microbial ecology microbial ecology chapter 30. principles of microbial ecology, definitions ecology...
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Microbial EcologyMicrobial Ecology
Chapter 30Chapter 30
Principles of Microbial Ecology, Principles of Microbial Ecology, DefinitionsDefinitions
EcologyEcology The study of relationships among organisms and their The study of relationships among organisms and their
environment.environment.
EcosystemEcosystem Includes all of the biotic (living) components and the Includes all of the biotic (living) components and the
abiotic (physical and chemical) components of an abiotic (physical and chemical) components of an environment.environment.
BiosphereBiosphere That region of the earth that is inhibited by living That region of the earth that is inhibited by living
organisms.organisms.
DefinitionsDefinitions BiodiversityBiodiversity
Evenness of distribution of the # of species presentEvenness of distribution of the # of species present BiomassBiomass
Weight of all organisms presentWeight of all organisms present Ecological CommunityEcological Community
Comprised of a variety of different species in a given Comprised of a variety of different species in a given environment; more stable than an environment with environment; more stable than an environment with fewer organisms.fewer organisms.
Principles of Microbial EcologyPrinciples of Microbial Ecology
Principles of Microbial EcologyPrinciples of Microbial Ecology Ecological NicheEcological Niche
The role that an organism The role that an organism plays in its particular plays in its particular ecosystem as well as the ecosystem as well as the physical space it occupies.physical space it occupies.
MicroenvironmentMicroenvironment Environment immediately Environment immediately
surrounding an individual surrounding an individual cellcell
Biofilm (Fig. 30.1, pg. 766)Biofilm (Fig. 30.1, pg. 766)
Principles of Microbial EcologyPrinciples of Microbial Ecology
IndigenousIndigenous Native organismsNative organisms
NonindigenousNonindigenous Temporary inhabitantsTemporary inhabitants
Principles of Microbial EcologyPrinciples of Microbial Ecology
Nutrient AcquisitionNutrient Acquisition Primary ProducersPrimary Producers
AutotrophsAutotrophs Convert COConvert CO22 organic material organic material Photoautotrophs – plants, algae, cyanobacteriaPhotoautotrophs – plants, algae, cyanobacteria Anoxygenic phototrophsAnoxygenic phototrophs
Use sunlight for energyUse sunlight for energy ChemolithoautotrophsChemolithoautotrophs
Oxidize inorganic compounds for energyOxidize inorganic compounds for energy
Food source for consumers and decomposersFood source for consumers and decomposers
Principles of Microbial EcologyPrinciples of Microbial Ecology
ConsumersConsumers HeterotrophsHeterotrophs
Utilize organic materialUtilize organic material Food chainFood chain
Herbivores – primary consumersHerbivores – primary consumers Carnivores – secondary consumersCarnivores – secondary consumers Carnivores – tertiary consumersCarnivores – tertiary consumers
Food webFood web Interacting food chainsInteracting food chains
Principles of Microbial EcologyPrinciples of Microbial Ecology
DecomposersDecomposers HeterotrophsHeterotrophs
Primarily bacteria and fungiPrimarily bacteria and fungi Digest remains or primary producers and consumersDigest remains or primary producers and consumers
Detritus - Fresh or partially decomposed organic matterDetritus - Fresh or partially decomposed organic matter Specialize in digesting complex materialsSpecialize in digesting complex materials
MineralizationMineralization Complete breakdown of organic matter into inorganic Complete breakdown of organic matter into inorganic
molecules such as ammonia, sulfates, phosphates & COmolecules such as ammonia, sulfates, phosphates & CO22
Principles of Microbial EcologyPrinciples of Microbial Ecology
Low Nutrient EnvironmentsLow Nutrient Environments Common in natureCommon in nature
Dilute aqueous solutionsDilute aqueous solutions Lakes, rivers, streamsLakes, rivers, streams Distilled water reservoirsDistilled water reservoirs Respiratory equipmentRespiratory equipment
Principles of Microbial EcologyPrinciples of Microbial Ecology
Microbial CompetitionMicrobial Competition Ability of microbes to Ability of microbes to
compete successfully for compete successfully for a habitat generally a habitat generally related torelated to
Rate at which organism Rate at which organism multiplesmultiples
Ability to withstand Ability to withstand adverse environmental adverse environmental conditionsconditions
Principles of Microbial EcologyPrinciples of Microbial Ecology
AntagonismAntagonism Promotes biodiversity through competitionPromotes biodiversity through competition
BactericinsBactericins Proteins produced by some soil microbes that kill closely Proteins produced by some soil microbes that kill closely
related strains of bacteriarelated strains of bacteria
Principles of Microbial EcologyPrinciples of Microbial Ecology
Microbes and Environmental ChangeMicrobes and Environmental Change ExamplesExamples
Enzyme inductionEnzyme induction Inactivates mercuryInactivates mercury Only formed when mercury is presentOnly formed when mercury is present
Antibiotic resistant bacteriaAntibiotic resistant bacteria Growth and metabolism of organism can change Growth and metabolism of organism can change
environment.environment. Figure 30..4, pg. 768Figure 30..4, pg. 768
Principles of Microbial EcologyPrinciples of Microbial Ecology Microbial CommunitiesMicrobial Communities
Biofilms (discussed in ch. 4)Biofilms (discussed in ch. 4) Microbial MatMicrobial Mat
A thick, dense, highly organized structure composed of A thick, dense, highly organized structure composed of distinctive layers (fig. 30.5, pg. 769)distinctive layers (fig. 30.5, pg. 769)
Principles of Microbial EcologyPrinciples of Microbial Ecology Microbial Ecology StudiesMicrobial Ecology Studies
TraditionalTraditional CulturesCultures MicroscopyMicroscopy
Molecular TechniquesMolecular Techniques MicroscopyMicroscopy
Dyes that made are fluorescent by metabolic activitiesDyes that made are fluorescent by metabolic activities Fluorescence in situ hybridization (FISH)Fluorescence in situ hybridization (FISH)
Nucleic acid probes to observe only cells with specific Nucleic acid probes to observe only cells with specific nucleotide sequencesnucleotide sequences
Principles of Microbial EcologyPrinciples of Microbial Ecology Confocal scanning laser microscopesConfocal scanning laser microscopes
To observe sectional views of a 3-dimensional specimen To observe sectional views of a 3-dimensional specimen (biofilm)(biofilm)
Polymerase chain reaction (PCR)Polymerase chain reaction (PCR) To detect only certain organismsTo detect only certain organisms Denaturing gradient gel electrophoresis (DGGE)Denaturing gradient gel electrophoresis (DGGE) PCR & DGGE studies conform that standard cultures PCR & DGGE studies conform that standard cultures
techniques can be poor indicators of natural microbial techniques can be poor indicators of natural microbial population compositionpopulation composition
GenomicsGenomics Sequence information can apply to more than one group Sequence information can apply to more than one group
of microbesof microbes
Aquatic HabitatsAquatic Habitats
WaterWater Extremely efficient solventExtremely efficient solvent Can absorb various wavelengths of lightCan absorb various wavelengths of light
Important aspect relating to photosynthesisImportant aspect relating to photosynthesis
Aquatic HabitatsAquatic Habitats Marine EnvironmentMarine Environment
OceansOceans Cover more than 70% of earth’s surfaceCover more than 70% of earth’s surface Most abundant aquatic habitatMost abundant aquatic habitat Represent 95% of global waterRepresent 95% of global water
Fresh Water EnvironmentFresh Water Environment Lakes, RiversLakes, Rivers
Fraction of global water sourceFraction of global water source Important source of fresh waterImportant source of fresh water
Aquatic HabitatsAquatic Habitats Oceans and lakesOceans and lakes
Characteristic zones influence distribution of Characteristic zones influence distribution of microbial populationsmicrobial populations
Upper layersUpper layers Sufficient light penetration - photosynthetic microorganismsSufficient light penetration - photosynthetic microorganisms
Oligotrophic watersOligotrophic waters Nutrient poorNutrient poor Growth of photosynthetic organisms & autotrophs Growth of photosynthetic organisms & autotrophs
limited by lack of phosphate, nitrate and ironlimited by lack of phosphate, nitrate and iron
Aquatic HabitatsAquatic Habitats
Eutrophic watersEutrophic waters Nutrient rich (fig. 30.6, pg. 770)Nutrient rich (fig. 30.6, pg. 770)
Photosynthetic activities in upper layers produce organic Photosynthetic activities in upper layers produce organic compoundscompounds
Organic compounds permit growth of heterotrophs in lower Organic compounds permit growth of heterotrophs in lower layerslayers
Heterotrophs consume dissolved OHeterotrophs consume dissolved O22 during metabolism during metabolism
OO22 consumption can outpace slow rate of atmospheric O consumption can outpace slow rate of atmospheric O22
diffusion into waterdiffusion into water Can create a hypoxic environmentCan create a hypoxic environment
Aquatic HabitatsAquatic Habitats DefinitionsDefinitions
EutrophicEutrophic A body of water rich in nutrientsA body of water rich in nutrients
swamps, bog lakes, etc.swamps, bog lakes, etc.
OligotrophicOligotrophic A body of water low in nutrientsA body of water low in nutrients
EutrophicationEutrophication Natural nutrient enrichment of watersNatural nutrient enrichment of waters
Accelerated EutrophicationAccelerated Eutrophication Rapid loading of nutrientsRapid loading of nutrients
Aquatic HabitatsAquatic Habitats Potable WaterPotable Water
Safe for drinkingSafe for drinking RainwaterRainwater
DistillateDistillate contaminated by air pollutantscontaminated by air pollutants
Ground WaterGround Water aquifers, underground lakes & riversaquifers, underground lakes & rivers
Surface WatersSurface Waters Creeks, rivers, ponds, lakesCreeks, rivers, ponds, lakes
Aquatic HabitatsAquatic Habitats
Factors Affecting Presence of OrganismsFactors Affecting Presence of Organisms NutrientsNutrients
Oceans typically oligotrophicOceans typically oligotrophic Inshore areas not as stable as deep oceanInshore areas not as stable as deep ocean
Dramatically affected by run-offDramatically affected by run-off Dead zone in Gulf of Mexico every springDead zone in Gulf of Mexico every spring
Aquatic HabitatsAquatic Habitats
Oxygen (limiting factor)Oxygen (limiting factor) low solubility in water, quantities limitedlow solubility in water, quantities limited well mixed cold water ~8-9mg/lwell mixed cold water ~8-9mg/l warm water ~ 5mg/lwarm water ~ 5mg/l Deep marine water is ODeep marine water is O22 saturated due to mixing saturated due to mixing
associated with tides, currents and windassociated with tides, currents and wind Temperature - Worldwide 0Temperature - Worldwide 0ooC to ~100C to ~100ooC C
Aquatic HabitatsAquatic Habitats Freshwater environmentsFreshwater environments
Oligotrophic lakes may have anaerobic layers due to Oligotrophic lakes may have anaerobic layers due to thermal stratificationthermal stratification
EpilimmionEpilimmion Warm upper layer (25Warm upper layer (25oo-22-22ooC)C) Generally oxygen rich due to photosynthetic organismsGenerally oxygen rich due to photosynthetic organisms Generally aerobicGenerally aerobic
HypolimmionHypolimmion Colder deeper layers (~5Colder deeper layers (~5oo-4-4ooC)C) May be anaerobic due consumption of OMay be anaerobic due consumption of O22 by heterotrophs by heterotrophs Water most dense at 4Water most dense at 4ooC (39C (39ooF)F)
Thermocline (~20Thermocline (~20oo-10-10ooC)C) Zone (layer) of rapid temperature changeZone (layer) of rapid temperature change
As weather cools, water mixes oxygenating deep water As weather cools, water mixes oxygenating deep water
Aquatic HabitatsAquatic Habitats
Freshwater EnvironmentsFreshwater Environments Rivers and StreamsRivers and Streams
Usually shallow and turbulentUsually shallow and turbulent Facilitates OFacilitates O22 circulation circulation Generally aerobicGenerally aerobic Generally good sunlight penetration for photosynthesisGenerally good sunlight penetration for photosynthesis Sheathed bacteria adhere to stable structures to allow Sheathed bacteria adhere to stable structures to allow
utilization of nutrients flowing passutilization of nutrients flowing pass Examples: Examples: SphaerotilusSphaerotilus & & LeptothrixLeptothrix
Aquatic HabitatsAquatic Habitats Factors Affecting Presence of OrganismsFactors Affecting Presence of Organisms
Sunlight Penetration (Photic Zone)Sunlight Penetration (Photic Zone) depth of sunlight penetrationdepth of sunlight penetration algae & cyanobacteria algae & cyanobacteria photosynthesis provides nutrients & oxygen for other photosynthesis provides nutrients & oxygen for other
organismsorganisms pH Range 2 - 9pH Range 2 - 9
fish hypersensitive to bacterial parasites at pH 5.5, fish hypersensitive to bacterial parasites at pH 5.5, usually die if pH drops below 4.5usually die if pH drops below 4.5
Aquatic HabitatsAquatic Habitats
Specialized Aquatic EnvironmentsSpecialized Aquatic Environments Salt lakes – no outletsSalt lakes – no outlets
Water evaporates, concentrates saltWater evaporates, concentrates salt Halophilic organismsHalophilic organisms
Iron springsIron springs Contain large quantities of ferrous ionsContain large quantities of ferrous ions
Sulfur SpringsSulfur Springs Support both photosynthetic and non-photosynthetic Support both photosynthetic and non-photosynthetic
sulfur bacteriasulfur bacteria
Aquatic HabitatsAquatic Habitats Lake ZonesLake Zones
Littoral ZoneLittoral Zone Extending from shore to the limit of occupancy of rooted Extending from shore to the limit of occupancy of rooted
plantsplants Part of the photic zonePart of the photic zone
Limnetic ZoneLimnetic Zone Region of open water bounded by zone of emergent Region of open water bounded by zone of emergent
(rooted) vegetation(rooted) vegetation Benthic ZoneBenthic Zone
Sediment (regardless of depth)Sediment (regardless of depth)
Aquatic HabitatsAquatic Habitats
FreshwaterFreshwater Composition of the water reflects its sourceComposition of the water reflects its source
Stagnant ponds to free flowing rivers and lakesStagnant ponds to free flowing rivers and lakes Ground waterGround water
Normally relatively free of nutrients and toxinsNormally relatively free of nutrients and toxins Surface waterSurface water
Affected by surface runoff of materialsAffected by surface runoff of materials Organics, fertilizers, herbicides, pesticides, etc.Organics, fertilizers, herbicides, pesticides, etc.
Inshore MarineInshore Marine Affected by freshwater runoff and pollutantsAffected by freshwater runoff and pollutants
Aquatic HabitatsAquatic Habitats
Marine EnvironmentMarine Environment Factors affecting presence of miroorganismsFactors affecting presence of miroorganisms
Same Factors as Fresh Water plusSame Factors as Fresh Water plus Barometric pressure (hydrostatic pressure)Barometric pressure (hydrostatic pressure)
1 atm / 33 feet of seawater1 atm / 33 feet of seawater ocean 35,750 feet (11,000 meters) deep, hydrostatic pressure - ocean 35,750 feet (11,000 meters) deep, hydrostatic pressure -
1,083 atm1,083 atm Organisms are Organisms are barophilic (barophiles)barophilic (barophiles)
SalinitySalinity Marine averages 3.5% (fresh averages ~0.5%)Marine averages 3.5% (fresh averages ~0.5%) Organisms are Organisms are halophilic (halophiles) or halotoleranthalophilic (halophiles) or halotolerant
Aquatic HabitatsAquatic Habitats Microbial Flora Microbial Flora
Dictated by Available NutrientsDictated by Available Nutrients Bulk of Microbial MassBulk of Microbial Mass
algae, cyanobacteria & protozoaalgae, cyanobacteria & protozoa
Aerobic Chemoheterotrophic BacteriaAerobic Chemoheterotrophic Bacteria degrade organic materialsdegrade organic materials Cytophaga, CaulobacterCytophaga, Caulobacter
Chemoautotrophic BacteriaChemoautotrophic Bacteria obtain energy from aerobic oxidation of reduced inorganic obtain energy from aerobic oxidation of reduced inorganic
compoundscompounds
Aquatic HabitatsAquatic Habitats
Sulfur Oxidizers - Sulfur Oxidizers - ThiobacillusThiobacillus oxidize Hoxidize H22S dissolved in water to inorganic sulfur or sulfateS dissolved in water to inorganic sulfur or sulfate
NitrifiersNitrifiers more important in marine environmentsmore important in marine environments oxidize ammonia - nitrite - nitrateoxidize ammonia - nitrite - nitrate
Sediment Sediment Methanogenic BacteriaMethanogenic Bacteria
Foraminiferans & Radiolarians (oil and gas markers)Foraminiferans & Radiolarians (oil and gas markers)
Aquatic HabitatsAquatic Habitats Marine WatersMarine Waters
Microbial FloraMicrobial Flora Most bacteria are foundMost bacteria are found
In association with organic particles (often less than 0.1mm in In association with organic particles (often less than 0.1mm in size) near the surfacesize) near the surface
In association with skin or gut of fishIn association with skin or gut of fish
Deep ocean ventsDeep ocean vents Chemoautotrophic bacteriaChemoautotrophic bacteria
Some Some VibriosVibrios are of major importance as fish pathogens are of major importance as fish pathogens Some microbes cause human-like diseases in fishSome microbes cause human-like diseases in fish
Pasteuralla piscicidaPasteuralla piscicida (like tularemia) (like tularemia) Mycobacterium marinumMycobacterium marinum (TB like disease) (TB like disease)
Aquatic HabitatsAquatic Habitats
Major Functions of Freshwater and Marine Major Functions of Freshwater and Marine BacteriaBacteria Decompose Organic MatterDecompose Organic Matter
liberate mineral nutrientsliberate mineral nutrients Transform Essential MineralsTransform Essential Minerals
cycling them through forms other organisms can usecycling them through forms other organisms can use Release Dissolved Organic CompoundsRelease Dissolved Organic Compounds
into the food web to support growth of other organismsinto the food web to support growth of other organisms
Aquatic HabitatsAquatic Habitats Determining Microbial Flora Determining Microbial Flora
Epifluorescence CountingEpifluorescence Counting Stain with acridine orange (stains DNA)Stain with acridine orange (stains DNA) view slide under UV lightview slide under UV light
tedious and can be inaccurate, counts DNA from living and tedious and can be inaccurate, counts DNA from living and dead organismsdead organisms
Luciferin-luciferase Enzyme SystemLuciferin-luciferase Enzyme System Gives estimate of the number of viable organisms in a Gives estimate of the number of viable organisms in a
given volume of watergiven volume of water Based on carbon:ATP ratio (~250 for most microbes)Based on carbon:ATP ratio (~250 for most microbes)
Terrestrial HabitatsTerrestrial Habitats Characteristics of SoilCharacteristics of Soil
Composed ofComposed of Pulverized rocks, decaying organic material, air & waterPulverized rocks, decaying organic material, air & water
LifeLife Bacteria, fungi, algae, protozoa, worms, insects, and Bacteria, fungi, algae, protozoa, worms, insects, and
plants rootsplants roots May containMay contain
More than 4,000 different species per gram of soilMore than 4,000 different species per gram of soil More than 2 tons of bacteria and fungi per acreMore than 2 tons of bacteria and fungi per acre
Can be a rapidly and dramatically changing Can be a rapidly and dramatically changing environmentenvironment
Terrestrial HabitatsTerrestrial Habitats Soil Layers (Horizons) Soil Layers (Horizons)
Topsoil (A Horizon)Topsoil (A Horizon) Dark, nutrient-richDark, nutrient-rich Supports plant growthSupports plant growth Depth – few inches to several feetDepth – few inches to several feet
Subsoil (B Horizon)Subsoil (B Horizon) Accumulation of clays, salts & various nutrientsAccumulation of clays, salts & various nutrients
C HorizonC Horizon Partially weathered bedrockPartially weathered bedrock
R HorizonR Horizon Unweathered bedrockUnweathered bedrock
Terrestrial HabitatsTerrestrial Habitats
Microorganisms in SoilMicroorganisms in Soil Composition affected by environmental conditionsComposition affected by environmental conditions
MoistureMoisture Finely textured soils (clay) tend to be waterlogged and Finely textured soils (clay) tend to be waterlogged and
anaerobicanaerobic Sandy soils (dry quickly) tend to be aerobicSandy soils (dry quickly) tend to be aerobic
AcidityAcidity Suppresses bacterial growthSuppresses bacterial growth Fungi thrive with less competition for nutrientsFungi thrive with less competition for nutrients
Terrestrial HabitatsTerrestrial Habitats
TemperatureTemperature Mesophiles comprise the bulk of the soil bacteria, they grow Mesophiles comprise the bulk of the soil bacteria, they grow
best between 20best between 20ooC and 50C and 50ooCC Thermophiles occur in compost piles where they generate heatThermophiles occur in compost piles where they generate heat
Available NutrientsAvailable Nutrients The size of the microbial population in soil is limited by on the The size of the microbial population in soil is limited by on the
amount of organic matter availableamount of organic matter available
Terrestrial HabitatsTerrestrial Habitats Soil OrganismsSoil Organisms
ProkaryotesProkaryotes Most numerous soil inhabitantsMost numerous soil inhabitants Most common generaMost common genera
Nocardia, Arthrobacter, StreptomycesNocardia, Arthrobacter, Streptomyces StreptomycesStreptomyces
Produce conidia (dessication resistant spore)Produce conidia (dessication resistant spore) Produce geosmins (give soil musty odor)Produce geosmins (give soil musty odor) Produce many medically useful antibioticsProduce many medically useful antibiotics
Gram (+) bacteria more abundant than Gram (-) bacteria Gram (+) bacteria more abundant than Gram (-) bacteria
Terrestrial HabitatsTerrestrial Habitats Not all Soil Organisms are BeneficialNot all Soil Organisms are Beneficial
Human Bacterial PathogensHuman Bacterial Pathogens ClostridiumClostridium and and NorcardiaNorcardia
Human Fungal PathogensHuman Fungal Pathogens CoccidioidesCoccidioides, , HistoplasmaHistoplasma, and , and BlastomycesBlastomyces
Terrestrial HabitatsTerrestrial Habitats FungiFungi
Make up bulk of soil biomassMake up bulk of soil biomass Most are aerobicMost are aerobic
Usually found in top 10 cm of soilUsually found in top 10 cm of soil Crucial in decomposing plant matterCrucial in decomposing plant matter
Some are free-livingSome are free-living Some occur in symbiotic relationship with plant rootsSome occur in symbiotic relationship with plant roots
MycorrhizaeMycorrhizae
AlgaeAlgae Live mostly on or near surfaceLive mostly on or near surface
Terrestrial HabitatsTerrestrial Habitats AlgaeAlgae
Dependent on sunlight and photosynthesis to provide energy needs.Dependent on sunlight and photosynthesis to provide energy needs. Sensitive to environmental conditions of drought and low Sensitive to environmental conditions of drought and low
temperaturetemperature Major nutrient source forMajor nutrient source for
Earthworms and nematodesEarthworms and nematodes
ProtozoaProtozoa Aerobic - generally found near the surfaceAerobic - generally found near the surface Found in moist soils at a density of ~10Found in moist soils at a density of ~1044 to 10 to 1055 organisms per gram organisms per gram
of soilof soil Predators of soil bacteria and algaePredators of soil bacteria and algae
Terrestrial HabitatsTerrestrial Habitats
RhizosphereRhizosphere Zone of soil that adheres to plant rootsZone of soil that adheres to plant roots Roots cells extract organic moleculesRoots cells extract organic molecules
Sugars, amino acids and vitaminsSugars, amino acids and vitamins Fosters growth of microorganismsFosters growth of microorganisms
Gram (-) more prevalent than surrounding soilGram (-) more prevalent than surrounding soil Certain grasses – enriched with Certain grasses – enriched with AzospirillumAzospirillum species species
Biochemical Cycling & Energy FlowBiochemical Cycling & Energy Flow Biochemical CyclesBiochemical Cycles
Cyclical paths elements take as they flow through Cyclical paths elements take as they flow through living (biotic) and non-living (abiotic) components living (biotic) and non-living (abiotic) components of ecosystemof ecosystem
Fixed and limited amount of elements availableFixed and limited amount of elements available Carbon and nitrogen particularly importantCarbon and nitrogen particularly important
Stable gaseous forms COStable gaseous forms CO22 and N gas enter atmosphere and N gas enter atmosphere Global impactsGlobal impacts
Elements continually cycle in ecosystemElements continually cycle in ecosystem Energy does not, must be continually added to fuel life Energy does not, must be continually added to fuel life
Biochemical CyclingBiochemical Cycling Elements - three general purposesElements - three general purposes
Biomass productionBiomass production Incorporated into cell materialIncorporated into cell material
All organisms require nitrogen to produce amino acidsAll organisms require nitrogen to produce amino acids
Energy sourceEnergy source Reduced form of element is used to generate energy – Reduced form of element is used to generate energy –
ATPATP Energy yielding reactions oxidize the energy sourceEnergy yielding reactions oxidize the energy source
Chemoorganotrophs use reduced carbon compounds – sugar, Chemoorganotrophs use reduced carbon compounds – sugar, lipids and amino acidslipids and amino acids
Chemolithotrophs use reduced inorganic molecules – HChemolithotrophs use reduced inorganic molecules – H22S, S,
ammonia (NHammonia (NH33) and hydrogen gas (H) and hydrogen gas (H44))
Biochemical CyclingBiochemical Cycling Terminal electron acceptorTerminal electron acceptor
Electrons from energy source transferred to an oxidized Electrons from energy source transferred to an oxidized form of element during respirationform of element during respiration
Aerobic conditionsAerobic conditions OO22 is terminal electron acceptor is terminal electron acceptor
Anaerobic conditions some prokaryotes use Anaerobic conditions some prokaryotes use Nitrate (NONitrate (NO33), nitrite (NO), nitrite (NO22), sulfate (SO), sulfate (SO44)and CO)and CO22
The following pages will review cycling The following pages will review cycling processes for oxygen, carbon, nitrogen, processes for oxygen, carbon, nitrogen, phosphorus and sulfur phosphorus and sulfur
Oxygen CycleOxygen Cycle
During photosynthesis During photosynthesis cyanobacteria, algae and cyanobacteria, algae and green plants produce green plants produce oxygen from water. The oxygen from water. The oxygen is utilized via oxygen is utilized via respiration.respiration. The level of oxygen in the The level of oxygen in the
atmosphere is maintained by atmosphere is maintained by chemical reactions in the chemical reactions in the upper atmosphere, aerobic upper atmosphere, aerobic respiration and photosynthesisrespiration and photosynthesis
Carbon CycleCarbon Cycle CarbonCarbon
Carbon enters producers during photosynthesis or Carbon enters producers during photosynthesis or chemosynthesis chemosynthesis
In turn enters consumers via consumption of the producers.In turn enters consumers via consumption of the producers. Carbon returned to the atmosphere in the form of COCarbon returned to the atmosphere in the form of CO22 by by
respiration and the actions of decomposers consuming dead respiration and the actions of decomposers consuming dead or decaying waste.or decaying waste.
Oxygen has profound influence on cycleOxygen has profound influence on cycle Allows degradation of certain compoundsAllows degradation of certain compounds Helps determine the types of carbon containing gases producedHelps determine the types of carbon containing gases produced Aerobic decompositionAerobic decomposition Great deal of OC2 formed through aerobic respirationGreat deal of OC2 formed through aerobic respiration (CH(CH22O)O)nn + (O + (O22))nn CO CO22 + H + H22OO
Carbon CycleCarbon Cycle Low oxygen (wet soils, marshes, swamps, etc.)Low oxygen (wet soils, marshes, swamps, etc.)
Degradation is incompleteDegradation is incomplete Generate COGenerate CO22 and other gases and other gases
Some COSome CO22 used by methanogens (ex: used by methanogens (ex: ArchaeaArchaea) as ) as
terminal electron acceptor generating methane (CHterminal electron acceptor generating methane (CH44))
4H4H22 + CO + CO22 CH CH44 + H + H22OO Methane entering atmosphere is oxidized by UV light and Methane entering atmosphere is oxidized by UV light and
chemical ions to CO and COchemical ions to CO and CO22
Nitrogen CycleNitrogen Cycle Nitrogen (Fig. 30.11; pg. 775)Nitrogen (Fig. 30.11; pg. 775)
Most important constituent of proteins and nucleic Most important constituent of proteins and nucleic acidsacids
Consumers obtain required nitrogen from ingested Consumers obtain required nitrogen from ingested plants and animals and use it to build biomass plants and animals and use it to build biomass
Prokaryotes – diverse in use of nitrogen compoundsProkaryotes – diverse in use of nitrogen compounds Some use oxidized compounds like nitrate and nitriteSome use oxidized compounds like nitrate and nitrite Some use reduced nitrogen compounds like ammoniumSome use reduced nitrogen compounds like ammonium
All of these metabolic activities represent steps in the N All of these metabolic activities represent steps in the N cyclecycle
Nitrogen CycleNitrogen Cycle Nitrogen FixationNitrogen Fixation
Nitrogen gas reduced to form ammoniumNitrogen gas reduced to form ammonium Ammonium can be incorporated into cellular materialAmmonium can be incorporated into cellular material Atmosphere 79% NAtmosphere 79% N22
Relatively few organisms use atmospheric (gaseous) Relatively few organisms use atmospheric (gaseous) nitrogen – rely on prokaryotes to convert atmospheric nitrogen – rely on prokaryotes to convert atmospheric nitrogen into a useable formnitrogen into a useable form
NitrogenaseNitrogenase Enzyme complex that mediates nitrogen fixation and is Enzyme complex that mediates nitrogen fixation and is
readily inactivated by oxygenreadily inactivated by oxygen Nitrogen fixing aerobes must have a mechanism for Nitrogen fixing aerobes must have a mechanism for
protectionprotection
Nitrogen CycleNitrogen Cycle Nitrogen fixing prokaryotes (diazotrophs)Nitrogen fixing prokaryotes (diazotrophs)
Free livingFree living Azotobacter - cAzotobacter - chief suppliers of fixed nitrogen in grasslands & hief suppliers of fixed nitrogen in grasslands &
similar ecosystemssimilar ecosystems Cyanobacteria - most significant nitrogen fixer in aquatic Cyanobacteria - most significant nitrogen fixer in aquatic
environmentsenvironments ClostridiumClostridium spp. - dominant free-living anaerobes in soils spp. - dominant free-living anaerobes in soils
Symbiotic - significant in benefiting plant growthSymbiotic - significant in benefiting plant growth Found in association with all leguminous plants including Found in association with all leguminous plants including
alfalfa, clover, peas, beans, peanuts and vetchalfalfa, clover, peas, beans, peanuts and vetch RhizobiumRhizobium
Synthetic nitrogen compoundsSynthetic nitrogen compounds
Nitrogen CycleNitrogen Cycle
AmmonificationAmmonification The decomposition of organic nitrogen into ammoniaThe decomposition of organic nitrogen into ammonia
Occurs when extracellular proteolytic enzymes convert Occurs when extracellular proteolytic enzymes convert proteins into amino acids.proteins into amino acids.
Other enzymes then decompose amino acids into ammonium Other enzymes then decompose amino acids into ammonium (NH(NH44
++) and sulfate ions.) and sulfate ions.
Ammonium ions in turn can be oxidized to nitrite (NOAmmonium ions in turn can be oxidized to nitrite (NO22--) and ) and
nitrate (NOnitrate (NO33--) through Nitrification) through Nitrification
Nitrogen CycleNitrogen Cycle NitrificationNitrification
Oxidation of ammonium to nitrite Oxidation of ammonium to nitrite Nitrifiers - encompass two groups of chemolithotrophic bacteriaNitrifiers - encompass two groups of chemolithotrophic bacteria
Ammonia oxidizers - Ammonia oxidizers - NitrosomonasNitrosomonas - (NH - (NH44
++ to NO to NO22--) (ammonium to nitrite)) (ammonium to nitrite)
Nitrite oxidizersNitrite oxidizers NitrobacterNitrobacter & & NitrospiraNitrospira (NO (NO22
-- to NO to NO33--) (nitrite to nitrate)) (nitrite to nitrate)
Obligate aerobes – use molecular OObligate aerobes – use molecular O22 as final electron acceptor as final electron acceptor Nitrification does not occur in waterlogged soils or anaerobic Nitrification does not occur in waterlogged soils or anaerobic
aquatic environmentsaquatic environments Important because it supplies plants with nitrates which is the most Important because it supplies plants with nitrates which is the most
useable form of nitrogen for plant metabolismuseable form of nitrogen for plant metabolism
Nitrogen CycleNitrogen Cycle DenitificationDenitification
Process to convert nitrate to gaseous nitrogenProcess to convert nitrate to gaseous nitrogen Nitrate represents fully oxidized nitrogenNitrate represents fully oxidized nitrogen
PseudomonasPseudomonas spp. can use nitrate as terminal electron acceptor spp. can use nitrate as terminal electron acceptor Anaerobic respirationAnaerobic respiration
Nitrate reduced to gaseous nitrogen compounds – nitrous oxide and Nitrate reduced to gaseous nitrogen compounds – nitrous oxide and molecular nitrogenmolecular nitrogen
Release to atmosphere represents a loss of nitrogen and contributes to Release to atmosphere represents a loss of nitrogen and contributes to global warmingglobal warming
Benefit – waste water treatment processes to remove nitrateBenefit – waste water treatment processes to remove nitrate
AnammoxAnammox Brocadia anamoxidansBrocadia anamoxidans oxidizes ammonium anaerobically oxidizes ammonium anaerobically Potential benefit in waste water treatmentPotential benefit in waste water treatment
Sulfur CycleSulfur Cycle SulfurSulfur
Occurs in all living thingsOccurs in all living things Chiefly a compound of amino acids methioine & Chiefly a compound of amino acids methioine &
cysteinecysteine Key steps of cycle rely on prokaryotesKey steps of cycle rely on prokaryotes
Some use reduced form of HSome use reduced form of H22S, some elemental SS, some elemental S Others use sulfateOthers use sulfate Most plants and microbes assimulate sulfur as sulfate Most plants and microbes assimulate sulfur as sulfate
(SO(SO442-2-))
Is present in the soil (like nitrogen) chiefly as a part of Is present in the soil (like nitrogen) chiefly as a part of proteinsproteins
Sulfur CycleSulfur Cycle Hydrogen sulfide is toxic to lining thingsHydrogen sulfide is toxic to lining things
Under aerobic conditions, HUnder aerobic conditions, H22S oxidizes spontaneously to S oxidizes spontaneously to
sulfur and is then converted to sulfate (SOsulfur and is then converted to sulfate (SO442-2-) (its most readily ) (its most readily
utilized form) by sulfur bacteriautilized form) by sulfur bacteria Under anaerobic conditions sulfate-reducing bacteria reduce Under anaerobic conditions sulfate-reducing bacteria reduce
sulfate to hydrogen sulfidesulfate to hydrogen sulfide
Oxidation of hydrogen sulfide to sulfate carried out Oxidation of hydrogen sulfide to sulfate carried out principally by nonphotosynthetic autotrophs, principally by nonphotosynthetic autotrophs, Thiobacillus, ThiothrixThiobacillus, Thiothrix and and BeggiatoaBeggiatoa and less and less commonly by photosynthetic autotrophs (green and commonly by photosynthetic autotrophs (green and purple sulfur bacteria)purple sulfur bacteria)
Sulfur CycleSulfur Cycle
Sulfur ReductionSulfur Reduction Reduction of sulfate to sulfideReduction of sulfate to sulfide
Carried out by anaerobic bacteria that are capable of utilizing Carried out by anaerobic bacteria that are capable of utilizing sulfate as the final electron acceptor in their anaerobic sulfate as the final electron acceptor in their anaerobic respirationrespiration
Include Include DesulfovibrioDesulfovibrio and and DesulfomonasDesulfomonas
Phosphorus CyclePhosphorus Cycle
Involves movement of phosphorus between Involves movement of phosphorus between inorganic and organic formsinorganic and organic forms Microorganisms play three major roles in Microorganisms play three major roles in
phosphorus transformationsphosphorus transformations Mineralize organic phosphorusMineralize organic phosphorus Convert insoluble forms of inorganic phosphorus to Convert insoluble forms of inorganic phosphorus to
soluble formssoluble forms Immobilize inorganic phosphorusImmobilize inorganic phosphorus
Phosphorus CyclePhosphorus Cycle Overall Transformations of PhosphorusOverall Transformations of Phosphorus
Soil OrganismsSoil Organisms Break down organic phosphate into to inorganic Break down organic phosphate into to inorganic
phosphatesphosphates Then convert inorganic phosphates to orthophosphate Then convert inorganic phosphates to orthophosphate
(PO(PO443-3-))
Orthophosphate is water soluble and readily used by most plants Orthophosphate is water soluble and readily used by most plants and microorganismsand microorganisms
When plants & animals die decomposers convert organic When plants & animals die decomposers convert organic phosphate back into inorganic phosphatephosphate back into inorganic phosphate
Phosphorus is often the limiting nutrient in many Phosphorus is often the limiting nutrient in many environmentsenvironments