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Martin Carr - One of the best experts on this subject based on the ideXlab platform.
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A genomic survey of transposable elements in the Choanoflagellate Salpingoeca rosetta reveals selection on codon usage
Mobile Dna, 2019Co-Authors: Jade Southworth, Alan O. Marron, C. Alastair Grace, Nazeefa Fatima, Martin CarrAbstract:Unicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The Choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the Choanoflagellate Monosiga brevicollis revealed the presence of only three families of LTR retrotransposons, all of which appeared to be active. Salpingoeca rosetta is the second Choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans. Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the Choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage. S. rosetta increases the known diversity of Choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in Choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.
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A genomic survey of transposable elements in the Choanoflagellate Salpingoeca rosetta reveals selection on codon usage
Mobile DNA, 2019Co-Authors: Jade Southworth, Alan O. Marron, C. Alastair Grace, Nazeefa Fatima, Martin CarrAbstract:Background Unicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The Choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the Choanoflagellate Monosiga brevicollis revealed the presence of only three families of LTR retrotransposons, all of which appeared to be active. Salpingoeca rosetta is the second Choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans. Results Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the Choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage. Conclusions S. rosetta increases the known diversity of Choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in Choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.
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A six-gene phylogeny provides new insights into Choanoflagellate evolution
Molecular Phylogenetics and Evolution, 2017Co-Authors: Martin Carr, Barry S C Leadbeater, Daniel J Richter, Parinaz Fozouni, Timothy J. Smith, Alexandra Jeuck, Frank NitscheAbstract:Recent studies have shown that molecular phylogenies of the Choanoflagellates (Class Choanoflagellatea) are in disagreement with their traditional taxonomy, based on morphology, and that Choanoflagellatea requires considerable taxonomic revision. Furthermore, phylogenies suggest that the morphological and ecological evolution of the group is more complex than has previously been recognized. Here we address the taxonomy of the major Choanoflagellate order Craspedida, by erecting four new genera. The new genera are shown to be morphologically, ecologically and phylogenetically distinct from other Choanoflagellate taxa. Furthermore, we name five novel craspedid species, as well as formally describe ten species that have been shown to be either misidentified or require taxonomic revision. Our revised phylogeny, including 18 new species and sequence data for two additional genes, provides insights into the morphological and ecological evolution of the Choanoflagellates. We examine the distribution within Choanoflagellates of these two additional genes, EF-1A and EFL, closely related translation GTPases which are required for protein synthesis. Mapping the presence and absence of these genes onto the phylogeny highlights multiple events of gene loss within the Choanoflagellates.
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three families of ltr retrotransposons are present in the genome of the Choanoflagellate monosiga brevicollis
Protist, 2008Co-Authors: Martin Carr, Michaela Nelson, Barry S C Leadbeater, Sandra L BaldaufAbstract:The Choanoflagellates are a ubiquitous group of nanoflagellates and the sister group of Metazoa. Examination of the initial draft version of the first Choanoflagellate genome, that of Monosiga brevicollis, reveals the presence of three novel families of long terminal repeat (LTR) retrotransposons and an apparent absence of non-LTR retrotransposons and transposons. One of the newly discovered LTR families falls in the chromovirus clade of the Ty3/gypsy group while the other two families are closely related members of the Ty1/copia group. Examination of EST sequences and nucleotide analyses show that all three families are transcriptionally active and potentially functional within the genome of M. brevicollis.
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Molecular phylogeny of Choanoflagellates, the sister group to Metazoa
Proceedings of the National Academy of Sciences of the United States of America, 2008Co-Authors: Martin Carr, Michaela Nelson, Barry S C Leadbeater, Ruhana Hassan, Sandra L BaldaufAbstract:Choanoflagellates are single-celled aquatic flagellates with a unique morphology consisting of a cell with a single flagellum surrounded by a "collar" of microvilli. They have long interested evolutionary biologists because of their striking resemblance to the collared cells (choanocytes) of sponges. Molecular phylogeny has confirmed a close relationship between Choanoflagellates and Metazoa, and the first Choanoflagellate genome sequence has recently been published. However, molecular phylogenetic studies within Choanoflagellates are still extremely limited. Thus, little is known about Choanoflagellate evolution or the exact nature of the relationship between Choanoflagellates and Metazoa. We have sequenced four genes from a broad sampling of the morphological diversity of Choanoflagellates including most species currently available in culture. Phylogenetic analyses of these sequences, alone and in combination, reject much of the traditional taxonomy of the group. The molecular data also strongly support Choanoflagellate monophyly rejecting proposals that Metazoa were derived from a true Choanoflagellate ancestor. Mapping of a complementary matrix of morphological and ecological traits onto the phylogeny allows a reinterpretation of Choanoflagellate character evolution and predicts the nature of their last common ancestor.
Alan O. Marron - One of the best experts on this subject based on the ideXlab platform.
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Technical note: The silicon isotopic composition of Choanoflagellates: implications for a mechanistic understanding of isotopic fractionation during biosilicification
Biogeosciences, 2019Co-Authors: Alan O. Marron, Lucie Cassarino, Paul Curnow, Jade E. Hatton, Katharine R. HendryAbstract:Abstract. The marine silicon cycle is intrinsically linked with carbon cycling in the oceans via biological production of silica by a wide range of organisms. The stable silicon isotopic composition (denoted by δ30Si ) of siliceous microfossils extracted from sediment cores can be used as an archive of past oceanic silicon cycling. However, the silicon isotopic composition of biogenic silica has only been measured in diatoms, sponges and radiolarians, and isotopic fractionation relative to seawater is entirely unknown for many other silicifiers. Furthermore, the biochemical pathways and mechanisms that determine isotopic fractionation during biosilicification remain poorly understood. Here, we present the first measurements of the silicon isotopic fractionation during biosilicification by loricate Choanoflagellates, a group of protists closely related to animals. We cultured two species of Choanoflagellates, Diaphanoeca grandis and Stephanoeca diplocostata, which showed consistently greater isotopic fractionation (approximately −5 ‰ to −7 ‰) than cultured diatoms ( −0.5 ‰ to −2.1 ‰). Instead, Choanoflagellate silicon isotopic fractionation appears to be more similar to sponges grown under similar dissolved silica concentrations. Our results highlight that there is a taxonomic component to silicon isotope fractionation during biosilicification, possibly via a shared or related biochemical transport pathway. These findings have implications for the use of biogenic silica δ30Si produced by different silicifiers as proxies for past oceanic change.
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A genomic survey of transposable elements in the Choanoflagellate Salpingoeca rosetta reveals selection on codon usage
Mobile DNA, 2019Co-Authors: Jade Southworth, Alan O. Marron, C. Alastair Grace, Nazeefa Fatima, Martin CarrAbstract:Background Unicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The Choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the Choanoflagellate Monosiga brevicollis revealed the presence of only three families of LTR retrotransposons, all of which appeared to be active. Salpingoeca rosetta is the second Choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans. Results Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the Choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage. Conclusions S. rosetta increases the known diversity of Choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in Choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.
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A genomic survey of transposable elements in the Choanoflagellate Salpingoeca rosetta reveals selection on codon usage
Mobile Dna, 2019Co-Authors: Jade Southworth, Alan O. Marron, C. Alastair Grace, Nazeefa Fatima, Martin CarrAbstract:Unicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The Choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the Choanoflagellate Monosiga brevicollis revealed the presence of only three families of LTR retrotransposons, all of which appeared to be active. Salpingoeca rosetta is the second Choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans. Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the Choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage. S. rosetta increases the known diversity of Choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in Choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.
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Aerotaxis in the closest relatives of animals
eLife, 2016Co-Authors: Julius B. Kirkegaard, Alan O. Marron, Ambre Bouillant, Kyriacos C. Leptos, Raymond E. GoldsteinAbstract:Most animals are made up of millions of cells, yet all animals evolved from ancestors that spent their whole lives as single cells. Today the closest single-celled relatives of animals are a group of aquatic organisms called Choanoflagellates. Certain species of Choanoflagellates can also form swimming colonies. This kind of multicellularity might resemble that seen in the earliest of animals. As such, studies into modern-day Choanoflagellates can give insights into how the first animals to evolve might have behaved. Many organisms can find their way towards favorable areas using different strategies. For instance, bacteria can bias their tumbling to gradually swim towards food, and algae can turn and move directly towards light. While Choanoflagellates require oxygen, it was not known if they could also actively navigate towards it, or any other resource. Now, Kirkegaard et al. find that the Choanoflagellate Salpingoeca rosetta can indeed navigate towards oxygen – an ability called aerotaxis. This was true for both individual cells and for colonies made up of many cells. This discovery suggests that the transition from living as a single cell to living as a simple multicellular organism could still have allowed the earliest animals to seek out and move towards resource-rich areas. Aerotaxis requires cells to both sense oxygen and react appropriately to changes in its concentration. Kirkegaard et al. watched Choanoflagellate colonies swimming under controlled conditions and varied the oxygen concentration in the water over time. These experiments revealed that the colonies navigate based on the logarithm of the oxygen concentration, so that at low oxygen levels the cells were even more sensitive to small changes in oxygen concentration. This type of ‘logarithmic sensing’ is similar to how our ears sense sounds and our eyes sense light. Kirkegaard et al. went on to conclude that the colonies were not actively steering in the correct direction directly. Instead, the colonies appeared to choose directions at random and later decide whether such a turn was correct. It remains unclear whether the common ancestor of animals and Choanoflagellates could also perform aerotaxis, and if so what mechanisms this involved. Further studies to compare aerotaxis and aerotaxis-related genes in simple animals and other single-celled relatives of animals would be needed to illuminate this. Future studies could also explore the maximum and minimum oxygen concentrations that Choanoflagellates can detect, and how well they navigate at these upper and lower limits.
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A Duplex PCR-Based Assay for Measuring the Amount of Bacterial Contamination in a Nucleic Acid Extract from a Culture of Free-Living Protists
2016Co-Authors: Alan O. Marron, Michael Akam, Giselle WalkerAbstract:Background: Cultures of heterotrophic protists often require co-culturing with bacteria to act as a source of nutrition. Such cultures will contain varying levels of intrinsic bacterial contamination that can interfere with molecular research and cause problems with the collection of sufficient material for sequencing. Measuring the levels of bacterial contamination for the purposes of molecular biology research is non-trivial, and can be complicated by the presence of a diverse bacterial flora, or by differences in the relative nucleic acid yield per bacterial or eukaryotic cell. Principal Findings: Here we describe a duplex PCR-based assay that can be used to measure the levels of contamination from marine bacteria in a culture of loricate Choanoflagellates. By comparison to a standard culture of known target sequence content, the assay can be used to quantify the relative proportions of bacterial and Choanoflagellate material in DNA or RNA samples extracted from a culture. We apply the assay to compare methods of purifying Choanoflagellate cultures prior to DNA extraction, to determine their effectiveness in reducing bacterial contamination. Together with measurements of the total nucleic acid concentration, the assay can then be used as the basis for determining the absolute amounts of Choanoflagellate DNA or RNA present in a sample. Conclusions: The assay protocol we describe here is a simple and relatively inexpensive method of measuring contamination levels in nucleic acid samples. This provides a new way to establish quantification and purification protocol
Nicole King - One of the best experts on this subject based on the ideXlab platform.
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Colonial Choanoflagellate isolated from Mono Lake harbors a microbiome
2021Co-Authors: K. Hake, Pawel Burkhardt, Davis Laundon, Kent L. Mcdonald, P. T. West, C. Feng, D. J. Richter, Jillian F. Banfield, Nicole KingAbstract:Choanoflagellates offer key insights into bacterial influences on the origin and early evolution of animals. Here we report the isolation and characterization of a new colonial Choanoflagellate species, Salpingoeca monosierra, that, unlike previously characterized species, harbors a stable microbiome. S. monosierra was isolated from Mono Lake, California and forms large spherical colonies that are more than an order of magnitude larger than those formed by the closely related S. rosetta. By designing fluorescence in situ hybridization probes from metagenomic sequences, we found that S. monosierra colonies are colonized by members of the halotolerant and closely related Saccharospirillaceae and Oceanospirillaceae, as well as purple sulfur bacteria (Ectothiorhodospiraceae) and non-sulfur Rhodobacteraceae. This relatively simple microbiome in a close relative of animals presents a new experimental model for investigating the evolution of stable interactions among eukaryotes and bacteria. IMPORTANCEThe animals and bacteria of Mono Lake (California) have evolved diverse strategies for surviving the hypersaline, alkaline, arsenic-rich environment. We sought to investigate whether the closest living relatives of animals, the Choanoflagellates, exist among the relatively limited diversity of organisms in Mono Lake. We repeatedly isolated members of a single species of Choanoflagellate, which we have named Salpingoeca monosierra, suggesting that it is a stable and abundant part of the ecosystem. Characterization of S. monosierra revealed that it forms large spherical colonies that each contain a microbiome, providing an opportunity to investigate the evolution of stable physical associations between eukaryotes and bacteria.
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a flagellate to amoeboid switch in the closest living relatives of animals
eLife, 2021Co-Authors: Nicole King, Thibaut Brunet, Marvin Albert, William Roman, Danielle C Spitzer, Maxwell C CoyleAbstract:Amoeboid cell types are fundamental to animal biology and broadly distributed across animal diversity, but their evolutionary origin is unclear. The closest living relatives of animals, the Choanoflagellates, display a polarized cell architecture (with an apical flagellum encircled by microvilli) that resembles that of epithelial cells and suggests homology, but this architecture differs strikingly from the deformable phenotype of animal amoeboid cells, which instead evoke more distantly related eukaryotes, such as diverse amoebae. Here, we show that Choanoflagellates subjected to confinement become amoeboid by retracting their flagella and activating myosin-based motility. This switch allows escape from confinement and is conserved across Choanoflagellate diversity. The conservation of the amoeboid cell phenotype across animals and Choanoflagellates, together with the conserved role of myosin, is consistent with homology of amoeboid motility in both lineages. We hypothesize that the differentiation between animal epithelial and crawling cells might have evolved from a stress-induced switch between flagellate and amoeboid forms in their single-celled ancestors.
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a flagellate to amoeboid switch in the closest living relatives of animals
bioRxiv, 2020Co-Authors: Nicole King, Thibaut Brunet, Marvin Albert, William Roman, Danielle C SpitzerAbstract:The evolution of different cell types was a key process of early animal evolution1-3. Two fundamental cell types, epithelial cells and amoeboid cells, are broadly distributed across the animal tree of life4,5 but their origin and early evolution are unclear. Epithelial cells are polarized, have a fixed shape and often bear an apical cilium and microvilli. These features are shared with Choanoflagellates - the closest living relatives of animals - and are thought to have been inherited from their last common ancestor with animals1,6,7. The deformable amoeboid cells of animals, on the other hand, seem strikingly different from Choanoflagellates and instead evoke more distantly related eukaryotes, such as diverse amoebae - but it has been unclear whether that similarity reflects common ancestry or convergence8. Here, we show that Choanoflagellates subjected to spatial confinement differentiate into an amoeboid phenotype by retracting their flagella and microvilli, generating blebs, and activating myosin-based motility. Choanoflagellate cell crawling is polarized by geometrical features of the substrate and allows escape from confined microenvironments. The confinement-induced amoeboid switch is conserved across diverse Choanoflagellate species and greatly expands the known phenotypic repertoire of Choanoflagellates. The broad phylogenetic distribution of the amoeboid cell phenotype across animals9-14 and Choanoflagellates, as well as the conserved role of myosin, suggests that myosin-mediated amoeboid motility was present in the life history of their last common ancestor. Thus, the duality between animal epithelial and crawling cells might have evolved from a temporal phenotypic switch between flagellate and amoeboid forms in their single-celled ancestors3,15,16.
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3D cellular architecture of Choanoflagellates and collar cells across the Choanozoa.
2019Co-Authors: Davis Laundon, Nicole King, Ben T. Larson, Kent Mcdonald, Pawel BurkhardtAbstract:(A) Phylogenetic distribution of collar cells across the Choanozoa (Choanoflagellata + Metazoa [1,5]) showing the presence (black circle), absence (white circle), and putative losses (brown cross) of collar cells across lineages. The origin of collar cells is marked by the orange circle. Adapted from [1]. *Some lineages within the Bilateria have secondarily lost collar cells. (B) The Choanoflagellate S. rosetta exhibits a complex life cycle, transitioning through both single and colonial collar cell types. The development of rosette colonies can be induced by RIF. Choanoflagellate colonies form through cytokinesis. (C–D) Characterisation of major organelles in S. rosetta labelled with fluorescent vital dyes (C) and by immunofluorescence (D). Arrowhead indicates nucleus of Choanoflagellates cell; asterisks indicate the stained nucleoids of engulfed prey bacteria. Scale bar = 1 μm. (E–L) 3D ssTEM reconstruction of three single (S1–3) and three colonial (C1–3) S. rosetta cells (E, F). The association of the three colonial cells in context with each other are shown in the white box. The plasma membrane was made transparent (G, J), and glycogen and ER were removed to allow better visualisation of subcellular structures (H, K) and vesicle populations (I, L). Shown are apical vesicles (pink), food vacuoles (green), endocytotic vacuoles (fuschia), ER (yellow), extracellular vesicles (grey), filopodia (external, purple), flagellar basal body (light blue), flagellum (dark green), glycogen storage (white), Golgi apparatus and vesicles (purple), intercellular bridges (external, yellow; septa, red), large vesicles (brown), microvillar collar (light orange), mitochondria (red), nonflagellar basal body (dark orange), and nuclei (dark blue). Scale bar = approximately 1 μm (depending on position of structure along the z-axis). ER, endoplasmic reticulum; RIF, rosette-inducing factor; ssTEM, serial ultrathin transmission electron microscopy.
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The architecture of cell differentiation in Choanoflagellates and sponge choanocytes
bioRxiv, 2018Co-Authors: Davis Laundon, Nicole King, Kent L. Mcdonald, Ben T. Larson, Pawel BurkhardtAbstract:Collar cells are ancient animal cell types which are conserved across the animal kingdom and their closest relatives, the Choanoflagellates. However, little is known about their ancestry, their subcellular architecture, or how they differentiate. The Choanoflagellate Salpingoeca rosetta expresses genes necessary for animal multicellularity and development and can alternate between unicellular and multicellular states making it a powerful model to investigate the origin of animal multicellularity and mechanisms underlying cell differentiation. To compare the subcellular architecture of solitary collar cells in S. rosetta with that of multicellular 9rosettes9 and collar cells in sponges, we reconstructed entire cells in 3D through transmission electron microscopy on serial ultrathin sections. Structural analysis of our 3D reconstructions revealed important differences between single and colonial Choanoflagellate cells, with colonial cells exhibiting a more amoeboid morphology consistent with relatively high levels of macropinocytotic activity. Comparison of multiple reconstructed rosette colonies highlighted the variable nature of cell sizes, cell-cell contact networks and colony arrangement. Importantly, we uncovered the presence of elongated cells in some rosette colonies that likely represent a distinct and differentiated cell type. Intercellular bridges within Choanoflagellate colonies displayed a variety of morphologies and connected some, but not all, neighbouring cells. Reconstruction of sponge choanocytes revealed both ultrastructural commonalities and differences in comparison to Choanoflagellates. Choanocytes and colonial Choanoflagellates are typified by high amoeboid cell activity. In both, the number of microvilli and volumetric proportion of the Golgi apparatus are comparable, whereas choanocytes devote less of their cell volume to the nucleus and mitochondria than Choanoflagellates and more of their volume to food vacuoles. Together, our comparative reconstructions uncover the architecture of cell differentiation in Choanoflagellates and sponge choanocytes and constitute an important step in reconstructing the cell biology of the last common ancestor of the animal kingdom.
Katharine R. Hendry - One of the best experts on this subject based on the ideXlab platform.
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Technical note: The silicon isotopic composition of Choanoflagellates: implications for a mechanistic understanding of isotopic fractionation during biosilicification
Biogeosciences, 2019Co-Authors: Alan O. Marron, Lucie Cassarino, Paul Curnow, Jade E. Hatton, Katharine R. HendryAbstract:Abstract. The marine silicon cycle is intrinsically linked with carbon cycling in the oceans via biological production of silica by a wide range of organisms. The stable silicon isotopic composition (denoted by δ30Si ) of siliceous microfossils extracted from sediment cores can be used as an archive of past oceanic silicon cycling. However, the silicon isotopic composition of biogenic silica has only been measured in diatoms, sponges and radiolarians, and isotopic fractionation relative to seawater is entirely unknown for many other silicifiers. Furthermore, the biochemical pathways and mechanisms that determine isotopic fractionation during biosilicification remain poorly understood. Here, we present the first measurements of the silicon isotopic fractionation during biosilicification by loricate Choanoflagellates, a group of protists closely related to animals. We cultured two species of Choanoflagellates, Diaphanoeca grandis and Stephanoeca diplocostata, which showed consistently greater isotopic fractionation (approximately −5 ‰ to −7 ‰) than cultured diatoms ( −0.5 ‰ to −2.1 ‰). Instead, Choanoflagellate silicon isotopic fractionation appears to be more similar to sponges grown under similar dissolved silica concentrations. Our results highlight that there is a taxonomic component to silicon isotope fractionation during biosilicification, possibly via a shared or related biochemical transport pathway. These findings have implications for the use of biogenic silica δ30Si produced by different silicifiers as proxies for past oceanic change.
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The silicon isotopic composition of Choanoflagellates: implications for a mechanistic understanding of isotopic fractionation during biosilicification
2019Co-Authors: Alan Marron, Lucie Cassarino, Jade Hatton, Paul Curnow, Katharine R. HendryAbstract:Abstract. The marine silicon cycle is intrinsically linked with carbon cycling in the oceans via biological production of silica by a wide range of organisms. The stable silicon isotopic composition (denoted by δ30Si) of siliceous microfossils extracted from sediment cores can be used as an archive of past oceanic silicon cycling. However, the silicon isotopic composition of biogenic silica has only been measured in diatoms, sponges and radiolarians, and isotopic fractionation relative to seawater is entirely unknown for many other silicifiers. Furthermore, the biochemical pathways and mechanisms that determine isotopic fractionation during biosilicification remain poorly understood. Here, we present the first measurements of the silicon isotopic fractionation during biosilicification by loricate Choanoflagellates, a group of protists closely related to animals. We cultured two species of Choanoflagellates, Diaphanoeca grandis and Stephanoeca diplocostata, which showed consistently greater isotopic fractionation (approximately −5 to −7 ‰) than cultured diatoms (−0.5 to −2 ‰). Instead, Choanoflagellate silicon isotopic fractionation appears to be more similar to sponges grown under similar DSi concentrations. Our results highlight that there is a taxonomic component to silicon isotope fractionation during biosilicification, possibly via a shared or related biochemical transport pathway. These findings have implications for the use of biogenic silica δ30Si produced by different silicifiers as proxies for past oceanic change.
Frank Nitsche - One of the best experts on this subject based on the ideXlab platform.
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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).
European journal of protistology, 2018Co-Authors: Sabine Schiwitza, Hartmut Arndt, Frank NitscheAbstract:Abstract With this study we aim to extend the knowledge on the biogeography of craspedid Choanoflagellates with additional data from extreme environments. Up to now, very little is known about Choanoflagellates from extreme saline environments, as most studies have focused on marine and freshwater habitats. Though previously investigated high saline ice biota communities have indicated a possible adaptation to environments with high salt concentrations. Hypersaline endorheic basins, so-called salt flats or salares from the Atacama Desert in Northern Chile provide an intense environment regarding fluctuating and extreme salinities, which allow for studies on evolutionary adaptations of protists to hypersaline conditions. This study focused on Choanoflagellate species isolated from different salt flats, their morphological characteristics using light and electron microscopy, molecular marker genes (SSU and LSU rDNA) and their salinity tolerance. Here, we described four new craspedid Choanoflagellate species, highly adapted to the hypersaline environment of the Atacama Desert. This study extends our knowledge on Choanoflagellate phylogeny and ecology and can become the basis for further molecular studies to understand the mechanisms of adaptations. Additionally, we emphasize the need of adding additional data such as autecological characteristics to amend species definitions, which is only possible from cultivated strains. This data would support the use of molecular data originating from metagenomic analyses also in an ecological context.
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First Efficient Transfection in Choanoflagellates using Cell-Penetrating Peptides
2018Co-Authors: Ines Neundorf, Frank NitscheAbstract:Only recently, based on phylogenetic studies Choanoflagellates have been confirmed to form the sister group to metazoan. The mechanisms and genes behind the step from single to multicellular organisation and as a consequence the evolution of metazoan multicellularity could not be verified yet, as no reliable and efficient method for transfection of Choanoflagellates was available. Here we present cell-penetrating peptides (CPPs) as an alternative to conventional transfection methods. In a series of experiments with the Choanoflagellate Diaphanoeca grandis we proof for the first time that the use of CPPs is a reliable and highly efficient method for the transfection of Choanoflagellates. We were able to silence the silicon transporter gene (SIT) by siRNA, and hence, to suppress the lorica (characteristic siliceous basket) formation. High gene silencing efficiency was determined and measured by light microscope and RT-qPCR. In addition, only low cytotoxic effects of CPP were detected. Our new method allows the reliable and efficient transfection of Choanoflagellates, finally enabling us to verify the function of genes, thought to be involved in cell adhesion or cell signaling by silencing them via siRNA. This is a step stone for the research on the origin of multicellularity in metazoans.
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A six-gene phylogeny provides new insights into Choanoflagellate evolution
Molecular Phylogenetics and Evolution, 2017Co-Authors: Martin Carr, Barry S C Leadbeater, Daniel J Richter, Parinaz Fozouni, Timothy J. Smith, Alexandra Jeuck, Frank NitscheAbstract:Recent studies have shown that molecular phylogenies of the Choanoflagellates (Class Choanoflagellatea) are in disagreement with their traditional taxonomy, based on morphology, and that Choanoflagellatea requires considerable taxonomic revision. Furthermore, phylogenies suggest that the morphological and ecological evolution of the group is more complex than has previously been recognized. Here we address the taxonomy of the major Choanoflagellate order Craspedida, by erecting four new genera. The new genera are shown to be morphologically, ecologically and phylogenetically distinct from other Choanoflagellate taxa. Furthermore, we name five novel craspedid species, as well as formally describe ten species that have been shown to be either misidentified or require taxonomic revision. Our revised phylogeny, including 18 new species and sequence data for two additional genes, provides insights into the morphological and ecological evolution of the Choanoflagellates. We examine the distribution within Choanoflagellates of these two additional genes, EF-1A and EFL, closely related translation GTPases which are required for protein synthesis. Mapping the presence and absence of these genes onto the phylogeny highlights multiple events of gene loss within the Choanoflagellates.
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Comparison of Similar Arctic and Antarctic Morphotypes of Heterotrophic Protists Regarding their Genotypes and Ecotypes
Protist, 2014Co-Authors: Frank Nitsche, Hartmut ArndtAbstract:The polar regions offer the opportunity to study possible diversification processes of spatially and temporally separated populations. We focused our study on similar morphotypes/species (e. g. species with the same morphology) of heterotrophic flagellates and ciliates originating from both, Antarctic and Arctic waters: 38 populations of six Choanoflagellate morphospecies (Acanthocorbis unguiculata, Helgoeca nana, Diaphanoeca grandis, Savillea micropora, Stephanoeca apheles, Salpingoeca tuba), four other flagellate morphospecies (Cafeteria roenbergensis, Podomonas magma, Procryptobia sorokini, Protaspis sp.) and three ciliate morphospecies (Holosticha sp., Uronema marinum, Pseudocohnilembus persalinus). We analysed similarities and differences regarding their genotypes (SSU rDNA) and for several species regarding morphotypes and autecology (temperature and salinity tolerance). Most of the investigated polar protists were psychrophilic and showed a high salinity tolerance. Morphologically well defined acanthoecid Choanoflagellates isolated from both poles showed the lowest intraspecific diversity (< 0.5% p-distance). No intragenomic polymorphism of SSU rDNA within one individual and among clones from one population occurred. The way of dispersal for acanthoecid Choanoflagellates still remains unclear. Even under extreme stress none of the examined cultures formed cysts. Single cell PCR appeared to be an appropriate method to investigate species not available as monoclonal cultures. As a prerequisite for barcoding, acanthoecid Choanoflagellate species have a very low intraspecific variability regarding SSU rDNA. There was a clear correlation between autecological, morphological and molecular data sets, which may help interpreting molecular data from clone libraries or next generation sequencing.
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Cryptic diversity within the Choanoflagellate morphospecies complex Codosiga botrytis - phylogeny and morphology of ancient and modern isolates.
European journal of protistology, 2012Co-Authors: Daniel Stoupin, Hartmut Arndt, Áron Keve Kiss, A. V. Shatilovich, David Gilichinsky, Frank NitscheAbstract:Abstract Choanoflagellates are closely related to metazoans and fungi according to recent phylogenetic studies; therefore the systematics of these organisms is of particular interest. The Choanoflagellate morphospecies Codosiga botrytis is the first described Choanoflagellate, and is one of the most frequently reported Choanoflagellate species. In this study we present phylogenetic and morphological data on eight different strains of Codosiga botrytis . Among these there are five ancient strains; these cultures have been established from up to 43,000 years old cysts from Siberian permafrost. We found that based on the variable V4 region of the small subunit (SSU) of the rDNA, all the investigated freshwater isolates of Codosiga botrytis , together with Sphaeroeca volvox , form a cluster at the base of all other Choanoflagellate species. Moreover, the morphospecies described classically as Codosiga botrytis contains at least four different genotypes separated by considerably high genetic distance. All these ‘cryptic species’ have identical general morphology and cell structure. Strains have a similar life cycle with several different life forms and large morphological plasticity. For the first time we were able to establish cultures from cryo-conserved cysts of Choanoflagellates. The ancient strains did not differ significantly in partial SSU rDNA from the modern ones. Besides, no biogeographically pattern could be established. This fact and the low genetic distances of some strains from remote locations support the distribution of dormant stages via air.