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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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2
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McKeown MM, Burge OR, Richardson SJ, Wood JR, Mitchell EAD, Wilmshurst JM. Biomonitoring tool for New Zealand peatlands: Testate amoebae and vascular plants as promising bioindicators. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120243. [PMID: 38422571 DOI: 10.1016/j.jenvman.2024.120243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/14/2024] [Accepted: 01/27/2024] [Indexed: 03/02/2024]
Abstract
In the last two centuries, a high proportion of peatlands have been lost or severely degraded across the world. The value of peatlands is now well-recognised for biodiversity conservation, flood management, and carbon mitigation, with peatland restoration now central to many government policies for climate action. A challenge, however, is to determine 'natural' and 'disturbed' conditions of peatlands to establish realistic baselines for assessing degradation and setting restoration targets. This requires a tool or set of tools that can rapidly and reliably capture peatland condition across space and time. Our aim was to develop such a tool based on combined analysis of plant and testate amoebae; a group of shelled protists commonly used as indicators of ecological change in peatlands. The value of testate amoebae is well established in Northern Hemisphere Sphagnum-dominated peatlands; however, relatively little work has been undertaken for Southern Hemisphere peat forming systems. Here we provide the first assessment and comparison of the bioindicator value of testate amoebae and vascular plants in the context of Southern Hemisphere peatlands. Our results further demonstrate the unique ecohydrological dynamics at play in New Zealand peat forming systems that set them apart from Northern Hemisphere peatlands. Our results show that plant and testate amoeba communities provided valuable information on peatland condition at different scales, we found that testate amoebae tracked changes in the abiotic variables (depth to water table, pH, and conductivity) more closely than vascular plants. Our results further demonstrate that functional traits of testate amoebae showed promising relationships with disturbance. Amoeba test compression, aperture position and test size were linked to changes in hydrology driven by fluctuations in ground water tables; however, trait responses manifested differently in ombrotrophic and minerotrophic peatlands. Overall, testate amoebae provide a promising bioindicator for tracking degradation in New Zealand peatlands and a potential additional tool to assess peatland condition.
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Affiliation(s)
- Michelle M McKeown
- Department of Geography, University College Cork, Cork T23 TK30, Ireland; Environmental Research Institute, University College Cork, Cork T23 TK30, Ireland.
| | - Olivia R Burge
- Manaaki Whenua-Landcare Research, 54 Gerald Street, Lincoln, 7640, New Zealand
| | - Sarah J Richardson
- Manaaki Whenua-Landcare Research, 54 Gerald Street, Lincoln, 7640, New Zealand
| | - Jamie R Wood
- Ecology and Evolutionary Biology Unit, University of Adelaide, Darling, South Australia, Australia
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
| | - Janet M Wilmshurst
- Manaaki Whenua-Landcare Research, 54 Gerald Street, Lincoln, 7640, New Zealand
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3
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Dumack K, Lara E, Duckert C, Ermolaeva E, Siemensma F, Singer D, Krashevska V, Lamentowicz M, Mitchell EAD. It's time to consider the Arcellinida shell as a weapon. Eur J Protistol 2024; 92:126051. [PMID: 38194835 DOI: 10.1016/j.ejop.2024.126051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/29/2023] [Accepted: 01/01/2024] [Indexed: 01/11/2024]
Abstract
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.
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Affiliation(s)
- Kenneth Dumack
- Terrestrial Ecology, Zülpicher Straße 47b, University of Cologne, Germany.
| | - Enrique Lara
- Real Jardín Botánico-CSIC, C. Moyano 1 28014, Madrid, Spain
| | - Clément Duckert
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile Argand 11 2000, Neuchâtel, Switzerland
| | - Elizaveta Ermolaeva
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile Argand 11 2000, Neuchâtel, Switzerland
| | | | - David Singer
- Soil Science and Environment Group, Changins, HES-SO University of Applied Sciences and Arts Western Switzerland, Nyon, Switzerland
| | - Valentyna Krashevska
- Senckenberg Biodiversity and Climate Research Centre, Functional Environmental Genomics, Senckenberganlage 25 60325, Frankfurt, Germany
| | - Mariusz Lamentowicz
- Climate Change Ecology Research Unit, Faculty of Geographical and Geological Sciences Adam Mickiewicz University in Poznan, Bogumiła Krygowskiego 10 61-680, Poznan, Poland
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile Argand 11 2000, Neuchâtel, Switzerland
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4
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Ribeiro GM, Useros F, Dumack K, González-Miguéns R, Siemensma F, Porfírio-Sousa AL, Soler-Zamora C, Pedro Barbosa Alcino J, Lahr DJG, Lara E. Expansion of the cytochrome C oxidase subunit I database and description of four new lobose testate amoebae species (Amoebozoa; Arcellinida). Eur J Protistol 2023; 91:126013. [PMID: 37690315 DOI: 10.1016/j.ejop.2023.126013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023]
Abstract
Arcellinida is ascending in importance in protistology, but description of their diversity still presents multiple challenges. Furthermore, applicable tools for surveillance of these organisms are still in developing stages. Importantly, a good database that sets a correspondence between molecular barcodes and species morphology is lacking. Cytochrome oxidase (COI) has been suggested as the most relevant marker for species discrimination in Arcellinida. However, some major groups of Arcellinida are still lacking a COI sequence. Here we expand the database of COI marker sequences for Arcellinids, using single-cell PCR, transcriptomics, and database scavenging. In the present work, we added 24 new Arcellinida COI sequences to the database, covering all unsampled infra- and suborders. Additionally, we added six new SSUrRNA sequences and described four new species using morphological, morphometrical, and molecular evidence: Heleopera steppica, Centropyxis blatta, Arcella uspiensis, and Cylindrifflugia periurbana. This new database will provide a new starting point to address new research questions from shell evolution, biogeography, and systematics of arcellinids.
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Affiliation(s)
- Giulia M Ribeiro
- Department of Zoology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | | | - Kenneth Dumack
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Germany
| | | | | | | | | | | | - Daniel J G Lahr
- Department of Zoology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
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5
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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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6
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Loron CC, Rodriguez Dzul E, Orr PJ, Gromov AV, Fraser NC, McMahon S. Molecular fingerprints resolve affinities of Rhynie chert organic fossils. Nat Commun 2023; 14:1387. [PMID: 36914650 PMCID: PMC10011563 DOI: 10.1038/s41467-023-37047-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
The affinities of extinct organisms are often difficult to resolve using morphological data alone. Chemical analysis of carbonaceous specimens can complement traditional approaches, but the search for taxon-specific signals in ancient, thermally altered organic matter is challenging and controversial, partly because suitable positive controls are lacking. Here, we show that non-destructive Fourier Transform Infrared Spectroscopy (FTIR) resolves in-situ molecular fingerprints in the famous 407 Ma Rhynie chert fossil assemblage of Aberdeenshire, Scotland, an important early terrestrial Lagerstätte. Remarkably, unsupervised clustering methods (principal components analysis and K-mean) separate the fossil spectra naturally into eukaryotes and prokaryotes (cyanobacteria). Additional multivariate statistics and machine-learning approaches also differentiate prokaryotes from eukaryotes, and discriminate eukaryotic tissue types, despite the overwhelming influence of silica. We find that these methods can clarify the affinities of morphologically ambiguous taxa; in the Rhynie chert for example, we show that the problematic "nematophytes" have a plant-like composition. Overall, we demonstrate that the famously exquisite preservation of cells, tissues and organisms in the Rhynie chert accompanies similarly impressive preservation of molecular information. These results provide a compelling positive control that validates the use of infrared spectroscopy to investigate the affinity of organic fossils in chert.
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Affiliation(s)
- C C Loron
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
| | - E Rodriguez Dzul
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - P J Orr
- UCD School of Earth Sciences, University College Dublin, Dublin, Ireland
| | - A V Gromov
- EastCHEM and School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - N C Fraser
- Natural Sciences Department, National Museums Scotland, Edinburgh, UK
| | - S McMahon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK. .,School of Geosciences, University of Edinburgh, Edinburgh, UK.
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7
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Creevy AL, Wilkinson DM, Andersen R, Payne deceased RJ. Testate amoebae response and vegetation composition after plantation removal on a former raised bog. Eur J Protistol 2023; 89:125977. [PMID: 37060794 DOI: 10.1016/j.ejop.2023.125977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/09/2023]
Abstract
Extensive drainage of peatlands in north-west Europe for the purposes of afforestation for timber production and harvesting has altered the carbon balance and biodiversity value. Large-scale restoration projects aim to reinstate hydrological conditions to keep carbon locked up in the peat and to restart active peat growth. Testate amoebae are an informal grouping of well-studied protists in peatland environments and as microbial consumers play an important role in nutrient and carbon cycling. Using a space for time substitution approach, this study investigated the response of testate amoebae assemblages and vegetation composition after tree removal on a drained raised bog. There was a clear difference in microbial assemblages between open and a chronosequenceof restoration areas. Results suggest microbial recovery after rewetting is a slow process with plant composition showing a faster response than the microbial assemblage. Mixotrophic testate amoebae had not recovered seventeen years following plantation removal and the establishment of Sphagnum mosses in the wetter microforms. These results suggest that vegetation composition and Testate amoeba assemblages respond differently to environmental drivers at forest-to-bog restoration areas. Local physicochemical peat properties were a stronger driver of the testate assemblage compared with vegetation. Complete recovery of microbial assemblages may take place over decadal timescales.
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8
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Pérez-Uz B, Galfione VC, Ochoa-Hueso R, Martín-Cereceda M. Protist Diversity Responses to Experimental N Deposition in Biological Crusts of a Semiarid Mediterranean Ecosystem. Protist 2023; 174:125929. [PMID: 36455480 DOI: 10.1016/j.protis.2022.125929] [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: 08/24/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/17/2022]
Abstract
Biological soil crusts (BSC) are associations of different macro and microorganisms and aggregated soil particles located on the surface of soils in many different habitats. BSC harbour a diverse and complex community of ciliates and testate amoebae. These phagotrophic protists play an important role in C and N recycling in soil ecosystems but have not been frequently studied in BSC. In this context, the effects of three increasing N inputs on ciliates and testate amoebae in crusts from a semi-arid Mediterranean ecosystem were evaluated. A field experiment with artificial N-deposition was designed to mimic the effects caused by anthropogenic N depositions. The results have shown that the protist populations of these semi-arid Mediterranean environments have lower species richness than other soil environments. The increase in N produces a net loss of diversity in the populations studied and shifts in the community structure. It has also been shown that some ciliates and testate amoebae, due to their population responses to increased N concentrations, could potentially be used as bio-indicators of N contamination in these BSCs.
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Affiliation(s)
- Blanca Pérez-Uz
- Dept. Genética, Fisiología y Microbiología, Fac. Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain.
| | - Virginia C Galfione
- Dept. Genética, Fisiología y Microbiología, Fac. Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Raul Ochoa-Hueso
- Instituto de Investigación Vitivinicola y Agroalimentaria, Universidad de Cádiz, Puerto Real, Spain
| | - Mercedes Martín-Cereceda
- Dept. Genética, Fisiología y Microbiología, Fac. Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
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9
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Bobrov A, Wetterich S, Schirrmeister L. Testate Amoebae in Historical parks of Potsdam, Germany. Protist 2022; 173:125911. [PMID: 36194982 DOI: 10.1016/j.protis.2022.125911] [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: 12/17/2021] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 12/30/2022]
Abstract
To explore the potential of urban settings as habitats for testate amoebae, five historical parks in Potsdam (Germany) were sampled at different sites. A total of 32 sampling sites was chosen in proximity to deciduous (Acer, Castanea, Fagus, Tilia, Platanus, Quercus) and coniferous (Fraxinus, Picea, Pinus, Tsuga) trees. Meadows and creeks were also sampled. The overall taxonomic record comprises 76 species and sub-species. High species numbers of >20 per sample were found in meadows and below Fagus, Tilia, and Quercus trees. The species richness per park ranges from 33 to 46 taxa. Most species belong to the eurybiontic ecological group, although litter-inhabiting and hygrophilic and hydrophilic species were also present. Common species found in more than 50% of all samples (superdominants) belong to the genera Centropyxis, Cyclopyxis, Euglypha, and Trinema. Interestingly, the rare Frenopyxis stierlitzi which inhabits tree hollows was found as a recently described species in a new genus FrenopyxisBobrov&Mazei2020 in the Babelsberg Park. The studied testate amoebae are characterized by a high degree of morphological and morphometric plasticity. Therefore, the study of testate amoebae in urban settings will reveal new insights into their ecology and enhance the definition of morphometric variability for single species.
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Affiliation(s)
- Anatoly Bobrov
- Department of Soil Science, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
| | - Sebastian Wetterich
- Department of Permafrost Research, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Telegrafenberg A45, 14473 Potsdam, Germany
| | - Lutz Schirrmeister
- Department of Permafrost Research, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Telegrafenberg A45, 14473 Potsdam, Germany.
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10
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Free-Living Amoebas in Extreme Environments: The True Survival in our Planet. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2359883. [PMID: 36303587 PMCID: PMC9596261 DOI: 10.1155/2022/2359883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/08/2022] [Indexed: 12/03/2022]
Abstract
Free-living amoebas (FLAs) are microorganisms, unicellular protozoa widely distributed in nature and present in different environments, such as water or soil; they are maintained in ecosystems and play a fundamental role in the biological control of bacteria, other protozoa, and mushrooms. In particular circumstances, some can reach humans or animals, promoting several health complications. Notably, FLAs are characterized by a robust capacity to survive in extreme environments. However, currently, there is no updated information on the existence and distribution of this protozoan in inhospitable places. Undoubtedly, the cellular physiology of these protozoan microorganisms is very particular. They can resist and live in extreme environments due to their encysting capacity and tolerance to different osmolarities, temperatures, and other environmental factors, which give them excellent adaptative resistance. In this review, we summarized the most relevant evidence related to FLAs and the possible mechanism, which could explain their adaptative capacity to several extreme environments.
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11
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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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12
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González-Miguéns R, Soler-Zamora C, Useros F, Nogal-Prata S, Berney C, Blanco-Rotea A, Carrasco-Braganza MI, de Salvador-Velasco D, Guillén-Oterino A, Tenorio-Rodríguez D, Velázquez D, Heger TJ, Sanmartín I, Lara E. Cyphoderia ampulla (Cyphoderiidae: Rhizaria), a tale of freshwater sailors. The causes and consequences of ecological transitions through the salinity barrier in a family of benthic protists. Mol Ecol 2022; 31:2644-2663. [PMID: 35262986 PMCID: PMC9311665 DOI: 10.1111/mec.16424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/17/2022] [Accepted: 03/02/2022] [Indexed: 11/29/2022]
Abstract
The salinity barrier that separates marine and freshwater biomes is probably the most important division in biodiversity on Earth. Those organisms that successfully performed this transition had access to new ecosystems while undergoing changes in selective pressure, which often led to major shifts in diversification rates. While these transitions have been extensively investigated in animals, the tempo, mode, and outcome of crossing the salinity barrier have been scarcely studied in other eukaryotes. Here, we reconstructed the evolutionary history of the species complex Cyphoderia ampulla (Euglyphida: Cercozoa: Rhizaria) based on DNA sequences from the nuclear SSU rRNA gene and the mitochondrial cytochrome oxidase subunit I gene, obtained from publicly available environmental DNA data (GeneBank, EukBank) and isolated organisms. A tree calibrated with euglyphid fossils showed that four independent transitions towards freshwater systems occurred from the Mid Miocene onwards, coincident with important fluctuations in sea level. Ancestral trait reconstructions indicated that the whole family Cyphoderiidae had a marine origin and suggest that ancestors of the freshwater forms were euryhaline and lived in environments with fluctuating salinity. Diversification rates did not show any obvious increase concomitant with ecological transitions, but morphometric analyses indicated that species increased in size and homogenized their morphology after colonizing the new environments. This suggests adaptation to changes in selective pressure exerted by life in freshwater sediments.
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Affiliation(s)
| | - Carmen Soler-Zamora
- Real Jardín Botánico de Madrid (RJB-CSIC), Plaza Murillo 2, 28014, Madrid, Spain
| | - Fernando Useros
- Real Jardín Botánico de Madrid (RJB-CSIC), Plaza Murillo 2, 28014, Madrid, Spain
| | - Sandra Nogal-Prata
- Real Jardín Botánico de Madrid (RJB-CSIC), Plaza Murillo 2, 28014, Madrid, Spain
| | - Cédric Berney
- Université de la Sorbonne CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France.,Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 10, Paris, France
| | - Andrés Blanco-Rotea
- Estación Biológica Internacional Duero-Douro, (EUROPARQUES-EBI), Buque hidrográfico Helios-Cousteau en el Lago de Sanabria, 49632, Ribadelago, Castilla y León, Spain
| | - María Isabel Carrasco-Braganza
- Estación Biológica Internacional Duero-Douro, (EUROPARQUES-EBI), Buque hidrográfico Helios-Cousteau en el Lago de Sanabria, 49632, Ribadelago, Castilla y León, Spain
| | - David de Salvador-Velasco
- Estación Biológica Internacional Duero-Douro, (EUROPARQUES-EBI), Buque hidrográfico Helios-Cousteau en el Lago de Sanabria, 49632, Ribadelago, Castilla y León, Spain
| | - Antonio Guillén-Oterino
- Estación Biológica Internacional Duero-Douro, (EUROPARQUES-EBI), Buque hidrográfico Helios-Cousteau en el Lago de Sanabria, 49632, Ribadelago, Castilla y León, Spain
| | - Daniel Tenorio-Rodríguez
- Estación Biológica Internacional Duero-Douro, (EUROPARQUES-EBI), Buque hidrográfico Helios-Cousteau en el Lago de Sanabria, 49632, Ribadelago, Castilla y León, Spain
| | - David Velázquez
- Dpt. of Biology, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Thierry J Heger
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260, Nyon, Switzerland
| | - Isabel Sanmartín
- Real Jardín Botánico de Madrid (RJB-CSIC), Plaza Murillo 2, 28014, Madrid, Spain
| | - Enrique Lara
- Real Jardín Botánico de Madrid (RJB-CSIC), Plaza Murillo 2, 28014, Madrid, Spain
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13
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Gooday AJ, Holzmann M, Majewski W, Pawlowski J. New species of Gromia (Protista, Rhizaria) from South Georgia and the Falkland Islands. Polar Biol 2022. [DOI: 10.1007/s00300-022-03017-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Baković N, Matoničkin Kepčija R, Siemensma FJ. Transitional and small aquatic cave habitats diversification based on protist assemblages in the Veternica cave (Medvednica Mt., Croatia). SUBTERRANEAN BIOLOGY 2022. [DOI: 10.3897/subtbiol.42.78037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Protists in caves are scarcely researched. Most cave studies address the diversity of protists, but very little is known about their habitats and spatio-temporal dynamics. The aim of this study was to investigate the diversity and abundance of protists in the Veternica cave in the Medvednica mountain in Croatia on hygropetric and sinter and clay pools during six months. During this study, 47 protists taxa were distinguished belonging to the groups of heterotrophic flagellates, ciliates, heliozoans, stramenopiles and testate and naked amoebae. The highest taxon richness was found at the sinter pool site richest in bats guano (36 taxa). Most diverse were testate amoebae and ciliates. The number of taxa and their abundance differed significantly between the sampling sites. The prospected habitats supported different protist assemblages, proved by ordination analysis. The most distinctive habitat was the hygropetric. Habitat heterogeneity could be attributed to the presence of inorganic and organic sediments at the sites and habitat microhydrology (lotic or lentic system). Kendall’s concordance coefficient showed a good synchronicity between the habitats in the Veternica cave, based on taxon richness and abundance of protists indicating similar seasonal trends. Seasonality in the studied habitats is attributed to the hydro-meteorological conditions in the Veternica cave drainage area. This study is one of the few studies of spatio-temporal diversity and abundance of protists in caves. Despite the similar appearance of small transitional and aquatic habitats in caves, an example of this study showed specific habitat diversification.
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15
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González-Miguéns R, Soler-Zamora C, Villar-Depablo M, Todorov M, Lara E. Multiple convergences in the evolutionary history of the testate amoeba family Arcellidae (Amoebozoa: Arcellinida: Sphaerothecina): when the ecology rules the morphology. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Protists are probably the most species-rich eukaryotes, yet their systematics are inaccurate, leading to an underestimation of their actual diversity. Arcellinida (= lobose testate amoebae) are amoebozoans that build a test (a hard shell) whose shape and composition are taxonomically informative. One of the most successful groups is Arcellidae, a family found worldwide in many freshwater and terrestrial environments where they are indicators of environmental quality. However, the systematics of the family is based on works published nearly a century ago. We re-evaluated the systematics based on single-cell barcoding, morphological and ecological data. Overall, test shape appears to be more related to environmental characteristics than to the species’ phylogenetic position. We show several convergences in organisms with similar ecology, some traditionally described species being paraphyletic. Based on conservative traits, we review the synapomorphies of the infraorder Sphaerothecina, compile a list of synonyms and describe a new genus Galeripora, with five new combinations. Seven new species: Arcella guadarramensis sp. nov., Galeripora balari sp. nov., Galeripora bufonipellita sp. nov., Galeripora galeriformis sp. nov., Galeripora naiadis sp. nov., Galeripora sitiens sp. nov. andGaleripora succelli sp. nov. are also described here.
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Affiliation(s)
| | | | - Mar Villar-Depablo
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, Madrid, Spain
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), Serrano 115 bis, Madrid, Spain
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Science, Sofia, Bulgaria
| | - Enrique Lara
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, Madrid, Spain
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16
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McKeown MM, Mitchell EA, Amesbury MJ, Blandenier Q, Charman D, Duckert C, Roland TP, Swindles GT, Wood JR, Wilmshurst JM. The testate amoebae of New Zealand: A checklist, identification key and assessment of biogeographic patterns. Eur J Protistol 2021; 81:125789. [DOI: 10.1016/j.ejop.2021.125789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 10/21/2022]
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Arcellinida testate amoebae as climate miner's canaries in Southern Spain. Eur J Protistol 2021; 81:125828. [PMID: 34487957 DOI: 10.1016/j.ejop.2021.125828] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/29/2021] [Accepted: 07/18/2021] [Indexed: 12/12/2022]
Abstract
Southern Spain is currently under threat of desertification as a consequence of global climate change, which pressures on fragile ecosystems such as caves. The organisms living in these extremely stable environments are particularly sensitive and prone to extinction, therefore they can be used as bioindicators for climate change. Cyanobacterial mats form peculiar and vulnerable micro-ecosystems at the entrance of caves and house a diversity of protists. Amongst them, Arcellinida testate amoebae have been traditionally used as bioindicators for environmental quality, notably because their narrow ecological tolerance and their key ecological position as top predators of the microbial foodwebs. We report here two new species of Arcellinida found in the cyanobacterial mats of cave Hundidero, in Sierra de Grazalema, Malaga province, whose traits suggest a narrow tolerance for changes in humidity. We provide a formal description for Difflugia alhadiqa sp. nov. and Heleopera baetica sp. nov. based on morphometrics and 18S rRNA gene data, and propose using the presence of these species to indicate the good health of the cyanobacterial mats, like miner's canaries for local climate.
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Lahr DJ. An emerging paradigm for the origin and evolution of shelled amoebae, integrating advances from molecular phylogenetics, morphology and paleontology. Mem Inst Oswaldo Cruz 2021; 116:e200620. [PMID: 34406221 PMCID: PMC8370470 DOI: 10.1590/0074-02760200620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 07/05/2021] [Indexed: 11/22/2022] Open
Abstract
The phylogenetic paradigm of eukaryotic evolution has changed dramatically over the past two decades, with profound reflections on the understanding of life on earth. Arcellinida testate (shelled) amoebae lineages represent some of the oldest fossils of eukaryotes, and the elucidation of their phylogenetic relationships opened a window to the distant past, with important implications for understanding the evolution of life on earth. This four-part essay summarises advances made in the past 20 years regarding: (i) the phylogenetic relationships among amoebae with shells evolving in concert with the advances made in the phylogeny of eukaryotes; (ii) paleobiological studies unraveling the biological affinities of Neoproterozoic vase-shaped microfossils (VSMs); (iii) the interwoven interpretation of these different sets of data concluding that the Neoproterozoic contains a surprising diversity of organisms, in turn demanding a reinterpretation of the most profound events we know in the history of eukaryotes, and; (iv) a synthesis of the current knowledge about the evolution of Arcellinida, together with the possibilities and pitfalls of their interpretation.
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Affiliation(s)
- Daniel Jg Lahr
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brasil
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Burdman L, Mataloni G, Mitchell EAD, Lara E. A reassessment of testate amoebae diversity in Tierra del Fuego peatlands: Implications for large scale inferences. Eur J Protistol 2021; 80:125806. [PMID: 34280730 DOI: 10.1016/j.ejop.2021.125806] [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: 01/25/2021] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 11/15/2022]
Abstract
Testate amoebae are a diverse group of shelled protists frequently used as model organisms in microbial biogeography. Relatively few species have been reported for the Southern Hemisphere, however, it remains unclear whether this lower diversity is real or an artifact of under-sampling or misidentifications, which would reduce their potential to address macroecological questions. We evaluated testate amoebae diversity from the full range of habitats occurring within two Tierra del Fuego peatlands and compared it with the reported diversity for the area and from the Northern Hemisphere peatlands. We recorded 87 species, of which 69 are new for the region and 45 of them probably new to science and likely to have restricted geographical distributions. Combined with previous studies, the total diversity of testate amoebae only from Tierra del Fuego peatlands now reaches 119, as compared with 183 reported from all Northern Hemisphere peatlands. Our results demonstrate that the number of Gondwanian and Neotropical endemic testate amoeba may be substantially higher than currently known. Previous reports of Holarctic taxa in Tierra del Fuego may result from forcing the identification of morphotypes to the descriptions in the most common literature (force-fitting) South American species into species common in literature from other regions.
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Affiliation(s)
- Luciana Burdman
- Laboratorio de Biodiversidad, Limnología y Biología de la Conservación, Instituto de Investigación e Ingeniería Ambiental (IIIA CONICET-UNSAM), Campus Miguelete, Universidad Nacional de San Martín. 25 de Mayo y Francia, 1650 San Martin, Provincia de Buenos Aires, Argentina; Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Center for Conservation and Sustainable Development, Missouri Botanical Garden, St.Louis, MO, USA.
| | - Gabriela Mataloni
- Laboratorio de Biodiversidad, Limnología y Biología de la Conservación, Instituto de Investigación e Ingeniería Ambiental (IIIA CONICET-UNSAM), Campus Miguelete, Universidad Nacional de San Martín. 25 de Mayo y Francia, 1650 San Martin, Provincia de Buenos Aires, Argentina
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Jardin Botanique de Neuchâtel, Neuchâtel, Switzerland
| | - Enrique Lara
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Department of Mycology, Real Jardín Botánico, CSIC. Plaza de Murillo 2, 28014 Madrid, Spain.
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20
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Dumack K, Duckert C, Meinhardt R, Lara E, Bonkowski M. Description of Phaeobola aeris gen. nov., sp. nov (Rhizaria, Cercozoa, Euglyphida) Sheds Light on Euglyphida's Dark Matter. J Eukaryot Microbiol 2020; 68:e12835. [PMID: 33222324 DOI: 10.1111/jeu.12835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/06/2020] [Accepted: 10/26/2020] [Indexed: 11/30/2022]
Abstract
The majority of Euglyphida species are characterised by shells with imbricated silica scales. Environmental surveys indicate a large unexplored diversity and recent efforts hinted at a certain diversity of yet undescribed, inconspicuous, scale-lacking Euglyphida. Here we describe Phaeobola aeris gen. nov., sp. nov. that shows a variety of morphological characters typical for the Euglyphida but lacks silica scales-instead, this species bears an agglutinated test. Neither its morphology nor phylogenetic placement allows its assignment to any currently described family. We erected the yet monospecific genus Phaeobola gen. nov., which with yet available data remain Euglyphida incertae sedis.
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Affiliation(s)
- Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, Köln, 50674, Germany
| | - Clément Duckert
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland
| | - Raphaela Meinhardt
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, Köln, 50674, Germany
| | - Enrique Lara
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, Köln, 50674, Germany
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21
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Macumber AL, Roe HM, Prentice SV, Sayer CD, Bennion H, Salgado J. Freshwater Testate Amoebae (Arcellinida) Response to Eutrophication as Revealed by Test Size and Shape Indices. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.568904] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We review the potential for applying traits-based approaches to freshwater testate amoeba, a diverse protist group that are abundant in lakes and are valuable ecological indicators. We investigated the efficacy of geometric morphometric analysis to define Arcellinida test size and shape indices that could summarize freshwater testate amoeba community dynamics along a temporal gradient of eutrophication in Loch Leven, Scotland (United Kingdom). A cluster analysis of test size and shape indices yielded three clusters, each dominated by a single shape: elongate, spherical and ovoid. When plotted stratigraphically, we observed increases in spherical tests, decreases in elongate tests and shrinking of test size coeval with eutrophication in Loch Leven. Decreases in the elongate cluster may reflect benthic conditions with reduced oxygen levels, while increases in the spherical cluster are likely associated with an expanding macrophyte community that promoted pelagic and epibiotic life habits. Shrinking of test size may be a stress response to eutrophication and/or warming temperatures. Tracking community dynamics using test size and shape indices was found to be as effective as using species-based approaches to summarize key palaeolimnological changes, with the added benefits of being free from taxonomic bias and error. The approach thus shows significant potential for future studies of aquatic community change in nutrient impacted lakes.
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de Klerk P, Bobrov A, Theuerkauf M, Joosten H. Short-distance distribution patterns of testate amoebae in an Arctic ice-wedge polygon mire (Berelekh-Indigirka lowlands, NE Siberia). Polar Biol 2020. [DOI: 10.1007/s00300-020-02711-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractThe Arctic is experiencing substantial warming with possibly large consequences for global climate when its large soil carbon stocks are mobilized. Yet the functioning of permafrost peatlands, which contain considerable amounts of carbon, is still not fully understood. Palaeoecological studies may contribute to unravelling this functioning but require actuo-ecological calibration of the environmental proxies used. Testate amoebae may be valuable proxies for palaeoecological reconstruction, but indeed still large gaps exist regarding their present-day distribution in Arctic peatlands. This study presents the distribution of testate amoebae taxa with high (1 m) spatial resolution along a transect crossing an Arctic ice-wedge polygon mire. Whereas the polygon ridges are characterised by taxa that are known to be typical of dry environments or hydrologically indifferent, the low-lying wet settings show a mixture of wet- and dry-living taxa, indicating seasonally rapidly changing conditions. High testate amoebae concentrations were only found on the dry polygon ridges. Archerella flavum occurs in various moss species in drier polygon settings, in contrast to temperate regions where the species is exclusively known from wet sites with Sphagnum, which probably relates to the special moisture conditions associated with permafrost. To compare the results of full testate amoebae analysis with those of palynology, each surface sample was split into two parts and prepared and analysed following standard testate amoebae analysis and palynological methods, respectively. Clear differences in qualitative content were found and can be attributed to the different preparation methods and to possible small (a few cm) differences in sample location. Nevertheless, the indicative value of testate amoebae found in pollen samples adds importantly to the ecological inference of palynological studies. Overall testate amoebae research is very valuable for the recognition of past ecological settings and the accurate reconstruction of past hydrological regimes in Arctic mires. Considerably more research is, however, necessary to cover the total (ecological) diversity of testate amoebae populations in NE Siberia.
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Öztoprak H, Walden S, Heger T, Bonkowski M, Dumack K. What Drives the Diversity of the Most Abundant Terrestrial Cercozoan Family (Rhogostomidae, Cercozoa, Rhizaria)? Microorganisms 2020; 8:E1123. [PMID: 32722603 PMCID: PMC7463998 DOI: 10.3390/microorganisms8081123] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/25/2022] Open
Abstract
Environmental sequencing surveys of soils and freshwaters revealed high abundance and diversity of the Rhogostomidae, a group of omnivorous thecate amoebae. This is puzzling since only a few Rhogostomidae species have yet been described and only a handful of reports mention them in field surveys. We investigated the putative cryptic diversity of the Rhogostomidae by a critical re-evaluation of published environmental sequencing data and in-depth ecological and morphological trait analyses. The Rhogostomidae exhibit an amazing diversity of genetically distinct clades that occur in a variety of different environments. We further broadly sampled for Rhogostomidae species; based on these isolates, we describe eleven new species and highlight important morphological traits for species delimitation. The most important environmental drivers that shape the Rhogostomidae community were soil moisture, soil pH, and total plant biomass. The length/width ratio of the theca was a morphological trait related to the colonized habitats, but not the shape and size of the aperture that is often linked to moisture adaption in testate and thecate amoebae.
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Affiliation(s)
- Hüsna Öztoprak
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany; (H.Ö.); (S.W.); (M.B.)
| | - Susanne Walden
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany; (H.Ö.); (S.W.); (M.B.)
| | - Thierry Heger
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland;
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany; (H.Ö.); (S.W.); (M.B.)
| | - Kenneth Dumack
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany; (H.Ö.); (S.W.); (M.B.)
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Lara E, Dumack K, García-Martín JM, Kudryavtsev A, Kosakyan A. Amoeboid protist systematics: A report on the "Systematics of amoeboid protists" symposium at the VIIIth ECOP/ISOP meeting in Rome, 2019. Eur J Protistol 2020; 76:125727. [PMID: 32755801 DOI: 10.1016/j.ejop.2020.125727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/22/2020] [Accepted: 06/25/2020] [Indexed: 01/21/2023]
Abstract
Amoeboid protists are extremely abundant and diverse in natural systems where they often play outstanding ecological roles. They can be found in almost all major eukaryotic divisions, and genomic approaches are bringing major changes in our perception of their deep evolutionary relationships. At fine taxonomic levels, the generalization of barcoding is revealing a considerable and unsuspected specific diversity that can be appreciated with careful morphometric analyses based on light and electron microscopic observations. We provide examples on the difficulties and advances in amoeboid protists systematics in a selection of groups that were presented at the VIIIth ECOP/ISOP meeting in Rome, 2019. We conclude that, in all studied groups, important taxonomical rearrangements will certainly take place in the next few years, and systematics must be adapted to incorporate these changes. Notably, nomenclature should be flexible enough to integrate many new high level taxa, and a unified policy must be adopted to species description and to the establishment of types.
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Affiliation(s)
- Enrique Lara
- Real Jardín Botánico de Madrid, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain.
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | | | - Alexander Kudryavtsev
- Laboratory of Cellular and Molecular Protistology, Zoological Institute of the Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint-Petersburg, Russia; Department of Invertebrate Zoology, Faculty of Biology, Saint-Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint-Petersburg, Russia
| | - Anush Kosakyan
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice, Czech Republic
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Bian P, Steinitz-Kannan M, McCarthy TJ. Reply to Comment on "Amoebae Assemble Synthetic Spherical Particles To Form Reproducible Constructs". LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4564. [PMID: 32298127 DOI: 10.1021/acs.langmuir.0c00903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Pei Bian
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Miriam Steinitz-Kannan
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky 41099, United States
| | - Thomas J McCarthy
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003, United States
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Ruggiero A, Grattepanche JD, Weiner AKM, Katz LA. High Diversity of Testate Amoebae (Amoebozoa, Arcellinida) Detected by HTS Analyses in a New England Fen using Newly Designed Taxon-specific Primers. J Eukaryot Microbiol 2020; 67:450-462. [PMID: 32145128 DOI: 10.1111/jeu.12794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 01/01/2023]
Abstract
Testate (shell-building) amoebae, such as the Arcellinida (Amoebozoa), are useful bioindicators for climate change. Though past work has relied on morphological analyses to characterize Arcellinida diversity, genetic analyses revealed the presence of multiple cryptic species underlying morphospecies. Here, we design and deploy Arcellinida-specific primers for the SSU-rDNA gene to assess the community composition on the molecular level in a pilot study of two samplings from a New England fen: (1) 36-cm horizontal transects and vertical cores; and (2) 26-m horizontal transects fractioned into four size classes (2-10, 10-35, 35-100, and 100-300 μm). Analyses of these data show the following: (1) a considerable genetic diversity within Arcellinida, much of which comes from morphospecies lacking sequences on GenBank; (2) communities characterized by DNA (i.e. active + quiescent) are distinct from those characterized by RNA (i.e. active, indicator of biomass); (3) active communities on the surface tend to be more similar to one another than to core communities, despite considerable heterogeneity; and (4) analyses of communities fractioned by size find some lineages (OTUs) that are abundant in disjunct size categories, suggesting the possibility of life-history stages. Together, these data demonstrate the potential of these primers to elucidate the diversity of Arcellinida communities in diverse habitats.
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Affiliation(s)
- Alistaire Ruggiero
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063
| | - Jean-David Grattepanche
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063
| | - Agnes K M Weiner
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063
| | - Laura A Katz
- Department of Biological Science, Smith College, 44 College Lane, Northampton, Massachusetts, 01063.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
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Dumack K, Siemensma F. Shell Colour in Cercozoa; a Simple Trait to Distinguish Thecofilosea from Imbricatea? Protist 2020; 171:125718. [DOI: 10.1016/j.protis.2020.125718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 01/29/2023]
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Macumber AL, Blandenier Q, Todorov M, Duckert C, Lara E, Lahr DJ, Mitchell EA, Roe HM. Phylogenetic divergence within the Arcellinida (Amoebozoa) is congruent with test size and metabolism type. Eur J Protistol 2020; 72:125645. [DOI: 10.1016/j.ejop.2019.125645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/01/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022]
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29
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Siemensma F, Dumack K. SSU rDNA Phylogeny Indicates the Scale-lacking Trivalvulariida ord. nov. as a Sister Group to the Euglyphida (Cercozoa, Rhizaria). Protist 2020; 171:125701. [DOI: 10.1016/j.protis.2019.125701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 01/21/2023]
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30
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Lamentowicz M, Kajukało-Drygalska K, Kołaczek P, Jassey VEJ, Gąbka M, Karpińska-Kołaczek M. Testate amoebae taxonomy and trait diversity are coupled along an openness and wetness gradient in pine-dominated Baltic bogs. Eur J Protistol 2020; 73:125674. [PMID: 32200296 DOI: 10.1016/j.ejop.2020.125674] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/08/2020] [Accepted: 01/22/2020] [Indexed: 11/26/2022]
Abstract
Sphagnum peatlands host a high abundance of protists, especially testate amoebae. Here, we designed a study to investigate the functional diversity of testate amoebae in relation to wetness and forest cover in Baltic bogs. We provided new data on the influence of openness/wetness gradient on testate amoebae communities, showing significant differences in selected testate amoebae (TA) traits. Three key messages emerged from our investigations: 1) we recorded an effect of peatland surface openness on testate amoebae functional traits that led us to accept the hypothesis that TA traits differ according to light intensity and hydrology. Mixotrophic species were recorded in high relative abundance in open plots, whereas they were nearly absent in forested sites; 2) we revealed a hydrological threshold for the occurrence of mixotrophic testate amoebae that might be very important in terms of peatland functioning and carbon sink vs. source context; and 3) mixotrophic species with organic tests were nearly absent in forested sites that were dominated by heterotrophic species with agglutinated or idiosomic tests. An important message from this study is that taxonomy of TA rather indicates the hydrological gradient whereas traits of mixotrophs the openness gradient.
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Affiliation(s)
- Mariusz Lamentowicz
- Laboratory of Climate Change Ecology, Faculty of Geographical and Geological Sciences, Adam Mickiewicz University, Poznań, Poland.
| | - Katarzyna Kajukało-Drygalska
- Laboratory of Climate Change Ecology, Faculty of Geographical and Geological Sciences, Adam Mickiewicz University, Poznań, Poland
| | - Piotr Kołaczek
- Laboratory of Climate Change Ecology, Faculty of Geographical and Geological Sciences, Adam Mickiewicz University, Poznań, Poland
| | - Vincent E J Jassey
- ECOLAB, Laboratoire d'Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Maciej Gąbka
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland
| | - Monika Karpińska-Kołaczek
- Laboratory of Climate Change Ecology, Faculty of Geographical and Geological Sciences, Adam Mickiewicz University, Poznań, Poland; Center for the Study of Demographic and Economic Structures in Preindustrial Central and Eastern Europe University of Białystok, Poland
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31
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Aoki Y, Sogame Y, Wanner M, Mazei Y, Shimano SD. A New Testate Amoeba, Matsakision ogawaraensis sp. nov. (Silicofilosea: Incertae sedis Euglyphida) from Lake Shore Sand of Northern Japan. ACTA PROTOZOOL 2020. [DOI: 10.4467/16890027ap.20.008.12676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A new species of a testate amoeba, Matsakision ogawaraensis sp. nov., is described from Ogawara pond, Aomori Prefecture, Japan. This is the third species in the genus Matsakision. Matsakision ogawaraensis sp. nov. is distinguished from two other species by the specific form of the shell in apertural view, which is triangular (the shells of other species are circular or elliptic). In addition, it has a chitinous lip around the aperture. For the first time, long needle-like pseudopodia have been observed.
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32
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Whittle A, Amesbury MJ, Charman DJ, Hodgson DA, Perren BB, Roberts SJ, Gallego-Sala AV. Salt-Enrichment Impact on Biomass Production in a Natural Population of Peatland Dwelling Arcellinida and Euglyphida (Testate Amoebae). MICROBIAL ECOLOGY 2019; 78:534-538. [PMID: 30535652 PMCID: PMC6647189 DOI: 10.1007/s00248-018-1296-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
Unicellular free-living microbial eukaryotes of the order Arcellinida (Tubulinea; Amoebozoa) and Euglyphida (Cercozoa; SAR), commonly termed testate amoebae, colonise almost every freshwater ecosystem on Earth. Patterns in the distribution and productivity of these organisms are strongly linked to abiotic conditions-particularly moisture availability and temperature-however, the ecological impacts of changes in salinity remain poorly documented. Here, we examine how variable salt concentrations affect a natural community of Arcellinida and Euglyphida on a freshwater sub-Antarctic peatland. We principally report that deposition of wind-blown oceanic salt-spray aerosols onto the peatland surface corresponds to a strong reduction in biomass and to an alteration in the taxonomic composition of communities in favour of generalist taxa. Our results suggest novel applications of this response as a sensitive tool to monitor salinisation of coastal soils and to detect salinity changes within peatland palaeoclimate archives. Specifically, we suggest that these relationships could be used to reconstruct millennial scale variability in salt-spray deposition-a proxy for changes in wind-conditions-from sub-fossil communities of Arcellinida and Euglyphida preserved in exposed coastal peatlands.
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Affiliation(s)
- Alex Whittle
- Department of Geography, University of Exeter, Exeter, EX4 4RJ, UK.
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - Matthew J Amesbury
- Department of Geography, University of Exeter, Exeter, EX4 4RJ, UK
- Environmental Change Research Unit (ECRU), Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Dan J Charman
- Department of Geography, University of Exeter, Exeter, EX4 4RJ, UK
| | - Dominic A Hodgson
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Department of Geography, Durham University, Durham, DH1 3LE, UK
| | - Bianca B Perren
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Stephen J Roberts
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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33
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Ntakou E, Siemensma F, Bonkowski M, Dumack K. The Dancing Star: Reinvestigation of Artodiscus saltans (Variosea, Amoebozoa) Penard 1890. Protist 2019; 170:349-357. [PMID: 31295666 DOI: 10.1016/j.protis.2019.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 06/05/2019] [Accepted: 06/13/2019] [Indexed: 01/03/2023]
Abstract
Artodiscus saltans, first described by Penard (1890), has a unique morphology. Without genetic data it could not yet been reliably placed into a wider taxonomical context. We present morphological data for A. saltans from different aquatic habitats of four European countries. We subjected three cells of one strain from Germany to molecular analyses and, interestingly, obtained six different rDNA sequences. Phylogenetic analyses of these SSU rDNA sequences revealed that A. saltans branches close to the amoebozoan Multicilia marina (Variosea, Amoebozoa).
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Affiliation(s)
- Efthymia Ntakou
- University of Cologne, Terrestrial Ecology, Institute of Zoology, Zülpicher Str. 47b, 50674 Köln, Germany
| | | | - Michael Bonkowski
- University of Cologne, Terrestrial Ecology, Institute of Zoology, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Kenneth Dumack
- University of Cologne, Terrestrial Ecology, Institute of Zoology, Zülpicher Str. 47b, 50674 Köln, Germany.
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34
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Bian P, Strano J, Zheng P, Steinitz-Kannan M, Clarson SJ, Kannan R, McCarthy TJ. Amoebae Assemble Synthetic Spherical Particles To Form Reproducible Constructs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5069-5074. [PMID: 30888172 DOI: 10.1021/acs.langmuir.9b00333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Difflugia are testate amoebae that use particulate inorganic matter to build a protective shell (generally called a test or theca). Difflugia globulosa were grown both in culture containing only naturally occurring theca-building materials and under conditions where synthetic particles were present also. The presence of monodisperse Stöber silica microspheres of 1, 3, and 6 μm in diameter or 4 μm polystyrene spheres dramatically increased the rate of Difflugia growth, and foreign microspheres became the overwhelmingly dominant construction material. Optical and electron microscopy of the 6 μm particle studies revealed that Difflugia construct spherical vase-shaped thecae with strikingly reproducible composition, morphology, and size. Time-lapse photography revealed construction techniques and masonry skills as Difflugia herded particles together, trapped them using phagocytosis, and applied the particles with biocement from inside the developing theca. The reported observations identify taxonomy complications, biomicrofabrication possibilities, and a discrete environmental impact of synthetic particle pollutants.
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Affiliation(s)
- Pei Bian
- Polymer Science and Engineering Department , University of Massachusetts , Amherst , Massachusetts 01003 , United States
| | - Joseph Strano
- Department of Biological Sciences , Northern Kentucky University , Highland Heights , Kentucky 41099 , United States
| | - Peiwen Zheng
- Polymer Science and Engineering Department , University of Massachusetts , Amherst , Massachusetts 01003 , United States
| | - Miriam Steinitz-Kannan
- Department of Biological Sciences , Northern Kentucky University , Highland Heights , Kentucky 41099 , United States
| | - Stephen J Clarson
- Department of Materials Science and Engineering , University of Cincinnati , Cincinnati , Ohio 45221 , United States
| | - Ramamurthi Kannan
- Department of Biological Sciences , Northern Kentucky University , Highland Heights , Kentucky 41099 , United States
| | - Thomas J McCarthy
- Polymer Science and Engineering Department , University of Massachusetts , Amherst , Massachusetts 01003 , United States
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35
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McKeown MM, Wilmshurst JM, Duckert C, Wood JR, Mitchell EA. Assessing the ecological value of small testate amoebae (<45 μm) in New Zealand peatlands. Eur J Protistol 2019; 68:1-16. [DOI: 10.1016/j.ejop.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 11/16/2022]
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36
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Lahr DJG, Kosakyan A, Lara E, Mitchell EAD, Morais L, Porfirio-Sousa AL, Ribeiro GM, Tice AK, Pánek T, Kang S, Brown MW. Phylogenomics and Morphological Reconstruction of Arcellinida Testate Amoebae Highlight Diversity of Microbial Eukaryotes in the Neoproterozoic. Curr Biol 2019; 29:991-1001.e3. [PMID: 30827918 DOI: 10.1016/j.cub.2019.01.078] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/26/2018] [Accepted: 01/30/2019] [Indexed: 11/26/2022]
Abstract
Life was microbial for the majority of Earth's history, but as very few microbial lineages leave a fossil record, the Precambrian evolution of life remains shrouded in mystery. Shelled (testate) amoebae stand out as an exception with rich documented diversity in the Neoproterozoic as vase-shaped microfossils (VSMs). While there is general consensus that most of these can be attributed to the Arcellinida lineage in Amoebozoa, it is still unclear whether they can be used as key fossils for interpretation of early eukaryotic evolution. Here, we present a well-resolved phylogenomic reconstruction based on 250 genes, obtained using single-cell transcriptomic techniques from a representative selection of 19 Arcellinid testate amoeba taxa. The robust phylogenetic framework enables deeper interpretations of evolution in this lineage and demanded an updated classification of the group. Additionally, we performed reconstruction of ancestral morphologies, yielding hypothetical ancestors remarkably similar to existing Neoproterozoic VSMs. We demonstrate that major lineages of testate amoebae were already diversified before the Sturtian glaciation (720 mya), supporting the hypothesis that massive eukaryotic diversification took place in the early Neoproterozoic and congruent with the interpretation that VSM are arcellinid testate amoebae.
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Affiliation(s)
- Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil.
| | - Anush Kosakyan
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 37005, České Budějovice, Czech Republic
| | - Enrique Lara
- Real Jardín Botánico, CSIC, Plaza Murillo 2, ES 28014 Madrid, Spain; Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland; Botanical Garden of Neuchâtel, Pertuis-du-Sault 58, 2000 Neuchâtel, Switzerland
| | - Luana Morais
- Department of Geophysics, Institute of Astronomy, Geophysics and Atmospheric Sciences, University of São Paulo, Brazil
| | | | - Giulia M Ribeiro
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA
| | - Tomáš Pánek
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA; Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Seungho Kang
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA.
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37
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Baković N, Siemensma FJ, Baković R, Rubinić J. Testate Amoebae in Karst Caves of the Dinaric Arc (South-Eastern Europe) with a Description of Centropyxis bipilata sp. nov. ACTA PROTOZOOL 2019. [DOI: 10.4467/16890027ap.19.018.12020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Karst freshwater caves are subterranean habitats characterized by the constant absence of light and relatively small variations of temperature and air humidity. They are mostly food deprived environments, with the exception if large bat colonies are present or if they are intensively supplied with organic matter by sinking rivers. Even though these habitats are often described as harsh, they have enabled the evolution of highly specialized and often endemic animals. The cave eukaryotic micro-organisms, on the other hand, are scarcely researched. The results of research of testate amoebae in the caves of the Dinaric arc detected 23 species, 12 of which were first found in caves. Also, a description of Centropyxis bipilata sp. nov. is presented. This species is clearly distinguished from other described species based on shell size, the presence of two struts and the usually dark ring around the aperture. Testate amoebae were registered on aquatic and terrestrial cave sediments and transitional habitats (like hygropetric and wet walls). The most frequent species within the samples were: Trinema lineare, Cryptodifflugia oviformis and Centropyxis bipilata sp. nov. Maximum diversity of testate amoebae was registered in Ponor Kovači with twenty species. In 24.4 % of the investigated samples microphototrophs were found, implying good surface-subsurface connectivity that could also affect testate amoebae diversity. This research showed that caves are underestimated habitats that can provide us with new data about the testate amoebae biogeography and diversity.
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38
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Dumack K, Kahlich C, Lahr DJG, Bonkowski M. Reinvestigation of Phryganella paradoxa
(Arcellinida, Amoebozoa) Penard 1902. J Eukaryot Microbiol 2018; 66:232-243. [DOI: 10.1111/jeu.12665] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/27/2018] [Accepted: 06/19/2018] [Indexed: 02/03/2023]
Affiliation(s)
- Kenneth Dumack
- Terrestrial Ecology; Institute of Zoology; University of Cologne; Zülpicher Str. 47b 50674 Köln Germany
- Department of Zoology; Institute of Biosciences; University of São Paulo; Rua do Matão, tv. 14, 101 05508-090 São Paulo Brazil
| | - Christopher Kahlich
- Terrestrial Ecology; Institute of Zoology; University of Cologne; Zülpicher Str. 47b 50674 Köln Germany
| | - Daniel J. G. Lahr
- Department of Zoology; Institute of Biosciences; University of São Paulo; Rua do Matão, tv. 14, 101 05508-090 São Paulo Brazil
| | - Michael Bonkowski
- Terrestrial Ecology; Institute of Zoology; University of Cologne; Zülpicher Str. 47b 50674 Köln Germany
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39
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Bankov N, Todorov M, Ganeva A. Checklist of Sphagnum-dwelling testate amoebae in Bulgaria. Biodivers Data J 2018; 6:e25295. [PMID: 29861653 PMCID: PMC5974006 DOI: 10.3897/bdj.6.e25295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/16/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Until now, a complete checklist of Sphagnum-dwelling testate amoebae in Bulgaria has never been published. Records for species diversity and distribution in the country were scattered in many faunistic and ecological publications. The aim of the present study is to summarise all data for the species distribution at the level of country by reviewing the existing literature and by additional data obtained in our research over the past two years. NEW INFORMATION The checklist comprises 171 species, classified into 43 genera, 20 families, three orders, three classes and three phyla. We present data for 16 new Sphagnum-dwelling testate amoebae in Bulgaria and new distribution data for 134 species. Of them, 99 species are recorded from Stara Planina Mt., for which there was no available data to date. Additionally are recorded 69 new species for Pirin Mt., 21 for Vitosha Mt. and 18 for Rila Mt. Thirty six species are synonymised according to the latest taxonomic changes. Two misidentified taxa (Euglypha brachiata Penard, 1902 and Difflugia compressa var. africana Gauthier-Lièvre et Thomas, 1958) are transferred into valid species E. acanthophora and Zivkovicia compressa, respectively. Three of the recorded species have not been included in the checklist, because they are currently not refering to testate amoebae (Cochliopodium bilimbosum (Auerbach 1856) and Cochliopodium echinatum Korotneef, 1879 are gymnamoebae (naked amoebae) and Microgromia elegantula (Penard 1904) = Paralieberkuehnia elegantula (Penard 1904) is freshwater foraminifera).
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Affiliation(s)
- Nikola Bankov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Anna Ganeva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
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40
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Schulz G, Maraun M, Völcker E, Scheu S, Krashevska V. Evaluation of Morphological Characteristics to Delineate Taxa of the Genus Trigonopyxis (Amoebozoa, Arcellinida). Protist 2018; 169:190-205. [PMID: 29614434 DOI: 10.1016/j.protis.2018.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 10/17/2022]
Abstract
Morphological features are often the only characteristics suitable for identification of taxa in testate amoebae, especially in ecological and palaeoecological studies. However, whereas the morphology of some species is rather stable it may vary considerably in others. Within the order Arcellinida the genus Trigonopyxis with the type species Trigonopyxis arcula is morphologically highly variable. To identify reliable characteristics for morphology-based taxon delineation we investigated variations in shell size, pseudostome diameter and pseudostome form in T. arcula from three different sites of the Ecuadorian Andes, where these characteristics vary even more than previously described. Further, we investigated if morphological characteristics in Trigonopyxis varied with changes in environmental factors. We studied 951 shells of Trigonopyxis collected along an altitudinal gradient with varying abiotic factors. We established a method for characterization of the pseudostome form, which lead to five different morphotypes. Our results suggest that shell size alone is not an appropriate character for taxon delineation but can be used as an indicator for changes in environmental conditions. In contrast, the pseudostome form might be used for taxon delineation, but likely also varies considerably within taxa. Overall, the study provides an overview of the morphological variability of the genus Trigonopyxis.
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Affiliation(s)
- Garvin Schulz
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, D-37073 Göttingen, Germany.
| | - Mark Maraun
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, D-37073 Göttingen, Germany
| | - Eckhard Völcker
- Penard Laboratory, 18 Stellenberg Avenue, Cape Town 7708, South Africa
| | - Stefan Scheu
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, D-37073 Göttingen, Germany
| | - Valentyna Krashevska
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, D-37073 Göttingen, Germany
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41
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Dumack K, Siemensma F, Bonkowski M. Rediscovery of the Testate Amoeba Genus Penardeugenia (Thaumatomonadida, Imbricatea). Protist 2018; 169:29-42. [DOI: 10.1016/j.protis.2017.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/23/2017] [Accepted: 12/09/2017] [Indexed: 11/28/2022]
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42
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Dumack K, Bonkowski M, Clauß S, Völcker E. Phylogeny and Redescription of the Testate Amoeba Diaphoropodon archeri
(Chlamydophryidae, Thecofilosea, Cercozoa), De Saedeleer 1934, and Annotations on the Polyphyly of Testate Amoebae with Agglutinated Tests in the Cercozoa. J Eukaryot Microbiol 2017; 65:308-314. [DOI: 10.1111/jeu.12474] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/27/2017] [Accepted: 09/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Kenneth Dumack
- Department of Terrestrial Ecology; Faculty of Zoology; University of Cologne; Zülpicher Str. 47b Köln 50674 Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology; Faculty of Zoology; University of Cologne; Zülpicher Str. 47b Köln 50674 Germany
| | - Steffen Clauß
- Penard Laboratory; 18 Stellenberg Avenue Cape Town 7708 South Africa
| | - Eckhard Völcker
- Penard Laboratory; 18 Stellenberg Avenue Cape Town 7708 South Africa
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43
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Morphology and phylogeny of the testate amoebae Euglypha bryophila Brown, 1911 and Euglypha cristata Leidy, 1874 (Rhizaria, Euglyphida). Eur J Protistol 2017; 61:76-84. [DOI: 10.1016/j.ejop.2017.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 09/04/2017] [Accepted: 09/11/2017] [Indexed: 11/21/2022]
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44
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Roland TP, Amesbury MJ, Wilkinson DM, Charman DJ, Convey P, Hodgson DA, Royles J, Clauß S, Völcker E. Taxonomic Implications of Morphological Complexity Within the Testate Amoeba Genus Corythion from the Antarctic Peninsula. Protist 2017; 168:565-585. [PMID: 28961456 DOI: 10.1016/j.protis.2017.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 07/03/2017] [Accepted: 07/28/2017] [Indexed: 11/16/2022]
Abstract
Precise and sufficiently detailed morphological taxonomy is vital in biology, for example in the accurate interpretation of ecological and palaeoecological datasets, especially in polar regions, where biodiversity is poor. Testate amoebae on the Antarctic Peninsula (AP) are well-documented and variations in their population size have recently been interpreted as a proxy for microbial productivity changes in response to recent regional climate change. AP testate amoeba assemblages are dominated by a small number of globally ubiquitous taxa. We examine morphological variation in Corythion spp. across the AP, finding clear evidence supporting the presence of two morphospecies. Corythion constricta (Certes 1889) was identified on the AP for the first time and has potentially been previously misidentified. Furthermore, a southerly trend of decreasing average test size in Corythion dubium (Taránek 1881) along the AP suggests adaptive polymorphism, although the precise drivers of this remain unclear, with analysis hindered by limited environmental data. Further work into morphological variation in Corythion is needed elsewhere, alongside molecular analyses, to evaluate the potential for (pseudo)cryptic diversity within the genus. We advocate a parsimonious taxonomical approach that recognises genetic diversity but also examines and develops accurate morphological divisions and descriptions suitable for light microscopy-based ecological and palaeoecological studies.
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Affiliation(s)
- Thomas P Roland
- Geography, College of Life and Environmental Sciences, University of Exeter, UK.
| | - Matthew J Amesbury
- Geography, College of Life and Environmental Sciences, University of Exeter, UK
| | | | - Dan J Charman
- Geography, College of Life and Environmental Sciences, University of Exeter, UK
| | | | | | - Jessica Royles
- British Antarctic Survey, Cambridge, UK; Department of Plant Sciences, University of Cambridge, UK
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Dumack K, Mylnikov AP, Bonkowski M. Evolutionary Relationship of the Scale-Bearing Kraken (incertae sedis, Monadofilosa, Cercozoa, Rhizaria): Combining Ultrastructure Data and a Two-Gene Phylogeny. Protist 2017; 168:362-373. [DOI: 10.1016/j.protis.2017.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/24/2017] [Accepted: 04/30/2017] [Indexed: 11/29/2022]
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46
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Gomaa F, Lahr DJG, Todorov M, Li J, Lara E. A contribution to the phylogeny of agglutinating Arcellinida (Amoebozoa) based on SSU rRNA gene sequences. Eur J Protistol 2017; 59:99-107. [PMID: 28433921 DOI: 10.1016/j.ejop.2017.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 03/17/2017] [Accepted: 03/22/2017] [Indexed: 10/19/2022]
Abstract
Arcellinid testate amoebae include a wide variety of amoeboid organisms whose test (shell) varies in shape, composition and size. A decade ago, we initiated molecular phylogenetic analyses based on SSU rRNA gene sequences and a taxonomic revision of Arcellinida. However, many lineages within Arcellinida still lack molecular data, and the phylogeny of this group is largely incomplete. In this study, we obtained SSU rRNA gene sequences from seven taxa, of which six have agglutinated shell (Difflugia oblonga, D. labiosa, D. gramen, Mediolus corona, Netzelia wailesi, and N. tuberculata), and one has an entirely proteinaceous shell (Arcella intermedia). All species but Difflugia oblonga branched within the recently erected suborder Sphaerothecina, confirming the synapomorphic value of an oviform or discoid shell. Thus, we propose that species with an oviform or discoid shell currently classified within genus Difflugia must be transferred to other genera, thus continuing the process of taxonomic revision of genus Difflugia, the largest Arcellinida genus. We therefore transferred the current and the previously sequenced oviform Difflugia spp. to Netzelia spp., based on the shared globular/oviform shell shape and their monophyly. Another species, D. labiosa, formed an independent lineage that branched as a sister clade to Arcella spp.; based on the shell morphology and their phylogenetic position, we considered D. labiosa as incertae sedis.
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Affiliation(s)
- Fatma Gomaa
- Department of Organismic and Evolutionary Biology, Biological Laboratory, Harvard University, Cambridge, Massachusetts, USA; Ain Shams University, Faculty of Science, Zoology Department, Cairo, Egypt.
| | - Daniel J G Lahr
- Department of Zoology, University of Sao Paulo, Sao Paulo, Brazil
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin St., 1113 Sofia, Bulgaria
| | - Jingchun Li
- Department of Organismic and Evolutionary Biology, Biological Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - Enrique Lara
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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Blandenier Q, Lara E, Mitchell EA, Alcantara DM, Siemensma FJ, Todorov M, Lahr DJ. NAD9/NAD7 (mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene)—A new “Holy Grail” phylogenetic and DNA-barcoding marker for Arcellinida (Amoebozoa)? Eur J Protistol 2017; 58:175-186. [DOI: 10.1016/j.ejop.2016.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 11/22/2016] [Accepted: 12/12/2016] [Indexed: 11/17/2022]
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48
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Porfírio-Sousa AL, Ribeiro GM, Lahr DJ. Morphometric and genetic analysis of Arcella intermedia and Arcella intermedia laevis (Amoebozoa, Arcellinida) illuminate phenotypic plasticity in microbial eukaryotes. Eur J Protistol 2017; 58:187-194. [DOI: 10.1016/j.ejop.2016.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 11/26/2022]
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49
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Polyphyly in the Thecate Amoeba Genus Lecythium (Chlamydophryidae, Tectofilosida, Cercozoa), Redescription of its Type Species L. hyalinum, Description of L. jennyae sp. nov. and the Establishment of Fisculla gen. nov. and Fiscullidae fam. nov. Protist 2017; 168:294-310. [PMID: 28499131 DOI: 10.1016/j.protis.2017.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 02/21/2017] [Accepted: 03/04/2017] [Indexed: 11/21/2022]
Abstract
Although testate amoebae have attracted great interest of protistologists for more than a century, some groups, especially those with a hyaline, organic test (=theca) are still poorly known. One of those is the genus Lecythium Hertwig et Lesser, 1874. Only recently Lecythium spp. were characterized by morphological and molecular means, but data on the type species Lecythium hyalinum Hertwig et Lesser, 1874, was still lacking. In this study, we screened for L. hyalinum in freshwater samples of Germany and the Netherlands. Four different isolates of L. hyalinum and one novel species were cultured and characterized by light microscopy. Phylogenetic analyses based on the small ribosomal subunit (SSU) RNA gene show that the genus Lecythium forms two robust clades, one forming a sister group to the Rhizaspididae/Pseudodifflugiidae clade (Tectofilosida), the other branching within 'Novel Clade 4' (Tectofilosida). We untangle this polyphyly by establishing Fisculla gen. nov. and the Fiscullidae fam. nov. for the former of these two clades.
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Bondarenko NI, Bondarenko AS, Smirnov AV. Lineage-Specific and Highly Derived Gene Sequences Among Amoebozoa, Revealed by the Comparative Analysis of Transcriptomes from Twelve Amoebozoan Species. J Eukaryot Microbiol 2017; 64:622-631. [PMID: 28166371 DOI: 10.1111/jeu.12397] [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: 12/03/2016] [Revised: 01/11/2017] [Accepted: 01/19/2017] [Indexed: 11/28/2022]
Abstract
Amoebozoa represent a difficult group for traditional morphology-based taxonomy. Molecular approaches, such as gene sequencing and DNA barcoding have greatly enhanced our knowledge of the diversity of these organisms. However, metagenomic studies of Amoebozoa still did not provide as impressive results as they did among some other groups of protists. In environmental DNA surveys done on fragments of SSU rDNA gene and other traditional DNA barcodes, Amoebozoa genes normally constitute a minor part of the total gene diversity and represent only the most abundant lineages. A potential way to resolve this problem is the usage of DNA barcodes based on genes, which are unique or highly derived in this group of organisms. In the present study, we attempted to find such genes and gene families with a low level of paralogy, potentially appropriate as Amoebozoa-specific DNA barcodes. For this we re-assembled transcriptomes of 12 amoebozoan species available from the public databases and performed gene annotation and identification of orthologous genes. In our analysis Amoebozoa-specific and highly derived sequences formed 53,182 clusters of orthologs, containing from 2 to 299 proteins each. Some of these genes may be a potential target for DNA barcoding of Amoebozoa.
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Affiliation(s)
- Natalya I Bondarenko
- Department of Invertebrate Zoology, Faculty of Biology, Saint-Petersburg State University, Universitetskaja nab. 7/9, St. Petersburg, 199034, Russia
| | - Anton S Bondarenko
- Faculty of Physics, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Alexey V Smirnov
- Department of Invertebrate Zoology, Faculty of Biology, Saint-Petersburg State University, Universitetskaja nab. 7/9, St. Petersburg, 199034, Russia
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