IF 1.9 3区生物学

Protist Pub Date : 2025-01-20 DOI: 10.1016/j.protis.2025.126086

Hitoshi Iida

引用次数: 0

Slowly evolving proteins support the monophyly of Craspedida (Choanoflagellatea) and a marine origin of choanoflagellates 缓慢进化的蛋白质支持石门（长鞭毛虫）的单一性和长鞭毛虫的海洋起源。

IF 1.9 3区生物学

Protist Pub Date : 2025-01-17 DOI: 10.1016/j.protis.2025.126085

Juan J. Ginés-Rivas, Martin Carr

{"title":"Slowly evolving proteins support the monophyly of Craspedida (Choanoflagellatea) and a marine origin of choanoflagellates","authors":"Juan J. Ginés-Rivas, Martin Carr","doi":"10.1016/j.protis.2025.126085","DOIUrl":"10.1016/j.protis.2025.126085","url":null,"abstract":"<div><div>Choanoflagellate species have been taxonomically divided upon the morphological and developmental basis of their extracellular coat (periplast). Species within the order Craspedida possess a purely organic periplast, whereas taxa of the order Acanthoecida have an additional silica based periplast termed the lorica. Whilst small-scale phylogenetic studies have recovered the two orders as monophyletic, recent phylogenomic analyses have rejected the monophyly of the craspedids. These analyses suggest that the freshwater craspedid <em>Codosiga hollandica</em> falls within the earliest branching choanoflagellate lineage; however, it has also been noted that phylogenomic studies result in inconsistent phylogenies, with unstable long-branched species being recovered as basal choanoflagellates. Presented here are phylogenetic analyses, based upon slowly evolving ribosomal proteins, which consistently recover both craspedid monophyly and a derived placement of <em>C. hollandica</em>. The addition of further, long-branched, ribosomal proteins to phylogenetic analyses are shown to generate longer terminal branches and a weakening of the support for Craspedida. The analyses highlight the requirement for an increase in data, in terms of both taxa and gene coverage, to successfully resolve the earliest craspedid branches. In addition, phylogenetically unstable species are identified that are recommended to be omitted from phylogenomic studies as they have the potential to disrupt recovered relationships.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"176 ","pages":"Article 126085"},"PeriodicalIF":1.9,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular phylogeny, morphology, and ultrastructure of a Mesomycetozoea member, Sphaeroforma nootkatensis isolated from Pacific oyster, Crassostrea gigas, on the Southern coast of Korea 从朝鲜南部海岸的太平洋牡蛎中分离出的一种中菌科成员Sphaeroforma nootkatensis的分子系统发育、形态和超微结构

IF 1.9 3区生物学

Protist Pub Date : 2024-12-24 DOI: 10.1016/j.protis.2024.126084

Seung-Hyeon Kim , S.D.N.K. Bathige , Donghyun Lee , W.A.A.H. Kalhari , Hyoun Joong Kim , Kyung-Il Park

{"title":"Molecular phylogeny, morphology, and ultrastructure of a Mesomycetozoea member, Sphaeroforma nootkatensis isolated from Pacific oyster, Crassostrea gigas, on the Southern coast of Korea","authors":"Seung-Hyeon Kim , S.D.N.K. Bathige , Donghyun Lee , W.A.A.H. Kalhari , Hyoun Joong Kim , Kyung-Il Park","doi":"10.1016/j.protis.2024.126084","DOIUrl":"10.1016/j.protis.2024.126084","url":null,"abstract":"<div><div>This study discovered the first Asian population of <em>Sphaeroforma nootkatensis</em> (SphX), a member of Mesomycetozoea, in the southern coastal region of South Korea. Although investigating parasites in Pacific oysters (<em>Crassostrea gigas</em>), a single-cell microorganism was isolated from gill tissues. Comprehensive phylogenetic analysis of its 18S rDNA revealed its placement within the order Ichthyophonida, class Mesomycetozoea. SphX formed a distinct cluster within <em>Sphaeroforma</em> spp., separate from <em>Pseudoperkinsus tapetis</em>. Morphological examinations of in vitro cultured cells revealed two distinctive life stages characterized by multilobe and granular sporangium, accompanied by corresponding non-motile larger and motile smaller endospores, respectively. Scanning electron microscope analysis depicted lobular and smooth surfaces on vegetative cells, indicative of differing life cycle stages. Transmission electron microscope observations revealed intriguing features consistent with previous reports on Mesomycetozoea. A prominent fibrillar structure was noted in a vegetative cell. In contrast, smaller endospores were observed with cilia-like structures surrounding the cell wall, indicating their mode of movement. The Ray's fluid thioglycollate medium assay showed that SphX cells were digested, whereas some small endospores remained resistant. This discovery provides novel insights into the life stages of Mesomycetozoans and geographical distribution and underscores the importance of monitoring oyster health for effective aquaculture management.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"176 ","pages":"Article 126084"},"PeriodicalIF":1.9,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142915088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Protist Pub Date : 2024-12-17 DOI: 10.1016/j.protis.2024.126083

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

{"title":"Environmental interactions between protists and bacterial communities in hydrocarbon degradation","authors":"Komal A. Chandarana, Sapna Chandwani, Harshida A. Gamit, Hetvi Naik, Natarajan Amaresan","doi":"10.1016/j.protis.2024.126083","DOIUrl":"10.1016/j.protis.2024.126083","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"176 ","pages":"Article 126083"},"PeriodicalIF":1.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Protist Pub Date : 2024-12-01 DOI: 10.1016/j.protis.2024.126073

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

{"title":"Comparative chloroplast genome analysis of two Desmodesmus species reveals genome diversity within Scenedesmaceae (Sphaeropleales, Chlorophyceae)","authors":"Yan Xu , Xiayi Chen , Michael Melkonian , Sibo Wang , Sunil Kumar Sahu","doi":"10.1016/j.protis.2024.126073","DOIUrl":"10.1016/j.protis.2024.126073","url":null,"abstract":"<div><div><em>Desmodesmus</em> (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 <em>Desmodesmus</em> species, <em>D. hystrix</em> and <em>D. perforatus</em>. 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 <em>D. perforatus</em>. 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 <em>Desmodesmus</em> 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.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 6","pages":"Article 126073"},"PeriodicalIF":1.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142747697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

New and noteworthy chrysophycean stomatocysts from the Steppe zone of South Urals (Russia) with comments on the morphological variability 南乌拉尔（俄罗斯）草原带新发现的值得注意的chrysophysp口囊及其形态学变异。

IF 1.9 3区生物学

Protist Pub Date : 2024-11-28 DOI: 10.1016/j.protis.2024.126075

Marina Ignatenko , Tatyana Yatsenko-Stepanova , Dmitry Kapustin

引用次数: 0

Protists and Society: A report on the 2024 autumn meeting of Protistology-UK, at the natural history museum, London 原生生物与社会：英国原生生物学2024年秋季会议报告，伦敦自然历史博物馆

IF 1.9 3区生物学

Protist Pub Date : 2024-11-27 DOI: 10.1016/j.protis.2024.126072

David J.S. Montagnes

引用次数: 0

Integrative studies shed light on the pseudocryptic genus Crassohymena n. gen. (Protozoa, Ciliophora) 综合研究揭示了假隐属（原生动物，纤毛虫目）。

IF 1.9 3区生物学

Protist Pub Date : 2024-11-27 DOI: 10.1016/j.protis.2024.126074

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

{"title":"Integrative studies shed light on the pseudocryptic genus Crassohymena n. gen. (Protozoa, Ciliophora)","authors":"Atef Omar , Jiwon Jung , Gaeul Lee , Jae-Ho Jung","doi":"10.1016/j.protis.2024.126074","DOIUrl":"10.1016/j.protis.2024.126074","url":null,"abstract":"<div><div>The morphology, morphogenesis, molecular phylogeny, and the resting cyst morphology of the freshwater ciliate, <em>Crassohymena primicirrata</em> (<span><span>Berger and Foissner, 1987</span></span>) 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 <em>Crassohymena</em> 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 <em>Cyrtohymena</em> 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 <em>Crassohymena primicirrata</em> 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 <em>Australocirrus</em> and <em>Notohymena</em>.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"176 ","pages":"Article 126074"},"PeriodicalIF":1.9,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Protist Pub Date : 2024-11-22 DOI: 10.1016/j.protis.2024.126071

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

{"title":"Long-read DNA sequencing reveals the organization of the mitochondrial genome in the early-branching dinoflagellate Oxyrrhis marina.","authors":"Ronie Haro , Nikita Walunjkar , Soham Jorapur , Claudio H. Slamovits","doi":"10.1016/j.protis.2024.126071","DOIUrl":"10.1016/j.protis.2024.126071","url":null,"abstract":"<div><div>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 <em>Breviolum minutum</em>. 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 <em>Oxyrrhis marina</em>. We found that the mitochondrial genome of <em>O. marina</em> consists of 3 linear chromosomes sized 15.9, 33.8 and 40.6 kbp for a total of 90.3 kbp. It contains the <em>cox</em>1, <em>cox</em>3 and <em>cob</em> 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.</div></div>","PeriodicalId":20781,"journal":{"name":"Protist","volume":"175 6","pages":"Article 126071"},"PeriodicalIF":1.9,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142720748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Protist Pub Date : 2024-10-26 DOI: 10.1016/j.protis.2024.126070

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

引用次数: 0

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