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Microbial ecology The study of the interactions of microorganisms with each other and their nonliving physical environment Environmental microbiology relates to the broad-scale effects microorganisms and their activities have on the planet Microbial interactions Some interactions can be beneficial for both participants (mutualism and cooperation) Some interactions benefit one participant but do not affect the other (commensalism) Some interactions benefit one participant at the expense of the other (predation and parasitism) Mutualism An obligatory relationship in which the mutualist and the host are metabolically dependent on each other Examples include the tube worm-bacterial relationship and the rumen ecosystem The tube worm-bacterial relationship Tube worm hemoglobin transports H2S to bacteria Bacteria fix CO2 using reducing power of H2S Tube worm supplied with organic molecules by bacteria The rumen ecosystem Ruminants are herbivorous animals (cattle, deer, sheep, etc.) Require microorganisms to degrade cellulose Anaerobic process produces CO2, H2 and CH4 Cooperation Both organisms benefit but the interaction is not obligatory Organisms can exist separately if required nutrients are supplied in the growth environment Commensalism A relationship in which one symbiont (the commensal) benefits while the other (the host) is not harmed The commensal feeds on substances captured or ingested by the host Commensals can become pathogens under certain circumstances Predation Relationship in which a predator attacks or engulfs a prey Predator may be larger or smaller than the prey Predation may have beneficial results for the prey (protection or enhancement of virulence) Parasitism One organism benefits and the other is harmed The line between parasitism and predation is hard to define (parasitism may eventually lead to predation) Parasitism usually is a long-term relationship whereas predation tends to end abruptly Amensalism One organism produces a compound that has a negative effect on another organism Production of antibiotics by certain bacteria is an example of amensalism Competition Microorganisms can compete for a physical location or a limiting nutrient 2 possible outcomes 1. One organism may outcompete the other 2. Both organisms may co-exist at lower levels Biogeochemical cycling Cycling of nutrients in the environment involving both biological and chemical processes Nutrients are transformed (often by oxidation-reduction reactions) and cycled Biogeochemical cycling Influence of oxygen on organic matter decomposition Oxidized products will accumulate when decomposition occurs under aerobic conditions Reduced products will accumulate when decomposition occurs under anaerobic conditions Mineralization The release of excess nitrogen and other minerals into the environment as a result of the decomposition of organic matter The carbon cycle Carbon exists in reduced forms (CH4 and organic matter) and oxidized forms (CO and CO2) Photosynthetic organisms fix carbon (reduced form) The carbon cycle Respiration produces oxidized form CO2 Methane is generated under anaerobic conditions (eventually oxidized to CO2) The sulfur cycle H2S can serve as an electron donor for photosynthetic bacteria H2S(ide) Sº, SO32-(ite), SO42-(ate) Different oxidized forms of sulfur diffuse into a reduced environment Other bacteria perform dissimilatory and assimilatory reductions The nitrogen cycle Requires several different processes including: Nitrification Denitrification Nitrogen assimilation Nitrogen fixation Nitrification Involves the aerobic oxidation of ammonium ion to nitrite and then to nitrate NH4+ NO2- NO3Can occur anaerobically by coupling oxidation of NH4+ with reduction of NO2- to produces nitrogen gas (N2) Commercial process referred to as the anamox process (anoxic ammonium oxidation) Denitrification Use of nitrate as an electron acceptor in anaerobic respiration (dissimilatory reduction) NO3- NO2 - N2O N2 Nitrogen assimilation NH4+ can be directly incorporated into organic matter NO3- assimilation is much more energetically expensive Nitrogen fixation Carried out by both aerobic and anaerobic prokaryotes Cannot be carried out by eukaryotes Nitrogen fixation Involves a sequence of reduction steps that require major expenditures of energy Produces ammonia which is immediately incorporated into organic matter The iron cycle Cycling between ferrous (2+) and ferric (3+) forms of iron Iron reduction occurs under anaerobic conditions Other cycles Manganese and other metals cycle between oxidized and reduced forms Cycling of different elements may be metabolically linked (e.g. Desulfobulbus propionicus oxidation of sulfate is linked to the reduction of manganese) The physical environment Microorganisms occupy specific environments in nature referred to as microenvironments Fluxes and gradients of nutrients, reductants and oxidants and waste products will influence the rate of growth and create a unique niche The physical environment Biofilms and microbial mats are microenvironments or niches created by microorganisms Microorganisms and ecosystems Microorganisms play two complementary roles in ecosystems Primary production - the synthesis of organic matter from CO2 and other inorganic molecules Microorganisms and ecosystems Consumption and decomposition - the breakdown of organic matter with the release of energy and inorganic molecules Extremophiles Some microorganisms have evolved to survive in extreme environments extremophiles Extreme environments include: High sodium concentrations High pressure Extreme acidic or alkaline conditions High temperature Microorganisms existing in such environments must possess unique adaptations Extremophiles Methods used in microbial ecology Isolation of organisms from environmental samples Standard media does not support the growth of many microorganisms PCR amplification and sequencing of extracted DNA Extracted DNA may not be representative of living microorganisms Methods used in microbial ecology Direct observation - slides or EM grids placed in location, recovered and observed Methods used in microbial ecology Microbial activity and turnover rates at which nutrients are incorporated into organic matter can give an indication of the metabolic activity of a microbial population Often make use of radioactive isotopes Methods used in microbial ecology Recovery or addition of individual microorganisms - individual microorganism may be removed and DNA analyzed after PCR Methods used in microbial ecology Microorganisms with reporter genes may be placed into environments to monitor specific changes (e.g. oxygen availability or UV radiation exposure)