5a and 5b

• Taxonomy


  Classifying, describing, identifying and naming the organisms

  
• Physical traits used to classify bacteria

  • Shape (cocci, rod, spiral, filamentous)
  • Number of cells (single, two, tetra, chain etc)
  • Cell wall (Gram staining)
  • Growth temperature range
  • Anaerobic/aerobic/facultative anaerobe
  • Mode of metabolism

  
• Modern classification started with Carl Linnaeus in 18th century
• Scientific nomenclature


  2 scientific (latin) names: 1st name is genus, 2nd name is species
• Examples of scientific names: Homo sapiens, Escherichia coli
• 16S rRNA


  A sequence of DNA that encodes the RNA component of the smaller subunit of the bacterial ribosome

  
• Carl Woese rewrote the tree of life
• Why use 16S rRNA?

  • Present in all cells
  • Conserved across all prokaryotic species
  • Essential for cell survival
  • Changes at DNA level acquired slowly
  • Unlikely to go through lateral or horizontal transfer
• The three domain model is the accepted biological classification
• Woese's classification emphasises separation between Bacteria and Archaea

  
• The split is based on genetic rather than morphological traits
• Comparison of 16S rRNA sequences

  • Methanococcus
  • Thermococcus
  • E.coli
  • Humans
• Analysis of SSU rRNA allows construction of "The Tree of Life"
• Prokaryotic Microbes


  • Bacteria
  • Archaea
• Eukaryotic Microbes


  • Fungi
  • Protozoa
  • Algae
• Principle differences between prokaryotic and eukaryotic microbes

  • Size of cell
  • Nucleus
  • Membrane-enclosed organelles
  • Flagella
  • Cell membrane
  • Cell wall
  • Ribosomes

  
• Bacterial Classification


  • Cyanobacteria
  • Proteobacteria
  • Firmicutes

  
• Archaea


  • More closely related to humans than bacteria
  • Found in extreme environments
  • Have structural, chemical and metabolic adaptations
• Archaeal Diversity


  • Euryarchaeota
  • Crenarchaeota
  • Asgard
  • DPANN
  • TACK

  
• Microbial Eukaryotes


  Unicellular and multicellular eukaryotes, have membrane bound organelles, include plants, animals etc.
• Microbial Eukaryotes


  • Fungi
  • Protozoa
  • Algae
• Unicellular Eukaryotes


  • Typically microscopic (from 2.5 µm)
  • Single-celled, sometimes form colonies with division of labour
• Multicellular Eukaryotes


  • At least 20 cells
  • Typically have tissues and organs
  • Can be self-propelled
• Classification of Microbial Eukaryotes

  • Environment (terrestrial, freshwater, marine)
  • Body size (picoplankton, nanoplankton)
  • Functional ecology (phytoplankton)
  • Feeding strategy (photosynthesisers, predators)
• Trophic level of Microbial Eukaryotes

  • Autotrophic (produce own carbon compounds)
  • Phagotrophic (ingest particles)
• Plankton


  Typically small, multicellular organisms, especially animals, critical part of aquatic ecology, present in huge numbers and major components of ecosystems
• Dinoflagellates


  • Unicellular protists, marine plankton but can be found in freshwater, photosynthetic and heterotrophic, about 1555 described species

  
• Diatoms


  • Group of algae, very large in size, account for ~20% of global photosynthetic carbon fixation, unicellular but can form filaments and stars, have calcium carbonate shells, very important for carbon cycle
• The fossil record is a tool to investigate and understand paleoclimates and how climate has changed
• Freshwater diatoms and other planktonic micro-algae are important indicators of water type and conditions
• The fossil record is an important source of historical data on the nature of the water, changes in environment, and past changes in nutrients
• 55 described species!
• Diatoms


  Group of algae (very common)
• Diatoms


  • Very large in size and significant because they account for ~20% of global photosynthetic carbon fixation
  • They are unicellular but can form a shape of filaments, stars
  • They have calcium carbonate shells
  • Very important for carbon cycle
• A teacup of Lake Windermere water contains approx. 2 million Asterionella
• Annual production 400 tons!
• Fossil record


  A tool to investigate and understand paleoclimates, i.e. the Earth's past climates and environments, and how climate has changed
• Freshwater diatoms and other planktonic micro-algae

  • Important indicators of water type and conditions
• Information available from fossil record

  • The nature of the water where they live
  • Changes in environment e.g. changes in sea levels reflected by species in saline vs brackish waters
  • Indicate past changes in nutrients in the water. Diatoms from nutrient-poor lakes (oligotrophic) are different in abundance and species composition than those that grow in nutrient-rich (eutrophic) lakes
  • pH variation over time e.g. acidification of lakes
• Information available from fossil record


  • The community itself, e.g. the species that live in the sampled area. Different aquatic animal communities thrive in different salinity concentrations
  • The community assemblage (composition and abundance): how it varies over time and season
  • The morphology of shells - smooth, lobate, chamber size, spines. No spines in low oxygen concentrations
  • Chemical composition of shells