Microbial Diversity Scott Clingenpeel
Complete Genomes • 2671 Prokaryotic genomes in GenBank • 114 Eukaryotic genomes • 9 Plants • 52 Animals Do we really need more microbial genomes?
Microbial Diversity • Less than 0.1% of known microbes have been grown in the lab • The uncultured microbes were completely unknown until the relatively recent development of DNA techniques • The vast majority of microbes known today don’t have a formal species name
Cell Morphology Image from Wikimedia Commons
Cell Morphology Clostridium sp. Escherichia coli Bacteroidesfragilis Images from Wikimedia Commons
Colony Morphology Image from Wikimedia Commons
Colony Morphology Brian Traw, U. Pittsburgh NOAA Office of Exploration & Research Wikimedia Commons
Biochemistry Images from ASM MicrobeLibrary
DNA (Finally!) • Need a gene present in all life • Need a gene that is the right size • Need a gene with slow and fast evolving parts • The gene that was chosen as just right is the 16S/18S ribosomal RNA gene • Arbitrary cutoff of 97% identity was decided to be the definition of a microbial species
Taxonomy Group Humans Dogs Domain EukaryaEukarya Kingdom AnimaliaAnimalia Phylum ChordataChordata Class Mammalia Mammalia Order Primates Carnivora Family HominidaeCanidae Genus Homo Canis Species sapiens lupus
Tree of Life Bacteria Archaea Eukarya Euryarchaeota Crenarchaeota Thaumarchaeota Nanoarchaeota Korarchaeota Modified from: Madigan et al., Brock Biology of Microorganisms 12th ed.
Extremes of Life • Temperature range: -18°C – 121°C (0°F – 250°F) • Eukaryotes: 0°C – 60°C (32°F - 140°F) • pH: 0 – 13 • Salinity: 5M NaCl = 10x sea water = 30% salt • Radiation: 3000x the dose that kills humans pH Scale
Microbial Physiologies Oxygen + Food →Carbon Dioxide + Water Molecules that can be used as Food Hydrogen gas Hydrogen Sulfide Sulfur Ammonia Nitrite Carbon Monoxide Phosphite Iron Molecules that can be used in place of Oxygen Nitrate Nitrite Nitric Oxide Nitrous Oxide Sulfate (sulfuric acid) Carbon Dioxide Chlorine Iron Manganese Selenium Arsenic
Microbial Physiologies • At least 10,000,000 organic molecules are made by living things • These are grouped into ~100 classes of molecules • Only about half of these have a known microbial pathway for making them or for breaking them down
Do We Really Need More Microbial Genomes? • 80% of current genomes come from only three bacterial kingdoms • ~30 bacterial kingdoms have no sequenced genomes • The number of genes shared between two species in different kingdoms are <5% • Only two genes are shared in all sequenced prokaryotic genomes