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

What is a Microbial Species?

Cell Morphology

Image from Wikimedia Commons

Cell Morphology

Images from Wikimedia CommonsEscherichia coliBacteroides fragilis

Clostridium sp.

Colony Morphology

Image from Wikimedia Commons

Colony Morphology

NOAA Office of Exploration & Research

Brian Traw, U. Pittsburgh

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 DogsDomain Eukarya EukaryaKingdom Animalia AnimaliaPhylum Chordata ChordataClass Mammalia MammaliaOrder Primates CarnivoraFamily Hominidae CanidaeGenus Homo CanisSpecies sapiens lupus

Tree of Life

Bacteria Archaea Eukarya

Modified from: Madigan et al., Brock Biology of Microorganisms 12th ed.

Thaumarchaeota Nanoarchaeota

Korarchaeota

Crenarchaeota

Euryarchaeota

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 PhysiologiesOxygen + Food → Carbon Dioxide + Water

Molecules that can be used in place of Oxygen

NitrateNitrite

Nitric OxideNitrous Oxide

Sulfate (sulfuric acid)Carbon Dioxide

ChlorineIron

ManganeseSeleniumArsenic

Molecules that can be used as Food

Hydrogen gasHydrogen Sulfide

SulfurAmmonia

NitriteCarbon Monoxide

PhosphiteIron

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

• 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

Do We Really Need More Microbial Genomes?