2: Classification and Phylogeny
- Page ID
- 131102
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“The tree of life as we know it has dramatically expanded due to new genomic sampling of previously enigmatic or unknown microbial lineages.”
—-Hug et al. (2016)
Historically, the breadth of microbial life was vastly underestimated. Scientists used microscopes to see microorganisms as early as the 17th century (Gest, 2004) and they developed enrichment culturing techniques by the 19th century (Austin, 2017). Although valuable advancements, the ability of these techniques to survey microbial communities and assess evolutionary relationships is limited. Microorganisms have relatively simple morphologies that poorly reflect their great diversity (Woese, 1987) and the vast majority of microorganisms have not been successfully cultured (Stewart, 2012). However, technological advances in molecular biology in recent decades have helped overcome these limitations and our view of microbial life and its significance is rapidly growing.
This chapter describes some basic concepts necessary to understand the classification microbial life. We will consider the tree of life and the concepts of phylogeny and taxonomy. We will also consider a common approach used to directly analyze microbial communities based on the 16S rRNA gene. Many new and powerful molecular biology techniques have emerged in recent years. This chapter does not attempt to provide a summary of these techniques. Instead, we focus on some basic concepts that will help you understand the breadth of microbial life and relationships between different groups of microorganisms.
- 2.1: Three domains of cellular life
- Overview of the phylogenetic tree and its three major divisions: Bacteria, Archaea, and Eukarya.
- 2.2: Evaluating phylogeny
- Genes and how they can be used to evaluate the evolutional relationships between different organisms.
- 2.3: What is taxonomy?
- How biologists use the taxonomic system to classify organisms.
- 2.4: Analyzing microbial populations using 16S rRNA genes
- Basics of how to analyze a microbial population by extracting, processing and sequencing the 16S rRNA gene.
- 2.5: Example analysis
- 16S rRNA analysis of methanogenic microorganisms in coalbed environments, performed by Kirk et al. (2015).
- 2.6: Viruses
- The difference between viruses and living organisms. The importance of studying viruses in microbiology.