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Porfirio-Sousa AL, Tice AK, Morais L, Ribeiro GM, Blandenier Q, Dumack K, Eglit Y, Fry NW, Gomes E Souza MB, Henderson TC, Kleitz-Singleton F, Singer D, Brown MW, Lahr DJG. Amoebozoan testate amoebae illuminate the diversity of heterotrophs and the complexity of ecosystems throughout geological time. Proc Natl Acad Sci U S A 2024; 121:e2319628121. [PMID: 39012821 PMCID: PMC11287125 DOI: 10.1073/pnas.2319628121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 06/01/2024] [Indexed: 07/18/2024] Open
Abstract
Heterotrophic protists are vital in Earth's ecosystems, influencing carbon and nutrient cycles and occupying key positions in food webs as microbial predators. Fossils and molecular data suggest the emergence of predatory microeukaryotes and the transition to a eukaryote-rich marine environment by 800 million years ago (Ma). Neoproterozoic vase-shaped microfossils (VSMs) linked to Arcellinida testate amoebae represent the oldest evidence of heterotrophic microeukaryotes. This study explores the phylogenetic relationship and divergence times of modern Arcellinida and related taxa using a relaxed molecular clock approach. We estimate the origin of nodes leading to extant members of the Arcellinida Order to have happened during the latest Mesoproterozoic and Neoproterozoic (1054 to 661 Ma), while the divergence of extant infraorders postdates the Silurian. Our results demonstrate that at least one major heterotrophic eukaryote lineage originated during the Neoproterozoic. A putative radiation of eukaryotic groups (e.g., Arcellinida) during the early-Neoproterozoic sustained by favorable ecological and environmental conditions may have contributed to eukaryotic life endurance during the Cryogenian severe ice ages. Moreover, we infer that Arcellinida most likely already inhabited terrestrial habitats during the Neoproterozoic, coexisting with terrestrial Fungi and green algae, before land plant radiation. The most recent extant Arcellinida groups diverged during the Silurian Period, alongside other taxa within Fungi and flowering plants. These findings shed light on heterotrophic microeukaryotes' evolutionary history and ecological significance in Earth's ecosystems, using testate amoebae as a proxy.
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Affiliation(s)
- Alfredo L. Porfirio-Sousa
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo05508-090, Brazil
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
| | - Alexander K. Tice
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
- Department of Biological Sciences, Texas Tech University, Lubbock, TX79409
| | - Luana Morais
- Department of Geophysics, Institute of Astronomy, Geophysics and Atmospheric Sciences, University of São Paulo, São Paulo05508-090, Brazil
- Department of Applied Geology, Institute of Geosciences and Exact Sciences, São Paulo State University, Rio Claro13506-900, Brazil
| | - Giulia M. Ribeiro
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo05508-090, Brazil
| | - Quentin Blandenier
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
| | - Kenneth Dumack
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne50674, Germany
| | - Yana Eglit
- Department of Biology, Dalhousie University, Halifax, NSB3H 4R2, Canada
- Department of Biology, Institute for Comparative Genomics, Dalhousie University, Halifax, NSV8P 3E6, Canada
- Department of Biology, University of Victoria, Victoria, BCV8P 3E6, Canada
| | - Nicholas W. Fry
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
| | | | - Tristan C. Henderson
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
| | | | - David Singer
- Soil Science and Environment Group, Changins, Haute école spécialisée de Suisse occidentale University of Applied Sciences and Arts Western Switzerland, Nyon1148, Switzerland
| | - Matthew W. Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS39762
- Department of Biological Sciences, Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS39762
| | - Daniel J. G. Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo05508-090, Brazil
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Useros F, García-Cunchillos I, Henry N, Berney C, Lara E. How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation. Environ Microbiol 2024; 26:e16606. [PMID: 38509748 DOI: 10.1111/1462-2920.16606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Metabarcoding approaches targeting microeukaryotes have deeply changed our vision of protist environmental diversity. The public repository EukBank consists of 18S v4 metabarcodes from 12,672 samples worldwide. To estimate how far this database provides a reasonable overview of all eukaryotic diversity, we used Arcellinida (lobose testate amoebae) as a case study. We hypothesised that (1) this approach would allow the discovery of unexpected diversity, but also that (2) some groups would be underrepresented because of primer/sequencing biases. Most of the Arcellinida sequences appeared in freshwater and soil, but their abundance and diversity appeared underrepresented. Moreover, 84% of ASVs belonged to the suborder Phryganellina, a supposedly species-poor clade, whereas the best-documented suborder (Glutinoconcha, 600 described species) was only marginally represented. We explored some possible causes of these biases. Mismatches in the primer-binding site seem to play a minor role. Excessive length of the target region could explain some of these biases, but not all. There must be some other unknown factors involved. Altogether, while metabarcoding based on ribosomal genes remains a good first approach to document microbial eukaryotic clades, alternative approaches based on other genes or sequencing techniques must be considered for an unbiased picture of the diversity of some groups.
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Affiliation(s)
| | - Iván García-Cunchillos
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Nicolas Henry
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, Paris, France
- CNRS, FR2424, ABiMS, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Cédric Berney
- CNRS, FR2424, ABiMS, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
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Wang K, Xu HH, Liu BC, Bai J, Wang Y, Tang P, Lu JF, Wang Y. Shallow-marine testate amoebae with internal structures from the Lower Devonian of China. iScience 2023; 26:106678. [PMID: 37182111 PMCID: PMC10173733 DOI: 10.1016/j.isci.2023.106678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/08/2023] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Abstract
Testate amoebae, a polyphyletic protist group inhabiting a wide variety of extant ecosystems, have evolved as far back as early Neoproterozoic. However, their fossil record is discontinuous and biased toward empty shells. Here, we report an arcellinid testate amoeba species, Cangwuella ampulliformis gen. nov., sp. nov., from a shallow-marine community in the Early Devonian of Guangxi, southwestern China. With the aid of scanning electron microscopy and X-ray micro-tomography, we find that the shell of our testate amoeba contains some acetabuliform structures. Although such configuration does not match exactly with the known internal structures in extant testate amoebae, our fossils highlight the potential of exploring the ecological relationships between fossil testate amoebae and their associated organisms, and increase our knowledge on the diversity of testate amoebae in Early Devonian environments.
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Affiliation(s)
- Kai Wang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-He Xu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- Corresponding author
| | - Bing-Cai Liu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiao Bai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Wang
- School of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Peng Tang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jian-Feng Lu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yi Wang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
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Woyzichovski J, Shchepin ON, Schnittler M. High Environmentally Induced Plasticity in Spore Size and Numbers of Nuclei per Spore in Physarum albescens (Myxomycetes). Protist 2022; 173:125904. [PMID: 36037769 DOI: 10.1016/j.protis.2022.125904] [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: 02/18/2022] [Revised: 06/23/2022] [Accepted: 07/28/2022] [Indexed: 12/30/2022]
Abstract
Spore size enables dispersal in plasmodial slime molds (Myxomycetes) and is an important taxonomic character. We recorded size and the number of nuclei per spore for 39 specimens (colonies of 50-1000 sporocarps) of the nivicolous myxomycete Physarum albescens, a morphologically defined taxon with several biological species. For each colony, three sporocarps were analyzed from the same spore mount under brightfield and DAPI-fluorescence, recording ca. 14,000 spores per item. Diagrams for spore size distribution showed narrow peaks of mostly uninucleate spores. Size was highly variable within morphospecies (10.6-13.5 µm, 11-13%), biospecies (3-13%), even within spatially separated colonies of one clone (ca. 8%); but fairly constant for a colony (mean variation 0.4 µm, ca. 1.5%). ANOVA explains most of this variation by the factor locality (within all colonies: 32.7%; within a region: 21.4%), less by biospecies (13.5%), whereas the contribution of intra-colony variation was negligible (<0.1%). Two rare aberrations occur: 1) multinucleate spores and 2) oversized spores with a double or triple volume of normal spores. Both are not related to each other or limited to certain biospecies. Spore size shows high phenotypic plasticity, but the low variation within a colony points to a strong genetic background.
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Affiliation(s)
- Jan Woyzichovski
- Institute of Botany and Landscape Ecology, Greifswald University, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Oleg N Shchepin
- Institute of Botany and Landscape Ecology, Greifswald University, Soldmannstr. 15, 17487 Greifswald, Germany; Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Greifswald University, Soldmannstr. 15, 17487 Greifswald, Germany
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González-Miguéns R, Todorov M, Blandenier Q, Duckert C, Porfirio-Sousa AL, Ribeiro GM, Ramos D, Lahr DJG, Buckley D, Lara E. Deconstructing Difflugia: The tangled evolution of lobose testate amoebae shells (Amoebozoa: Arcellinida) illustrates the importance of convergent evolution in protist phylogeny. Mol Phylogenet Evol 2022; 175:107557. [PMID: 35777650 DOI: 10.1016/j.ympev.2022.107557] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 10/17/2022]
Abstract
Protists, the micro-eukaryotes that are neither plants, animals nor fungi build up the greatest part of eukaryotic diversity on Earth. Yet, their evolutionary histories and patterns are still mostly ignored, and their complexity overlooked. Protists are often assumed to keep stable morphologies for long periods of time (morphological stasis). In this work, we test this paradigm taking Arcellinida testate amoebae as a model. We build a taxon-rich phylogeny based on two mitochondrial (COI and NADH) and one nuclear (SSU) gene, and reconstruct morphological evolution among clades. In addition, we prove the existence of mitochondrial mRNA editing for the COI gene. The trees show a lack of conservatism of shell outlines within the main clades, as well as a widespread occurrence of morphological convergences between far-related taxa. Our results refute, therefore, a widespread morphological stasis, which may be an artefact resulting from low taxon coverage. As a corollary, we also revise the groups systematics, notably by emending the large and highly polyphyletic genus Difflugia. These results lead, amongst others, to the erection of a new infraorder Cylindrothecina, as well as two new genera Cylindrifflugia and Golemanskia.
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Affiliation(s)
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Science, 1113 Sofia, Bulgaria
| | - Quentin Blandenier
- Laboratory of Soil Biodiversity, University of Neuchâtel, Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Clément Duckert
- Laboratory of Soil Biodiversity, University of Neuchâtel, Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | | | - Giulia M Ribeiro
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil
| | - Diana Ramos
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, 28014 Madrid, Spain
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil
| | - David Buckley
- Department of Biology (Genetics), Universidad Autónoma de Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Spain
| | - Enrique Lara
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, 28014 Madrid, Spain.
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