Ecology: study of organisms in their natural and managed environmentsBiogeochemical CyclesMMG 301 Dr. Frank DazzoMicrobial Ecology I: General Concepts & BiogeochemistryEcology: study of organisms in their natural and managed environmentsHierarchy of ecological order for microorganisms:• Individual cells of the same type multiply to form populations• Metabolically related populations constitute groups called guilds• Mixtures of different guilds conducting complementaryphysiological processes interact to form microbial communities• Microbial communities then interact with communities ofmacroorganisms and the physicochemical environment to definethe entire ecosystembaThe science of Microbial Ecology has 2 broad objectives:1. To understand the biodiversity of microorganisms in nature andhow different guilds interact in microbial communities2. To measure the behavior and activities of microorganisms innatural environments and monitor their effects on ecosystemsA few important concepts:1. Much is known about the activities of only a small proportion ofthe microbial world: there are many microorganisms left to bediscovered and this is a major goal of microbial ecology.2. Each type of microorganism has at least one ecological niche, i.e.,a function that it can successfully compete for in a habitat.3. Countless microbial niches exist in the biosphere and are in largepart responsible for the great metabolic diversity and biodiversityof microorganisms on Earth.4. Since microbes are small, their habitats are small, and theirecological niches can also cover small spatial scales. Despitetheir small size, microbes nevertheless affect ecosystems ongreater scales, including global-level effects, e.g., biogeochemicalcycling of C, N, S needed to sustain life on Earth.5. The concept of microenvironment becomes important inunderstanding how microbes actually live and metabolize withintheir natural habitats.6. Such microenvironments commonly undergo profound changes inphysicochemical characteristics, resulting in gradients.7. Example: respiratory consumption of oxygen by largepopulations of aerobic microbes on biofilms within the humanmouth creates anoxic microenvironments that allow anaerobicmicrobes to produce various volatile fermentation waste productsthat cause “bad breath” odor.Microbes participate in both positive (+) and negative (-) interactions: Description and microbial example:Bidirectional; some reciprocal benefitaccrues to both partners. Examples:lichen symbiosis: fungus (mycobiont)and algae or cyanobacteria phycobiont);rumen-microbe symbiosis (cow andanaerobic bacteria), nitrogen-fixingRhizobium-legume root nodule symbiosisUnidirectional: one partner benefits whilethe other is neither benefited nor harmed.Examples: many interactions in microbialbiofilms and indigenous normal microfloraof the intact human bodyPredator engulfs, attacks and kills the prey.Examples: density-dependent predation ofbacteria by protozoans in aquatic and soilhabitats.Parasite infects host, who is harmed.Examples; bacteriophage infecting bacteria,human infectious diseases.Unidirectional release of an inhibitorycompound by one organisms that harms asusceptible microorganism. Example:production of antibiotics or bacteriocins.The demand for a food resourceexceeds the supply: a majorcause of restricted microbialproductivity in soil and marineecosystems (limitation ofenergy-yielding organic carbon).Biogeochemical Cycles• Biogeochemical cycling involves both biological and chemicalprocesses that result in the cyclic interconversion of certain keyelements (e.g., C, N, S, others) needed to sustain productive lifeprocesses in the biosphere.• The most important role of microorganisms in the biosphere istheir participation in the biogeochemical cycling of nutrients.• Life as we know it would ultimately cease to exist without thiscontribution of microorganisms to biogeochemical cycling.Bacteria are essential for life on Earth• These cycles are driven by microbial metabolism that transformsnutrients, often by oxidation-reduction reactions, therebychanging their physical and chemical characteristics.• All biogeochemical cycles are interlinked and these nutrienttransformations have global-level impacts.ReducedOxidizedPresence of O2 significantly influences biogeochemical cycling,as illustrated by its influence on organic matter decompositon:• Microorganisms form different products when decomposingcomplex organic matter. Oxidized products accumulateaerobically, while reduced products accumulate anaerobically.• These reactions also illustrate commensalistic transformations,where the waste products from one microbial group are used assubstrates by other microbial groups (syntrophy).Biogeochemical Carbon Cycle:1. CO2 fixation by photoautotrophs and chemoautotrophs.2. Methanogenesis from inorganic (CO2 + H2) or organic matter,involves various archaea methanogens (Methanobacterium,others). Global CH4 production ∼∼∼∼1011 kg / yr (∼∼∼∼ 85% biogenic)AerobicAnaerobic122Biogeochemical Nitrogen cycle:Examples of bacteria involved in box numbered steps:1. Nitrogen fixation N2 →→→→ NH3 (aerobic) free-living: Azotobacter,cyanobacteria; symbiotic: Rhizobium, Frankia. (anaerobic):Clostridium perfringens, purple & green sulfur phototrophs.2. NH3 assimilation (aerobic & anaerobic) many organisms3. Ammonification (organic N→→→→ NH3) many organisms4. Nitrosification (aerobic), Nitrosomonas5. Nitrification (aerobic), Nitrobacter6. Nitrate assimilation (NO3-→→→→ NH3 →→→→ amino acids) many organisms7. Dissimilatory nitrate reduction (NO3-→→→→ NO2-) many organisms8. Denitrification (NO3- →→→→ →→→→ →→→→ →→→→ N2) Bacillus, Pseudomonas, others1111378263245Biogeochemical Sulfur Cycle:1. Sulfur oxidation (S°°°°→→→→ SO3-2→→→→ SO4-2): (aerobic) manychemolithotrophs; (anaerobic) purple & green photoautotrophs2. Assimilatory sulfate reduction (SO4-2→→→→ organic S) many microbes3. Desulfurylation (organic S decomposition →→→→ H2S) many microbes4. H2S oxidation (H2S →→→→ S°°°°) Aerobic: Thiobacillus, Beggiotoa(chemolithotrophs). Anaerobic: Chlorobium, Chromatium(anoxigenic photoautotrophs)5. Dissimilatory sulfate and sulfite reduction (solid purple arrows)SO4-2 or SO3-2 →→→→ H2S: Desulfovibrio and related organisms6. Elemental sulfur reduction
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