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（生物）的进化和生态研究。由于它们的外观通常不能反映他们的进化关系，因此通常只有在我们拥有形态学和遗传数据并可以使用系统发育分析来重建其进化关系时，通常才能正确理解生物群体。最近以这种方式阐明了许多原生群体。此外，相关的分子技术已被用来表明大多数环境中生物的遗传多样性是巨大的 - 等待发现的生物比在形态学上所知要多。然而，一组在很大程度上避免了基于培养的生物和分子研究的生物是大型非壳的变形虫，其细胞（乳胶假卵形）的长度，通常是分支的分支扩展，其中一些融合形成了细胞质的“网络”（网络网络）（网状网络）（网状尺寸）。我们称它们为NRRA-裸露的拉丝/网状变形虫。 NRRA可能几乎是固定的，附着在表面上，或在土壤或沉积物颗粒之间延伸其假地，或者它们可以是活跃的捕食者，跨表面或通过颗粒物材料移动以寻找猎物。培养的NRRA并不多，因为它们很难生长，但是所有已知的菌株都在广泛的食物来源（其他原生动物，单细胞和多细胞藻类）上备受追捧，包括许多类型的真菌，包括已知的真菌，包括引起农作物或其他植物的疾病，甚至是小动物，甚至是诸如Nematode蠕虫和牛皮机的小动物。有些攻击可能甚至更大的生物。因此，NRRA可能是生物控制的重要药物，影响其他微生物活性，包括引起疾病的生物以及参与分解和营养循环的生物。 NRRA仍然非常众所周知，因为它们细腻的细胞形状意味着它们通常被抽样技术破坏。他们需要很长时间才能出现在实验室中的环境样本中，并且通常需要特定的（但通常是未知的！）生长。此外，通过分子研究，它们相对较少检测到它们，因为它们用于此类研究的基因的版本通常与许多其他生物体如此不同，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，描述其形态和生命周期，并衡量其食欲的大小 - 在饮食的多样性以及饮食量的多样性方面（包括真菌和其他生物体）（包括引起较高植物的疾病））。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。我们将在许多不同的环境条件下衡量它们的多样性（尽管这在许多生物中通常是一个不清楚的概念）。进一步进行研究，我们将与三个研究计划合作，这些研究计划在1）森林土壤上进行长期实验，2）农业与未耕种和未耕种的土壤以及3）淡水湖泊。这些实验具有良好的采样策略和从样本站点收集的其他数据，这将为我们关于NRRA的新数据提供非常有用的背景。通过对所有三个实验的贡献的深入采样位点，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）组的变化相关。如果他们这样做，我们将提出相关性的可能原因，可以在以后的研究中进行测试。我们还将确定NRRA最多样化和丰富的环境条件（温度，pH，死机材料的量等）。这些结果结合在一起，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