KINGDOMS & DOMAINS An Illustrated Guide to the Phyla of Life on Earth Lynn Margulis University of Massachusetts at Amherst Michael J. Chapman Marine Biological Laboratory Woods Hole, Massachusetts, USA AMSTERDAM • BOSTON • HEIDELBERG • LONDON • NEW YORK • OXFORD • PARIS • SAN DIEGO • SAN FRANCISCO ' SINGAPORE • SYDNEY • TOKYO ELSEVIER Academic Press is an imprint of Elsevier CONTENTS List of Figures xi SUBKINGDOM (DOMAIN) EUBACTERIA 65 List of Tables lix Division Gracilicutes (Gram-negative bacteria) Foreword E. O. Wilson lxi Phylum B-3 Proteobacteria purple bacteria: phototrophs, Foreword to 1st to 3rd editions Stephen Jay Gould lxiii heterotrophs 68 Preface lxvii Azotohacter, Escherichia, Nitrobacter Acknowledgments lxxi Phylum B-4 Spirochaetae helical motile heterotrophs, periplasmic flagella 76 INTRODUCTION 3 Diplocalyx, Spirochaeta, Spirosymplokos Phylum B-5 Bacteroides-Saprospirae gliding fermenters, Box I-i: The wisdom of Darwin and Gould 5 heterotrophs 80 Classification of life, names of organisms • The cell as a Bacteroides, Saprospira, Spowcytophaga unit; the kingdoms of life • Plant or animal? History of the Phylum B-6 Cyanobacteria oxygenic highest taxa • Undulipodia, centrioles, and kinetosomes • photoautotrophs 82 Sex and reproduction • Kingdoms and domain criteria • Anabaena, Nostoc, Oscillatoria Viruses Phylum B-7 Chloroflexa gliding nonsulfur oxygen- Box I-ii: Life is growth 19 tolerant photoautotrophs 86 Chloroflexus, Heliothrix, Oscillochbris The Environment 23 Earth history: The geologic record • Seven "ecostrips": Phylum B-8 Chlorobia sulfur oxygen-intolerant photoautotrophs 88 Ecosystems and their habitats • Evolution and taxa • Chlorobium, Chlorochromatium, Chloronema Environmental evolution and Gaia theory • Chapters, Figures and Table Numbers in this book • Bibliography Division Tenericutes (wall-less eubacteria) Phylum B-9 Aphragmabacteria mycoplasmas no SUPERKINGDOM PROKARYA 33 cell walls 90 Origins not by symbiogenesis Acholeplasma, Ehrlichia, Mycoplasma, Wolbachia CHAPTER ONE Division Firmicutes (Gram-positive and protein-walled bacteria) KINGDOM PROKARYOTAE (BACTERIA, Phylum B-10 Endospora low-G+C endospore-forming MONERA, PROKARYA) 35 Gram-positives and relatives 92 Bacillus, Clostridium, Peptococcus Box Prokaryotae-i: Whole organism criteria, not partial Phylum B-11 Pirellulae proteinaceous wall-formers and phytogenies 50 relatives 94 Box Prokaryotae-ii: Two superkingdoms, not three Chlamydia, Gemmata, Planctomyces domains 53 Phylum B-l2 Actinobacteria fungoid multicellular Box Prokaryotae-iii: Modes of multicellularity 55 Gram-positives and relatives 98 Actinomyces, Frankia, Streptomyces SUBKINGDOM (DOMAIN) ARCHAEA 58 Phylum B-13 Deinococci radiation- or heat-resistant Division Mendosicutes (deficient-walled archaebacteria) Gram-positives 100 Phylum B-l Euryarchaeota methanogens and Deinococcus, Thermus halophils 60 Phylum B-14 Thermotogae thermophilic Halobacter, Halococcus, Methanobacterium fermenters 102 Phylum B-2 Crenarchaeota thermoacidophils 62 Aquifex, Fervidobacterium, Thermotoga Pyrobaculum, Pyrodictium, Sulfolobus, Thermoplasma Bibliography 104 vii SUPERKINGDOM EUKARYA 109 Phylum Pr-10 Proteromonadida (III) small mastigotes, intestinal in animals 156 Origins by symbiogenesis Kawtomorpha, Proteromonas Box Eukarya-i: Undulipodia from sulfur syntrophies 110 Phylum Pr-11 Kinetoplastida (III) kinetoplastids, most Box Eukarya-ii: Eukaryosis—Life histories, life cycles 111 symbiotrophic mastigotes 158 Bodo, Crithidia, Trypanosoma CHAPTER TWO Phylum Pr-12 Euglenida (III) euglenids 162 KINGDOM PROTOCTISTA117 Colacium, Euglena, Pemnema Phylum Pr-13 Hemimastigota (III) Gondwanaland Four modes: phyla whose members 119 mastigotes 164 I. Lack both undulipodia and meiotic sex 119 Hemimastix, Spironema II. Lack undulipodia but have meiotic sex 119 III. Have undulipodia but lack meiotic sexual life cycles 119 Phylum Pr-14 Hyphochytriomycota (III) hyphochytrid IV. Have undulipodia and meiotic sexual life cycles 119 water molds 166 Anisolpidium, Hyphochytrium, Rhizidiomyces SUBKINGDOM (Division) AMITOCHONDRIA Phylum Pr-15 Chrysomonada (IV) chrysophytes, Box Pr-i: Symbiogenesis and the origin of organelles 124 golden-yellow algae 168 Box Pr-ii: Mitosomes and hydrogenosomes 127 Chrysosphaerella, Ochromonas, Synura Phylum Pr-1 Archeaprotista (III) motile with no Phylum Pr-16 Xanthophyta (IV) yellow-green algae 172 mitochondria 130 Botrydium, Ophiocytium, Vaucheria Mastigamoeba, Pelomyxa, Staurojoenina, Trichonympha Phylum Pr-17 Phaeophyta (IV) brown algae 174 Ascophyllum, Fucus, Macrocystis SUBKINGDOM (Division) AMOEBAMORPHA Phylum Pr-18 Bacillariophyta (IV) diatoms, silica Phylum Pr-2 Rhizopoda (I) Amostigota, amoebae, tests 176 cellular slime molds 134 Diploneis, Melosira, Thalassiosira Acrasia, Arcella, Dictyostelium, Mayorella Phylum Pr-19 Labyrinthulata (IV) slime nets and Phylum Pr-3 Granuloreticulosa (Foraminifera and thraustochytrids 178 unshelled relatives) (IV) reticulomyxids, foraminifera, Althornia, Aplanochytrium, Labyrinthula chlorarachnids 138 Allogromia, Globigerina, Rotaliella Phylum Pr-20 Plasmodiophora (IV) plasmodiophoran plant symbiotrophs 182 Box Pr-iii: Fossil record insights—Calibration of molecular Ligniera, Plasmodiophora, Sorodiscus clocks to the geologic record 140 Phylum Pr-21 Oomycota (IV) oomycete water molds Phylum Pr-4 Xenophyophora (I) barite skeleton ( = egg molds) 184 deep sea protists 142 Achlya, Phytophthora, Saprolegnia Galatheammina, Psammetta, Reticulammina SUBKINGDOM (Division) ALVEOLATA SUBKINGDOM (Division) ISOKONTA Phylum Pr-5 Dinomastigota (IV) Dinoflagellata, Phylum Pr-22 Amoebomastigota, Heterolobosea (III) Dinophyta 144 amoebomastigotes, heteroloboseans 188 Gonyaulax, Gymnodinium, Peridinium Naegleria, Paratetramitus, Vahlkampfia, Willaertia Phylum Pr-6 Ciliophora (IV) ciliates 146 Phylum Pr-23 Myxomycota (IV) plasmodial slime Gastrostyla, Paramecium, Tetrahymena molds 190 Phylum Pr-7 Apicomplexa (IV) apicomplexan animal- Cercomonas, Echinostelium, Physarum, Stemonitis symbiotrophs 148 Phylum Pr-24 Pseudociliata (III) polyundulipodiated Eimeria, Plasmodium, Toxoplasma animal symbiotrophs 192 SUBKINGDOM (Division) HETEROKONTA Opalina, Stephanopogon, Zelleriella (Stramenopiles) Phylum Pr-25 Haptomonada (III) Prymnesiophyta hap- Phylum Pr-8 Bicosoecida (III) small mastigotes, some tophytes, coccolithophorids 194 form colonies 152 Emiliania, Phaeocystis, Prymnesium Acronema, Cafeteria, Pseudobodo Phylum Pr-26 Cryptomonada (III) cryptomonads, Phylum Pr-9 Jakobida (III) bactivorous mastigotes, some cryptophytes 196 loricate attached to sediment 154 Chilomonas, Cryptomonas, Cyathomonas, Histiona, Jakoba, Reclinomonas Nephroselmis vm Phylum Pr-27 Eustigmatophyta (III) eye-spot Phylum A-4 Coelenterata sea anemones, hydroid- algae 198 medusas 250 Chlorobotrys, Eustigmatos, Vischeria Craspedacusta, Hydra, Physalia Phylum Pr-28 Chlorophyta (IV); green algae, plant Phylum A-5 Ctenophora comb jellies 256 ancestors 200 Beroe, Bolinopsis, Ocryopsis Acetabularia, Chlamydomonas, Volvox SUBKINGDOM (Division) EUMETAZOA (nervous and SUBKINGDOM (Division) AKONTA muscular systems) Phylum Pr-29 Haplospora (II) haplosporan animal Phylum A-6 Gnathostomulida gnathostome worms 260 symbiotrophs 202 Austrognatharia, Gnathostomula, Problognathia Haplosporidium, Minchinia, Urosporidium Phylum A-7 Platyhelminthes flat worms, flukes 262 Phylum Pr-30 Paramyxa (I) cell-inside-cell marine animal Convoluta, Dugesia, Planaria symbiotrophs 204 Phylum A-8 Rhombozoa tiny animal symbiotrophs 264 Marteilia, Paramarteilia, Paramyxa Conocyema, Dicyema, Microcyema Phylum Pr-31 Actinopoda (II) ray animalcules; Phylum A-9 Orthonectida tiny animal symbiotrophs 268 acantharia, heliozoa, radiolaria 206 Ciliocincta, Rhopalura, Stoecharthrum Acanthocystis, Clathrulina, Sticholonche Phylum A-10 Nemertina nemertine worms 270 Phylum Pr-32 Gamophyta (II) conjugating green Cerebratulus, Linens, Prostoma algae 210 Phylum A-11 Nematoda nematode worms 274 Micmsterias, Mougeotia, Zygnema Ascaris, Caenorhabditis, Rhabdias Phylum Pr-33 Rhodophyta (II) red algae 212 Phylum A-12 Nematomorpha nematomorph worms 276 Amphiroa, Bangia, Gracilaria, Porphyra Chordodes, Gordius, Nectonema SUBKINGDOM (Division) OPISTHOKONTA Phylum A-13 Acanthocephala spiny-headed worms 278 Phylum Pr-34 Blastocladiomycota (IV) polyzoosporic Acanthogyrus, Leptorhynchoides, Macracanthorhynchus water molds 216 Phylum A-14 Rotifera rotifers; wheel-animals 282 Allomyces, Blastocladiella Brachionus, Euchlanis, Philodina Phylum Pr-35 Chytridiomycota (IV); undulipodiated Phylum A-15 Kinorhyncha kinorhynch worms 284 water molds, fungal ancestors 218 Catena, Echinoderes, Semnoderes Monobkpharis, Neocallimastix, Polyphagus Phylum A-16 Priapulida priapulid worms 286 Phylum Pr-36 Choanomastigota (III); collared protists, Halicryptus, Priapulus, Tubiluchus animal ancestors 222 Phylum A-17 Gastrotricha gastrotrich worms 288 Dermocystidium, Nuclearia, Salpingoeca Acanthodasys, Macrodasys, Urodasys Bibliography 224 Phylum A-18 Loricifera loriciferans 290 Nanaloricus, Pliciloricus, Rugiloricus CHAPTER THREE Phylum A-19 Entoprocta entoprocts 292 KINGDOM ANIMALIA 231 Barentsia, Loxosoma, Pedkellina Phylum A-20 Chelicerata spider, scorpions, ticks 294 Box A-i: Larval transfer 238 Amblopygis, Ixodes, Scorpio SUBKINGDOM (Division) PLACOZOA (no nerves or Phylum A-21 Mandibulata insects, crustaceans 298 antero-posterior asymmetry) Cambarus Drosophila, Polistes, Pterotermes Phylum A-1 Placozoa free-living marine dorsal-ventral Phylum A-22 Annelida earthworms, polychaete