DOCSLIB.ORG

Phylogenetic Classification of Life

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Phylogenetic Classification of Life Proc. Natl. Accad. Sci. USA Vol. 93, pp. 1071-1076, February 1996 Evolution Archaeal- eubacterial mergers in the origin of Eukarya: Phylogenetic classification of life (centriole-kinetosome DNA/Protoctista/kingdom classification/symbiogenesis/archaeprotist) LYNN MARGULIS Department of Biology, University of Massachusetts, Amherst, MA 01003-5810 Conitribluted by Lynnl Marglulis, September 15, 1995 ABSTRACT A symbiosis-based phylogeny leads to a con- these features evolved in their ancestors by inferable steps (4, sistent, useful classification system for all life. "Kingdoms" 20). rRNA gene sequences (Trichomonas, Coronympha, Giar- and "Domains" are replaced by biological names for the most dia; ref. 11) confirm these as descendants of anaerobic eu- inclusive taxa: Prokarya (bacteria) and Eukarya (symbiosis- karyotes that evolved prior to the "crown group" (12)-e.g., derived nucleated organisms). The earliest Eukarya, anaero- animals, fungi, or plants. bic mastigotes, hypothetically originated from permanent If eukaryotes began as motility symbioses between Ar- whole-cell fusion between members of Archaea (e.g., Thermo- chaea-e.g., Thermoplasma acidophilum-like and Eubacteria plasma-like organisms) and of Eubacteria (e.g., Spirochaeta- (Spirochaeta-, Spirosymplokos-, or Diplocalyx-like microbes; like organisms). Molecular biology, life-history, and fossil ref. 4) where cell-genetic integration led to the nucleus- record evidence support the reunification of bacteria as cytoskeletal system that defines eukaryotes (21)-then an Prokarya while subdividing Eukarya into uniquely defined optimal explanation for Table I's large quantity of otherwise subtaxa: Protoctista, Animalia, Fungi, and Plantae. baffling sequence data ensues (Table 2). Nucleoid membranes are known in at least one prokaryote, Gemmata obscuriglobus (24), and membrane hypertrophy is Bacterial Symbioses Form Cells of Eukarya common in invasive associations implying nuclear-endomem- brane systems originated as defensive response in bacterial Here I detail implications of serial endosymbiotic theory (SET; mergers (4). Centriole-kinetosomes are thought derived from ref. 1) of origins of nucleated organisms for interpretation of attached eubacteria (Fig. 1) such that centriole-kinetosome molecular data and classification of all life. Eukaryotes evolved DNA (c-kDNA; refs. 25 and 26) is their vestige (4, 21). when archaeal (2) (=archaebacterial) and eubacterial cells A great distinction is made between prokaryotic genomes no merged in ahaerobic symbiosis. Nucleocytoplasm (from Ar- matter their recombinant source or number per cell (e.g., chaea) acquired swimming motility (from fermenting Eubac- Escherichia coli's same-genome multiple nucleoids when fis- teria) becoming mastigotes prior to acquisition of mitochon- sion is retarded) and composite genomes derived from genetic dria or plastids (3, 4). Some mastigotes then incorporated integration of symbionts. Archaea and eubacteria, no matter purple Eubacteria (mitochondria precursors) to become oxy- their vast RNA, protein, and metabolic differences, are nev- gen-respiring aerobes from which most protoctists, animals, ertheless prokaryotes. They lack the system that underlies and fungi evolved. Aerobes in later permanent association with mendelian genetics (composite heterospecific genomes, intra- plastid-precursor cyanobacteria became algae-i.e., phototro- cellular motility, and cell fusion) and therefore are united into phic protoctists (5). one most inclusive taxon: Prokarya. Nucleated organisms, Individuality reappears as former symbionts integrate and products of symbiont integration of two or more former branches on bifurcating phylogenies anastomose to generate prokaryotes, are placed in the second taxon: Eukarya. new name-requiring taxa. The necessary and sufficient expla- nation of simultaneous archaeal and eubacterial protein and Protoctista nucleic acid sequences (refs. 2, 5-13; Table 1) even in amito- chondriate eukaryotes is their origin as genetically integrated The Eukarya taxon (equivalent to "Superkingdom" or "Do- bacterial symbionts. The consequences of the SET phylogeny main") includes amitochondriate mastigotes [Archeozoa (27), for systematics (evolutionary classification) includes replace- Hypochondria (13), here Archaeprotista], organisms derived ment of ad hoc gene transfer hypotheses (10), social-political from symbioses between as few as two prokaryote types. terms like Kingdom or Domain (2), and other confusion with Meiosis and fertilization are known in some: parabasalids a consistent taxonomy for identifying, naming, and classifying (Barbulanympha) and pyrsonymphids (Notila; ref. 28). Meio- all life. tic-sexual cycles did not evolve in all Archaeprotista as Kirby Comparable to extant prokaryotic consortia-e.g., Thioden- showed for large Calonymphidae trichomonads (29). These dron (15), Methanobacillus omelianski (16), and Daptobacter- amitochondriate multikinetosome mastigotes are multinucle- infected chromatia (17)-the earliest symbioses that became ated. They bear numerous akaryomastigonts (four-kinetosome eukaryotic cells lacked mitosis and meiosis. Abiding in anoxic structures that lack their connected nucleus) and karyomas- environments today are free-living amitochondriate motile tigonts (four-kinetosome organelles attached to a nucleus) heterotrophs, mastigotes, related to animal intestinal symbi- peculiar to the family. Akaryomastigont kinesis outpaced onts (18, 19). They vary in number of nuclei, organization of karyomastigont kinesis such that the akaryomastigonts out- chromatin, kinetochores, Golgi-parabasal bodies, rhizoplast number the nuclei in the genera Calonympha, Stephanoniym- nucleus-kinetosome connectors, [9(2)+21 microtubule-based pha, and Snyderella (29). From DNA staining in Calonympha intracellular motility organelles (undulipodia), centriole- grassii akarymastigonts (*) we infer that certain centriole- kinetosome-mitotic spindles, and meiotic sexuality, suggesting kinetosomes retained their genes. The nuclear internalization of c-kDNA (i.e., in Chlamydomonas; ref. 26) probably oc- The publication costs of this article were defrayed in part by page charge payment. This articlc must therefore be hereby marked "advertisement" in *Dolan, M., Second European Congress of Protistology, July 24-28, accordance with 18 U.S.C. §1734 solely to indicate this fact. 1995, Clermont-Ferrand, France, p. 42 (abstr.). 1071 1072 Evolution: Margulis Proc. Natl. Acad. Sci. USA 93 (1996) Table 1. Prokarya origins of Eukarya components: Eubacterial Table 2. Hypothetical source of eukaryotic features and archacal protein contributions to the nucleocytoplasm of eukaryotes Spirochaeta sp. Thermoplasnma sp. (or related eubacterium) (or related archae) Eubacteria Archaea Undulipodium: undulating Acid, heat resistance Aminto acid metabolism/proteini synthesis swimming motility Aspartate aminotransferase Arginosuccinate synthetase Centriole-kinetosomes Membrane ATPases and lipids, Glutamine synthetase Elongation factor 2 (centrosomes, centroplasts) H +-ATPase Glutamate dehydrogenase Elongation factor Tu Spindle tubules, axonemes Chromatin with nucleosomal Aminoacyl tRNA synthetase organization, histones, (isoleucyl-, leucyl-, valyl-) (8) lamins Ubiquitin; proteosomes* Eubacterial genes, proteins* Archaebacterial polymerases Modified rRNA3, 5' ppp on 5SrRNA* and protein-synthetic Methionine initiation apparatus; other Fermentation/energy metabolism archaebacterial enzymes* Ferredoxin Cytoplasmic a-chain, /3-chain HI 02 hypersensitivity 02 microaerophilia vacuolar-type ATPase Retractiont Pleiomorphism (absence of cell Glyceraldehyde-3- Phosphoglycerol kinase wall) phosphate H2 productiont Sulfur respiration§ dchydrogenase (9) Resistant propagule formationt Cytoskeletal fibers$ Nutcleotide/lnlcleic acid metabolisnm Emergent after fusion and integration: amitochondriate mastigotes Formylglycinylmide Carbamoyl-phosphate synthaset (Phylum Archaeprotista of Table 4), nuclear envelope with 8-fold ribonucleotide symmetrical pores, mitosis, Ca2+-sensitive physiologies, actin- and synthetaset myosin-based phagocytosis, fluid (reversibly fusing) membranes, mo- Pyrroline-5-carboxylate Indole-3-glycerol phosphate tility-based morphogenesis, programmed cell hybrid formation. reductase DNA-directed RNA polymerase *See Table 1 (6, 7). DNA polymerase tSpirosynmplokos deltaeiberi provides an example of a spirochete pre- DNA topoisomeraset adaptation of undulipodial withdrawal into the cell and perhaps even Histone-DNA binding proteins resistant propagule formation (22). Histidine pathwayt tFermentation product. Fibrillamina of nucleolus §Thermoplasma grows anaerobically if in contact with elemental sulfur particles as electron acceptors. Most membranes SThese structures reported in mycoplasms (23); their presence in Ester-linked lipids, Amino acid-Na+ cotransport protein Thermoplasma requires investigation. phospholipids Isoprenoid membrane lipids (ethers) Striess proteinl mitochondriate aerobes (nucleocytoplasm/centriole-kineto- hsp7O (DnaK) hsp6() chaperonin, cocytes (TCP-1) some/mitochondria). These include malarial parasites, cili- Vitaninl antd storage metabolism ates, and amoebae, whereas those of at least four genomes Dihydrofolate reductase (nucleocytoplasm/centriole- kinetosome/mitochondria/ Glycogen or cytoplasmic "floridean" plastids) include euglenids, diatoms, chrysophytes, coccolith- starch ophorids, and brown and red algae (Table 3). Protoctists in Carbolhydrate metabolism which the cells are large (30-500
Load more

Recommended publications
  • Genome Sequence of the Hyperthermophilic Crenarchaeon Pyrobaculum Aerophilum
    Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum Sorel T. Fitz-Gibbon*†, Heidi Ladner*‡, Ung-Jin Kim§, Karl O. Stetter¶, Melvin I. Simon§, and Jeffrey H. Miller*ʈ *Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California, Los Angeles, CA 90095-1489; †IGPP Center for Astrobiology, University of California, Los Angeles, CA 90095-1567; §Division of Biology, 147-75, California Institute of Technology, Pasadena, CA 91125; and ¶Archaeenzentrum, Regensburg University, 93053 Regensburg, Germany Contributed by Melvin I. Simon, November 30, 2001 We determined and annotated the complete 2.2-megabase genome sequence of Pyrobaculum aerophilum, a facultatively aerobic nitrate- C) crenarchaeon. Clues were°100 ؍ reducing hyperthermophilic (Topt found suggesting explanations of the organism’s surprising intoler- ance to sulfur, which may aid in the development of methods for genetic studies of the organism. Many interesting features worthy of further genetic studies were revealed. Whole genome computational analysis confirmed experiments showing that P. aerophilum (and perhaps all crenarchaea) lack 5؅ untranslated regions in their mRNAs and thus appear not to use a ribosome-binding site (Shine–Dalgarno)- .based mechanism for translation initiation at the 5؅ end of transcripts Inspection of the lengths and distribution of mononucleotide repeat- tracts revealed some interesting features. For instance, it was seen that mononucleotide repeat-tracts of Gs (or Cs) are highly unstable, a pattern expected for an organism deficient in mismatch repair. This result, together with an independent study on mutation rates, sug- gests a ‘‘mutator’’ phenotype. ϭ yrobaculum aerophilum is a hyperthermophilic (Tmax 104°C, Fig. 1. Small subunit rRNA-based phylogenetic tree of the crenarchaea.
    [Show full text]
  • Phylogenetic Classification of Life
    Proc. Natl. Accad. Sci. USA Vol. 93, pp. 1071-1076, February 1996 Evolution Archaeal- eubacterial mergers in the origin of Eukarya: Phylogenetic classification of life (centriole-kinetosome DNA/Protoctista/kingdom classification/symbiogenesis/archaeprotist) LYNN MARGULIS Department of Biology, University of Massachusetts, Amherst, MA 01003-5810 Conitribluted by Lynnl Marglulis, September 15, 1995 ABSTRACT A symbiosis-based phylogeny leads to a con- these features evolved in their ancestors by inferable steps (4, sistent, useful classification system for all life. "Kingdoms" 20). rRNA gene sequences (Trichomonas, Coronympha, Giar- and "Domains" are replaced by biological names for the most dia; ref. 11) confirm these as descendants of anaerobic eu- inclusive taxa: Prokarya (bacteria) and Eukarya (symbiosis- karyotes that evolved prior to the "crown group" (12)-e.g., derived nucleated organisms). The earliest Eukarya, anaero- animals, fungi, or plants. bic mastigotes, hypothetically originated from permanent If eukaryotes began as motility symbioses between Ar- whole-cell fusion between members of Archaea (e.g., Thermo- chaea-e.g., Thermoplasma acidophilum-like and Eubacteria plasma-like organisms) and of Eubacteria (e.g., Spirochaeta- (Spirochaeta-, Spirosymplokos-, or Diplocalyx-like microbes; like organisms). Molecular biology, life-history, and fossil ref. 4) where cell-genetic integration led to the nucleus- record evidence support the reunification of bacteria as cytoskeletal system that defines eukaryotes (21)-then an Prokarya while
    [Show full text]
  • Plant Evolution an Introduction to the History of Life
    Plant Evolution An Introduction to the History of Life KARL J. NIKLAS The University of Chicago Press Chicago and London CONTENTS Preface vii Introduction 1 1 Origins and Early Events 29 2 The Invasion of Land and Air 93 3 Population Genetics, Adaptation, and Evolution 153 4 Development and Evolution 217 5 Speciation and Microevolution 271 6 Macroevolution 325 7 The Evolution of Multicellularity 377 8 Biophysics and Evolution 431 9 Ecology and Evolution 483 Glossary 537 Index 547 v Introduction The unpredictable and the predetermined unfold together to make everything the way it is. It’s how nature creates itself, on every scale, the snowflake and the snowstorm. — TOM STOPPARD, Arcadia, Act 1, Scene 4 (1993) Much has been written about evolution from the perspective of the history and biology of animals, but significantly less has been writ- ten about the evolutionary biology of plants. Zoocentricism in the biological literature is understandable to some extent because we are after all animals and not plants and because our self- interest is not entirely egotistical, since no biologist can deny the fact that animals have played significant and important roles as the actors on the stage of evolution come and go. The nearly romantic fascination with di- nosaurs and what caused their extinction is understandable, even though we should be equally fascinated with the monarchs of the Carboniferous, the tree lycopods and calamites, and with what caused their extinction (fig. 0.1). Yet, it must be understood that plants are as fascinating as animals, and that they are just as important to the study of biology in general and to understanding evolutionary theory in particular.
    [Show full text]
  • Displacement of the Canonical Single-Stranded DNA-Binding Protein in the Thermoproteales
    Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales Sonia Paytubia,1,2, Stephen A. McMahona,2, Shirley Grahama, Huanting Liua, Catherine H. Bottinga, Kira S. Makarovab, Eugene V. Kooninb, James H. Naismitha,3, and Malcolm F. Whitea,3 aBiomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, United Kingdom; and bNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 AUTHOR SUMMARY Proteins are the major structural and biochemical route involved direct puri- operational components of cells. Even fication and identification of proteins the simplest organisms possess hundreds thatcouldbindtossDNAinoneofthe of different proteins, and more complex Thermoproteales, Thermoproteus tenax. organisms typically have many thou- This approach resulted in the identifi- sands. Because all living beings, from cation of the product of the gene ttx1576 microbes to humans, are related by as a candidate for the missing SSB. evolution, they share a core set of pro- We proceeded to characterize the teins in common. Proteins perform properties of the Ttx1576 protein, (which fundamental roles in key metabolic we renamed “ThermoDBP” for Ther- processes and in the processing of in- moproteales DNA-binding protein), formation from DNA via RNA to pro- showing that it has all the biochemical teins. A notable example is the ssDNA- properties consistent with a role as a binding protein, SSB, which is essential functional SSB, including a clear prefer- for DNA replication and repair and is ence for ssDNA binding and low se- widely considered to be one of the quence specificity. Using crystallographic few core universal proteins shared by analysis, we solved the structure of the alllifeforms.Herewedemonstrate Fig.
    [Show full text]
  • Kingdom Animalia: Phylum Summary Table
    KINGDOM ANIMALIA: PHYLUM SUMMARY TABLE Phylum PORIFERA CNIDARIA PLATYHELMINTHES (flatworms) NEMATODA (roundworms) ANNELIDA (segmented worms) Examples Sponges Sea jellies, Hydra, coral Planaria, tapeworm Trichinella, hookworm, Earthworm, polychaete worms, colonies, sea anemones nematode leech Body type Asymmetry Radial symmetry Bilateral symmetry Bilateral symmetry Bilateral symmetry (Symmetry) Ecological roles Food source Food source Food source Food source Food source home / shelter Reef- home, protect Parasitic Parasitic Parasitic symbiotic with shores Eat dead animals – Aerate soil Aerate soil bacteria Chem. – anticancer saprophyte Breakdown material Breakdown material Body organization 2 germ layers 2 layers: ecto & endo 3 layers: ectoderm, mesoderm, 3 layers: ectoderm, 3 layers: ectoderm, mesoderm, (# germ layers) Ectoderm, endoderm With mesoglea between endoderm mesoderm, endoderm endoderm Body cavity Acoelom Acoelom Acoelom Pseudocoelom Coelom Digestive system Filter feed: collar cells, Gastrovascular cavity, Mouth and gastrovascular Complete digestive Complete digestive system: food vacuoles, mouth, and cavity system: mouth & anus mouth & anus osculum nematocysts to capture food Mouth also serves as anus Special organs Special organs Reproduction Sexual: Sexual: male & female Sexual: hermaphroditic – Sexual: separate sexes = Sexual: hermaphroditic – heramaphroditic – medusa – gametes fuse cross fertilization dioecious cross fertilization gametes released in H2O Asexual: budding, Asexual: fragmentation Asexual: budding, regeneration
    [Show full text]
  • Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma Divulgatum
    microorganisms Article Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum Rafael Bargiela 1 , Karin Lanthaler 1,2, Colin M. Potter 1,2 , Manuel Ferrer 3 , Alexander F. Yakunin 1,2, Bela Paizs 1,2, Peter N. Golyshin 1,2 and Olga V. Golyshina 1,2,* 1 School of Natural Sciences, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK; [email protected] (R.B.); [email protected] (K.L.); [email protected] (C.M.P.); [email protected] (A.F.Y.); [email protected] (B.P.); [email protected] (P.N.G.) 2 Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor LL57 2UW, UK 3 Systems Biotechnology Group, Department of Applied Biocatalysis, CSIC—Institute of Catalysis, Marie Curie 2, 28049 Madrid, Spain; [email protected] * Correspondence: [email protected]; Tel.: +44-1248-388607; Fax: +44-1248-382569 Received: 27 April 2020; Accepted: 15 May 2020; Published: 19 May 2020 Abstract: The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation.
    [Show full text]
  • Fungi-Chapter 31 Refer to the Images of Life Cycles of Rhizopus, Morchella and Mushroom in Your Text Book and Lab Manual
    Fungi-Chapter 31 Refer to the images of life cycles of Rhizopus, Morchella and Mushroom in your text book and lab manual. Chytrids Chytrids (phylum Chytridiomycota) are found in terrestrial, freshwater, and marine habitats including hydrothermal vents They can be decomposers, parasites, or mutualists Molecular evidence supports the hypothesis that chytrids diverged early in fungal evolution Chytrids are unique among fungi in having flagellated spores, called zoospores Zygomycetes The zygomycetes (phylum Zygomycota) exhibit great diversity of life histories They include fast-growing molds, parasites, and commensal symbionts The life cycle of black bread mold (Rhizopus stolonifer) is fairly typical of the phylum Its hyphae are coenocytic Asexual sporangia produce haploid spores The zygomycetes are named for their sexually produced zygosporangia Zygosporangia are the site of karyogamy and then meiosis Zygosporangia, which are resistant to freezing and drying, can survive unfavorable conditions Some zygomycetes, such as Pilobolus, can actually “aim” and shoot their sporangia toward bright light Glomeromycetes The glomeromycetes (phylum Glomeromycota) were once considered zygomycetes They are now classified in a separate clade Glomeromycetes form arbuscular mycorrhizae by growing into root cells but covered by host cell membrane. Ascomycetes Ascomycetes (phylum Ascomycota) live in marine, freshwater, and terrestrial habitats Ascomycetes produce sexual spores in saclike asci contained in fruiting bodies called ascocarps Ascomycetes are commonly
    [Show full text]
  • Pyrobaculum Igneiluti Sp. Nov., a Novel Anaerobic Hyperthermophilic Archaeon That Reduces Thiosulfate and Ferric Iron
    TAXONOMIC DESCRIPTION Lee et al., Int J Syst Evol Microbiol 2017;67:1714–1719 DOI 10.1099/ijsem.0.001850 Pyrobaculum igneiluti sp. nov., a novel anaerobic hyperthermophilic archaeon that reduces thiosulfate and ferric iron Jerry Y. Lee, Brenda Iglesias, Caleb E. Chu, Daniel J. P. Lawrence and Edward Jerome Crane III* Abstract A novel anaerobic, hyperthermophilic archaeon was isolated from a mud volcano in the Salton Sea geothermal system in southern California, USA. The isolate, named strain 521T, grew optimally at 90 C, at pH 5.5–7.3 and with 0–2.0 % (w/v) NaCl, with a generation time of 10 h under optimal conditions. Cells were rod-shaped and non-motile, ranging from 2 to 7 μm in length. Strain 521T grew only in the presence of thiosulfate and/or Fe(III) (ferrihydrite) as terminal electron acceptors under strictly anaerobic conditions, and preferred protein-rich compounds as energy sources, although the isolate was capable of chemolithoautotrophic growth. 16S rRNA gene sequence analysis places this isolate within the crenarchaeal genus Pyrobaculum. To our knowledge, this is the first Pyrobaculum strain to be isolated from an anaerobic mud volcano and to reduce only either thiosulfate or ferric iron. An in silico genome-to-genome distance calculator reported <25 % DNA–DNA hybridization between strain 521T and eight other Pyrobaculum species. Due to its genotypic and phenotypic differences, we conclude that strain 521T represents a novel species, for which the name Pyrobaculum igneiluti sp. nov. is proposed. The type strain is 521T (=DSM 103086T=ATCC TSD-56T). Anaerobic respiratory processes based on the reduction of recently revealed by the receding of the Salton Sea, ejects sulfur compounds or Fe(III) have been proposed to be fluid of a similar composition at 90–95 C.
    [Show full text]
  • Differences in Lateral Gene Transfer in Hypersaline Versus Thermal Environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1
    Rhodes et al. BMC Evolutionary Biology 2011, 11:199 http://www.biomedcentral.com/1471-2148/11/199 RESEARCH ARTICLE Open Access Differences in lateral gene transfer in hypersaline versus thermal environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1 Abstract Background: The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these “long distance” LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles. Results: We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles. Conclusions: Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA.
    [Show full text]
  • Biology of Fungi, Lecture 2: the Diversity of Fungi and Fungus-Like Organisms
    Biology of Fungi, Lecture 2: The Diversity of Fungi and Fungus-Like Organisms Terms You Should Understand u ‘Fungus’ (pl., fungi) is a taxonomic term and does not refer to morphology u ‘Mold’ is a morphological term referring to a filamentous (multicellular) condition u ‘Mildew’ is a term that refers to a particular type of mold u ‘Yeast’ is a morphological term referring to a unicellular condition Special Lecture Notes on Fungal Taxonomy u Fungal taxonomy is constantly in flux u Not one taxonomic scheme will be agreed upon by all mycologists u Classical fungal taxonomy was based primarily upon morphological features u Contemporary fungal taxonomy is based upon phylogenetic relationships Fungi in a Broad Sense u Mycologists have traditionally studied a diverse number of organisms, many not true fungi, but fungal-like in their appearance, physiology, or life style u At one point, these fungal-like microbes included the Actinomycetes, due to their filamentous growth patterns, but today are known as Gram-positive bacteria u The types of organisms mycologists have traditionally studied are now divided based upon phylogenetic relationships u These relationships are: Q Kingdom Fungi - true fungi Q Kingdom Straminipila - “water molds” Q Kingdom Mycetozoa - “slime molds” u Kingdom Fungi (Mycota) Q Phylum: Chytridiomycota Q Phylum: Zygomycota Q Phylum: Glomeromycota Q Phylum: Ascomycota Q Phylum: Basidiomycota Q Form-Phylum: Deuteromycota (Fungi Imperfecti) Page 1 of 16 Biology of Fungi Lecture 2: Diversity of Fungi u Kingdom Straminiplia (Chromista)
    [Show full text]
  • Picrophilus Oshimae and Picrophilus Tomdus Fam. Nov., Gen. Nov., Sp. Nov
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1996, p. 814-816 Vol. 46, No. 3 0020-77 13/96/$04.00+0 Copyright 0 1996, International Union of Microbiological Societies Picrophilus oshimae and Picrophilus tomdus fam. nov., gen. nov., sp. nov., Two Species of Hyperacidophilic, Thermophilic, Heterotrophic, Aerobic Archaea CHRISTA SCHLEPER, GABRIELA PUHLER, HANS- PETER KLENK, AND WOLFRAM ZILLIG* Max Plank Institut fur Biochemie, 0-82152 Martinsried, Germany We describe two species of hyperacidophilic, thermophilic, heterotrophic, aerobic archaea that were isolated from solfataric hydrothermal areas in Hokkaido, Japan. These organisms, Picrophilus oshimae and Picrophilus torridus, represent a novel genus and a novel family, the Picrophilaceae, in the kingdom Euryarchaeota and the order Thermoplasmales. Both of these bacteria are more acidophilic than the genus Thermoplasma since they are able to grow at about pH 0. The moderately thermophilic, hyperacidophilic, aerobic ar- which comprises acid-loving (i.e., hyperacidophilic) organisms. chaea (archaebacteria) (7) Picrophilus oshimae and Picrophilus Separation of these taxa is justified by their phylogenetic dis- rorridus, which have been described previously (4, 5), were tance, (9.5% difference in the 16s rRNA sequences of mem- isolated from moderately hot hydrothermal areas in solfataric bers of the Picrophilaceae and T. acidophilum), by the lack of fields in Hokkaido, Japan. One of the sources of isolation was immunochemical cross-reactions in Ouchterlony immunodif- a solfataric spring which had a temperature of 53°C and a pH fusion assays between the RNA polymerases of P. oshimae and of 2.2, and the other was a rather dry hot soil which had a pH T. acidophilum, which also do not occur between members of of <OS.
    [Show full text]
  • Animal Phylum Poster Porifera
    Phylum PORIFERA CNIDARIA PLATYHELMINTHES ANNELIDA MOLLUSCA ECHINODERMATA ARTHROPODA CHORDATA Hexactinellida -- glass (siliceous) Anthozoa -- corals and sea Turbellaria -- free-living or symbiotic Polychaetes -- segmented Gastopods -- snails and slugs Asteroidea -- starfish Trilobitomorpha -- tribolites (extinct) Urochordata -- tunicates Groups sponges anemones flatworms (Dugusia) bristleworms Bivalves -- clams, scallops, mussels Echinoidea -- sea urchins, sand Chelicerata Cephalochordata -- lancelets (organisms studied in detail in Demospongia -- spongin or Hydrazoa -- hydras, some corals Trematoda -- flukes (parasitic) Oligochaetes -- earthworms (Lumbricus) Cephalopods -- squid, octopus, dollars Arachnida -- spiders, scorpions Mixini -- hagfish siliceous sponges Xiphosura -- horseshoe crabs Bio1AL are underlined) Cubozoa -- box jellyfish, sea wasps Cestoda -- tapeworms (parasitic) Hirudinea -- leeches nautilus Holothuroidea -- sea cucumbers Petromyzontida -- lamprey Mandibulata Calcarea -- calcareous sponges Scyphozoa -- jellyfish, sea nettles Monogenea -- parasitic flatworms Polyplacophora -- chitons Ophiuroidea -- brittle stars Chondrichtyes -- sharks, skates Crustacea -- crustaceans (shrimp, crayfish Scleropongiae -- coralline or Crinoidea -- sea lily, feather stars Actinipterygia -- ray-finned fish tropical reef sponges Hexapoda -- insects (cockroach, fruit fly) Sarcopterygia -- lobed-finned fish Myriapoda Amphibia (frog, newt) Chilopoda -- centipedes Diplopoda -- millipedes Reptilia (snake, turtle) Aves (chicken, hummingbird) Mammalia
    [Show full text]