microbial ecology microbial ecology chapter 30. principles of microbial ecology, definitions ecology...

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)


IndigenousIndigenous Native organismsNative organisms

NonindigenousNonindigenous Temporary inhabitantsTemporary inhabitants


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


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


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


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


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


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


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


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


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


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


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


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)


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


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


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)


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


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


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

microbial ecology microbial ecology chapter 30. principles of microbial ecology, definitions ecology...

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microbial ecologymicrobes

microbial ecologychapter

microbial mata thick

given environment

fewer organisms

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