Protist Diversity and Seasonal Dynamics in Skagerrak Plankton Communities As Revealed by Metabarcoding and Microscopy
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University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
Based on SSU Rdna Sequences
J. Eukaryot. Microbiol., 48(5), 2001 pp. 604±607 q 2001 by the Society of Protozoologists Phylogenetic Position of Sorogena stoianovitchae and Relationships within the Class Colpodea (Ciliophora) Based on SSU rDNA Sequences ERICA LASEK-NESSELQUISTa and LAURA A. KATZa,b aDepartment of Biological Sciences, Smith College, Northampton, Massachusetts 01063, and bProgram in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA ABSTRACT. The ciliate Sorogena stoianovitchae, which can form a multicellular fruiting body, has been classi®ed based upon its ultrastructure and morphology: the oral and somatic infraciliature of S. stoianovitchae most closely resemble those of members of the order Cyrtolophosidida in the class Colpodea. We characterized the small subunit ribosomal DNA (SSU rDNA) gene sequence from S. stoianovitchae and compared this sequence with those from representatives of all ciliate classes. These analyses placed S. stoianovitchae as either sister to members of the class Nassophorea or Colpodea. In an in-group analysis, including all SSU rDNA sequences from members of the classes Nassophorea and Colpodea and representatives of appropriate outgroups, S. stoianovitchae was always sister to Platyophrya vorax (class Colpodea, order Cyrtolophosidida). However, our analyses failed to support the monophyly of the class Colpodea. Instead, our data suggest that there are essentially three unresolved clades: (1) the class Nassophorea; (2) Bresslaua vorax, Colpoda in¯ata, Pseudoplatyophrya nana, and Bursaria truncatella (class Colpodea); and (3) P. vorax and S. stoianovitchae (class Colpodea). Key Words. Bursariomorphida, ciliate phylogeny, Colpodida, Cyrtolophosidida, molecular systematics, Nassophorea, Sorogenida. OROGENA stoianovitchae is a unique ciliate that aggregates partial B. sphagni sequence), provide the ®rst molecular hy- S to produce an aerial fruiting body when cells are starved. -
A Survey of Selected Economic Plants Virgil S
Eastern Illinois University The Keep Masters Theses Student Theses & Publications 1981 A Survey of Selected Economic Plants Virgil S. Priebe Eastern Illinois University This research is a product of the graduate program in Botany at Eastern Illinois University. Find out more about the program. Recommended Citation Priebe, Virgil S., "A Survey of Selected Economic Plants" (1981). Masters Theses. 2998. https://thekeep.eiu.edu/theses/2998 This is brought to you for free and open access by the Student Theses & Publications at The Keep. It has been accepted for inclusion in Masters Theses by an authorized administrator of The Keep. For more information, please contact [email protected]. T 11 F:SIS H El"">RODUCTION CERTIFICATE TO: Graduate Degree Candidates who have written formal theses. SUBJECT: Permission to reproduce theses. The University Library is rece1vrng a number of requests from other institutions asking permission to reproduce disse rta tions for inclusion in their library holdings. Although no copyright laws are involved, we feel that professional courtesy demands that permission be obtained from the author before we allow theses to be copied. Please sign one of the following statements: Booth Library of Eastern Illinois University has my permission to l end my thesis to a reputable college or university for the purpose of copying it for inclusion in that institution's library or res e ar ch holdings• . �� /ft/ ff nfl. Author I respectfully request Booth Library of Eastern Illinois University not allow my thesis be reproduced because -----� ---------- ---··· ·--·· · ----------------------------------- Date Author m A Survey o f Selected Economic Plants (TITLE) BY Virgil S. -
Phylogenomic Analysis of Balantidium Ctenopharyngodoni (Ciliophora, Litostomatea) Based on Single-Cell Transcriptome Sequencing
Parasite 24, 43 (2017) © Z. Sun et al., published by EDP Sciences, 2017 https://doi.org/10.1051/parasite/2017043 Available online at: www.parasite-journal.org RESEARCH ARTICLE Phylogenomic analysis of Balantidium ctenopharyngodoni (Ciliophora, Litostomatea) based on single-cell transcriptome sequencing Zongyi Sun1, Chuanqi Jiang2, Jinmei Feng3, Wentao Yang2, Ming Li1,2,*, and Wei Miao2,* 1 Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan 430023, PR China 2 Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan 430072, Hubei Province, PR China 3 Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, PR China Received 22 April 2017, Accepted 12 October 2017, Published online 14 November 2017 Abstract- - In this paper, we present transcriptome data for Balantidium ctenopharyngodoni Chen, 1955 collected from the hindgut of grass carp (Ctenopharyngodon idella). We evaluated sequence quality and de novo assembled a preliminary transcriptome, including 43.3 megabits and 119,141 transcripts. Then we obtained a final transcriptome, including 17.7 megabits and 35,560 transcripts, by removing contaminative and redundant sequences. Phylogenomic analysis based on a supermatrix with 132 genes comprising 53,873 amino acid residues and phylogenetic analysis based on SSU rDNA of 27 species were carried out herein to reveal the evolutionary relationships among six ciliate groups: Colpodea, Oligohymenophorea, Litostomatea, Spirotrichea, Hetero- trichea and Protocruziida. The topologies of both phylogenomic and phylogenetic trees are discussed in this paper. In addition, our results suggest that single-cell sequencing is a sound method of obtaining sufficient omics data for phylogenomic analysis, which is a good choice for uncultivable ciliates. -
Terrestrial Cryptogam Diversity Across Productivity Gradients of Southern
Distribution and diversity of terrestrial mosses, liverworts and lichens along productivity gradients of a southern boreal forest J.M. Kranabetter1, P. Williston2, and W.H. MacKenzie3 1British Columbia Ministry of Forests and Range Bag 6000, Smithers, B.C., Canada, V0J 2N0 Ph# (250) 847-6389; Fax# (250) 847-6353 [email protected] 2Gentian Botanical Research 4861 Nielsen Road, Smithers B.C., Canada, V0J 2N2 Ph# (250) 877-7702 [email protected] 3British Columbia Ministry of Forests and Range Bag 6000, Smithers, B.C., Canada, V0J 2N0 Ph# (250) 847-6388; Fax# (250) 847-6353 [email protected] Abstract Terrestrial cryptogams (mosses, liverworts and lichens) provide a useful suite of species for monitoring forests, especially when species distributions and diversity attributes are well defined from benchmark sites. To facilitate this, we surveyed contrasting plant associations of an upland boreal forest (in British Columbia, Canada) to explore the association of soil productivity with cryptogam distribution and diversity. Total terrestrial cryptogam richness of the study sites (19 plots of 0.15 ha each) was 148 taxa, with 47 mosses, 23 liverworts, and 78 lichens. Soil productivity was strongly related to the distribution of cryptogams by guild (i.e. lichen species richness declined with productivity, while moss and liverwort richness increased) and substrate (i.e. species richness on forest floor and cobbles declined with productivity as species richness increased on coarse woody debris). Generalists comprised only 15% of the cryptogam community by species, and mesotrophic sites lacked some of the species adapted to the dry-poor or moist-rich ends of the producitivity spectrum. -
Diversity of Microorganisms in Biocrusts Surrounding Highly Saline Potash Tailing Piles in Germany
microorganisms Communication Diversity of Microorganisms in Biocrusts Surrounding Highly Saline Potash Tailing Piles in Germany Ekaterina Pushkareva 1,2,* , Veronika Sommer 1, Israel Barrantes 3 and Ulf Karsten 1 1 Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, 18059 Rostock, Germany; [email protected] (V.S.); [email protected] (U.K.) 2 Department of Biology, Botanical Institute, University of Cologne, 50674 Cologne, Germany 3 Research Group Translational Bioinformatics, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, 18057 Rostock, Germany; [email protected] * Correspondence: [email protected] Abstract: Potash tailing piles located in Germany represent extremely hypersaline locations that negatively affect neighbouring environments and limit the development of higher vegetation. How- ever, biocrusts, as cryptogamic covers, inhabit some of these areas and provide essential ecological functions, but, nevertheless, they remain poorly described. Here, we applied high-throughput sequencing (HTS) and targeted four groups of microorganisms: bacteria, cyanobacteria, fungi and other eukaryotes. The sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Cyanobacteria and Actinobacteria. Additionally, we applied yanobacteria-specific primers for a detailed assessment of the cyanobacterial community, which was dominated by members of the filamentous orders Synechococcales and Oscillatoriales. Furthermore, the majority of reads in the studied biocrusts obtained by sequencing of the 18S rRNA gene belonged to eukaryotic microalgae. In addition, sequencing of the internal rDNA transcribed spacer region (ITS) showed the dominance Citation: Pushkareva, E.; Sommer, V.; of Ascomycota within the fungal community. Overall, these molecular data provided the first detailed Barrantes, I.; Karsten, U. -
The Life Cycles of Cryptogams 7
Acta Botanica Malacitana, 16(1): 5-18 Málaga, 1991 E IE CYCES O CYOGAMS Peter R. BELL SUMMARY: Meiosis and karyogamy are recognized as control points in the life cycle of cryptogams. The control of meiosis is evidently complex and in yeast, and by analogy in all cryptogams, involves progressive gene activation. The causes of the delay in meiosis in diplohaplontic and diplontic organisms, and the manner in which the block is removed remain to be discovered. There is accumulating evidence that cytoplasmic RNA plays an important role in meiotic division. Many features of tn are still obscure. The tendency to oogamy has provided the opportunity for the laying down of long-lived messenger RNA in the abundant cytoplasm of the female gamete. The sporophytic nature of the developing zygote can in this way be partially pre-determined. There is evidence that this is the situation in the ferns. Specific molecules (probably arabino-galacto-proteins) on the surface of the plasma membrane are likely to account both for gametic selection, and the readiness with which appropriate gametes fuse. The dikaryotic condition indicates that nuclear fusion is not inevitable following plasmogamy. The ultimate fusion of the nuclei may result from quite simple changes in the nuclear surface. Exposure of lipid, for example, would lead to fusion as a result of hydrophobic forces. Aberrations of cryptogamic life cycles are numerous. The nuclear relationships of many aberrant cycles are unknown. In general it appears that the maintenance of sporophytic growth depends upon the presence of at least two sets of chromosomes. Conversely the maintenance of gametophytic growth in cultures obtained aposporously appears to be impossible in the presence of four sets of chromosomes, or more. -
Tracing the Origin of Planktonic Protists in an Ancient Lake
microorganisms Article Tracing the Origin of Planktonic Protists in an Ancient Lake Nataliia V. Annenkova 1,* , Caterina R. Giner 2,3 and Ramiro Logares 2,* 1 Limnological Institute Siberian Branch of the Russian Academy of Sciences 3, Ulan-Batorskaya St., 664033 Irkutsk, Russia 2 Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, ES08003 Barcelona, Spain; [email protected] 3 Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada * Correspondence: [email protected] (N.V.A.); [email protected] (R.L.) Received: 26 February 2020; Accepted: 7 April 2020; Published: 9 April 2020 Abstract: Ancient lakes are among the most interesting models for evolution studies because their biodiversity is the result of a complex combination of migration and speciation. Here, we investigate the origin of single celled planktonic eukaryotes from the oldest lake in the world—Lake Baikal (Russia). By using 18S rDNA metabarcoding, we recovered 1414 Operational Taxonomic Units (OTUs) belonging to protists populating surface waters (1–50 m) and representing pico/nano-sized cells. The recovered communities resembled other lacustrine freshwater assemblages found elsewhere, especially the taxonomically unclassified protists. However, our results suggest that a fraction of Baikal protists could belong to glacial relicts and have close relationships with marine/brackish species. Moreover, our results suggest that rapid radiation may have occurred among some protist taxa, partially mirroring what was already shown for multicellular organisms in Lake Baikal. We found 16% of the OTUs belonging to potential species flocks in Stramenopiles, Alveolata, Opisthokonta, Archaeplastida, Rhizaria, and Hacrobia. -
Protozoologica
Acta Protozool. (2014) 53: 207–213 http://www.eko.uj.edu.pl/ap ACTA doi:10.4467/16890027AP.14.017.1598 PROTOZOOLOGICA Broad Taxon Sampling of Ciliates Using Mitochondrial Small Subunit Ribosomal DNA Micah DUNTHORN1, Meaghan HALL2, Wilhelm FOISSNER3, Thorsten STOECK1 and Laura A. KATZ2,4 1Department of Ecology, University of Kaiserslautern, 67663 Kaiserslautern, Germany; 2Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; 3FB Organismische Biologie, Universität Salzburg, A-5020 Salzburg, Austria; 4Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA Abstract. Mitochondrial SSU-rDNA has been used recently to infer phylogenetic relationships among a few ciliates. Here, this locus is compared with nuclear SSU-rDNA for uncovering the deepest nodes in the ciliate tree of life using broad taxon sampling. Nuclear and mitochondrial SSU-rDNA reveal the same relationships for nodes well-supported in previously-published nuclear SSU-rDNA studies, al- though support for many nodes in the mitochondrial SSU-rDNA tree are low. Mitochondrial SSU-rDNA infers a monophyletic Colpodea with high node support only from Bayesian inference, and in the concatenated tree (nuclear plus mitochondrial SSU-rDNA) monophyly of the Colpodea is supported with moderate to high node support from maximum likelihood and Bayesian inference. In the monophyletic Phyllopharyngea, the Suctoria is inferred to be sister to the Cyrtophora in the mitochondrial, nuclear, and concatenated SSU-rDNA trees with moderate to high node support from maximum likelihood and Bayesian inference. Together these data point to the power of adding mitochondrial SSU-rDNA as a standard locus for ciliate molecular phylogenetic inferences. -
Interaction Between Metarhizium Anisopliae and Its Host, the Subterranean Termite Coptotermes Curvignathus During the Infection Process
biology Article Interaction between Metarhizium anisopliae and Its Host, the Subterranean Termite Coptotermes curvignathus during the Infection Process Samsuddin Ahmad Syazwan 1,2 , Shiou Yih Lee 1, Ahmad Said Sajap 1, Wei Hong Lau 3, Dzolkhifli Omar 3 and Rozi Mohamed 1,* 1 Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, Serdang 43400, Malaysia; [email protected] (S.A.S.); [email protected] (S.Y.L.); [email protected] (A.S.S.) 2 Mycology and Pathology Branch, Forest Biodiversity Division, Forest Research Institute Malaysia (FRIM), Kepong 52109, Malaysia 3 Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia; [email protected] (W.H.L.); zolkifl[email protected] (D.O.) * Correspondence: [email protected]; Tel.: +60-397-697-183 Simple Summary: The use of Metarhizium anisopliae as a biological control of insect pests has been experimented in the laboratory as well as in field trials. This includes against the termite Coptotermes curvignathus, however the results have varying degrees of success. One reason could be due to the lack of detailed knowledge on the molecular pathogenesis of M. anisopliae. In the current study, the conidial suspension of M. anisopliae isolate PR1 was first inoculated on the C. curvignathus, after which the pathogenesis was examined using two different approaches: electron microscopy and protein expression. At the initiation stage, the progression observed and documented including Citation: Syazwan, S.A.; Lee, S.Y.; adhesion, germination, and penetration of the fungus on the cuticle within 24 h after inoculation. Sajap, A.S.; Lau, W.H.; Omar, D.; Later, this was followed by colonization and spreading of the fungus at the cellular level. -
Ciliate Biodiversity and Phylogenetic Reconstruction Assessed by Multiple Molecular Markers Micah Dunthorn University of Massachusetts Amherst, [email protected]
University of Massachusetts Amherst ScholarWorks@UMass Amherst Open Access Dissertations 9-2009 Ciliate Biodiversity and Phylogenetic Reconstruction Assessed by Multiple Molecular Markers Micah Dunthorn University of Massachusetts Amherst, [email protected] Follow this and additional works at: https://scholarworks.umass.edu/open_access_dissertations Part of the Life Sciences Commons Recommended Citation Dunthorn, Micah, "Ciliate Biodiversity and Phylogenetic Reconstruction Assessed by Multiple Molecular Markers" (2009). Open Access Dissertations. 95. https://doi.org/10.7275/fyvd-rr19 https://scholarworks.umass.edu/open_access_dissertations/95 This Open Access Dissertation is brought to you for free and open access by ScholarWorks@UMass Amherst. It has been accepted for inclusion in Open Access Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. CILIATE BIODIVERSITY AND PHYLOGENETIC RECONSTRUCTION ASSESSED BY MULTIPLE MOLECULAR MARKERS A Dissertation Presented by MICAH DUNTHORN Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of Doctor of Philosophy September 2009 Organismic and Evolutionary Biology © Copyright by Micah Dunthorn 2009 All Rights Reserved CILIATE BIODIVERSITY AND PHYLOGENETIC RECONSTRUCTION ASSESSED BY MULTIPLE MOLECULAR MARKERS A Dissertation Presented By MICAH DUNTHORN Approved as to style and content by: _______________________________________ -
F. Y. B. Sc.(Botany) Question Bank
Question bank for F.Y. B.Sc. Botany Paper-I Diversity Of Lower And Higher Cryptogams Paper-II Economic And Applied Botany -Prepared by- Chairperson, Members Of Board of Studies and Experienced teachers in Botany Of North Maharashtra University, Jalgaon. -Approved by- Dean, Science faculty, North Maharashtra University, Jalgaon. Botany paper I Diversity of Lower and Higher cryptogams Term-I Chapter: 1 Diversity of Lower cryptogams 2 Marks Questions: 1. Define diversity? Explain diversity in algae 2.What is diversity? Explain diversity in fungi 3.The study of algae is known as -------- a) Mycology b) Phycology c) Taxonomy d) Physiology 4. The branch which deals with study of fungi is known as-------- a) Physiology b) Ecology c) Mycology d) Phycology 5.Thalloid and non flowering plants are known as ------- a)Angiosperm b)Thallophyta c)Gymnosperm d) Dicotyledons Chapter: 2 Algae 2 Marks Questions: 1. What is epiphytic algae 2. What is symbiotic algae 3. The reserve food material in algae is -------- a) cellulose b) starch c) protein d) glycogen 4.The cell wall in algae is made up of-------- a) Chitin b) cellulose c) pectin d) glycogen 5. Fusion between gametes of equal sizes is called ------ a) Isogamy b) Anisogamy c) Oogamy d) Dichotogamy 6. Fusion between gametes of unequal sizes is called ------ a) Dichotogamy b) Anisogamy c) Oogamy d) Isogamy 7. An alga growing on aquatic animal is called-------- a) Epizoic b) Endozoic c) Epiphytic d) Terrestrial 8. The algae growing in seawater is known as ------- a) Freshwater algae b) Terrestrial algae c) Marine algae d) Lithophytic algae 4 Marks Questions: 1.Give the general characters of algae.