Geomicrobiology Microbes are any life form too small to be seen with the naked eye Classification of life forms Eukaryotic Plants animals fungus algae and even protozoa Prokaryotic archaea and bacteria Living cells can Self feed Replicate grow Differentiate change in form function Communicate Archaea and Bacteria can vary in size Some are as large as 600 x 80 m Most are on the order of a 0 5 2 m Some are thought to be as small as 100 nm or smaller nanobacteria Your hair is around 35 m thick 35 000 nm Archaea and bacteria come in many shapes Cocci Bacilli rods Many others corkscrews helices spirals stars squares and more Spores analogous to seeds Why size is important Food air nutrients diffuse in and out of the cell smaller size faster these things move faster metabolism faster rate of division How small can microbes get Minimum amount of material to have enough chemical diversity to support basic life functions 0 3 MBp with cell around 170 m 100 m 20 m Microbes on the head of a pin false color SEM images from j Rogers http people westminstercollege edu faculty jrogers V 20prokaryotes ppt 298 3 Slide 3 0 5 m S8 in biofilms at Frasassi Images courtesy Jenn Macalady Penn State Environmental limits on life Liquid H2O life as we know it requires liquid water Redox gradient conditions which limit this Range of conditions for prokaryotes much more than that of eukaryotes inactive stasis Spores can take a lot of abuse and last very long times Tougher living less diversity Closer to the limits of life Fewer microbes able to function Life at pH 0 Significant communities of bacteria archaea fungi and protists A Slump Diversity There are likely millions of different microbial species Scientists have identified and characterized 5 000 of these Typical soils contain hundreds thousands of different species Very extreme environments contain as little as a few different microbes Characterizing microbes Morphological and functional what they look like and what they eat breathe Based primarily on culturing grow microbes on specific media trying to get pure culture Genetic Determine sequence of the DNA or RNA only need a part of this for good identification Probes Based on genetic info design molecule to stick to the DNA RNA and be visible in a microscope Classification of life forms Eukaryotic Plants animals fungus algae and even protozoa Prokaryotic archaea and bacteria Living cells can Self feed Replicate grow Differentiate change in form function Communicate Evolve Can purely chemical systems do these things All of these things Why do we care to go through this Tree of life Cell Metabolism Based on redox reactions Substrate food electron is lost from this which is oxidized by this process that electron goes through enzymes to harness the energy for the production of ATP Electron eventually ends up going to another molecule which is reduced by this The Redox ladder O2 Oxic Aerobes H2O NO3 Dinitrofiers Post oxic N2 MnO2 Mn2 Sulfidic Methanic Maganese reducers Fe OH 3 Fe2 Iron reducers SO42H2S Sulfate reducers CO2 CH4 Methanogens H2O H2 The redox couples are shown on each stair step where the most energy is gained at the top step and the least at the bottom step Gibb s free energy becomes more positive going down the steps Nutrition value Eukaryotes like us eat organics and breathe oxygen Prokaryotes can use other food sources and acceptors Redox gradients and life Microbes harness the energy present from DISEQUILIBRIUM Manipulate flow of electrons O2 H2 O C2HO Phototrophic mats PSB Purple sulfur bacteria mats 0 100 200 Depth microns Respond to light level changes in minutes position in sediment and water column can vary significantly Purple sulfur bacteria mats 300 400 500 600 700 800 0 500 1000 1500 H2 S aq Concentration M 2000 Microbes e flow Catabolism breakdown of any compound for energy Anabolism consumption of that energy for biosynthesis Transfer of e facilitated by e carriers some bound to the membrane some freely diffusible thiovulum mats Pozzo di Cristale Frassassi caves Profiles and microbial habitats O2 3 2 depth O2 Minerals Expected H2S Fe2 4 H2S 1 Org C Concentration Org C Other nutrients needed for life Besides chemicals for metabolic energy microbes need other things for growth Carbon Oxygen Sulfur Phosphorus Nitrogen Iron Trace metals including Mo Cu Ni Cd etc What limits growth Nutrients Lakes are particularly sensitive to the amount of nutrients in it Oligotrophic low nutrients low photosynthetic activity low organics clear clean Eutrophic high nutrients high photosynthetic activity high organics mucky plankton cyanobacterial population high Plankton growth 106 CO2 16 NO3 HPO42 122 H2O 18 H trace elements light C106H263O110N16P1 138 O2 organic material composing plankton This C N P ratio 106 16 1 is the Redfield Ratio What nutrients are we concerned with in Lake Champlain Nutrient excess can result in blooms Lake Champlain Phosphorus limited Algal blooms What controls P Nutrient cycling linked to SRB IRBMRB activity PO43 PO43 FeOOH PO43 Org C SO42H2S PO43 Sulfate Reducers PO4 FeS2 3 PO43 PO43 PO43Blue Green Algae blooms Redox Fronts Oxic Anoxic Boundary between oxygen rich oxic and more reduced anoxic waters Oxygen input through entrainment wind wave action photosynthesis Oxygen consumption from heterotrophic consumption reaction with reduced forms of Fe Mn S Methods Voltammetric microelectrodes In situ pore water measurements to determine redox front by real time analysis of O2 Fe2 Fe3 Mn2 H2S DGT Diffusive Gradients in Thin films to monitor P fluxes through sediment Gravity Coring and chemical extractions of iron manganese and phosphorus in the sediment Inductively coupled plasma optical emission spectroscopy ICP OES to measure iron manganese and phosphorus from extractant Voltammetric data St Albans Bay Sediments Current 0 304 0 106 0 100 0 280 0 260 0 090 0 240 0 080 0 220 0 070 0 200 0 180 0 060 0 160 0 050 0 140 0 040 0 120 H2O2 2e 2H 2H2O 0 100 0 080 0 030 0 020 O2 2e 2H H2O2 0 060 0 040 0 010 0 000 0 020 0 004 1 800 Mn2 2e Mn0 Hg Fe 1e Fe 3 1 600 1 400 1 200 blue 0 00 0 00 red 0 00 0 00 1 000 0 800 0 600 0 400 2 0 010 0 100 0 019 1 800 1 600 0 341 1 400 1 200 blue 1 56 0 04 red 1 34 0 01 1 000 0 800 0 600 0 400 0 100 0 300 0 250 0 200 0 150 0 100 FeS aq 0 050 0 000 0 058 1 800 1 600 1 400 blue 1 200 0 00 0 00 1 000 0 800 0 600 0 400 0 100 7 19 04 Core 1 Profile 1 10 10 5 5 0 0 5 5 Mn nA 10 O2 nA 15 Fe3 nA 20 20 FeS nA 25 25 30 30 10 O2 nA 15 Depth mm Depth mm 6 23 04