4: Microbial Diversity

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Life appeared on Earth approximately 3.7 billion years ago. For a billion years all life was prokaryotic and mainly anaerobic until eukaryotes evolved from a symbiosis between a larger archaeal cell and aerobically-respiring bacteria in response to increasing levels of atmospheric oxygen. In this symbiosis, aerobic respiration was critical to providing the high levels of energy necessary to support the evolution of the large, complex eukaryotic cells we are familiar with today.

In the course of 3.7 billion years, prokaryotes have evolved to take advantage of almost every imaginable carbon and energy source in every possible niche and environment. This has resulted in a huge diversity of microbial life, which today is formally classified through a taxonomic system based on evolutionary relationships (phylogeny) and informally based on organismal characteristics (phenotype). Some of the most familiar groups of microbes are discussed here as representatives of this diversity.

Chapter 4 BSC 3271 Learning Outcomes

Provide a rough timeline of the evolution of life on Earth, including: formation of the Earth, first cells, increase in atmospheric oxygen, first eukaryotes, multicellular life, humans.
Distinguish between vertical and horizontal gene transfer and explain why evolution is now thought to be more of a web than a tree (although usually represented in tree form)
Describe the endosymbiotic theory for the evolution of certain eukaryotic organelles and provide at least three pieces of evidence to support the theory
In the framework of the endosymbiotic theory and environmental conditions at the time of the evolution of eukaryotic cells, explain the benefits of the relationship to both host and symbiont
Describe both the beneficial and harmful implications of the reactivity of oxygen.
Explain how either phenotype characteristics or molecular characteristics can be used to classify organisms.
Order the levels of classification from more general to more specific, from domain to strain.
Explain why ribosomal sequences are a good choice for determining relationships of organisms.
Use a phylogenetic tree to determine an organism’s closest relatives.
Properly apply the terminology for nutritional types (metabolic lifestyles): chemo/phototroph, auto/heterotroph.
Describe the major characteristics of the following taxonomic groups: Bacteria (Domain), Archaea (Domain), Eukaryotes (Domain), Cyanobacteria (Phylum), Firmicutes (Phylum), Proteobacteria (Phylum), Bacillus (Genus), Clostridium (Genus)
List the characteristics commonly associated with Archaea, in particular the thermophiles, halophiles, and methanogens
Give one characteristic NOT associated with Archaea
Given a description of an organism, select the taxonomic group (of those above) with which the organism would best be classified

4.1: Taxonomy and Evolution
It is believed that the Earth is 4.6 billion year old, with the first cells appearing approximately 3.8 billion years ago. Those cells were undoubtedly microbes, eventually giving rise to all the life forms that we envision today, as well as the life forms that went extinct before we got here. How did this progression occur?
4.2: A Systematic Approach
Carolus Linnaeus developed a taxonomic system for categorizing organisms into related groups. Binomial nomenclature assigns organisms Latinized scientific names with a genus and species designation. A phylogenetic tree is a way of showing how different organisms are thought to be related to one another from an evolutionary standpoint. The first phylogenetic tree contained kingdoms for plants and animals; Ernst Haeckel proposed adding a kingdom for protists. Our modern understanding of taxonomy
4.3: Representative Groups
This chapter will examine the diversity, structure, and function of prokaryotes. Prokaryotes have an important role in changing, shaping, and sustaining the entire biosphere. They can produce proteins and other substances used by molecular biologists in basic research and in medicine and industry

Thumbnail: "Hot water running over mineral and bacteria deposits yellowstone wyoming wy" by Tim Pearce, Los Gatos is licensed under CC BY 2.0