4/21/2025 Notes | BIOL 412

Topic: Diversity

  • Diversity: variability among living organisms

    • Functional - metabolic types

    • Species - phylogenetic and evolutionary relationships

    • Mechanisms that promote genetic diversity

  • Eukarya and Archaea derived from Bacteria evolutionarily

    • rRNA-based genetic findings

  • What is a species?

    • a group of organisms with a shared evolutionary history

    • find statistical threshold (70% of genome should hybridize with each other)

      • Genomic DNA-DNA hybridization

      • most bacteria’s whole genome isn’t available due to difficulty in culturing and isolating colonies

      • rRNA is used instead of DNA

      • a bacterial species is a 97% similarity in 16S rRNA gene

        • Species: organisms with 97% similarity in the 16S rRNA gene

    • Phylogenetic Species Concept

      • genetically and phenotypically cohesive

      • functional traits should be distinct

      • monophyletic

      • majority of genes have congruent phylogenies

      • does not imply an evolutionary model of speciation

  • How many species?

    • Seawater: 20,000 sp/L
      Soil: 5,000-20,000 sp/g

    • predicted ~ 1 trillion species around the world

    • OTU: Operational Taxonomic Unit

      • equivalent to that 97% similarity 16S rRNA gene benchmark

    • 10,000 described species (textbook)

    • ~30,000 described species (ICNP)

      • 30 major phyla

      • 80 phyla predicted from rRNA sequences

    • 6 phyla have vast majority of info. collected

    • most species derived from molecular genetic approaches

      • culturing is a barrier

    • 90% of cultural taxa are from:

      • Proteobacteria —> Pseudomonadota

      • Actinobacteria —> Actinomycetota

      • Firmicutes —> Bacillota

      • Bacteroidetes —> Bacteroidota

      • Tenericutes

  • Archaeal Diversity

    • ~6/27 phyla have cultural representatives

    • 357 species published

    • majority of taxa are unculturable (discovered via genomic analysis)

  • enormous genetic diversity

    • functional and metabolic taxa are not phylogenetically constrained

    • Cyanobacteria have constrained traits

EXAMPLES (use study guide 13)

  • Ch. 16 on bacterial diversity

    • differences in structural anatomy

    • bacterial internal structures

    • free-living vs endosymbiotic microorganisms

  • pick 2 taxa we didn’t learn about and learn about them

  • focus on habitat, morphology, physiology, applications to industry, etc.

PROTEOBACTERIA

  • largest and most metabolically diverse taxa

  • >1/3 of characterized species

  • grows well in our environment

  • medical, industrial, ecological, and agricultural significance

  • all Gram negative

  • horizontal gene transfer (HGT) shapes metabolic diversity

    • ~70% of Proteobacteria have HGT at least once

    • occurs at species level and shared between phylogenetically constrained individuals

    • free-living organisms more likely to share than endosymbionts

    • conjugation most common

  • Classes are separated by Greek letters

  • CLASS: Alphaproteobacteria

    • ~1000 described species

    • oligotrophs

    • aerobic or facultative anaerobic

    • ORDER: Rhizobiales

      • form nodules with roots

      • nitrogen fixation

      • not monophyletic (HGT)

      • chemoorganotrophs

      • obligate aerobes

  • Pelagibacter ubique’s class is either Rhizobiales or Rhickettsiales (depends on source)

    • very oligotrophic

    • chemoorganotrophs

    • obligate areobic

    • 25% of cells in photic zone

    • 50% in temperate oceans

    • smallest genome of any free-living bacteria (135 ORFs)

  • ORDER: Hyphomicrobiales

    • fluctuating environment

    • purple sulfur bacteria