1
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Abraham JS, Somasundaram S, Maurya S, Sood U, Lal R, Toteja R, Makhija S. Insights into freshwater ciliate diversity through high throughput DNA metabarcoding. FEMS MICROBES 2024; 5:xtae003. [PMID: 38450097 PMCID: PMC10917447 DOI: 10.1093/femsmc/xtae003] [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: 09/01/2023] [Revised: 01/03/2024] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
The freshwater bodies of India are highly biodiverse but still understudied, especially concerning ciliates. Ciliates constitute a significant portion of eukaryotic diversity and play crucial roles in microbial loops, nutrient recycling, and ecosystem maintenance. The present study aimed to elucidate ciliate diversity in three freshwater sites in the Delhi region of India: Okhla Bird Sanctuary (OBS), Sanjay Lake (SL), and Raj Ghat pond (RJ). This study represents the first investigation into the taxonomic diversity and richness of freshwater ciliates in India using a high-throughput DNA metabarcoding approach. For the analysis, total environmental DNA was extracted from the three freshwater samples, followed by sequencing of the 18S V4 barcode region and subsequent phylogenetic analyses. Operational taxonomic units (OTU) analyses revealed maximum species diversity in OBS (106), followed by SL (104) and RJ (99) sites. Ciliates from the classes Oligohymenophorea, Prostomatea, and Spirotrichea were dominant in the three sites. The study discusses the ability of the metabarcoding approach to uncover unknown and rare species. The study highlights the need for refined reference databases and cautious interpretation of the high-throughput sequencing-generated data while emphasizing the complementary nature of molecular and morphological approaches in studying ciliate diversity.
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Affiliation(s)
- Jeeva Susan Abraham
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Sripoorna Somasundaram
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Swati Maurya
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi 110007, India
| | - Rup Lal
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Ravi Toteja
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Seema Makhija
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
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2
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Ahsan R, Blanche W, Katz LA. Macronuclear development in ciliates, with a focus on nuclear architecture. J Eukaryot Microbiol 2022; 69:e12898. [PMID: 35178799 DOI: 10.1111/jeu.12898] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/20/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
Abstract
Ciliates are defined by the presence of dimorphic nuclei as they have both a somatic macronucleus and germline micronucleus within each individual cell. The size and structure of both germline micronuclei and somatic macronuclei varies tremendously among ciliates. Except just after conjugation (i.e. the nuclear exchange in sexual cycle), the germline micronucleus is transcriptionally-inactive and contains canonical chromosomes that will be inherited between generations. In contrast, the transcriptionally-active macronucleus contains chromosomes that vary in size in different classes of ciliates, with some lineages having extensively-fragmented gene-sized somatic chromosomes while others contain longer multigene chromosomes. Here, we describe the variation in somatic macronuclear architecture in lineages sampled across the ciliate tree of life, specifically focusing on lineages with extensively fragmented chromosomes (e.g. the classes Phyllopharyngea and Spirotrichea). Further, we synthesize information from the literature on the development of ciliate macronuclei, focusing on changes in nuclear architecture throughout life cycles. These data highlight the tremendous diversity among ciliate nuclear cycles, extend our understanding of patterns of genome evolution, and provide insight into different germline and somatic nuclear features (e.g. nuclear structure and development) among eukaryotes.
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Affiliation(s)
- Ragib Ahsan
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, 01003, USA
| | - Wumei Blanche
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA.,University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, 01003, USA
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3
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Ma M, Xu Y, Yan Y, Li Y, Warren A, Song W. Taxonomy and molecular phylogeny of four karyorelictid species belonging to the genera Apotrachelocerca and Tracheloraphis (Protozoa: Ciliophora), with descriptions of two new species. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The taxonomy and phylogeny of four trachelocercid ciliates, Apotrachelocerca orientalis sp. nov., Tracheloraphis apoligostriata sp. nov., T. oligostriata and T. prenanti, isolated from marine habitats in Qingdao, China, were studied. The new species, A. orientalis sp. nov., can be distinguished from its most closely related congener, A. arenicola, by the absence of cortical granules and its conspicuously different SSU rDNA sequence. Tracheloraphis apoligostriata sp. nov. differs from the similar T. oligostriata by its body shape, distribution pattern of the cortical granules and SSU rDNA sequence. Based on available data, we suggest that T. prenanti can be defined by its colourless, globular cortical granules, which indicates that this species should be removed from the T. phoenicopterus-complex. Phylogenetic analyses based on SSU rDNA sequence data indicates that: A. orientalis sp. nov. groups with A. arenicola with full support, together sister to all other trachelocercid species; and T. cf. phoenicopterus, T. prenanti, T. oligostriata and T. apoligostriata sp. nov. form a clearly outlined clade.
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Affiliation(s)
- Mingzhen Ma
- College of Fisheries, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yuan Xu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Ying Yan
- College of Fisheries, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yuqing Li
- College of Fisheries, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK
| | - Weibo Song
- College of Fisheries, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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4
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Kassinger SJ, van Hoek ML. Biofilm architecture: An emerging synthetic biology target. Synth Syst Biotechnol 2020; 5:1-10. [PMID: 31956705 PMCID: PMC6961760 DOI: 10.1016/j.synbio.2020.01.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/29/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023] Open
Abstract
Synthetic biologists are exploiting biofilms as an effective mechanism for producing various outputs. Metabolic optimization has become commonplace as a method of maximizing system output. In addition to production pathways, the biofilm itself contributes to the efficacy of production. The purpose of this review is to highlight opportunities that might be leveraged to further enhance production in preexisting biofilm production systems. These opportunities may be used with previously established production systems as a method of improving system efficiency further. This may be accomplished through the reduction in the cost of establishing and maintaining biofilms, and maintenance of the enhancement of product yield per unit of time, per unit of area, or per unit of required input.
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Affiliation(s)
| | - Monique L. van Hoek
- George Mason University, School of Systems Biology, George Mason University, 10920 George Mason Circle, Manassas, VA, 20110, USA
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5
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Rossi A, Bellone A, Fokin SI, Boscaro V, Vannini C. Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study. MICROBIAL ECOLOGY 2019; 78:232-242. [PMID: 30411190 DOI: 10.1007/s00248-018-1279-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.
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Affiliation(s)
- Alessia Rossi
- Department of Biology, University of Pisa, Pisa, Italy
| | | | - Sergei I Fokin
- Department of Biology, University of Pisa, Pisa, Italy
- Department of Invertebrate Zoology, St.-Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch of the S.I. Vavilov Institute of History of Science and Technology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Vittorio Boscaro
- Department of Biology, University of Pisa, Pisa, Italy
- Department of Botany, University of British Columbia, Vancouver, Canada
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6
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Illa K, Shameem U, Serra V, Melai M, Mangam S, Basuri CK, Petroni G, Modeo L. Multidisciplinary investigation on the catfish parasite Hamatopeduncularia Yamaguti, 1953 (Monogenoidea: Dactylogyridae): description of two new species from India, and phylogenetic considerations. EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2019.1597931] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- K. Illa
- Department of Zoology, Andhra University, Visakhapatnam, India
| | - U. Shameem
- Department of Zoology, Andhra University, Visakhapatnam, India
| | - V. Serra
- Department of Biology, University of Pisa, Pisa, Italy
| | - M. Melai
- Department of Biology, University of Pisa, Pisa, Italy
| | - S. Mangam
- Department of Zoology, Andhra University, Visakhapatnam, India
| | - C. K. Basuri
- National Centre for Coastal Research, NIOT Campus, Ministry of Earth Science, Chennai, India
| | - G. Petroni
- Department of Biology, University of Pisa, Pisa, Italy
| | - L. Modeo
- Department of Biology, University of Pisa, Pisa, Italy
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7
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Fokin SI, Serra V, Ferrantini F, Modeo L, Petroni G. "Candidatus Hafkinia simulans" gen. nov., sp. nov., a Novel Holospora-Like Bacterium from the Macronucleus of the Rare Brackish Water Ciliate Frontonia salmastra (Oligohymenophorea, Ciliophora): Multidisciplinary Characterization of the New Endosymbiont and Its Host. MICROBIAL ECOLOGY 2019; 77:1092-1106. [PMID: 30627761 DOI: 10.1007/s00248-018-1311-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/19/2018] [Indexed: 05/09/2023]
Abstract
We characterized a novel Holospora-like bacterium (HLB) (Alphaproteobacteria, Holosporales) living in the macronucleus of the brackish water ciliate Frontonia salmastra. This bacterium was morphologically and ultrastructurally investigated, and its life cycle and infection capabilities were described. We also obtained its 16S rRNA gene sequence and performed in situ hybridization experiments with a specifically-designed probe. A new taxon, "Candidatus Hafkinia simulans", was established for this HLB. The phylogeny of the family Holosporaceae based on 16S rRNA gene sequences was inferred, adding to the already available data both the sequence of the novel bacterium and those of other Holospora and HLB species recently characterized. Our phylogenetic analysis provided molecular support for the monophyly of HLBs and placed the new endosymbiont as the sister genus of Holospora. Additionally, the host ciliate F. salmastra, recorded in Europe for the first time, was concurrently described through a multidisciplinary study. Frontonia salmastra's phylogenetic position in the subclass Peniculia and the genus Frontonia was assessed according to 18S rRNA gene sequencing. Comments on the biodiversity of this genus were added according to past and recent literature.
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Affiliation(s)
- Sergei I Fokin
- Department of Biology, University of Pisa, 56126, Pisa, Italy.
- Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia, 199034.
- St. Petersburg Branch of the S.I. Vavilov Institute of History of Science and Technology, Russian Academy of Sciences, St. Petersburg, Russia, 199034.
| | - Valentina Serra
- Department of Biology, University of Pisa, 56126, Pisa, Italy.
| | | | - Letizia Modeo
- Department of Biology, University of Pisa, 56126, Pisa, Italy
| | - Giulio Petroni
- Department of Biology, University of Pisa, 56126, Pisa, Italy
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8
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Koehler L, Flemming FE, Schrallhammer M. Towards an ecological understanding of the killer trait - A reproducible protocol for testing its impact on freshwater ciliates. Eur J Protistol 2019; 68:108-120. [PMID: 30826731 DOI: 10.1016/j.ejop.2019.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/04/2019] [Accepted: 02/04/2019] [Indexed: 11/19/2022]
Abstract
Paramecium strains with the ability to kill other paramecia often harbour intracellular bacteria belonging to the genera Caedibacter or Caedimonas. Central structures of this killer trait are refractile bodies (R-bodies) produced by the endosymbionts. Once ingested by a sensitive Paramecium, R-bodies presumably act as delivery system for an unidentified toxin which causes the death of endosymbiont-free paramecia while those infected gain resistance from their symbionts. The killer trait is therefore considered as competitive advantage for the hosts of R-body producers. While its effectiveness against paramecia is well documented, the effects on other aquatic ciliates are much less studied. In order to address the broadness of the killer trait, a reproducible killer test assay considering the effects on predatory ciliates (Climacostomum virens and Dileptus jonesi) as well as potential bacterivorous Paramecium competitors (Dexiostoma campyla, Euplotes aediculatus, Euplotes woodruffi, and Spirostomum teres) as possibly susceptible species was established. All used organisms were molecularly characterized to increase traceability and reproducibility. The absence of any lethal effects in both predators and competitors after exposure to killer paramecia strongly suggests a narrow action range for the killer trait. Thus, R-body producing bacteria provide their host with a complex, costly strategy to outcompete symbiont-free congeners only.
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Affiliation(s)
- Lars Koehler
- Institute of Biology II, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany; Institute of Hydrobiology, Technische Universität Dresden, 01217 Dresden, Germany
| | - Felicitas E Flemming
- Institute of Biology II, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| | - Martina Schrallhammer
- Institute of Biology II, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany.
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9
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Seah BKB, Schwaha T, Volland JM, Huettel B, Dubilier N, Gruber-Vodicka HR. Specificity in diversity: single origin of a widespread ciliate-bacteria symbiosis. Proc Biol Sci 2018; 284:rspb.2017.0764. [PMID: 28701560 PMCID: PMC5524500 DOI: 10.1098/rspb.2017.0764] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/06/2017] [Indexed: 12/03/2022] Open
Abstract
Symbioses between eukaryotes and sulfur-oxidizing (thiotrophic) bacteria have convergently evolved multiple times. Although well described in at least eight classes of metazoan animals, almost nothing is known about the evolution of thiotrophic symbioses in microbial eukaryotes (protists). In this study, we characterized the symbioses between mouthless marine ciliates of the genus Kentrophoros, and their thiotrophic bacteria, using comparative sequence analysis and fluorescence in situ hybridization. Ciliate small-subunit rRNA sequences were obtained from 17 morphospecies collected in the Mediterranean and Caribbean, and symbiont sequences from 13 of these morphospecies. We discovered a new Kentrophoros morphotype where the symbiont-bearing surface is folded into pouch-like compartments, illustrating the variability of the basic body plan. Phylogenetic analyses revealed that all investigated Kentrophoros belonged to a single clade, despite the remarkable morphological diversity of these hosts. The symbionts were also monophyletic and belonged to a new clade within the Gammaproteobacteria, with no known cultured representatives. Each host morphospecies had a distinct symbiont phylotype, and statistical analyses revealed significant support for host–symbiont codiversification. Given that these symbioses were collected from two widely separated oceans, our results indicate that symbiotic associations in unicellular hosts can be highly specific and stable over long periods of evolutionary time.
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Affiliation(s)
- Brandon K B Seah
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Thomas Schwaha
- Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Jean-Marie Volland
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
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10
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Unusual features of non-dividing somatic macronuclei in the ciliate class Karyorelictea. Eur J Protistol 2017; 61:399-408. [PMID: 28673471 DOI: 10.1016/j.ejop.2017.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 05/06/2017] [Accepted: 05/09/2017] [Indexed: 01/01/2023]
Abstract
Genome structure and nuclear organization have been intensely studied in model ciliates such as Tetrahymena and Paramecium, yet few studies have focused on nuclear features of other ciliate clades including the class Karyorelictea. In most ciliates, both the somatic macronuclei and germline micronuclei divide during cell division and macronuclear development only occurs after conjugation. However, the macronuclei of Karyorelictea are non-dividing (i.e. division minus (Div-)) and develop anew from micronuclei during each asexual division. As macronuclei age within Karyorelictea, they undergo changes in morphology and DNA content until they are eventually degraded and replaced by newly developed macronuclei. No less than two macronuclei and one micronucleus are present in karyorelictid species, which suggests that a mature macronucleus 1) might be needed to sustain the cell while a new macronucleus is developing and 2) likely plays a role in guiding the development of the new macronucleus. Here we use a phylogenetic framework to compile information on the morphology and development of nuclei in Karyorelictea, largely relying on the work of Dr. Igor Raikov (1932-1998). We synthesize data to speculate on the functional implications of key features of Karyorelictea including the presence of at least two macronuclei in each cell and the inability for macronuclei to divide.
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11
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Lanzoni O, Fokin SI, Lebedeva N, Migunova A, Petroni G, Potekhin A. Rare Freshwater Ciliate Paramecium chlorelligerum Kahl, 1935 and Its Macronuclear Symbiotic Bacterium "Candidatus Holospora parva". PLoS One 2016; 11:e0167928. [PMID: 27992463 PMCID: PMC5161471 DOI: 10.1371/journal.pone.0167928] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/18/2016] [Indexed: 11/19/2022] Open
Abstract
Ciliated protists often form symbioses with many diverse microorganisms. In particular, symbiotic associations between ciliates and green algae, as well as between ciliates and intracellular bacteria, are rather wide-spread in nature. In this study, we describe the complex symbiotic system between a very rare ciliate, Paramecium chlorelligerum, unicellular algae inhabiting its cytoplasm, and novel bacteria colonizing the host macronucleus. Paramecium chlorelligerum, previously found only twice in Germany, was retrieved from a novel location in vicinity of St. Petersburg in Russia. Species identification was based on both classical morphological methods and analysis of the small subunit rDNA. Numerous algae occupying the cytoplasm of this ciliate were identified with ultrastructural and molecular methods as representatives of the Meyerella genus, which before was not considered among symbiotic algae. In the same locality at least fifteen other species of "green" ciliates were found, thus it is indeed a biodiversity hot-spot for such protists. A novel species of bacterial symbionts living in the macronucleus of Paramecium chlorelligerum cells was morphologically and ultrastructurally investigated in detail with the description of its life cycle and infection capabilities. The new endosymbiont was molecularly characterized following the full-cycle rRNA approach. Furthermore, phylogenetic analysis confirmed that the novel bacterium is a member of Holospora genus branching basally but sharing all characteristics of the genus except inducing connecting piece formation during the infected host nucleus division. We propose the name "Candidatus Holospora parva" for this newly described species. The described complex system raises new questions on how these microorganisms evolve and interact in symbiosis.
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Affiliation(s)
| | - Sergei I. Fokin
- Department of Biology, University of Pisa, Pisa, Italy
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Natalia Lebedeva
- Centre of Core Facilities “Culture Collections of Microorganisms”, Research Park, Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexandra Migunova
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
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12
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Yan Y, Xu Y, Al-Farraj SA, Al-Rasheid KAS, Song W. Morphology and phylogeny of three trachelocercids (Protozoa, Ciliophora, Karyorelictea), with description of two new species and insight into the evolution of the family Trachelocercidae. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12364] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ying Yan
- State Key Laboratory of Estuarine and Coastal Research; East China Normal University; Shanghai 200062 China
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Yuan Xu
- State Key Laboratory of Estuarine and Coastal Research; East China Normal University; Shanghai 200062 China
| | - Saleh A. Al-Farraj
- Zoology Department; College of Science; King Saud University; Riyadh 11451 Saudi Arabia
| | | | - Weibo Song
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
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13
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Rossi A, Boscaro V, Carducci D, Serra V, Modeo L, Verni F, Fokin SI, Petroni G. Ciliate communities and hidden biodiversity in freshwater biotopes of the Pistoia province (Tuscany, Italy). Eur J Protistol 2016; 53:11-9. [DOI: 10.1016/j.ejop.2015.12.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/02/2015] [Accepted: 12/16/2015] [Indexed: 11/26/2022]
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14
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Castelli M, Lanzoni O, Rossi L, Potekhin A, Schrallhammer M, Petroni G. Evaluation of Enrichment Protocols for Bacterial Endosymbionts of Ciliates by Real-Time PCR. Curr Microbiol 2016; 72:723-32. [PMID: 26894821 DOI: 10.1007/s00284-016-1006-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/03/2016] [Indexed: 11/30/2022]
Abstract
Large-scale studies on obligate bacterial endosymbionts may frequently require preliminary purification and enrichment protocols, which are often elaborate to set up and to evaluate, especially if the host organism is a protist. The purpose of this study was to develop a real-time PCR-based strategy and employ it for assessing two of such enrichment protocols for Holospora caryophila, hosted by the ciliate Paramecium. Four SSU rRNA gene-targeted real-time PCR assays were designed, which allowed to compare the amount of H. caryophila to other organisms, namely the host, its food bacterium (Raoultella planticola), and free-living bacteria present in the culture medium. By the use of the real-time PCR assays in combination, it was possible to conclude that the "cell fractionation" protocol was quite successful in the enrichment of the symbiont, while the "Percoll gradient" protocol will need further refinements to be fully repeatable. The proposed approach has the potential to facilitate and encourage future studies on the yet underexplored field of bacterial endosymbionts of ciliates and other protists. It can also find valuable applications for experimental questions other than those tested, such as fast and precise assessment of symbiont abundance in natural populations and comparison among multiple coexisting symbionts.
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Affiliation(s)
| | - Olivia Lanzoni
- Department of Biology, University of Pisa, 56126, Pisa, Italy
| | - Leonardo Rossi
- Department of Clinical and Experimental Medicine, University of Pisa, 56126, Pisa, Italy
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, St. Petersburg State University, Saint Petersburg, Russia, 199034
| | - Martina Schrallhammer
- Microbiology, Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
| | - Giulio Petroni
- Department of Biology, University of Pisa, 56126, Pisa, Italy.
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Xu Y, Yan Y, Li L, Al-Rasheid KAS, Al-Farraj SA, Song W. Morphology and phylogeny of three karyorelictean ciliates (Protista, Ciliophora), including two novel species, Trachelocerca chinensis sp. n. and Tracheloraphis dragescoi sp. n. Int J Syst Evol Microbiol 2014; 64:4084-4097. [PMID: 25238761 DOI: 10.1099/ijs.0.068783-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper investigates the morphology and infraciliature of three karyorelictean ciliates, Trachelocerca chinensis sp. n., Tracheloraphis dragescoi sp. n. and a rarely known form, Geleia acuta (Dragesco, 1960) Foissner, 1998, which were isolated from the intertidal zone of sandy beaches at Zhanjiang and Qingdao, China. Trachelocerca chinensis sp. n. is distinguished from related forms by having 26-30 somatic kineties, a narrow glabrous stripe and a single nuclear group composed of approximately four to six macronuclei and two micronuclei. Tracheloraphis dragescoi sp. n. can be recognized through its 14-22 somatic kineties, wide glabrous stripe and a single nuclear group composed of about four macronuclei. Phylogenetic analyses based on small-subunit (SSU) rRNA gene sequences indicated that the genera Trachelocerca and Tracheloraphis are closely related but that neither of them appears to be a clearly monophyletic group. Nonetheless, the monophyly of Trachelocerca is not rejected by the approximately unbiased (AU) test (P = 0.143, >0.05), although that of Tracheloraphis is rejected (P = 0.011, <0.05). Geleia acuta, meanwhile, branched with Geleia fossata and falls in the Geleia clade.
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Affiliation(s)
- Yuan Xu
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China.,State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, PR China
| | - Ying Yan
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Lifang Li
- Marine College, Shandong University, Weihai 264209, PR China
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Weibo Song
- Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
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Xu Y, Pan H, Miao M, Hu X, Al-Farraj SA, Al-Rasheid KAS, Song W. Morphology and phylogeny of two species of Loxodes (Ciliophora, Karyorelictea), with description of a new subspecies, Loxodes striatus orientalis subsp. n. J Eukaryot Microbiol 2014; 62:206-16. [PMID: 25155338 DOI: 10.1111/jeu.12162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 06/30/2014] [Accepted: 07/21/2014] [Indexed: 11/28/2022]
Abstract
The morphology and phylogeny of Loxodes vorax and L. striatus orientalis subsp. n. were investigated based on infraciliature and small subunit (SSU) rRNA gene sequence data. Loxodes striatus orientalis subsp. n. was separated from L. striatus striatus stat. n. by having fewer dikinetids in the intrabuccal kinety (35-55 vs. 50-70) and a variable number of macronuclei (2-4 vs. 2). In addition, the SSU rRNA gene sequence of the new subspecies differs in 13 and 11 nucleotides from that of two populations of the nominotypic subspecies. We also summarized the morphological differences between Loxodes and Remanella based on the data available. Phylogenetic analyses revealed that the genus Loxodes was monophyletic and nested within Remanella species. This study might, therefore, support the hypothesis that the freshwater genus Loxodes evolved from the marine genus Remanella.
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Affiliation(s)
- Yuan Xu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China; Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
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Yan Y, Gao F, Xu Y, Al-Rasheid KAS, Song W. Morphology and Phylogeny of Three Trachelocercid Ciliates, with Description of a New Species, Trachelocerca orientalis
spec. nov. (Ciliophora, Karyorelictea). J Eukaryot Microbiol 2014; 62:157-66. [DOI: 10.1111/jeu.12154] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 07/02/2014] [Accepted: 07/04/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Ying Yan
- Laboratory of Protozoology; Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Feng Gao
- Laboratory of Protozoology; Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Yuan Xu
- State Key Laboratory of Estuarine and Coastal Research; East China Normal University; Shanghai 200062 China
| | | | - Weibo Song
- Laboratory of Protozoology; Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
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Focusing on Genera to Improve Species Identification: Revised Systematics of the Ciliate Spirostomum. Protist 2014; 165:527-41. [DOI: 10.1016/j.protis.2014.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/18/2014] [Accepted: 05/21/2014] [Indexed: 11/20/2022]
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Xu Y, Gao S, Hu X, Al-Rasheid KA, Song W. Phylogeny and systematic revision of the karyorelictid genus Remanella (Ciliophora, Karyorelictea) with descriptions of two new species. Eur J Protistol 2013; 49:438-52. [DOI: 10.1016/j.ejop.2012.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 12/05/2012] [Accepted: 12/11/2012] [Indexed: 11/29/2022]
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Xu Y, Li J, Song W, Warren A. Phylogeny and Establishment of a New Ciliate Family, Wilbertomorphidae fam. nov. (Ciliophora, Karyorelictea), a Highly Specialized Taxon Represented by Wilbertomorpha colpoda
gen. nov., spec. nov. J Eukaryot Microbiol 2013; 60:480-9. [DOI: 10.1111/jeu.12055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 03/28/2013] [Accepted: 04/08/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Yuan Xu
- Laboratory of Protozoology; Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Jiamei Li
- Laboratory of Protozoology; Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Weibo Song
- Laboratory of Protozoology; Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao 266003 China
| | - Alan Warren
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD United Kingdom
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Survey of Paramecium duboscqui using three markers and assessment of the molecular variability in the genus Paramecium. Mol Phylogenet Evol 2012; 65:1004-13. [DOI: 10.1016/j.ympev.2012.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/12/2012] [Accepted: 09/03/2012] [Indexed: 11/22/2022]
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Xu Y, Miao M, Warren A, Song W. Diversity of the karyorelictid ciliates:Remanella(Protozoa, Ciliophora, Karyorelictida) inhabiting intertidal areas of Qingdao, China, with descriptions of three species. SYST BIODIVERS 2012. [DOI: 10.1080/14772000.2012.681713] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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XU YUAN, LI JIAMEI, GAO FENG, HU XIAOZHONG, AL-RASHEID KHALEDA. Apotrachelocerca arenicola (Kahl, 1933) n. g., comb. n. (Protozoa, Ciliophora, Trachelocercidae): Morphology and Phylogeny. J Eukaryot Microbiol 2011; 58:504-10. [DOI: 10.1111/j.1550-7408.2011.00578.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Morphological and molecular information of a new species of Geleia (Ciliophora, Karyorelictea), with redescriptions of two Kentrophoros species from China. Eur J Protistol 2011; 47:172-85. [DOI: 10.1016/j.ejop.2011.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/28/2011] [Accepted: 03/30/2011] [Indexed: 11/20/2022]
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Lynn DH, Pinheiro M. A survey of polymerase chain reaction (PCR) amplification studies of unicellular protists using single-cell PCR. J Eukaryot Microbiol 2009; 56:406-12. [PMID: 19737192 DOI: 10.1111/j.1550-7408.2009.00439.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We surveyed a variety of studies that have used single-cell polymerase chain reaction (SC-PCR) to examine the gene sequences of a diversity of unicellular protists. Representatives of all the Super-Groups of eukaryotes have been subjected to SC-PCR with ciliates and dinoflagellates being most commonly examined. The SC-PCR was carried out either by directly amplifying a single lysed cell or by first extracting DNA and following this with amplification of the DNA extract. Cell lysis methods included heating, freezing, mechanical rupture, and enzyme digestion. Cells fixed or preserved with ethanol, methanol, and Lugol's have also been used successfully. Heminested or seminested PCR might follow the initial PCR, whose products were then directly sequenced or cloned and then sequenced. The methods are not complicated. This should encourage protistologists to use SC-PCR in the description of new or revised taxa, especially rare and unculturable forms, and it should also enable the probing of gene expression in relation to life history stages.
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Affiliation(s)
- Denis H Lynn
- Department of Integrative Biology, University of Guelph, Ontario, Canada.
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