7. Microbiology - Soil Flashcards
DEFINE:
- ecosystem
- habitat
- population
- community
ECOSYSTEM:
The sum of all organisms and abiotic factors in a particular environment. An ecosystem is a dynamic complex of plants, animals, microbial communities and the nonliving surroundings, which interact as a functional unit.
HABITAT:
Portion of an ecosystem where a community could reside. Many habitats are unsuitable for plants and animals, and some habitats are almost exclusively microbial.
POPULATION
group of microorganisms of the same species residing in the same place at the same time.
ie E. coli population in GI tract
COMMUNITY
a group of populations. (typically act together)
an ____________ contains many different ______________
*habitat, ecosystem: which word goes where
- microbes account for ____% of all biomass on Earth. They are __________ on the (2) of Earth
- microbes show great WHAT and are the major players in WHAT
- ecosystem contains many habitats!
- 50% of all biomass –> are ubiquitous on surface and deep within earth
- great metabolic diversity and are major players in nutrient cycles
*their metabolic diversity shapes/dictates where microorg will thrive
The diversity of microbial species in an ecosystem is expressed in 2 ways:
- Species ____A______: DEFINE + example of high vs low
- Species _____B____: DEFINE + example of high vs low
- Microbial species ___A____ and ____B_____ are a function WHAT
- species richness: total number of dif species present
- species abundance: proportion of each species in an ecosystem
ex.: high richness, low abundance: lots of diversity but each species has low abundance –> happens in usually very permissive environments (ie GI tract)
ex.: low richness, high abundance: all cells look the same/from same species
- species richness and abundance are a function of the kinds and amounts of nutrients available in a given habitat!
define:
GUILDS
NICHE
- give examples of guilds (6)
- what are the energy inputs? (3)
GUILDS:
Metabolically related microbial populations. Sets of guilds form microbial communities that interact with macroorganisms and abiotic factors in the ecosystem.
NICHE:
Habitat shared by a guild. Supplies nutrients as well as conditions for growth.
- oxygenic phototrophs (light)
- aerobic respiration (O2)
- denitrifying bacteria (NO3-)
- sulfate reducers (SO4^2-)
- fermenters (lots of org molecules)
- anoxygenic phototrophs (light and H2S)
*guilds can use energy inputs produced by other guilds! ie aerobic respiration guild uses organic material from oxygenic phototroph guild
ENERGY INPUTS:
- sunlight
- organic carbon
- reduced inorganic substances.
- growth of microbes depends on (2)
- what defines the niche for each microbe? (2 ish)
- what is the prime niche?
- define microenvironment
- give an example of a microenvironment
- resources and growth conditions
- difference in type and quantity of resources and physiochemical conditions of a habitat define niche of each microbe
- for each organism, there exists at least one niche in which that organism is most successful (prime niche)
MICROENVIRONMENT:
- immediate environmental surroundings of a microbial cell or group of cell
- ie Soil particles contain many microenvironments OR grains of sand = microenvironment: grains of sand and water: gradient of O2 and CO2 and sand
- ____________ conditions in a microenvironment are subject to rapid change, both ________ and __________
- Resources in natural environments are highly variable and many microbes in nature face a ________________existence (____________ is important)
- are growth rates of microbes in nature higher or lower than growth rates defined in laboratory?
- what (2) occur between microbes in natural systems and btw microbes and higher organisms
- what are 3 relationship types btw other organisms?
- Physiochemical conditions in a microenvironment are subject to rapid change, both spatially and temporally.
- face a feast-or-famine existence (storage is important).
- Growth rates of microbes in nature are usually WELL BELOW maximum growth rates defined in the laboratory.
- Competition and cooperation occur between microbes in natural systems and between microbes and higher organisms.
- PARASITISM: one member in the relationship is harmed and the other benefits.
- MUTUALISM: both species benefit.
- COMMENSALISM: one species benefits and the other is neither harmed nor helped.
BIOGEOCHEMISTRY
- define
- what does a biogeochemical cycle define?
- typically proceed by what reactions?
- microbes play critical roles in energy transformation and biogeochemical processes –> give examples of 3 cycles
- the study of biologically mediated chemical transformations.
- defines the transformations of a key elements by biological
and chemical agents. - Typically proceed by oxidation–reduction reactions
- carbon cycle (CO2 to organic compounds to CO2)
- nitrogen cycle (N2, NH3, NO2, NO3-, NO2-, NO, N2O, N2) (nitrification and denitrification)
- sulfur cycle (H2S, SO4^2-, H2S)
- define soil
- soil can be divided into which 2 broad groups? describe
- soils are composed of (4)
SOIL: The loose outer material of Earth’s surface, distinct from bedrock.
a) MINERAL soils: derived from rock weathering and other inorganic materials
- ie sand! from rocks breaking down
b) ORGANIC soils: derived from sedimentation in bogs and marshes (organic material)
- ie leaves from trees that fall on ground)
1) Inorganic mineral matter (~40% of soil volume)
2) Organic matter (~5%)
3) Air and water (~50%)
4) Living organisms
what are the 5 “layers” of soil? + describe
- what is another name for “layers”?
horizons!
1) ORGANIC HORIZON (O)
- undecomposed organic material
- leaves, dead rabbit…
2) SURFACE HORIZON (A)
- rich in organic material
- high microbial activity: lots of chemoorganotrops and phototrophs
- decomposition of organic material (actively being decomposed!)
3) SUBSOIL (B)
- rich in humus (dead plant material that is resistant to decomposition. keep water and nutrients in soil)
- minerals
- lower microbial activity
4) SUBSTRATUM (C)
5) BEDROCK (R)
both 4 and 5:
- rich in minerals
- poor in organic material
- microbial activity very low: chemolitotrophs
- most microbial growth takes place on WHICH PART of soil particles?
- ____A_____ is the most important factor influencing microbial activity in ___WHICH PART_____ soils –> 3 types of soil: describe their relationship with ___A_____
- vs what is the most important factor in __________ environments
- on surfaces of soil particles!
WATER! - SAND (big): water drains quickly: so very dry
- SILT (medium): retains water to the right extent –> dries a bit but enough water to promote microbial growth
- CLAY (small): water retained too well –> blocks diffusion of fas –> soil becomes anoxic/anaerobic metabolism
NUTRIENT availability! in subsurface environments
MICROORGANISMS IN SOIL:
- what type of orgs (4) can you find in the top few cms (which horizon?)?
- the most common type of microorg (out of the 4 listed in Q1) are largely responsible for (4)
DEFINE:
- rhizosphere
- mycorrhizae
- Bacteria/Archaea: up to 2.5 x 10^2
- Fungi: upto2x10^5
- Protozoa: up to 3 x 10^4
- Algae: up to 2.5 x 10^4
Bacteria and archaea are largely responsible for:
- production of the humus
- release of minerals from soil particles (production of acids (bc fermentation) from organic compounds solubilize the minerals)
- cycling of nutrients (C, N, S)
- nitrogen fixation.
- RHIZOSPHERE: soil that surrounds plant roots and receive plant secretions (plant secretions give nutrients to microorgs)
- MYCCORHIZAE: association of fungi with plant roots.
- who can fix nitrogen?
- does it take a lot of energy to fix N2? why or why not?
- why is nitrogen fixation one of the most important microbial processes on earth? (2 ish)
- 2 types ish of nitrogen fixers
- reaction catalyzed by WHAT? requires what? (2) what is lost in the process?
*source of electron? - enzyme inhibited by what? why is that a problem?
- what is the final product of N fixation?
- only certain prokaryotes!
- yes! a lot of E bc N2 in atmosphere has a triple bond!
- bc use N2 from atmosphere and convert it to smtg that can be used for metabolic properties in organisms! (ie amino acids)
*in the absence of fertilizers, other organisms are dependent on nitrogen fixers
free living (cyanobacteria)
- can live where there’s no N bc can use N2 from air
VS symbotic (ie rhizobium)
- give aa to org and org give them sugar/energy so they can fix N2
- catalyzed by nitrogenase complex (metal cofactors): 16 ATP and 8 e- are required, 2 are lost as H2 in the process
*source of electron = NADH! - dinitrogenase reductase is INHIBITED by presence of oxygen –> problematic bc aerobic respiration is the best way to make ATP and need lots of ATP to fix nitrogen
- ammonia! used to produce aa
FREE-LIVING NITROGEN FIXERS
- widespread where?
- produce WHAT that can be used by WHAT
- give 3 examples + describe if they are aerobes or anaerobes + characteristics
- widespread in soil, require a soil rich in organic matter to provide energy for
nitrogen fixation. - Produce ammonia that can be used by plants (NH3, dissolves in water to produce ammonium NH4)
1) CLOSTRIDIUM: strict anaerobe. chemoheterotrophs
2) AZOTOBACTER: strict aerobe + chemoheterotrophs. The enzyme (dinitrogenase reductase) is protected by a very high rate of O2
consumption, which keeps the intracellular environment anaerobic (ie very high metabolic activity: no accumulation of O2 bc as soon as O2 comes, reduced to H2O
3) CYANOBACTERIA: only some species are capable of N2 fixation. MAJOR nitrogen- fixing organisms in nature. Cyanobacteria produce energy by oxygenic photosynthesis, oxygen is produced in the cell –> oxygenic and anoxygenic photosynthesis
CYANOBACTERIA
- live as single cells or colonies?
- free-living or symbiotic N fixers?
- Nitrogen fixation occurs where? describe
- the specialized cell (name?) have what morphotology?
- specialized cells live close to which cells? HOW?
- colonies! (picture: filaments)
- free-living!
- occurs in specialized anaerobic cells (heterocysts) –> lack photosystem II (so no oxygenic photosynthesis –> would be bad bc produces O2) –> photosystem I produces ATP by cyclic phosphorylation
- heterocysts have a thick cell wall that stops diffusion of O2
- REGULAR CELLS provide the heterocysts with CHO (sucrose) from which NADPH (source of e-) is produced in the pentose phosphate pathways
*heterocyst use NH3 (ammonia) to produce aa glutamine (2 N groups) from glutamate (1 N group) –> aa are used by the regular cells
SYMBIOTIC NITROGEN FIXERS
- what is one of the most important symbioses known?
- examples?
- what is the best-known nitrogen-fixing bacteria engaging in these symbioses?
- mutualistic relationship btw leguminous plants and N-fixing bacteria
- ex of legumes: soybeans, clover, alfalfa, beans, peas
- Rhizobium!
SYMBIOTIC NITROGEN FIXERS:
- colonization of legume roots by N-fixing bacteria leads to formation of WHAT?
- explain its formation (7 steps)
- of root nodules that fix nitrogen!
1) When nitrogen is limited, plants produce chemicals that attracts nitrogen-fixing bacteria
2) Recognition and attachment of bacterium to root hairs
3) excretion of nod factors by the bacterium –> “proposal/key” to enter the root
4) Bacterial invasion of the root hair –> highly regulated pathway
5) Travel to the main root via the infection thread (tube composed of cellulose)
6) Formation of bacteroid (version of Rhizobium that will fix N) state within plant cell (swollen and misshapen bacteria - fix N2) –> give N compound to plant and take sugar from plant
7) Continued plant and bacterial division, forming the mature root nodule
NODULE FORMATION:
- O2 levels are controlled by what?
- what are bacteroids?
- bacteroids are a _________ state and cannot be shed in the _____________
- the nodules contain regular Rhizobium cells that serve to do what?
- how does plant create perfect niche for N fixers to live?
- by O2-binding protein leghemoglobin, produced by plant cells
- version of bacteria that will fix Nitrogen
- terminal state and cannot be shed in the environment
- serve to inoculate the environment
Plant creates perfect niche for N. fixers to live:
1) plant produces sugars through photosynthesis –> sugars become organic acids which are taken in by the bacteria (succinate, malate, fumarate) –> intermediates of TCA cycle –> brings e- to ETC, proton motive force makes ATP –> ATP powers nitrogenase to convert N2 to NH3 –> NH3 used to produce glutamine and asparagine (which bacteriod gives to the plant)
2) bacteria does aerobic respiration –> PLANT controls level of O2 bacteria receives through Leghemoglobin enzyme
IMPLICATION OF N FIXATION FOR AGRICULTURE:
- most plants will use N compounds produced by WHO or WHO during ________________
- nitrate is more/less soluble than ammonium and is more/less readily available to plants
- what reactions do nitrifying bacteria do? need O2?
- what happens when the soil is poorly drained and becomes waterlogged?
- anaerobic conditions promote WHAT reduction –> consequence?
- by free-living Nitrogen fixers OR by other organisms during ammonification (ie urine)
- more soluble than ammonium and more readily available in plants
- NH3 –> NO2- –> NO3- –> O2 as e- acceptor! but no O2 in clay bc too much water and anoxic
- soil becomes anaerobic which promotes denitrification! NO3 –> NO2- –> NO –> N2O –> N2
- anaerobic conditions promote sulfur and sulfate reduction which produce H2S (toxic for plants bc inhibit PSII for plants)
