Ecological and morphological characterisation, and phylogeny of Endomyxa: poorly known but widespread and diverse protozoan parasites and omnivores

Endomyxa 的生态和形态特征以及系统发育：鲜为人知但广泛且多样化的原生动物寄生虫和杂食动物

• 批准号: NE/H000887/1
• 负责人: David Bass
• 金额: $ 19.26万
• 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%2FH000887%2F1
• 关键词: Ecological; morphological; characterisation; phylogeny; Endomyxa

Endomyxa are a very poorly known but large and diverse group of organisms in the protozoan phylum Cercozoa. Endomyxa includes the commercially important plasmodiophorid plant parasites, and haplosporidia and relatives, which include parasites of a wide range of invertebrates, most famously MSX disease of oysters. The evolutionary relationships of both of these groups were for a long time unknown (plasmodiophorids were considered fungi for a long time), but good ribosomal DNA trees show that they are related to each other (a relationship reinforced by morphological synapomorphies) and several lines of molecular evidence show that they belong within the eukaryotic supergroup Rhizaria, specifically as a subphylum within Cercozoa, but separately from the so-called 'core' Cercozoa. More recently, free-living relatives of these parasites have been found through culturing/cell isolation and rDNA sequencing. These include the large testate marine filose amoeba Gromia, and large reticulose, naked amoebae: the bacterivorous Filoreta and the predatory Arachnula and Platyreta. Such organisms represent very distinct and poorly studied protozoan morphotypes whose ecological roles are almost completely unknown. Other research has revealed more endomyxan parasites, for example the spot prawn parasite, and Paradinium, a parasite of copepods. Culture-independent environmental rDNA libraries show that there are a large diversity of other endomyxan clades and lineages which remain uncharacterised - the only information we have for them is the provenance of the samples in which the sequences were detected. The environmental libraries also show that there is very strong ecological structuring - many endomyxan clades have so far only been found in quite specific habitats, for example deep-sea samples, anaerobic marine, anaerobic freshwater, or phylloplane communities. These patterns suggest high levels of ecological specialization, perhaps involving interactions with other organisms. This project aims to identify as many of these novel lineages and clades as possible, whether they are free-living, symbiotic, or parasitic, using a combination of intensive selective culturing using a diversity of food sources and culture conditions informed by the results of the environmental libraries, and fluorescent in situ hybridization (FISH) using fluorescent probes that will specifically detect chosen uncharacterized lineages. FISH will also show the relative abundance of endomyxan lineages in different habitats, and whether they are associated with, or are found inside, other eukaryote cells, and if so, which organisms they co-occur with (and are therefore perhaps parasites of). Multiple and diverse SSU rDNA environmental libraries will be constructed, using a set of overlapping PCR primers covering all Endomyxa, to show much more clearly and realistically than previously possible the true diversity of Endomyxa, and their ecological nature by analyzing the sequence data in the context of other biotic and abiotic variables co-measured at each sampling site. The libraries will be made using both rDNA and crDNA reverse transcribed from rRNA: the latter is generally taken as a surrogate for the level of activity of the cells (more ribosomes will be present in more active cells), rather than just presence/absence and biomass as indicated by rDNA. This approach will provide more informative about the ecological characteristics than rDNA libraries alone. The environmental sequences will be used to improve phylogenetic reconstructions of Endomyxa and their relationships to the rest of Rhizaria both by increasing taxon sampling of this part of the tree, and by providing sequence data that can be used to obtain LSU rDNA sequences for representative genotypes directly from environmental DNA samples. Where cultures are available, other genes can be targeted by PCR, to be combined with existing data in multigene phylogenies.

Endomyxa是一个非常众所周知的，但在原生动物核生物中的大量生物群。 Endomyxa包括商业上重要的疟原虫植物寄生虫以及单倍孢子虫和亲戚，其中包括多种无脊椎动物的寄生虫，最著名的是牡蛎的MSX疾病。 The evolutionary relationships of both of these groups were for a long time unknown (plasmodiophorids were considered fungi for a long time), but good ribosomal DNA trees show that they are related to each other (a relationship reinforced by morphological synapomorphies) and several lines of molecular evidence show that they belong within the eukaryotic supergroup Rhizaria, specifically as a subphylum within Cercozoa, but separately from the所谓的“核心” Cercozoa。最近，通过培养/细胞分离和rDNA测序发现了这些寄生虫的自由生活亲戚。其中包括大型睾丸海洋伪造的变形虫Gromia和大的网状，裸露的变形虫：细菌丝状fileta和掠夺性的芳香虫和帕特氏菌。这样的生物代表了非常不同且研究不足的原生动物形态，其生态作用几乎是完全未知的。其他研究表明，更多的内肌寄生虫，例如斑点寄生虫和寄生虫，寄生虫。与文化无关的环境rDNA库表明，其他内肌肉进化枝和谱系的多样性仍然没有特征 - 我们唯一的信息是检测到序列的样品的出处。环境图书馆还表明，存在非常强大的生态结构 - 到目前为止，许多内肌肉进化枝仅在非常特定的栖息地中发现，例如深海样品，厌氧海洋，厌氧淡水或植物素社区。这些模式表明，高水平的生态专业化，也许涉及与其他生物的相互作用。该项目的目的是通过使用多种食物来源和培养条件结合使用，由环境库的结果和荧光杂交的荧光概念不适合使用，以确定荧光概念的素养，该项目旨在使用多种食物来源和培养条件来确定这些新颖的谱系和进化剂，无论它们是自由生活，共生还是寄生的，无论是自由生活，共生还是寄生虫，使用多种食物来源和培养条件。 FISH还将显示不同栖息地中内肌谱系的相对丰度，以及它们是否与其他真核生物细胞相关或在内部发现，如果是的，则它们与哪些有机体相同（因此也许是寄生虫）。将使用一组涵盖所有内肌的重叠PCR引物来构建多个和多样的SSU RDNA环境库，与以前可能的真实多样性相比，在每个生物和原始变量的上下文中分析了Endomyxa的真实多样性及其生态性质，以更清晰，更真实地显示出其生态性质。将使用从rRNA转录的rDNA和crDNA进行库制作：后者通常被视为细胞活性水平的替代物（更多的核糖体在更活跃的细胞中存在更多的核糖体），而不仅仅是存在/不存在和不存在和生物量，如RDNA所示。这种方法将与单独的rDNA库有关生态特征提供更多信息。环境序列将用于改善内肌的系统发育重建及其与Rhizaria其余部分的关系，都通过增加树的这一部分的分类量采样，并通过提供可用于直接从环境DNA样本中获得代表性基因型的LSU rDNA序列的序列数据。在有培养物的地方，可以将其他基因靶向PCR，并将其与多基因系统发育中的现有数据结合使用。

项目成果

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes.

• DOI: 10.1111/jeu.12691
• 发表时间: 2019-01
• 期刊: The Journal of eukaryotic microbiology
• 作者: Adl SM;Bass D;Lane CE;Lukeš J;Schoch CL;Smirnov A;Agatha S;Berney C;Brown MW;Burki F;Cárdenas P;Čepička I;Chistyakova L;Del Campo J;Dunthorn M;Edvardsen B;Eglit Y;Guillou L;Hampl V;Heiss AA;Hoppenrath M;James TY;Karnkowska A;Karpov S;Kim E;Kolisko M;Kudryavtsev A;Lahr DJG;Lara E;Le Gall L;Lynn DH;Mann DG;Massana R;Mitchell EAD;Morrow C;Park JS;Pawlowski JW;Powell MJ;Richter DJ;Rueckert S;Shadwick L;Shimano S;Spiegel FW;Torruella G;Youssef N;Zlatogursky V;Zhang Q
• 通讯作者: Zhang Q

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 Pathobiome in Animal and Plant Diseases

• DOI: 10.1016/j.tree.2019.07.012
• 发表时间: 2019-11-01
• 期刊: TRENDS IN ECOLOGY & EVOLUTION
• 影响因子: 16.8
• 作者: Bass, David;Stentiford, Grant D.;Tyler, Charles R.
• 通讯作者: Tyler, Charles R.

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