1
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Zhang T, Rurik I, Vďačný P. A holistic approach to inventory the diversity of mobilid ciliates (Protista: Ciliophora: Peritrichia). ORG DIVERS EVOL 2023. [DOI: 10.1007/s13127-022-00601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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2
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Rataj M, Zhang T, Vd’ačný P. Nuclear and Mitochondrial SSU rRNA Genes Reveal Hidden Diversity of Haptophrya Endosymbionts in Freshwater Planarians and Challenge Their Traditional Classification in Astomatia. Front Microbiol 2022; 13:830951. [PMID: 35495648 PMCID: PMC9048206 DOI: 10.3389/fmicb.2022.830951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Like many other aquatic animals, freshwater planarians have also become partners of symbiotic ciliates from the class Oligohymenophorea. In the present study, we explored the hidden diversity and addressed the questionable systematic position of mouthless obligatory gut endosymbionts of freshwater planarians, using the nuclear and mitochondrial SSU rRNA genes. Although all isolated ciliates morphologically corresponded to a single species, molecular analyses suggested the existence of three genetically distinct entities: Haptophrya planariarum, Haptophrya dugesiarum nov. spec., and Haptophrya schmidtearum nov. spec. The two former species share the same planarian host, which indicates a speciation model involving one duplication event without host switching. Such a diversification pattern was recognized also in astome ciliates inhabiting megascolecid and glossoscolecid earthworms. The present multi-gene phylogenies along with the secondary structure of the mitochondrial 16S rRNA molecule, however, challenge the traditional classification of Haptophrya within the subclass Astomatia. Haptophrya very likely evolved from an orphan scuticociliate lineage by the loss of oral apparatus and by the transformation of the thigmotactic field into an adhesive sucker. Since astomy evolved multiple times independently within the Oligohymenophorea, the loss of cell mouth cannot be used as a sole argument for the assignment of Haptophrya to the Astomatia anymore.
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Affiliation(s)
| | | | - Peter Vd’ačný
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
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3
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Paramecium bursaria—A Complex of Five Cryptic Species: Mitochondrial DNA COI Haplotype Variation and Biogeographic Distribution. DIVERSITY 2021. [DOI: 10.3390/d13110589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ciliates are a diverse protistan group and many consist of cryptic species complexes whose members may be restricted to particular biogeographic locations. Mitochondrial genes, characterized by a high resolution for closely related species, were applied to identify new species and to distinguish closely related morphospecies. In the current study, we analyzed 132 sequences of COI mtDNA fragments obtained from P. bursaria species collected worldwide. The results allowed, for the first time, to generate a network of COI haplotypes and demonstrate the relationships between P. bursaria strains, as well as to confirm the existence of five reproductively isolated haplogroups. The P. bursaria haplogroups identified in the present study correspond to previously reported syngens (R1, R2, R3, R4, and R5), thus we decided to propose the following binominal names for each of them: P. primabursaria, P. bibursaria, P. tribursaria, P. tetrabursaria, and P. pentabursaria, respectively. The phylogeographic distribution of P. bursaria species showed that P. primabursaria and P. bibursaria were strictly Eurasian, except for two South Australian P. bibursaria strains. P. tribursaria was found mainly in Eastern Asia, in two stands in Europe and in North America. In turn, P. tetrabursaria was restricted to the USA territory, whereas P. pentabursaria was found in two European localities.
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4
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Dong C, Jia Y, Han M, Chen W, Mou D, Feng C, Jia J, Liu X. Phylogenetic analysis of eight species of Anomopoda based on transcriptomic and mitochondrial DNA sequences. Gene 2021; 787:145639. [PMID: 33848576 DOI: 10.1016/j.gene.2021.145639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/10/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Anomopoda is the widespread planktonic microcrustacean, which plays a crucial role in aquatic ecosystem. There are few studies about the evolutionary relationships among various Anomopoda basing on molecular data. In the present study, phylogenetic analysis of eight Anomopoda was carried out. Firstly, the culture system was developed to breed cladocerans. By using this system, eight species (Daphnia magna, D. pulex, D. sinensis, Ceriodaphnia reticulata, Moina micrura, Scapholeberis kingi, Simocephalus vetulus and Eurycercus lamellatus) were purified and cultured stably in the laboratory. Then, transcriptomic sequences and partial mitochondrial DNA sequences were both used to reconstruct the phylogenetic tree among 8 species. Transcriptomic sequences were sequenced on Illumina Hiseq 2500 platform. After assembly and annotation, transcriptomic sequences were spliced together and aligned for phylogenetic analysis. Basing on the orthologous genes derived from transcriptomic sequences, the phylogenetic analysis showed that 4 genera of Daphniidae were clustered into one group, and among the 4 genera, Ceriodaphnia was closer to Daphnia than Simocephalus, while Scapholeberis was farthest from other species. In addition, Eurycercidae was closer to Daphniidae than Moinidae. The phylogenetic trees based on both 12S rRNA and 16S rRNA sequences were similar with that based on transcriptomic sequences. Meanwhile, the phylogenetic tree based on 16S rRNA sequences was more suitable than that based on 12S rRNA sequences. These results suggested that the phylogenetic analysis basing on the transcriptomic sequences was available in cladocerans, which will help us to effectively understand the phylogenetic relationships among various cladocerans.
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Affiliation(s)
- Chenchen Dong
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongyi Jia
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China
| | - Mengqi Han
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenkai Chen
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Dezhen Mou
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Cui Feng
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingyi Jia
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangjiang Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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5
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Schiwitza S, Nitsche F. A Needle in the Haystack – Mapping Sequences to Morphology Exemplified by the Loricate Choanoflagellate Enibas thessalia sp. nov. (Acanthoecida, Acanthoecidae). Protist 2021; 172:125782. [DOI: 10.1016/j.protis.2020.125782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/16/2020] [Accepted: 11/22/2020] [Indexed: 01/28/2023]
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6
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Coenen AR, Hu SK, Luo E, Muratore D, Weitz JS. A Primer for Microbiome Time-Series Analysis. Front Genet 2020; 11:310. [PMID: 32373155 PMCID: PMC7186479 DOI: 10.3389/fgene.2020.00310] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 03/16/2020] [Indexed: 12/22/2022] Open
Abstract
Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.
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Affiliation(s)
- Ashley R. Coenen
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Sarah K. Hu
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA, United States
| | - Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, United States
| | - Daniel Muratore
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Joshua S. Weitz
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
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7
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Sandin MM, Pillet L, Biard T, Poirier C, Bigeard E, Romac S, Suzuki N, Not F. Time Calibrated Morpho-molecular Classification of Nassellaria (Radiolaria). Protist 2019; 170:187-208. [DOI: 10.1016/j.protis.2019.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/21/2019] [Accepted: 02/07/2019] [Indexed: 02/01/2023]
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8
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Zhao Y, Yi Z, Warren A, Song W. Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus Euplotes (Alveolata, Ciliophora). Proc Biol Sci 2019; 285:rspb.2017.2159. [PMID: 29367393 DOI: 10.1098/rspb.2017.2159] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/03/2018] [Indexed: 11/12/2022] Open
Abstract
Recent advances in high-throughput sequencing and metabarcoding technologies are revolutionizing our understanding of the diversity and ecology of microbial eukaryotes (protists). The interpretation of protist diversity and the elucidation of their ecosystem function are, however, impeded by problems with species delimitation, especially as it applies to molecular taxonomy. Here, using the ciliate Euplotes as an example, we describe approaches for species delimitation based on integrative taxonomy by using evolutionary and ecological perspectives and selecting the most appropriate metabarcoding gene markers as proxies for species units. Our analyses show that: Euplotes (sensu lato) comprises six distinct clades, mainly as result of ecological speciation; the validity of the genera Euplotes (sensu stricto), Euplotoides, Euplotopsis and Moneuplotes are not supported; the vannus-type group, which includes species without distinct morphological differences, seems to be undergoing incipient speciation and contains cryptic species; the hypervariable V4 region of the small subunit rDNA and D1-D2 region of the large subunit rDNA are the promising candidates for general species delimitation in Euplotes.
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Affiliation(s)
- Yan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China .,Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, People's Republic of China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Weibo Song
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, People's Republic of China
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9
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Przyboś E, Rautian M, Beliavskaia A, Tarcz S. Evaluation of the molecular variability and characteristics of Paramecium polycaryum and Paramecium nephridiatum, within subgenus Cypriostomum (Ciliophora, Protista). Mol Phylogenet Evol 2018; 132:296-306. [PMID: 30528084 DOI: 10.1016/j.ympev.2018.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 11/05/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022]
Abstract
Although some Paramecium species are suitable research objects in many areas of life sciences, the biodiversity structure of other species is almost unknown. In the current survey, we present a molecular analysis of 60 Cypriostomum strains, which for the first time allows for the study of intra- and interspecific relationships within that subgenus, as well as the assessment of the biogeography patterns of its morphospecies. Analysis of COI mtDNA variation revealed three main clades (separated from each other by approximately 130 nucleotide substitutions), each one with internal sub-clusters (differing by 30 to 70 substitutions - a similar range found between P. aurelia cryptic species and P. bursaria syngens). The first clade is represented exclusively by P. polycaryum; the second one includes only four strains identified as P. calkinsi. The third cluster seems to be paraphyletic, as it includes P. nephridiatum, P. woodruffi, and Eucandidatus P. hungarianum. Some strains, previously identified as P. calkinsi, had COI sequences identical or very similar to P. nephridiatum ones. Morphological reinvestigation of several such strains revealed common morphological features with P. nephridiatum. The paper contains new information concerning speciation within particular species, i.e. existence of cryptic species within P. polycaryum (three) and in P. nephridiatum (six).
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Affiliation(s)
- Ewa Przyboś
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, Poland
| | - Maria Rautian
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexandra Beliavskaia
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia; Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sebastian Tarcz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, Poland.
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10
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Caron DA, Hu SK. Are We Overestimating Protistan Diversity in Nature? Trends Microbiol 2018; 27:197-205. [PMID: 30455081 DOI: 10.1016/j.tim.2018.10.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/04/2018] [Accepted: 10/25/2018] [Indexed: 12/30/2022]
Abstract
Documenting the immense diversity of single-celled, eukaryotic organisms (protists) has been a formidable challenge for ecologists. These species were originally defined by morphological criteria, but shortcomings of the morphospecies concept, and a bewildering array of sizes and cellular attributes, has made constructing a taxonomy that is useful for ecologists nearly impossible. Consequently, physiological and genetic information has been integrated to address these shortcomings, and to develop the framework of a unifying taxonomy. DNA sequence information, in particular, has revolutionized studies of protistan diversity. However, the exponential increase in sequence-based protistan species richness published from field surveys in recent years raises the question of whether we have moved beyond characterizing species-level diversity and begun to reveal intraspecies diversity. The answer to that question appears to be 'yes', at least for some protistan lineages. The need to document such microdiversity may be justified, but it is important for protistologists to recognize and acknowledge that possibility, and its consequences.
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Affiliation(s)
- David A Caron
- Department of Biological Sciences, 3616 Trousdale Parkway, University of Southern California, Los Angeles, CA 90089-0371, USA.
| | - Sarah K Hu
- Department of Biological Sciences, 3616 Trousdale Parkway, University of Southern California, Los Angeles, CA 90089-0371, USA
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11
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Eitel M, Francis WR, Varoqueaux F, Daraspe J, Osigus HJ, Krebs S, Vargas S, Blum H, Williams GA, Schierwater B, Wörheide G. Comparative genomics and the nature of placozoan species. PLoS Biol 2018; 16:e2005359. [PMID: 30063702 PMCID: PMC6067683 DOI: 10.1371/journal.pbio.2005359] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Placozoans are a phylum of nonbilaterian marine animals currently represented by a single described species, Trichoplax adhaerens, Schulze 1883. Placozoans arguably show the simplest animal morphology, which is identical among isolates collected worldwide, despite an apparently sizeable genetic diversity within the phylum. Here, we use a comparative genomics approach for a deeper appreciation of the structure and causes of the deeply diverging lineages in the Placozoa. We generated a high-quality draft genome of the genetic lineage H13 isolated from Hong Kong and compared it to the distantly related T. adhaerens. We uncovered substantial structural differences between the two genomes that point to a deep genomic separation and provide support that adaptation by gene duplication is likely a crucial mechanism in placozoan speciation. We further provide genetic evidence for reproductively isolated species and suggest a genus-level difference of H13 to T. adhaerens, justifying the designation of H13 as a new species, Hoilungia hongkongensis nov. gen., nov. spec., now the second described placozoan species and the first in a new genus. Our multilevel comparative genomics approach is, therefore, likely to prove valuable for species distinctions in other cryptic microscopic animal groups that lack diagnostic morphological characters, such as some nematodes, copepods, rotifers, or mites.
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Affiliation(s)
- Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
| | - Warren R. Francis
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Frédérique Varoqueaux
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Jean Daraspe
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Hans-Jürgen Osigus
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gray A. Williams
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Bernd Schierwater
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Department of Ecology & Evolution, Yale University, New Haven, Connecticut, United States of America
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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12
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Atherton S, Jondelius U. Wide distributions and cryptic diversity within a Microstomum
(Platyhelminthes) species complex. ZOOL SCR 2018. [DOI: 10.1111/zsc.12290] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sarah Atherton
- Department of Zoology; Naturhistoriska riksmuseet; Stockholm Sweden
| | - Ulf Jondelius
- Department of Zoology; Naturhistoriska riksmuseet; Stockholm Sweden
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13
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Rachik S, Christaki U, Li LL, Genitsaris S, Breton E, Monchy S. Diversity and potential activity patterns of planktonic eukaryotic microbes in a mesoeutrophic coastal area (eastern English Channel). PLoS One 2018; 13:e0196987. [PMID: 29746519 PMCID: PMC5944946 DOI: 10.1371/journal.pone.0196987] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/24/2018] [Indexed: 01/02/2023] Open
Abstract
The diversity of planktonic eukaryotic microbes was studied at a coastal station of the eastern English Channel (EEC) from March 2011 to July 2015 (77 samples) using high throughput sequencing (454-pyrosequencing and Illumina) of the V2-V3 hypervariable region of the 18S SSU rDNA gene. Similar estimations of OTU relative abundance and taxonomic distribution for the dominant higher taxonomic groups (contributing >1% of the total number of OTUs) were observed with the two methods (Kolmogorov-Smirnov p-value = 0.22). Eight super-groups were identified throughout all samples: Alveolata, Stramenopiles, Opisthokonta, Hacrobia, Archeaplastida, Apusozoa, Rhizaria, and Amoebozoa (ordered by decreasing OTU richness). To gain further insight into microbial activity in the EEC, ribosomal RNA was extracted for samples from 2013–2015 (30 samples). Analysis of 18S rDNA and rRNA sequences led to the detection of 696 and 700 OTUs, respectively. Cluster analysis based on OTUs’ abundance indicated three major seasonal groups that were associated to spring, winter/autumn, and summer conditions. The clusters inferred from rRNA data showed a clearer seasonal representation of the community succession than the one based on rDNA. The rRNA/rDNA ratio was used as a proxy for relative cell activity. When all OTUs were considered, the average rRNA:rDNA ratio showed a linear trend around the 1:1 line, suggesting a linear relation between OTU abundance (rDNA) and activity (rRNA). However, this ratio was highly variable over time when considering individual OTUs. Interestingly, the OTU affiliated with P. globosa displayed rRNA:rDNA ratio that allowed to delimit high vs low abundance and high vs low activity periods. It unveiled quite well the Phaeocystis bloom dynamic regarding cell proliferation and activity, and could even be used as early indicator of an upcoming bloom.
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Affiliation(s)
- Sara Rachik
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Urania Christaki
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Luen Luen Li
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Savvas Genitsaris
- International Hellenic University, School of Economics, Business Administration & Legal Studies, Thessaloniki, Greece
| | - Elsa Breton
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Sébastien Monchy
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR, LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
- * E-mail:
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14
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Lim AS, Jeong HJ, Ok JH, Kim SJ. Feeding by the harmful phototrophic dinoflagellate Takayama tasmanica (Family Kareniaceae). HARMFUL ALGAE 2018; 74:19-29. [PMID: 29724340 DOI: 10.1016/j.hal.2018.03.009] [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: 01/05/2018] [Revised: 03/25/2018] [Accepted: 03/25/2018] [Indexed: 06/08/2023]
Abstract
The trophic mode of a phototrophic dinoflagellate is a critical factor in the dynamics of its harmful algal bloom. Recent discoveries of the mixotrophic capabilities of phototrophic dinoflagellates have changed the traditional view of bloom dynamics and prediction models. Here, mixotrophy in the harmful phototrophic dinoflagellate Takayama tasmanica was examined. Moreover, growth and ingestion rates of T. tasmanica on each of Alexandrium minutum CCMP1888 and Alexandrium tamarense CCMP1493, suitable prey, were determined as a function of prey concentration. This study reported for the first time that T. tasmanica is a mixotrophic species. Among the phytoplankton species offered as prey, T. tasmanica fed on all prey species whose equivalent spherical diameter (ESD) was greater than 30 μm, but also A. minutum whose ESD was 19 μm. In contrast, T. tasmanica did not feed on the phototrophic dinoflagellates Heterocapsa triquetra, Gymnodinium aureolum, Scrippsiella acuminata (previously S. trochoidea), Cochlodinium polykrikoides, Alexandrium affine, Alexandrium insuetum, and Alexandrium pacificum that its sister species Takayama helix is able to feed on. With increasing mean prey concentration, ingestion rates of T. tasmanica on A. minutum increased, but became saturated at the prey concentrations of >2130 cells mL-1 (1070 ng C mL-1). The maximum ingestion rate (MIR) of T. tasmanica on A. minutum was 0.5 ng C predator-1 d-1 (1.0 cells predator-1 d-1) which is only 64% of the body carbon of a T. tasmanica cell. Growth rates of T. tasmanica on A. minutum were not affected by prey concentrations. Thus, the low maximum ingestion rate is likely to be responsible for the small increases of its growth rate through mixotrophy. In addition, neither growth nor ingestion rates of T. tasmanica feeding on Alexandrium tamarense were affected by prey concentrations. The maximum ingestion rate of T. tasmanica on A. minutum was considerably lower than that of T. helix on the same prey species. Therefore, the mixotrophic ability of T. tasmanica is weaker than that of T. helix, and also T. tasmanica may have an ecological niche different from that of T. helix in marine ecosystems.
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Affiliation(s)
- An Suk Lim
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea; Brain Korea 21 Plus Program, School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hae Jin Jeong
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea; Advanced Institutes of Convergence Technology, Suwon, Gyeonggi-do, 16229, Republic of Korea.
| | - Jin Hee Ok
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - So Jin Kim
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
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15
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Worldwide sampling reveals low genetic variability in populations of the freshwater ciliate Paramecium biaurelia (P. aurelia species complex, Ciliophora, Protozoa). ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-017-0357-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Tan S, Liu H. Unravel the hidden protistan diversity: application of blocking primers to suppress PCR amplification of metazoan DNA. Appl Microbiol Biotechnol 2017; 102:389-401. [PMID: 29080999 DOI: 10.1007/s00253-017-8565-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/08/2017] [Accepted: 09/28/2017] [Indexed: 11/28/2022]
Abstract
Planktonic protists, including both autotroph and heterotroph, have been recognized as a major contributor to primary production and consumers of bacteria, archaea and picophytoplankton. However, the understanding of protistan diversity is typically impeded by the large amount of metazoans when employing universal primers to environmental samples. In this study, we developed 3 blocking primers to inhibit the amplification of metazoan DNA in PCR. First, we optimized the design and concentration of blocking primers by using 2 metazoans and 3 protists in quantitative PCR. No significant difference (q > 0.05) was found in protistan community structure at phylum, family or OTU levels and genetic diversity between samples amplified with and without adding blocking primers, indicating that the blocking primer does not alter the composition of protistan community. An application to samples with a high abundance of metazoans showed that the blocking primer can reduce 42.1-72.4% of metazoan sequences, resulting the retrieval of a higher protistan richness and diversity. The use of the blocking primer helped to identify protistan community composition from a large size fraction, which is usually dominated by metazoans. Protistan community from the small (0.2-10 μm) and large (> 10 μm) size fractions exhibited a low similarity of 36.6% and shared 14.7% OTUs. About 63.8% of the OTUs were unique to the large fraction. Species from groups, such as Lepidodinium, Warnowia, Kareniaceae, Torodiniales, Phaeocystis, Chrysochromulina and Chrysophyceae, were enriched in the large fraction, indicating that they could be largely underestimated in studies that exclude the large-sized cells. Blocking primers are a promising tool to increase the efficiency for the characterization of protistan diversity in aquatic planktonic ecosystems.
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Affiliation(s)
- Shangjin Tan
- Division of Life Science, The Hong Kong University of Science and Technology, CYT5004, Clear Water Bay, Kowloon, Hong Kong, SAR, China
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, CYT5004, Clear Water Bay, Kowloon, Hong Kong, SAR, China.
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17
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Santoferrara LF, McManus GB. Integrating dimensions of biodiversity in choreotrichs and oligotrichs of marine plankton. Eur J Protistol 2017; 61:323-330. [DOI: 10.1016/j.ejop.2017.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/22/2017] [Accepted: 04/04/2017] [Indexed: 01/01/2023]
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18
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Caron DA, Alexander H, Allen AE, Archibald JM, Armbrust EV, Bachy C, Bell CJ, Bharti A, Dyhrman ST, Guida SM, Heidelberg KB, Kaye JZ, Metzner J, Smith SR, Worden AZ. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat Rev Microbiol 2016; 15:6-20. [DOI: 10.1038/nrmicro.2016.160] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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19
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Walker LM, Stephenson SL. The Species Problem in Myxomycetes Revisited. Protist 2016; 167:319-338. [DOI: 10.1016/j.protis.2016.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 05/12/2016] [Accepted: 05/27/2016] [Indexed: 11/27/2022]
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20
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Paz-Y-Miño-C G, Espinosa A. Kin Discrimination in Protists: From Many Cells to Single Cells and Backwards. J Eukaryot Microbiol 2016; 63:367-77. [PMID: 26873616 PMCID: PMC4856593 DOI: 10.1111/jeu.12306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 02/03/2016] [Accepted: 02/07/2016] [Indexed: 12/16/2022]
Abstract
During four decades (1960-1990s), the conceptualization and experimental design of studies in kin recognition relied on work with multicellular eukaryotes, particularly Unikonta (including invertebrates and vertebrates) and some Bikonta (including plants). This pioneering research had an animal behavior approach. During the 2000s, work on taxa-, clone- and kin-discrimination and recognition in protists produced genetic and molecular evidence that unicellular organisms (e.g. Saccharomyces, Dictyostelium, Polysphondylium, Tetrahymena, Entamoeba and Plasmodium) could distinguish between same (self or clone) and different (diverse clones), as well as among conspecifics of close or distant genetic relatedness. Here, we discuss some of the research on the genetics of kin discrimination/recognition and highlight the scientific progress made by switching emphasis from investigating multicellular to unicellular systems (and backwards). We document how studies with protists are helping us to understand the microscopic, cellular origins and evolution of the mechanisms of kin discrimination/recognition and their significance for the advent of multicellularity. We emphasize that because protists are among the most ancient organisms on Earth, belong to multiple taxonomic groups and occupy all environments, they can be central to reexamining traditional hypotheses in the field of kin recognition, reformulating concepts, and generating new knowledge.
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Affiliation(s)
- Guillermo Paz-Y-Miño-C
- New England Center for the Public Understanding of Science, Roger Williams University, One Old Ferry Road, Bristol, Rhode Island, 02809
| | - Avelina Espinosa
- New England Center for the Public Understanding of Science, Roger Williams University, One Old Ferry Road, Bristol, Rhode Island, 02809
- Department of Biology, Roger Williams University, One Old Ferry Road, Bristol, Rhode Island, 02809
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21
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Morard R, Escarguel G, Weiner AKM, André A, Douady CJ, Wade CM, Darling KF, Ujiié Y, Seears HA, Quillévéré F, de Garidel-Thoron T, de Vargas C, Kucera M. Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera. Syst Biol 2016; 65:925-40. [PMID: 27073250 DOI: 10.1093/sysbio/syw031] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/04/2016] [Indexed: 11/12/2022] Open
Abstract
Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists, and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible, and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently, we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.
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Affiliation(s)
- Raphaël Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany,
| | - Gilles Escarguel
- Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Agnes K M Weiner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany, Japan Agency for Marine Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Kanagawa, Japan
| | - Aurore André
- Université de Reims-Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, Batiment 18, 51100 REIMS, France
| | - Christophe J Douady
- Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France, Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
| | - Christopher M Wade
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Kate F Darling
- School of GeoSciences, University of Edinburgh, Edinburgh EH9 3JW, UK, School of Geography and GeoSciences, University of St Andrews, Fife KY16 9AL, UK
| | - Yurika Ujiié
- Department of Biology, Shinshu University, Asahi3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Heidi A Seears
- Department of Biology, Gilmer Hall, University of Virginia, 485 McCormick Road, Charlottesville, VA 22904, USA
| | - Frédéric Quillévéré
- Univ Lyon, Université Lyon 1, ENS de Lyon, CNRS, UMR 5276 LGL-TPE, F-69622 Villeurbanne, France
| | - Thibault de Garidel-Thoron
- Centre Européen de Recherche et d'Enseignement de Géosciences de l'Environnement, Centre National de la Recherche Scientifique, et Aix-Marseille Université, Aix-en-Provence, France
| | - Colomban de Vargas
- Centre National de la Recherche Scientifique, UMR 7144, EPEP, Station Biologique de Roscoff, 29680 Roscoff, France, and Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany
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22
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Pagenkopp Lohan KM, Fleischer RC, Carney KJ, Holzer KK, Ruiz GM. Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships' Ballast Water: Implications for Biogeography and Infectious Diseases. MICROBIAL ECOLOGY 2016; 71:530-42. [PMID: 26476551 DOI: 10.1007/s00248-015-0684-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/28/2015] [Indexed: 05/22/2023]
Abstract
Ships' ballast water (BW) commonly moves macroorganisms and microorganisms across the world's oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships' BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world's oceans.
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Affiliation(s)
- K M Pagenkopp Lohan
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.
- Marine Invasions Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA.
| | - R C Fleischer
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA
| | - K J Carney
- Marine Invasions Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - K K Holzer
- Marine Invasions Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - G M Ruiz
- Marine Invasions Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
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23
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Santoferrara LF, Bachy C, Alder VA, Gong J, Kim YO, Saccà A, da Silva Neto ID, Strüder-Kypke MC, Warren A, Xu D, Yi Z, Agatha S. Updating Biodiversity Studies in Loricate Protists: The Case of the Tintinnids (Alveolata, Ciliophora, Spirotrichea). J Eukaryot Microbiol 2016; 63:651-6. [DOI: 10.1111/jeu.12303] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/03/2016] [Accepted: 02/03/2016] [Indexed: 11/29/2022]
Affiliation(s)
| | - Charles Bachy
- Monterey Bay Aquarium Research Institute; Moss Landing California 95039 USA
| | - Viviana A. Alder
- Instituto de Ecología, Genética y Evolución de Buenos Aires (UBA-CONICET) y Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; Buenos Aires C1428EHA Argentina
- Instituto Antártico Argentino, Dirección Nacional del Antártico; Buenos Aires C1010AAZ Argentina
| | - Jun Gong
- Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai 264003 China
| | - Young-Ok Kim
- South Sea Environment Research Division; Korea Institute of Ocean Science & Technology; Geoje 656-834 Korea
| | - Alessandro Saccà
- Dipartimento di Scienze Biologiche e Ambientali; Università degli Studi di Messina; Messina 98166 Italy
| | - Inácio D. da Silva Neto
- Departamento de Zoologia; Universidade Federal do Rio de Janeiro; Rio de Janeiro 21941-590 Brazil
| | | | - Alan Warren
- Department of Life Sciences; Natural History Museum; London SW75BD United Kingdom
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Sciences; Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen 361102 China
| | - Zhenzhen Yi
- School of Life Science; South China Normal University; Guangzhou 510631 China
| | - Sabine Agatha
- Department of Ecology and Evolution; University of Salzburg; Salzburg A-5020 Austria
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24
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Przyboś E, Tarcz S. Paramecium jenningsicomplex: existence of three cryptic species confirmed by multi-locus analysis and strain crosses. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2015.1134701] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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25
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Molecular Identification of Soil Eukaryotes and Focused Approaches Targeting Protist and Faunal Groups Using High-Throughput Metabarcoding. Methods Mol Biol 2016; 1399:125-40. [PMID: 26791500 DOI: 10.1007/978-1-4939-3369-3_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
While until recently the application of high-throughput sequencing approaches has mostly been restricted to bacteria and fungi, these methods have now also become available to less often studied (eukaryotic) groups, such as fauna and protists. Such approaches allow routine diversity screening for large numbers of samples via DNA metabarcoding. Given the enormous taxonomic diversity within the eukaryote tree of life, metabarcoding approaches targeting a single specific DNA region do not allow to discriminate members of all eukaryote clades at high taxonomic resolution. Here, we report on protocols that enable studying the diversity of soil eukaryotes and, at high taxonomic resolution, of individual faunal and protist groups therein using a tiered approach: first, the use of a general eukaryotic primer set targeting a wide range of eukaryotes provides a rough impression on the entire diversity of protists and faunal groups. Second, more focused approaches enable deciphering subsets of soil eukaryotes in higher taxonomic detail. We provide primers and protocols for two examples: soil microarthropods and cercozoan protists.
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26
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Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists. Mol Phylogenet Evol 2016; 94:718-729. [DOI: 10.1016/j.ympev.2015.10.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/08/2015] [Accepted: 10/16/2015] [Indexed: 11/20/2022]
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27
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Przyboś E, Tarcz S, Rautian M, Sawka N. Delimiting Species Boundaries within a Paraphyletic Species Complex: Insights from Morphological, Genetic, and Molecular Data on Paramecium sonneborni (Paramecium aurelia species complex, Ciliophora, Protozoa). Protist 2015; 166:438-56. [PMID: 26277215 DOI: 10.1016/j.protis.2015.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 07/01/2015] [Accepted: 07/12/2015] [Indexed: 02/06/2023]
Abstract
The demarcation of boundaries between protist species is often problematic because of the absence of a uniform species definition, the abundance of cryptic diversity, and the occurrence of convergent morphology. The ciliates belonging to the Paramecium aurelia complex, consisting of 15 species, are a good model for such systematic and evolutionary studies. One member of the complex is P. sonneborni, previously known only from one stand in Texas (USA), but recently found in two new sampling sites in Cyprus (creeks running to Salt Lake and Oroklini Lake near Larnaca). The studied Paramecium sonneborni strains (from the USA and Cyprus) reveal low viability in the F1 and F2 generations of interstrain hybrids and may be an example of ongoing allopatric speciation. Despite its molecular distinctiveness, we postulate that P. sonneborni should remain in the P. aurelia complex, making it a paraphyletic taxon. Morphological studies have revealed that some features of the nuclear apparatus of P. sonneborni correspond to the P. aurelia spp. complex, while others are similar to P. jenningsi and P. schewiakoffi. The observed discordance indicates rapid splitting of the P. aurelia-P. jenningsi-P. schewiakoffi group, in which genetic, morphological, and molecular boundaries between species are not congruent.
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Affiliation(s)
- Ewa Przyboś
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków 31-016, Sławkowska 17, Poland
| | - Sebastian Tarcz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków 31-016, Sławkowska 17, Poland.
| | - Maria Rautian
- Laboratory of Protistology and Experimental Zoology, Faculty of Biology and Soil Science, St. Petersburg State University, Saint Petersburg 199034, Universitetskaya nab. 7/9, Russia
| | - Natalia Sawka
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków 31-016, Sławkowska 17, Poland
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28
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Reñé A, Camp J, Garcés E. Diversity and Phylogeny of Gymnodiniales (Dinophyceae) from the NW Mediterranean Sea Revealed by a Morphological and Molecular Approach. Protist 2015; 166:234-63. [DOI: 10.1016/j.protis.2015.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 02/21/2015] [Accepted: 03/02/2015] [Indexed: 12/01/2022]
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29
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Hu SK, Liu Z, Lie AAY, Countway PD, Kim DY, Jones AC, Gast RJ, Cary SC, Sherr EB, Sherr BF, Caron DA. Estimating Protistan Diversity Using High-Throughput Sequencing. J Eukaryot Microbiol 2015; 62:688-93. [PMID: 25851049 DOI: 10.1111/jeu.12217] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/17/2015] [Accepted: 01/26/2015] [Indexed: 11/28/2022]
Abstract
Sequencing hypervariable regions from the 18S rRNA gene is commonly employed to characterize protistan biodiversity, yet there are concerns that short reads do not provide the same taxonomic resolution as full-length sequences. A total of 7,432 full-length sequences were used to perform an in silico analysis of how sequences of various lengths and target regions impact downstream ecological interpretations. Sequences that were longer than 400 nucleotides and included the V4 hypervariable region generated results similar to those derived from full-length 18S rRNA gene sequences. Present high-throughput sequencing capabilities are approaching protistan diversity estimation comparable to whole gene sequences.
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Affiliation(s)
- Sarah K Hu
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Zhenfeng Liu
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Alle A Y Lie
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Peter D Countway
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Diane Y Kim
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Adriane C Jones
- Mount St. Mary's College, Los Angeles, California, 90049, USA
| | - Rebecca J Gast
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - S Craig Cary
- Environmental Research Institute, School of Science, University of Waikato, Hamilton, 3240, New Zealand.,College of Earth and Ocean Science, University of Delaware, Newark, Delaware, 19716, USA
| | - Evelyn B Sherr
- College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Barry F Sherr
- College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, 97331, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
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30
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Santoferrara LF, Tian M, Alder VA, McManus GB. Discrimination of Closely Related Species in Tintinnid Ciliates: New Insights on Crypticity and Polymorphism in the Genus Helicostomella. Protist 2015; 166:78-92. [DOI: 10.1016/j.protis.2014.11.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 10/20/2014] [Accepted: 11/29/2014] [Indexed: 11/15/2022]
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31
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Dirren S, Salcher MM, Blom JF, Schweikert M, Posch T. Ménage-à-trois: The Amoeba Nuclearia sp. from Lake Zurich with its Ecto- and Endosymbiotic Bacteria. Protist 2014; 165:745-58. [DOI: 10.1016/j.protis.2014.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 11/28/2022]
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32
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Espinosa A, Paz-Y-Miño-C G. Evidence of Taxa-, Clone-, and Kin-discrimination in Protists: Ecological and Evolutionary Implications. Evol Ecol 2014; 28:1019-1029. [PMID: 25400313 DOI: 10.1007/s10682-014-9721-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Unicellular eukaryotes, or protists, are among the most ancient organisms on Earth. Protists belong to multiple taxonomic groups; they are widely distributed geographically and in all environments. Their ability to discriminate among con- and heterospecifics has been documented during the past decade. Here we discuss exemplar cases of taxa-, clone-, and possible kin-discrimination in five major lineages: Mycetozoa (Dictyostelium, Polysphondylium), Dikarya (Saccharomyces), Ciliophora (Tetrahymena), Apicomplexa (Plasmodium) and Archamoebae (Entamoeba). We summarize the proposed genetic mechanisms involved in discrimination-mediated aggregation (self versus different), including the csA, FLO and trg (formerly lag) genes, and the Proliferation Activation Factors (PAFs), which facilitate clustering in some protistan taxa. We caution about the experimental challenges intrinsic to studying recognition in protists, and highlight the opportunities for exploring the ecology and evolution of complex forms of cell-cell communication, including social behavior, in a polyphyletic, still superficially understood group of organisms. Because unicellular eukaryotes are the evolutionary precursors of multicellular life, we infer that their mechanisms of taxa-, clone-, and possible kin-discrimination gave origin to the complex diversification and sophistication of traits associated with species and kin recognition in plants, fungi, invertebrates and vertebrates.
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Affiliation(s)
- Avelina Espinosa
- Department of Biology, Roger Williams University, One Old Ferry Road, Bristol, Rhode Island 02809, USA
| | - Guillermo Paz-Y-Miño-C
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, Massachusetts 02747-2300, USA
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33
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The first European stand of Paramecium sonneborni (P. aurelia complex), a species known only from North America (Texas, USA). Eur J Protistol 2014; 50:236-47. [DOI: 10.1016/j.ejop.2014.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 02/15/2014] [Accepted: 03/03/2014] [Indexed: 11/18/2022]
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Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes. Appl Environ Microbiol 2014; 80:4363-73. [PMID: 24814788 DOI: 10.1128/aem.00057-14] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.
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Tarcz S, Rautian M, Potekhin A, Sawka N, Beliavskaya A, Kiselev A, Nekrasova I, Przyboś E. Paramecium putrinum (Ciliophora, Protozoa): The first insight into the variation of two DNA fragments – Molecular support for the existence of cryptic species. Mol Phylogenet Evol 2014; 73:140-5. [DOI: 10.1016/j.ympev.2014.01.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 01/18/2014] [Accepted: 01/21/2014] [Indexed: 11/25/2022]
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Kaczmarska I, Mather L, Luddington IA, Muise F, Ehrman JM. Cryptic diversity in a cosmopolitan diatom known as Asterionellopsis glacialis (Fragilariaceae): Implications for ecology, biogeography, and taxonomy. AMERICAN JOURNAL OF BOTANY 2014; 101:267-286. [PMID: 24509794 DOI: 10.3732/ajb.1300306] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Diatoms have long been known as the most species-rich of algal groups, with a wide range of estimates for species number (20-200 k) due to differing species concepts. The fine valve structure in Asterionellopsis glacialis, a diatom believed cosmopolitan and eurytopic, has never been systematically examined using modern microscopy and is an excellent candidate to genetically test morphology-based conspecificity among its geographically distant culture isolates. METHODS Isolates from the Atlantic and Pacific Oceans that were morphologically delineated as A. glacialis were genetically characterized using three nuclear DNA regions (two 18S rDNA fragments and ITS region) and one plastidal (rbcL) and one mitochondrial gene (cox1) and related to SEM-based morphometrics. KEY RESULTS Five genetically distinct groupings were found, four of which are new to science. ITS2 RNA transcript secondary structure was species specific as were plastidal and mitochondrial genes, while the 18S gene fragments did not diverge sufficiently to segregate new species efficiently. We genetically circumscribed the A. glacialis epitype. CONCLUSIONS The morphological diversification of the species examined in this study lags behind their genetic divergence. The currently accepted 2% cutoff level of operational taxonomic unit (OTU) clustering in 18S rDNA environmental sequencing is too high to recognize genetic diversity in Asterionellopsis and very likely in many other species. Our results support the notion that a considerable number of species and diversity remain to be discovered among diatoms and that species number may be more in line with higher estimates. Molecular signatures of the species discovered here will aid in their globally consistent identification and ultimate understanding of their ecology.
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Affiliation(s)
- Irena Kaczmarska
- Biology Department, Mount Allison University, Sackville, New Brunswick E4L 1G7 Canada
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Okamoto N, Tai V. Assessing protistan diversity and genetic variance: a symposium presented at the Protist2012 meeting in Oslo, Norway. J Eukaryot Microbiol 2013; 60:406. [PMID: 23710580 DOI: 10.1111/jeu.12045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 03/05/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Noriko Okamoto
- Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, Canada, V6T 1Z4
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