Lecture 20

• Phylogeny is the history of branching divergence of multiple species and strains.
• A phylogenetic tree is a series of branching groups of related organisms generated from phylogeny.
• A clade is a group of related organisms that share a common ancestor.
• A node is a branch point.
• The root is a node for a group of branches, representing the common ancestor. Moving from the root to the tips of the branches means moving forward in time.
• Random mutation is a mechanism of evolution.
• Natural selection and adaptation are mechanisms of evolution.
• Reductive evolution is a mechanism of evolution.
• Horizontal gene transfer is a mechanism of evolution.
• Enrichment culture is a method in microbial ecology where the addition of a particular class of nutrient favors the growth of microbes that can use that nutrient.
• Microbial communities are living organisms that evolve in an ecosystem of organisms interacting within a given habitat.
• A microbiome, also known as microbiota or microbial community, is the microbes found in a defined habitat.
• Microbial ecology methods include sequencing a metagenome, which is the alignment of reads.
• Microbial ecology studies the questions of who is there, what are they doing, and how do microbiomes vary under different conditions.
• A community is the sum of populations of different species in an ecosystem, which includes animals, plants, and microbes.
• Microbiomes may be associated with a host animal or plant or with a region of soil or water, etc.
• An ideal molecular clock gene has the following features: the gene has the same function across all types of organisms compared, the generation time is the same for all organisms compared, the average mutation rate remains constant among organisms and across generations, and it is small-subunit ribosomal RNA (SSU rRNA) or 16S rRNA in bacteria and archaea, or 18S rRNA in eukaryotes.
• Small-subunit ribosomal RNA (16S or 18S) is used in phylogenetic studies.
• Small-subunit rDNA sequencing is used in phylogenetic studies.
• Small-subunit rDNA alignment is used in phylogenetic studies.
• Divergence is calculated as 100% - % similarity in a phylogenetic tree.
• Deep-branching Gram-negative bacteria are most (but not all) obligate anaerobes, with Chlorobi being green sulfur bacteria, Bacteroidetes found in the gut or soil, and Spirochetes forming tightly coiled spirals.
• Proteobacteria are broken up into classes: alpha, beta, gamma, delta, epsilon, and have a more diverse metabolism than any other phylum.
• Actinobacteria are Gram-positive, have a high GC content, are ubiquitous in soil and water, and some form arthrospores.
• Mycoplasma are related to Firmicutes but lack a cell wall and require an animal host.
• Proteobacteria have an outer membrane of lipopolysaccharides (LPS) and are Gram-negative.
• Deep-branching thermophiles have the fastest doubling rates and high mutation rates, share habitats with Archaea as well as archaeal traits (membrane lipids).
• Firmicutes are Gram-positive, have a thick cell wall supported with teichoic or mycolic acids, and contain a S-layer of glycoproteins.
• Cyanobacteria perform oxygenic photosynthesis and share a common metabolism, but have a wide range of cell shape and physiology.
• The PVC superphylum consists of irregular cells with no cell walls or diminished cell walls, including Planctomycetes, Verrucomicrobia, Chlamydiae, and Intracellular parasites.