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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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Weiner AKM, Sehein T, Cote-L’Heureux A, Sleith RS, Greco M, Malekshahi C, Ryan-Embry C, Ostriker N, Katz LA. Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes. Evolution 2023; 77:2472-2483. [PMID: 37672006 PMCID: PMC10629589 DOI: 10.1093/evolut/qpad158] [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: 08/03/2022] [Revised: 08/13/2023] [Accepted: 09/05/2023] [Indexed: 09/07/2023]
Abstract
The enormous population sizes and wide biogeographical distribution of many microbial eukaryotes set the expectation of high levels of intraspecific genetic variation. However, studies investigating protist populations remain scarce, mostly due to limited 'omics data. Instead, most genetics studies of microeukaryotes have thus far relied on single loci, which can be misleading and do not easily allow for detection of recombination, a hallmark of sexual reproduction. Here, we analyze >40 genes from 72 single-cell transcriptomes from two morphospecies-Hyalosphenia papilio and Hyalosphenia elegans-of testate amoebae (Arcellinida, Amoebozoa) to assess genetic diversity in samples collected over four years from New England bogs. We confirm the existence of cryptic species based on our multilocus dataset, which provides evidence of recombination within and high levels of divergence between the cryptic species. At the same time, total levels of genetic diversity within cryptic species are low, suggesting that these abundant organisms have small effective population sizes, perhaps due to extinction and repopulation events coupled with efficient modes of dispersal. This study is one of the first to investigate population genetics in uncultivable heterotrophic protists using transcriptomics data and contributes towards understanding cryptic species of nonmodel microeukaryotes.
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Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bergen, Norway
| | - Taylor Sehein
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Robin S Sleith
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Mattia Greco
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Clara Malekshahi
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Chase Ryan-Embry
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Naomi Ostriker
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, MA, United States
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3
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Weiner AKM, Katz LA. Epigenetics as Driver of Adaptation and Diversification in Microbial Eukaryotes. Front Genet 2021; 12:642220. [PMID: 33796133 PMCID: PMC8007921 DOI: 10.3389/fgene.2021.642220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Affiliation(s)
- Agnes K M Weiner
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States.,Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States
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4
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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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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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6
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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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7
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Tikhonenkov DV, Jhin SH, Eglit Y, Miller K, Plotnikov A, Simpson AGB, Park JS. Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats. PLoS One 2019; 14:e0216188. [PMID: 31465455 PMCID: PMC6715209 DOI: 10.1371/journal.pone.0216188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/14/2019] [Indexed: 12/26/2022] Open
Abstract
The heterotrophic flagellate Percolomonas cosmopolitus (Heterolobosea) is often observed in saline habitats worldwide, from coastal waters to saturated brines. However, only two cultures assigned to this morphospecies have been examined using molecular methods, and their 18S rRNA gene sequences are extremely different. Further the salinity tolerances of individual strains are unknown. Thus, our knowledge on the autecology and diversity in this morphospecies is deficient. Here, we report 18S rRNA gene data on seven strains similar to P. cosmopolitus from seven geographically remote locations (New Zealand, Kenya, Korea, Poland, Russia, Spain, and the USA) with sample salinities ranging from 4‰ to 280‰, and compare morphology and salinity tolerance of the nine available strains. Percolomonas cosmopolitus-like strains show few-to-no consistent morphological differences, and form six clades separated by often extremely large 18S rRNA gene divergences (up to 42.4%). Some strains grow best at salinities from 75 to 125‰ and represent halophiles. All but one of these belong to two geographically heterogeneous clusters that form a robust monophyletic group in phylogenetic trees; this likely represents an ecologically specialized subclade of halophiles. Our results suggest that P. cosmopolitus is a cluster of several cryptic species (at least), which are unlikely to be distinguished by geography. Interestingly, the 9 Percolomonas strains formed a clade in 18S rRNA gene phylogenies, unlike most previous analyses based on two sequences.
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Affiliation(s)
- Denis V. Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Soo Hwan Jhin
- Department of Oceanography, Research Institute for Dok-do and Ulleung-do Island and Kyungpook Institute of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, Korea
| | - Yana Eglit
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kai Miller
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrey Plotnikov
- Center of Shared Scientific Equipment “Persistence of Microorganisms”, Institute for Cellular and Intracellular Symbiosis UB RAS, Orenburg, Russia
| | - Alastair G. B. Simpson
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, Program in Integrated Microbial Diversity, Toronto, Ontario, Canada
| | - Jong Soo Park
- Department of Oceanography, Research Institute for Dok-do and Ulleung-do Island and Kyungpook Institute of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, Korea
- * E-mail:
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8
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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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Kosakyan A, Lahr DJG, Mulot M, Meisterfeld R, Mitchell EAD, Lara E. Phylogenetic reconstruction based on
COI
reshuffles the taxonomy of hyalosphenid shelled (testate) amoebae and reveals the convoluted evolution of shell plate shapes. Cladistics 2016; 32:606-623. [DOI: 10.1111/cla.12167] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2016] [Indexed: 11/28/2022] Open
Affiliation(s)
- Anush Kosakyan
- Laboratory of Evolutionary Protistology Institute of Biosciences University of Sao Paulo Matão Travessa 14 Cidade Universitária Sao Paulo 05508‐090 SP Brazil
| | - Daniel J. G. Lahr
- Laboratory of Evolutionary Protistology Institute of Biosciences University of Sao Paulo Matão Travessa 14 Cidade Universitária Sao Paulo 05508‐090 SP Brazil
| | - Matthieu Mulot
- Laboratory of Soil Biodiversity University of Neuchatel Rue Emile‐Argand 11 Neuchatel 2000 Switzerland
| | - Ralf Meisterfeld
- Institute for Biology II (Zoology) RWTH Aachen University Worringerweg 3 Aachen 52056 Germany
| | - Edward A. D. Mitchell
- Laboratory of Soil Biodiversity University of Neuchatel Rue Emile‐Argand 11 Neuchatel 2000 Switzerland
- Jardin Botanique de Neuchâtel Chemin du Perthuis‐du‐Sault 58 Neuchâtel 2000 Switzerland
| | - Enrique Lara
- Laboratory of Soil Biodiversity University of Neuchatel Rue Emile‐Argand 11 Neuchatel 2000 Switzerland
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15
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Royles J, Amesbury MJ, Roland TP, Jones GD, Convey P, Griffiths H, Hodgson DA, Charman DJ. Moss stable isotopes (carbon-13, oxygen-18) and testate amoebae reflect environmental inputs and microclimate along a latitudinal gradient on the Antarctic Peninsula. Oecologia 2016; 181:931-45. [PMID: 27003701 PMCID: PMC4912596 DOI: 10.1007/s00442-016-3608-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 03/08/2016] [Indexed: 11/27/2022]
Abstract
The stable isotope compositions of moss tissue water (δ(2)H and δ(18)O) and cellulose (δ(13)C and δ(18)O), and testate amoebae populations were sampled from 61 contemporary surface samples along a 600-km latitudinal gradient of the Antarctic Peninsula (AP) to provide a spatial record of environmental change. The isotopic composition of moss tissue water represented an annually integrated precipitation signal with the expected isotopic depletion with increasing latitude. There was a weak, but significant, relationship between cellulose δ(18)O and latitude, with predicted source water inputs isotopically enriched compared to measured precipitation. Cellulose δ(13)C values were dependent on moss species and water content, and may reflect site exposure to strong winds. Testate amoebae assemblages were characterised by low concentrations and taxonomic diversity, with Corythion dubium and Microcorycia radiata types the most cosmopolitan taxa. The similarity between the intra- and inter-site ranges measured in all proxies suggests that microclimate and micro-topographical conditions around the moss surface were important determinants of proxy values. Isotope and testate amoebae analyses have proven value as palaeoclimatic, temporal proxies of climate change, whereas this study demonstrates that variations in isotopic and amoeboid proxies between microsites can be beyond the bounds of the current spatial variability in AP climate.
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Affiliation(s)
- Jessica Royles
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
| | - Matthew J Amesbury
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4RJ, UK
| | - Thomas P Roland
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4RJ, UK
| | - Glyn D Jones
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Peter Convey
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Dominic A Hodgson
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Dan J Charman
- Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4RJ, UK
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16
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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: 49] [Impact Index Per Article: 6.1] [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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17
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Oliverio AM, Lahr DJG, Grant J, Katz LA. Are microbes fundamentally different than macroorganisms? Convergence and a possible case for neutral phenotypic evolution in testate amoeba (Amoebozoa: Arcellinida). ROYAL SOCIETY OPEN SCIENCE 2015; 2:150414. [PMID: 27019725 PMCID: PMC4807447 DOI: 10.1098/rsos.150414] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
This study reveals extensive phenotypic convergence based on the non-monophyly of genera and morphospecies of testate (shelled) amoebae. Using two independent markers, small subunit ribosomal DNA (ssu-rDNA) and mitochondrial cytochrome oxidase I (COI), we demonstrate discordance between morphology and molecules for 'core Nebela' species (Arcellinida; Amoebozoa). Prior work using just a single locus, ssu-rDNA, also supported the non-monophyly of the genera Hyalosphenia and Nebela as well as for several morphospecies within these genera. Here, we obtained COI gene sequences of 59 specimens from seven morphospecies and ssu-rDNA gene sequences of 50 specimens from six morphospecies of hyalosphenids. Our analyses corroborate the prior ssu-rDNA findings of morphological convergence in test (shell) morphologies, as COI and ssu-rDNA phylogenies are concordant. Further, the monophyly of morphospecies is rejected using approximately unbiased tests. Given that testate amoebae are used as bioindicators in both palaeoecological and contemporary studies of threatened ecosystems such as bogs and fens, understanding the discordance between morphology and genetics in the hyalosphenids is essential for interpretation of indicator species. Further, while convergence is normally considered the result of natural selection, it is possible that neutrality underlies phenotypic evolution in these microorganisms.
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Affiliation(s)
- Angela M. Oliverio
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Daniel J. G. Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Jessica Grant
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
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18
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Lahr DJG, Bosak T, Lara E, Mitchell EAD. The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems. PeerJ 2015; 3:e1234. [PMID: 26734499 PMCID: PMC4699787 DOI: 10.7717/peerj.1234] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/19/2015] [Indexed: 11/20/2022] Open
Abstract
The terrestrial cycling of Si is thought to have a large influence on the terrestrial and marine primary production, as well as the coupled biogeochemical cycles of Si and C. Biomineralization of silica is widespread among terrestrial eukaryotes such as plants, soil diatoms, freshwater sponges, silicifying flagellates and testate amoebae. Two major groups of testate (shelled) amoebae, arcellinids and euglyphids, produce their own silica particles to construct shells. The two are unrelated phylogenetically and acquired biomineralizing capabilities independently. Hyalosphenids, a group within arcellinids, are predators of euglyphids. We demonstrate that hyalosphenids can construct shells using silica scales mineralized by the euglyphids. Parsimony analyses of the current hyalosphenid phylogeny indicate that the ability to “steal” euglyphid scales is most likely ancestral in hyalosphenids, implying that euglyphids should be older than hyalosphenids. However, exactly when euglyphids arose is uncertain. Current fossil record contains unambiguous euglyphid fossils that are as old as 50 million years, but older fossils are scarce and difficult to interpret. Poor taxon sampling of euglyphids has also prevented the development of molecular clocks. Here, we present a novel molecular clock reconstruction for arcellinids and consider the uncertainties due to various previously used calibration points. The new molecular clock puts the origin of hyalosphenids in the early Carboniferous (∼370 mya). Notably, this estimate coincides with the widespread colonization of land by Si-accumulating plants, suggesting possible links between the evolution of Arcellinid testate amoebae and the expansion of terrestrial habitats rich in organic matter and bioavailable Si.
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Affiliation(s)
- Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo , Rua do Matão, São Paulo , Brazil
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary Sciences, Massachussetts Institute of Technology , Cambridge, MA , USA
| | - Enrique Lara
- Laboratory of Soil Biology, University of Neuchatel , Neuchatel , Switzerland
| | - Edward A D Mitchell
- Laboratory of Soil Biology, University of Neuchatel, Neuchatel, Switzerland; Jardin Botanique de Neuchâtel, Neuchatel, Switzerland
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19
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Fučíková K, Lahr DJG. Uncovering Cryptic Diversity in Two Amoebozoan Species Using Complete Mitochondrial Genome Sequences. J Eukaryot Microbiol 2015. [PMID: 26211788 DOI: 10.1111/jeu.12253] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Amoebozoa are a major eukaryotic lineage that encompasses a wide range of amoeboid organisms. The group is understudied from a systematic perspective: molecular tools have only been applied in the last 15 yr. Hence, there is an undersampling of both genes and taxa in the group especially compared to plants, animals, and fungi. Here, we present the complete mitochondrial genomes of two ubiquitous and abundant morpho-species (Acanthamoeba castellanii and Vermamoeba vermiformis). Both have mitochondrial genomes of close relatives previously available, enabling insights into recent divergences at a genomic scale, while simultaneously offering comparisons with divergence estimates obtained from traditionally used single genes, SSU rDNA and cox1. The newly sequenced mt genomes are significantly divergent from their previously sequenced conspecifics (A. castellannii 16.4% divergence at nucleotide level and 10.4% amino acid; V. vermiformis 21.6% and 13.1%, respectively), while divergence at the small subunit ribosomal DNA is below 1% within both species. Morphological analyses determined that these lineages are indistinguishable from their previously sequenced counterparts. Phylogenetic reconstructions using 26 mt genes also indicate a level of divergence that is comparable to divergence among species, while reconstructions using the small subunit ribosomal DNA (SSU rDNA) do not. In addition, we demonstrate that between closely related taxa, there are high levels of synteny, which can be explored for primer design to obtain larger fragments than the traditional barcoding genes. We conclude that, although most systematic work has relied on SSU, this gene alone can severely underestimate diversity. Thus, we suggest that the mt genome emerges as an alternative for unraveling the lower level phylogenetic relationships of Amoebozoa.
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Affiliation(s)
- Karolina Fučíková
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-090, Brazil
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20
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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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21
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Lahr DJG, Laughinghouse HD, Oliverio AM, Gao F, Katz LA. How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth. Bioessays 2014; 36:950-9. [PMID: 25156897 DOI: 10.1002/bies.201400056] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on both the molecular and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are genetically distinct and (ii) morphologically distinct individuals that are genetically the same. We argue that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis.
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Affiliation(s)
- Daniel J G Lahr
- Department of Zoology, University of Sao Paulo, Sao Paulo, Brazil
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22
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Grattepanche JD, Santoferrara LF, McManus GB, Katz LA. Diversity of diversity: conceptual and methodological differences in biodiversity estimates of eukaryotic microbes as compared to bacteria. Trends Microbiol 2014; 22:432-7. [PMID: 24814699 DOI: 10.1016/j.tim.2014.04.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 03/31/2014] [Accepted: 04/11/2014] [Indexed: 01/05/2023]
Abstract
Recent advances such as high-throughput sequencing (HTS) have changed conceptions about the magnitude of diversity on Earth. This is especially true for microbial lineages, which have seen the discovery of great numbers of rare forms in places such as the human gut as well as diverse environments (e.g., freshwater, marine, and soil). Given the differences in perceptions of diversity for bacterial and eukaryotic microbes, including divergent species concepts, HTS tools used to eliminate errors and population-level variation in bacteria may not be appropriate for microbial eukaryotes and may eliminate valid species from the data. We discuss here how the nature of biodiversity varies among microbial groups and the extent to which HTS tools designed for bacteria are useful for eukaryotes.
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Affiliation(s)
| | | | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA.
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