Soil Microorganisms Lecture 3 Sep 13th

1. Soil Microorganisms Lecture 3 Sep 13th • TODAY: • Discussion Questions • Reading Assignments from last week • Smith et al. (Eutrophication) – will discuss beginning of N lecture (9-26) • Condron et al. 98-108 – will discuss beginning of metabolism lecture (9-19) • Lecture

2. Outline • Bacterial Morphology • 1. Cell Structure • 2. Cell Motility • 3. Cell Wall Structures • a. Odd Soil and Water Bacteria • B. Intro to Bacterial Growth • C. Intro to Bacterial Genetics • 1. Central Dogma • 2. Gene Exchange

3. New Course Schedule 9/12 Intro to Bacteria and Viruses – Structure and Genetics 9/19 Bacterial Diversity, Metabolism, and Viruses 9/26 Bacterial-mediated Nitrogen Cycling 10/03 Exam 1 10/10 Bacterial-mediated Sulfur and Phosphorus Cycling Plant-Bacteria Interactions 10/17 Methods of Assessment of Soil Bacteria 10/24 Soil Fungi – Diversity, Function, and Competition 10/31 Mycorrhizae and N Fixation 11/7 Exam 2 11/14 Soil Microfauna 11/21 Soil Mesofauna 11/28 Soil Macrofauna 12/5 Frontiers of Research in Soil Biology 12/14 Final Exam

4. I. Bacteria & Archaea • Prokaryotic • Lack organelles • No true nucleus • Unicellular • Range in size from 0.1 um to > um • Why would it be disadvantageous for bacteria to be large? • Most abundant “living” organisms in soil

5. Prokaryotes: The unseen majority ~108 – 1010 bacteria g-1 soil 1019 grains of sand in the world 1023 stars in the observable universe 1027 bacteria in tropical rain forest soils 1030 bacteria on earth biomass exceeds that of all plants and animals 1013 cells in human body 1014 bacterial cells on and in the human body Can persist for eons 8 million yr old bacteria revived from Antarctic ice

6. Bacterial Morphology cocci (spheres) filamentous spirilla bacilli (rods)

7. Bacterial Morphology Pili “Walking” Polar flagella motility

8. Bacterial Morphology Gliding Slime Layer Capsule • Slime layer capsule • Polysaccharide layer • Antibiotics, dessication, chemical attack • Endospore • Long-term survival • Dormant state • Nutrient deficiency

9. Bacterial Morphology Gram + and Gram - • Two main sub-groups of bacteria • Based on differences in the structure of the ________

10. Bacterial Morphology Bacteria vs. Archaea Eukaryota Bacteria Archaea

11. Strange Bacteria Beggiatoa (genus) 2H2S + O2 → 2S + 2H2O • Oxidize Hydrogen Sulfide to S • Store S intracellular (golden granules) • Visible with naked eye • Marine sediments • Move up and down for optimum balance • Single cells or in filaments

12. Strange Bacteria Pseudomonas fluorescens • 1 um short rods • Siderophore producing

13. Strange Bacteria • Actinobacteria (phylum) • Used to be classified as a fungus, Actinomycetes • Some form branching filaments • Geosmin • Petrichor - Frankia – N2 Fixing Bacteria Oldest living thing on Earth? 500,000 yo Nocardia – Lignin and Gingival Pockets

14. Strange Bacteria • Burkholderia (genus) • ~35 species • Cystic Fibrosis • Chloroorganic pesticides • PCB • Agricultural • Biocontrol Agents • PGP • Biowarfare Agents

15. Strange Bacteria • Deinococcus radiodurans • Soil bacteria • Toughest bacteria on Earth • Radiation, acid, dehydration, vacuum • 5 gy kills human, 800 gy kill E. coli, 5000 kills radiodurans • Conan the bacterium Tetrads, 4 cells sticking together

16. II. Bacterial Growth "The mathematics of uncontrolled growth are frightening. A single cell of the bacterium E. coli would, under ideal circumstances, divide every twenty minutes. That is not particularly disturbing until you think about it, but the fact is that bacteria multiply geometrically: one becomes two, two become four, four become eight, and so on. In this way it can be shown that in a single day, one cell of E. coli could produce a super-colony equal in size and weight to the entire planet Earth." Michael Crichton (1969) The Andromeda Strain, Dell, N.Y. p247

17. Is he correct? 272 = 4.7*1021 10-12 g/cell = 4.72* 106 kg Mass of Earth = 5.98*1024 kg Would actually take about 40 hours

18. Factors affecting growth are: • 1. • 2. • 3. • Limiting nutrient: • CLASSIC GROWTH CURVE

19. Killham and Prosser, 2007 umax A umax B Copiotrophy (r-strategists) vs. oligotrophy (K-strategists)

20. umax A ½ umax A Ks

21. Higher Ks: Lower KS: umax B ½ umax B Ks B Ks A

22. Bacterial Evolution – NichingEveryone Competes • 12 identical populations of E. Coli over 23 years • 50,000 generations • After 20,000 grew 70% faster than parent strain • 120 mutations were fixed in the populations • Some could not repair DNA any more • Some could use citrate under aerobic conditions • Never seen in the wild

23. Everyone Competes……But Will Also Cooperate • Bacterial Crosstalk • “Please pass the sugar” • Rhizobia inoculation • Quorom Sensing • Is everyone ready? • Putting relatives first • Bacterial “suicide bombers”

24. C. Intro to Bacterial Genetics 1. Central Dogma 2. Gene Exchange 3. Examples in Soil

25. CENTRAL DOGMA The ability to extract DNA (deoxyribonucleic acids (DNA) and ribonucleic acids (RNA) from cells within soils have given us great new insights into soil microbial communities A T G C

26. CENTRAL DOGMA

27. CENTRAL DOGMA Ribonucleic Acid – Secondary Structure

29. CENTRAL DOGMA The Ribosome • Translates mRNA (gene transcript) • mRNA  Protein • Consists of protein and RNA • Active sites are conserved • Genes encoding protein and RNA are conserved

30. Replication

31. Transcription

32. Translation

33. 16S rRNA 16S rRNA gene • Acts as scaffold for ribosomal proteins • Conserved and hypervariable regions • Basis of bacterial taxonomy

34. 2. Gene Exchange • Plasmid • Extrachromosomal circular genetic structure that can reproduce autonomously but is not essential • Generally 1-10% the size of the chromosome • Provides genetic diversity and enables bacteria to rapidly adapt to a wide range of ecological niches

35. 2. Gene Exchange • Some plasmid – encoded functions • Antibiotic and toxin resistance • Enzymes for xenobiotic degradation • N2 fixation genes • Transfer Method #1: Conjugation • Requires cell to cell contact, usually plasmid mediated • Most important mechanism • Uses pili • Does not have to be • closely related • Does not involve the • chromosome SOUND

36. 2. Gene Exchange • Transfer Method #2: Transduction • Bacteriophage infection • Transfer by delivery of viral DNA • Sometimes species or strain specific due to attachment sites • Phage attached to pili • Bacteria change their pili • May become adsorbed to soil SOUND

37. 2. Gene Exchange • Transfer Method #2: Transduction • Lytic Phage: Inserted phage DNA is copied by cell machinery • Many copies are made • Phage components assemble themselves • Cell wall bursts and phage replicates are released • Lysogenic Phage: Integration of phage DNA into host chromosome • Replicated as part of chromosome • ~10% of human genome is ancient viruses • May enter lytic cycle • Sometimes mistakes are made in copying viral DNA • Portion of host DNA integrated into viral DNA • Transfer of genes among hosts via viral infection

38. 2. Gene Exchange • Transfer Method #3: Transformation • Uptake of naked extracellular DNA – closely related species • Incorporation into the genome • Originated as a way to obtain nutrients • Extracellular DNA can be stabilized onto soil • Least important of three genetic exchange mechanisms