Microbial Ecology Chapter 30

Principles of Microbial Ecology, Definitions The study of relationships among organisms and their environment. Ecosystem Includes all of the biotic (living) components and the abiotic (physical and chemical) components of an environment. Biosphere That region of the earth that is inhibited by living organisms.

Principles of Microbial Ecology Definitions Biodiversity Evenness of distribution of the # of species present Biomass Weight of all organisms present Ecological Community Comprised of a variety of different species in a given environment; more stable than an environment with fewer organisms.

Principles of Microbial Ecology Ecological Niche The role that an organism plays in its particular ecosystem as well as the physical space it occupies. Microenvironment Environment immediately surrounding an individual cell Biofilm (Fig. 30.1, pg. 766)

Principles of Microbial Ecology Indigenous Native organisms Nonindigenous Temporary inhabitants

Principles of Microbial Ecology Nutrient Acquisition Primary Producers Autotrophs Convert CO2 organic material Photoautotrophs – plants, algae, cyanobacteria Anoxygenic phototrophs Use sunlight for energy Chemolithoautotrophs Oxidize inorganic compounds for energy Food source for consumers and decomposers

Principles of Microbial Ecology Consumers Heterotrophs Utilize organic material Food chain Herbivores – primary consumers Carnivores – secondary consumers Carnivores – tertiary consumers Food web Interacting food chains

Principles of Microbial Ecology Decomposers Heterotrophs Primarily bacteria and fungi Digest remains or primary producers and consumers Detritus - Fresh or partially decomposed organic matter Specialize in digesting complex materials Mineralization Complete breakdown of organic matter into inorganic molecules such as ammonia, sulfates, phosphates & CO2

Principles of Microbial Ecology Low Nutrient Environments Common in nature Dilute aqueous solutions Lakes, rivers, streams Distilled water reservoirs Respiratory equipment

Principles of Microbial Ecology Microbial Competition Ability of microbes to compete successfully for a habitat generally related to Rate at which organism multiples Ability to withstand adverse environmental conditions

Principles of Microbial Ecology Antagonism Promotes biodiversity through competition Bactericins Proteins produced by some soil microbes that kill closely related strains of bacteria

Principles of Microbial Ecology Microbes and Environmental Change Examples Enzyme induction Inactivates mercury Only formed when mercury is present Antibiotic resistant bacteria Growth and metabolism of organism can change environment. Figure 30..4, pg. 768

Principles of Microbial Ecology Microbial Communities Biofilms (discussed in ch. 4) Microbial Mat A thick, dense, highly organized structure composed of distinctive layers (fig. 30.5, pg. 769)

Principles of Microbial Ecology Microbial Ecology Studies Traditional Cultures Microscopy Molecular Techniques Dyes that made are fluorescent by metabolic activities Fluorescence in situ hybridization (FISH) Nucleic acid probes to observe only cells with specific nucleotide sequences

Principles of Microbial Ecology Confocal scanning laser microscopes To observe sectional views of a 3-dimensional specimen (biofilm) Polymerase chain reaction (PCR) To detect only certain organisms Denaturing gradient gel electrophoresis (DGGE) PCR & DGGE studies conform that standard cultures techniques can be poor indicators of natural microbial population composition Genomics Sequence information can apply to more than one group of microbes

Aquatic Habitats Water Extremely efficient solvent Can absorb various wavelengths of light Important aspect relating to photosynthesis

Aquatic Habitats Marine Environment Fresh Water Environment Oceans Cover more than 70% of earth’s surface Most abundant aquatic habitat Represent 95% of global water Fresh Water Environment Lakes, Rivers Fraction of global water source Important source of fresh water

Aquatic Habitats Oceans and lakes Characteristic zones influence distribution of microbial populations Upper layers Sufficient light penetration - photosynthetic microorganisms Oligotrophic waters Nutrient poor Growth of photosynthetic organisms & autotrophs limited by lack of phosphate, nitrate and iron

Aquatic Habitats Eutrophic waters Nutrient rich (fig. 30.6, pg. 770) Photosynthetic activities in upper layers produce organic compounds Organic compounds permit growth of heterotrophs in lower layers Heterotrophs consume dissolved O2 during metabolism O2 consumption can outpace slow rate of atmospheric O2 diffusion into water Can create a hypoxic environment

Aquatic Habitats Definitions Eutrophic Oligotrophic Eutrophication A body of water rich in nutrients swamps, bog lakes, etc. Oligotrophic A body of water low in nutrients Eutrophication Natural nutrient enrichment of waters Accelerated Eutrophication Rapid loading of nutrients

Aquatic Habitats Potable Water Rainwater Ground Water Surface Waters Safe for drinking Rainwater Distillate contaminated by air pollutants Ground Water aquifers, underground lakes & rivers Surface Waters Creeks, rivers, ponds, lakes

Aquatic Habitats Factors Affecting Presence of Organisms Nutrients Oceans typically oligotrophic Inshore areas not as stable as deep ocean Dramatically affected by run-off Dead zone in Gulf of Mexico every spring

Aquatic Habitats Oxygen (limiting factor) low solubility in water, quantities limited well mixed cold water ~8-9mg/l warm water ~ 5mg/l Deep marine water is O2 saturated due to mixing associated with tides, currents and wind Temperature - Worldwide 0oC to ~100oC

Aquatic Habitats Freshwater environments Oligotrophic lakes may have anaerobic layers due to thermal stratification Epilimmion Warm upper layer (25o-22oC) Generally oxygen rich due to photosynthetic organisms Generally aerobic Hypolimmion Colder deeper layers (~5o-4oC) May be anaerobic due consumption of O2 by heterotrophs Water most dense at 4oC (39oF) Thermocline (~20o-10oC) Zone (layer) of rapid temperature change As weather cools, water mixes oxygenating deep water

Aquatic Habitats Freshwater Environments Rivers and Streams Usually shallow and turbulent Facilitates O2 circulation Generally aerobic Generally good sunlight penetration for photosynthesis Sheathed bacteria adhere to stable structures to allow utilization of nutrients flowing pass Examples: Sphaerotilus & Leptothrix

Aquatic Habitats Factors Affecting Presence of Organisms Sunlight Penetration (Photic Zone) depth of sunlight penetration algae & cyanobacteria photosynthesis provides nutrients & oxygen for other organisms pH Range 2 - 9 fish hypersensitive to bacterial parasites at pH 5.5, usually die if pH drops below 4.5

Aquatic Habitats Specialized Aquatic Environments Salt lakes – no outlets Water evaporates, concentrates salt Halophilic organisms Iron springs Contain large quantities of ferrous ions Sulfur Springs Support both photosynthetic and non-photosynthetic sulfur bacteria

Aquatic Habitats Lake Zones Littoral Zone Limnetic Zone Benthic Zone Extending from shore to the limit of occupancy of rooted plants Part of the photic zone Limnetic Zone Region of open water bounded by zone of emergent (rooted) vegetation Benthic Zone Sediment (regardless of depth)

Aquatic Habitats Freshwater Composition of the water reflects its source Stagnant ponds to free flowing rivers and lakes Ground water Normally relatively free of nutrients and toxins Surface water Affected by surface runoff of materials Organics, fertilizers, herbicides, pesticides, etc. Inshore Marine Affected by freshwater runoff and pollutants

Aquatic Habitats Marine Environment Factors affecting presence of miroorganisms Same Factors as Fresh Water plus Barometric pressure (hydrostatic pressure) 1 atm / 33 feet of seawater ocean 35,750 feet (11,000 meters) deep, hydrostatic pressure - 1,083 atm Organisms are barophilic (barophiles) Salinity Marine averages 3.5% (fresh averages ~0.5%) Organisms are halophilic (halophiles) or halotolerant

Aquatic Habitats Microbial Flora Dictated by Available Nutrients Bulk of Microbial Mass algae, cyanobacteria & protozoa Aerobic Chemoheterotrophic Bacteria degrade organic materials Cytophaga, Caulobacter Chemoautotrophic Bacteria obtain energy from aerobic oxidation of reduced inorganic compounds

Aquatic Habitats Sediment Sulfur Oxidizers - Thiobacillus Nitrifiers oxidize H2S dissolved in water to inorganic sulfur or sulfate Nitrifiers more important in marine environments oxidize ammonia - nitrite - nitrate Sediment Methanogenic Bacteria Foraminiferans & Radiolarians (oil and gas markers)

Aquatic Habitats Marine Waters Microbial Flora Most bacteria are found In association with organic particles (often less than 0.1mm in size) near the surface In association with skin or gut of fish Deep ocean vents Chemoautotrophic bacteria Some Vibrios are of major importance as fish pathogens Some microbes cause human-like diseases in fish Pasteuralla piscicida (like tularemia) Mycobacterium marinum (TB like disease)

Aquatic Habitats Major Functions of Freshwater and Marine Bacteria Decompose Organic Matter liberate mineral nutrients Transform Essential Minerals cycling them through forms other organisms can use Release Dissolved Organic Compounds into the food web to support growth of other organisms

Aquatic Habitats Determining Microbial Flora Epifluorescence Counting Stain with acridine orange (stains DNA) view slide under UV light tedious and can be inaccurate, counts DNA from living and dead organisms Luciferin-luciferase Enzyme System Gives estimate of the number of viable organisms in a given volume of water Based on carbon:ATP ratio (~250 for most microbes)

Terrestrial Habitats Characteristics of Soil Composed of Life Pulverized rocks, decaying organic material, air & water Life Bacteria, fungi, algae, protozoa, worms, insects, and plants roots May contain More than 4,000 different species per gram of soil More than 2 tons of bacteria and fungi per acre Can be a rapidly and dramatically changing environment

Terrestrial Habitats Soil Layers (Horizons) Topsoil (A Horizon) Dark, nutrient-rich Supports plant growth Depth – few inches to several feet Subsoil (B Horizon) Accumulation of clays, salts & various nutrients C Horizon Partially weathered bedrock R Horizon Unweathered bedrock

Terrestrial Habitats Microorganisms in Soil Composition affected by environmental conditions Moisture Finely textured soils (clay) tend to be waterlogged and anaerobic Sandy soils (dry quickly) tend to be aerobic Acidity Suppresses bacterial growth Fungi thrive with less competition for nutrients

Terrestrial Habitats Temperature Available Nutrients Mesophiles comprise the bulk of the soil bacteria, they grow best between 20oC and 50oC Thermophiles occur in compost piles where they generate heat Available Nutrients The size of the microbial population in soil is limited by on the amount of organic matter available

Terrestrial Habitats Soil Organisms Prokaryotes Most numerous soil inhabitants Most common genera Nocardia, Arthrobacter, Streptomyces Streptomyces Produce conidia (dessication resistant spore) Produce geosmins (give soil musty odor) Produce many medically useful antibiotics Gram (+) bacteria more abundant than Gram (-) bacteria

Terrestrial Habitats Not all Soil Organisms are Beneficial Human Bacterial Pathogens Clostridium and Norcardia Human Fungal Pathogens Coccidioides, Histoplasma, and Blastomyces

Terrestrial Habitats Fungi Algae Make up bulk of soil biomass Most are aerobic Usually found in top 10 cm of soil Crucial in decomposing plant matter Some are free-living Some occur in symbiotic relationship with plant roots Mycorrhizae Algae Live mostly on or near surface

Terrestrial Habitats Algae Protozoa Dependent on sunlight and photosynthesis to provide energy needs. Sensitive to environmental conditions of drought and low temperature Major nutrient source for Earthworms and nematodes Protozoa Aerobic - generally found near the surface Found in moist soils at a density of ~104 to 105 organisms per gram of soil Predators of soil bacteria and algae

Terrestrial Habitats Rhizosphere Zone of soil that adheres to plant roots Roots cells extract organic molecules Sugars, amino acids and vitamins Fosters growth of microorganisms Gram (-) more prevalent than surrounding soil Certain grasses – enriched with Azospirillum species

Biochemical Cycling & Energy Flow Biochemical Cycles Cyclical paths elements take as they flow through living (biotic) and non-living (abiotic) components of ecosystem Fixed and limited amount of elements available Carbon and nitrogen particularly important Stable gaseous forms CO2 and N gas enter atmosphere Global impacts Elements continually cycle in ecosystem Energy does not, must be continually added to fuel life

Biochemical Cycling Elements - three general purposes Biomass production Incorporated into cell material All organisms require nitrogen to produce amino acids Energy source Reduced form of element is used to generate energy – ATP Energy yielding reactions oxidize the energy source Chemoorganotrophs use reduced carbon compounds – sugar, lipids and amino acids Chemolithotrophs use reduced inorganic molecules – H2S, ammonia (NH3) and hydrogen gas (H4)

Biochemical Cycling Terminal electron acceptor Electrons from energy source transferred to an oxidized form of element during respiration Aerobic conditions O2 is terminal electron acceptor Anaerobic conditions some prokaryotes use Nitrate (NO3), nitrite (NO2), sulfate (SO4)and CO2 The following pages will review cycling processes for oxygen, carbon, nitrogen, phosphorus and sulfur

Oxygen Cycle During photosynthesis cyanobacteria, algae and green plants produce oxygen from water. The oxygen is utilized via respiration. The level of oxygen in the atmosphere is maintained by chemical reactions in the upper atmosphere, aerobic respiration and photosynthesis

Carbon Cycle Carbon Carbon enters producers during photosynthesis or chemosynthesis In turn enters consumers via consumption of the producers. Carbon returned to the atmosphere in the form of CO2 by respiration and the actions of decomposers consuming dead or decaying waste. Oxygen has profound influence on cycle Allows degradation of certain compounds Helps determine the types of carbon containing gases produced Aerobic decomposition Great deal of OC2 formed through aerobic respiration (CH2O)n + (O2)n CO2 + H2O

Carbon Cycle Low oxygen (wet soils, marshes, swamps, etc.) Degradation is incomplete Generate CO2 and other gases Some CO2 used by methanogens (ex: Archaea) as terminal electron acceptor generating methane (CH4) 4H2 + CO2 CH4 + H2O Methane entering atmosphere is oxidized by UV light and chemical ions to CO and CO2

Nitrogen Cycle Nitrogen (Fig. 30.11; pg. 775) Most important constituent of proteins and nucleic acids Consumers obtain required nitrogen from ingested plants and animals and use it to build biomass Prokaryotes – diverse in use of nitrogen compounds Some use oxidized compounds like nitrate and nitrite Some use reduced nitrogen compounds like ammonium All of these metabolic activities represent steps in the N cycle

Nitrogen Cycle Nitrogen Fixation Nitrogen gas reduced to form ammonium Ammonium can be incorporated into cellular material Atmosphere 79% N2 Relatively few organisms use atmospheric (gaseous) nitrogen – rely on prokaryotes to convert atmospheric nitrogen into a useable form Nitrogenase Enzyme complex that mediates nitrogen fixation and is readily inactivated by oxygen Nitrogen fixing aerobes must have a mechanism for protection

Nitrogen Cycle Nitrogen fixing prokaryotes (diazotrophs) Free living Azotobacter - chief suppliers of fixed nitrogen in grasslands & similar ecosystems Cyanobacteria - most significant nitrogen fixer in aquatic environments Clostridium spp. - dominant free-living anaerobes in soils Symbiotic - significant in benefiting plant growth Found in association with all leguminous plants including alfalfa, clover, peas, beans, peanuts and vetch Rhizobium Synthetic nitrogen compounds

Nitrogen Cycle Ammonification The decomposition of organic nitrogen into ammonia Occurs when extracellular proteolytic enzymes convert proteins into amino acids. Other enzymes then decompose amino acids into ammonium (NH4+) and sulfate ions. Ammonium ions in turn can be oxidized to nitrite (NO2-) and nitrate (NO3-) through Nitrification

Nitrogen Cycle Nitrification Oxidation of ammonium to nitrite Nitrifiers - encompass two groups of chemolithotrophic bacteria Ammonia oxidizers - Nitrosomonas - (NH4+ to NO2-) (ammonium to nitrite) Nitrite oxidizers Nitrobacter & Nitrospira (NO2- to NO3-) (nitrite to nitrate) Obligate aerobes – use molecular O2 as final electron acceptor Nitrification does not occur in waterlogged soils or anaerobic aquatic environments Important because it supplies plants with nitrates which is the most useable form of nitrogen for plant metabolism

Nitrogen Cycle Denitification Anammox Process to convert nitrate to gaseous nitrogen Nitrate represents fully oxidized nitrogen Pseudomonas spp. can use nitrate as terminal electron acceptor Anaerobic respiration Nitrate reduced to gaseous nitrogen compounds – nitrous oxide and molecular nitrogen Release to atmosphere represents a loss of nitrogen and contributes to global warming Benefit – waste water treatment processes to remove nitrate Anammox Brocadia anamoxidans oxidizes ammonium anaerobically Potential benefit in waste water treatment

Sulfur Cycle Sulfur Occurs in all living things Chiefly a compound of amino acids methioine & cysteine Key steps of cycle rely on prokaryotes Some use reduced form of H2S, some elemental S Others use sulfate Most plants and microbes assimulate sulfur as sulfate (SO42-) Is present in the soil (like nitrogen) chiefly as a part of proteins

Sulfur Cycle Hydrogen sulfide is toxic to lining things Under aerobic conditions, H2S oxidizes spontaneously to sulfur and is then converted to sulfate (SO42-) (its most readily utilized form) by sulfur bacteria Under anaerobic conditions sulfate-reducing bacteria reduce sulfate to hydrogen sulfide Oxidation of hydrogen sulfide to sulfate carried out principally by nonphotosynthetic autotrophs, Thiobacillus, Thiothrix and Beggiatoa and less commonly by photosynthetic autotrophs (green and purple sulfur bacteria)

Sulfur Cycle Sulfur Reduction Reduction of sulfate to sulfide Carried out by anaerobic bacteria that are capable of utilizing sulfate as the final electron acceptor in their anaerobic respiration Include Desulfovibrio and Desulfomonas

Phosphorus Cycle Involves movement of phosphorus between inorganic and organic forms Microorganisms play three major roles in phosphorus transformations Mineralize organic phosphorus Convert insoluble forms of inorganic phosphorus to soluble forms Immobilize inorganic phosphorus

Phosphorus Cycle Overall Transformations of Phosphorus Soil Organisms Break down organic phosphate into to inorganic phosphates Then convert inorganic phosphates to orthophosphate (PO43-) Orthophosphate is water soluble and readily used by most plants and microorganisms When plants & animals die decomposers convert organic phosphate back into inorganic phosphate Phosphorus is often the limiting nutrient in many environments