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Schiwitza S, Thomsen HA, Leadbeater BSC. Morphological and molecular reinvestigation of acanthoecid species III. - Kalathoeca cupula (Leadbeater, 1972) gen. et comb. nov. (=Stephanoeca cupula (Leadbeater) Thomsen, 1988). Eur J Protistol 2023; 87:125943. [PMID: 36610374 DOI: 10.1016/j.ejop.2022.125943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/10/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Abstract
Based on a further re-examination of loricate choanoflagellate species with detailed morphological (SEM/TEM) and molecular data of the SSU and LSU rRNA, the present study aims to give new insights for Stephanoeca cupula. In contrast to the original allocation within the family of tectiform reproducing species, morphological and molecular data of S. cupula sensu Leadbeater, 1972 points towards an affiliation within the nudiform reproducing family. Based on these new data, we here erect the nudiform genus Kalathoeca with its type species K. cupula gen. et comb. nov. Our data challenges morphological species assignments, as K. cupula shares its morphological lorica characteristics with tectiform reproducing species of Stephanoeca sensu stricto. Kalathoeca cupula is an interesting candidate for further investigating and understanding the evolutionary relationship of tectiform and nudiform reproducing species. Stephanoeca cupula sensu Thomsen, 1988 has been morphologically re-examined based on the renewed understanding of the morphological variability associated with S. cupula sensu Leadbeater, 1972 (=K. cupula), allowing us now to distribute the different morphological forms investigated within K. cupula and Pseudostephanoeca quasicupula.
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Affiliation(s)
- Sabine Schiwitza
- University of Cologne, Cologne Biocenter, Institute of Zoology, General Ecology, Zuelpicher Str. 47b, D-50674 Cologne, Germany.
| | - Helge A Thomsen
- Technical University of Denmark, National Institute of Aquatic Resources (DTU Aqua), Kemitorvet, Bygning 201, DK 2800 Kgs Lyngby, Denmark.
| | - Barry S C Leadbeater
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Leadbeater BSC, Carr M. Significance of the Nudiform and Tectiform Modes of Silica Deposition, Lorica Assembly and Cell Division in Choanoflagellates as Exemplified by Stephanoeca diplocostata and Enibas spp. Protist 2022; 173:125923. [PMID: 36370514 DOI: 10.1016/j.protis.2022.125923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
Abstract
The deposition of silicified costal strips and lorica assembly in choanoflagellates is precisely linked to the cell cycle. A minority of species undergo nudiform division whereby a loricate cell divides to produce a naked daughter cell that deposits a set of costal strips and then assembles a lorica. Most species undergo tectiform division whereby a parent loricate cell produces a set of costal strips, divides and passes on the stored strips to a daughter cell that immediately assembles a lorica. Many phylogenetic analyses recover nudiform and tectiform species as sister-clades giving the impression that they are distinct evolutionary lineages. However, the tectiform species Stephanoeca diplocostata is capable of undergoing nudiform division and depositing costal strips and assembling a lorica with certain modifications in a nudiform manner. The recent discovery of a new genus, Enibas, comprising species with Stephanoeca-like loricae that undergo nudiform cell division and on phylogenetic analysis occur as a sister group to other nudiform species has drawn attention to whether there are also unique features in lorica construction. A range of Enibas loricae is illustrated and it appears that there are unique features which might be interpreted as being derived from a Stephanoeca-like ancestor.
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Affiliation(s)
- Barry S C Leadbeater
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.
| | - Martin Carr
- Department of Biological & Geographical Sciences, University of Huddersfield, Queensgate, Huddersfield, West Yorkshire HD1 3DH, United Kingdom
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Carr M, Leadbeater BSC. Re-evaluating Loricate Choanoflagellate Phylogenetics: Molecular Evidence Points to the Paraphyly of Tectiform Species. Protist 2022; 173:125924. [PMID: 36327744 DOI: 10.1016/j.protis.2022.125924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/16/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Lorica-bearing choanoflagellates belong to the order Acanthoecida, a taxon which has been consistently recovered as monophyletic in molecular phylogenies. Based upon differences in lorica development and morphology, as well as the presence or absence of a motile dispersal stage, species are labelled as either nudiform or tectiform. Whilst Acanthoecida is robustly resolved in molecular phylogenies, the placement of the root of the clade is less certain with two different positions identified in past studies. One recovered root has been placed between the nudiform family Acanthoecidae and the tectiform family Stephanoecidae. An alternative root placement falls within the tectiform species, recovering the monophyletic Acanthoecidae nested within a paraphyletic Stephanoecidae. Presented here is a 14-gene phylogeny, based upon nucleotide and amino acid sequences, which strongly supports tectiform paraphyly. The horizontal transfer of a ribosomal protein gene, from a possible SAR donor, into a subset of acanthoecid species provides further, independent, support for this root placement. Differing patterns of codon usage bias across the choanoflagellates are proposed as the cause of artefactual phylogenetic signals that lead to the recovery of tectiform monophyly.
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Affiliation(s)
- Martin Carr
- Department of Biological & Geographical Sciences, University of Huddersfield, Queensgate, Huddersfield, West Yorkshire HD1 3DH, United Kingdom.
| | - Barry S C Leadbeater
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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Morphological and molecular reinvestigation of acanthoecid species II. – Pseudostephanoeca paucicostata (Tong et al., 1998) gen. et comb. nov. (= Stephanoeca diplocostata var. paucicostata Throndsen, 1969) including also the description of Pseudostephanoeca quasicupula sp. nov. and Stephanoeca ellisfiordensis sp. nov. Eur J Protistol 2022; 86:125919. [DOI: 10.1016/j.ejop.2022.125919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/23/2022] [Accepted: 08/27/2022] [Indexed: 11/23/2022]
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Junqueira Alves C, Silva Ladeira J, Hannah T, Pedroso Dias RJ, Zabala Capriles PV, Yotoko K, Zou H, Friedel RH. Evolution and Diversity of Semaphorins and Plexins in Choanoflagellates. Genome Biol Evol 2021; 13:6149127. [PMID: 33624753 PMCID: PMC8011033 DOI: 10.1093/gbe/evab035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2021] [Indexed: 12/22/2022] Open
Abstract
Semaphorins and plexins are cell surface ligand/receptor proteins that affect cytoskeletal dynamics in metazoan cells. Interestingly, they are also present in Choanoflagellata, a class of unicellular heterotrophic flagellates that forms the phylogenetic sister group to Metazoa. Several members of choanoflagellates are capable of forming transient colonies, whereas others reside solitary inside exoskeletons; their molecular diversity is only beginning to emerge. Here, we surveyed genomics data from 22 choanoflagellate species and detected semaphorin/plexin pairs in 16 species. Choanoflagellate semaphorins (Sema-FN1) contain several domain features distinct from metazoan semaphorins, including an N-terminal Reeler domain that may facilitate dimer stabilization, an array of fibronectin type III domains, a variable serine/threonine-rich domain that is a potential site for O-linked glycosylation, and a SEA domain that can undergo autoproteolysis. In contrast, choanoflagellate plexins (Plexin-1) harbor a domain arrangement that is largely identical to metazoan plexins. Both Sema-FN1 and Plexin-1 also contain a short homologous motif near the C-terminus, likely associated with a shared function. Three-dimensional molecular models revealed a highly conserved structural architecture of choanoflagellate Plexin-1 as compared to metazoan plexins, including similar predicted conformational changes in a segment that is involved in the activation of the intracellular Ras-GAP domain. The absence of semaphorins and plexins in several choanoflagellate species did not appear to correlate with unicellular versus colonial lifestyle or ecological factors such as fresh versus salt water environment. Together, our findings support a conserved mechanism of semaphorin/plexin proteins in regulating cytoskeletal dynamics in unicellular and multicellular organisms.
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Affiliation(s)
- Chrystian Junqueira Alves
- Friedman Brain Institute, Nash Family Department of Neuroscience and Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Júlia Silva Ladeira
- Programa de Pós-graduação em Modelagem Computacional, Universidade Federal de Juiz de Fora, Minas Gerais, Brazil
| | - Theodore Hannah
- Friedman Brain Institute, Nash Family Department of Neuroscience and Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Roberto J Pedroso Dias
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Minas Gerais, Brazil
| | - Priscila V Zabala Capriles
- Programa de Pós-graduação em Modelagem Computacional, Universidade Federal de Juiz de Fora, Minas Gerais, Brazil
| | - Karla Yotoko
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - Hongyan Zou
- Friedman Brain Institute, Nash Family Department of Neuroscience and Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Roland H Friedel
- Friedman Brain Institute, Nash Family Department of Neuroscience and Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
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Schiwitza S, Nitsche F. A Needle in the Haystack – Mapping Sequences to Morphology Exemplified by the Loricate Choanoflagellate Enibas thessalia sp. nov. (Acanthoecida, Acanthoecidae). Protist 2021; 172:125782. [DOI: 10.1016/j.protis.2020.125782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/16/2020] [Accepted: 11/22/2020] [Indexed: 01/28/2023]
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Thomsen HA, Østergaard JB. Loricate choanoflagellates (Acanthoecida) from warm water seas. III. Acanthocorbis Hara and Takahashi and Stephanoeca Ellis. Eur J Protistol 2019; 69:52-69. [DOI: 10.1016/j.ejop.2019.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/29/2019] [Accepted: 02/04/2019] [Indexed: 11/25/2022]
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First description of an euryoecious acanthoecid choanoflagellate species, Enibas tolerabilis gen. et sp. nov. from a salar in the Chilean Andes based on morphological and transcriptomic data. Eur J Protistol 2019; 67:106-113. [DOI: 10.1016/j.ejop.2018.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/16/2018] [Accepted: 11/26/2018] [Indexed: 01/13/2023]
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Schiwitza S, Arndt H, Nitsche F. Four new choanoflagellate species from extreme saline environments: Indication for isolation-driven speciation exemplified by highly adapted Craspedida from salt flats in the Atacama Desert (Northern Chile). Eur J Protistol 2018; 66:86-96. [DOI: 10.1016/j.ejop.2018.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 10/28/2022]
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Arroyo AS, López-Escardó D, Kim E, Ruiz-Trillo I, Najle SR. Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00099] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Venter PC, Nitsche F, Arndt H. The Hidden Diversity of Flagellated Protists in Soil. Protist 2018; 169:432-449. [PMID: 29870898 DOI: 10.1016/j.protis.2018.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 11/18/2022]
Abstract
Protists are among the most diverse and abundant eukaryotes in soil. However, gaps between described and sequenced protist morphospecies still present a pending problem when surveying environmental samples for known species using molecular methods. The number of sequences in the molecular PR2 database (∼130,000) is limited compared to the species richness expected (>1 million protist species) - limiting the recovery rate. This is important, since high throughput sequencing (HTS) methods are used to find associative patterns between functional traits, taxa and environmental parameters. We performed HTS to survey soil flagellates in 150 grasslands of central Europe, and tested the recovery rate of ten previously isolated and cultivated cercomonad species, among locally found diversity. We recovered sequences for reference soil flagellate species, but also a great number of their phylogenetically evaluated genetic variants, among rare and dominant taxa with presumably own biogeography. This was recorded among dominant (cercozoans, Sandona), rare (apusozoans) and a large hidden diversity of predominantly aquatic protists in soil (choanoflagellates, bicosoecids) often forming novel clades associated with uncultured environmental sequences. Evaluating the reads, instead of the OTUs that individual reads are usually clustered into, we discovered that much of this hidden diversity may be lost due to clustering.
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Affiliation(s)
- Paul Christiaan Venter
- University of Cologne, Cologne Biocenter, Institute of Zoology, Department of General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany
| | - Frank Nitsche
- University of Cologne, Cologne Biocenter, Institute of Zoology, Department of General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany
| | - Hartmut Arndt
- University of Cologne, Cologne Biocenter, Institute of Zoology, Department of General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany.
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Circumstantial evidence of life history events in loricate choanoflagellates. Eur J Protistol 2017; 58:26-34. [DOI: 10.1016/j.ejop.2016.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/30/2016] [Accepted: 12/20/2016] [Indexed: 11/19/2022]
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Bridging the gap between morphological species and molecular barcodes – Exemplified by loricate choanoflagellates. Eur J Protistol 2017; 57:26-37. [DOI: 10.1016/j.ejop.2016.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/07/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
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A six-gene phylogeny provides new insights into choanoflagellate evolution. Mol Phylogenet Evol 2017; 107:166-178. [DOI: 10.1016/j.ympev.2016.10.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 12/17/2022]
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A phylogenetic and morphological re-investigation of Diaphanoeca spiralifurca, Didymoeca elongata and Polyoeca dichotoma (Acanthoecida/Choanomonadida) from the Caribbean Sea. Eur J Protistol 2016; 52:58-64. [DOI: 10.1016/j.ejop.2015.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/21/2015] [Accepted: 11/02/2015] [Indexed: 11/21/2022]
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Extended phylogeny of the Craspedida (Choanomonada). Eur J Protistol 2014; 50:430-43. [DOI: 10.1016/j.ejop.2014.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/13/2014] [Accepted: 06/19/2014] [Indexed: 11/17/2022]
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