Microbes and the Environment

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Microbes and the Environment
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Microbial Ecology
Definition the study of the behavior and
activities of microorganisms in their natural
environment
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Environments

• Two scales
• ________________ environment
• ________________ environment

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Example Termite Hindgut
anoxic
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Example Termite Hindgut
Model system (1) symbiosis microbe and
relationship with host (2) ecology relationship
with other microbes and the environment
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Mutualism

• some reciprocal benefit to both partners
• an ________________ relationship
• often partners cannot live separately
• mutualist and host are metabolically dependent on
  each other
• termite provides food for protozoan
• protozoan digests cellulose in wood particles,
  providing nutrients for termite

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Example Termite Hindgut
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Foundations of Microbial Ecology

• ________________
• relationships among organisms in an ecosystem
• populations
• assemblages of similar organisms
• communities
• mixtures of different populations
• ecosystems
• self-regulating biological communities and their
  physical environment

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Another example lichens

• mycobiont
• fungal partner
• provides water, minerals, sheltered environment
  and firm substratum for growth
• phycobiont________________
• alga or cyanobacterium
• provides organic carbon and oxygen

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Roles of microbes

• primary producers
• decomposers (often carry out mineralization)
• food source for other organisms
• biogeochemical cycling
• change amounts of materials in soluble and
  gaseous form
• produce inhibitory compounds that limit microbial
  activity or limit survival and functioning of
  plants and animals
• impact function of plants and animals through
  symbiotic interactions

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Microorganism Movement between Ecosystems

• movement occurs in many ways
• in soil transported by windstorms
• in rivers containing eroded materials, sewage
  plant effluents and urban wastes
• by plants and animals
• waste products
• dead organisms
• intentional or accidental transport by human
  activity

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Fate of transported microbes

• usually do not survive well in new environment
• often unable to compete effectively with
  indigenous organisms
• nonculturable microorganisms
• alive, but unable to be cultured using techniques
  normally used for that microbe

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Cycles in the Environment
Water Elements (carbon, nitrogen, sulfur etc)
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Hydrologic Cycle
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Carbon Cycle
CH4
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Carbon Chemistry

• Carbon Fixation
• Convert CO2 to organic matter (example
  photosynthesis)
• Mineralization
• Convert organic matter to inorganic counterparts
  (CO2, CH4 etc..)

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Microbes and Agriculture

• The Nitrogen Cycle

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Sulfur Cycle
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Winogradsky Column
demonstrates gradients often observed in aquatic
environ- ments and under- lying sediments
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Cycles in the Environment
Water Elements (carbon, nitrogen, sulfur etc)
Metals Iron, Manganese
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Acid Mine Drainage
Sulfide oxidation by oxygen to sulfate (initiator
reaction)
4FeS2(pyrite) 14O2 4H2O  ---gt  4Fe2 8SO42-
8H Fe2 ---gt   Fe3 FeS2(pyrite) 14Fe3
8H2O   ---gt   15Fe2 2SO42- 16H   
Sulfide oxidation by Thiobacillus ferrooxidans
(propagation cycle)
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Magnetospirillum magnetotacticum
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Microorganisms and Metal Toxicity

• microorganisms can modify toxicity of metals
• differing sensitivities of multicellular
  organisms and microorganisms to metals are basis
  of many antiseptic procedures

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Lets consider some environemnts
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Marine Environments

• contain 97 of Earths water
• often called high pressure refrigerator
• temperatures near 3C
• pressures up to 1,000 atm

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Nutrient cycling

• most occurs in upper 300 meters
• organic matter falls
• only 1 of photosynthetically derived materials
  reach deep-sea floor unaltered
• conditions in deep sea are oligotrophic

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Sea ice environments

• interfaces between ice an sea water
• pockets of salt brine

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Freshwater Environments

• lakes, rivers and streams
• provide microbial environments that are very
  different from marine environments

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Lakes
oligotrophic
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eutrophic nutrient rich
epilimnion warm, aerobic
hypolimnion cold, anaerobic
thermocline zone of rapid temperature decrease

• usually little mixing of layers
• in spring and fall layers turn over and mixing
  occurs

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Microorganisms in Freshwater Ice

• e.g., Antarctic lakes
• important habitats for microorganisms
• microbial growth occurs during summer when some
  of ice melts

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Waters and Disease Transmission

• numerous diseases are waterborne

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Waterborne Pathogens and Water Purification

• water purification
• critical link in controlling waterborne disease

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sedimentation basin
settling basins
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Problem microbes

• not consistently removed by coagulation, rapid
  sand filtration, and disinfection processes
• Giardia lamblia
• backpackers disease
• slow sand filters effectively remove Giardia
  cysts
• Cryptosporidium
• small protozoan, with oocysts that escape usual
  purification schemes
• Cyclosporan
• protozoan that causes diarrhea
• viruses
• up to 99.9 are removed by usual purification
  schemes, but this not considered sufficient
  protection

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Sanitary Analysis of Waters

• based on detecting ________________
• indicate fecal contamination of water supplies
• indicate possible contamination by human pathogens

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Ideal indicator organism

• suitable for analysis of all types of water
• present whenever enteric pathogens are present
• survives longer than hardiest enteric pathogen
• does not reproduce in contaminated water
• detected by highly specific test
• test easy to do and sensitive
• harmless to humans
• its level in water reflects degree of fecal
  pollution

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Two commonly used indicators

• coliforms
• fecal streptococci
• increasingly used to test brackish and marine
  water

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Coliforms

• facultative anaerobic, ________________,
  nonsporing, rod-shaped bacteria that ferment
  lactose with gas formation within 48 hours at 35C

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MPN most probable number
Figure 29.22
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Wastewater Treatment

• decreases organic matter and number of
  microorganisms in human waste-impacted water
• has lead to major reduction in spread of pathogens

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Eutrophication

• Process whereby water bodies receive excess
  nutrients that stimulate excessive algal growth
  called an algal bloom
• results from addition of nutrients to water
• e.g., addition of phosphorus to oligotrophic
  water can stimulate cyanobacterial and algal
  growth
• e.g., addition of nutrients to eutrophied lakes
  can cause blooms
• stimulates growth of plants, algae, and bacteria
• can occur slowly (over centuries) or very rapidly
• This reduces dissolved oxygen in the water (when
  dead plant material decomposes)

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Oxygen Sag Curve
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back to some environments
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Soil as an Environment for Microorganisms

• dominated by inorganic geological material, which
  is modified by organisms to form soils
• typically not water saturated, so O2 readily
  available
• can contain mini aquatic environments

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Microorganisms in the Soil Environment
peds aggregated soil particles
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Microbial populations in soils

• numbers can be very high
• only small portion have been cultured
• microbes are constantly being added to soil
• most do not survive
• make important contributions to biogeochemical
  cycling
• gram-positive bacteria are important members of
  soil communities

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Deserts Soils

• desert crusts
• microbial communities on soil surface
• cyanobacteria and associated commensals
• help retain water from infrequent rainfalls
• are fragile and easily damaged

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Mycorrhizae

• fungus-root associations
• can increase plants competitiveness
• e.g., increase availability of nutrients
• e.g., aid in water uptake
• can influence plant communities
• sharing of nutrients
• mycorrhizosphere
• region around mycorrhizal fungi having increased
  microbial populations due to release of materials
  by fungus

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Agrobacterium

• induce tumor formation in plants
• controlled by Ti (Ri) plasmid
• used by biotechnologists to modify plant DNA

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Fungi and Bacteria as Plant Pathogens

• fungal pathogens cause diseases called rusts,
  powdery mildews, and smuts
• bacterial pathogens also cause a variety of plant
  diseases

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Viruses

• wide range of viruses infect plants
• e.g., tobacco mosaic virus (TMV)
• one virus of note infects fungus that causes
  chestnut blight
• may be used to control fungal pathogen

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Understanding Microbial Diversity in the Soil

• estimated that only 1-10 of microscopically
  observable microbes have been cultured
• molecular techniques are allowing microbiologists
  to detect and identify noncultured microbes

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Methods in Microbial Ecology

• microscopy
• chemical and biochemical analyses
• culturing techniques
• many microorganisms cannot be cultured
• molecular techniques
• hybridization
• PCR
• microarrays
• arrays of gene probes that allow detection of
  ssRNA from mixed populations