Parts and During Physiological Reorganization, When New Oral Structures Replace the Pre-Existing Ones for Reasons That Are Not Well Understood
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Molecular Data and the Evolutionary History of Dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Un
Molecular data and the evolutionary history of dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Universitat Heidelberg, 1993 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES Department of Botany We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA November 2003 © Juan Fernando Saldarriaga Echavarria, 2003 ABSTRACT New sequences of ribosomal and protein genes were combined with available morphological and paleontological data to produce a phylogenetic framework for dinoflagellates. The evolutionary history of some of the major morphological features of the group was then investigated in the light of that framework. Phylogenetic trees of dinoflagellates based on the small subunit ribosomal RNA gene (SSU) are generally poorly resolved but include many well- supported clades, and while combined analyses of SSU and LSU (large subunit ribosomal RNA) improve the support for several nodes, they are still generally unsatisfactory. Protein-gene based trees lack the degree of species representation necessary for meaningful in-group phylogenetic analyses, but do provide important insights to the phylogenetic position of dinoflagellates as a whole and on the identity of their close relatives. Molecular data agree with paleontology in suggesting an early evolutionary radiation of the group, but whereas paleontological data include only taxa with fossilizable cysts, the new data examined here establish that this radiation event included all dinokaryotic lineages, including athecate forms. Plastids were lost and replaced many times in dinoflagellates, a situation entirely unique for this group. Histones could well have been lost earlier in the lineage than previously assumed. -
The Macronuclear Genome of Stentor Coeruleus Reveals Tiny Introns in a Giant Cell
University of Pennsylvania ScholarlyCommons Departmental Papers (Biology) Department of Biology 2-20-2017 The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell Mark M. Slabodnick University of California, San Francisco J. G. Ruby University of California, San Francisco Sarah B. Reiff University of California, San Francisco Estienne C. Swart University of Bern Sager J. Gosai University of Pennsylvania See next page for additional authors Follow this and additional works at: https://repository.upenn.edu/biology_papers Recommended Citation Slabodnick, M. M., Ruby, J. G., Reiff, S. B., Swart, E. C., Gosai, S. J., Prabakaran, S., Witkowska, E., Larue, G. E., Gregory, B. D., Nowacki, M., Derisi, J., Roy, S. W., Marshall, W. F., & Sood, P. (2017). The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. Current Biology, 27 (4), 569-575. http://dx.doi.org/10.1016/j.cub.2016.12.057 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/biology_papers/49 For more information, please contact [email protected]. The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell Abstract The giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor [1, 2] is a heterotrichous ciliate distantly related to familiar ciliate models, such as Tetrahymena or Paramecium. The primary distinguishing feature of Stentor is its incredible size: a single cell is 1 mm long. Early developmental biologists, including T.H. Morgan [3], were attracted to the system because of its regenerative abilities—if large portions of a cell are surgically removed, the remnant reorganizes into a normal-looking but smaller cell with correct proportionality [2, 3]. -
Eukaryotes Microbes
rator abo y M L ic ve ro IV Eukaryote Microbes 1–7 ti b c i a o r l o e t g y n I 1 Algae, 2 Lichens, 3 Fungi, I I I I I I I I I I I B 4 Fleshy Fungi, 5 Protozoa, s a e s c ic n , A ie 6 Slime Molds, 7 Water Molds p Sc pl h ied & Healt Eukaryotes 1 Algae top of page ● Objectives/Key Words ✟ 9 motility & structure videos ● Algal Thallus ✟ Carpenter’s diatom motility ● Algal Wet Mount (Biosafety Level 1)✲✱✓ ✟ Chlamydomonas motility ● Algal Wet Mount (Biosafety Level 2)✲✱✓ ✟ Diatom gliding movement ● Algal Wet Mount (disposable loop) ✲✱✱✓ ✟ Euglena motility ● Microscopic Algae✓ ✟ Gyrosigma motility ✟ ❍ Green Algae (Chlorophyta) ✟ Noctiluca scintillans motility ✟ ❍ Chlamydomonas ✟ Peridinium dinoflagellate motility ✟ ❍ Euglenoids (Euglenophyta) ✟ Synura cells & colony ❍ Diatoms (Chrysophyta) ✟ Volvox flagellate cells ✟✟ ❍ 1 frustules & motility ◆ ❍ 2 cell division ❖14 scenic microbiology, 60 images, 9 videos ❍ 3 sexual reproduction ❖ Biofouling 1, 2 ❍ 4 striae ❖ Coral Bleaching: Hawaii ✟◆ ◆ Volvox ❍ Dinoflagellates (Pyrrophyta) ❖ Coral Reefs: Pacific Ocean ❍ Red Tide 1–2 ❖ Coral Reefs 2: Andaman Sea, Indian Ocean◆ ❖ “Doing the Laundry”, India◆◆ ● Eukaryotes Quick Quiz 1A: Algae ❖ Green Lake, Lanzarote◆ ● Eukaryotes Quick Quiz 1B: Best Practice ❖ Garden Pond, British Columbia Canada, 1◆, 2 ● Eukaryotes Question Bank1.1✓–1.16◆◆◆◆◆◆◆◆✟✟✟ ❖ Marine Luminescence, Sucia Island, WA, US◆ ❖ Red Tide, Vancouver & Comox, Canada ● 35 interactive pdf pages ❖ Sea Turtle Tracks, Galápagos Islands◆ ● 112 illustrations, 80 images of algae ❖ Sea Turtles & Sea -
An Integrative Approach Sheds New Light Onto the Systematics
www.nature.com/scientificreports OPEN An integrative approach sheds new light onto the systematics and ecology of the widespread ciliate genus Coleps (Ciliophora, Prostomatea) Thomas Pröschold1*, Daniel Rieser1, Tatyana Darienko2, Laura Nachbaur1, Barbara Kammerlander1, Kuimei Qian1,3, Gianna Pitsch4, Estelle Patricia Bruni4,5, Zhishuai Qu6, Dominik Forster6, Cecilia Rad‑Menendez7, Thomas Posch4, Thorsten Stoeck6 & Bettina Sonntag1 Species of the genus Coleps are one of the most common planktonic ciliates in lake ecosystems. The study aimed to identify the phenotypic plasticity and genetic variability of diferent Coleps isolates from various water bodies and from culture collections. We used an integrative approach to study the strains by (i) cultivation in a suitable culture medium, (ii) screening of the morphological variability including the presence/absence of algal endosymbionts of living cells by light microscopy, (iii) sequencing of the SSU and ITS rDNA including secondary structures, (iv) assessment of their seasonal and spatial occurrence in two lakes over a one‑year cycle both from morphospecies counts and high‑ throughput sequencing (HTS), and, (v) proof of the co‑occurrence of Coleps and their endosymbiotic algae from HTS‑based network analyses in the two lakes. The Coleps strains showed a high phenotypic plasticity and low genetic variability. The algal endosymbiont in all studied strains was Micractinium conductrix and the mutualistic relationship turned out as facultative. Coleps is common in both lakes over the whole year in diferent depths and HTS has revealed that only one genotype respectively one species, C. viridis, was present in both lakes despite the diferent lifestyles (mixotrophic with green algal endosymbionts or heterotrophic without algae). -
Analysis of the Mechanism of Dinoflagellate Flagella Contraction-Relaxation Cycle
Biol Cell (1992) 76, 33-42 33 © Elsevier, Paris Original article Analysis of the mechanism of dinoflagellate flagella contraction-relaxation cycle Monique Cachon a, Claude Greuet b, Jacky Cosson a, Philippe Huitorel" a Groupe de Motilitd Cellulaire, URA 671 du CNRS, Universit~ Pet M Curie, Observatoire Ocdanologique, 06230 Villefranche-sur-Mer; b Centre de Biologie Marine, Laboratoire de Cytophysiologie des Protistes, Universitd de Nice-Sophia Antipolis, 06108 Nice Cedex, France (Received 11 May 1992; accepted 29 September 1992) Summary - Dinoflagellates possess two flagella. One of them, the longitudinal flagellum, retracts from time to time in some species, such as Ceratium and Peridinium. Additional structures which run along the axoneme seem to be responsible for this particular beha- viour. The retraction which is rapid (less than 60 ms) may be subdivided into several steps: i) the undulating movement stops; ii) the flagellum appears then as a jagged line during 20 ms; iii) finally a rapid retraction (20 ms) takes place, the flagellum being folded 20 times inside the cylindrical flagellar pocket. The measurements on video-records suggest that the R-fibre shortens to 30°7o of its original length. The contraction and relaxation mechanism of nanofilaments is proposed to be through coiling and uncoiling depen- dent on Ca 2+ concentration. protist / flagellar contraction / nanofilaments Introduction Motility observations Dinoflagellates possess two flagella, one longitudinal and These were made using Leitz and Reichert microscopes equipped one transverse, whose properties are not yet fully under- with differential interference contrast (DIC) Nomarski optics. stood [1-10]. These flagella appear to beat according to Video recordings were made with a Panasomic CCD camera sinusoidal waves [11] but in fact the transverse has a heli- (F. -
Lobban & Schefter 2008
Micronesica 40(1/2): 253–273, 2008 Freshwater biodiversity of Guam. 1. Introduction, with new records of ciliates and a heliozoan CHRISTOPHER S. LOBBAN and MARÍA SCHEFTER Division of Natural Sciences, College of Natural & Applied Sciences, University of Guam, Mangilao, GU 96923 Abstract—Inland waters are the most endangered ecosystems in the world because of complex threats and management problems, yet the freshwater microbial eukaryotes and microinvertebrates are generally not well known and from Guam are virtually unknown. Photo- documentation can provide useful information on such organisms. In this paper we document protists from mostly lentic inland waters of Guam and report twelve freshwater ciliates, especially peritrichs, which are the first records of ciliates from Guam or Micronesia. We also report a species of Raphidiophrys (Heliozoa). Undergraduate students can meaningfully contribute to knowledge of regional biodiversity through individual or class projects using photodocumentation. Introduction Biodiversity has become an important field of study since it was first recognized as a concept some 20 years ago. It includes the totality of heritable variation at all levels, including numbers of species, in an ecosystem or the world (Wilson 1997). Biodiversity encompasses our recognition of the “ecosystem services” provided by organisms, the interconnectedness of species, and the impact of human activities, including global warming, on ecosystems and biodiversity (Reaka-Kudla et al. 1997). Current interest in biodiversity has prompted global bioinformatics efforts to identify species through DNA “barcodes” (Hebert et al. 2002) and to make databases accessible through the Internet (Ratnasingham & Hebert 2007, Encyclopedia of Life 2008). Biodiversity patterns are often contrasted between terrestrial ecosystems, with high endemism, and marine ecosystems, with low endemism except in the most remote archipelagoes (e.g., Hawai‘i), but patterns in Oceania suggest that this contrast may not be so clear as it seemed (Paulay & Meyer 2002). -
Phylogenetic Position of Three Condylostoma Species (Protozoa, Ciliophora, Heterotrichea) Inferred from the Small Subunit Rrna Gene Sequence
Available online at www.sciencedirect.com Progress in Natural Science 18 (2008) 1089–1093 www.elsevier.com/locate/pnsc Phylogenetic position of three Condylostoma species (Protozoa, Ciliophora, Heterotrichea) inferred from the small subunit rRNA gene sequence Wenbo Guo a, Weibo Song a,*, Khaled A.S. Al-Rasheid b, Chen Shao a, Miao Miao a, Saleh A. Al-Farraj b, Saleh A. Al-Qurishy b, Zigui Chen a, Zhenzhen Yi a, Shan Gao a a Laboratory of Protozoology, Ocean University of China, Minxing Building B, 5 Yushan Road, Qingdao 266003, China b Zoology Department, King Saud University, Riyadh 11451, Saudi Arabia Received 24 January 2008; received in revised form 9 April 2008; accepted 9 April 2008 Abstract The systematically poorly known ciliate genus Condylostoma was erected by Vincent in 1826. About 10 morphotypes have been reported, but any molecular investigations concerning this group so far are lacking. In this work, the small subunit ribosomal RNA (SS rRNA) gene of three marine Condylostoma species was sequenced, by which the phylogenetic trees were constructed by distance- matrix, maximum parsimony and Bayesian inference methods. The results show that (1) all the trees have similar topologies with high supports; (2) Condylostoma is mostly related to the genus Condylostentor; and (3) three Condylostoma species as well as Condylostentor auriculatus cluster together and form a sister group with other heterotrichs. This is moderately consistent with the assessment of phylo- genetic relationships of Condylostoma-related heterotrichs from the morphological information. The phylogenetic relationship of some other related heterotrichs, Peritromus, Folliculina, Stentor and Blepharisma, has been also discussed. Ó 2008 National Natural Science Foundation of China and Chinese Academy of Sciences. -
The Planktonic Protist Interactome: Where Do We Stand After a Century of Research?
The ISME Journal (2020) 14:544–559 https://doi.org/10.1038/s41396-019-0542-5 ARTICLE The planktonic protist interactome: where do we stand after a century of research? 1 1 1 1 Marit F. Markussen Bjorbækmo ● Andreas Evenstad ● Line Lieblein Røsæg ● Anders K. Krabberød ● Ramiro Logares 1,2 Received: 14 May 2019 / Revised: 17 September 2019 / Accepted: 24 September 2019 / Published online: 4 November 2019 © The Author(s) 2019. This article is published with open access Abstract Microbial interactions are crucial for Earth ecosystem function, but our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2500 ecological interactions from ~500 publications, spanning the last 150 years. All major protistan lineages were involved in interactions as hosts, symbionts (mutualists and commensalists), parasites, predators, and/or prey. Predation was the most common interaction (39% of all records), followed by symbiosis (29%), parasitism (18%), and ‘unresolved interactions’ fi 1234567890();,: 1234567890();,: (14%, where it is uncertain whether the interaction is bene cial or antagonistic). Using bipartite networks, we found that protist predators seem to be ‘multivorous’ while parasite–host and symbiont–host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e., Stramenopiles, Alveolata, and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (TARA Oceans) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the recorded interactions. -
UC San Francisco Electronic Theses and Dissertations
UCSF UC San Francisco Electronic Theses and Dissertations Title Reviving Stentor coeruleus as a Modern Model for Morphogenesis: RNA interference reveals Mob1 as an asymmetrically localized polarity protein. Permalink https://escholarship.org/uc/item/6tb3c3h1 Author Slabodnick, Mark Maddock Publication Date 2014 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California asvmm by OlCH DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in CELL BIOLOGY in the ii Dedications and Acknowledgements I will start by saying that my thesis project was certainly a unique one. I will never forget the experiences I gathered during my graduate career and time in the Marshall lab, and I will always look back on this time fondly. Here I wish to recognize the many people who have contributed to my success as well as those who have kept and continue to keep me sane. But before I begin I first wish to dedicate my work to my family. I was fortunate to have a great group of classmates to share in my time at UCSF. The Tetrad program does a wonderful job of bringing together groups of people with rather diverse interests and experiences. I learned a good deal through my interactions with all of them over the years and I hope they all know that it has meant a lot to get to know them and call them friends. Whether we were studying, relaxing, playing indoor soccer, board games, camping, skiing, or working – I was always happy to be around them. -
Spatial and Temporal Distribution of Free-Living Protozoa in Aquatic Environments of a Brazilian Semi-Arid Region
ISSN = 1980-993X – doi:10.4136/1980-993X www.ambi-agua.net E-mail: [email protected] Tel.: (12) 3631-8004 ISSN = 1980-993X – doi:10.4136/1980-993X Spatial and temporal distributionwww.ambi of-agua free.net-living protozoa in aquatic E-mail: [email protected] environments of aTel.: B razilian(12) 3625-4212 semi -arid region doi: 10.4136/ambi-agua.1129 Maria Luisa Quinino de Medeiros1; Magnólia Fernandes Florêncio de Araújo*1; Luiz Sodré Neto2; Aline de Souza Amorim1 1Universidade Federal do Rio Grande do Norte - Natal, RN, Brasil Departamento de Microbiologia e Parasitologia 2Universidade Federal de Campina Grande - Cuité, PB, Brasil Centro de Educação e da Saúde * Corresponding author: e-mail: [email protected], [email protected], [email protected], [email protected] ABSTRACT Free-living protozoa organisms are distributed in aquatic environments and vary widely in both qualitative and quantitative terms. The unique ecological functions they exhibit in their habitats help to maintain the dynamic balance of these environments. Despite their wide range and abundance, studies on geographical distribution and ecology, when compared to other groups, are still scarce. This study aimed to identify and record the occurrence of free- living protozoa at three points in Piancó-Piranhas-Açu basin, in a semi-arid area of Rio Grande do Norte (RN) state, and to relate the occurrence of taxa with variations in chlorophyll a, pH and temperature in the environments. Samples were collected in the Armando Ribeiro Gonçalves Dam, from two lentic environments upstream and a lotic ecosystem downstream. Sixty-five taxa of free-living protozoa were found. -
Acquired Phototrophy in Aquatic Protists
Vol. 57: 279–310, 2009 AQUATIC MICROBIAL ECOLOGY Printed December 2009 doi: 10.3354/ame01340 Aquat Microb Ecol Published online November 24, 2009 Contribution to AME Special 3 ‘Rassoulzadegan at Villefranche-sur-Mer: 3 decades of aquatic microbial ecology’ OPENPEN ACCESSCCESS Acquired phototrophy in aquatic protists Diane K. Stoecker1,*, Matthew D. Johnson2, Colomban de Vargas3, Fabrice Not3 1University of Maryland Center for Environmental Science, Horn Point Laboratory, PO Box 775, 2020 Horns Point Rd, Cambridge, Maryland 21613, USA 2Woods Hole Oceanographic Institution, Watson Building 109, MS#52, Woods Hole, Massachusetts 02543, USA 3Evolution du Plancton et PaleOceans (EPPO) Lab., UMR 7144 - CNRS & Univ. Paris VI, Station Biologique de Roscoff - SBR, Place George Teissier, BP 74, 29682 Roscoff, Cedex, France ABSTRACT: Acquisition of phototrophy is widely distributed in the eukaryotic tree of life and can involve algal endosymbiosis or plastid retention from green or red origins. Species with acquired phototrophy are important components of diversity in aquatic ecosystems, but there are major differ- ences in host and algal taxa involved and in niches of protists with acquired phototrophy in marine and freshwater ecosystems. Organisms that carry out acquired phototrophy are usually mixotrophs, but the degree to which they depend on phototrophy is variable. Evidence suggests that ‘excess car- bon’ provided by acquired phototrophy has been important in supporting major evolutionary innova- tions that are crucial to the current ecological roles of these protists in aquatic ecosystems. Acquired phototrophy occurs primarily among radiolaria, foraminifera, ciliates and dinoflagellates, but is most ecologically important among the first three. Acquired phototrophy in foraminifera and radiolaria is crucial to their contributions to carbonate, silicate, strontium, and carbon flux in subtropical and trop- ical oceans. -
Characterization of a Green Stentor with Symbiotic Algae Growing in An
www.nature.com/scientificreports OPEN Characterization of a green Stentor with symbiotic algae growing in an extremely oligotrophic environment and storing large amounts of starch granules in its cytoplasm Ryo Hoshina1*, Yuuji Tsukii2, Terue Harumoto3 & Toshinobu Suzaki4 The genus Stentor is a relatively well-known ciliate owing to its lucid trumpet shape. Stentor pyriformis represents a green, short, and fat Stentor, but it is a little-known species. We investigated 124 ponds and wetlands in Japan and confrmed the presence of S. pyriformis at 23 locations. All these ponds were noticeably oligotrophic. With the improvement of oligotrophic culture conditions, we succeeded in long-term cultivation of three strains of S. pyriformis. The cytoplasm of S. piriformis contains a large number of 1–3 μm refractive granules that turn brown by Lugol’s staining. The granules also show a typical Maltese-cross pattern by polarization microscopy, strongly suggesting that the granules are made of amylopectin-rich starch. By analyzing the algal rDNA, it was found that all S. pyriformis symbionts investigated in this study were Chlorella variabilis. This species is known as the symbiont of Paramecium bursaria and is physiologically specialized for endosymbiosis. Genetic discrepancies between C. variabilis of S. pyriformis and P. bursaria may indicate that algal sharing was an old incident. Having symbiotic algae and storing carbohydrate granules in the cytoplasm is considered a powerful strategy for this ciliate to withstand oligotrophic and cold winter environments in highland bogs. Mixotrophic protists are reported to live in a wide range of environments1, even in highly oligotrophic environ- ments where other photoautotrophic and heterotrophic organisms cannot survive2,3.