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Dufour OK, Hoffman E, Sleith RS, Katz LA, Weiner AKM, Sehein TR. Testate amoebae (Arcellinida, Amoebozoa) community diversity in New England bogs and fens assessed through lineage-specific amplicon sequencing. Eur J Protistol 2024; 92:126049. [PMID: 38163403 PMCID: PMC11130782 DOI: 10.1016/j.ejop.2023.126049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Testate amoebae (order Arcellinida) are abundant in freshwater ecosystems, including low pH bogs and fens. Within these environments, Arcellinida are considered top predators in microbial food webs and their tests are useful bioindicators of paleoclimatic changes and anthropogenic pollutants. Accurate species identifications and characterizations of diversity are important for studies of paleoclimate, microbial ecology, and environmental change; however, morphological species definitions mask cryptic diversity, which is a common phenomenon among microbial eukaryotes. Lineage-specific primers recently designed to target Arcellinida for amplicon sequencing successfully captured a poorly-described yet diverse fraction of the microbial eukaryotic community. Here, we leveraged the application of these newly-designed primers to survey the diversity of Arcellinida in four low-pH New England bogs and fens, investigating variation among bogs (2018) and then across seasons and habitats within two bogs (2019). Three OTUs represented 66% of Arcellinida reads obtained across all habitats surveyed. 103 additional OTUs were present in lower abundance with some OTUs detected in only one sampling location, suggesting habitat specificity. By establishing a baseline for Arcellinida diversity, we provide a foundation to monitor key taxa in habitats that are predicted to change with increasing anthropogenic pressure and rapid climate change.
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Affiliation(s)
- Olivia K Dufour
- Smith College, Department of Biological Sciences, Northampton, MA, USA
| | - Evie Hoffman
- Smith College, Department of Biological Sciences, Northampton, MA, USA
| | - Robin S Sleith
- Smith College, Department of Biological Sciences, Northampton, MA, USA
| | - Laura A Katz
- Smith College, Department of Biological Sciences, Northampton, MA, USA; University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, MA, USA.
| | - Agnes K M Weiner
- Smith College, Department of Biological Sciences, Northampton, MA, USA; NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bergen, Norway
| | - Taylor R Sehein
- Smith College, Department of Biological Sciences, Northampton, MA, USA
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2
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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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3
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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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4
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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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5
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Marcisz K, Jassey VEJ, Kosakyan A, Krashevska V, Lahr DJG, Lara E, Lamentowicz Ł, Lamentowicz M, Macumber A, Mazei Y, Mitchell EAD, Nasser NA, Patterson RT, Roe HM, Singer D, Tsyganov AN, Fournier B. Testate Amoeba Functional Traits and Their Use in Paleoecology. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.575966] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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6
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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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7
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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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8
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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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9
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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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10
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Mulot M, Marcisz K, Grandgirard L, Lara E, Kosakyan A, Robroek BJM, Lamentowicz M, Payne RJ, Mitchell EAD. Genetic Determinism vs. Phenotypic Plasticity in Protist Morphology. J Eukaryot Microbiol 2017; 64:729-739. [DOI: 10.1111/jeu.12406] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/05/2017] [Accepted: 02/16/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Matthieu Mulot
- Laboratory of Soil Biodiversity; University of Neuchatel; Rue Emile-Argand 11 Neuchatel 2000 Switzerland
- EPEP - UMR 7144; CNRS - UPMC Roscoff Biological Station; Place Georges Teissier 29680 Roscoff France
| | - Katarzyna Marcisz
- Laboratory of Wetland Ecology and Monitoring & Department of Biogeography and Paleoecology; Adam Mickiewicz University; Krygowskiego 10 Poznan 61-680 Poland
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research; University of Bern; Altenbergrain 21 CH-3013 Bern Switzerland
| | - Lara Grandgirard
- Laboratory of Soil Biodiversity; University of Neuchatel; Rue Emile-Argand 11 Neuchatel 2000 Switzerland
| | - Enrique Lara
- Laboratory of Soil Biodiversity; University of Neuchatel; Rue Emile-Argand 11 Neuchatel 2000 Switzerland
| | - Anush Kosakyan
- Laboratory of Evolutionary Protistology, Institute of Biosciences; University of Sao Paulo; Matao Travessa 14 Cidade Universitaria Sao Paulo 05508-090 SP Brazil
- Biology Center (Institute of Parasitology); Czech Academy of Sciences; Branišovská 1160/31 37005 České Budějovice Czech Republic
| | - Bjorn J. M. Robroek
- Ecology and Biodiversity Group, Faculty of Science; Utrecht University; Padualaan 8 Utrecht 3585 CH The Netherlands
- Ecole Polytechnique Federale de Lausanne; Ecological Systems Laboratory; Lausanne CH-1015 Switzerland
- WSL Swiss Federal Institute for Forest, Snow and Landscape Research; Site Lausanne Lausanne CH-1015 Switzerland
| | - Mariusz Lamentowicz
- Laboratory of Wetland Ecology and Monitoring & Department of Biogeography and Paleoecology; Adam Mickiewicz University; Krygowskiego 10 Poznan 61-680 Poland
| | - Richard J. Payne
- Environment; University of York; York YO105DD United Kingdom
- Department of Zoology and Ecology; Penza State University; Krasnaya street 40 440026 Penza Russia
| | - Edward A. D. Mitchell
- Laboratory of Soil Biodiversity; University of Neuchatel; Rue Emile-Argand 11 Neuchatel 2000 Switzerland
- Jardin Botanique de Neuchatel; Chemin du Perthuis-du-Sault 58 Neuchatel 2000 Switzerland
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11
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Liu L, Liu M, Wilkinson DM, Chen H, Yu X, Yang J. DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes. Mol Ecol Resour 2017; 17:991-1002. [PMID: 28063202 DOI: 10.1111/1755-0998.12652] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 12/29/2016] [Accepted: 01/04/2017] [Indexed: 11/27/2022]
Abstract
Microeukaryotic plankton (0.2-200 μm) are critical components of aquatic ecosystems and key players in global ecological processes. High-throughput sequencing is currently revolutionizing their study on an unprecedented scale. However, it is currently unclear whether we can accurately, effectively and quantitatively depict the microeukaryotic plankton communities using traditional size-fractionated filtering combined with molecular methods. To address this, we analysed the eukaryotic plankton communities both with, and without, prefiltering with a 200 μm pore-size sieve -by using SSU rDNA-based high-throughput sequencing on 16 samples with three replicates in each sample from two subtropical reservoirs sampled from January to October in 2013. We found that ~25% reads were classified as metazoan in both size groups. The species richness, alpha and beta diversity of plankton community and relative abundance of reads in 99.2% eukaryotic OTUs showed no significant changes after prefiltering with a 200 μm pore-size sieve. We further found that both >0.2 μm and 0.2-200 μm eukaryotic plankton communities, especially the abundant plankton subcommunities, exhibited very similar, and synchronous, spatiotemporal patterns and processes associated with almost identical environmental drivers. The lack of an effect on community structure from prefiltering suggests that environmental DNA from larger metazoa is introduced into the smaller size class. Therefore, size-fractionated filtering with 200 μm is insufficient to discriminate between the eukaryotic plankton size groups in metabarcoding approaches. Our results also highlight the importance of sequencing depth, and strict quality filtering of reads, when designing studies to characterize microeukaryotic plankton communities.
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Affiliation(s)
- Lemian Liu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Min Liu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - David M Wilkinson
- School of Natural Science and Psychology, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK.,School of Life Sciences, University of Lincoln, Lincoln, LN6 7TS, UK
| | - Huihuang Chen
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Xiaoqing Yu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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12
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Relationships between environmental conditions and the morphological variability of planktonic testate amoeba in four neotropical floodplains. Eur J Protistol 2016; 56:180-190. [PMID: 27682890 DOI: 10.1016/j.ejop.2016.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 08/20/2016] [Accepted: 08/21/2016] [Indexed: 11/23/2022]
Abstract
Planktonic testate amoebae in floodplains exhibit a broad-range of morphological variability. The variation size is already known, but it is necessary to know how this is for morphological variables. This study aimed to identify the relationships between testate amoebae morphology and environmental factors in four neotropical floodplains. We conducted detailed morphometric analyses on 27 common species of planktonic testate amoebae from genera Arcella, Centropyxis, Cucurbitella, Suiadifflugia, Difflugia, Lesquereusia and Netzelia. We sampled subsurface water from each lake in 72 lakes in four Brazilian floodplain lakes. Our goals were to assess: (1) the range of their morphological variability (a) over space within each floodplain, and (b) among the four floodplains, and (c) over time, and (2) which environmental factors explained this variation. Mean shell height and breadth varied considerably among the different floodplain lakes, especially in the Pantanal and Amazonian floodplains. The morphological variability of testate amoeba was correlated to environmental conditions (ammonia, nitrate, phosphate, chlorophyll-a, turbidity, temperature, and depth). Thus, understanding the morphological variation of the testate amoeba species can elucidate many questions involving the ecology of these organisms. Furthermore, could help molecular studies, bioindicator role of these organisations, environmental reconstruction, among others.
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13
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Filker S, Sommaruga R, Vila I, Stoeck T. Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns. Mol Ecol 2016; 25:2286-301. [PMID: 27029537 DOI: 10.1111/mec.13633] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 02/11/2016] [Accepted: 03/29/2016] [Indexed: 11/27/2022]
Abstract
Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high-mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high-mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We therefore expected that these ecosystems support a plankton diversity that differs notably from other freshwater lakes. In addition, we hypothesized that the communities under study exhibit geographic structuring. Our rationale was that geographic dispersal of small-sized eukaryotes in high-mountain lakes over continental distances seems difficult. We analysed hypervariable V4 fragments of the SSU rRNA gene to compare the genetic microbial eukaryote diversity in high-mountain lakes located in the European Alps, the Chilean Altiplano and the Ethiopian Bale Mountains. Microbial eukaryotes were not globally distributed corroborating patterns found for bacteria, multicellular animals and plants. Instead, the plankton community composition emerged as a highly specific fingerprint of a geographic region even on higher taxonomic levels. The intraregional heterogeneity of the investigated lakes was mirrored in shifts in microbial eukaryote community structure, which, however, was much less pronounced compared with interregional beta-diversity. Statistical analyses revealed that on a regional scale, environmental factors are strong predictors for plankton community structures in high-mountain lakes. While on long-distance scales (>10 000 km), isolation by distance is the most plausible scenario, on intermediate scales (up to 6000 km), both contemporary environmental factors and historical contingencies interact to shift plankton community structures.
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Affiliation(s)
- Sabine Filker
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Ruben Sommaruga
- Institute of Ecology, Lake and Glacier Research Group, University of Innsbruck, Innsbruck, 6020, Austria
| | - Irma Vila
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, 67663, Germany
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14
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Kosakyan A, Gomaa F, Lara E, Lahr DJG. Current and future perspectives on the systematics, taxonomy and nomenclature of testate amoebae. Eur J Protistol 2016; 55:105-117. [PMID: 27004416 DOI: 10.1016/j.ejop.2016.02.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 12/09/2015] [Accepted: 02/08/2016] [Indexed: 10/22/2022]
Abstract
Testate amoebae are a polyphyletic assemblage of at least three major, unrelated taxonomic groups of unicellular amoeboid eukaryotes exhibiting a test. The focus on testate amoebae in scientific research has greatly increased in the past 20 years: from an average of about 5 papers a year in the mid-1990s to the current rate of more than 50 papers published yearly. The application range of these organisms is rapidly expanding as well: from the traditional fields of environmental monitoring and paleoecology, to forensic sciences and ecotoxicology studies. These developments are nevertheless strongly dependent on reliable taxonomy and nomenclature. However, scientometric data reveal that despite an ever-increasing necessity for the use of names (the product of taxonomy), the corresponding effort has not been achieved for improving testate amoebae systematics. As a consequence, inaccurate taxonomy yields to misinterpretations in the diversity of the organisms and to potentially incorrect conclusions. These and related problems are discussed in this study, highlighting the outcome of poor taxonomic expertise in accurate classification and phylogeny of testate amoebae, and the consequences derived from it. Additionally, this study is aimed to discuss the current status of testate amoebae classification, and to present all nomenclature and taxonomic changes in higher and lower taxonomic levels of testate amoebae, as a result of recent molecular reconstructions. Finally, we conclude with a list of the needs and suggestions toward a unified and modernized taxonomy of testate amoebae.
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Affiliation(s)
- Anush Kosakyan
- Institute of Biosciences, Department of Zoology, University of Sao Paulo, Rua do Matão, Travessa 14, Cidade Universitária, 05508-090 Sao Paulo, SP, Brazil
| | - Fatma Gomaa
- Department of Organismic and Evolutionary Biology, Biological Laboratory, Harvard University, Cambridge, MA, USA; Zoology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Enrique Lara
- Laboratory of Soil Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Switzerland
| | - Daniel J G Lahr
- Institute of Biosciences, Department of Zoology, University of Sao Paulo, Rua do Matão, Travessa 14, Cidade Universitária, 05508-090 Sao Paulo, SP, Brazil.
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Hydroecology of Amazonian lacustrine Arcellinida (testate amoebae): A case study from Lake Quistococha, Peru. Eur J Protistol 2015; 51:460-9. [PMID: 26410188 DOI: 10.1016/j.ejop.2015.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/11/2015] [Accepted: 06/30/2015] [Indexed: 11/22/2022]
Abstract
Organic rich sediments were obtained from seven core tops taken in Lake Quistococha, near the city of Iquitos in the Peruvian Amazon. Subsamples from 0 to 4cm depth in each core were analyzed under dissecting light microscopy to carry out the first investigation of Arcellinida (testate lobose amoebae) from a lacustrine environment in this ecologically important region. The fauna was characterized by a low diversity, low abundance community dominated by centropyxids. This fauna is similar to 'stressed' assemblages reported from temperate latitudes, except that test concentrations were two orders of magnitude lower than typical in temperate lakes. Principle arcellinidan stressors in Lake Quistococha likely include the low pH 4 conditions in the lake, and a general lack of suitable minerogenic material to construct tests in the organic rich lake substrate. The low pH conditions are the result of runoff and seepage of water high in dissolved organic carbon from the adjacent similarly low pH 4 terrestrial peatland. The dearth of minerogenic material is the result of the lake being isolated from riverine input for the past ∼2000 years, even during flooding events. Other limiting factors contributing to depressed arcellinidan populations may include nutrient supply, predation pressure, competition, and post-mortem taphonomic factors.
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