Lecture 6- Environmental Microbiology PDF

Readings Chapter 19 Taking the measurement of microbial systems (helpful for some tutorial presentations) molecular approaches Week 5 Microbial ecology lecture looks at the basics of ecology in microbial systems Chapter 20 Microbial ecosystems (Week 6 Environmental microbiolog...

Readings Chapter 19 Taking the measurement of microbial systems (helpful for some tutorial presentations) molecular approaches Week 5 Microbial ecology lecture looks at the basics of ecology in microbial systems Chapter 20 Microbial ecosystems (Week 6 Environmental microbiology lecture) Chapter 21 Nutrient cycles (Week 6 Environmental microbiology lecture) Chapter 23 Microbial symbioses with microbe, plant and animals (Lecture 7, Week 8, Microbial interactions) Last few slides of microbial ecology examinable for finals Indicator Species  Bioindicators Bioindicators can be a biological process, species or community A change in their size indicates a change in an environmental parameter originating in activity human ~ Usually anthropogenic but can also be natural An indicator species will have physiology that is responsive to the environmental variable e.g. Canaries in coal mines, frog spawn and pollution  & not too common not super rare ~ * & common very  Microbial Indicators Microbes are great indicators of biological processes as they do many of them from synthesis of organic C 102 ~ Primary productivity Respiration (BOD) - demand biogeochemistry biological oxygen 2 eg N fixate & etc. Microbes have been used as indicator species ~ faster & cheaper Direct (cfu counts) or indirectly (biomarker molecules) Biomarker molecules include diagnostic molecules for the presence of an organism such as fatty acid, DNA, protein Why are microbial systems so amenable to ecology?  Microbial systems Large populations size Short generation time budeif abundaneenies ~ can knockoutagene & Genetic manipulation (ultimate reduction) & not things just correlating Readily sampled Experimentally tractable Different modes of genetic inheritance Environmental Microbiology Introductory Microbiology Assoc. Prof. Rebecca Case SCELSE/SBS [email protected]  Life on earth Many ecosystems exist on earth. An ecosystem is an environmental unit in which the physical (abiotic) components interact with the community of organisms (biotic) Microbial photosynthesis produces: organic carbon from CO2 and oxygen (waste product) Primary productivity and the rate at which carbon dioxide is reduced into organic carbon CO2 fixation is the production of organic carbon compounds chemical exts to from CO2 ~ Yorganic o o ~ light energy uses to make food for itself Performed by chemoautotrophs and photoautotrophs Oxygen accumulated in the atmosphere making it habitable for humans and most other life forms we know This made Earth habitable to organisms that respire organic carbon with oxygen to carbon dioxide  Oxygenic photosynthesis made Earth habitable for eukaryotes in CO2 is high low in e pasta present metals became metal oxide then can be oxygen accumulated in atmosphere microbial fossils microbial fossils  inclusi bodies inside cell , forms a fillment so its multicellular ~800 myo fosilized cyanobacteria from stromatilites  have characteristic biochemical structures ~ Hopanoids – Molecular Fossils dructure eringdifficult is for microbes to digest & is biologically inaccessible , making it molecular fossils ~ characteristic of phototrophs Specific hopanoid for phototrophs (2-methylhopanes) and this has been used to data photosynthesis before the oxygenation of the atmosphere  Hopanoids ~ hydrophobic cructure Hopanoids are lipids found in cell membranes Thought to play a role in membrane fluidity, stress and protein localization much better than S They can be used as biomarkers just like DNA, RNA and proteins They are much more stable than DNA, RNA and proteins and therefore are used as biomarkers in fossils However, they do not contain sequence information and are therefore harder to identify 2-methylhopanoids as biomarkers for cyanobacteria and oxygenic photosynthesis date oxygenic photosynthesis can  Life on earth Microbes drive the biogeochemical cycles required for life Biogeochemical cycles allow essential elements to be cycled for reuse through habitats and spheres Think about the diversity of energy sources for chemo, e-acceptor & litho- and auto- trophic organisms elements/cmpds as these generate energy donor to arl can as These cycles are a series of redox reactions that Bacteria and Archaea use for energy (electron (e) acceptors and donors) and to make organic carbon Nitrogen, Phosphorus, Carbon (C:N:P) Bust don’t forget Oxygen, Hydrogen and Sulfur! These elements also make up the biomolecules that make life (DNA, RNA, proteins)  The Sulfur Cycle S04-2>SO3-2>SO2>S2O32-> different states of s >modendant S>H2S & & rotten eqp small yellow colour  Sulfate reduction ~ e-acceptor => [H) to - SO42- + 2H+ + 2e- > SO32- + H2O 1 ATP generated [H) S SO32- + 6H+ + 6e- > S2- +3H2O 3ATP Sulfate-reducing bacteria have very short electron transport chains (ETC) because little energy is available relative to O2 Sulfidogens are microbes that produce H2S. Obligate anaerobes are common in soil and marine environments - killed by normal atmospheric Very diverse. Best known example: Desulfovibrio From sulfate reducers to sulfidigens outside to protons pumped create electron potential generated e whole doesn't generallywouldexists in all be a usually one bacteria , sulfate reducer , another will be a sulfidogen lot from e [H) a more asi energy generated all member to converses is too much for e handle  Sulfur oxidation (chemoautotrophs) ~ reverse e-flow ETC can be reversed in sulfur oxidizers because HS-, S2O32- and S0 are weaker electron donors than NAD/NADH (NADH reduct generates NADH by equir for com & TH) as required for CO2 fixation) sulfur fixation as also oxidisers are & chemoautotrophs Electrons from these fuel sources fed into ETC at level need organic to reduce co2 C equivalent to their E0 Proton motive force formed at quinone (Q) and terminal oxidase (cytochrome – cyt) bringinginprora p The Nitrogen Cycle NO3 >NO2 >NO> - - N2O>N2>NH3>NH4+  I most oxidised form ~ takes back to N2 (neutral State) N fixate creduced forms most reduced ~ If n a form  ~ NO Stepwise Nitrate Reduction: Denitrification 1. NO3- + 2H+ + 2e- > NO2- + H2O 2 ATP some microbes can step but many microbes do> & 14 just doI step 2. 2NO2- + 2H+ + 2e- > 2NO + 2OH- 2 ATP produce enough energy for themselves 3. 2NO + 2H+ + 2e- > N2O + H2O 2 ATP 4. N2O + 2H+ + 2e- > N2 + H2O 2 ATP & most reduced form 1st step: nitrate respiration is carried out by E. coli and many other bacteria Sequential reduction of nitrate (NO3-) to N-gases (NO, N2O, and N2) = denitrification N2O (nitrous oxide) is a potent greenhouse gas produced mainly by denitrification in agricultural soils (and laughing gas)  Nitrogen Fixation Reduction of dinitrogen gas (N2) to ammonia (NH3) by the enzyme nitrogenase – very O2 sensitive (major process ~ anaerobic limitat ) = Life as we know it depends on the rapid cycling of nitrogen into biologically available forms Two enzyme complex (dinitrogenase and dinitrogenase reductase requirement of being process an anaerobic energetically~ expensive (triple bond) Only prokaryotes do it! And lots of different kinds symbiotic bacteria (e.g. Rhizobia that associated with plants) Cell differentiation (e.g. Cyanobacteria) Free-living aerobes (e.g. Azotobacter Free-living anaerobes (e.g. Clostridium) & N2 have 3 N hard to bonds , very break up , a lot of energy required N2 NH4+ - Soil (community) can Cultured microbe & look Gene for path e of NUnt & Study have Chizobia inoculated no Rhizobin on roots e on roofs in size & larger greener they are (more chlorophyll) - > more photosynthesis & grow better  see w dijih is what we called modules our eyes , not like that & they i are bacteria infects until k , a , e density of alls is immature organ I root of noduce which require I infects thread (in blue) anaerobic infeste multiply , it is & causes maturate of e organ Gene promoter e infecte thread-microbes colonizat fusions -Lac expression, Xgal BLUE - GREEN Fluorescent protein  Nitrogen fixing symbionts colonised Rhizobia (alpha proteobacteria) – terrestrial plants Eukaryotes unable to metabolise atmospheric nitrogen so access nitrogen from prokaryotes (symbiotic relationship) Rhizobia fix (or reduce) atmospheric nitrogen Make it available to plants form through a direct (symbiotic) of heterotrophic roof modules & consume plants organic feed i sugar solute toe (rhizobia interaction C are & in excess anaerobic c d also be organic can fixate for nitrogen Rhizobia induce cell differentiation in host plant to create niche (chemical communication) Root nodules have reduced oxygen as nitrogen fixation is an anaerobic process levels cyanobacteria polies O I out can carry & photosynthesis nitrogen fixate "strictly anaerobia process  red shows presence of chlorophyll Nitrogen fixation is anaerobic and therefore no -blue represents N fixntq photosynthesis cells (heterocuses) , they occurs in don't have chlorophyll heterocysts (blue)  complex morphologies ~ Heterocysts Cyanobacteria are also capable of fixing (reducing nitrogen) in aquatic systems Specialised cells called heterocysts fix nitrogen Heterocysts have several features for nitrogen fixation: thickened cell walls to reduce cell permeability to oxygen No chlorophyll so no photosynthesis (i.e. oxygen is not generated in the heterocyst) expression of photosynthetic genes - no Reduced nitrogen (NH4+ or organic N) is transported from the heterocyst to the vegetative cells doing photosynthesis who ~ are There is sugar transported from vegetative cells to heterocysts organic & C from photosynthesis ~ heterocysts Sugars are supplied in excess so they leak out of the cell, this attracts heterotrophic bacteria ~ that consume both oxygen and the sugars reducing O lowering heterocysts making => to colonise and I cell , it anaerobic The diffusion of these compounds (sugars and organic N) determines heterocyst spacing  A schematic diagram of the molecular regulation of heterocyst patterning. regulatoai make heterocupts ~ not literally cuffq but causes Hetre to be misfolded Peptide signal 5 amino acid signal ~ lots of it made in heterocycls cell d acts solikewhen a molecular scissors RESER birds to HetR , it degrades HetR HetR made reterocysts it is immediately degraded by pentapeptide although is in , inside ecell causing it to be recognised a degraded Starvation sensor from I further you more diffuses from heterocysts for all towell as organic N pentapeptides , induce an TRESURJt causing [HetR] ↑ accumulate this & can theres less chemicals Risser D D , Callahan S M PNAS 2009;106:19884-19888 away , thick cell wall d etc. of all e genes needed to make a heterocytes e. g expe.  Heterocyst spacing A schematic diagram of the molecular regulation of heterocyst patterning. The activator of heterocyst formation, HetR, is expressed under nitrogen starvation. The RGSGR pentapeptide (a signal) promotes HetR decay and therefore inhibits heterocyst formation. The RGSGR pentapeptide diffuses away from source cells (heterocysts) to neighbouring cells (vegetative) establishing an inhibitor concentration gradient along the filament, which in turn promotes an inverse gradient of the activator, HetR. Arrows indicate positive regulation. Scissors indicate decay.  Aerobic N2 fixation Azotobacter vinelandii Under low O2, no slime layer -acts as a barrier Under high O2, large slime layer upregulate Slime retards diffusion of O2 biosynthesis EPS > - into cell Nitrogenase will not be inactivated upregulate of nitrogenase & C Eps : extravellular geres polysaccharide very sticky & de,a The Phosphorus Cycle P>PO4 & more abundant  washed phosphate & out of rocks goes into water photo credit: Raven, Peter, Linda Berg. Environment third edition. Harcourt:2001 Lady Musgrave Island, GBR, Australia. The island is made of Guano (bird poop) which was mined for phosphate used in industry and agriculture.  Douglas-fir seedlings with and without mycorrhizae inoculation. phosphate mobilisate plants also rely on fungi as they can do roof associates transport into plants by plantgrowsthet are Redwood seedlings with (right) and without (left) mycorrhizae. Mike Amaranthus, USDA mushrooms (Borneo) mycelium  structures that penetrate on i surface surface layer epidermis ↑ e into dark yellow cells not inside cells but they are , I cells this maximises betw as SA to maximise exchange of befor unfrients a coupds fungus a plant  Phosphate Fungi secrete H+ to lower the pH of soil (from ~8 to 5), making metals more bio-available H+ displaces the metal cations in salts or complexes so available biologically ~ they can be taken up (dissolves them) ~ they exclude bacteria i This change in pH also serves to create a niche for the fungi as they are acid adapted and bacteria are less competitive in low pH environments Phosphatases (enzymes used for phosphate uptake) are adapted to a low pH in fungi and a neutral-basic pH in bacteria Bacterial phosphate uptake important in wastewater processing to accumulate polyphosphate removed - is Phosphorus is usually oxidized as PO4+2 in soils and this is the form microbes usually uptake  Mycorrhizae Mycorrhizae are the symbiotic system formed between plant roots and fungi Found on 95% of plants examined (small sample of real diversity, but prevalent) Symbiosis formed primarily for nutrition exchange Two Types: (slide 42) 1. VAM Arbuscular Mycorrhizae (inside plant root) 2. Ectomycorrhizae (outside plant root)  Mycorrhizae The fungus has enzymes that dissolve tightly bound minerals like phosphorus, sulfur, iron and all the major and minor nutrients used by plants The primary exchange usually found is: Fungus access phosphate from soil and exchanges it for Sugars produced by the plant through photosynthesis Essential in phosphate limited systems in type) : arbuscular means webbed-like struct > maximisa interface betw cells as it only imports phosphate I sells to specific cells & from there other cells and it transports it to however, phosphate is not equally distributed among I plant Diagram indicating possible sites of plant and fungal phosphate transporters and fungal glucose transporters in membranes of an arbuscular mycorrhiza. Phosphate transport: 1, phosphate uptake across membranes in the external hyphae; 2, phosphate efflux across the arbuscule membrane; 3, phosphate uptake across the peri-arbuscular membrane (2&3 inside plant). The net transfer is from the soil into the plant as the fungus is able to efficiently scavenge phosphate. Carbon transport: 2 and 4, possible sites of glucose uptake by the fungus. Carbon transport is inside the plant because the plant makes organic carbon through photosynthesis.  is maintained as wants it to differentiate betw self a fungus may < Himtransport is so  polymerised into n sugaa f art funsa wall throughall wall plant  Mycorrhizal Benefits Improved transplant survival and growth More effective rooting place holdsI soil in less eros? mycelium , Improved soil structure ~ organic c which is & also ofholds it a lot impt in fertiliser uptake of more nutrients Increased fertilizer utilization ~ plant by water soil @ greater Decreased drought stress depths - more held I in e in roots Tolerance of environmental extremes Reduces off-site pollution of surface and groundwater mycorrhizal gets & toxicof soil ecmpds out I Disease reduction  Mycorrhizae in succession mycorrhizae exports enzymes out of t cell Essential-role in developing soils Exo-enxymes make micronutrients available to biosphere enabling further succession Change soil (habitat) characteristics i dificatirreversibly so that their hosts are often excluded from the environment (acidification – conifer & forests the best example) forest diff plant diversity can lose exclude as acidificate can other plants Possible mechanisms of reduction of infection by root pathogens by mycorrhizae Production of antibiotics by fungal symbionts Mechanical barrier created by fungal mantle Chemical exudation of mycorrhizae & Protective microbial rhizosphere populations acidificat encourages specific bacteria acid-tolerant that are living in i chizosphere , shaping rhizosphere community  Relationships between phylotype diversity (Shannon index) and MAT, latitude, PET, and soil pH driven by corrhizal ~ my only acidificate forces diversity => downward influence on & able microbial diversity to exclude a lot of species a and root also living , diseases exclude many Fierer N , Jackson R B PNAS 2006;103:626-631 ©2006 by National Academy of Sciences  Past exam questions 2-methylhopanoids were proposed as biomarkers in paleobiology for: A.Anoxygenic photosynthesis B.Oxygenic photosynthesis C.Methanotrophy D.Alphaproteobacteria E.Gammaproteobacteria  Past exam questions ~ simpler form Anoxygenic photosynthesis: A.Postdates oxygenic photosynthesis and requires PhotoSystem I or II B.Postdates oxygenic photosynthesis and requires PhotoSystem I and II C.Predates oxygenic photosynthesis and requires PhotoSystem I or II D.Predates oxygenic photosynthesis and requires both PhotoSystem I and II E.Predates oxygenic photosynthesis and doesn’t require a PhotoSystem Definitys Past exam questions The energy and carbon sources for chemoheterotrophs, chemolithotrophs, photoheterotrophs and photoautotrophs are (respectively): A. Energy from light, carbon from CO2; energy from light, carbon from organic sources; energy from oxidation of inorganic compounds, carbon from CO2; energy and carbon from organic substrate B. Energy from organic substrate, carbon only from CO2; energy from oxidation of inorganic compounds, carbon from CO2; energy from light, carbon from organic sources; energy from light, carbon from CO2 C.Energy and carbon from organic substrate; energy from oxidation of inorganic compounds, carbon from CO2; energy from light, carbon from CO2; energy from light, carbon from organic sources D.Energy from oxidation of inorganic compounds, carbon from CO2; energy and carbon from organic substrate; energy from light, carbon from organic sources; energy from light, carbon from CO2 E. Energy and carbon from organic substrate; energy from oxidation of inorganic compounds, carbon from CO2; energy from light, carbon from organic sources; energy from light, carbon from CO2  Past exam questions Going from the most oxidized to the most reduced forms in the sulfur cycle can look like: SO4-2 > SO3-2 > SO2 > S2O3-2 > S > H2S more abundant & rea shorter ET ~ The reduction of SO4-2 to SO3-2, compared to the reduction of SO4-2 to H2S, is: A.More common and tightly controlled within a cell B.Less common and not as well controlled within a cell C.Less common and tightly controlled within a cell D.More common and not as well controlled within a cell E.More common and generates more ATP  Past exam questions The enzyme nitrogenase, an important part of nitrogen fixation, is responsible for the reduction of: A.NO2- to NO B.N2 to NH3 C.NH3 to NH4+ D.NO3- to NO2- E.NO to N2O  Past exam questions What type of cell do cyanobacteria use for nitrogen fixation? A.Akinetes B.Vegetative cells C.Hormogonia D.Heterocysts E.None, cyanobacteria cannot fix nitrogen