1. Are we human, or are we… The diversity of microbes

2. Diversity of Microbes Microbes are ubiquitous on our planet ◦ Found in every environment imaginable 50% of all biomass is thought to be made up of microbes Bacteria and other microbes help our world function as we know it ◦ Fermentationnitrogen fixation ◦ Biopharmaceuticalsdecomposition ◦ Digestionfood production

3. Diversity of Microbes 1 trillion vs 10 trillion 30k genes vs 30 million

4. Diversity of Microbes 5 Kingdoms system has been used since 1959 Grouping stated with Linnaeus (1700s) Can be grouped into eukaryotes and prokaryotes Late ‘80s Carl Woese used rRNA to identify differences in prokaryotes Led to a new classification system, the 3 Domains

5. Diversity of Microbes The 3 Domains are: ◦ Eubacteria: typical prokaryotes ◦ Archaea: extremophiles ◦ Eukarya: single and multicellular organisms with a membrane bound nucleus 5 kingdoms based on structural differences, 3 Domains molecular differences Variations in rRNA sequences led to a clear distinction within the three domains and provided another evolutionary piece of evidence Be familiar with the table on page 514

6. Diversity of Microbes The split into the 3 domains was really to help explain discrepancies that were seen within the 5 kingdoms Each of the 5 kingdoms would fit within one of the three domains Main problem archaea were classified within the same kingdom as bacteria ◦ Molecularly more closely related to eukaryotes (all based on rRNA structures)

7. Diversity of Microbes--Archaea These are the extremophiles—they live in very harsh conditions These conditions are thought to be similar to life on early Earth They can split into three main groups: ◦ Methanogens—used CO 2 to produce CH 4 ◦ Thermophiles—heat loving, usually acidic ◦ Halophiles—salt loving, 10x greater than oceans

8. Diversity of Microbes--Bacteria Typically found in arrangements with three different shapes ◦ Spherical (cocci) ◦ Rods (bacilli) ◦ Helices (spirilla) Can occur as single cells or groups of cells ◦ Staphylococcus—bunch of spheres ◦ Streptococcus—chain of spheres ◦ Diplococcus—pair of spheres These arrangements are used in part to identify bacteria

9. Diversity of Microbes--Bacteria Besides shape, one major way to differentiate between bacteria is cell wall morphology Gram staining is an easy way to differentiate between these differences Gram (+)Gram (-) PurplePink Lots of peptidoglycanLittle peptidoglycan No outer membraneOuter membrane More susceptible to antibioticsLess susceptible to antibiotics

10. Diversity of Microbes--Bacteria Bacteria have a way in which they can communicate with one another ◦ Quorum sensing relies on chemical signals Not all QS is cool…most pathogenic microbes also use QS to release toxins that cause illness

11. Diversity of Microbes--Viruses Viruses are not alive, but still considered microbes Come in a variety of shapes and with multiple methods of replicating Same general packaging regardless of type of virus ◦ Protein coat (encapsulated or not) ◦ Nucleic acid (ssDNA/RNA or dsDNA/RNA) ◦ Internal enzymes

12. Diversity of Microbes-eukaryotes Not all microbes are prokaryotes MEMBRANE BOUND NUCLEUS YEAST Fermentation  alcohol and CO 2 AMOEBA Pseudopodia & food vacuoles (intracellular digestion) PLASMODIA Parasitic heterotrophs PARAMECIUM Ciliate heterotrophs; food vacuole + lytic enzymes vacuole EUGLENA Heteroautotrophs, chlorophyll and photoreceptors CHLORELLA Single celled green algae Chlorphyll, non-motile, cellulose

13. Diversity of Microbes The world around you functions as a result of microbes in ways which we usually don’t recognize Two good examples of this would be the Nitrogen Cycle and Waste Water Treatment Section F.2 in the book discusses microbes in the environment, be sure to know the details from that section With all these examples, the natural metabolism of microbes is used in some way to benefit us

14. Diversity of Microbes Microbes can be producers, decomposers, and nitrogen fixers “fixing” a gas simply takes it from a gaseous state to a form which can be used by organisms The nitrogen cycle is responsible for taking nitrogenous wastes from plants and animals and turning it into nitrogen gas (N 2 ) It is also responsible for taking nitrogen gas and converting it into nitrates, nitrites, and ammonia which can be used metabolically by plants which are then consumed by animals

15. Diversity of Microbes AMMONIA NH 3 Gaseous Nitrogen N 2 1 NITRATES/NITRITES 2 3 4 5 6 7 1) Fixation 2) Nitrification 3) active transport of Nitrate ions 4) consumption 5) death and excretion 6) putrefaction 7) denitrification

16. Diversity of Microbes What happens to the water in your toilet after you flush? ◦ How would you feel knowing that it will be recycled and you could drink it later? It’s because of microbes, specifically saprotrophs, that this is possible Water from bath tubs, showers, toilets, washing machines, dishwashers, and business and industry all sent to treatment plants Water is treated and eventually reused ◦ Solid wastes are removed (in inorganic), consumed (by microbes), and concentrated and sent to a landfill (sludge)

17. Diversity of Microbes

18. Many food production processes require microbes Beer, wine, bread, sauerkraut/kimchi, yogurt, and soy sauce are all produced using microbes ◦ Make sure you can explain the production of soy sauce by using Aspergillus oryzae Processes are also in place to preserve food to prevent spoilage by microbes ◦ Canning/Pickling – uses pH (acids) and salt to prevent spoiling ◦ Preserves—uses high sugar concentration ◦ Pasteurization—uses heat and a sealed environment

19. Diversity of Microbes Food poisoning can occur if preservation techniques are done poorly or if fresh food is left to spoil Salmonella infections are common food-borne illnesses Studies have shown 80% or more of chicken at grocery stores are contaminated Fully cooking food will prevent illness Most infections result from undercooked food, irrigation with contaminated water, or cross- contamination

20. Diversity of Microbes With salmonellosis symptoms (cramps, diarrhea, fever) will develop 12 to 72 hours after infection Severe dehydration can result in hospitalization Without treatment, infection can spread to blood and lead to death (not typical) Antibiotics will take care of the infection To fully diagnose salmonellosis fecal samples must be tested for the presence of the bacterium ~40,000 cases reported in the U.S. each year