Soil Flashcards
What is the 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 non-living surroundings, which interact as a functional unit
What is a habitat
Portion of an ecosystem where a community could reside. An ecosystem contains many different habitats
Microbes account for ___ of all biomass on Earth
50%
What is the population
A group of microorganisms of the same species residing in the same place at the same time
What is a community
A group of populations
Two ways how microbial diversity is expressed in a ecosystem
- Species richness
- Species abundance
What is species richness
The total number of different species present
What is species abundance
The proportion of each species in an ecosystem
Microbial species richness and abundance depend on
Kinds and amounts of nutrients available in a given habitat
As well as temperature, salinity, pH, water availability, etc.
What are guilds
Metabolically related microbial populations. Sets of guilds form microbial communities that interact with mcroorganisms and abiotic factors in the ecosystem
What is the niche
Habitat shared by a guild. Supplies nutrients as well as conditions for growth.
They way in which an organism fits into an ecological community
kinds of energy inputs
Sunlight, organic carbon, reduced inorganic substances
If we consider a lake as one ecosystem what kind of bacteria we can find there
Community one, where photic zone is:
Oxygenic phototrophs
Community 2: Oxic zone. Aerobes and faculatative aerobes
Community 3: a bunch of different bacteria->denitrifying, sulfate-reducing,fermentative, methanogens,acetogens
The deeper into the ground the bacteria goes, ___ (energy yield)
Less energy yield the bacteria has
What is determining the niche for each microbe
Difference in the type and quantity of resources and the physiochemical conditions of a habitat
What is the prime niche
A niche ( at least one for each organism) in which that organism is most successful
What is the microenvironment
-The immediate environmental surroundings of a microbial cell or group of cells
Soil particle contain different ___
Microenvironments
Inside there is no oxygen , comparing to the outside
What are the top 3 important things affecting microbial growth in the soil and the least important
Top 3: soil pH,organic carbon quality and quantity, soil(o2) and redox status
Least: predation and viral lysis
What conditions change rapidly with time and place in the soil
physiochemical
The difference between growth rates in the lab and in the nature
Growth rates of microbes in nature are usually well below maximum growth rates defined in the lab
What is happening between microbes in natural systems and between microbes and higher organisms
Competition and cooperation
What is parasitism
One member in the relationship is harmed and the other benefits
What is mutualism
Both species benefit (symbiosis)
What is commensalism
One species benefits and the other is neither harmed nor helped
What is biogeochemistry
The study of biologically mediated chemical transformations
What does biogeochemistry define
the transformations of a key elements by biological and chemical agents
Biogeochemistry agents usually proceed through
Oxidation-reduction reactions
How do microbes play critical role in energy transformation and biogeochemical processes
-Carbon cycle
Nitrogen cycle
Sulfur cycle
Through oxidation-reduction reactions
What is the soil
The loose outer material of Earth’s surface, distinct from bedrock (solid rock)
What two groups soil can be divided into
Mineral soils
Organic soils
What is the mineral soil
Derived from rock weathering (breaking down of rocks) and other inorganic materials
What are organic soils
Derived from sedimentation in bogs and marshes
Soils are composed of
- Inorganic mineral matter (40% by volume)
- Organic matter (5)
- Air and water (50)
- Living organisms
What is humus
Dead plant material that is resistant to decomposition.
Keep water and nutrients in the soil. Good for soil fertility
Different soil horizons and its characterization
- O horizon.Very top. Layer of undecomposed plant material
- A horizon. Dark color, high in organic matter; a lot of nutrients in this environment; plants and large numbers of microorganims grow here; high microbial activity
-B horizon.Subsoil (minerals, humus, and so on, leached from soil surface accumulate here; little organic matter; microbial activity detectable but lower than at A horizon)
C horizon. Soil base (develops
directly from underlying
bedrock; microbial activity
generally very low)
How do you figure out what microorganisms live in the soil
- Extract soil microbial community DNA
- Isolate, sequence and analyze 16s rRNA genes
What organisms dominate soil environements
Bacteria, in specific proteobacteria
Where does the most of microbial growth takes place
On the surfaces of soil particles
What is the most important factor influencing microbial activity in surface soils
Availability of water
What is the most important component in subsurface environments
Nutrient availability
Different soil particles and what is their size
Sand( the largest 0.1-2mm)
Silt(0,002-0.1mm)
Clay( very small)
What is the best particle in the soil and why
Sand particles are too big and water drains quickly
Silt retains water to the right extent
Clay: water retained too well, soil becomes anoxic
What are rhizosphere
Soil that surrounds plant roots and receive plant secretions
What are mycorrhizae
Association of fungi with plant roots
Microorganisms in the top few centimeters of soil in the rank of their abundance
- Bacteria
- fungi
- Protozoa
- Algae
Explain carbon cycle
CO2 is fixed by photosynthetic land plants and marine microbes.
CO2 is returned to the atmosphere by respiration as well as anthropogenic activities ( the use of fossil fuels)
What is the largest producer of CO2 released to the atmosphere
Microbial decomposition
What is the other major end product of decomposition (besides CO2)
CH4
What is the most important reservoir of carbon in earth
Rocks and sediments
CO2
Why only certain prokaryotes can fix nitrogen N2
A lot of energy is required to break the bond because of the triple bond
What in general bacteria do with nitrogen
It is converting it to the sources that plants can use
Nitrogen fixation is ___ the process
the most important process on earth
In the absence of fertilizers, other organisms need
Nitrogen fixers
Two types of nitrogen fixers and their examples
Free-living (cyanobacteria)
Symbiotic (rhizobium)
The reaction of nitrogen fixation is catalyzed by
Nitrogenase complex (metal cofactors)
Nitrogenase complex requires
8 electrons from pyruvate , 2 are lost as H2 in the process and input of energy
What is the final product of nitrogen fixation
NH3
denitrogenase reductase is inhibited by
The presence of oxygen
How the electrons flow in nitrogen fixation reaction
The sequence of electron transfer in nitrogenase is as follows:
electron donor(flavodoxin) -> dinitrogenase reductase -> dinitrogenase ->
N2
Example of free-living nitrogen fixers
Azotobacter
Beijerinckia
Clostridium
Where do free-living nitrogen fixers live
Widespread in soil because require a soil rich in organic matter to provide energy for nitrogen fixation
Clostridium is ___ ( metabolism)
Strict anaerobe
Azotobacter is ___ ( metabolism)
Strict aerobe
How plants can use ammonia produced bu nitrogen fixers
NH3 dissolves in water to produce ammonium NH4
As denitrogenase reductase is inhibited by oxygen, how azotobacter keeps nitrogen fixing
They have a very rapid O2 consumption, which keeps the intracellular environment anaerobic
Why only some cyanobacteria are able of nitrogen fixation
Because they produce energy by oxygenic photosynthesis , oxygen is produced in the cell
As denitrogenase reductase is inhibited by oxygen, how cyanobacteria keeps nitrogen fixing
Nitrogen fixation occurs in specialized anaerobic cells (heterocysts), which lack photosystem II (does not produce O2)
How do heterocysts have their pyruvate and its structure
Heterocysts have a thick cell wall that slow down the diffusion of O2
The regular cells provide the heterocysts with carbohydrate (pyruvate)
What is the most important symbioses known
The mutualistic relationship between leguminous plants and nitrogen-fixing bacteria
Examples of legumes
Soybeans, clover, alfalfa,beans, and peas
What is the best-known bacteria, inolved in nitrogen -fixing bacteria engaged with soybeans
Rhizobium
What is happening with bacteria and soybean plants
Colonization of legume roots by nitrogen-fixing bacteria leads to the formation of root nodules that fix nitrogen
6 steps in nodule formation
- Recognition and attachment of bacterium to root hairs
- Excretion of nod factors by the bacterium
- bacterial invasion of the root hair
- Travel to the main root via infection thread( tube composed of cellulose)
- Formation of bacteriod state within plant cell (swollen and misshapen bacteria-fix N2). Surrounded by plant cytoplasm
- Continued plant and bacterial division, forming the mature root nodule
Oxygen levels are important for nitrogen fixation. How are they controlled
The O2 binding protein leghemoglobin, produced by plant cells
Do bacteriods go away with time?
No, they are terminal. The nodules contain regular Rhizobium cells that serve ti inoculate the environment
Explain in general what happens at nodules
Plant give bacteria organic acids, with NH3 produced inside bacteria, giving off glutamine and asparagine
Nitrogen fixation in aerial roots
through Mucilage-associated microbiota
Plant acquire ___% of its nitrogen from the air.
29-82%. At least some of this N is fixed by bacteria in the mucilage
What is mucilage
Viscous sugar-rich fluid secreted by some plants that includes diverse community of bacteria with N fixers
Examples of N fixers bacteria in sierra
Rhizobiaceae
What is amonification
Organic N->NH4
Most plants will use nitrogen compounds produced by ___
Free-living nitrogen fixers or by other organisms during ammonification, which is good for farmers because they do not need to use as much fertilizers
Nitrate is more ___ than ammonium and is more ____
Soluble and available to plasnts, though plasnts can use both ammonium and nitrate
Sources of nitrate and what is required
Nitrifying bacteria: NH3-> NO2->NO3
Requires O2
As both Nitrifying bacteria and plants need NH3, so there is
a competition for NH3
What is bad for plants and farmers with the soil
If the soil is poorly drained and becomes waterlogged, the soil becomes anaerobic, which promotes denitrification: NO3->NO2->NO->N2O->N2
Anaerobic conditions in the soil promote
Sulfur and sulfate reduction which produce H2S ( toxic for plants)
