IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2025-03-01 Epub Date: 2024-11-27 DOI: 10.1016/j.protis.2024.126074

Atef Omar , Jiwon Jung , Gaeul Lee , Jae-Ho Jung

The morphology, morphogenesis, molecular phylogeny, and the resting cyst morphology of the freshwater ciliate, Crassohymena primicirrata (Berger and Foissner, 1987) n. gen., n. comb., found in samples collected from South Korea, were investigated. The Korean two populations observed are identical to each other and are highly similar to the type population showing only few and minor differences in the size and arrangement of cortical granules and the length of dorsal kinety 4. The new genus Crassohymena n. gen. is established and characterized by a number of morphological and ontogenetic features: the thick undulating membranes comprising three or four rows of kinetosomes and in Cyrtohymena pattern; the anteriorly distinctly displaced transverse cirri; the posteriorly set-off cirrus V/3; the opisthe's anlagen IV–VI originate from cirri IV/2, V/4, and V/3, respectively; the proter's anlagen IV–VI originate from cirrus IV/3; and the enormous anlage I in each daughter cell. Phylogenetic analyses based on 18S rRNA gene sequences show that Crassohymena primicirrata n. gen., n. comb. is separated from all other morphologically most similar taxa and forms an adelphotaxon to the clade containing sequences of the families Neokeronopsidae and Spirofilidae, and the two oxytrichid genera Australocirrus and Notohymena.

淡水纤毛虫Crassohymena primicirrata的形态、形态发生、分子系统发育和静息囊形态（Berger and Foissner, 1987） n. gen. n. comb。从韩国采集的样本中发现的。观察到的朝鲜两个种群彼此完全相同，与型种群高度相似，在皮质颗粒的大小和排列以及背部运动的长度上只有很少和微小的差异4。新属（Crassohymena n. geng .）被建立，并具有许多形态学和个体发生特征：由三或四行动体组成的厚波状膜和细胞膜模式；前面明显移位的横卷；后抵消卷云V/3；蛇的胶原IV- vi分别来源于cirri IV/2、V/4和V/3；蛋白原IV- vi源自IV/3型卷病毒；以及每个子细胞中巨大的细胞I。基于18S rRNA基因序列的系统发育分析表明，原膜虫属（Crassohymena primicirrata n. gen., n. comb.）；从所有其他形态上最相似的分类群中分离出来，形成了一个adelphotaxon，它的进化枝包含了Neokeronopsidae和Spirofilidae家族的序列，以及两个oxytrichid属australcirrus和Notohymena。

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引用次数: 0

Environmental interactions between protists and bacterial communities in hydrocarbon degradation 碳氢化合物降解过程中原生生物与细菌群落之间的环境相互作用。

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2025-03-01 Epub Date: 2024-12-17 DOI: 10.1016/j.protis.2024.126083

Komal A. Chandarana, Sapna Chandwani, Harshida A. Gamit, Hetvi Naik, Natarajan Amaresan

Reclamation of petroleum-polluted environments is a key issue for today and in the future, as our reliance on oil will persist for decades. An eco-friendly solution is to use microbes that play a role in petroleum-hydrocarbon degradation. However, as hydrocarbon degradation involves a multi-step process involving different functional groups, focusing only on finding efficient bacterial species will not be the complete solution. Heterotrophic protists are unicellular eukaryotic microorganisms that could play a role in remediation of ecosystems by enhancing petroleum-hydrocarbon degradation through different mechanisms. This mini-review discusses the importance of protists in the degradation of petroleum-hydrocarbon and their predatory impact on hydrocarbon-degrading bacterial communities. Additionally, the effect of hydrocarbons on protistan community structure and protistan cells is discussed. A better understanding of the puzzle hydrocarbon-protist interactions will significantly increase our knowledge of how to employ these microbes for bioremediation of hydrocarbon pollutants.

由于我们对石油的依赖将持续几十年，石油污染环境的回收是当今和未来的一个关键问题。一个生态友好的解决方案是使用微生物，它们在石油碳氢化合物的降解中发挥作用。然而，由于碳氢化合物的降解是一个涉及不同官能团的多步骤过程，只关注于寻找有效的细菌种类并不是完整的解决方案。异养原生生物是一种单细胞真核微生物，可以通过不同的机制促进石油烃的降解，在生态系统中发挥修复作用。本文综述了原生生物在石油烃降解中的重要作用及其对烃类降解细菌群落的影响。此外，还讨论了碳氢化合物对原生生物群落结构和原生生物细胞的影响。更好地理解碳氢化合物与原生生物之间的相互作用，将大大增加我们对如何利用这些微生物对碳氢化合物污染物进行生物修复的认识。

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引用次数: 0

Characterization of the encystment-inducing activity of extracellular fluid from encysting vegetative cells in the terrestrial ciliated protozoa Colpoda cucullus 陆地纤毛原生动物包囊营养细胞胞外液诱导包囊活性的研究

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2025-03-01 Epub Date: 2025-02-12 DOI: 10.1016/j.protis.2025.126088

Yuto Shimada , Arisa Momota , Ayumu Onda , Mikihiko Arikawa

The terrestrial ciliated protozoan Colpoda cucullus transforms into a dehydration-resistant cyst upon sensing adverse signals. Recently, we identified a pheromone secreted by encysting vegetative cells of C. cucullus, termed “encystment-inducing pheromone” (EnIP), and characterized its properties. Overpopulated vegetative cells spontaneously encysted in ion-free ultrapure water without external stimuli. The external solution of encysting cells markedly induced encystment in vegetative cells under low cell density conditions, suggesting that EnIP, secreted by encysting cells into the external solution, induced encystment in vegetative cells. Further investigations revealed the following properties of EnIP: 1) EnIP retains encystment-inducing activity even in the presence of EGTA. 2) EnIP exhibits a concentration-dependent encystment effect. 3) EnIP is released within hours at high cell density. 4) EnIP is released by exocytosis. 5) EnIP loses its activity after 1–2 days. 6) EnIP is inactivated by heating and treatment with proteolytic enzymes. 7) The nominal molecular weight of EnIP was estimated to range between 10 and 100 kDa. These findings lead to the conclusion that encystment-induced C. cucullus vegetative cells secrete EnIP, a protein pheromone, with encystment-inducing activity for other cells. This study contributes to understanding microbial communication and reveals a novel mechanism for protist survival in harsh environments.

陆生纤毛原生动物囊足（Colpoda cucullus）在感知到不利信号后转变为抗脱水囊。最近，我们鉴定了一种由黄瓜营养细胞囊化分泌的信息素，称为“囊化诱导信息素”（EnIP），并对其性质进行了表征。在没有外界刺激的情况下，过剩的营养细胞自发地包裹在无离子的超纯水中。在低细胞密度条件下，囊泡细胞外源性溶液显著诱导营养细胞成囊，说明囊泡细胞分泌EnIP诱导营养细胞成囊。进一步的研究揭示了EnIP的以下特性：1)即使在EGTA存在的情况下，EnIP也能保持诱导系统的活性。2) EnIP表现出浓度依赖的囊化效应。3) EnIP以高细胞密度在数小时内释放。4) EnIP通过胞吐作用释放。5) EnIP在1-2天后失去活性。6) EnIP通过加热和蛋白水解酶处理灭活。7)估计EnIP的标称分子量在10 - 100 kDa之间。这些发现表明，囊化诱导的黄瓜营养细胞分泌一种蛋白信息素EnIP，对其他细胞具有囊化诱导活性。该研究有助于理解微生物的交流，揭示了原生生物在恶劣环境下生存的新机制。

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引用次数: 0

Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems 恐龙在进化过程中拥有两种不同的自噬相关泛素类连接系统

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-12-01 Epub Date: 2024-09-21 DOI: 10.1016/j.protis.2024.126067

Euki Yazaki , Tadaaki Uehara , Hirokazu Sakamoto , Yuji Inagaki

Autophagy is an intracellular degradation mechanism by which cytoplasmic materials are delivered to and degraded in the lysosome-fused autophagosome (autolysosome) and proposed to have been established at an early stage of eukaryotic evolution. Dinoflagellates harboring endosymbiotic diatoms (so-called “dinotoms”), which retain their own nuclei and mitochondria in addition to plastids, have been investigated as an intermediate toward the full integration of a eukaryotic phototroph into the host-controlled organelle (i.e., plastid) through endosymbiosis. Pioneering studies systematically evaluated the degree of host governance on several metabolic pathways in the endosymbiotic diatoms (ESDs). However, little attention has been paid to the impact of the endosymbiotic lifestyle on the autophagy operated in the ESDs. In this study, we searched for ATG3, ATG4, ATG5, ATG7, ATG8, ATG10, and ATG12, which are required for autophagosome formation, in the RNA-seq data from dinotoms Durinskia baltica and Kryptoperidinium foliaceum. We detected two evolutionally distinct sets of the ATG proteins in the dinotom species, one affiliated with the dinoflagellate homologs and the other with the diatom homologs in phylogenetic analyses. The results suggest that the ATG proteins descended from the diatom taken up by the dinoflagellate host persist for autophagosome formation and, most likely, autophagy.

自噬是一种细胞内降解机制，通过这种机制，细胞质物质被运送到溶酶体融合的自噬体（自溶酶体）中并在其中降解。内共生硅藻（即所谓的 "硅藻"）是真核生物光营养体通过内共生完全融入宿主控制的细胞器（即质体）的中间产物。开创性的研究系统地评估了宿主对内共生硅藻（ESD）中几种代谢途径的控制程度。然而，人们很少关注内共生生活方式对ESDs自噬的影响。在这项研究中，我们从Durinskia baltica和Kryptoperidinium foliaceum的RNA-seq数据中寻找了自噬体形成所需的ATG3、ATG4、ATG5、ATG7、ATG8、ATG10和ATG12。在系统进化分析中，我们在恐龙物种中发现了两组进化不同的 ATG 蛋白，一组与甲藻同源，另一组与硅藻同源。结果表明，被双鞭毛虫宿主吸收的硅藻后裔ATG蛋白持续用于自噬体的形成，并很可能用于自噬。

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引用次数: 0

Long-read DNA sequencing reveals the organization of the mitochondrial genome in the early-branching dinoflagellate Oxyrrhis marina. 长读DNA测序揭示了早期分支甲藻Oxyrrhis marina线粒体基因组的组织结构。

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-12-01 Epub Date: 2024-11-22 DOI: 10.1016/j.protis.2024.126071

Ronie Haro , Nikita Walunjkar , Soham Jorapur , Claudio H. Slamovits

The mitochondrial genomes of dinoflagellate protists are remarkable for their highly fragmented and heterogeneous organization. Early attempts to determine their structure without ‘next-generation’ DNA sequencing failed to recover a defined genome. Still, it coincided in showing that the proteins coding genes, three in total, and parts of the ribosomal RNA genes were spread across a diffuse assortment of small linear fragments. In contrast, a recent study employed Illumina sequencing to assemble a 326 kbp long single-molecule, circular mitochondrial genome in the symbiotic dinoflagellate Breviolum minutum. Here, we used a combination of short- and long-read massively-parallel DNA sequencing to analyze further the mitochondrial DNA of the early-branching dinoflagellate Oxyrrhis marina. We found that the mitochondrial genome of O. marina consists of 3 linear chromosomes sized 15.9, 33.8 and 40.6 kbp for a total of 90.3 kbp. It contains the cox1, cox3 and cob genes, the same three proteins encoded in the mitochondrion of all myzozoans (Apicomplexa and Dinophyceae), some fragments of ribosomal RNA genes as well as many non-functional gene fragments and extensive noncoding DNA. Our analysis unveiled segments syntenic patterns and rearrangements encompassing coding and non-coding regions, suggesting that recombination is a pervasive process driving the evolution of these genomes.

甲藻原生动物的线粒体基因组因其高度分散和异质的组织结构而引人注目。在没有进行 "下一代 "DNA 测序的情况下，确定其结构的早期尝试未能恢复一个确定的基因组。尽管如此，它还是不约而同地显示，蛋白质编码基因（共三个）和部分核糖体 RNA 基因分布在各种小的线性片段中。与此相反，最近的一项研究利用 Illumina 测序技术在共生甲藻 Breviolum minutum 中组装了一个 326 kbp 长的单分子环形线粒体基因组。在这里，我们结合使用了短线程和长线程大规模平行DNA测序技术，进一步分析了早枝甲藻（Oxyrrhis marina）的线粒体DNA。我们发现，O. marina 的线粒体基因组由 3 条线性染色体组成，大小分别为 15.9、33.8 和 40.6 kbp，总计 90.3 kbp。基因组中包含 cox1、cox3 和 cob 基因，这三种蛋白在所有无脊椎动物（拟尾柱虫纲和鼎足目）的线粒体中都有编码，还包含一些核糖体 RNA 基因片段以及许多无功能基因片段和大量非编码 DNA。我们的分析揭示了包括编码区和非编码区的片段同源模式和重排，表明重组是推动这些基因组进化的一个普遍过程。

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引用次数: 0

Dead reckoning of protist viability with propidium monoazide (PMA)-quantitative PCR; a case study using Neoparamoeba perurans 利用单氮化丙啶（PMA）-定量 PCR 对原生生物的存活率进行死算；以周龄新巴拉米阿米巴为例进行研究

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-12-01 Epub Date: 2024-09-24 DOI: 10.1016/j.protis.2024.126068

James W. Wynne , Anca G. Rusu , Ben T. Maynard , Megan L. Rigby , Richard S. Taylor

The ability to distinguish between viable and non-viable protozoan parasites is central to improved human and animal health management. While conceptually simple, methods to differentiate cell viability in situ remain challenging. Amoebic gill disease, caused by Neoparamoeba perurans is a parasitic disease impacting Atlantic salmon aquaculture globally. Although commercial freshwater treatments alleviate AGD, viable amoebae remain on gills or in used treatment water. Existing PCR-based assays are able to quantify N. perurans abundance but cannot discriminate amoeba viability. We investigated the use of propidium monoazide (PMA) application, prior to real-time PCR, to distinguish between alive and dead cells. We demonstrate that 200 μM PMA can significantly reduce amplification from non-viable (isopropanol treated) cultured amoebae across at least three logs of cell concentrations. Using a serial dilution of viable and non-viable cells, we show that non-PMA PCR amplifies both viable and non-viable amoebae, while PMA exposure suppresses (but does not completely inhibit) amplification from non-viable amoebae. The effect of freshwater treatment on N. perurans viability was assessed using the PMA-PCR. Following PMA exposure, amplification from freshwater treated amoebae was reduced by approximately 94–97 %. Taken together this study demonstrates that PMA combined with traditional real-time PCR can estimate amoeba viability.

区分有活力和无活力原生动物寄生虫的能力是改善人类和动物健康管理的核心。虽然概念上很简单，但在原位区分细胞活力的方法仍然具有挑战性。由周新巴拉米巴（Neoparamoeba perurans）引起的阿米巴鳃病是一种影响全球大西洋鲑水产养殖的寄生虫病。尽管商业淡水处理可减轻 AGD，但鳃上或使用过的处理水中仍残留着可存活的阿米巴。现有的基于 PCR 的检测方法能够量化 N. perurans 的数量，但无法区分阿米巴的存活率。我们研究了在实时 PCR 之前使用单氮化丙啶（PMA）来区分活细胞和死细胞的方法。我们证明，200 μM PMA 可显著降低未存活（异丙醇处理过的）培养阿米巴在至少三个对数的细胞浓度下的扩增。通过对有活力细胞和无活力细胞进行系列稀释，我们发现非 PMA PCR 可扩增有活力和无活力的变形虫，而 PMA 暴露可抑制（但不能完全抑制）无活力变形虫的扩增。使用 PMA-PCR 评估了淡水处理对 N. perurans 存活率的影响。暴露于 PMA 后，淡水处理变形虫的扩增率降低了约 94-97%。总之，这项研究表明，PMA 与传统的实时 PCR 相结合可以评估变形虫的存活率。

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引用次数: 0

Basic biology, ecology, and biotechnology of euglenids 八目鳗的基础生物学、生态学和生物技术

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-12-01 Epub Date: 2024-09-12 DOI: 10.1016/j.protis.2024.126066

Michael L. Ginger Guest Editor, Anna Karnkowska Guest Editor, Vladimír Hampl Guest Editor, Scott C. Farrow Guest Editor

引用次数: 0

The protists of Ernst Haeckel’s Kunstformen der Natur 恩斯特-海克尔《自然形态学》中的原生生物

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-12-01 Epub Date: 2024-10-05 DOI: 10.1016/j.protis.2024.126069

John R. Dolan

Haeckel’s ’art book’, Kunstformen der Natur, is likely familiar to most protistologists as it is probably Haeckel’s best known work, and it prominently featured protists. No doubt many of us have used some of the images from it in our lectures. Most familiar are perhaps the often-reproduced images of nassularian radiolaria, but plates were also devoted to phaeodarians, acantharia, foraminifera, ciliates, diatoms, dinoflagellates and desmids. Despite the fame of Kunstformen der Natur, there are aspects of the work that have received little attention, and are of potential interest to protistologists. These include the overall importance of protists in the work, compared to other taxa, the surprisingly under appreciated role of Haeckel’s collaborator, Adolph Giltsch in creating the figures, the disputed fidelity of the illustrations of protists, and Haeckel’s discrete inclusion of many descriptions of new species of protists, forcing us to consider Kunstformen a scientific publication. Here these aspects, and the 20 plates featuring protists will be reviewed. The goal of this review is to familiarize protistologists with the most famous work featuring protists, and point out the many particular figures of protists we may wish to avoid showcasing, as the illustrations are questionable. A supplemental file is provided listing the currently accepted names of the protist taxa (for names found in a database), and the reasons for considering some illustrations as questionable.

大多数原生生物学家可能对海克尔的 "艺术书"《Kunstformen der Natur》并不陌生，因为这本书可能是海克尔最著名的作品，其中突出介绍了原生生物。毫无疑问，我们中的许多人都曾在讲座中使用过其中的一些图片。大家最熟悉的可能是经常被复制的纳氏放射虫的图片，但也有专门介绍辉石虫、棘皮动物、有孔虫、纤毛虫、硅藻、甲藻和脱壳虫的图版。尽管《Kunstformen der Natur》声名远播，但该作品的某些方面却鲜有人关注，而原生动物学家却可能对此感兴趣。这些方面包括：与其他类群相比，原生动物在该著作中的整体重要性；海克尔的合作者阿道夫-吉尔施（Adolph Giltsch）在绘制图像中发挥的作用出人意料地未得到充分重视；原生动物插图的真实性存在争议；海克尔单独纳入了许多原生动物新物种的描述，迫使我们将《Kunstformen》视为一份科学出版物。在此，我们将对这些方面以及 20 幅以原生动物为主题的图版进行回顾。这篇评论的目的是让原生生物学家熟悉这本以原生生物为主题的最著名作品，并指出我们可能希望避免展示的许多特定的原生生物形象，因为这些插图是有问题的。我们还提供了一份补充文件，列出了目前公认的原生生物类群名称（针对数据库中找到的名称），以及认为某些插图有问题的原因。

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引用次数: 0

Comparative chloroplast genome analysis of two Desmodesmus species reveals genome diversity within Scenedesmaceae (Sphaeropleales, Chlorophyceae) 两种盘尾藻叶绿体基因组的比较分析揭示了盘尾藻科（Sphaeropleales，吊兰科）基因组多样性

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-12-01 Epub Date: 2024-11-28 DOI: 10.1016/j.protis.2024.126073

Yan Xu , Xiayi Chen , Michael Melkonian , Sibo Wang , Sunil Kumar Sahu

Desmodesmus (Sphaeropleales, Chlorophyceae) is a genus of freshwater green algae widely distributed in aquatic ecosystems and known for its potential in biotechnology and bioremediation. We present the complete chloroplast genome sequences of two Desmodesmus species, D. hystrix and D. perforatus. Comparative analysis revealed significant differences in their quadripartite structures, particularly in the lengths of the small single copy regions. We observed variations in G + C content across genomic regions, with inverted repeat regions showing a higher G + C content. Microsatellite analysis revealed that A/T mononucleotides were the most abundant type, while dispersed repeat analysis suggested a potential link to expansion of the single-copy region in D. perforatus. Gene annotation, codon usage analysis, and comparison of genome rearrangement highlighted both similarities and differences between the species. Nucleotide diversity analysis revealed higher variability in intergenic regions than in coding regions, with IR regions displaying relative conservation. Comparative analyses of genomes and IR border arrangements demonstrated that the Desmodesmus species exhibit substantial differences in genome structure and gene arrangement among Scenedesmaceae. Phylogenetic analysis, based on 51 single-copy genes from 34 species of Sphaeropleales provided additional information about phylogenetic relationships within Sphaeropleales. These findings contribute to our understanding of comparative plastid genomics in green algae.

鳞藻是一种广泛分布于水生生态系统中的淡水绿藻属，在生物技术和生物修复方面具有重要的应用价值。本文报道了两种连线虫的叶绿体基因组序列，即hystrix和perforatus。比较分析显示，它们的四分体结构存在显著差异，特别是在小的单拷贝区域的长度上。我们观察到不同基因组区域的G + C含量存在差异，反向重复区域的G + C含量较高。微卫星分析显示，A/T单核苷酸是最丰富的类型，而分散重复分析表明，A/T单拷贝区可能与孔雀桃单拷贝区扩展有关。基因注释、密码子使用分析和基因组重排比较突出了物种之间的相似性和差异性。核苷酸多样性分析显示，基因间区比编码区具有更高的变异性，红外区表现出相对的保守性。基因组和红外边界排列的比较分析表明，排尾蝇在基因组结构和基因排列上存在显著差异。对34种球梨属植物的51个单拷贝基因进行系统发育分析，进一步揭示了球梨属植物的系统发育关系。这些发现有助于我们对绿藻比较质体基因组学的理解。

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引用次数: 0

Flagellar proteomic analysis of the brown alga Mutimo cylindricus revealed a novel calcium-binding protein abundantly localized in the anterior flagellum 褐藻 Mutimo cylindricus 的鞭毛蛋白质组分析发现了一种新型钙结合蛋白，该蛋白大量定位于前鞭毛中

IF 1.9 3区生物学 Q4 MICROBIOLOGY

Protist

Pub Date : 2024-12-01 Epub Date: 2024-10-26 DOI: 10.1016/j.protis.2024.126070

Nana Kinoshita-Terauchi , Kogiku Shiba , Makoto Terauchi , Hideki Noguchi , Kazuo Inaba

Mutimo cylindricus gametes have two flagella with different structures : an anterior and a posterior flagellum. Their flagellar waveforms are regulated by calcium ions through various mechanisms, however the factors involved in this regulation remain largely unknown To elucidate the molecular basis underlying the difference between the two flagella, we performed a flagellar proteomic analysis of male M. cylindricus gametes. We identified 848 proteins shared with Ectocarpus siliculosus, including 28 calcium-binding proteins. Among the EF-hand proteins, a 111 kDa protein showed predominant localization along the anterior flagellum. Immunogold localization suggested that this protein is associated with outer doublet microtubules. This is the first report to show heterogeneous localization of a calcium-binding protein between two flagellar axonemes and suggests that calcium-binding proteins are involved in the specific regulation of the anterior flagellum.

圆柱木配子有两种不同结构的鞭毛：前鞭毛和后鞭毛。为了阐明两种鞭毛差异的分子基础，我们对雄性圆筒木配子进行了鞭毛蛋白质组分析。我们发现了848个与硅外皮藻共有的蛋白质，其中包括28个钙结合蛋白。在EF-手蛋白中，一个111 kDa的蛋白主要沿前鞭毛定位。免疫金定位表明，该蛋白与外双微管有关。这是首次报道钙结合蛋白在两个鞭毛轴丝之间的异质性定位，表明钙结合蛋白参与了前鞭毛的特异性调控。

引用次数: 0

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