Chapter 8
Microbial Evolution, Phylogeny, and Diversity
By Boundless
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Evidence for evolution has been obtained through fossil records, embryology, geography, and molecular biology.
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Key elements were needed for early life to start on earth.
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The question of how simple organic molecules formed a protocell is largely unanswered.
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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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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 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, one of Jupiter's four moons, is covered by a layer of ice/water and scientists have multiple hypotheses to explain its structure.
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Natural selection can only occur in the presence of genetic variation; environmental conditions determine which traits are selected.
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Similar traits can be either homologous structures that share an embryonic origin or analogous structures that share a function.
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Taxanomic classification divides species in a hierarchical system beginning with a domain and ending with a single species.
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Bacterial taxonomy is the rank-based classification of bacteria.
Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly.
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The number of species of bacteria and archaea is surprisingly small, despite their early evolution, genetic, and ecological diversity.
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Nomenclature is the set of rules and conventions that govern the names of taxa.
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Microorganisms can be classified on the basis of cell structure, cellular metabolism, or on differences in cell components.
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Prokaryotic organisms were the first living things on earth and still inhabit every environment, no matter how extreme.
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The molecular approach to microbial phylogenetic analysis revolutionized our thinking about evolution in the microbial world.
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In medicine, microorganisms are identified by morphology, physiology, and other attributes; in ecology by habitat, energy, and carbon source.
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The Proteobacteria are a major group (phylum) of bacteria.
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Alphaproteobacteria is a class of Proteobacteria; like all Proteobacteria, they are Gram-negative.
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Betaproteobacteria is a class of Proteobacteria that are all Gram-negative.
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The two main groups of morphologically unusual proteobacteria include spirillum and prosthecate bacteria.
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Gammaproteobacteria is a class of several medically, ecologically and scientifically important groups of bacteria.
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Deltaproteobacteria is a class of Proteobacteria that are Gram-negative.
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Epsilonproteobacteria is a class of Proteobacteria that are Gram-negative.
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Actinobacteria are Gram-positive bacteria with high guanine and cytosine content in their DNA and can be terrestrial or aquatic.
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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The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure and some of which can form endospores.
Actinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content in their DNA.
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The cyanobacteria, also known as blue-green bacteria, are a phylum of bacteria that obtain their energy through photosynthesis.
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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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Picoplankton is the fraction of plankton which can be photosynthetic or heterotrophic.
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Chlamydiae are a bacterial phylum and class whose members are obligate intracellular pathogens.
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Planctomycetes are a phylum of aquatic bacteria and are found in samples of brackish, marine, and fresh water.
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Verrucomicrobia is a recently described phylum of bacteria which is part of the PVC superphylum.
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Bacteroides and Flavobacterium are both Gram-negative bacteria that can be either motile or non-motile.
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Acidobacteria are a newly formed phylum of bacteria that are physiologically diverse and abundant in soil environments.
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Cytophaga are a type of bacteria characterized as Gram-negative, rod shaped bacteria that utilize a gliding mechanism for locomotion.
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Bacteria categorized under the Phylum Bacteroidetes and Phlyum Chlorobi are closely related base on comparative genomic analysis.
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Fusobacterium are anaerobic, non-spore forming, gram-negative bacteria that are associated with periodontal disease and Lemierre's syndrome.
Spirochaetes are characterized by the presence of a double-membrane and long, spiral-shaped cells that are chemoheterotrophic.
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Along with Thermotogae, members of Aquificae are thermophilic eubacteria.
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The Deinococcus-Thermus are a small group of bacteria composed of cocci highly resistant to environmental hazards.
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Chloroflexus are Gram-negative filamentous anoxygenic phototrophic organisms that utilize type II photosynthetic reaction centers.
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Nitrospirae is a phylum of bacteria; some nitrospirae species perform important functions in the nitrogen cycle.
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The Aquificae phylum is a diverse collection of bacteria found in harsh environments: hot springs, sulfur pools, and thermal ocean vents.
Crenarchaeota exist in a wide range of habitats and exhibit a great variety of chemical reactions in their metabolism.
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A hyperthermophile thrives at relatively high temperatures and can be found in geothermally heated regions of the Earth.
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Hyperthermophiles live in dark regions of the oceans and use chemosynthesis to produce biomass from single carbon molecules.
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Nonthermophilic Crenarchaeota can be extreme halophiles living in highly salty environments.
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Psychrophiles crenarchaeotes are extremophilic organisms that are capable of growth and reproduction in cold temperatures.
There are over 50 described species of methanogens, sharing over 30 signature proteins.
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Halophiles are extremophiles that thrive in environments with very high concentrations of salt.
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Methanogens are an important group of microoraganisms that produce methane as a metabolic byproduct under anaerobic conditions.
There are many classes in the phylum Euryarchaeota, many of which are extremophiles.
Archaeoglobus is a genus of Euryarchaeota found in high-temperature oil fields.
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Nanoarchaeum equitans is a species of marine Archaea discovered in a hydrothermal vent off the coast of Iceland.
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A hyperthermophile is an organism that thrives in extremely hot environments, from 60 degrees C (140 degrees F) and up.
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Eukaryotes are very diverse in phylogenic terms, the common feature being a membrane bound nucleus.
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Until more recent work, the historical view of eukaryotes has been anthropomorphic.
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Opisthokonts include the animal and fungus kingdoms.
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Genome fusion occurs during endosymbiosis, which is the mechanism proposed as responsible for the first eukaryotic cells.
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Protists are an incredibly diverse set of eukaryotes of various sizes, cell structures, metabolisms, and methods of motility.
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There are many new species to be discovered, including eukaryotic species.
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Fungi, latin for mushroom, are eukaryotes which are responsible for decomposition and nutrient cycling through the environment.
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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 are the major decomposers of nature; they break down organic matter which would otherwise not be recycled.
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Chytrids are the most primitive group of fungi and the only group that possess gametes with flagella.
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Zygomycota, a small group in the fungi kingdom, can reproduce asexually or sexually, in a process called conjugation.
Glomeromycetes are an important group of fungi that live in close symbiotic association with the roots of trees and plants.
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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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The basidiomycota are mushroom-producing fungi with developing, club-shaped fruiting bodies called basidia on the gills under its cap.
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Protists are eukaryotes that first appeared approximately 2 billion years ago with the rise of atmospheric oxygen levels.
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Excavata, defined by a feeding groove that is "excavated" from one side, includes Diplomonads, Parabasalids and Euglenozoans.
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Alveolates are defined by the presence of an alveolus beneath the cell membrane and include dinoflagellates, apicomplexans and ciliates.
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Stramenophiles include photosynthetic marine algae and heterotrophic protists such as diatoms, brown and golden algae, and oomycetes.
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Rhizaria are a supergroup of protists, typically amoebas, that are characterized by the presence of needle-like pseudopodia.
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Amoebozoa are a type of protist that is characterized by the presence of pseudopodia which they use for locomotion and feeding.
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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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Helminths, or parasitic worms, are eukaryotic parasites characterized by their ability to feed and live on living hosts.
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Parasitic worms, distributed worldwide, are hypothesized to have importance in immune system regulation.
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Arthropods are capable of functioning as vectors by transmitting diseases.