Microbial Origins of Life and Energy Conversions

1. Microbial Origins of Life and Energy Conversions Biol 251

2. Terms to Know for this Lecture • Science – Questioning • Religion - Believing • Fact – What most experts agree on… often becomes dogma (essentially the truth) • Truth – What is… does anyone really know what truth is? Inherent bias…

3. The “Big Bang” and Earth • The universe was created sometime about 13.5 billion years ago from a cosmic explosion that hurled matter and in all directions (the “big bang”) • The Earth is thought to have formed about 4.5-4.6 billion years ago

4. Geologic Time…. Oldest sedimentary rocks, Greenland  3.8 bya O2 accumulates rapidly CH4 dominated environment [CH4] [CO2] [H2O] Atmosphere is warm 2.3 bya photosynthetic cyanobacteria  3.5 bya anaerobic prokaryotes lithotrophic and or fermentative Atmosphere is cold 1.7 bya Western Australia South Africa 2.4 bya origin of eukaryotic cells

5. Origin of Early Life  3.8 bya The primitive Earth was hot (>100°C), anaerobic with warm oceans Simple organic molecules formed from atmospheric gases (CO2, NH3, H2S, CH4, HCN and CO) and dissolved in the oceans Lightning, heat & UV light - energy Simple macromolecules: sugars, amino acids, nucleotides, lipids How do simple organic molecules form a protocell? Spontaneous generation?

6. Experimental Results Laboratory experiments that attempt to address how cells developed

7. Primordial Soup Experiment 1953 • Replicate environmental conditions of prebiotic times • Atmosphere • H2O, H2, CH4 & NH3 • Organic compounds • Amino acids This experiment has been modified over the last 50 years and has yielded all 20 amino acids, nucleotides, lipids, sugars and ATP

8. Protocells • All cells have a outer plasma membrane • Protocells • 3.8 bya • Simple membrane bound sacs • Created simple membranes under laboratory conditions • Fatty acids & alcohols • Bubble hypothesis • Proteinoids • “protein-like” molecules that are produced when amino acid solutions are heated

9. What was hereditary material of early organisms? - RNA • Genetic & enzymatic components of early cells were probably RNA • Lab experiments have produced • RNA • Ribozymes • Enzymatic RNA molecule that catalyzes reactions during RNA splicing • Clay can concentrate charged molecules • Catalysis of polymers

10. Classification and naming of bacteria by how they derive energy and carbon 4 parts to name 1. How they get energy (chemo- versus photo-) 2. Where they get electrons from? Organic versus inorganic molecules (organo- versus litho- (rock eater) 3. Where do they get their carbon from? Auto- (CO2) versus hetero- (organic carbon source- e.g., glucose) 4. Add troph…

11. What were earliest organisms (bacteria?) like metabolically? • Aerobic versus anaerobic? • Photo- versus chemotrophic? • Litho- versus organotrophic? • Auto- versus heterotrophic? • Optimal growth temperature… • Psychrophile: <15° C • Mesophile: From 20 to 40° C • Moderate Thermophiles: 40 to 80° C • Hyperthermophiles: > 80°C

12. Stromatolites Banded domes of sedimentary rock similar to layered mats of heterotrophic bacteria & cyanobacteria Stromatolites in western Australia  3.5 billion years old microscopic resemblance to photosynthetic organisms

13. The Origin of Prokaryotes • Fossils of microbes dating from 950 mya • Palaeolyngbya from Shale in Siberia Divisions reminiscent of membranes or cell walls

14. When did eukaryotes arise? • Sterols, including cholesterol have been found in oil droplets within quartz crystals • Sterols are produced almost exclusively by eukaryotes • Quartz is dated at 2.4 bya • Predates the “Great Oxidation Event” • O2 production by cyanobacteria

15. The oldest eukaryotic fossils are 2.1 bya

16. How did organelles develop?

17. Theory of Endosymbiosis page 125 • Symbiotic relationship between two microorganisms, in which one is living inside the other • Chloroplast • Cyanobacterium engulfed by larger organism • Photosynthesis provided carbohydrates & produced O2 • Protected habitat for the cyanobacterium • Both organisms benefit - mutualism • Relationship became obligatory

18. Evidence for Endosymbiosis • Modern chloroplasts • Circular chromosome with prokaryotic-like genes • Independent division • Prokaryotic ribosomes • Has 16s rRNA gene in genome and 16s rRNA molecule in ribosome

19. Endosymbiosis • Mitochondria • Circular chromosome with prokaryotic like genes • Independent division • Prokaryotic like ribosomes • Prokaryotic like membranes • Has 16s rRNA gene in genome and 16s rRNA molecule in ribosome

20. Endosymbiosis • Eukaryotes • Fusion of bacterial & archaeal cells • Genomes fused • Eukaryotic flagella & cilia • Consequence of a spiral bacterium & a eukaryotic cell

21. Relationships that support the Theory of Endosymbiosis • Many protozoans are infected with bacteria in an Endosymbiotic relationship • Many symbiotic relationships between microorganisms in nature • Lichens • Cyanobacterium or alga with a fungus • Cyanobacteria are endosymbionts of plants, various protists and sponges

22. Bacteria Eukarya Archaea Node - LUCA Last Universal Common Ancestor Hyperthermophile Anaerobe Archaea or Bacteria?

23. ThermotogamaritimaA model for LUCA • Deep sea thermal vents • Grows at 90ºC so hyperthermophile (Domain Bacteria) • Anaerobic • Heterotroph • Must consume carbon compounds • Contains genes that can be classified as… • Bacterial • Archaeal • ¼ of the genes • Eukaryotic

24. Deep Sea Hydrothermal Vents Water temperatures >350°C Tremendous diversity of marine organisms surrounding thermal vents Minerals precipitate out of sea water “Black Smoker” … smoke is precipitate of metal sulfides from H2S

25. Global Energy Conversions –Microbes Rule the Earth!!

26. Microbes comprise nearly half of all biomass on Earth All habitats that support plants and animals have abundant populations of microorganims. Microorganisms also exist in habitats too extreme for plants and animals.

27. Prokaryotes are the most abundant form of life on Earth Greatest amount of biomass and total numbers of species Prokaryotes compose 90 % of the total combined weight of all organisms in the oceans > 109 bacterial cells are present in 1.0 g of agricultural soil Outnumber all eukaryotic cells by 10,000 : 1 • 3,000 species of Bacteria and Archaea are currently recognized

28. The main role of microorganisms in the biosphere is to act as catalysts of biogeochemical cycles. Microorganisms catalyze reactions that cycle C, N, O, P and many other elements.

29. BIOGEOCHEMICAL CYCLES • Elements required for cells are constantly • progressing through a cycle involving microorganisms • Leaf falls from tree • Decomposes • Elements making leaf used by microbes • Four key elements constitute four primary cycles • CARBON • NITROGEN • SULFUR • PHOSPHORUS

30. Carbon Cycle www.textbookofbacteriology.net

31. The Carbon Cycle • Carbon is fixed when photosynthetic organisms fix • CO2 into organic compounds • Herbivores consume plants • Carbon from herbivores recycled by four mechanisms • Exhaled CO2 is used by photosynthetic organisms • Feces utilized by soil microbes • Prey for carnivores • Dead animals are decomposed by soil microbes

32. The Carbon Cycle • Prehistoric decomposed • matter was converted into • fossil fuels • Burning of fossil fuels • generates CO2 • CO2 reenters cycle • through photosynthetic • plants • Methanogens reduce CO2 • anaerobically and give off CH4

33. Nitrogen Cycle • N2 gas is the most abundant (~80%) gas in Earth’s atmosphere • Involves several types of microbes • 4 types of reactions • Nitrogen fixation – ONLY by prokaryotes • N2 gas is converted to NO2- (nitrite), NO3- (nitrate), or NH3(ammonium salts) • Ammonification • Bacteria degrade of organic compounds to ammonia • Nitrification • Convert NH3 to NO2- and NO3- • Denitrification – ONLY by prokaryotes • Microbial conversion of various nitrogen salts back to atmospheric N2

34. Nitrogen Cycle www.textbookofbacteriology.net

36. Free Living Nitrogen-Fixing Organisms • NITROGENASE complex – ONLY in prokaryotes!!!!! • Enzyme of nitrogen-fixation • Two protein subunits that work together • Destroyed by O2 • Nitrogenase must be maintained in an anaerobic environment • Cyanobacteria - fix nitrogen in specialized cellsHETEROCYSTS • Provide anaerobic environment required for nitrogenase • Plant-associated bacteria – many produce nodules • In nodules, plant produces a unique form of hemoglobin called • leghemoglobin • This protein binds O2 and “protects” nitrogenase

37. Symbiotic Nitrogen Fixing Organisms • Rhizobium species - infect roots of legumes (Pea Family of Plants) • Alfalfa, peas, beans, clover, soybeans, & peanuts • Attach to root hair, “infection thread” forms • Bacteria enter through thread and penetrate root cells • Bacteria differentiate into BACTEROIDS • Thicker cell walls • Combination of plant & bacterial cell wall • Dense cytoplasm • Do not divide

38. Consume carbohydrates from the plant and fix N2 • Synthesize amino acids • Causes enlargement of root cells • Results in formation of a root NODULE • Bacteria within nodule fix nitrogen • Plant use amino acids

39. Nodules Rhizobium & Bradyrhizobium Symbiotic association with legume roots Alfalfa Beans Clover Peas N2 + 8H+ + 8e- + 16 ATP  2NH3 + H2 + 16 ADP + 16 Pi

40. Deamination • After N2 is fixed • Converted to biologically relevant molecules • Majority of atmospheric nitrogen is incorporated into amino • acids • Plant is consumed and amino acids incorporated into herbivore • Herbivore excretes waste • Microbes break down proteins into amino acids • A second set of microbes break amino acids down into ammonia • DEAMINATION • Often times NH3 is released into soil • AMMONIFICATION • Highly soluble in moist soil • Available to plants and other microbes

41. Nitrification – ONLY in prokaryotes • Not all NH3 is used by plants • Some moves to next step in cycle • Some organisms oxidize NH3 to produce nitrite (NO2-) • NITRIFICATION • Nitrosomonas • Nitrite is further oxidized to nitrate (NO3-) • Easily moves through soil via diffusion • Nitrobacter

42. Denitrification – ONLY in prokaryotes • NO3- (nitrate) can be used as terminal electron acceptor • under anaerobic conditions • Results in conversion of NO3- to atmospheric nitrogen N2 • Three reactions involved in process • Completes nitrogen cycle NO3- NO2- N2O N2