Microbes and Earth MaterialsSlide 2Tree of lifeSlide 4Slide 5Prokaryote StructureCell Nuclear MaterialMovementCell MetabolismNutrition valueRedox gradients and lifeOther nutrients needed for lifeSlide 13DiversityEnvironmental limits on lifeMicrobial evolutionSlide 17Identifying microbesSlide 19Microbes & MineralsSulfate reducing bacteriaSlide 22White biofilm pictureIron OxidizersSlide 25SEM of fluffysampling pictureIron ReducersMagnetotactic BacteriaMicrobes & Direct MineralizationSulfur oxidizing microorganismsH2S oxidationSlide 33Elemental Sulfur OxidationPyrite OxidationAMD neutralizationSlide 37Where is all the Fe2+ coming from?Slide 39Slide 40Slide 41Slide 42Slide 43Slide 44Microbes & PetroleumMicrobes & MethaneNatural AttenuationMineral Templatingfilaments in TEMminsheath2Slide 51Slide 52Microbes and Earth Materials•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)–CommunicateTree of lifediatomforams•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 seedsProkaryote StructureCell wallmembraneNuclear materialMembrane is critical part of how food and waste are transported - Selectively permeablePhospholipid layerTransport proteinsCell Nuclear Material•Genetic information in the nucleoid – single DNA molecule in a gel-like form, twisted and folded to fit inside the cell.•RNA around that – they do the work – both by carrying messages and catalyzing reactions•Why is DNA and RNA important in thinking about microbes as an Earth material??–Identify organisms in environments–Use genetic information for info about what they eat and how–Understand evolutionary relationshipsMovement•Flagella – spin corkscrew motion•Vesicles – gas filled for buoyancyCell 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)Nutrition value•Eukaryotes (like us) eat organics and breathe oxygen•Prokaryotes can use other food sources and acceptorsRedox gradients and life•Microbes harness the energy present from DISEQUILIBRIUM•Manipulate flow of electronsO2/H2OC2HOOther 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??Nutrient excess can resultin ‘blooms’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 microbesEnvironmental 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 functionMicrobial evolution•Oldest fossil evidence - ~3.5 g.a (Stromatolites)•Evidence for microbial activity argued for deposits > 3.7 g.a.•Couple fossil evidence with genomic information (analysis of function from genetic info)•Put against backdrop of early earth conditions–Significant atmospheric O2 after 2.0 g.a.•Look at most ‘primitive’ microbes in selected environments (similar to early earth)Tree of lifeIdentifying 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 microscopeMicrobes & Minerals•Direct precipitation/dissolution–Metabolism results in the precipitation of minerals – excrete something that reacts with other ions to form minerals–Utilize solids as e-donors/acceptors, resulting in dissolution•Indirect precipitation–Changes in local environments – e.g. pH–Microbes may induce mineralization by forming shells/testes–Microbes may serve as templates for minerals to easily form on themSulfate reducing bacteria•Eat organics – things like acetate and glucose•‘Breathe’ sulfate, exhale H2S•H2S really likes metals – form sulfide minerals:–Pyrite (FeS2), Sphalerite (ZnS), Galena (PbS), etc.White biofilm pictureIron Oxidizers•Eat Fe2+, Breathe O2•Fe3+ product likes O, OH – forms oxyhydroxides (FeOOH)–Goethite, Schwertmmanite, ‘Amorphous’ FeOOHSEM of fluffysampling pictureIron Reducers•Eat Organics, ‘breathe’ Fe3+, yielding Fe2+•Get Fe3+ from FeOOH minerals•How to eat/breathe a solid millions of times your size…–Solubilize the material–Iron reducers use organics called siderophores to solubilize Fe3+ and bring it inside the cell–Also use special organics as shuttles, which actually carry the electron between the microbe and the solid.Magnetotactic Bacteria•Form magnetic minerals from as a result of Fe3+ reduction (commonly magnetite, Fe3+2Fe2+O4, and greigite, Fe3+Fe2+S4) which are deposited inside the cell and used as a compass or sensor to guide the microbes’ position in an environmentMicrobes & Direct Mineralization•Through affecting metals, sulfur, and oxygen - a number of minerals may be precipitated as a result of microbial metabolisms•Microbes may also affect minerals through dissolution – which yields increased weatheringSulfur oxidizing microorganisms•Sulfur exists in different forms of varying redox state•Microbes can use many of them