Microbial ecology Flashcards
What is an ecosystem?
A group of micro habitats
What is a micro habitat?
Group of communities
What is a community?
A group of guilds
What is a guild?
Group of metabolically similar microbial population
What is a population?
Group of organisms of the same species living in the same place at the same time
List the levels of microbial complexity, with most complex first, the levels of microbial associations
- Ecosystem
- Micro habitat
- Community
- Guild
- Populat
Why is aquatic microbio important?
Aquatic environment covers 69% of the surface of the earth
What are the layers of soil? How do levels of nutrient differ?
- Topsoil- consist of organic horizon and then A horizon underneath= these have the most organic, nutrients but the least due to dead leaves and animals/microbes
- Subsoil- B horizon on top and C horizon on the bottom
- Bedrock on the bottom- consist of R horizon only, has the most inorganic nutrients but least organic nutrients and microbes
What is humus?
The organic material of the top soil, dead, alive and decaying organic matter such as plants
What is the rhizosphere?
The soil that is directly surrounding the plant roots
What is loam?
A soil that is a mix of sand,silt, and humus
What is inorganic material of soil composed of?
Composed of rock, which is broken down into small particles of stand,silt, and clay
What are the 2 categories of factors that affect the microbial abundance/population in soil?
Abiotic: non-living
Biotic: living
What are the biotic factors that affect microbial abundance/population in the terrestrial environment?
Biotic: living components
- producers(autotrophs) e.g., plants
- Consumers(heterotrophs) e.g. animals
- decomposes(detritivores) e.g., fungi and bacteria
All of these affect microbial population/ abundance
What are the abiotic factors of microbial abundance/population in the terrestrial environment?
Abiotic: non-living
Water availability and oxygen abundance (closely related)
- pH
- temperature
- nutrients
All of these affect microbial population/ abundance
What are the soil types and how do they differ?
Peaty soil- high water content(acidic)
Sand- easily loses water and nutrients
Clay - good water storage but loses nutrients
Silt- retains water longer as well as nutrients
What gives soil it’s characteristics?
Antinomyces
What is the most common micronutrient in soil?
Bacteria- 10^8-10^9.(g of soil ) Biomass =400-500
How abundant is antinomyces in soil?
10^7 - 10^8 (g of soil ) biomass= 400-500
How abundant is algae in soil?
10^4 - 10^5 (g of soil) biomass= 1-50(g/m^2)
How abundant are Protozoa in soil?
10^3-10^4 (microorganisms per gram of soil) biomass= varies (g/m^2)
How abundant are nematodes in soil?
10^2-10^3 (g of microorganisms) biomass= varies
What are the abiotic factors of microbial abundance in the aquatic ecosystems?
- sunlight, is it penetrating the water, by how much?
- dissolved oxygen
- salinity
- flow
- temperature
- depth of the water
- nutrients
What are the biotic factors that affect microbial abundance in aquatic environments?
Producers- autotrophs like algae and Cyanobacteria
Consumers- heterotrophs e.g., fish
Decomposers
Different water types
Differentiated by salinity/salt content
Fresh= 0.05% NaCl
- lentic -slow moving (lakes and ponds)/these have slow turnover of nutrients and oxygen replenishing than lotic, lotic is moving which helps replenish
- lytic- fast moving (rivers and streams) /paths to moving
- wetlands-saturated soil
Marine- 3.5% NaCl
Define freshwater
Typically low in salt (0.05% salt)
Exceptions: dead sea(30% salt)
Contrast the types of freshwater
Moving water(rivers) -high elevations
- cold
- high oxygen
- fish(trout), streamlined plants
Standing or slow moving water(lakes)
-lower elevations
- warmer
- less oxygen
- fish, amphibians, cattails, rushes
What are estuaries?
The area where fresh water(rivers/streams) meets ocean water such as bays, lagoons, harbors, inlets or sounds- they are a transitional aquatic ecosystem
Brackish- less salty than see but is not fresh water
Rich in sediments
More salt conc. increase the heterotrophic microbes
Why do mangroves grow in eustaries?
Grow in brackish, estuaries due to brackish environment
How much of the world is covered by marine water?
69% of earths surface is salt water covered
What is the salt content of marine water?
33-37 g/L
Give examples of marine waters?
Include nearshore systems(costal regions) , salt marshes, mudflats, Seagrass meadows, mangroves, rocky intertidal systems and coral reefs
They also extend outwards from the coast to include from the coast to include offshore systems, such as the surface ocean, pelagic ocean waters, the deep sea, oceanic hydrothermal vents and the sea floor
What microbes can be found in ground water/spring water?
Ground water/ spring water (low nutrient level) - micrococcus, pseudomonas, serratia, flavobacterium, chromobacterium, achromobacter
What microbes can be found in rivers?
Rivers (via contact with, nutrients nit enough for them to be naturally occurring) : Bacillus, actinomyces, streptomyces, fungi(polyphagus, penicllium, aspergillus)
Algae(Microcystis, nostoc)
-sewage pollutants: E. Coli, E. faecalis, P.vulgaris, clostridium spp.
What types of microbes are found in eustaries?
Eustaries: psuedomonas, flavobacterium, vibrio, other enterics
What is eutrophication?
Enrichment of water by nutrient salts that causes structural changes to the ecosystem such as:
- increased production of algae and aquatic plants
- depletion of fish species
- general deterioration of water quality and other effects that reduce and preclude use
- alters the dynamics of plant: animal: bacterial population
- is a form of water pollution
Give the types of eutrophication
Natural: lake/river ages with time
Anthropogenic/cultural: humans release nutrients(short, within decades)
What is the eutrophication process?
- Excess nitrates/artificial fertilizers/ phosphates
- Excess growth of plants/algae
- Dissolved oxygen not enough to cope with anaerobic decomposition
- NH3, H2S, PH3-poison water
- Aquatic species die
- Additional species die
- Additional anaerobic decay
- Lake devoid of life=eutrophication
What are the effects of eutrophication?
- decreased water translucency
- development of anoxic conditions(decreased oxygen levels)
- increased algal blooms
- loss of habitat (e.g., sea grass beds)
- changes in dominant biota(plankton and macrophytes) -> changes in fish composition
- changes in species diversity
- changes in the value of water
How does pH change with eutrophication?
pH: CO2 content, organic /inorganic acids
pH below 5 and above 9 are harmful to fish, limit algal and invertebrate growth
How does dissolved oxygen content differ as a result of eutrophication?
Dissolved O2: varies with temp. and pressure
-increased temp/pressure =decreased O2
- below 4- 5 mg/ml most invertebrates die
- game fish require 8-15 mg/ml
How does eutrophication affect water chemistry if CO2?
Aerobic/anaerobic decomposition organic matter
- carbonic acid
- normal= less than 1 mg/ml
How does eutrophication affect ammonia/ammonium water chemistry?
Ammonia(NH3+/NH4+)- decomposition of animal/plant protein.
Important plant nutrient
- less than 1mg/ml(natural water bodies )
-increases stimulate Alga growth/toxic to fish
How does eutrophication affect nitrates/nitrites in water chemistry?
Decomposition with inter conversion by some bacteria
-naturally, rarely increase above 10mg/ml, often less than 1mg/ml
Increase algal blooms
What are the affects of eutrophication on phosphates in water chemistry?
Released during decomposition
-natural = less than 0.01 mg/ml
-high levels stimulate algal blooms
How can water quality be measured?
Biological oxygen demand
This measures dissolved oxygen consumed by microbes during aerobic oxidation of substrates (organic matter/ammonia) in water
- Organics + O2 —> CO2 + H2O (heterotrophic bacteria)
- NH3 + 2O2—> NO3- + H2O + H+ (N2 reducing bacteria )
What are sources of pollution that may affect BOD?
Decaying plants, animal waste and human activity
Explain how BOD can be used to assess water quality
BOD level in mg/liter
1-2 = very good water quality: there will not be much organic matter present in the water supply
3-5 = fair: moderately clean
6-9= poor: somewhat polluted-usually indicates that organic matter present and microorganisms are decomposing that waste
100 or more= very poor-very polluted contains organic matter
Explain BOD(biological oxygen demand ) as a test
BOD aka BOD5 is a day process: [BOD]= [ DO]final- [DO] initial
DO= dissolved oxygen
Represents oxygen demand of aerobic microorganisms
Sample (along with prepared dilution water) placed into an air-tight bottle (300 ml volume)
- incubate @ 20 +/- 1 degree Celsius for 5 days
- DO measured initially, and again after 5 days
- bottle size, incubation temperature are all specified
Why do we use 5 days for BOD?
The reason we use 5 days for BOD is because there may also have eutrophic bacteria, and so heterotrophic and euterotroph both bacteria may use oxygen after 5 days, which makes the results more accurate
What are the problems of increased BOD?
- eutrophication
- algal blooms
- fish death
Rivers/streams: replenish BOD quickly
Lakes don’t replenish BOD as efficiently
Contrast COD and BOD
Not related to BOD
Much quicker than BOD
Typically higher values than BOD
The most popular alternative to BOD as it only takes hours
Explain COD
Importance: characterizing water bodies, sewage, industrial wastes and treatment plant effluents
It’s an independent measure of organic matter
Amount of O2 required to chemically oxidase biodegradable /non-biodegradable organic matter
Uses a strong oxidizing agent( Potassium dichromate)
-defined as the amount of a specified oxidant that reacts with the sample under controlled conditions
How do we test for COD?
- Organic and oxidizable inorganic substances in the sample are oxidized by potassium dichromate in 50% sulfric acid solution at reflux temperature
- Silver sulphate is used as a catalyst and mercuric sulphate is added to remove chloride interference
- Excess dichromate is titrated with standard ferrous ammonium sulphate, using orthophenanthroline ferrous complex as an indicator
- Typically higher values than BOD
Explain water as a vehicle for disease
Potential source: infectious agents and chemical intoxicants
Potable: fit for human consumption
- approximately 30 outbreaks per year (USA)
- Legionella (most common - 57%), other bacteria, viruses(Norovirus), parasites(Giarda)
Recreational- ponds, streams, lakes, public swimming baths
- approximately 20 outbreaks per year USA.
- Cryptosporidium most common
What is waste water?
Microbiological haven
Untreated domestic wastewater (Washing from a washing machine, flushing, sewage, etc.)
Can have organisms found in the body, or even intest8nal tract
How can wastewater be treated?
It can go to a wastewater plant based on the type of water present
Can be released to environment or reused
Goal: reduced organic/inorganic material
-Expressed: reduction of BOD (amount dissolved oxygen consumed by microbes to completely oxidize all organic /inorganic matter)
What are the types of wastewater?
Sewage= effluent contaminatedwith faeces(human or animal )
Domestic wastewater = sewage + grey water
Industrial wastewater= discharges from various processes and insustries
How many stages are in wastewater treatment?
3 stages
Discuss the primary stage in wastewater treatment
Raw sewage enters
- physical separation:
- sewage is stored, oils and microbes rise to the top, layers are removed and remaining liquid is taken to the secondary stage
- sewage sludge is treated via sludge digestion
- grates/screens remove large, floating suspended solids and grit 50-70% suspended solids removed
Polluted water:
-soluble/suspended organic matter
Reduce 30-35% BOD
What are the types of secondary wastewater treatments?
Secondary aerobic treatment and secondary anaerobic treatment
Discuss secondary anaerobic wastewater treatment
Typically used on high BOD wastewater
- used when Containing high insoluble organic matter
- food/dairy industry
- digestive and fermentative process
- large tanks: sludge digesters/bioreactor
- Products can be used to heat/run the plant
Discuss secondary aerobic wastewater treatment
Typically used on low organic levels
- used to treat non-industrial wastewater
- uses fixed film systems where water passes through them
Common processes:
-activated sludge
-trickling filter or rotating biological contractors
Explain the activated-sludge method:
Used in secondary aerobic wastewater treatment
Wastewater fed continuously fed into aerated tank
Decomposing bacteria mixed in sewage, sewage mixed with air to facilitate decomposition
-microbes (bacteria, Protozoa, fungi) form “flocs”, degrade organics by oxidation
NB: not complete oxidation of organic material
BOD reduced: up to 95%
Discuss advanced/tertiary wastewater treatment
Final stage, increases effluent quality before discharged to receiving environment (sea, river, lake ground, etc.)
Relatively expensive
Variety of possible tertiary methods, include:
-filtration: removes residual suspended material, I.e., activated carbon for toxin removal
-Lagooning: settlement and further biological improvement through storage filter-feeding invertebrates (Daphnia and Rotifera) remove fine particulates
Nutrient removal (nitrogen and phosphorus )
- Nitrogen removal: activated sludge process(anoxic tanks)
- enhanced biological Phosphorus removal: by chemical precipitation or polyphosphate accumulating organisms (PAOs)-these have a high nutrient value for fertilizers
Why is water a public health issue?
There are a variety of waterborne pathogens which are harmful to humans
We can be exposed by a variety of ways, ingestion, inspiration and expiration, direct contact
How do we asses for water quality ?
The WHO has routine methods to assess for potable, recreational and wastewater
Methods to identify potentially harmful microbes
- indicator test/organisms: coliforms
- facultative anaerobes
- gram negative
- rod-shaped
- non-sporulation bacteria
- ferment lactose + gas, within 46 hrs at 35 degrees Celsius
How can coliforms be tested for?
Coliforms are part of our GI tract (e coli, Enterobacter or klebseinna) we can use these
2 procedures:
most-probable number (MPN)
Membrane filtration (MF)
MPN- we use tubes to which we dilute water sample in and observe gas production and plate samples to agar plate and count the number of colonies
Assumption: coliforms presence= fecal contamination (remember fecal coliforms is a subgroup of coliforms)
Standards: Sade drinking water act
Routine testing: potable and recreational water
Explain the membrane filtration method
100ml sample through sterile membrane filter(0.45mm)
-removes bacteria
Filter placed on selective/differential media
-eosin-methylene blue (EMB) medium
MI agar (4-methylumbelliferyl—D-galactopyranoside (MUGal) and a chromogen indoxyl - -D- glucuronide (IBDG) (Fluorogen reacts with galactosidase + chromogen reacts with glucuronidase )
Exposure to UV light (366 nm, the coliforms are fluoresce it will indicate the coliforms)
What are the WHO guidelines?
E. Coli or thermotolerant coliforms bacteria must not be detectable in any 100 ml sample directly intended fir drinking, entering to a distribution system or treated water within a distribution system
Differentiate the stages of eutrophication according to nutrient build up
Oligotrophy-least nutrients
Mesotrophy -middle of build up
Eutrophication and hypereutrophy-lots of build up
Differentiate natural and anthropogenic eutrophication
Natural eutrophication -thousands of years to grow oligotrophy to mesotrophy. Hundreds of years to go from mesotrophy to eutrophication and hypereutrophy
Anthropogenic- oligotrophy to eutrophication and hypertrophy over decades
Due to urban runoff, industrial discharge, fertilizers and pesticides, erosion and sedimentation, no point source pollution from cottages
