Biodiversity, phylogeny, and ecology of large naked ramose/reticulose amoebae: barely studied but diverse and common components of many ecosystems

大型裸枝/网状变形虫的生物多样性、系统发育和生态学：很少研究，但许多生态系统的多样化和共同组成部分

• 批准号: NE/H009426/1
• 负责人: David Bass
• 金额: $ 38.81万
• 依托单位: Natural History Museum
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2010
• 资助国家: 英国
• 起止时间: 2010 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FH009426%2F1
• 关键词: Biodiversity; phylogeny; ecology; large; naked

Recent advances in molecular biology techniques and analyses have greatly advanced the evolutionary and ecological study of microbial eukaryotes (protists). Because their appearance often does not reflect their evolutionary relationships, protist groups can generally only be properly understood when we have both morphological and genetic data and can use phylogenetic analyses to reconstruct their evolutionary relationships. Many protist groups have recently been elucidated in this way. In addition, related molecular techniques have been used to show that the genetic diversity of protists in most environments is massive - many more organisms await discovery than are known morphologically. However, one group of protists that has largely eluded both culture-based and molecular studies is that of large, non-shelled amoebae with long, often branching extensions to their cells (ramose pseudopodia), some of which fuse to form cytoplasmic 'networks' (reticulopodia) of varying sizes. We call them NRRA - naked ramose/reticulose amoebae. NRRA may be almost stationary, attached to surfaces or extending their pseudopodia between soil or sediment particles, or they can be active predators, moving across surfaces or through particulate material in search of prey. There are not many cultured NRRA because they are difficult to grow, but all known strains feed voraciously on a wide range of food sources - other protozoa, unicellular and multicellular algae, many types of fungi including those known to cause diseases of crops or other plants, and even small animals like nematode worms and rotifers. It is possible that some attack even larger organisms. Therefore, NRRA are likely to be important agents of biological control, influencing other microbial activity including disease-causing organisms and those involved in decomposition and nutrient cycling. NRRA remain very poorly known because their delicate cell shape means they are often destroyed by sampling techniques. They take a long time to appear in environmental samples in the laboratory and often need particular (but usually unknown!) conditions to grow. Furthermore, they are relatively rarely detected by molecular studies because their versions of the genes used for such studies are often so different from many other organisms that the standard molecular probes fail to detect them. The aim of our project is to find more NRRA in a wide range of habitats and describe their morphologies and lifecycles, and to measure how big their appetites are - both in terms of the diversity of their diet and how much of it they eat (including fungi and other organisms which are known to cause diseases of higher plants). We will sequence genes from NRRA cells in order to understand their evolutionary relationships and histories. We will measure how diverse they are (how many 'species', although this is often an unclear concept in many protists) under many different environmental conditions. Taking this line of enquiry further, we will collaborate with three research programmes that run long-term experiments on 1) forest soils, 2) agricultural vs. unploughed and uncultivated soils, and 3) freshwater lakes. These experiments have well established sampling strategies and other data collected from the sample sites, which will provide a very informative context for our new data on NRRA. By intensively sampling sites contributing to all three experiments we will investigate whether changes in NRRA diversity and abundance correlate with changes in other microbial (and small animal and plant) groups. If they do we will suggest possible reasons for the correlations, which can be tested in future studies. We will also work out the environmental conditions (temperature, pH, amount of dead organic material, etc.) under which NRRA are most diverse and abundant. These results combined will help scientists and environmental agencies to assess the 'health' and carbon budgets of soil and freshwater environments.

分子生物学技术和分析的最新进展极大地推进了微生物真核生物（原生生物）的进化和生态研究。由于它们的外观通常不能反映它们的进化关系，因此原生生物群体通常只有在我们同时拥有形态学和遗传数据并且可以使用系统发育分析来重建它们的进化关系时才能正确理解。最近以这种方式阐明了许多原生生物群体。此外，相关的分子技术已被用来表明大多数环境中原生生物的遗传多样性是巨大的——等待发现的生物体比形态学上已知的生物体还要多。然而，一组在很大程度上避开了基于培养和分子研究的原生生物是大型无壳变形虫，它们的细胞具有长且经常分支的延伸（分枝伪足），其中一些融合形成细胞质“网络” （网状伪足）大小不等。我们称它们为 NRRA——裸枝/网状变形虫。 NRRA 可能几乎是静止的，附着在表面或在土壤或沉积物颗粒之间延伸伪足，或者它们可以是活跃的捕食者，在表面或颗粒物质中移动以寻找猎物。培养的 NRRA 并不多，因为它们难以生长，但所有已知的菌株都贪婪地捕食各种食物来源 - 其他原生动物、单细胞和多细胞藻类、许多类型的真菌，包括已知会引起农作物或其他植物疾病的真菌，甚至还有线虫和轮虫等小动物。有些可能会攻击更大的生物。因此，NRRA 可能是重要的生物控制剂，影响其他微生物活动，包括致病微生物以及参与分解和营养循环的微生物。 NRRA 仍然鲜为人知，因为它们脆弱的细胞形状意味着它们经常被采样技术破坏。它们需要很长时间才能出现在实验室的环境样本中，并且通常需要特定的（但通常未知！）条件才能生长。此外，它们相对很少被分子研究检测到，因为用于此类研究的基因版本通常与许多其他生物体非常不同，以至于标准分子探针无法检测到它们。我们项目的目的是在广泛的栖息地中找到更多的 NRRA，描述它们的形态和生命周期，并测量它们的胃口有多大 - 包括饮食的多样性和吃的量（包括真菌和其他已知会引起高等植物疾病的生物体）。我们将对 NRRA 细胞的基因进行测序，以了解它们的进化关系和历史。我们将测量它们在许多不同的环境条件下的多样性（有多少“物种”，尽管这对许多原生生物来说通常是一个不清楚的概念）。进一步推进这一研究，我们将与三个研究项目合作，对 1) 森林土壤、2) 农业土壤与未犁耕和未开垦的土壤以及 3) 淡水湖进行长期实验。这些实验已经制定了完善的采样策略以及从采样点收集的其他数据，这将为我们关于 NRRA 的新数据提供非常丰富的信息。通过对所有三个实验都有贡献的集中采样点，我们将研究 NRRA 多样性和丰度的变化是否与其他微生物（以及小动物和植物）群体的变化相关。如果确实如此，我们将提出相关性的可能原因，并可以在未来的研究中进行测试。我们还将计算出 NRRA 最多样化和最丰富的环境条件（温度、pH 值、死亡有机物质的量等）。这些结果相结合将帮助科学家和环境机构评估土壤和淡水环境的“健康”和碳预算。

项目成果

Reticulamoeba is a long-branched Granofilosean (Cercozoa) that is missing from sequence databases.

• DOI: 10.1371/journal.pone.0049090
• 发表时间: 2012
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Bass D;Yabuki A;Santini S;Romac S;Berney C
• 通讯作者: Berney C

Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists

• DOI: 10.1111/1462-2920.13235
• 发表时间: 2016-05-01
• 期刊: ENVIRONMENTAL MICROBIOLOGY
• 影响因子: 5.1
• 作者: Bass, David;Silberman, Jeffrey D.;Hartikainen, Hanna
• 通讯作者: Hartikainen, Hanna

The revised classification of eukaryotes.

• DOI: 10.1111/j.1550-7408.2012.00644.x
• 发表时间: 2012-09
• 期刊: The Journal of eukaryotic microbiology
• 作者: Adl SM;Simpson AG;Lane CE;Lukeš J;Bass D;Bowser SS;Brown MW;Burki F;Dunthorn M;Hampl V;Heiss A;Hoppenrath M;Lara E;Le Gall L;Lynn DH;McManus H;Mitchell EA;Mozley-Stanridge SE;Parfrey LW;Pawlowski J;Rueckert S;Shadwick L;Schoch CL;Smirnov A;Spiegel FW
• 通讯作者: Spiegel FW

Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of "Hidden" Diversity.

• DOI: 10.3389/fmicb.2018.00168
• 发表时间: 2018
• 期刊: Frontiers in microbiology
• 影响因子: 5.2
• 作者: Bass D;van der Gast C;Thomson S;Neuhauser S;Hilton S;Bending GD
• 通讯作者: Bending GD

Rhizarian 'Novel Clade 10' Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates, including Aquavolon n. gen.

• DOI: 10.1111/jeu.12524
• 发表时间: 2018-11
• 期刊: The Journal of eukaryotic microbiology
• 作者: Bass D;Tikhonenkov DV;Foster R;Dyal P;Janouškovec J;Keeling PJ;Gardner M;Neuhauser S;Hartikainen H;Mylnikov AP;Berney C
• 通讯作者: Berney C