LOE - Diversity of bacteria and archaea

• Antoni van Leuwenhoek - C17th. Made lenses and saw 'animalcules'.
• Belief in spontaneous generation before germ theory and knowledge of bacteria.
• Pasteur - C19th. Experiment with swan-necked flasks showed that when no air could enter a broth, it was preserved. This proved that outside agents cause spoilage.
• Pasteur's experiments supported Redi's work (C17th).

Archaea and bacteria differ from eukaryotes -

• Mostly by the complexity of cell structure.
• Archaea and bacteria are relatively simple - no membrane-bound organelles or nucleus, most have a single circular chromosome (but it also may be linear or multiple).
• Eukaryotes have linear chromosomes, compacted with histone proteins. These points are considered to be a distinction between bacteria and eukaryotes.

Archaea differ from bacteria -

• Appear similar but have very different biochemistry.
• Bacterial membrane lipids are similar to eukaryotic cells - contain D-glycerol and have ester linkages - but archaeal membrane lipids are very different, with L-glycerol and ether linkages.

• Genetic differences - Archaea have small subunit RNA sequences, distinct to those in bacteria.
• Archaea have similar intron-exon structures to eukaryotes - introns separated by exon. Exons are spliced out of RNA after transcription and before translation.
• Some groups are monophyletic, such as cyanobacteria, and others are paraphyletic, such as Gram-negative bacteria.

• Nuclear envelope: Absent in bacteria and archaea, present in eukaryotes.
• Membrane-bound organelles: Absent in bacteria and archaea, present in eukaryotes.
• Peptidoglycan cell wall: Present in bacteria, absent in archaea and eukaryotes.
• Membrane lipids: Unbranched hydrocarbons in eukaryotes and bacteria, some branched hydrocarbons in archaea.
• RNA polymerase: One type only in bacteria, several types in archaea and eukaryotes.
• Interior amino acid: Formyl-methionine in bacteria, methionine in archaea and eukaryotes.
• Introns in genes: Very rare in bacteria, more common in archaea and eukaryotes.
• Histones associated with DNA: Absent in bacteria, present in some archaea and all eukaryotes.
• Circular chromosomes: Circular or linear in bacteria, circular in archaea, linear in eukaryotes.
• Growth above 100˚C: In some archaeal species, not in bacteria or eukaryotes.

• Bacteria are ubiquitous - Found in many environments, e.g. human body, oceans, deep sea thermal vents, soils.
• Archaea can also be found in all these places, albeit found less easily than bacteria, as they are harder to grow in a lab.
• Archaea can also be found in extreme environments, e.g. hypersaline environments.

• Cyanobacteria: Gram-negative bacteria that can produce algal blooms.
• Fruit rotting: Needed for recycling organic material back into soil.
• Digestion: Live in cow rumens and digest cellulose - cows cannot do this, and having bacteria to do it for them allows them to live on poorly-digestible compounds.
• Cause disease: There are no known archaeal pathogens, but some are known to live in symbiosis with eukaryotes.

• Phototrophs: Use light as an energy source.
• Chemotrophs: Use chemical energy sources, e.g. bacteria living in deep sea vents.
• Autotrophs: Only require carbon dioxide as a source of carbon.
• Heterotrophs: Need 1+ organic molecules, e.g. glucose, as an energy source.

• Photoautotrophs: Photosynthetic bacteria, plants, some protists (algae).
• Chemoautotrophs: Some archaea (e.g. Sulfolobus), some bacteria (Thermus aquaticus). Use inorganic compounds e.g. ammonia, iron ions as energy sources.
• Photoheterotrophs: Certain bacteria (e.g. Rhodobacter).
• Chemoheterotrophs: Many bacteria, archaea, protists, fungi, animals, and some plants. Use organic compounds as energy sources.

Modern bacterial systematics is based on sequence divergence.

• Alpha proteobacteria: Many species closely associated with eukaryotic cells, e.g. Rhizobium in root nodules. Some species e.g. Agrobacterium produce plant tumours and are used to genetically modify plants. Mitochondria may have evolved by endosymbiosis in an alpha proteobacterium.
• Beta proteobacteria: Nutritionally-diverse subgroup, including Nitrosomonas (oxidises ammonium ions to nitrite). Wide range of aquatic species, and some pathogens e.g. Neisseria.
• Gamma proteobacteria: Auxotrophs, e.g. sulfur bacteria Thiomargarita namibiensis, obtain energy by oxidising hydrogen sulfide to sulfur. This group also includes some heterotrophic pathogens (Salmonella, Vibrio) and commensals (E. coli).
• Delta proteobacteria: Includes Myxobacteria - these can form fruiting bodies and release resistant myxospores. Bdellovibrio is small and motile. It preys on other Gram-negative bacteria by invading the periplasm and feeding on their biopolymers.
• Epsilon proteobacteria: Includes human pathogens Campylobacter (food-borne intestinal illness) and Helicobacter pylori (gastritis, gastric cancer - survives in acidic conditions of stomach). Also some non-pathogens e.g. Wollinella, found in soil.

• Chlamydias: Obligate intracellular pathogens - can only survive in host animal cells. Depend on the host cell for nutrients and ATP. Unusually for Gram-negative bacteria, they have no peptidoglycan in the cell wall. Includes some human pathogens, e.g. Chlamydia trachomatis (causes blindness, STI).
• Spirochetes: Heterotrophs with internal flagellum-like filaments, allowing them to spiral through viscour environments. Many are free-living, but includes some human pathogens too e.g. Borrelia burgdorferi (Lyme disease).
• Cyanobacteria: Photoautorophs - only photosynthetic bacteria. Responsible for producing oxygen in Earth's early atmopshere. Some species have specialised cells for nitrogen fixation. Chloroplasts may have evolved from an endosymbiotic cyanobacterium.
• All of the above groups are Gram-negative bacteria.
• Gram-positive bacteria: Very diverse - includes pathogens and free-living forms, e.g. Mycobacteria. Thick peptidoglycan outer surface, but lacking the outer membrane of Gram-negative bacteria. Mycoplasma lack cell walls entirely - smallest known cells (can be 0.1micrometres).

• Originally known for being extremophiles - halophiles and thermophiles.
• However, some live in moderate environments e.g. oceans, animal intestines.
• Some are methanogens - undergo anaerobic digestion, producing methane as a result.

• Extreme halophiles: Live in highly-saline environments. May be dependent on or just tolerant of high salinity. Unusual proteins to avoid denaturation - but this may mean that they are dependent on a hyper-saline environment to function.
• Extreme thermophiles: Sulfolobus inhabits sulfur-rich volcanic springs (up to 90˚C). 'Species 121' lives in hydrothermal vents (120˚C). Specially-adapted proteins to avoid denaturation. Enzymes from these species are used in biotech, e.g. DNA polymerase from P. furiosus is used in PCR, as it is resistant to the high temperatures needed for this process.

• Methanogens: Many use carbon dioxide to oxidise hydrogen to produce energy, and methane is produced as a by-product. Most are obligate anaerobes. Can live in extreme or moderate environments. Used industriallt in anaerobic digesters to break down organic waste and produce useful methane.

• Recycling organic compounds - decomposition.
• Carbon capture - photosynthesis.
• Nitrogen fixation.
• Bioremediation.
• Interactions with other organisms - symbiotic, pathogenic, commensal.