目2：我们的目标是解决真核生物深层进化中的一个深刻的谜团。我们将研究来自某些群体的细胞的内部结构（细胞骨架），这些群体被认为是远亲，但似乎共享一组与摄食系统相关的特定结构。我们还将比较具有和不具有这些结构的物种的基因组，以确定它们可能由其组成的新蛋白质。我们的目标是了解是否所有活的真核生物都是从具有这些相同结构的古代祖先传下来的。项目三：我们将使用直接从环境中收集的基因序列，以及从观察和/或培养的细胞，评估一个大的高盐（即咸）湖的水和沉积物中自由生活的原生动物的生物多样性。我们将测试我们是否发现新的群体是其他复杂细胞的专业捕食者（由于这些系统中动物的多样性有限），以及我们是否可以从遗传数据中的模式推断出它们的猎物。我们还将测试贫氧沉积层是否与以前在海底无氧盐水池中发现的物种相似。这些项目一起将从字面上'重绘复杂细胞生命的进化树'，因为它出现在所有生物学教科书中，例如，并大大提高了我们对地球上复杂生命形式多样化的认识。许多其他研究人员将在未来的研究中使用我们的发现，旨在了解复杂细胞的无数不同部分如何随着时间的推移而产生和变化。有些人可能会使用我们的一些新培养物进行各种细胞实验。我们的研究结果也将被世界各地的微生物生态学家使用，使他们能够在自己的遗传数据集中正确识别物种。

Eukaryotes are the lifeforms with complex cells. The most familiar eukaryotes are animals, fungi and land plants. Yet these represent only a small fraction of the `kingdoms' of eukaryotes - there are dozens of groups of algae, parasites and free-living protozoa that are equivalently distinct parts of Earth's biodiversity. In fact, free-living protozoa represent most of the diversity of eukaryote groups alive today, and have the most ancient roots: they gave rise to all the other eukaryotic lifeforms. They are also tremendously important parts of the ecosystem, as major predators of other microbes. Nonetheless, we know far less about free-living protozoa than other eukaryotes. The proposed research program consists of 3 projects that resolve fundamental questions about the biodiversity and evolution of free-living protozoa: Project 1: We will isolate protozoa that potentially represent `new kingdoms', using cell-culturing as well as methods to obtain large amounts of genetic data from cells that cannot be cultivated. We will then infer evolutionary trees from large databases of genetic information to place these new groups on the evolutionary tree of life. Project 2: We aim to resolve a profound mystery in the deep-level evolution of eukaryotes. We will examine the internal architecture (cytoskeleton) of cells from certain groups that are thought to be distantly related, yet seem to share a particular set of structures related to the feeding system. We will also compare the genomes of species with and without these structures to identify novel proteins that they might be made from. We aim to understand whether all living eukaryotes descended from an ancient ancestor with these same structures. Project 3: We will assess the biodiversity of free-living protozoa in water and sediments of a large hypersaline (i.e. briny) lake, using genetic sequences collected directly from the environment, as well from observed and/or cultivated cells. We will test whether we find new groups that are specialist predators of other complex cells (due to the limited diversity of animals in these systems), and whether we can infer their prey from patterns in the genetic data. We will also test whether oxygen-poor sediment levels have similar species to those found previously in oxygen-free brine pools on the sea floor. These projects together will literally `redraw the evolutionary tree' of complex-celled life, as it appears in all biology textbooks for example, and greatly improve our knowledge of how complex lifeforms diversified on Earth. Many other researchers will use our findings in future studies aimed at understanding how the myriad different parts of complex cells arose and changed over time. Some are likely to use some of our new cultures for various cell experiments. Our results will also be used by microbial ecologists worldwide to allow them to correctly identify species in their own genetic datasets.