Kenneth Dumack , Enrique Lara , Clément Duckert , Elizaveta Ermolaeva , Ferry Siemensma , David Singer , Valentyna Krashevska , Mariusz Lamentowicz , Edward A.D. Mitchell
{"title":"It's time to consider the Arcellinida shell as a weapon","authors":"Kenneth Dumack , Enrique Lara , Clément Duckert , Elizaveta Ermolaeva , Ferry Siemensma , David Singer , Valentyna Krashevska , Mariusz Lamentowicz , Edward A.D. Mitchell","doi":"10.1016/j.ejop.2024.126051","DOIUrl":"10.1016/j.ejop.2024.126051","url":null,"abstract":"<div><p>The shells of testate amoebae are morphologically diverse and persistent in the environment. Accordingly, the examination of the morphology and composition of shells became a standard tool in ecological, palaeoecological, and evolutionary studies. However, so far the function of the shell remains poorly understood and, although based on limited evidence, the shell was considered as a defense mechanism. Based on recent evidence, we propose that the shell of arcellinid testate amoebae is a crucial component facilitating the amoebae’s attack of large prey. Accordingly, the shell is not purely protective, but must be considered also as a weapon. This change in perspective opens up numerous new avenues in protistology and will lead to a substantial change in ecological, palaeoecological, and evolutionary research.</p></div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0932473924000014/pdfft?md5=53b8559b1fe719b469a1c20b3fb15cfb&pid=1-s2.0-S0932473924000014-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139082281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pavel Safonov , Mariia Berdieva , Elena Nassonova , Sergei Skarlato , Ilya Pozdnyakov
{"title":"The first arctic strain of Rhizochromulina: Morphology, ultrastructure, and position in the evolutionary tree of the order Rhizochromulinales (Heterokontophyta, Dictyochophyceae)","authors":"Pavel Safonov , Mariia Berdieva , Elena Nassonova , Sergei Skarlato , Ilya Pozdnyakov","doi":"10.1016/j.ejop.2023.126050","DOIUrl":"10.1016/j.ejop.2023.126050","url":null,"abstract":"<div><p><em>Rhizochromulina marina</em> is a unicellular amoeboid alga capable of forming flagellate cells; it is a single validly named species in the genus. Besides, there are numerous environmental sequences and undescribed strains designated as <em>Rhizochromulina</em> sp. or <em>R. marina</em>. The biogeography of the genus is understudied: rhizochromulines from the Indian, Southern, and Arctic Oceans are unknown. Here, we present the description of <em>Rhizochromulina</em> sp. B44, which was for the first time isolated from an arctic habitat. Biofilms of this microalga grow at the bottom of a culture vessel, where neighbouring amoeboid cells form associations through a common network of pseudopodia, i.e. meroplasmodia. Pseudopodia branch, anastomose mainly during meroplasmodia formation, and are supported by microtubules that arise from the perinuclear zone. Actin filaments are localized in the cytoplasm and can be revealed only near the bases of pseudopodia. We succeeded in inducing the transformation of amoeboid cells into flagellates using a prolonged agitation of cultures. Morphological and molecular analyses revealed that the studied strain is most closely related to the type strain of <em>R. marina</em>. At the same time, 18S rDNA sequences of early branching-off rhizochromulinids differ significantly from <em>Rhizochromulina</em> sp. B44, suggesting a high divergence at the genus level.</p></div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138690117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Olivia K. Dufour , Evie Hoffman , Robin S. Sleith , Laura A. Katz , Agnes K.M. Weiner , Taylor R. Sehein
{"title":"Testate amoebae (Arcellinida, Amoebozoa) community diversity in New England bogs and fens assessed through lineage-specific amplicon sequencing","authors":"Olivia K. Dufour , Evie Hoffman , Robin S. Sleith , Laura A. Katz , Agnes K.M. Weiner , Taylor R. Sehein","doi":"10.1016/j.ejop.2023.126049","DOIUrl":"10.1016/j.ejop.2023.126049","url":null,"abstract":"<div><p><span><span>Testate amoebae (order Arcellinida) are abundant in </span>freshwater ecosystems, including low pH </span>bogs<span> and fens. Within these environments, Arcellinida are considered top predators in microbial food webs and their tests are useful bioindicators of paleoclimatic changes and anthropogenic pollutants. Accurate species identifications and characterizations of diversity are important for studies of paleoclimate, microbial ecology<span>, and environmental change; however, morphological species definitions mask cryptic diversity, which is a common phenomenon among microbial eukaryotes. Lineage-specific primers recently designed to target Arcellinida for amplicon<span> sequencing successfully captured a poorly-described yet diverse fraction of the microbial eukaryotic community. Here, we leveraged the application of these newly-designed primers to survey the diversity of Arcellinida in four low-pH New England bogs and fens, investigating variation among bogs (2018) and then across seasons and habitats within two bogs (2019). Three OTUs represented 66% of Arcellinida reads obtained across all habitats surveyed. 103 additional OTUs were present in lower abundance with some OTUs detected in only one sampling location, suggesting habitat specificity. By establishing a baseline for Arcellinida diversity, we provide a foundation to monitor key taxa in habitats that are predicted to change with increasing anthropogenic pressure and rapid climate change.</span></span></span></p></div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138689985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ziyan Liu, Ziyu Wang, Qi Zhang, Qiukun Wang, Fengchao Li
{"title":"Description of Holostichides (Extraholostichides) eastensis tianjinensis subgen. nov. subspec. nov. (Ciliophora, Hypotricha) from northern China","authors":"Ziyan Liu, Ziyu Wang, Qi Zhang, Qiukun Wang, Fengchao Li","doi":"10.1016/j.ejop.2023.126048","DOIUrl":"10.1016/j.ejop.2023.126048","url":null,"abstract":"<div><p><span>The morphology and morphogenesis of a new urostylid, </span><em>Holostichides</em> (<em>Extraholostichides</em>) <em>eastensis tianjinensis</em><span> subgen. nov. subspec. nov. were analyzed. The new subspecies differs from the nominotypical subspecies </span><em>H.</em> (<em>Extraholostichides</em>) <em>eastensis eastensis</em><span> Wang et al., 2022 by the relatively long frontoterminal row (about 60% vs. 30% of body length), colorless cortical granules (vs. dark brown), two (vs. one) parabuccal cirri, and usually an extra cirrus behind the first midventral pair (vs. lacking). Based on the difference in the frontal ciliature, we split </span><em>Holostichides</em> into two subgenera: <em>H.</em> (<em>Extraholostichides</em>) subgen. nov. (type species <em>Holostichides eastensis</em> Wang et al., 2022; with a short cirral row behind the middle frontal cirrus) and <em>H.</em> (<em>Holostichides</em>) <span>Foissner, 1987</span> (type species Holostichides chardezi <span>Foissner, 1987</span>; lacking this short row). The main morphogenetic characters of the new subspecies are very similar to those of <em>H.</em> (<em>Extraholostichides</em>) <em>eastensis eastensis</em><span> except for some minor differences. Phylogenetic analyses based on SSU rDNA sequences indicate that </span><em>H.</em> (<em>Extraholostichides</em>) subgen. nov. is monophyletic and nested within the monophyletic genus <em>Holostichides</em>, which is sister to <em>Eschaneustyla lugeri</em>.</p></div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138572377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Morphology and molecular phylogeny of two hypotrichous ciliates (Ciliophora, Spirotrichea) from South Korea, including Hemiurosomoida koreana n. sp.","authors":"Atef Omar , Ji Hye Moon , Jae-Ho Jung","doi":"10.1016/j.ejop.2023.126045","DOIUrl":"10.1016/j.ejop.2023.126045","url":null,"abstract":"<div><p><span><span>The living morphology, infraciliature, and molecular phylogeny of a new soil </span>ciliate, </span><em>Hemiurosomoida koreana</em> n. sp., discovered in a sample collected from a mountain in the northeast of South Korea, were investigated. The new species possesses the characteristics of the genus <em>Hemiurosomoida</em><span><span>, i.e., a reduced number of frontal-ventral-transverse cirri, three dorsal kineties of which kineties 1 and 2 each bears a caudal cirrus, and a single dorsomarginal kinety. It is distinguishable from congeners and other similar species by at least one distinct qualitative or quantitative character including the body size, the presence and arrangement of cortical granules, the number of adoral membranelles, marginal cirri, and dorsal dikinetids, or by the arrangement of transverse cirri. </span>Phylogenetic analyses based on 18S rRNA gene sequences also support the assignment of the new species to the non-monophyletic genus </span><em>Hemiurosomoida</em>. In addition, the living morphology, infraciliature, and the 18S rRNA gene sequence of a Korean population of <em>Nothoholosticha flava</em> were studied.</p></div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138534298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Morphology, morphogenesis, and molecular phylogeny of Aspidisca koreana n. sp. (Ciliophora, Euplotida) from South Korea","authors":"Ji Hye Choi , Atef Omar , Jae-Ho Jung","doi":"10.1016/j.ejop.2023.126037","DOIUrl":"10.1016/j.ejop.2023.126037","url":null,"abstract":"<div><p><span><span>The morphology, morphogenesis<span>, and molecular phylogeny of a new </span></span>ciliate, </span><em>Aspidisca koreana</em> n. sp., discovered in the eastern coast of South Korea, were investigated. The morphological description is based on the observation of living cells, 4′-6-diamidino-2-phenylindole (DAPI) and silver-stained specimens (e.g., protargol, silver nitrate), and scanning electron micrographs. The new species is characterized by having a small body size (17–25 × 15–18 μm in vivo), a distinct peristomial spur on the posterior portion of left margin, seven frontoventral cirri in “<em>polystyla</em><span>-arrangement”, and the arrangement of the anterior portion of adoral zone of membranelles, i.e., anteriormost membranelle is distinctly separated from the other three membranelles. The morphogenesis follows the typical pattern of this genus. Phylogenetic analyses, using the 18S rDNA sequence, also support the establishment of a new species.</span></p></div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138534299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tushar Kaushik , Vaishnavi Dixit , Thirumalai Murugan
{"title":"Morphology and molecular phylogeny of two new species of Psammophaga (Rhizaria, Foraminifera) from the west coast of India","authors":"Tushar Kaushik , Vaishnavi Dixit , Thirumalai Murugan","doi":"10.1016/j.ejop.2023.126035","DOIUrl":"10.1016/j.ejop.2023.126035","url":null,"abstract":"<div><p>Benthic foraminifera are unicellular eukaryotic protists that construct an organic, agglutinated, or calcareous test wall. Although single-chambered (monothalamous) foraminifera are ubiquitous in marine habitats worldwide, they are poorly known compared to their multi-chambered relatives, notably from the tropical marine environments of India. In this study, we describe two new species of marine monothalamid genus <em>Psammophaga</em> Arnold, 1982, from the Rajapuri Creek, coastal Maharashtra, India (Arabian Sea). <em>Psammophaga holzmannae</em> sp. nov. is ovoid to spherical shaped, 103–246 µm in length, single aperture, translucent to orange color cytoplasm, outer surface is composed of agglutinated fine clay particles, and ingested mineral grains are concentrated near its aperture. <em>Psammophaga sinhai</em> sp. nov. is oblong, elliptical, or droplet-shaped, 279–448 µm in length, single aperture, yellow olive color cytoplasm, the exterior surface formed of agglutinated fine clay particles, and the ingested mineral grains are dispersed throughout the body. Phylogenetic analyses based on partial small subunit rRNA gene sequences position new species within the Clade E of monothalamids and are genetically distinct from other <em>Psammophaga</em>. Elemental (SEM–EDS) analysis of engulfed mineral grains revealed preferential selection and uptake of heavy opaque titaniferous minerals from the ambient environment in the cytoplasm.</p></div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138543329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Şeyma DURAN , Ayça Fulya ÜSTÜNTANIR DEDE , Yeliz DÜNDAR ORHAN , Muhittin ARSLANYOLU
{"title":"Genome-wide identification and in-silico analysis of papain-family cysteine protease encoding genes in Tetrahymena thermophila","authors":"Şeyma DURAN , Ayça Fulya ÜSTÜNTANIR DEDE , Yeliz DÜNDAR ORHAN , Muhittin ARSLANYOLU","doi":"10.1016/j.ejop.2023.126033","DOIUrl":"10.1016/j.ejop.2023.126033","url":null,"abstract":"<div><p><em>Tetrahymena thermophila</em> is a promising host for recombinant protein production, but its utilization in biotechnology is mostly limited due to the presence of intracellular and extracellular papain-family cysteine proteases (PFCPs). In this study, we employed bioinformatics approaches to investigate the <em>T. thermophila</em> PFCP genes and their encoded proteases (TtPFCPs), the most prominent protease family in the genome. Results from the multiple sequence alignment, protein modeling, and conserved motif analyses revealed that all TtPFCPs showed considerably high homology with mammalian cysteine cathepsins and contained conserved amino acid motifs. The total of 121 TtPFCP-encoding genes, 14 of which were classified as non-peptidase homologs, were found. Remaining 107 true TtPFCPs were divided into four distinct subgroups depending on their homology with mammalian lysosomal cathepsins: cathepsin L-like (TtCATLs), cathepsin B-like (TtCATBs), cathepsin C-like (TtCATCs), and cathepsin X-like (TtCATXs) PFCPs. The majority of true TtPFCPs (96 out of the total) were in TtCATL-like peptidase subgroup. Both phylogenetic and chromosomal localization analyses of TtPFCPs supported the hypothesis that TtPFCPs likely evolved through tandem gene duplication events and predominantly accumulated on micronuclear chromosome 5. Additionally, more than half of the identified TtPFCP genes are expressed in considerably low quantities compared to the rest of the TtPFCP genes, which are expressed at a higher level. However, their expression patterns fluctuate based on the stage of the life cycle. In conclusion, this study provides the first comprehensive <em>in-silico</em> analysis of TtPFCP genes and encoded proteases. The results would help designing an effective strategy for protease knockout mutant cell lines to discover biological function and to improve the recombinant protein production in <em>T. thermophila</em>.</p></div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135516519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ludmila V. Chistyakova , Alexei Yu. Kostygov , Andrew V. Goodkov , Anton V. Radaev , Alexander O. Frolov
{"title":"Phylogenetic position of the pelobiont Mastigamoeba aspera and revision of the family Mastigamoebidae (Archamoebae, Pelobiontida)","authors":"Ludmila V. Chistyakova , Alexei Yu. Kostygov , Andrew V. Goodkov , Anton V. Radaev , Alexander O. Frolov","doi":"10.1016/j.ejop.2023.126029","DOIUrl":"10.1016/j.ejop.2023.126029","url":null,"abstract":"<div><p><span>In this study, we presented the results of our molecular phylogenetic analysis<span> of Archamoebae<span> using a newly obtained sequence of the 18S rRNA gene of </span></span></span><em>Mastigamoeba aspera</em><span>, the type species of the genus. In addition, we characterized the general organization of the tubulin cytoskeleton of </span><em>M. aspera</em> by immunofluorescent microscopy and TEM. Our findings allowed us to revise the family Mastigamoebidae and establish within it two subfamilies: Mastigamoebinae for the genus <em>Mastigamoeba</em> and Seraviniinae subfam. nov. for the genera <em>Seravinia</em> gen. nov., <em>Paramastigamoeba</em> gen. nov., <em>Iodamoeba</em> and <span><em>Endolimax</em></span>. The type genera <em>Mastigamoeba</em> and <em>Seravinia</em> are clearly distinguished by the structure of the basal apparatus of flagella. In addition, the tubulin cytoskeleton of several <em>Mastigamoeba</em> spp. contains a rim of microtubules around the nuclei.</p></div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71421930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Re-isolation and revaluation of boundaries of Thecamoeba terricola Greeff, 1886 (Amoebozoa, Discosea, Thecamoebida), with description of Thecamoeba vicaria n. sp.","authors":"Yelisei Mesentsev , Alina Surkova , Oksana Kamyshatskaya , Elena Nassonova , Alexey Smirnov","doi":"10.1016/j.ejop.2023.126030","DOIUrl":"10.1016/j.ejop.2023.126030","url":null,"abstract":"<div><p>We studied a large species of <em>Thecamoeba</em> found in a glass dish with soaked moss and obtained 18s rRNA gene sequence of this organism. Morphologically, the strain was most similar to <em>T. terricola</em> sensu Page, but had significant differences in cell size and nuclear morphology. A more complete similarity was found with the original description of “<span><em>Amoeba</em><em> terricola”</em></span> by Greeff, as well as with Penard’s descriptions and slides. The analysis of literature data shows that the strain described by Page in 1977 as a re-isolated <em>T. terricola</em> differs from the original description of this species provided by Greeff in 1866 and data by Penard published in 1902 and 1913. Based on our observations as well as on Greeff’s and Penard’s data, we reassessed the species boundaries of <em>T. terricola</em> and established <em>T. vicaria</em> n. sp. for the organism described by Page in 1977. The species <em>T. terricola</em> was defined according to its original description. The observations of amoebae on agar have shown that <em>T. terricola</em> cells can form the “standing amoeba” stage, previously described only for <span><em>Sappinia</em><em> pedata</em></span>. This and some other “behaviour” features of <em>T. terricola</em> may be associated with living conditions in terrestrial habitats.</p></div>","PeriodicalId":12042,"journal":{"name":"European journal of protistology","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71479727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}