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Microbiology

Chapter 8

Microbial Evolution, Phylogeny, and Diversity

Book Version 6
By Boundless
Boundless Microbiology
Microbiology
by Boundless
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Section 1
Origins of Life
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Evidence of Evolution

Evidence for evolution has been obtained through fossil records, embryology, geography, and molecular biology.

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Elements of Life

Key elements were needed for early life to start on earth.

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Unresolved Questions About the Origins of Life

The question of how simple organic molecules formed a protocell is largely unanswered.

Section 2
Astrobiology
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Mars and a Biosphere

Mars, the fourth planet from the Sun, is currently undergoing a great deal of investigation concerning its capacity for maintaining life.

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Martian Biosignatures

A biosignature, a substance that provides scientific evidence of past or present life, is present in the form of fog on the planet Mars.

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Terraforming Mars

Terraforming Mars is the hypothetical idea that Mars could be altered in such a way to sustain human and terrestrial life forms.

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Europa's Possible Ocean

Europa, one of Jupiter's four moons, is covered by a layer of ice/water and scientists have multiple hypotheses to explain its structure.

Section 3
Microbial Phylogeny
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Processes and Patterns of Evolution

Natural selection can only occur in the presence of genetic variation; environmental conditions determine which traits are selected.

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Distinguishing between Similar Traits

Similar traits can be either homologous structures that share an embryonic origin or analogous structures that share a function.

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The Levels of Classification

Taxanomic classification divides species in a hierarchical system beginning with a domain and ending with a single species.

Section 4
Classification of Microorganisms
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The Taxonomic Scheme

Bacterial taxonomy is the rank-based classification of bacteria.

The Diagnostic Scheme

Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly.

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The Species Concept in Microbiology

The number of species of bacteria and archaea is surprisingly small, despite their early evolution, genetic, and ecological diversity.

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Classification and Nomenclature

Nomenclature is the set of rules and conventions that govern the names of taxa.

Section 5
Methods of Classifying and Identifying Microorganisms
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Phenotypic Analysis

Microorganisms can be classified on the basis of cell structure, cellular metabolism, or on differences in cell components.

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Classification of Prokaryotes

Prokaryotic organisms were the first living things on earth and still inhabit every environment, no matter how extreme.

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Phylogenetic Analysis

The molecular approach to microbial phylogenetic analysis revolutionized our thinking about evolution in the microbial world.

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Nongenetic Categories for Medicine and Ecology

In medicine, microorganisms are identified by morphology, physiology, and other attributes; in ecology by habitat, energy, and carbon source.

Section 6
Bacterial Diversity
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Common Bacterial Traits

Bacteria are a subset of prokaryotes and while very different, they still have some common features.

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Unclassified and Uncultured Bacteria

To classify a species of bacteria, one usually needs to isolate and grow up the species that is to be classified.

Section 7
Proteobacteria
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Overview of Proteobacteria

The Proteobacteria are a major group (phylum) of bacteria.

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Alphaproteobacteria

Alphaproteobacteria is a class of Proteobacteria; like all Proteobacteria, they are Gram-negative.

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Betaproteobacteria

Betaproteobacteria is a class of Proteobacteria that are all Gram-negative.

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Morphologically Unusual Proteobacteria

The two main groups of morphologically unusual proteobacteria include spirillum and prosthecate bacteria.

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Gammaproteobacteria

Gammaproteobacteria is a class of several medically, ecologically and scientifically important groups of bacteria.

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The Deltaproteobacteria

Deltaproteobacteria is a class of Proteobacteria that are Gram-negative.

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Epsilonproteobacteria

Epsilonproteobacteria is a class of Proteobacteria that are Gram-negative.

Section 8
Gram-Positive Bacteria and Actinobacteria
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Overview of Gram-Positive Bacteria and Actinobacteria

Actinobacteria are Gram-positive bacteria with high guanine and cytosine content in their DNA and can be terrestrial or aquatic.

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Non-Spore-Forming Firmicutes

The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure and some of which do not produce spores.

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Firmicutes

The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure and some of which can form endospores.

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Actinobacteria (High G + C Gram-Positive Bacteria)

Actinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content in their DNA.

Section 9
Nonproteobacteria Gram-Negative Bacteria
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Cyanobacteria

The cyanobacteria, also known as blue-green bacteria, are a phylum of bacteria that obtain their energy through photosynthesis.

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Anoxygenic Photosynthetic Bacteria

Some groups of bacteria can capture light energy and convert it to ATP without the production of oxygen through anoxygenic photosynthesis.

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Prochlorophytes

Picoplankton is the fraction of plankton which can be photosynthetic or heterotrophic.

Section 10
Irregular Bacterial Cells
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Chlamydiae

Chlamydiae are a bacterial phylum and class whose members are obligate intracellular pathogens.

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Planctomycetes

Planctomycetes are a phylum of aquatic bacteria and are found in samples of brackish, marine, and fresh water.

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Verrucomicrobia

Verrucomicrobia is a recently described phylum of bacteria which is part of the PVC superphylum.

Section 11
Other Bacterial Groups
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Bacteroides and Flavobacterium

Bacteroides and Flavobacterium are both Gram-negative bacteria that can be either motile or non-motile.

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Acidobacteria

Acidobacteria are a newly formed phylum of bacteria that are physiologically diverse and abundant in soil environments.

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Cytophaga and Relatives

Cytophaga are a type of bacteria characterized as Gram-negative, rod shaped bacteria that utilize a gliding mechanism for locomotion.

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Bacteroidetes and Chlorobi

Bacteria categorized under the Phylum Bacteroidetes and Phlyum Chlorobi are closely related base on comparative genomic analysis.

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Fusobacteria

Fusobacterium are anaerobic, non-spore forming, gram-negative bacteria that are associated with periodontal disease and Lemierre's syndrome.

Spirochaetes

Spirochaetes are characterized by the presence of a double-membrane and long, spiral-shaped cells that are chemoheterotrophic.

Section 12
Thermophiles
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Aquificales and Thermotogales

Along with Thermotogae, members of Aquificae are thermophilic eubacteria.

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Deinococcus and Thermus

The Deinococcus-Thermus are a small group of bacteria composed of cocci highly resistant to environmental hazards.

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Chloroflexus and Relatives

Chloroflexus are Gram-negative filamentous anoxygenic phototrophic organisms that utilize type II photosynthetic reaction centers.

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Nitrospirae and Deferribacter

Nitrospirae is a phylum of bacteria; some nitrospirae species perform important functions in the nitrogen cycle.

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Aquifex, Thermocrinis, and Related Bacteria

The Aquificae phylum is a diverse collection of bacteria found in harsh environments: hot springs, sulfur pools, and thermal ocean vents.

Section 13
Archaeal Diversity
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Energy Conservation and Autotrophy in Archaea

Archaea can use a number of different mechanisms to get nutrients and energy.

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Archaeal Gene Regulation

Archaea are very different genetically from bacteria and eukaryotes.

Section 14
Crenarchaeota
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Habitats and Energy Metabolism of Crenarchaeota

Crenarchaeota exist in a wide range of habitats and exhibit a great variety of chemical reactions in their metabolism.

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Hyperthermophiles from Terrestrial Volcanic Habitats

A hyperthermophile thrives at relatively high temperatures and can be found in geothermally heated regions of the Earth.

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Hyperthermophiles from Submarine Volcanic Habitats

Hyperthermophiles live in dark regions of the oceans and use chemosynthesis to produce biomass from single carbon molecules.

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Nonthermophilic Crenarchaeota

Nonthermophilic Crenarchaeota can be extreme halophiles living in highly salty environments.

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Psychrophilic Crenarchaeota

Psychrophiles crenarchaeotes are extremophilic organisms that are capable of growth and reproduction in cold temperatures.

Section 15
Euryarchaeota
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Diverse Cell Forms of Methanogens

There are over 50 described species of methanogens, sharing over 30 signature proteins.

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Extremely Halophilic Archaea

Halophiles are extremophiles that thrive in environments with very high concentrations of salt.

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Methane-Producing Archaea: Methanogens

Methanogens are an important group of microoraganisms that produce methane as a metabolic byproduct under anaerobic conditions.

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Thermoplasmatales, Thermocaccales, and Methanopyrus

There are many classes in the phylum Euryarchaeota, many of which are extremophiles.

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Archaeoglobus

Archaeoglobus is a genus of Euryarchaeota found in high-temperature oil fields.

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Nanoarchaeum and Aciduliprofundum

Nanoarchaeum equitans is a species of marine Archaea discovered in a hydrothermal vent off the coast of Iceland.

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Hyperthermophilic Archaea, H2, and Microbial Evolution

A hyperthermophile is an organism that thrives in extremely hot environments, from 60 degrees C (140 degrees F) and up.

Section 16
Eukaryotic Microbial Diversity
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Phylogeny of the Eukarya

Eukaryotes are very diverse in phylogenic terms, the common feature being a membrane bound nucleus.

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Historical Overview of Eukaryotes

Until more recent work, the historical view of eukaryotes has been anthropomorphic.

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Opisthokonts: Animals and Fungi

Opisthokonts include the animal and fungus kingdoms.

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Endosymbiotic Theory and the Evolution of Eukaryotes

Genome fusion occurs during endosymbiosis, which is the mechanism proposed as responsible for the first eukaryotic cells.

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Cell Structure, Metabolism, and Motility

Protists are an incredibly diverse set of eukaryotes of various sizes, cell structures, metabolisms, and methods of motility.

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Newly Discovered Eukaryotes

There are many new species to be discovered, including eukaryotic species.

Section 17
Fungi
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Characteristics of Fungi

Fungi, latin for mushroom, are eukaryotes which are responsible for decomposition and nutrient cycling through the environment.

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Fungi as Plant, Animal, and Human Pathogens

From crop and food spoilage to severe infections in animal species, fungal parasites and pathogens are wide spread and difficult to treat.

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Fungi Habitat, Decomposition, and Recycling

Fungi are the major decomposers of nature; they break down organic matter which would otherwise not be recycled.

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Chytridiomycota: The Chytrids

Chytrids are the most primitive group of fungi and the only group that possess gametes with flagella.

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Zygomycota: The Conjugated Fungi

Zygomycota, a small group in the fungi kingdom, can reproduce asexually or sexually, in a process called conjugation.

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Glomeromycota

Glomeromycetes are an important group of fungi that live in close symbiotic association with the roots of trees and plants.

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Ascomycota: The Sac Fungi

Most fungi belong to the Phylum Ascomycota, which uniquely forms of an ascus, a sac-like structure that contains haploid ascospores.

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Basidiomycota: The Club Fungi

The basidiomycota are mushroom-producing fungi with developing, club-shaped fruiting bodies called basidia on the gills under its cap.

Section 18
Protists
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Early Eukaryotes

Protists are eukaryotes that first appeared approximately 2 billion years ago with the rise of atmospheric oxygen levels.

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Excavata

Excavata, defined by a feeding groove that is "excavated" from one side, includes Diplomonads, Parabasalids and Euglenozoans.

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Chromalveolata: Alveolates

Alveolates are defined by the presence of an alveolus beneath the cell membrane and include dinoflagellates, apicomplexans and ciliates.

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Chromalveolata: Stramenopiles

Stramenophiles include photosynthetic marine algae and heterotrophic protists such as diatoms, brown and golden algae, and oomycetes.

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Rhizaria

Rhizaria are a supergroup of protists, typically amoebas, that are characterized by the presence of needle-like pseudopodia.

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Amoebozoa and Opisthokonta

Amoebozoa are a type of protist that is characterized by the presence of pseudopodia which they use for locomotion and feeding.

Section 19
Algae
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Archaeplastida

Archaeplastida are a supergroup of protists that comprise red and green algae, which include unicellular, multicellular, and colonial forms.

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Protists as Primary Producers, Food Sources, and Symbionts

Protists function as sources of food for organisms on land and sea.

Section 20
Helminths
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Characteristics of Helminths

Helminths are parasitic worms that live and feed on living hosts to receive nourishment and protection which results in illness of the host.

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Classification and Identification of Helminths

Helminths, or parasitic worms, are eukaryotic parasites characterized by their ability to feed and live on living hosts.

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Distribution and Importance of Parasitic Worms

Parasitic worms, distributed worldwide, are hypothesized to have importance in immune system regulation.

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Arthropods as Vectors

Arthropods are capable of functioning as vectors by transmitting diseases.

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Microbial Evolution, Phylogeny, and Diversity
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