Biology of Algae, Lichens and Bryophytes

Prolog
Contents
1 Introduction: The New Cryptogams
	1.1 Oxy-Phototroph Life Forms and Traditional Botany
	1.2 The New Cryptogams—a Modern Concept for the Non-Vascular Oxy-Phototroph Life Forms
	1.3 Functional Aspects of New Cryptogams: Hydro-Passivity
	1.4 The New Cryptogams Predated the Conquest of the Third Dimension on Land
	1.5 The New Cryptogams and Chapter Selection of This Textbook
	References
2 Endosymbioses: Origin and Diversity of Photosynthetic Eukaryotes and Their General Genetic Exchange Modes
	2.1 Introduction: The Role of Endosymbiosis in the Evolution of Eukaryotes
		2.1.1 Endosymbiotic Gene Transfer and Reductive Evolution
		2.1.2 Protein Import by Organelles
	2.2 Primary Endosymbiosis: The Endosymbiotic Origin of Plastids
		2.2.1 An Ancient Endosymbiotic Event and the Cyanobacterial Progenitor of Plastids
		2.2.2 The Origin of Archaeplastida
			2.2.2.1 Plastid Genomes
	2.3 Eukaryote-Eukaryote Endosymbioses
		2.3.1 A Brief Overview of the Endosymbiotic Potpourri
			2.3.1.1 Secondary Endosymbiosis: EGT Mayhem
			2.3.1.2 Complexities of Protein Targeting and Membrane
			2.3.1.3 Nucleomorphs
	2.4 A Modern Overview of Eukaryotic Diversity—The Opuntia-Tree-of-Life
	2.5 Life histories, Plastid Spread, and Sexual Reproduction in the New Cryptogams
	References
3 Cyanobacteria/Blue-Green Algae
	3.1 Short History of Cyanobacterial Research
	3.2 Origin of Cyanobacteria
		3.2.1 Cyanobacteria and the Origin of Plastids
	3.3 Structure and Function
		3.3.1 Cell Wall
		3.3.2 Cytoplasm
			3.3.2.1 Thylakoids
			3.3.2.2 Photosynthesis and Cellular Metabolism
			3.3.2.3 Carboxysomes
			3.3.2.4 Gas Vesicles and Buoyancy
			3.3.2.5 Glycogen Granules
			3.3.2.6 Polyphosphate Bodies
			3.3.2.7 Cyanophycin Granules
	3.4 Survival and Cell Specialization
		3.4.1 Heterocytes
		3.4.2 Akinetes
		3.4.3 Necridic Cells
		3.4.4 Hormogonia
	3.5 Reproduction, Life Cycle
		3.5.1 Unicellular Cyanobacteria
		3.5.2 Filamentous Cyanobacteria
			3.5.2.1 Life Cycle of Nostoc Species
	3.6 Phylogeny and Diversity
		3.6.1 Taxonomy and Systematics
			3.6.1.1 Order Gloeobacterales
			3.6.1.2 Order Synechococcales
			3.6.1.3 Order Spirulinales
			3.6.1.4 Order Chroococcales
			3.6.1.5 Order Pleurocapsales
			3.6.1.6 Order of Unsafe Systematic Position: Chroococcidiopsidales
			3.6.1.7 Order Oscillatoriales
			3.6.1.8 Order Nostocales
		3.6.2 Biogeography
	3.7 Ecology
		3.7.1 Rock and Soil
			3.7.1.1 Rock (Epilithic, Endolithic)
			3.7.1.2 Soil
		3.7.2 Epiphytic
			3.7.2.1 Phyllosphere
		3.7.3 Freshwater and Marine Habitats
			3.7.3.1 Lakes
			3.7.3.2 Watercourses
			3.7.3.3 Marine Plankton
		3.7.4 Eco-Physiology
			3.7.4.1 Desiccation Tolerance and Anhydrobiosis.
			3.7.4.2 Light and Carbon Dioxide-Exchange
			3.7.4.3 Temperature and Carbon Dioxide-Exchange
			3.7.4.4 Thallus Water Content and Carbon Dioxide-Exchange
			3.7.4.5 Effects of Phosphorous
	References
4 Algae from Primary Endosymbioses
	4.1 Rhodophyta, Red Algae
		4.1.1 Origin of Red Algae
			4.1.1.1 Fossil Record
		4.1.2 Morphology and Cell Structure
			4.1.2.1 General Morphology
			4.1.2.2 Cell Structure
		4.1.3 Reproduction, Life Cycle
			4.1.3.1 The Biphasic Life Cycle
			4.1.3.2 The Triphasic Life Cycle
		4.1.4 Phylogeny, Systematics, and Diversity
			4.1.4.1 Classification and Systematic Arrangement of the Rhodophyta
			4.1.4.2 Subdivision Cyanidiophytina
			4.1.4.3 Subdivision Rhodophytina
		4.1.5 Genome Reductions and Gains: The Ecological Imprint
		4.1.6 Ecology
			4.1.6.1 Freshwater
			4.1.6.2 Marine
			4.1.6.3 Ecophysiology
		4.1.7 Phylogeography
	4.2 Chloroplastida—Green Algae
		4.2.1 Ecological and Economic Importance
		4.2.2 Origin of Green Algae
		4.2.3 Defining Characters of the Green Algae
			4.2.3.1 General Morphology
			4.2.3.2 Chloroplasts
			4.2.3.3 Flagella
			4.2.3.4 Mitosis and Cytokinesis
			4.2.3.5 Cell Walls
			4.2.3.6 Giant Multinucleate Cells
		4.2.4 Reproduction and Life Cycle
		4.2.5 Systematics and Classification of the Chloroplastida
		4.2.6 Phylum Prasinodermophyta
		4.2.7 Phylum Chlorophyta and Prasinophytes
			4.2.7.1 Class Mamiellophyceae
			4.2.7.2 Class Pyramimonadophyceae
			4.2.7.3 Class Nephroselmidophyceae
			4.2.7.4 Class Chloropicophyceae
			4.2.7.5 Class Picocystophyceae
		4.2.8 The Core Chlorophyta, Chlorodendrophyceae, and Pedinophyceae
			4.2.8.1 Class Chlorodendrophyceae
			4.2.8.2 Class Pedinophyceae
		4.2.9 Class Trebouxiophyceae
		4.2.10 Class Chlorophyceae
		4.2.11 Class Ulvophyceae
			4.2.11.1 Orders Ulvales and Ulotrichales
			4.2.11.2 Order Cladophorales
			4.2.11.3 Order Bryopsidales
			4.2.11.4 Order Dasycladales
			4.2.11.5 Order Trentepohliales
		4.2.12 Phylum Streptophyta—The Streptophyte Algae Grade
			4.2.12.1 Class Mesostigmatophyceae
			4.2.12.2 Class Klebsormidiophyceae, Order Klebsormidiales
			4.2.12.3 Class Charophyceae, Order Charales
			4.2.12.4 Class Coleochaetophyceae, Order Coleochaetales
			4.2.12.5 Class Zygnematophyceae
			4.2.12.6 The Streptophyte Algae and Plant Terrestrialization
	4.3 Glaucophyta
		4.3.1 Origin of the Phylum Glaucophyta
		4.3.2 Morphology and Cell Structure/Function
			4.3.2.1 Cell Wall and Cell Surface
			4.3.2.2 The Muroplast
		4.3.3 Genome
		4.3.4 Classification and Systematic Arrangement of the Glaucophyta
			4.3.4.1 Gloeochaete
			4.3.4.2 Cyanoptyche
			4.3.4.3 Glaucocystis
			4.3.4.4 Cyanophora
		4.3.5 Ecology
	4.4 Cercozoa—A Second Primary Endosymbiosis
		4.4.1 Primary Endosymbiosis?
		4.4.2 Origin
		4.4.3 Morphology and Ultrastructure
		4.4.4 Classification and Systematic Arrangement
	References
5 Algae from Secondary Endosymbiosis
	5.1 Heterokontophyta—Photosynthetic Stramenopiles
		5.1.1 General Ecology and Importance
		5.1.2 General Description
			5.1.2.1 Flagella
			5.1.2.2 Chloroplast
			5.1.2.3 Cell Coverings
		5.1.3 Evolutionary History
		5.1.4 Taxonomic Classes
			5.1.4.1 Phaeophyceae
			5.1.4.2 Chrysophyceae
			5.1.4.3 Xanthophyceae
			5.1.4.4 Diatomeae—The Diatoms
			5.1.4.5 Raphidophyceae
			5.1.4.6 Eustigmatophyceae
			5.1.4.7 Dictyochophyceae
			5.1.4.8 Pelagophyceae
			5.1.4.9 Phaeothamniophyceae
			5.1.4.10 Bolidophyceae
			5.1.4.11 Pinguiophyceae
			5.1.4.12 Schizocladiophyceae
			5.1.4.13 Synchromophyceae
			5.1.4.14 Aurearenophyceae
			5.1.4.15 Chrysoparadoxophyceae
			5.1.4.16 Phaeosacciophyceae
			5.1.4.17 Olisthodiscophyceae
		5.1.5 Perspectives
			5.1.5.1 Heterokontophyta in the Genomics Era
			5.1.5.2 Evolutionary Trends
			5.1.5.3 Functional Genomics of the Heterokontophyta
			5.1.5.4 Genomics of Heterokontophyta in the Global Change Era
			5.1.5.5 Genomics, Taxonomy, and “Tradition”
	5.2 Dinoflagellates
		5.2.1 Organization and Structural Features of Dinoflagellates Cells
			5.2.1.1 General Morphology
			5.2.1.2 Coccoid Life Stages, Trophic Cysts, and Dormant Stages
			5.2.1.3 Unique Molecular Traits
		5.2.2 Reproduction
		5.2.3 Chloroplasts
		5.2.4 Kleptoplasty
		5.2.5 Non-Photosynthetic Nutrition
		5.2.6 Bioluminescence
		5.2.7 Toxins and Harmful Algal Blooms
		5.2.8 Phylogeny: Classification
	5.3 A Cercozoan Secondary Endosymbiosis: Chlorarachniophyta
		5.3.1 General Characters
		5.3.2 History of Research
		5.3.3 Morphology and Developmental Stages
			5.3.3.1 Pseudopods
			5.3.3.2 Chloroplasts and Nucleomorph
			5.3.3.3 Pyrenoids and Pyrenoid Caps
			5.3.3.4 Developmental Stages
		5.3.4 Reproduction and Life Cycle
		5.3.5 Phylogeny and Systematics
	5.4 Euglenids—(Excavates, Discoba, Euglenozoa, and Euglenida)
		5.4.1 Short Introduction—what Are Euglenids? Why Are They Called Augentierchen?
			5.4.1.1 Ambiregnal Status
		5.4.2 Taxonomic Classification
		5.4.3 Origin and Fossil Record
		5.4.4 History of Research
		5.4.5 General Information and Diversity of Nutrition Modes
			5.4.5.1 Nutrition—You Are What You Eat
			5.4.5.2 Cells Eating Other Cells—A Variety of Feeding Apparatuses Evolved in Euglenids
		5.4.6 Characters Uniting Euglenids—An Overview of Morphology and Cell Structure
			5.4.6.1 Pellicle and Metaboly
			5.4.6.2 Extrusomes—Trichocysts and Mucocysts Produce Extracellular Matrix
			5.4.6.3 Canal and Reservoir
			5.4.6.4 Thick Flagella Mark the Euglenids
			5.4.6.5 Reproduction and Nucleus
			5.4.6.6 Euglenid Chloroplasts Evolved by Secondary Endosymbiosis
			5.4.6.7 A Photosensory System Enables the Cell to Respond to Light Changes
			5.4.6.8 An Unusual Storage Polymer—Paramylon
			5.4.6.9 Mitochondria Are Different in Euglenids
			5.4.6.10 Ribosomal Operon
		5.4.7 Phylogenetic Position—Euglenida
		5.4.8 Ecology—Where Do We Find Euglenids?
		5.4.9 Description of Easily Observed Taxa
	5.5 Haptista
		5.5.1 General Description
		5.5.2 Fossil Record
		5.5.3 Molecular Clock Record
		5.5.4 Morphology and Ultrastructure
		5.5.5 Life Cycle
		5.5.6 Phylogeny and Classification
		5.5.7 Eco-Physiology
			5.5.7.1 Photosynthesis, Calcification, and CO2—Concentrating Mechanism
			5.5.7.2 Carbon Partitioning
			5.5.7.3 Role of Coccolithophores in Biogeochemical Cycles
	5.6 Cryptista
		5.6.1 Cell Structure and Function
		5.6.2 Habitats and Survival Strategies
		5.6.3 Origin and Evolution of the Cryptista
	References
6 Symbioses
	6.1 Algal Symbioses
		6.1.1 Symbiogenesis and Symbioses
			6.1.1.1 Origin of Symbioses in Theory and Nature
		6.1.2 Symbiotic Cyanobacteria and Algae—The Photoautotrophic Partner
			6.1.2.1 Cyanobacteria
			6.1.2.2 Algae
		6.1.3 Cyanobacteria Associated with Heterotrophic Protists and Algae
		6.1.4 Cyanobacteria and Algae Associated with Fungi (Excluding Lichens)
			6.1.4.1 Geosiphon Pyriforme (Glomeromycota) and Cyanobacteria
		6.1.5 Cyanobacteria and Bryophytes
			6.1.5.1 Hornworts
			6.1.5.2 Cyanobacteria and Liverworts
			6.1.5.3 Associations of Cyanobacteria, Algae and Mosses
		6.1.6 Cyanobacteria and Azolla (Ferns)
		6.1.7 Cyanobacteria and the Gymnosperm Cycads
		6.1.8 Cyanobacteria and the Angiosperm Gunnera
		6.1.9 Algae Associated with Invertebrates
			6.1.9.1 Sponges (Porifera)
			6.1.9.2 Cnidaria
			6.1.9.3 Acoela
			6.1.9.4 Bivalves
			6.1.9.5 Sacoglossan Sea Slugs
		6.1.10 Algal—Vertebrate Symbioses
	6.2 Lichens
		6.2.1 Short History of Lichen Research
		6.2.2 Evolution and Diversity of Lichens
			6.2.2.1 Mycobionts
			6.2.2.2 The Fossil Record
			6.2.2.3 Molecular Dating
			6.2.2.4 Photobionts
			6.2.2.5 New Insight: Lichens as Multi-Species Symbioses
			6.2.2.6 Phylogenetic Systematics of the Lichenized Fungi (Frey 2016, 2018, Nelsen et al. 2007)
		6.2.3 Morphology
			6.2.3.1 Growth Forms
		6.2.4 Anatomy
			6.2.4.1 Upper Cortex
			6.2.4.2 Medulla with Photobiont Layer
			6.2.4.3 Lower Cortex
			6.2.4.4 Cephalodia, Photosymbiodemes
			6.2.4.5 Mycobiont-Photobiont Contact
		6.2.5 Sexual Reproduction of Lichens
			6.2.5.1 Fruiting Structures
		6.2.6 Asexual Reproduction of Lichens
		6.2.7 Short Treatise on Lichen Physiology
			6.2.7.1 Signaling and Recognition of the Symbiotic Partners
			6.2.7.2 Systems Biology Approach
		6.2.8 Ecology and Eco-Physiology of Lichens
			6.2.8.1 Phylogeography
			6.2.8.2 Lichens on Rock and Soil
			6.2.8.3 Epiphytic Lichens
			6.2.8.4 Aquatic Lichens
			6.2.8.5 Eco-Physiology
	References
7 Bryophytes
	7.1 Introduction
	7.2 Division: Marchantiophyta—The Liverworts
		7.2.1 Oil Bodies
		7.2.2 The Gametophyte
			7.2.2.1 Leafy Liverworts
			7.2.2.2 Simple Thalloids
			7.2.2.3 Complex Thalloids
		7.2.3 The Sporophyte
			7.2.3.1 Embryo
			7.2.3.2 Foot and Seta
			7.2.3.3 Capsule
			7.2.3.4 Spores and Spore Germination
		7.2.4 Classification
			7.2.4.1 Class Haplomitriopsida
			7.2.4.2 Class Marchantiopsida
			7.2.4.3 Class Jungermanniopsida
	7.3 Division Bryophyta—The Mosses
		7.3.1 The Gametophyte
			7.3.1.1 Protonema
			7.3.1.2 Stems
			7.3.1.3 Phylloids (“Leaves”)
			7.3.1.4 Rhizoids
			7.3.1.5 Sexual Organs and Fertilization
		7.3.2 The Sporophyte
			7.3.2.1 Embryo
			7.3.2.2 Foot and Seta
			7.3.2.3 Capsule and Calyptra
			7.3.2.4 Spores
			7.3.2.5 Peristome
		7.3.3 Classification
			7.3.3.1 Class Takakiopsida
			7.3.3.2 Class Sphagnopsida—Peat Mosses
			7.3.3.3 Class Andreaeopsida—Lantern Mosses
			7.3.3.4 Class Andreaeobryopsida
			7.3.3.5 Class Oedipodiopsida
			7.3.3.6 Class Polytrichopsida—Hair-Cap Mosses
			7.3.3.7 Class Tetraphidopsida—Four-Toothed Mosses
			7.3.3.8 Class Bryopsida—Mosses s. Str.
	7.4 Division: Anthocerotophyta—The Hornworts
		7.4.1 The Gametophyte
			7.4.1.1 General Structure
			7.4.1.2 Symbiotic Associations (See also Sect. 6.1.5.1)
			7.4.1.3 Antheridia and Archegonia
			7.4.1.4 Asexual Reproduction (See also Sect. 7.5)
		7.4.2 The Sporophyte
			7.4.2.1 Spores
		7.4.3 Classification
			7.4.3.1 Class Leiosporocerotopsida
			7.4.3.2 Class Anthocerotopsida
	7.5 Asexual Reproduction
		7.5.1 Asexual Reproduction s. str.
		7.5.2 Fragmentation of Gametophytes into Unspecialized Fragments
		7.5.3 Clonal Reproduction
		7.5.4 Apospory
		7.5.5 Apogamy
	7.6 Physiology and Physiological Ecology
		7.6.1 Water Relations
			7.6.1.1 Two Opposing Strategies
			7.6.1.2 Water Uptake and Transport
			7.6.1.3 Cell Water Relations
			7.6.1.4 Water Content and Storage
			7.6.1.5 Desiccation Tolerance
		7.6.2 Photosynthesis and Respiration
			7.6.2.1 Photosynthesis and Light
			7.6.2.2 Photosynthesis and Temperature
			7.6.2.3 Photosynthesis and CO2
			7.6.2.4 Photosynthesis and Thallus Water Content
			7.6.2.5 Dark Respiration
		7.6.3 Mineral Nutrition
			7.6.3.1 Nutrient Sources
			7.6.3.2 Nutrient Uptake
			7.6.3.3 Nutrient Content and Distribution Within the Thallus
			7.6.3.4 Desiccation Effects
	7.7 Ecology
		7.7.1 Autecology: Substratum Ecology
			7.7.1.1 Calcicoles and Calcifuges
			7.7.1.2 Epiliths
			7.7.1.3 Epiphytes
			7.7.1.4 Epiphylls
			7.7.1.5 Specialists
		7.7.2 Population and Community Ecology
			7.7.2.1 Life History Traits and Population Dynamics
			7.7.2.2 Bryophytic Metapopulations
			7.7.2.3 Community Ecology
			7.7.2.4 Interactions Among Bryophytes
			7.7.2.5 Interactions of Bryophytes with Vascular Plants
			7.7.2.6 Interactions with Animals
			7.7.2.7 Parasitic Interactions
			7.7.2.8 Species Composition and Diversity
		7.7.3 Systems Ecology
			7.7.3.1 Bryophytes and Succession
			7.7.3.2 Carbon and Nutrient Cycling
			7.7.3.3 The Genus Sphagnum and Its Role in Peatlands and Bogs
			7.7.3.4 Bryophyte-Rich Ecosystems
			7.7.3.5 Bryophytes and Climate Change
	References
Glossary
Index